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1. (WO2008008284) CANCER BIOMARKERS AND METHODS OF USE THREOF
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CANCER BLOM ARKERS AND METHODS OF USE THEREOF
BACKGROUND
[0001] Cancer, like many diseases, is not the result of a single, well-defined cause, but rather can be viewed as several diseases, each caused by different aberrations in informational pathways, that
ultimately result in apparently similar pathologic phenotypes. Identification of polynucleotides that correspond to genes that are differentially expressed in cancerous, pre-cancerous, or low metastatic potential cells relative to normal cells of the same tissue type, provides the basis for diagnostic tools, facilitates drug discovery by providing for targets for candidate agents, and further serves to identify therapeutic targets for cancer therapies that are more tailored for the type of cancer to be treated.
Literature
[0002] Crawford et al. (2004) Cancer Cell 5:263; McDermott et al. (2006) PLoS Biol. 4:e51 ; Berman et al. (2005) Cold Spring Harbor Symp. Quant. Biol. 70:317; Gauthier et al. (2005) Cancer Res.
65:1792; Shim et al. (2003) Cancer Res. 63:2347; Hoist et al. (2003) Cancer Res. 63:1596; Tlsty et al. (2004) . Mammary Gland Biol. Neoplasia 9:263; Kriiger et al. (1991) 5r. J. Cancer 63:114-118.

SUMMARY OF THE INVENTION
[0003] The present invention provides detection methods for detecting a pre-cancerous epithelial cell signature. The present invention further provides reagents for use in the detection methods. A subject detection method is useful in various imaging, diagnostic, prognostic, and patient monitoring methods, which are also provided.

BRIEF DESCRIPTION OF THE DRAWINGS
[0004] Figure 1 is a growth curve of normal human mammary epithelial cells (HMEC) and variant human mammary epithelial cells (vHMEC).
[0005] Figure 2 depicts fluorescence activated cell sorting (FACS) analysis of CD73, CD90, CDl 38, and Notch receptor-3 expression on vHMEC and HMEC cells.
[0006] Figure 3 depicts plό™*43 promoter methylation status in HMEC and vHMEC cells.
[0007] Figure 4 depicts isolation of CD73+ CD90" vHMEC from disease-free mammary reduction tissue.
[0008] Figure 5 depicts unsorted HMEC, CD73+ CD90" vHMEC, and CD73- CD90+ HMEC from mammary reduction tissue, cultured in vitro.
[0009] Figure 6 depicts paraffin-embedded section of normal mammary tissue stained with anti-CD73 antibody.
[0010] Figures 7A-D depict correlation of pi 6 overexpression, coupled with proliferation, with
increased risk of subsequent tumor events among women with ductal carcinoma in situ (DCIS).

[0011] Figures 8A-D depict concordance between pi 6 or COX-2 mRNA and protein expression in tumors.
[0012] Figures 9A-C depict the correlation between COX-2 overexpression, coupled with
proliferation, with increased risk of subsequent tumor events among women with DCIS.
[0013] Figure 10 is a diagram representing DCIS lesions expressing combinations of plό, COX-2 and

Ki67.
[0014] Figures 1 IA-C depict the relationship between overexpression of COX-2, in the absence or presence of proliferation, and pl6/Rb dysfunction.
[0015] Figures 12 A-E depict differential regulation of COX-2 by deregulation of distinct members of the pl6/cyclin Dl /Rb pathway.
[0016] Figure 13 depicts identification by pi 6 and COX-2 overexpression of a subset of epithelial cells in normal breast tissue and atypical ductal hyperplasias, for use in risk stratification.
[0017] Figure 14 depicts mRNAs that are over-expressed or under-expressed in vHMEC, compared to normal HMEC.
[0018] Figures 15A-C depict immunoblot analysis (Figure 15A), cell cycle analysis (Figure 15B), and chromosome analysis (Figure 15C) of vHMEC comprising a control expression vector or a Ha-rasV12 expression vector.
[0019] Figures 16A and 16B depict the effect of serum-induced extracellular signaling and
intracellular ras activation on immortalization of vHMEC (Figure 16A) and vHMEC telomerase
activity (Figure 16B).
[0020] Figures 17A-D depict the effect of extracellular signaling and intracellular ras activation on cellular morphology and methylation in HMEC.
[0021] Figures 18A-D depict the effect of TGFβ on EMT in vHMEC-rasO.5 cells.
[0022] Figure 19 depicts anchorage independent growth of vHMEC immortalized with Ha-ras.
[0023] Figure 20 depicts association of telomere Content with COX-2 expression.
[0024] Figure 21 depicts up-regulation of γH2AX in vHMEC expressing TRF2.
[0025] Figures 22A-C depict the effect of over-expressing TRF2 on COX-2 in vHMEC.
[0026] Figures 23 A-D depict up-regulation of Activin A in vHMEC and the effect of up-regulation of

Activin A on COX-2.
[0027] Figures 24 A-C depict marker analysis of vHMEC and HMEC.

DEFINITIONS
[0028] A "gene product" is a biopolymeric product that is expressed or produced by a gene, such as a peptide or protein. A gene product may be, for example, an unspliced RNA, an mRNA, a splice variant mRNA, a polypeptide, a post-translationally modified polypeptide, a splice variant polypeptide etc.
Also encompassed by this term are biopolymeric products that are made using an RNA gene product as a template (i.e., cDNA of the RNA). A gene product may be made enzymatically, recombinantly,
chemically, or within a cell to which the gene is native. In many embodiments, if the gene product is proteinaceous, it exhibits a biological activity. In many embodiments, if the gene product is a nucleic acid, it can be translated into a proteinaceous gene product that exhibits a biological activity.
[0029] The terms "polypeptide" and "protein," used interchangeably herein, refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or
biochemically modified or derivatized amino acids, and polypeptides having modified peptide
backbones. The term includes fusion proteins, including, but not limited to, fusion proteins with a
heterologous amino acid sequence, fusions with heterologous and homologous leader sequences, with or without N-terminal methionine residues; immunologically tagged proteins; and the like.
[0030] The term "polynucleotide" refers to polymeric forms of nucleotides of any length, either
ribonucleotides or deoxynucleotides. Thus, these terms include, but are not limited to, single-, double-, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases. These terms further include, but are not limited to, mRNA or cDNA that comprise intronic sequences (see, e.g., Niwa et al. (1999) Cell 99(7):691-702). The backbone of the polynucleotide can comprise sugars and phosphate groups (as may typically be found in RNA or DNA), or modified or substituted sugar or phosphate groups. Alternatively, the backbone of the polynucleotide can comprise a polymer of synthetic subunits such as phosphoramidites and thus can be an
oligodeoxynucleoside phosphoramidate or a mixed phosphoramidate-phosphodiester oligomer.
Peyrottes et al. (1996) Nucl. Acids Res. 24:1841-1848; Chaturvedi et al. (1996) Nucl. Acids Res.
24:2318-2323. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs, uracyl, other sugars, and linking groups such as fluororibose and thioate, and nucleotide branches. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component. Other types of modifications included in this definition are caps, substitution of one or more of the naturally occurring nucleotides with an analog, and introduction of means for attaching the polynucleotide to proteins, metal ions, labeling components, other polynucleotides, or a solid support. The term "polynucleotide" also encompasses peptidic nucleic acids (Pooga et al Curr Cancer Drug
Targets. (2001) 1 :231-9).
[0031] The term "capture agent" refers to an agent that binds a target molecule through an interaction that is sufficient to permit the agent to bind and concentrate the target molecule from a homogeneous mixture of different molecules. The binding interaction is typically mediated by an affinity region of the capture agent. Typical capture agents include any moiety that can specifically bind to a target molecule. In certain embodiments, a polypeptide, e.g., an antibody protein, may be employed. Capture agents usually "specifically bind" a target molecule. Accordingly, the term "capture agent" refers to a
molecule or a multi-molecular complex which can specifically bind a target molecule, e.g., a phosphorylated polypeptide, with a dissociation constant (K0) of less than about 10"6 M (e.g., less than about 10"7M, less than about 10"8M, less than about 10"9M, less than about 10"10 M, less than about 10" 11 M, less than about 10"12 M, to up to about 10'lδ M) without significantly binding to other molecules.

[0032] The term "specific binding" refers to the ability of a capture agent to preferentially bind to a particular target molecule that is present in a homogeneous mixture of different target molecule. In certain embodiments, a specific binding interaction will discriminate between desirable and undesirable target molecules in a sample, typically more than about 10 to 100-fold or more (e.g., more than about 1000- or 10,000-fold).
[0033] The term "capture agent/target complex" is a complex that results from the specific binding of a capture agent with a target, i.e., a "binding partner pair". A capture agent and an target for the capture agent will usually specifically bind to each other under "conditions suitable for specific binding", where such conditions are those conditions (in terms of salt concentration, pH, detergent, protein
concentration, temperature, etc.) which allow for binding to occur between capture agents and targets to bind in solution. Such conditions, particularly with respect to proteins and antibodies, include those described in Harlow and Lane (Antibodies: A Laboratory Manual Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989)) and Ausubel, et al (Short Protocols in Molecular Biology, 5th ed., Wiley & Sons, 2002).
[0034] As used herein, "binding partners" and equivalents thereof refer to pairs of molecules that can be found in a capture agent/target complex, i.e., exhibit specific binding with each other.
[0035] The phrase "surface-bound capture agent" refers to a capture agent that is immobilized on a surface of a substrate. In certain embodiments, the capture agent employed herein may be present on a surface of the same support, e.g., in the form of an array.
[0036] The term "pre-determined" refers to an element whose identity is known prior to its use. An element may be known by name, sequence, molecular weight, its function, or any other attribute or identifier. In some embodiments, the term "polypeptide of interest", i.e., a known polypeptide that is of interest, is used synonymously with the term "pre-determined polypeptide".
[0037] The term "antibody protein" is used herein to refer to a capture agent that has at least an epitope binding domain of an antibody. These terms are well understood by those in the field, and refer to a protein containing one or more polypeptides that specifically binds an antigen. One form of antibody constitutes the basic structural unit of an antibody. This form is a tetramer and consists of two identical pairs of antibody chains, each pair having one light and one heavy chain. In each pair, the light and heavy chain variable regions are together responsible for binding to an antigen, and the constant regions are responsible for the antibody effector functions. Types of antibodies, including antibody isotypes, monoclonal antibodies and antigen-binding fragments thereof (e.g., Fab, Fv, scFv, and Fd fragments, chimeric antibodies, humanized antibodies, single-chain antibodies, etc) are known and need not be described in any further detail.

[0038] A polynucleotide "derived from" or "specific for" a designated sequence, such as a target sequence of a target nucleic acid, refers to a polynucleotide sequence which comprises a contiguous sequence of approximately at least about 6 nucleotides, at least about 8 nucleotides, at least about 10-12 nucleotides, or at least about 15-20 nucleotides corresponding to, i.e., identical or complementary to, a region of the designated nucleotide sequence. The derived polynucleotide will not necessarily be
derived physically from the nucleotide sequence of interest, but may be generated in any manner, including, but not limited to, chemical synthesis, replication, reverse transcription or transcription, which is based on the information provided by the sequence of bases in the region(s) from which the polynucleotide is derived or specific for. Polynucleotides that are derived from" or "specific for" a designated sequence include polynucleotides that are in a sense or an antisense orientation relative to the original polynucleotide.
[0039] A polynucleotide or polypeptide has a certain percent "sequence identity" to another
polynucleotide or polypeptide, meaning that, when aligned, that percentage of bases or amino acids are the same, and in the same relative position, when comparing the two sequences. Sequence similarity can be determined in a number of different manners. To determine sequence identity, sequences can be aligned using the methods and computer programs, including BLAST, available over the world wide web at ncbi.nlm.nih.gov/BLAST. See, e.g., Altschul et al (1990), J. MoI. Biol. 215:403-10. Another alignment algorithm is FASTA, available in the Genetics Computing Group (GCG) package, from
Madison, Wisconsin, USA, a wholly owned subsidiary of Oxford Molecular Group, Inc. Other
techniques for alignment are described in Methods in Enzymology, vol. 266: Computer Methods for
Macromolecular Sequence Analysis (1996), ed. Doolittle, Academic Press, Inc., a division of Harcourt Brace & Co., San Diego, California, USA. Of particular interest are alignment programs that permit gaps in the sequence. The Smith-Waterman is one type of algorithm that permits gaps in sequence alignments. See Meth. MoI. Biol. 70: 173-187 (1997). Also, the GAP program using the Needleman and Wunsch alignment method can be utilized to align sequences. See J. MoI. Biol. 48: 443-453 (1970).
[0040] A nucleic acid is "hybridizable" to another nucleic acid, such as a cDNA, genomic DNA, or
RNA, when a single stranded form of the nucleic acid can anneal to the other nucleic acid under the appropriate conditions of temperature and solution ionic strength. Hybridization and washing
conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring
Harbor (1989), particularly Chapter 11 and Table 11.1 therein; and Sambrook, J. and Russell, W.,
Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor (2001). The conditions of temperature and ionic strength determine the "stringency" of the hybridization. Stringency conditions can be adjusted to screen for moderately similar fragments, such as homologous sequences from distantly related organisms, to highly similar fragments, such as genes that duplicate functional enzymes from closely related organisms.

[0041] Hybridization conditions and post-hybridization washes are useful to obtain the desired
determine stringency conditions of the hybridization. One set of illustrative post-hybridization washes is a series of washes starting with 6 x SSC (where SSC is 0.15 M NaCl and 15 mM citrate buffer), 0.5% SDS at room temperature for 15 minutes, then repeated with 2 x SSC, 0.5% SDS at 45°C for 30
minutes, and then repeated twice with 0.2 x SSC, 0.5% SDS at 500C for 30 minutes. Other stringent conditions are obtained by using higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 minute washes in 0.2 x SSC, 0.5% SDS, which is
increased to 600C. Another set of highly stringent conditions uses two final washes in 0.1 x SSC, 0.1% SDS at 65°C. Another example of stringent hybridization conditions is hybridization at 500C or higher and O.lxSSC (15 mM sodium chloride/1.5 mM sodium citrate). Another example of stringent
hybridization conditions is overnight incubation at 420C in a solution: 50% formamide, 5 * SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5 x Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1 x SSC at about 650C. Stringent hybridization conditions and post-hybridization wash conditions are hybridization conditions and post-hybridization wash conditions that are at least as stringent as the above representative conditions.
[0042] In certain embodiments, the stringency of the wash conditions that set forth the conditions which determine whether a nucleic acid is specifically hybridized to a probe. Wash conditions used to identify nucleic acids may include, e.g.: a salt concentration of about 0.02 molar at pH 7 and a
temperature of at least about 50. 0C. or about 55°C. to about 600C; or, a salt concentration of about
0.15 M NaCl at 72°C. for about 15 minutes; or, a salt concentration of about 0.2xSSC at a temperature of at least about 500C. or about 55. 0C. to about 600C. for about 15 to about 20 minutes; or, the
hybridization complex is washed twice with a solution with a salt concentration of about 2xSSC
containing 0.1% SDS at room temperature for 15 minutes and then washed twice by O.lxSSC
containing 0.1% SDS at 68°C. for 15 minutes; or, equivalent conditions. Stringent conditions for
washing can also be, e.g., 0.2xSSC/0.1% SDS at 42°C. In instances wherein the nucleic acid molecules are deoxyoligonucleotides ("oligos"), stringent conditions can include washing in 6xSSC/0.05%
sodium pyrophosphate at 37. °C. (for 14-base oligos), 48. 0C. (for 17-base oligos), 55°C. (for 20-base oligos), and 600C. (for 23-base oligos). See Sambrook, Ausubel, or Tijssen (cited below) for detailed descriptions of equivalent hybridization and wash conditions and for reagents and buffers, e.g., SSC buffers and equivalent reagents and conditions.
[0043] Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The
appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of the melting temperature (Tm) for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNArRNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Sambrook et al., supra, 9.50-9.51). For hybridizations with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Sambrook et al., supra, 11.7-11.8). Typically, the length for a hybridizable nucleic acid is at least about 10 nucleotides. Illustrative minimum lengths for a hybridizable nucleic acid are: at least about 15 nucleotides; at least about 20 nucleotides; and at least about 30 nucleotides. Furthermore, the skilled artisan will recognize that the temperature and wash solution salt concentration may be
adjusted as necessary according to factors such as length of the probe.
[0044] A "DNA-dependent DNA polymerase" is an enzyme that synthesizes a complementary DNA copy from a DNA template. Examples include DNA polymerase I from E. coli and bacteriophage T7
DNA polymerase. All known DNA-dependent DNA polymerases require a complementary primer to initiate synthesis. Under suitable conditions, a DNA-dependent DNA polymerase may synthesize a complementary DNA copy from an RNA template.
[0045] A "DNA-dependent RNA polymerase" or a "transcriptase" is an enzyme that synthesizes
multiple RNA copies from a double-stranded or partially-double stranded DNA molecule having a
(usually double-stranded) promoter sequence. The RNA molecules ("transcripts") are synthesized in the 51 to 3' direction beginning at a specific position just downstream of the promoter. Examples of
transcriptases are the DNA-dependent RNA polymerase from E. coli and bacteriophages T7, T3, and
SP6.
[0046] An "RNA-dependent DNA polymerase" or "reverse transcriptase" is an enzyme that
synthesizes a complementary DNA copy from an RNA template. All known reverse transcriptases also have the ability to make a complementary DNA copy from a DNA template; thus, they are both RNA- and DNA-dependent DNA polymerases. A primer is required to initiate synthesis with both RNA and
DNA templates.
[0047] "RNAse H" is an enzyme that degrades the RNA portion of an RNA:DNA duplex. These
enzymes may be endonucleases or exonucleases. Most reverse transcriptase enzymes normally contain an RNAse H activity in addition to their polymerase activity. However, other sources of the RNAse H are available without an associated polymerase activity. RNA degradation mediated by an RNAse H may result in separation of RNA from a RNA: DNA complex, or the RNAse H may cut the RNA at various locations such that portions of the RNA melt off or permit enzymes to unwind portions of the
RNA.
[0048] As used herein, the term "target nucleic acid region" or "target nucleic acid" or "target
molecules" refers to a nucleic acid molecule with a "target sequence" to be detected (e.g., in a method involving nucleic acid hybridization and/or amplification). The target nucleic acid may be either single- stranded or double-stranded and may or may not include other sequences besides the target sequence (e.g., the target nucleic acid may or may not include nucleic acid sequences upstream or 5' flanking sequence, may or may not include downstream or 3 ' flanking sequence, and in some embodiments may not include either upstream (5') or downstream (3') nucleic acid sequence relative to the target
sequence. Where detection is by amplification, these other sequences in addition to the target sequence may or may not be amplified with the target sequence.
[0049] The term "target sequence" or "target nucleic acid sequence" refers to the particular nucleotide sequence of the target nucleic acid to be detected (e.g., through amplification). The target sequence may include a probe-hybridizing region contained within the target molecule with which a probe will form a stable hybrid under desired conditions. The "target sequence" may also include the complexing
sequences to which the oligonucleotide primers complex and be extended using the target sequence as a template. Where the target nucleic acid is originally single-stranded, the term "target sequence" also refers to the sequence complementary to the "target sequence" as present in the target nucleic acid. If the "target nucleic acid" is originally double-stranded, the term "target sequence" refers to both the plus (+) and minus (-) strands. Moreover, where sequences of a "target sequence" are provided herein, it is understood that the sequence may be either DNA or RNA. Thus where a DNA sequence is provided, the RNA sequence is also contemplated and is readily provided by substituting "T" of the DNA
sequence with "U" to provide the RNA sequence.
[0050] The term "primer" or "oligonucleotide primer" as used herein, refers to an oligonucleotide which acts to initiate synthesis of a complementary nucleic acid strand when placed under conditions in which synthesis of a primer extension product is induced, e.g., in the presence of nucleotides and a polymerization-inducing agent such as a DNA or RNA polymerase and at suitable temperature, pH, metal ion concentration, and salt concentration. Primers are generally of a length compatible with its use in synthesis of primer extension products, and are in many embodiments in the range of between 8 nucleotides and 100 nucleotides (nt) in length, such as 10 nt to 75 nt, 15 nt to 60 nt, 15 nt to 40 nt, 18 nt to 30 nt, 20 nt to 40 nt, 21 nt to 50 nt, 22 nt to 45 nt, 25 nt to 40 nt, and so on, e.g., in the range of between 18 nt and 40 nt, between 20 nt and 35 nt, between 21 and 30 nt in length, inclusive, and any length between the stated ranges. Primers can be in the range of between 10-50 nucleotides long, such as 15-45, 18-40, 20-30, 21-25 nt and so on, and any length between the stated ranges. In some
embodiments, the primers are not more than about 10, 12, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, or 70 nucleotides in length.
[0051] Primers are in many embodiments single-stranded for maximum efficiency in amplification, but may alternatively be double-stranded. If double-stranded, the primer is in many embodiments first treated to separate its strands before being used to prepare extension products. This denaturation step is typically effected by heat, but may alternatively be carried out using alkali, followed by neutralization. Thus, a "primer" is complementary to a template, and complexes by hydrogen bonding or hybridization with the template to give a primer/template complex for initiation of synthesis by a polymerase, which is extended by the addition of covalently bonded bases linked at its 31 end complementary to the
template in the process of DNA synthesis.
[0052] A "primer pair" as used herein refers to first and second primers having nucleic acid sequence suitable for nucleic acid-based amplification of a target nucleic acid. Such primer pairs generally
include a first primer having a sequence that is the same or similar to that of a first portion of a target nucleic acid, and a second primer having a sequence that is complementary to a second portion of a target nucleic acid to provide for amplification of the target nucleic acid or a fragment thereof.
Reference to "first" and "second" primers herein is arbitrary, unless specifically indicated otherwise.
For example, the first primer can be designed as a "forward primer" (which initiates nucleic acid
synthesis from a 5' end of the target nucleic acid) or as a "reverse primer" (which initiates nucleic acid synthesis from a 5' end of the extension product produced from synthesis initiated from the forward primer). Likewise, the second primer can be designed as a forward primer or a reverse primer.
[0053] As used herein, the term "probe" or "oligonucleotide probe", used interchangeable herein, refers to a structure comprised of a polynucleotide, as defined above, which contains a nucleic acid sequence complementary to a nucleic acid sequence present in the target nucleic acid analyte (e.g., a nucleic acid amplification product). The polynucleotide regions of probes may be composed of DNA, and/or RNA, and/or synthetic nucleotide analogs. Probes are generally of a length compatible with its use in specific detection of all or a portion of a target sequence of a target nucleic acid, and are in many embodiments in the range of between 8 nt and 100 nt in length, such as 8 to 75 nt, 10 to 74 nt, 12 to 72 nt, 15 to 60 nt, 15 to 40 nt, 18 to 30 nt, 20 to 40 nt, 21 to 50 nt, 22 to 45 nt, 25 to 40 nt in length, and so on, e.g., in the range of between 18-40 nt, 20-35 nt, or 21-30 nt in length, and any length between the stated ranges. In some embodiments, a probe is in the range of between 10-50 nucleotides long, such as 15-45, 18-40, 20-30, 21-28, 22-25 and so on, and any length between the stated ranges. In some
embodiments, the primers are not more than about 10, 12, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, or 70 nucleotides in length.
[0054] Probes contemplated herein include probes that include a detectable label. For example, when an "oligonucleotide probe" is to be used in a 5' nuclease assay, such as the TAQMAN™ assay, the
probe includes at least one fluorescer and at least one quencher which is digested by the 5' endonuclease activity of a polymerase used in the reaction in order to detect any amplified target oligonucleotide sequences. In this context, the oligonucleotide probe will have a sufficient number of phosphodi ester linkages adjacent to its 51 end so that the 5' to 3' nuclease activity employed can efficiently degrade the bound probe to separate the fluorescers and quenchers. When an oligonucleotide probe is used in the
TMA technique, it will be suitably labeled, as described below.
[0055] Probes and primers contemplated herein include those useful in various amplification and/or detection systems, including those in which primers and probes are provided as bi-functional molecules. Exemplary amplification and/or detection systems include Sunrise™ primer-based systems, Molecular Beacons, the Taqman™ system, an Amplifluor™ hairpin primer-based system, a Scorpions technology (e.g., bi-fiinctional molecules containing a PCR primer element covalently linked to a probe element), and a Light Upon Extension or LUX™-based system. Further exemplary detection systems include those based on a melt-curve analysis, and using intercalating dyes such as the fluorescent dye SYBR
Green.
[0056] As used herein, the terms "label" and "detectable label" refer to a molecule capable of
detection, including, but not limited to, radioactive isotopes, fluorescers, chemiluminescers,
chromophores, enzymes, enzyme substrates, enzyme cofactors, enzyme inhibitors, chromophores, dyes, metal ions, metal sols, ligands (e.g., biotin, avidin, strepavidin or haptens), intercalating dyes and the like. The term "fluorescer" refers to a substance or a portion thereof which is capable of exhibiting fluorescence in the detectable range.
[0057] The terms "hybridize" and "hybridization" refer to the formation of complexes between
nucleotide sequences which are sufficiently complementary to form complexes via Watson-Crick base pairing. Where a primer "hybridizes" with target (template), such complexes (or hybrids) are
sufficiently stable to serve the priming function required by, e.g., the DNA polymerase to initiate DNA synthesis.
[0058] The term "stringent conditions" refers to conditions under which a primer will hybridize
preferentially to, or specifically bind to, its complementary binding partner, and to a lesser extent to, or not at all to, other sequences. Put another way, the term "stringent hybridization conditions" as used herein refers to conditions that are compatible to produce duplexes on an array surface between
complementary binding members, e.g., between probes and complementary targets in a sample, e.g., duplexes of nucleic acid probes, such as DNA probes, and their corresponding nucleic acid targets that are present in the sample, e.g., their corresponding mRNA analytes present in the sample.
[0059] An "array," includes any one, two-dimensional or substantially two-dimensional (as well as a three-dimensional) arrangement of addressable regions bearing a particular chemical moiety or moieties (e.g., polynucleotide or oligonucleotide sequences (nucleic acids), polypeptides (e.g., proteins such antibodies) associated with that region. In the broadest sense, arrays are arrays of polymeric binding agents, where the polymeric binding agents may be any of: polypeptides, proteins (e.g., antibodies), nucleic acids, synthetic mimetics of such polymeric binding agents, etc. In some embodiments of
interest, the arrays are arrays of nucleic acids, including oligonucleotides, polynucleotides, cDNAs, mRNAs, synthetic mimetics thereof, and the like. Where the arrays are arrays of nucleic acids, the nucleic acids may be covalently attached to the arrays at any point along the nucleic acid chain, but are generally attached at one of their termini (e.g. the 3' or 5' terminus). In other embodiments, the arrays are arrays of polypeptides, e.g., proteins or fragments thereof, antibodies, and the like.
[0060] Any given substrate may carry one, two, four or more or more arrays disposed on a front
surface of the substrate. Depending upon the use, any or all of the arrays may be the same or different from one another and each may contain multiple spots or features. An array can contain more than ten, more than one hundred, more than one thousand more ten thousand features, or even more than one hundred thousand features, in an area of less than 20 cm2 or even less than 10 cm2. For example,
features may have widths (that is, diameter, for a round spot) in the range from a 10 μm to 1.0 cm. In other embodiments each feature may have a width in the range of 1.0 μm to 1.0 mm, from 5.0 μm to
500 μm,or from 10 μm to 200 μm. Non-round features may have area ranges equivalent to that of
circular features with the foregoing width (diameter) ranges. At least some, or all, of the features are of different compositions (for example, when any repeats of each feature composition are excluded the remaining features may account for at least 5%, 10%, or 20% of the total number of features).
Interfeature areas will typically (but not essentially) be present which do not carry any polynucleotide
(or other polymer or chemical moiety of a type of which the features are composed). Such interfeature areas typically will be present where the arrays are formed by processes involving drop deposition of reagents but may not be present when, for example, photolithographic array fabrication processes are used. It will be appreciated though, that the interfeature areas, when present, could be of various sizes and configurations.
[0061] Each array may cover an area of less than 100 cm2, or even less than 50 cm2, 10 cm2 or 1 cm2.

In many embodiments, the substrate carrying the one or more arrays will be shaped generally as a
rectangular solid (although other shapes are possible), having a length of more than 4 mm and less than 1 m, than 4 mm and less than 600 mm, or less than 400 mm; a width of more than 4 mm and less than 1 m, less than 500 mm, or less than 400 mm; and a thickness of more than 0.01 mm and less than 5.0 mm, more than 0.1 mm and less than 2 mm, or more than 0.2 and less than 1 mm. With arrays that are read by detecting fluorescence, the substrate may be of a material that emits low fluorescence upon
illumination with the excitation light. Additionally in this situation, the substrate may be relatively
transparent to reduce the absorption of the incident illuminating laser light and subsequent heating if the focused laser beam travels too slowly over a region. For example, substrate 10 may transmit at least
20%, or 50% (or even at least 70%, 90%, or 95%), of the illuminating light incident on the front as may be measured across the entire integrated spectrum of such illuminating light or alternatively at 532 nm or 633 nm.
[0062] Arrays can be fabricated using drop deposition from pulse jets of either polynucleotide
precursor units (such as monomers) in the case of in situ fabrication, or the previously obtained
polynucleotide. Such methods are described in detail in, for example, US 6,242,266, US 6,232,072, US 6,180,351, US 6,171,797, US 6,323,043, and the references cited therein. As already mentioned, these references are incorporated herein by reference. Other drop deposition methods can be used for
fabrication, as previously described herein. Also, instead of drop deposition methods, photolithographic array fabrication methods may be used. Interfeature areas need not be present particularly when the arrays are made by photolithographic methods.
[0063] An array is "addressable" when it has multiple regions of different moieties (e.g., different polynucleotide sequences) such that a region (i.e., a "feature" or "spot" of the array) at a particular predetermined location (i.e., an "address") on the array will detect a particular target or class of targets (although a feature may incidentally detect non-targets of that feature). Array features are typically, but need not be, separated by intervening spaces. In the case of an array, the "target" will be referenced as a moiety in a mobile phase (typically fluid), to be detected by probes ("target probes") which are bound to the substrate at the various regions. However, either of the "target" or "target probe" may be the one which is to be evaluated by the other (thus, either one could be an unknown mixture of polynucleotides to be evaluated by binding with the other). A "scan region" refers to a contiguous (e.g., rectangular) area in which the array spots or features of interest, as defined above, are found. The scan region is that portion of the total area illuminated from which the resulting fluorescence is detected and recorded. For the purposes of this invention, the scan region includes the entire area of the slide scanned in each pass of the lens, between the first feature of interest, and the last feature of interest, even if there exist
intervening areas which lack features of interest. An "array layout" refers to one or more characteristics of the features, such as feature positioning on the substrate, one or more feature dimensions, and an indication of a moiety at a given location. "Hybridizing" and "binding", with respect to
polynucleotides, are used interchangeably.
[0064] A "scanner" is device for evaluating arrays. In scanners, an optical light source, particularly a laser light source, generates a light which is focused on the array and sequentially illuminates surface regions of known location (for example, a point or line) on an array substrate. The resulting signals from the surface regions are collected either employing the same lens used to focus the light onto the array or using a separate lens positioned to one side of the lens used to focus the onto the array. The collected signals may be then transmitted through appropriate spectral filters, to an optical detector. A recording device, such as a computer memory, records the detected signals and builds up a scan file of intensities as a function of position, or time as it relates to the position, hi the case of spot illumination, such intensities, as a function of position, are typically referred to in the art as "pixels". Biopolymer arrays are often scanned and/or scan results are often represented at 5 or 10 micron pixel resolution. To achieve the precision required for such activity, components such as the lasers must be set and
maintained with particular alignment. Scanners may be bi-directional, or unidirectional, as is known in the art.
[0065] The scanner typically used for the evaluation of arrays includes a scanning fluorimeter. A
number of different types of such devices are commercially available from different sources, such as such as Perkin-Elmer, Agilent, or Axon Instruments, etc., and examples of suitable scanners are
described in U.S. Patent Nos: 5,091 ,652; 5,760,951, 6,320,196 and 6,355,934.
[0066] The term "assessing" includes any form of measurement, and includes determining if an
element is present or not. The terms "determining," "measuring," "evaluating," "assessing," and
"assaying" are used interchangeably and includes quantitative and qualitative determinations. Assessing may be relative or absolute. "Assessing the presence of includes determining the amount of something present, and/or determining whether it is present or absent. As used herein, the terms "determining," "measuring," and "assessing," and "assaying" are used interchangeably and include both quantitative and qualitative determinations.
[0067] The term "binds specifically," in the context of a specific binding reagent, e.g., in the context of antibody binding, refers to high avidity and/or high affinity binding of an antibody to a specific
polypeptide i.e., epitope of a polypeptide, e.g., a CD73 polypeptide, a CDl 38 polypeptide, a notch receptor-3 polypeptide, a CD90 polypeptide, a BMI-I polypeptide, or a Cox-2 polypeptide. For
example, antibody binding to an epitope on a specific a target gene product or fragment thereof is
stronger than binding of the same antibody to any other epitope, particularly those which may be
present in molecules in association with, or in the same sample, as the specific polypeptide of interest, e.g., binds more strongly to a specific target polypeptide than to any other epitopes so that by adjusting binding conditions the antibody binds almost exclusively to the specific target epitope and not to any other epitope, or to any other polypeptide which does not comprise the epitope. Antibodies that bind specifically to a polypeptide may be capable of binding other polypeptides at a weak, yet detectable, level (e.g., 10% or less of the binding shown to the polypeptide of interest). Such weak binding, or background binding, is readily discernible from the specific antibody binding to a target polypeptide, e.g. by use of appropriate controls. In general, specific antibodies bind to a given polypeptide with a binding affinity of 10"7 M or more, e.g., 10'8 M or more (e.g., 10"9 M, 10"10 M, 10"11 M, etc.). In general, an antibody with a binding affinity of 10"6 M or less is not useful in that it will not bind an antigen at a detectable level using conventional methodology currently used.
[0068] A composition (e.g. a polynucleotide, polypeptide, antibody, or host cell) that is "isolated" or
"in substantially isolated form" refers to a composition that is in an environment different from that in which the composition naturally occurs. For example, a polynucleotide that is in substantially isolated form is outside of the host cell in which the polynucleotide naturally occurs, and could be a purified fragment of DNA, could be part of a heterologous vector, or could be contained within a host cell that is not a host cell from which the polynucleotide naturally occurs. The term "isolated" does not refer to a genomic or cDNA library, whole cell total protein or mRNA preparation, genomic DNA preparation, or an isolated human chromosome. A composition which is in substantially isolated form is usually
substantially purified.
[0069] As used herein, the term "substantially purified" refers to a compound (e.g., a polynucleotide, a polypeptide or an antibody, etc.) that is removed from its natural environment and is at least 60% free, 75% free, at least 90%, at least 95%, at least 98%, or at least 99% free from other components with which it is naturally associated. Thus, for example, a composition containing A is "substantially free of B when at least 85% by weight of the total A+B in the composition is A. For example, A comprises at least about 90% by weight of the total of A+B in the composition, or at least about 95% or even 99% by weight. In the case of polynucleotides, "A" and "B" may be two different genes positioned on different chromosomes or adjacently on the same chromosome, or two isolated cDNA species, for example.

[0070] If one composition is "bound" to another composition, the compositions do not have to be in direct contact with each other. In other words, bonding may be direct or indirect, and, as such, if two compositions (e.g., a substrate and a polypeptide) are bound to each other, there may be at least one other composition (e.g., another layer) between to those compositions. Binding between any two
compositions described herein may be covalent or non-covalent. The terms "bound" and "linked" are used interchangeably herein.
[0071] As used herein, "subject," "host," "patient," and "individual" are used interchangeably to refer to a mammal, e.g., a human, a non-human primate, ungulates, canines, felines, equines, and the like.
[0072] "Diagnosis" as used herein generally includes determination of a subject's susceptibility to a disease or disorder, determination as to whether a subject is presently affected by a disease or disorder, prognosis of a subject affected by a disease or disorder (e.g., identification of pre-metastatic or
metastatic cancerous states, stages of cancer, or responsiveness of cancer to therapy), and use of
therametrics (e.g., monitoring a subject's condition to provide information as to the effect or efficacy of therapy).
[0073] As used herein, the term "a polypeptide associated with cancer" refers to a polypeptide encoded by a polynucleotide that is differentially expressed in a cancer cell.
[0074] The term "biological sample" encompasses a variety of sample types obtained from an
organism and can be used in an imaging, a diagnostic, a prognostic, or a monitoring assay. The term encompasses blood and other liquid samples of biological origin, solid tissue samples, such as a biopsy specimen or tissue cultures or cells derived therefrom and the progeny thereof. The term encompasses samples that have been manipulated in any way after their procurement, such as by treatment with
reagents, solubilization, or enrichment for certain components. The term encompasses a clinical sample, and also includes cells in cell culture, cell supernatants, cell lysates, serum, plasma, biological fluids, and tissue samples.
[0075] The terms "treatment," "treating," "treat" and the like are used herein to generally refer to
obtaining a desired pharmacologic and/or physiologic effect. The effect may be prophylactic in terms of completely or partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete stabilization or cure for a disease and/or adverse effect attributable to the disease.
"Treatment" as used herein covers any treatment of a disease in a mammal, particularly a human, and includes: (a) preventing the disease or symptom from occurring in a subject which may be predisposed to the disease or symptom but has not yet been diagnosed as having it; (b) inhibiting the disease
symptom, i.e., arresting its development; or (c) relieving the disease symptom, i.e., causing regression of the disease or symptom.
[0076] The terms "cancer," "neoplasm," and "tumor" are used interchangeably herein to refer to cells which exhibit relatively autonomous growth, so that they exhibit an aberrant growth phenotype
characterized by a significant loss of control of cell proliferation. In general, cells of interest for
detection or treatment in the present application include precursors, precancerous (e.g., benign), malignant, pre-metastatic, metastatic, and non-metastatic cells. Detection of pre-cancerous cells is of particular interest.
[0077] "Cancerous phenotype" generally refers to any of a variety of biological phenomena that are characteristic of a cancerous cell, which phenomena can vary with the type of cancer. The cancerous phenotype is generally identified by abnormalities in, for example, cell growth or proliferation (e.g., uncontrolled growth or proliferation), regulation of the cell cycle, cell mobility, cell-cell interaction, or metastasis, etc.
[0078] The term "assessing" includes any form of measurement, and includes determining if an
element is present or not. The terms "determining", "measuring", "evaluating", "assessing" and
"assaying" are used interchangeably and include quantitative and qualitative determinations. Assessing may be relative or absolute. "Assessing the presence of includes determining the amount of
something present, and/or determining whether it is present or absent. As used herein, the terms
"determining," "measuring," and "assessing," and "assaying" are used interchangeably and include both quantitative and qualitative determinations.
[0079] The term "transformation" is used interchangeably herein with "genetic modification" and refers to a permanent or transient genetic change induced in a cell following introduction of new
nucleic acid (i.e., DNA exogenous to the cell). Genetic change ("modification") can be accomplished either by incorporation of the new DNA into the genome of the host cell, or by transient or stable
maintenance of the new DNA as an episomal element. A permanent genetic change is generally
achieved by introduction of the DNA into the genome of the cell. Suitable methods of genetic
modification include viral infection, transfection, conjugation, protoplast fusion, electroporation,
particle gun technology, calcium phosphate precipitation, direct microinjection, and the like. A general discussion of these methods can be found in Ausubel, et al, Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995.
[0080] "Operably linked" refers to a juxtaposition wherein the components so described are in a
relationship permitting them to function in their intended manner. For instance, a promoter is operably linked to a coding sequence if the promoter affects its transcription or expression. As used herein, the terms "heterologous promoter" and "heterologous control regions" refer to promoters and other control regions that are not normally associated with a particular nucleic acid in nature. For example, a
"transcriptional control region heterologous to a coding region" is a transcriptional control region that is not normally associated with the coding region in nature.
[0081] A "host cell," as used herein, denotes an in vivo or in vitro eukaryotic cell, or a cell from a multicellular organism (e.g., a primary cell, a cell line) cultured as a unicellular entity, which
eukaryotic cell can be, or has been, used as a recipient for a nucleic acid (e.g., an exogenous nucleic acid), and include the progeny of the original cell which has been genetically modified by the nucleic acid. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation. A "recombinant host cell" (also referred to as a "genetically modified host cell") is a host cell into which has been introduced a heterologous nucleic acid, e.g., an expression vector.

[0082] Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the
appended claims.
[0083] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.
[0084] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the
practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the
methods and/or materials in connection with which the publications are cited.
[0085] It must be noted that as used herein and in the appended claims, the singular forms "a," "and," and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "an epithelial cell" includes a plurality of such cells and reference to "the biomarker"
includes reference to one or more biomarkers and equivalents thereof known to those skilled in the art, and so forth. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as "solely," "only" and the like in connection with the recitation of claim elements, or use of a "negative"
limitation.
[0086] The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently
confirmed.

DETAILED DESCRIPTION
[0087] The present invention provides reagents and methods for detecting a pre-cancerous or
cancerous epithelial cell. It has been found that certain signatures associated with mammary epithelial cells identify pre-cancerous cells, and indicate a level of risk that a malignant tumor will develop.
Mammary epithelial cell signatures include, for example, the presence and/or levels and/or
posttranslation modification of a protein or collection of proteins; the presence and/or level of a nucleic acid; and the integrity or methylation status or other parameter of a nucleic acid.
[0088] A variant mammary epithelial cell (vMEC) appears morphological normal, e.g., a vMEC is morphologically indistinguishable from a normal mammary epithelial cell. However, a vMEC has a
"signature" that indicates its potential for developing into a cancerous cell, e.g., a vMEC is a pre- malignant cell. Thus, e.g., a vMEC signature distinguishes it from an MEC (e.g., a control, normal
MEC that is not pre-malignant) by one or more of: 1) a lower than normal level of an mRNA, compared to the level of the mRNA in a MEC; 2) a higher than normal level of an mRNA, compared to the level of the mRNA in a MEC; 3) a lower than normal level of a protein, compared to the level of the protein in a MEC; 4) a higher than normal level of a protein, compared to the level of the protein in an MEC; 5) a higher level of a post-translationally modified protein,compared to the level of the post-translationally modified protein in an MEC; 6) an increased level of genomic DNA abnormalities, compared to the level found in an MEC; and 7) an increased level of methylation of a particular promoters), compared to the level of methylation of the promoter(s) in an MEC.
[0089] For example, an mRNA or a protein that is differentially expressed in a vMEC, compared to a control, normal MEC, is present in the vMEC at a level from about 1.5-fold to 100-fold higher or lower than the level of the mRNA or protein in a control, normal MEC, e.g., an mRNA or a protein that is differentially expressed in a vMEC is present in the vMEC at a level of from about 1.5-fold to about 2- fold, from about 2-fold to about 2.5-fold, from about 2.5-fold to about 5-fold, from about 5-fold to about 10-fold, from about 10-fold to about 15-fold, from about 15-fold to about 20-fold, from about 20- fold to about 25-fold, from about 25-fold to about 50-fold, from about 50-fold to about 75-fold, or from about 75-fold to about 100-fold, or more, higher or lower than the level of the mRNA or protein in a control, normal MEC. In some embodiments, a control, normal MEC is a primary MEC isolated from an individual, where the control, normal MEC is a CD73" MEC, e.g., is substantially negative for
CD73.
[0090] Methods for detecting a pre-cancerous or cancerous epithelial cell find use in various clinical settings, e.g., imaging methods, diagnostic methods, prognostic methods, and monitoring methods.
Reagents suitable for use in a subject method include: 1) reagents that detect the presence and/or level of a selected protein or collection of proteins; 2) reagents that detect posttranslational modifications of gene expression-controlling proteins; 3) reagents that detect the level of a selected DNA; 4) reagents that detect the integrity of a selected DNA; 5) reagents that detect methylation status of a selected
DNA; 6) reagents that detect the presence and/or a level of a selected mRNA or collection of mRNA; T) reagents that detect the presence and/or level of a selected microRNA; 8) reagents for proteomics
analyses; and 9) reagents for biological assays.
REAGENTS
[0091] As noted above, the present invention provides reagents for detecting a mammary epithelial cell signature that provides for identification of risk that a mammary epithelial cell will become malignant. These reagents are described in more detail below.
Reagents for detecting a mammary epithelial cell signature
[0092] The present invention provides reagents for detecting a mammary epithelial cell (MEC)
signature, e.g., an MEC signature that is indicative of a pre-cancerous MEC. An "MEC signature"
includes, but is not limited to: 1) the presence and/or level of a selected protein or collection of proteins; 2) the presence or absence of a posttranslational modification of a selected protein or collection of
proteins; 3) the presence of a chromatin modification; 4) the level of a selected DNA or collection of
DNA; 5) the integrity of a selected DNA or collection of DNA; 6) the methylation status of a selected
DNA or collection of DNA; 7) the presence and/or level of a selected mRNA or collection of mRNA; 8) the presence and/or level of a selected microRNA or collection of microRNA; and 9) secretion
and/or release of a factor from an MEC.
[0093] Suitable reagents include, but are not limited to, 1) reagents that detect the presence and/or level of a selected protein or collection of proteins; 2) reagents that detect posttranslational
modifications of gene expression-controlling proteins; 3) reagents that detect the level of a selected
DNA; 4) reagents that detect the integrity of a selected DNA; 5) reagents that detect methylation status of a selected DNA; 6) reagents that detect the presence and/or a level of a selected mRNA or collection of mRNA; 7) reagents that detect the presence and/or level of a selected microRNA; 8) reagents for proteomics analyses; and 9) reagents for use in biological assays.
Specific binding agents
[0094] Specific binding agents (also referred to as "capture agents") are provided, which are useful in a subject detection method, where specific binding agents include specific binding agents that detect the presence and/or level of a protein in an MEC, specific binding agents that detect the presence and/or levels of a selected posttranslationally modified protein, and the like. "Specific binding agents" include, e.g., antibodies, antigen-binding fragments of an antibody; an epitope-binding fragment of an antibody; or other protein that bind specifically to an epitope on a target polypeptide. The discussion below refers to antibody reagents. However, any specific binding agent is suitable for use. Hence, where the
disclosure refers to "antibody reagents," other specific binding agents are also contemplated.
[0095] Antibody reagents are provided, which are useful in a subject detection method. In some
embodiments, an antibody reagent detects the presence and/or levels of a selected protein or collection of proteins in an MEC. In other embodiments, an antibody reagent detects the presence and/or levels of a selected posttranslationally modified protein, e.g., a protein that controls gene expression.

[0096] A subject antibody reagent can be in substantially isolated form, e.g., in an environment other than its naturally-occurring environment. In some embodiments, a subject antibody reagent is a
synthetic antibody reagent, or a recombinant antibody reagent. In some embodiments, the antibody reagents are immobilized on an insoluble support. In some embodiments, a panel of antibodies is
provided, where a panel of antibodies is two or more different antibodies, each specific for a different polypeptide that comprises an MEC signature. The antibody reagents bind specifically to a selected target polypeptide or collection of selected target polypeptides.
[0097] Suitable antibody reagents include antibodies of any isotype; single-chain Fv; Fab; Fab; Fv;
F(ab')2; artificial antibodies; and the like. Suitable antibodies also include "artificial" antibodies, e.g., antibodies and antibody fragments produced and selected in vitro, In some embodiments, such
antibodies are displayed on the surface of a bacteriophage or other viral particle. In many embodiments, such artificial antibodies are present as fusion proteins with a viral or bacteriophage structural protein, including, but not limited to, Ml 3 gene m protein. Methods of producing such artificial antibodies are well known in the art. See, e.g., U.S. Patent Nos. 5,516,637; 5,223,409; 5,658,727; 5,667,988;
5,498,538; 5,403,484; 5,571,698; and 5,625,033. In some embodiments, the antibodies are monoclonal antibodies. In some embodiments, an antibody reagent is directly or indirectly detectably labeled.
[0098] Direct labels include radioisotopes; enzymes having detectable products (e.g., luciferase, β- galactosidase, and the like); fluorescent labels (e.g., fluorescein isothiocyanate, rhodamine,
phycoerythrin, and the like); fluorescence emitting metals, e.g., 152Eu, or others of the lanthanide series, attached to the antibody through metal chelating groups such as EDTA; chemiluminescent compounds, e.g., luminol, isoluminol, acridinium salts, and the like; bioluminescent compounds, e.g., luciferin, aequorin (green fluorescent protein), and the like. Other suitable detectable labels include fluorescent dyes, e.g., Fluorescein, Rhodamine, Texas Red, Cy2, Cy3, Cy5, VECTOR Red, ELF™ (Enzyme- Labeled Fluorescence), CyO, CyO.5, CyI, CyI .5, Cy3, Cy3.5, Cy5, Cy7, FluorX, Calcein, Calcein-AM, CRYPTOFLUOR™, Orange (42 kDa), Tangerine (35 kDa), Gold (31 kDa), Red (42 kDa), Crimson (40 kDa), BHMP, BHDMAP, Br-Oregon, Lucifer Yellow, Alexa dye family, N-[6-(7-nitrobenz-2-oxa-l, 3- diazol-4-yl)amino]caproyl] (NBD), BOD1PY™, boron dipyrromethene difluoride, Oregon Green,
MΓTOTRACKER™ Red, DiOC7 (3), DiICi8, Phycoerythrin, Phycobiliproteins BPE (240 kDa) RPE
(240 kDa) CPC (264 kDa) APC (104 kDa), Spectrum Blue, Spectrum Aqua, Spectrum Green, Spectrum Gold, Spectrum Orange, Spectrum Red, NADH, NADPH, FAD, Infra-Red (IR) Dyes, Cyclic GDP- Ribose (cGDPR), Calcofluor White, Tyrosine and Tryptophan.
[0099] In some embodiments, an antibody reagent comprises, covalently linked to the antibody
reagent, a protein that provides for a detectable signal. Suitable proteins include, but are not limited to, fluorescent proteins and enzymes (e.g., β-galactosidase, luciferase, horse radish peroxidase, alkaline phosphatase, etc.). Polypeptides that provide a detectable signal include fluorescent proteins,
chromogenic proteins, enzymes that catalyze the production of a product that is luminescent,
fluorescent, or colored, etc. Suitable fluorescent proteins include, but are not limited to, a green fluorescent protein (GFP; Chalfie, et al., Science 263(5148):802-805 (Feb 11, 1994); an enhanced GFP (EGFP), Clontech - Genbank Accession Number U55762); a blue fluorescent protein (BFP; 1. Quantum Biotechnologies, Inc. 1801 de Maisonneuve Blvd. West, 8th Floor, Montreal (Quebec) Canada H3H
1 J9; 2. Stauber, R. H. Biotechniques 24(3):462-471 (1998); 3. Heim, R. and Tsien, R. Y. Curr. Biol.
6:178-182 (1996)); an enhanced yellow fluorescent protein (EYFP; Clontech Laboratories, Inc., 1020 East Meadow Circle, Palo Alto, CA 94303); a fluorescent protein as described in, e.g., WO 92/15673, WO 95/07463, WO 98/14605, WO 98/26277, WO 99/49019, U.S. Patent No. 5,292,658, U.S. Patent
No. 5,418,155, U.S. Patent No. 5,683,888, U.S. Patent No. 5,741,668, U.S. Patent No. 5,777,079, U.S. Patent No. 5,804,387, U.S. Patent No. 5,874,304, U.S. Patent No. 5,876,995, and U.S. Patent No.
5,925,558; a GFP from species such as Renilla reniformis, Renilla mulleri, or Ptilosarcus guernyi, as described in, e.g., WO 99/49019 and Peelle et al. (2001) J. Protein Chem. 20:507-519; "humanized" recombinant GFP (hrGFP) (Stratagene); any of a variety of fluorescent and colored proteins from
Anthozoan species, as described in, e.g., Matz et al. (1999) Nature Biotechnol. 17:969-973, U.S. Patent Publication No. 2002/0197676, or U.S. Patent Publication No. 2005/0032085; and the like.
[00100] Indirect labels include second antibodies specific for an antibody reagent, wherein the second antibody is labeled as described above; and members of specific binding pairs, e.g., biotin-avidin, and the like.
[00101] In some embodiments, the antibodies are immobilized on an insoluble support, e.g., in an
antibody diagnostic device, in an antibody array, etc. Antibodies can be immobilized directly or
indirectly (e.g., via a linker molecule) to an insoluble support for use in a diagnostic assay to detect a target polypeptide in a biological sample. An antibody reagent can be immobilized by covalent or non- covalent attachment to an insoluble support. Insoluble supports include, but are not limited to, beads
(e.g., polystyrene beads, magnetic beads, and the like); plastic surfaces (e.g., polystyrene or
polycarbonate multi-well plates typically used in an enzyme-linked immunosorbent assay (ELISA) or radioimmunoassay (RIA), and the like); sheets, e.g., nylon, nitrocellulose, and the like; and chips, e.g., SiO2 chips such as those used in microarrays. Accordingly, the invention further provides assay devices comprising one or more antibody reagents attached to a solid support.
[00102] The present invention further provides an array of antibodies, e.g., monoclonal antibodies, attached to an insoluble support in an array. In some embodiments, a subject antibody array provides for detection of a target polypeptide that is indicative of a pre-cancerous epithelial cell.
[00103] Suitable antibodies are obtained by immunizing a host animal with peptides comprising all or a portion of a target protein. Suitable host animals include mouse, rat sheep, goat, hamster, rabbit, etc.
The host animal will generally be from a different species than the immunogen where the immunogen is from a naturally occurring source, e.g., a human sample, where representative host animals include, but are not limited to, e.g., rabbits, goats, mice, etc.
[00104] Methods for producing and using antibody arrays are known in the art; and any known method can be used. See, e.g., U.S. Patent No. 6,797,393.

[00105] In one embodiment, the antibody reagents are arranged in the form of an array. An array can be created by spotting captures agents onto a substrate (e.g., glass, nitrocellulose, etc.) and attaching those capture agents to the substrate. The antibody reagents can be bound to the substrate by either covalent bonds or by non-specific interactions, such as hydrophobic interactions. Techniques for constructing arrays and methods of using these arrays are described in, for example, Schena et al. (1996) Proc Natl Acad Set USA. 93(20): 10614-9; Schena et al. (1995) Science 270(5235):467-70; Shalon ef α/. (1996) Genome Res. 6(7):639-45, USPN 5,807,522, EP 799 897; WO 97/29212; WO 97/27317; EP 785 280; WO 97/02357; USPN 5,593,839; USPN 5,578,832; EP 728 520; USPN 5,599,695; EP 721 016; USPN 5,556,752; WO 95/22058; and USPN 5,631,734. The antibody reagents utilized in the arrays can be of varying types and can include, for example, antibodies, including antibody fragments, aptamers,
avimers, or peptidomimetics.
[00106] Common physical substrates for making protein arrays include glass or silicon slides, magnetic particles or other micro beads, functionalized with aldehyde or other chemical groups to help
immobilize proteins. The substrate can also be coated with PLL (polylysine), nitrocellulose, PVDF membranes or modified with specific chemical reagents to adsorb capture agents. The desirable
properties of an ideal surface include: chemical stability before, during, and after the coupling
procedure, suitability for a wide range of capture agents (e.g., hydrophilic and hydrophobic, low MW and high MW), minimal non-specific binding, low or no intrinsic background in detection, presentation of the capture agents in a fully-functional orientation, production of spots with predictable and regular morphology (shape, signal uniformity).
[00107] The variables in the immobilization of proteins include: type of capture agent (e.g., antibody reagent), nature of surface (including any pretreatment prior to use), and the immobilization method.
Both adsorption and covalent attachment have been used for protein arrays. Orientation of the capture agent is very important in presenting it to the ligand or the surface in a functional state. Although
covalent attachment using a variety of chemically activated surfaces (e.g., aldehyde, amino, epoxy) as well as attachment by specific biomolecular interactions (e.g., biotin-streptavidin) provide a stable linkage and good reproducibility, chemical derivatization of the surface may alter the biological activity of the capture agent and/or may result in multi-site attachment.
[00108] In one embodiment, antibody arrays are made with a non-contact deposition printer. The printer uses thermal ink jet heads that can print many solutions simultaneously to produce hundreds of spots of 50-60 μm in diameter with a spacing of 150 μm between spots. The droplet volume ranges between 35 pL to 1.5 nL. The heating element is made out of TaAl or other suitable materials, and is capable of achieving temperatures that can vaporize a sufficient volume of printing buffer to produce a bubble that will push out a precise volume of the antibody solution on the substrate. Selection of printing buffer is important, in that the buffer accomplishes the following: increases printing efficiency (measure of the number of spots that are printed to the total number of spots that are attempted), reduces sample
spreading, promotes uniform delivery, stabilizes the capture agents that are being printed, reduces sample drying, and increases the visibility of the printed spots. In addition to the printing buffer, other variables that affect printing include: size of the drops, the method of washing and drying the print head, and the speed at which the dispensing head moves. Various modifications may be within these conditions.
Antibody reagents that detect the presence and/or level of a selected protein or collection of proteins
[00109] In some embodiments, a subject antibody (or panel of antibodies) detects the presence and/or level of a selected protein (or collection of proteins) produced by an MEC. Detection of the presence and/or level of a selected protein or collection of proteins produced by an MEC allows prediction of the likelihood that the MEC is pre-cancerous, e.g., will progress to form a tumor. For example, in some embodiments, a subject antibody or antibody array detects the presence and/or level of a selected target polypeptide, or collection of target polypeptides, that constitute a vMEC signature, e.g., the
polypeptide(s) are present in a vMEC at a higher or lower than normal level, compared to a control, normal MEC (e.g., compared to a CD73' MEC).
[00110] Suitable antibodies include antibodies that bind specifically to a target polypeptide identified in

Figure 14. Suitable antibodies include antibodies that bind specifically to a target polypeptide selected from: CD73, CDl 38, notch receptor-3, CD90, BMI-I, COX-2, Ki67, pl6, IGF2, YKL-40, EGF-R, c- jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK, MAPKK, DDR, TRF2, activin, and MEK1/2. These proteins are discussed in greater detail below.
[00111] CD73 (also referred to as 5 '-ribonucleotide phosphohydrolase) is a membrane-bound enzyme that catalyzes the conversion of AMP to bioactive adenosine at neutral pH; and also has functions independent of its enzyme activity. CD73 is expressed on various cells include endothelial cells,
pericytes, follicular dendritic cells, and subsets of T cells. Amino acid sequences of human CD73 are known, and are presented in, e.g., GenBank Accession Nos. AAH65937, NP_002517, and AI40168.
[00112] CD90, also known as Thy-1, is a 25-37 kD, glycosylphosphatidylinositol-anchored, cell surface glycoprotein found on many cell types. Amino acid sequences of human CD90 are known, and are presented in, e.g., GenBank Accession Nos. P04216, AAG13904, AAH65559, and NP_006279. See also, Seki et al. (1985) Proc. Natl. Acad. ScL U.S.A. 82:6657-6661.
[00113] CD138, also known as syndecan-1, is a transmembrane heparan sulfate proteoglycans. Amino acid sequences of human CDl 38 are known, and are presented in, e.g., GenBank Accession Nos.
AAH08765, P18827, and NP_002988.
[00114] Notch3 (or "notch-3 receptor") is a membrane-spanning protein that comprises multiple tandem repeats of a calcium-binding, epidermal growth factor (EGF)-like domain. Amino acid sequences of human notch3 are known and are presented in, e.g., GenBank Accession Nos. AAB91371, AACl 5789, AAC14346, and NP_000426.
[00115] COX-2 ("cyclooxygenase-2") is an enzyme that converts arachidonic acid to prostaglandin H2.

Amino acid sequences of human COX-2 are known, and are presented in, e.g., GenBank Accession
Nos. AAA58433 and NP_000954.

[00116] Ki67 (also referred to as "Ki67 antigen") is a nuclear antigen expressed in proliferating cells but not in quiescent cells, and thus is used as a "proliferation marker" to measure proliferation of cells. Multiple isoforms of Ki 67 have been identified. Ki67 includes multiple repeats of an approximately 22 amino acid motif, referred to as the "Ki67" motif. Schluter et al. (1993) J. Cell Biol. 123:513-522.
Amino acid sequences of a 3256-amino acid isoform of human Ki-67 are known, and are presented in, e.g., GenBank Accession Nos. CAA46519, CAIl 6902, CAH73169, and EAW49178. Amino acid
sequences of a 2896-amino acid isoform of human Ki-67 are known, and are presented in, e.g.,
GenBank Accession Nos. CAA46520, CAIl 6903, CAH73170, and EAW49179. Amino acid sequences of a 2801-amino acid isoform of human Ki-67 are known, and are presented in, e.g., GenBank
Accession No. EAW49177.
[00117] pl6 (also known as INK4a, MTSl, CDK4I, and cyclin dependent kinase inhibitor 2A) is a cyclin dependent kinase inhibitor, pi 6, a member of the INK4 family, binds to and inhibits cyclin- dependent kinase-4 (CDK4). Amino acid sequences of human pl6 are known, and are presented in, e.g., GenBank Accession Nos. P42771 (156 amino acid form); NP_000068 (156 amino acid form);
NP_478102 (173 amino acid form); and NP_478104 (116 amino acid form).
[00118] IGF2 (also known as somatomedin A) is a single chain polypeptide that shares amino acid sequence identity of about 47% with insulin. Amino acid sequences of 180 amino acid human IGF2 are known, and are presented in, e.g, GenBank Accession No. ABD93451 , and GenBank Accession No.
ABM83647.
[00119] YKL-40 is a secreted glycoprotein of the chitinase family. YKL-40 is a major secretory protein of human chondrocytes and synoviocytes. Hakala et al. J. Biol. Chem. 268 (34), 25803-25810 (1993). Amino acid sequences of human YKL-40 are known, and are presented in, e.g., GenBank Accession
No. AAA16074; and U.S. Patent No. 6,579,684.
[00120] Epidermal growth factor receptor (EGF-R) is also referred to as ErbB-1 or HERl . EGF-R is the cell-surface receptor for members of the epidermal growth factor family (EGF-family) of extracellular protein ligands. EGFR (epidermal growth factor receptor) exists on the cell surface and is activated by binding of its specific ligands, including epidermal growth factor and transforming growth factor α
(TGFα). Amino acid sequences of human EGF-R are known, and are presented in, e.g,. GenBank
Accession Nos. AAG35786 (pi 10); and AAG35787 (p60).
[00121] c-jun is the cellular counterpart of the transforming protein of the chicken retrovirus ASV17.

Via a leucine zipper, c-Jun forms homodimers and heterodimers with Fos and other jun-related proteins which, together, comprise the AP-I transcription factor that binds TPA response elements (TREs). c- Jun therefore mediates transcriptional regulation in response to a variety of stimulants. Amino acid sequences of human c-jun are known, and are presented in, e.g., GenBank Accession Nos. AAH68522 and NP 002219.

[00122] Proliferating cell nuclear antigen (PCNA) (also referred to as cyclin, or DNA polymerase delta auxiliary protein) is involved in DNA replication and repair. Amino acid sequences of human PCNA are known, and are presented in, e.g,. GenBank Accession Nos. AAH00491 and NP_872590.
[00123] Cyclin Bl plays a role in cell cycle control. M-phase promoting factor or maturation promoting factor (MPF), the key regulator of the G2 M transition during the cell cycle, is regulated by
phosphorylation of both of its component proteins: the serine/threonine protein kinase cdc2 and a B- type cyclin. Amino acid sequences of human cyclin Bl are known, and are presented in, e.g,. GenBank Accession Nos. NP_114172, EAW51306, and AAP88038.
[00124] C-kit, also known as CDl 17, is a cytokine receptor expressed on the surface of hematopoietic stem cells as well as other cell types. C-kit is the receptor for the cytokine stem cell factor (SCF), also known as "steel factor" or "c-kit ligand." Amino acid sequences of human c-kit are known, and are presented in, e.g,. GenBank Accession Nos. AAH71593 and AAC50968.
[00125] Signal Transducer and Activator of Transcription-3 (STAT3) is a member of a family of
STATs. STATS are transcription factors that are phosphorylated by JAK kinases in response to
cytokine activation of a cell surface receptor tyrosine kinases. Bromberg et al. (1999) Cell 98:295-303; and DiIe (2001) Curr. Opin. Cell Biol. 13:211-217. Amino acid sequences of human STAT3 are known, and are presented in, e.g,. GenBank Accession Nos. NP_644805, NP_003141 , NP_998827, and .
CAAl 0032.
[00126] The cyclin Dl proto-oncogene is an important regulator of Gl to S-phase transition and an important cofactor for several transcription factors in numerous cell types. Amino acid sequences of human cyclin Dl are known, and are presented in, e.g,. GenBank Accession Nos. NP_444284,
AAH23620, AAH25302, AAH01501, and AAH14078.
[00127] Phosphatidylinositol 3-kinases (PI3K) generate lipids that control a wide variety of intracellular signalling pathways.. Mammals have eight distinct catalytic subunits and seven regulatory subunits.
Catalytic subunit isoforms include pi 10a, pi lOβ, pi 105, and pi lOγ. Amino acid sequences of human
PI3K catalytic subunits are known, and are presented in, e.g., GenBank Accession Nos. NP 005017,
000329, and CAIl 5702 (pi lOδ); NP_006209, AAIl 3604, and P42336 (pi 10a); NP_0O2640, P48736, and AAH35683 (pi lOγ); and NP_006210, AAI14433, and P42338 (pi lOβ). See also, Kang et al.
(2006) Proc. Natl. Acad. ScL USA 103:1289; and Vanhaesebroeck et al. (2005) TRENDS Biochem. Sd. 30:194.
[00128] Mitogen-activated protein (MAP) kinases (MAPK) are serine/threonine-specific protein kinases that respond to extracellular stimuli (e.g., mitogens) and regulate various cellular activities, such as gene expression, mitosis, differentiation, and cell survival/apoptosis. MAPK include MAPKl (ERK2, MAPKl), MAPK3 (ERKl), MAPK6 (ERK3), MAPK7 (ERK7), MAPK8 (JNKl), MAPK9 (JNK2),
MAPKlO (JNK3), MAPKl 1 (p38bMAPK), MAPK12 (p38gMAPK), MAPK13, and MAPK14 (p38
MAPK). Amino acid sequences of human MAPK are known, and are presented in, e.g., GenBank
Accession Nos. NP_002736, NP_620407, and AAH99905 (MAPKl); AAHl 3992, P27361, EAW79912, EAW79912, EAW77913, EAW79914, and EAW79915 (MAPK3); NP_002739,
AAH35492, and EAW77434 (MAPK6); NP_620603, NP_620601, and EAW50887 (MAPK7);
AAI30571, NP_620637, and NP_620635 (MAPK8); CAG38817, AAH32539, and AAY46156
(MAPK9); AAH65516, AAH51731, and P53779 (MAPKlO); CAG30400, NP_002742, and
AAH27933 (MAPKI l); CAG30401, NP_002960, and AAH15741 (MAPK12); CAG46488, CAI9690, and CAB08438 (MAPKl 3); CAG38743, AAH31574, and AAH00092 (MAPKl 4).
[00129] Mitogen-activated protein (MAP) kinases require dual phosphorylation on threonine and
tyrosine residues in order to gain enzymatic activity. This activation is carried out by a family of
enzymes known as MAP kinase kinases (MAPKKs, MKKs, or MEKs). MAPKK include MAP2K1
(MEKl), MAP2K2 (MEK2), MAP2K3 (MEK3), MAP2K4 (Mkk4, JNKKl), MAP2K5 (MEK5),
MAP2K6 (MKK6), MAP2K7 (JNKK2). Amino acid sequences of human MAPKKs are known, and are presented in, e.g., GenBank Accession Nos. AAI39730, NP_002746, and Q02750 (MAP2K1);
NP_109587, AAH18645, and P36507 (MAP2K2).
[00130] TRF2 is a telomere-binding protein. Telomere-binding proteins TRFl and TRF2 interact with several other telomere regulators including TIN2, PTOP, POTl, and RAPl to ensure proper
maintenance of telomeres. TRF2 mediates t-loop formation and end protection. Liu et al. (2004) J. Biol. Chem. 279:51338. Amino acid sequences of human TRF2 (500 amino acids) are known, and are
presented in, e.g., GenBank Accession Nos. NP_05643, Ql 5554, and AAB81135.
[00131] Activin A is a homodimer of the activin βA subunits. The activin βA monomer can also form a heterodimer with inhibin α, to produce the activin A antagonist, inhibin A. Amino acid sequences of human activin βA (426 amino acids) are known, and are presented in, e.g, GenBank Accession Nos.
EAL24001, EAW94141, and AAH07858.
[00132] In some embodiments, the present invention provides an antibody panel, comprising two or more antibodies with specificity for two or more polypeptides that are differentially expressed in precancerous epithelial cells or surrounding epithelial cells, hi some embodiments, a subject antibody panel comprises antibody reagents that provide for detection of two, three, four, five, or all of CD73,
CDl 38, notch receptor-3, CD90, BMI-I, and COX-2. In other embodiments, a subject antibody panel comprises antibody reagents that provide for detection of CD90 and CD73. In other embodiments, a subject antibody panel comprises antibody reagents that provide for detection of Ki67 and COX-2. In other embodiments, a subject antibody panel comprises antibody reagents that provide for detection of Ki67 and pi 6. In other embodiments, a subject antibody panel comprises antibody reagents that provide for detection of Ki67, COX-2, and pi 6. In other embodiments, a subject antibody panel comprises antibody reagents that provide for detection of TRF2 and activin. In other embodiments, a subject antibody panel comprises antibody reagents that provide for detection of activin, and markers that are induced by activin.

Antibody reagents that detect the presence and/or level of posttranslationally modified polypeptides
[00133] In some embodiments, a subject antibody detects the presence and/or level of a
posttranslationally modified polypeptide produced by an MEC. Posttranslationally modified
polypeptides that are targets for a subject antibody reagent include histone deacetylase (HDAC)
polypeptides. Posttranslational modifications of HDAC polypeptides include methylation and
acetylation. In some embodiments, an antibody reagent specifically binds to an HDAC epitope(s) that is not modified, e.g., the antibody reagent binds specifically to an HDAC epitope that comprises only encoded amino acids. In other embodiments, an antibody reagent specifically binds to an acetylated
HDAC polypeptide, e.g., the antibody reagents binds specifically to an HDAC epitope that is
acetylated. In other embodiments, an antibody reagent specifically binds to a methylated HDAC
polypeptide, e.g., the antibody reagents binds specifically to an HDAC epitope that is methylated.
Antibody reagents that detect a chromatin modification
[00134] In some embodiments, an antibody reagent for use in a subject detection method includes an antibody reagent that detects a modification of one or more intracellular proteins. Modification of an intracellular protein includes, e.g., modification of chromatin, e.g., acetylation of chromatin by an
HDAC (e.g., polycomb-group (PcG) protein modifications; histone modifications); etc. In some
embodiments, an antibody reagent detects a chromatin epitope that is acetylated. In other embodiments, an antibody reagent detects a chromatin epitope that is deacetylated. In other embodiments, an antibody reagent detects a chromatin epitope that is methylated. In other embodiments, an antibody reagent detects a chromatin epitope that is demethylated.
Antibody reagents that detect modification of an extracellular matrix component
[00135] hi some embodiments, an antibody reagent for use in a subject detection method includes an antibody reagent that detects a modification in an extracellular matrix (ECM) component. ECM
modifications that can be detected using a subject antibody reagent include, but are not limited to, enzymatic cleavage of an ECM component into fragments; sulfation; removal of one or more sulfate groups; phosphorylation; dephosphorylation; glycosylation; deglycosylation; and the like. ECM
includes, but is not limited to, collagen, fibronectin, elastin, laminin, etc.
Antibody reagents that detect secretion and/or release of a molecule
[00136] hi some embodiments, an antibody reagent for use in a subject detection method includes an antibody reagent that detects a secreted or released molecule from a cell, e.g., an MEC, a fibroblast that is cultured in vitro with a reporter epithelial cell, etc. Secreted or released molecules that can be
detected using an antibody reagent include, e.g., proteins. MEC can also secrete one or more of a
nucleic acid, a calcium ion, etc., and such molecules can be detected using other reagents, as described below.
Binding reagents that detect methylated DNA
[00137] hi some embodiments, a binding reagent for use in a subject detection method includes a
binding reagent that detects methylated DNA, e.g., where the methylation status of a selected DNA provides an indication as to whether a cell, e.g., an MEC, is pre-cancerous. Binding reagents that detect methylated DNA are known in the art and include binding reagents that specifically bind a nucleotide sequence comprising a C1^pG sequence, where Cme is methylated cytosine. Suitable CmBpG-specific binding reagents include methylated-CpG binding domain proteins (MBD) (e.g., MECP2; MBD2; etc.); a methylated-CpG-binding domain of an MBD protein; an antibody reagent specific for a methylated- CpG; and the like. See, e.g., Yegnasubramanian et al. (2006) Nucl. Acids Res. 34:el9. Proteins
containing a methyl-binding domain include, but are not limited to, MBDl, MBD2, MBD3, MBD4,
MeCPl and MeCP2. See, for example, Bird et al. (1999) Cell 99:451-454.
Specific binding reagent panels
[00138] Specific binding reagent panels are provided. As noted above, in some embodiments, a specific binding reagents is an antibody; however, specific binding reagents other than antibodies are also
contemplated. Where the disclosure refers to an "antibody reagent panel," it should be understood that the disclosure applies as well to panels of other specific binding reagents. Antibody reagent panels
(specific binding reagent panels) are provided, where a subject antibody reagent panel includes two or more of: 1) an antibody reagent that provides for detection of the presence and/or level of a selected protein or collection of proteins, e.g., a selected protein or collection of proteins that provide for
detection of a pre-cancerous MEC; 2) an antibody reagent that provides for detection of the presence and/or level of a posttranslationally modified polypeptide; 3) an antibody reagent that provides for detection of a chromatin modification; 4) an antibody reagent that provides for detection of
modification of an ECM component; 5) an antibody reagent that provides for detection of secretion or release of a molecule from a cell, e.g., from an MEC, from a fibroblast that is cultured in vitro with a reporter epithelial cell, etc; and 6) a binding reagent that provides for detection of a methylated DNA.

[00139] In some embodiments, a subject antibody reagent panel includes two or more of: 1) two or more different antibody reagents that provide for detection of the presence and/or level of two or more selected proteins, e.g., two or more selected proteins that provide for detection of a pre-cancerous MEC; 2) an antibody reagent that provides for detection of the presence and/or level of a posttranslationally modified polypeptide; 3) an antibody reagent that provides for detection of a chromatin modification; 4) an antibody reagent that provides for detection of modification of an ECM component; 5) an antibody reagent that provides for detection of secretion or release of a molecule from a cell; and 6) a binding reagent that provides for detection of a methylated DNA.
[00140] In some embodiments, a subject antibody reagent panel includes two or more antibodies that bind specifically to two or more of the protein markers identified in Figure 14. In some embodiments, a subject antibody reagent panel includes two or more of: 1) two or more different antibody reagents that provide for detection of the presence and/or level of two or more of CD73, CD138, notch receptor-3,
CD90, BMI-I, COX-2, Ki67, pi 6, IGF2, YKL-40, EGR-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2; 2) an antibody reagent that provides for detection of the presence and/or level of a posttranslationally modified polypeptide; 3) an antibody reagent that provides for detection of a chromatin modification; 4) an antibody reagent that provides for detection of modification of an ECM component; 5) an antibody reagent that provides for detection of secretion or release of a molecule from a cell; and 6) a binding reagent that provides for detection of a methylated DNA.
[00141] In some embodiments, a subject antibody reagent panel includes two or more of: 1) two or more different antibody reagents that provide for detection of the presence and/or level of two or more of CD73, CDl 38, notch receptor-3, CD90, BMI-I, and COX-2; 2) an antibody reagent that provides for detection of the presence and/or level of a posttranslationally modified polypeptide; 3) an antibody reagent that provides for detection of a chromatin modification; 4) an antibody reagent that provides for detection of modification of an ECM component; 5) an antibody reagent that provides for detection of secretion or release of a molecule from a cell; and 6) a binding reagent that provides for detection of a methylated DNA.
[00142] In some embodiments, a subject antibody reagent panel includes two or more of: 1) two or more different antibody reagents that provide for detection of the presence and/or level of COX-2,
Ki 67, and pi 6; 2) an antibody reagent that provides for detection of the presence and/or level of a
posttranslationally modified polypeptide; 3) an antibody reagent that provides for detection of a
chromatin modification; 4) an antibody reagent that provides for detection of modification of an ECM component; 5) an antibody reagent that provides for detection of secretion or release of a molecule from a cell.; and 6) a binding reagent that provides for detection of a methylated DNA.
[00143] In some embodiments, a subject antibody reagent panel includes two or more of: 1) two or more different antibody reagents that provide for detection of the presence and/or level of TRF2 and activin; 2) an antibody reagent that provides for detection of the presence and/or level of a
posttranslationally modified polypeptide; 3) an antibody reagent that provides for detection of a
chromatin modification; 4) an antibody reagent that provides for detection of modification of an ECM component; 5) an antibody reagent that provides for detection of secretion or release of a molecule from a cell.; and 6) a binding reagent that provides for detection of a methylated DNA.
[00144] As noted above, in some embodiments, an antibody reagent panel comprises two or more
antibody reagents immobilized onto an insoluble support. In some embodiments, a subject antibody reagent panel comprises an array of antibody reagents.
Nucleic acid reagents
[00145] The present invention provides nucleic acid reagents for use in a subject detection method (e.g., in a subject imaging method, a subject diagnostic method, a subject prognostic method, a subject
method for determining efficacy of a treatment method, etc.). The nucleic acid reagents are in
substantially isolated form, and can be synthetic or recombinant. The nucleic acid reagents include reagents that provide for one or more of: 1) detection of the level of a selected DNA; 2) detection of the integrity of a selected DNA; 3) detection of the methylation status of a selected DNA; 4) detection of the presence and/or a level of a selected mRNA or collection of mRNA; and 5) detection of the
presence and/or level of a selected microRNA or collection of microRNAs.
Reagents for detecting the level of a selected DNA
[00146] In some embodiments, a subject nucleic acid reagent provides for detection of the level of a selected DNA in an MEC. For example, in some embodiments, a selected DNA is amplified (e.g., present in greater than the normal copy number) in an MEC that is pre-cancerous. In other
embodiments, a selected DNA is deleted (entirely or in part) in an MEC that is pre-cancerous. Suitable nucleic acid reagents for detecting the level of a selected DNA in an MEC include nucleic acid reagents that function as primers for nucleic acid amplification; nucleic acid reagents that function as nucleic acid probes; and the like. In some embodiments, one or more additional, non-nucleic acid, reagent is provided in a system for use in detecting the level of a selected DNA in an MEC. Such additional
reagents include, for example, a restriction endonuclease that cuts at a site adjacent to and/or within an amplified region of a selected DNA; and the like. As an example, a subject system can include a
restriction endonuclease that cuts at a site adjacent to and/or within an amplified region of a selected
DNA; and a nucleic acid reagent that functions as a probe and provides for determination of the relative levels of the selected DNA in a test MEC, compared to one or more control MEC. Genomic loci that are amplified in a pre-cancerous MEC include loci in chromosome 14q. Genomic loci that are deleted in a pre-cancerous MEC include loci in chromosomes 3p, 4, 5, and 6q. Such amplifications and/or deletions can be detected by array profiling, by karyotyping, etc.
Reagents for detecting the integrity of a selected DNA
[00147] In some embodiments, a subject nucleic acid reagent provides for detection of the integrity of a selected DNA in an MEC. For example, in some embodiments, a subject nucleic acid reagent provides for detection of one or more of: a translocation of a selected DNA, an inversion of a selected DNA, deletion of all or a portion of a selected DNA, and telomere integrity, in an MEC. Suitable nucleic acid reagents for detecting the integrity of a selected DNA in an MEC include nucleic acid reagents that function as primers for nucleic acid amplification; nucleic acid reagents that function as nucleic acid probes; and the like. In some embodiments, one or more additional, non-nucleic acid, reagent is
provided in a system for use in detecting the integrity of a selected DNA in an MEC. Such additional reagents include, for example, a restriction endonuclease that cuts at a site adjacent to and/or within a selected DNA; and the like. As an example, a subject system can include a restriction endonuclease that cuts at a site adjacent to and at a site within a selected DNA; and a nucleic acid reagent that functions as a probe and provides for determination of the integrity of the selected DNA in a test MEC, compared to one or more control MEC.
Reagents that provide for detection of the methylation status of a selected DNA
[00148] In some embodiments, a subject nucleic acid reagent provides for detection of the methylation status of a selected DNA in an MEC. Suitable nucleic acid reagents include nucleic acid reagents that function as primers for nucleic acid amplification; nucleic acid reagents that function as nucleic acid probes; and the like. Nucleic acid reagents can be used in a variety of methods to detect DNA
methylation status, where suitable methods include, but are not limited to, methylation-specific
polymerase chain reaction (MSP; Herman et al. (1996) Proc. Natl. Acad. ScL USA 93:9821-9826);
MethylLight (Eads et al. (2000) Nucl Acids Res. 28:E32; and U.S. Pat. No. 6,331,393); HeavyMethyl (Cottrell et al. (2004) Nucl. Acids Res. 32:el 0); MethylQuant (Thomassin et al. (2004) Nucl. Acids Res. 32:el68; and the like.
[00149] A number of methods involve treatment of DNA with a bisulfite reagent, which converts
unmethylated cytosines to uracils, leaving only methylated cytosines unchanged (see, e.g., WO
05/038051). Following bisulfite treatment, individual cytosine positions can be detected by a primer extension reaction (Gonzalgo and Jones (1997) Nucleic Acids Res. 25:2529-31; and WO 95/00669) or by enzymatic digestion (Xiong and Laird (1997) Nucleic Acids Res. 25: 2535-4). Alternatively,
following bisulfite treatment, a methylation-specific polymerase chain reaction (PCR) can be carried out, using primers that bind either to methylated or unmethylated DNA only and that therefore
selectively amplify only DNA with a defined methylation. MethylLight is a variation of MSP, and involves use of a methylation-specific real-time detection probe (MethyLight), which makes the assay both homogenous and quantitative. HeavyMethyl is also a variation on MSP. In the HeavyMethyl method, the priming is methylation specific, but non-extendable oligonucleotide blockers provide this specificity instead of the primers themselves. The blockers bind to bisulfite-treated DNA in a
methylation-specific manner, and their binding sites overlap the primer binding sites. When the blocker is bound, the primer cannot bind and therefore the amplicon is not generated. When the blocker is not bound, the primer-binding site is accessible and the amplicon is generated. HeavyMethyl in
combination with real-time detection with methylation-specific fluorogenic probes provides sensitive and specific detection of DNA methylation.
[00150] In some embodiments, a subject system will include, in addition to a nucleic acid reagent, one or more additional reagents, e.g., a methylation-sensitive restriction endonuclease (e.g., a restriction endonuclease that recognizes and cleaves a nucleic acid having a particular nucleotide sequence only when the sequence is unmethylated); a methylation-insensitive restriction endonuclease (e.g., a
restriction endonuclease that recognizes and cleaves a nucleic acid having a particular nucleotide
sequence, regardless of the methylation status of the nucleotide sequence); and the like. The term
"methylation-sensitive enzyme" refers to a restriction enzymes that does not cleave DNA (or cleaves
DNA poorly) if one or more nucleotides in its recognition site are methylated. Suitable methylation- sensitive and methylation-insensitive restriction endonucleases that are suitable for use include, but are not limited to, Mbol, DpnII, HpaH, BsmBL Sau3A, and CIaI.
Reagents that provide for detection of the level and/or presence of an mRNA
[00151] A subject nucleic acid reagent includes a nucleic acid probe, or collection of nucleic acid
probes, that provides for detection of the presence and/or level of an mRNA (or a cDNA copy of an mRNA) in an MEC. In some embodiments, a subject nucleic acid reagent is a nucleic acid primer, or a collection of nucleic acid primers, that provides for detection of the presence and/or level of an mRNA (or a cDNA copy of an mRNA) in an MEC. For example, a subject nucleic acid reagent includes a
nucleic acid probe, or collection of nucleic acid probes, a nucleic acid primer, or a collection of nucleic acid primers, that provides for detection of the presence and/or level of an mRNA (or a cDNA copy of an mRNA) that is differentially expressed in a pre-cancerous MEC. For example, an mRNA (or a
cDNA copy) that is differentially expressed in a pre-cancerous MEC can be expressed at a level that is at least about 25%, at least about 50%, at least about 75%, at least about 100% (or 2-fold), at least about 5-fold, at least about 10-fold, at least about 50-fold, or at least about 100-fold, or more, higher than the level of the mRNA in a normal (non-pre-cancerous) MEC. As another example, an mRNA (or a cDNA copy) that is differentially expressed in a pre-cancerous MEC can be expressed at a level that is at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90% lower than the level of the mRNA in a normal (e.g., non- pre-cancerous) MEC.
[00152] Exemplary nucleic acid probes include probes that detect, in an MEC (e.g., a vMEC, or a
normal MEC), one or more of the mRNA set forth in Figure 14. Exemplary nucleic acid probes include probes that detect, in an MEC (e.g., a vMEC, or a normal MEC), one or more of the following mRNA
(or cDNA copy of an mRNA): CD73, CD138, notch receptor-3, CD90, BMI-I, COX-2, Ki67, pl6,
IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK,
MAPKK, DDR2, TRF2, activin, and MEK1/2.
[00153] In some embodiments, a subject nucleic acid reagent is a collection of nucleic acid probes that provides for detection of two or more of the following mRNA (or cDNA copy of an mRNA): CD73,
CD138, notch receptor-3, CD90, BMI-I5 COX-2, Ki67, pl6, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2.
[00154] In some embodiments, a subject nucleic acid reagent is a collection of nucleic acid probes that provides for detection of the presence and/or level of two, three, four, five, or all of CD73, CD138, notch receptor-3, CD90, BMI-I, and COX-2 mRNAs (or cDNA copies of same). In other embodiments, a subject nucleic acid reagent is a collection of nucleic acid probes that provides for detection of the presence and/or level of Ki67, COX-2, and pl6 mRNA (or cDNA copies of same).
[00155] Nucleic acid probes that are suitable for detecting the presence and/or level of an mRNA that is differentially expressed in a pre-cancerous MEC can have a length of from about 10 nucleotides to about 100 nucleotides (nt), e.g., from about 10 nt to about 15 nt, from about 15 nt to about 20 nt, from about 20 nt to about 25 nt, from about 25 nt to about 30 nt, from about 30 nt to about 40 nt, from about 40 nt to about 50 nt, from about 50 nt to about 60 nt, from about 60 nt to about 70 nt, from about 70 nt to about 80 nt, from about 80 nt to about 90 nt, or from about 90 nt to about 100 nt.
[00156] Nucleic acids comprising nucleotide sequences encoding CD73, CDl 38, notch receptor-3,
CD90, BMI-I, COX-2, Ki67, pl6, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK, MAPKK1 DDR2, TRF2, activin, and MEK1/2 are known in the art; and can form the basis for the design and preparation of a nucleic acid reagent, or collection of nucleic acid reagents, including probes and primers. For example, nucleotide sequences encoding human CD73 are presented in GenBank Accession Nos. BC065937, NM_002526, and AL589666; nucleotide sequences encoding human CD90 are presented in GenBank Accession Nos. AF261093, NM_006288, and
BC065559; nucleotide sequences encoding human CDl 38 are presented in GenBank Accession Nos.
NM_002997, and BC008765; nucleotide sequences encoding human notch-3 receptor are presented in GenBank Accession Nos. U97669, AC004663, AH006054, and NM000435; nucleotide sequences encoding human COX-2 are presented in GenBank Accession Nos. M90100, and NM_000963;
nucleotide sequences encoding human Ki-67 are presented in GenBank Accession Nos. X65551 ,
X65550, AL355529, and AL390236; nucleotide sequences encoding human pi 6 are presented in
GenBank Accession Nos. NM_000077, NM_058195, and NM_058197; nucleotide sequences encoding human TRF2 are presented in GenBank Accession Nos NM 005652 and AF002999; and nucleotide sequences encoding human activin βA chain are presented in GenBank Accession Nos CH236951 and BC007858.
Reagents that provide for detection of the presence and/or level of a microRNA
[00157] In some embodiments, a subject nucleic acid reagent provides for detection of the presence and/or level of a microRNA that is expressed in a pre-cancerous MEC, e.g., that is differentially
expressed in a pre-cancerous MEC, compared to a normal (non-precancerous MEC). MicroRNAs that can be detected using a subject nucleic acid reagent include, but are not limited to, mir 196b (HoxA9), (pl4), 328, 30A-3P, 125b5 30E-3P, 680, 134, 604, 128b, 128a, 331, 520F, 299-3P, 520H, 510, 365,
520G, 9, 324-3P, 351, 125A, 764-5P, 302D, 520D, 652, 520C, 350, 585, 621, 542-5P, 560, 126, and
341. See, e.g., Griffiths-Jones et al. (2006) "miRBase: microRNA sequences, targets and gene
nomenclature" Nucleic Acids Res. 34:D140-D144; GenBank Accession No. NT_007819; Kim et al.
(2004) Proc. Natl. Acad. Sd. USA 101:360-365; Weber (2005) FEBSJ. 272:59-73.
[00158] For specific microRNA sequences, see, e.g.: 1) 328: Kim et al. (2004) Proc. Natl. Acad. Sd.
USA 101 :360-365; and Weber (2005) FEBSJ. 272:59-73; 2) 196b: Yekta et al. (2004) Science 304:594- 596; 3) 3OA-3p: Kasashima et al. ((2004) Biochem. Biophys. Res. Comm. 322:403-410; 4) 125b: Lee et al. (2005) J. Biol. Chem. 280:16635-16641; 5) 30e-3p: Kasashima et al. (2004) Biochem. Biophys. Res. Comm. 322:403-410; and Weber (2005) FEBSJ. 272:59-73; 6) 680: Weber (2005) FEBSJ 272:59-73; and Fu et al. (2005) FEBS Lett. 579:3849-3854; 7) 134: Altuvia et al. (2005) Nucl. Acids Res. 33:2697- 2706; and Suh et al. (2004) DevBiol. 270:488-498; 8) 604: Cummins et al. (2006) Proc Natl Acad Sd
USA. 103:3687-3692; 9) 128b: Lim et al. (2003) Science 299:1540; 10) 128a: Kasashima et al. ((2004) Biochem. Biophys. Res. Comm. 322:403-410; 11) 331 : Kim et al. (2004) Proc. Natl. Acad. Sd. USA
101 :360-365; and Weber (2005) FEBSJ. 272:59-73; 12) 520F: Bentwich et al. (2005) Nat. Genet.
37:766-770; 13) 299-3P: Altuvia et al. (2005) Nucl. Acids Res. 33:2697-2706; and Weber (2005) FEBS J. 272:59-73; 14) 520H: Bentwich et al. (2005) Nat Genet. 31-.166-71Q; 15) 510: Bentwich et al. (2005) Nat. Genet. 31:166-110; 16) 365: Bentwich et al. (2005) Nat. Genet. 31:166-710; 17) 520G: Bentwich et al. (2005) Nat. Genet. 37:766-770; 18) 324-3P: Kim et al. (2004) Proc. Natl. Acad. Sci. USA
101 :360-365; and Weber (2005) FEBSJ. 272:59-73; 19) 125A: Lagos-Quintana et al. (2002) CurrBiol. 12:735-739; 20) 302D: Suh et al. (2004) Dev Biol. 270:488-498; 21) 520D: Bentwich et al. (2005) Na/. Genet. 37:766-770; 22) 652: 22) 652: Cummins et al. (2006) Proc Natl Acad Sci USA. 103:3687-3692; 23) 520C: Bentwich et al. (2005) Nat. Genet. 37:766-770; 24) 585: Cummins et al. (2006) Proc Natl
Acad Sci USA. 103:3687-3692; 25) 621 : Cummins et al. (2006) Proc Natl Acad Sci USA. 103:3687- 3692; 26) 542-5p: Sewer et al. (2005) BMC Bioinformatics. 6:267; 27) 560: Cummins et al. (2006)
Proc Natl Acad Sci USA. 103:3687-3692; and 28) 126: Lagos-Quintana et al. (2002) CurrBiol.
12:735-739.
[00159] A suitable sequence includes a stem-loop sequence; a mature sequence; a sequence
complementary to a stem-loop sequence; and a sequence complementary to a mature sequence.
[00160] MicroRΝA sequences include, e.g.,
[00161] 1) 328: stem-loop sequence:
UGGAGUGGGGGGGCAGGAGGGGCUCAGGGAGAAAGUGCAUACAGCCCCUGGCCCUCUC UGCCCUUCCGUCCCCUG (SEQ ID NO: 1); mature sequence: CUGGCCCUCUCUGCCCUUCCGU (SEQ ID NO:2); nucleotide sequence complementary to mature sequence: 5'- ACGGAAGGGC AGAGAGGGCCAG-3' (SEQ ID NO:3);
[00162] 2) 196b: stem-loop sequence:
ACUGGUCGGUGAUUUAGGUAGUUUCCUGUUGUUGGGAUCCACCUUUCUCUCGACAGCA CGACACUGCCUUCAUUACUUCAGUUG (SEQ ID NO:4); mature sequence:
UAGGUAGUUUCCUGUUGUUGG (SEQ ID NO:5); nucleotide sequence complementary to mature sequence: 5'-CCAACAACAGGAAACTACCTA-S' (SEQ ID NO:6);
[00163] 3) 30A-3P: stem-loop sequence:
GCGACUGUAAACAUCCUCGACUGGAAGCUGUGAAGCCACAGAUGGGCUUUCAGUCGGA UGUUUGCAGCUGC (SEQ ID NO:7); mature sequence: UGUAAACAUCCUCGACUGGAAG (SEQ ID NO:8); nucleotide sequence complementary to mature sequence: 5'- CTTCC AGTCG AGG ATGTTTACA-3' (SEQ ED NO:9);
[00164] 4) 125b: stem-loop sequence:
UGCGCUCCUCUCAGUCCCUGAGACCCUAACUUGUGAUGUUUACCGUUUAAAUCCACGGG UUAGGCUCUUGGGAGCUGCGAGUCGUGCU (SEQ ID NO: 10); mature sequence:
UCCCUGAGACCCUAACUUGUGA (SEQ ID NO: 11); nucleotide sequence complementary to
mature sequence: 5'-TCACAAGTTAGGGTCTCAGGGT-S' (SEQ ID NO:12);
[00165] 5) 30e-3p: stem-loop sequence:
GGGCAGUCUUUGCUACUGUAAACAUCCUUGACUGGAAGCUGUAAGGUGUUCAGAGGAG CUUUCAGUCGGAUGUUUACAGCGGCAGGCUGCCA (SEQ ID NO: 13); mature sequence:
CUUUCAGUCGGAUGUUUACAGC (SEQ ID NO: 14); nucleotide sequence complementary to
mature sequence: 5'-GCTGTAAACATCCGACTGAAAG-S' (SEQ ID NO: 15);

[00166] 6) 680: stem-loop sequence:
CCUGCCGGGGCUAAAGUGCUGACAGUGCAGAUAGUGGUCCUCUCCGUGCUACCGCACUG UGGGUACUUGCUGCUCCAGCAGG (SEQ ID NO: 16); mature sequence: mature sequence:
UAAAGUGCUGACAGUGCAGAU (SEQ ID NO: 17); nucleotide sequence complementary to mature sequence: 5'-ATCTGCACTGTCAGCACTTTA-S' (SEQ ID NO: 18);
[00167] 7) 134: stem-loop sequence:
CAGGGUGUGUGACUGGUUGACCAGAGGGGCAUGCACUGUGUUCACCCUGUGGGCCACC UAGUCACCAACCCUC (SEQ ID NO: 19); mature sequence: UGUGACUGGUUGACCAGAGGG
(SEQ ID NO:20); nucleotide sequence complementary to mature sequence: 5'- CCCTCTGGTC AACC AGTC AC A-3' (SEQ ID NO:21);
[00168] 8) 604: stem-loop sequence:
AGAGCAUCGUGCUUGACCUUCCACGCUCUCGUGUCCACUAGCAGGCAGGUUUUCUGACA CAGGCUGCGGAAUUCAGGACAGUGCAUCAUGGAGA (SEQ ID NO:22); mature sequence:
AGGCUGCGGAAUUCAGGAC (SEQ ID NO: 23); nucleotide sequence complementary to mature sequence: 5' -GTCCTG AATTCCGC AGCCT-3' (SEQ ID NO:24);
[00169] 9) 128b: stem-loop sequence:
UGUGCAGUGGGAAGGGGGGCCGAUACACUGUACGAGAGUGAGUAGCAGGUCUCACAGU GAACCGGUCUCUUUCCCUACUGUGUC (SEQ ID NO:25); mature sequence:
UCACAGUGAACCGGUCUCUUUC (SEQ ID NO:26); nucleotide sequence complementary to
mature sequence: S'-GAAAGAGACCGGTTCACTGTGA-S' (SEQ ID NO :27);
[00170] 10) 128a: stem-loop sequence:
UGAGCUGUUGGAUUCGGGGCCGUAGCACUGUCUGAGAGGUUUACAUUUCUCACAGUGA ACCGGUCUCUUUUUCAGCUGCUUC (SEQ ID NO:28); mature sequence:
UCACAGUGAACCGGUCUCUUUU (SEQ ID NO:29); nucleotide sequence complementary to
mature sequence: 5'-AAAAGAGACCGGTTCACTGTGA-S' (SEQ ID NO:30);
[00171] 11) 331: stem-loop sequence:
GAGUUUGGUUUUGUUUGGGUUUGUUCUAGGUAUGGUCCCAGGGAUCCCAGAUCAAACC AGGCCCCUGGGCCUAUCCUAGAACCAACCUAAGCUC (SEQ ID NO:31); mature sequence:
GCCCCUGGGCCUAUCCUAGAA (SEQ ID NO:32); nucleotide sequence complementary to mature sequence: 5 '-TTCTAGGATAGGCCCAGGGGC-S' (SEQ ID NO:33);
[00172] 12) 520F: stem-loop sequence:
UCUCAGGCUGUGACCCUCUAAAGGGAAGCGCUUUCUGUGGUCAGAAAGAAAAGCAAGU GCUUCCUUUUAGAGGGUUACCGUUUGGGA (SEQ ID NO:34); mature sequence:
AAGUGCUUCCUUUUAGAGGGUU (SEQ ID NO: 35); nucleotide sequence complementary to mature sequence: 5'-AACCCTCTAAAAGGAAGCACTT-S' (SEQ ID NO:36);
[00173] 13) 299-3P: stem-loop sequence:
AAGAAAUGGUUUACCGUCCCACAUACAUUUUGAAUAUGUAUGUGGGAUGGUAAACCGC UUCUU (SEQ ID NO:37); mature sequence: UAUGUGGGAUGGUAAACCGCUU (SEQ ID NO:38); nucleotide sequence complementary to mature sequence: 5'-AAGCGGTTTACCATCCCACATA-S'
(SEQ BD NO:39);
[00174] 14) 520H: stem-loop sequence:
UCCCAUGCUGUGACCCUCUAGAGGAAGCACUUUCUGUUUGUUGUCUGAGAAAAAACAA AGUGCUUCCCUUUAGAGUUACUGUUUGGGA (SEQ ID NO:40; mature sequence:
ACAAAGUGCUUCCCUUUAGAGU (SEQ ID NO:41); nucleotide sequence complementary to
mature sequence: 5'-ACTCTAAAGGGAAGCACTTTGA-S' (SEQ ID NO:42);
[00175] 15) 510: stem-loop sequence:
GUGGUGUCCUACUCAGGAGAGUGGCAAUCACAUGUAAUUAGGUGUGAUUGAAACCUCU AAGAGUGGAGUAACAC (SEQ ID NO:43); mature sequence:
UACUCAGGAGAGUGGCAAUCACA (SEQ ID NO:44); nucleotide sequence complementary to mature sequence: 5'-TGTGATTGCCACTCTCCTGAGTA-S' (SEQ ID NO:45);
[00176] 16) 365: stem-loop sequence:
ACCGCAGGGAAAAUGAGGGACUUUUGGGGGCAGAUGUGUUUCCAUUCCACUAUCAUAA UGCCCCUAAAAAUCCUUAUUGCUCUUGCA (SEQ ID NO:46); mature sequence:
UAAUGCCCCUAAAAAUCCUUAU (SEQ ED NO:47); nucleotide sequence complementary to
mature sequence: 5'-ATAAGGATTTTTAGGGGCATTA-S ' (SEQ ID NO:48);
[00177] 17) 520G: stem-loop sequence:
UCCCAUGCUGUGACCCUCUAGAGGAAGCACUUUCUGUUUGUUGUCUGAGAAAAAACAA AGUGCUUCCCUUUAGAGUGUUACCGUUUGGGA (SEQ ID NO:49); mature sequence:
ACAAAGUGCUUCCCUUUAGAGUGU (SEQ ID NO:50); nucleotide sequence complementary to mature sequence: 5'-ACACTCTAAAGGGAAGCACTTTGA-S' (SEQ BD NO:51);
[00178] 18) 324-3P: stem-loop sequence:
CUGACUAUGCCUCCCCGCAUCCCCUAGGGCAUUGGUGUAAAGCUGGAGACCCACUGCCC CAGGUGCUGCUGGGGGUUGUAGUC (SEQ ID NO:52); mature sequence:
CCACUGCCCCAGGUGCUGCUGG (SEQ ID NO:53); nucleotide sequence complementary to mature sequence: 5'-CCAGCAGCACCTGGGGCAGTGG-S' (SEQ ID NO:54);
[00179] 19) 125 A: stem-loop sequence:
UGCCAGUCUCUAGGUCCCUGAGACCCUUUAACCUGUGAGGACAUCCAGGGUCACAGGUG AGGUUCUUGGGAGCCUGGCGUCUGGCC (SEQ ID NO:55); mature sequence:
UCCCUGAGACCCUUUAACCUGUG (SEQ ID NO:56); nucleotide sequence complementary to mature sequence: 5'-CACAGGTTAAAGGGTCTCAGGGT-S ' (SEQ ID NO:57);
[00180] 20) 302D: stem-loop sequence:
CCUCUACUUUAACAUGGAGGCACUUGCUGUGACAUGACAAAAAUAAGUGCUUCCAUGU UUGAGUGUGG(SEQ IDNO:58); mature sequence: UAAGUGCUUCCAUGUUUGAGUGU (SEQ ID NO:59); nucleotide sequence complementary to mature sequence: 5'- ACACTCAAAC ATGGAAGCACTT A-3' (SEQ ID NO:60);
[00181] 21) 520D: stem-loop sequence:
UCUCAAGCUGUGAGUCUACAAAGGGAAGCCCUUUCUGUUGUCUAAAAGAAAAGAAAGU GCUUCUCUUUGGUGGGUUACGGUUUGAGA (SEQ ID NO:61); mature sequence:
UCUACAAAGGGAAGCCCUUUCUG (SEQ ID NO:62); nucleotide sequence complementary to mature sequence: 5'-CAGAAAGGGCTTCCCTTTGTAGA-S' (SEQ ED NO:63);
[00182] 22) 652: stem-loop sequence:
ACGAAUGGCUAUGCACUGCACAACCCUAGGAGAGGGUGCCAUUCACAUAGACUAUAAU UGAAUGGCGCCACUAGGGUUGUGCAGUGCACAACCUACAC (SEQ ID NO:64); mature
sequence: AAUGGCGCCACUAGGGUUGUGCA (SEQ ID NO:65); nucleotide sequence
complementary to mature sequence: 5'-TGCACAACCCTAGTGGCGCCATT-S ' (SEQ ID NO:66);
[00183] 23) 520C: stem-loop sequence:
UCUCAGGCUGUCGUCCUCUAGAGGGAAGCACUUUCUGUUGUCUGAAAGAAAAGAAAGU GCUUCCUUUUAGAGGGUUACCGUUUGAGA (SEQ ID NO:67); mature sequence:
AAAGUGCUUCCUUUUAGAGGGUU (SEQ ID NO: 68); nucleotide sequence complementary to mature sequence: 5'-AACCCTCTAAAAGGAAGCACTTT-S' (SEQ ID NO:69);
[00184] 24) 585: stem-loop sequence:
UGGGGUGUCUGUGCUAUGGCAGCCCUAGCACACAGAUACGCCCAGAGAAAGCCUGAAC GUUGGGCGUAUCUGUAUGCUAGGGCUGCUGUAACAA (SEQ ID NO:70); mature sequence:
UGGGCGUAUCUGUAUGCUA (SEQ ID NO:71); nucleotide sequence complementary to mature sequence: 5'-TAGCATACAGATACGCCCA-S' (SEQ ID NO.72);
[00185] 25) 621: stem-loop sequence:
UAGAUUGAGGAAGGGGCUGAGUGGUAGGCGGUGCUGCUGUGCUCUGAUGAAGACCCAU GUGGCUAGCAACAGCGCUUACCUUUUGUCUCUGGGUCC (SEQ ID NO:73); mature sequence: GGCUAGCAACAGCGCUUACCU (SEQ ID NO:74); nucleotide sequence complementary to mature sequence: 5'-AGGTAAGCGCTGTTGCTAGCC-S ' (SEQ ID NO: 75);
[00186] 26) 542-5p: stem-loop sequence:
CAGAUCUCAGACAUCUCGGGGAUCAUCAUGUCACGAGAUACCAGUGUGCACUUGUGAC AGAUUGAUAACUGAAAGGUCUGGGAGCCACUCAUCUUCA (SEQ ID NO:76); mature
sequence: UCGGGGAUCAUCAUGUCACGAG (SEQ ID NO:77); nucleotide sequence
complementary to mature sequence: 5'-CTCGTGACATGATGATCCCCGA-S' (SEQ ID NO:78);
[00187] 27) 560: stem-loop sequence:
UCCCCUCUGGCGGCUGCGCACGGGCCGUGUGAGCUAUUGCGGUGGGCUGGGGCAGAUG ACGCGUGCGCCGGCCGGCCGCCGAGGGGCUACCGUUC (SEQ ID NO:79); mature sequence: GCGUGCGCCGGCCGGCCGCC (SEQ ID NO: 80); nucleotide sequence complementary to mature sequence: 5'-GGCGGCCGGCCGGCGCACGC-S' (SEQ ID NO:81); and [00188] 28) 126: stem-loop sequence:
CGCUGGCGACGGGACAUUAUUACUUUUGGUACGCGCUGUGACACUUCAAACUCGUACC GUGAGUAAUAAUGCGCCGUCCACGGCA (SEQ ED NO: 82); mature sequence:
CAUUAUUACUUUUGGUACGCG (SEQ ID NO: 83); nucleotide sequence complementary to mature sequence: 5'-CGCGTACCAAAAGTAATAATG-S ' (SEQ ID NO:84).
[00189] Nucleic acids that provide for detection of the presence and/or level of a microRNA that is differentially expressed in a pre-cancerous HMEC can comprises a nucleotide sequence that is
complementary to all or a portion of a target microRNA. For example, the nucleotide sequence 5'- CGCGTACC AAAAGT AAT AATG-3' is complementary to the mature sequence of the 126
microRNA.
[00190] Nucleic acid reagents that provide for detection of the presence and/or level of a microRNA that is differentially expressed in a pre-cancerous HMEC can have a length of from about 10
nucleotides to about 100 nucleotides (nt), e.g., from about 10 nt to about 15 nt, from about 15 nt to about 20 nt, from about 20 nt to about 25 nt, from about 25 nt to about 30 nt, from about 30 nt to about 40 nt, from about 40 nt to about 50 nt, from about 50 nt to about 60 nt, from about 60 nt to about 70 nt, from about 70 nt to about 80 nt, from about 80 nt to about 90 nt, or from about 90 nt to about 100 nt.
[00191] In some embodiments, a subject nucleic acid reagent provides for detection of the presence and/or level of a microRNA that is differentially expressed in a pre-cancerous MEC is immobilized onto an insoluble support. In some embodiments, the reagents include two or more nucleic acid probes that provide for detection of the presence and/or level of two or more microRNAs that are differentially expressed in a pre-cancerous MEC. Ih some embodiments, the two or more nucleic acid probes that provide for detection of the presence and/or level of two or more microRNAs that are differentially expressed in a pre-cancerous MEC are immobilized onto an insoluble support.
Target nucleic acids
[00192] Target nucleic acids include nucleic acids that are abnormally expressed in a pre-cancerous epithelial cell, where the abnormal expression levels are thus associated with an increased risk of
developing cancer (e.g., a carcinoma, e.g., breast cancer) and/or are associated with a pre-cancerous or cancerous state of a cell such as an epithelial cell and/or are indicative of the presence of a precancerous cell in the individual. For example, abnormal expression levels of a target nucleic acid will in some cases be associated with abnormal levels of target mRNA and/or target polypeptide in an
epithelial cell. Exemplary, non-limiting target nucleic acids are the nucleic acids listed in Figure 14.
Exemplary, non-limiting target nucleic acids are CD73, CD138, notch receptor-3, CD90, BMI-I , COX- 2, Ki67, pl6, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K,
MAPK, MAPKK, DDR, TRP2, activin, and MEK1/2. Exemplary, non-limiting target nucleic acids are CD73, CD138, notch receptor-3, CD90, BMI-I, and Cox-2 nucleic acids.
[00193] In some embodiments, abnormal levels of a target mRNA that, when present in a cell, are associated with a precancerous or cancerous state of the cell, are levels that are significantly higher or lower than normal levels of the target mRNA found in a non-cancerous cell of the same cell type. In some embodiments, abnormal levels of a target mRNA that, when present in a test cell, are indicative of the presence of a cancerous cell in the individual from whom the test cell was obtained, are levels that are significantly higher or lower than normal levels of the target mRNA typically found in the test cell in an individual who does not have cancer.
[00194] An abnormally high level of a target mRNA that, when present in a cell, is associated with a precancerous or cancerous state of the cell, is a level that is at least about 25%, at least about 50%, at least about 100% (or 2-fold), at least about 3-fold, at least about 5-fold, at least about 10-fold, at least about 25-fold, or at least about 50-fold, or more, higher than the level of the target mRNA in a noncancerous cell of the same cell type, e.g., an epithelial cell.
[00195] For example, an abnormally high level of a target mRNA that, when present in an epithelial cell, is associated with a precancerous state of the cell, is a level that is at least about 25%, at least about 50%, at least about 100% (or 2-fold), at least about 3-fold, at least about 5-fold, at least about 10-fold, at least about 25-fold, or at least about 50-fold, or more, higher than the level of the target mRNA in a non-cancerous epithelial cell.
[00196] An abnormally low level of a target mRNA that, when present in a cell, is associated with a precancerous or cancerous state of the cell, is a level that is about 75% or less, about 60% or less, about 50% or less, about 25% or less, or about 10% or less, than the level of the target mRNA in a noncancerous cell of the same cell type
[00197] For example, an abnormally low level of a target mRNA that, when present in an epithelial cell, is associated with a precancerous state of the epithelial cell, is a level that is about 75% or less, about
60% or less, about 50% or less, about 25% or less, or about 10% or less, than the level of the target mRNA in a non-cancerous epithelial cell.
Sources of target nucleic acids
[00198] Where the detection methods involve detection of a target nucleic acid, the target nucleic acids are detected in samples obtained from a tissue comprising cells. In some embodiments, the cells are obtained from a tissue suspected of comprising cancer cells.
[00199] The source of the tissue will depend, at least in part, on the type of pre-cancerous epithelial cell that is being detected. For example, target nucleic acids can be obtained from lung tissue (for detection of a pre-cancerous lung epithelial cell); from pancreas; from prostate; etc.
[00200] In the context of breast cancer, the source of target nucleic acid is breast tissue. In some
embodiments, the tissue is a breast biopsy. In other embodiments, the tissue is an axillary lymph node tissue. In the context of breast cancer, suitable sources of target nucleic acids include breast cells and lymph node cells, e.g., cells obtained via fine needle aspiration biopsy; cells obtained via core needle biopsy; cells obtained from lymph nodes in the vicinity of the breast (e.g., axillary lymph nodes); and the like.

[00201] In the context of breast cancer, breast cancers that can be detected using a subject method
include mammary carcinoma, adenocarcinoma, ductal carcinoma in situ, lobular (small cell) carcinoma, intraductal carcinoma, medullary breast cancer, mucinous breast cancer, tubular breast cancer, papillary breast cancer, Paget's disease, inflammatory breast cancer, and hormone dependent tumors of the
breast.
Nucleic acid probes
[00202] The present invention provides detection, diagnostic, and staging methods, e.g., methods for detecting and diagnosing cancer (e.g., breast cancer and other carcinomas) in an individual; methods of identifying individuals at risk of developing cancer (e.g., breast cancer); and methods of staging cancer (e.g., breast cancer). The methods generally involve detecting an abnormal level of a target mRNA in a biological sample obtained from the individual. The subject methods can be carried out using a method involving nucleic acid hybridization, amplification, or both.
[00203] Nucleic acid hybridization can be carried out using a nucleic acid probe that detects a level of a target mRNA that is abnormally expressed in a pre-cancerous epithelial cell. Where abnormal
expression of a target nucleic acid is to be detected, nucleic acid probes suitable for use include nucleic acid probes that hybridize to and provide for detection of a target nucleic acid that is overexpressed or underexpressed in an epithelial cell, e.g., a pre-cancerous epithelial cell. The present invention provides such nucleic acid probes
[00204] Suitable nucleic acid probes are in some embodiments in the range of between 10-50
nucleotides long, such as 10 to 50, 12 to 45, 15 to 40, 20 to 35, 25 to 30 nucleotides, and the like. For example, probes will in some embodiments be in the range of between 18 to 40, 19 to 35, 20 to 30, 21 to 29, 22 to 28, 23 to 27, 24-25 nucleotides long, and any length between the stated ranges. Probes of about 20 to 22 nucleotides in length are of particular interest in some embodiments.
[00205] A suitable probe may be coupled to a label for detection. There are several methods and
compositions known for derivatizing oligonucleotides with reactive functionalities which permit the addition of a label. For example, several approaches are available for biotinylating probes so that
radioactive, fluorescent, chemiluminescent, enzymatic, or electron dense labels can be attached via avidin. See, e.g., Broken et al., Nucl. Acids Res. (1978) 5:363-384 which discloses the use of ferritin- avidin-biotin labels; and Chollet et al. Nucl. Acids Res. (1985) 13:1529-1541 which discloses
biotinylation of the 5' termini of oligonucleotides via an aminoalkylphosphoramide linker arm. Several methods are also available for synthesizing amino-derivatized oligonucleotides which are readily
labeled by fluorescent or other types of compounds derivatized by amino-reactive groups, such as
isothiocyanate, N-hydroxysuccinimide, or the like, see, e.g., Connolly (1987) Nucl. Acids Res.
15:3131-3139, Gibson et al. (1987) Nucl. Acids Res. 15:6455-6467 and U.S. Pat. No. 4,605,735 to
Miyoshi et al. Methods are also available for synthesizing sulfhydryl-derivatized oligonucleotides
which can be reacted with thiol-specific labels, see, e.g., U.S. Pat. No. 4,757,141 to Fung et al.,
Connolly et al. (1985) Nuc. Acids Res. 13:4485-4502 and Spoat et al. (1987) Nucl. Acids Res. 15:4837- 4848. A comprehensive review of methodologies for labeling DNA fragments is provided in Matthews et al., Anal. Biochem. (1988) 169:1-25.
[00206] For example, probes may be fluorescently labeled by linking a fluorescent molecule to the non- ligating terminus of the probe. Guidance for selecting appropriate fluorescent labels can be found in
Smith et al., Meth. Enzymol. (1987) 155:260-301; Karger et al., Nucl. Acids Res. (1991) 19:4955-4962; Haugland (1989) Handbook of Fluorescent Probes and Research Chemicals (Molecular Probes, Inc.,
Eugene, Oreg.). Exemplary fluorescent labels include fluorescein and derivatives thereof, such as
disclosed in U.S. Pat. No. 4,318,846 and Lee et al., Cytometry (1989) 10:151-164, and 6-FAM, JOE,
TAMRA, ROX, HEX-I , HEX-2, ZOE, TET-I or NAN-2, and the like.
[00207] Additionally, probes can be labeled with an acridinium ester (AE). Current technologies allow the AE label to be placed at any location within the probe. See, e.g., Nelson et al. (1995) "Detection of Acridinium Esters by Chemiluminescence" in Nonisotopic Probing, Blotting and Sequencing, Kricka L. J. (ed) Academic Press, San Diego, Calif.; Nelson et al. (1994) "Application of the Hybridization
Protection Assay (HPA) to PCR" in The Polymerase Chain Reaction, Mullis et al. (eds.) Birkhauser,
Boston, Mass.; Weeks et al., Clin. Chem. (1983) 29:1474-1479; Berry et al., Clin. Chem. (1988)
34:2087-2090. An AE molecule can be directly attached to the probe using non-nucleotide-based linker arm chemistry that allows placement of the label at any location within the probe. See, e.g., U.S. Pat.
Nos. 5,585,481 and 5,185,439.
[00208] If a solid support is used in the assay (e.g., to capture amplicons of target nucleic acid using a probe), the oligonucleotide probe may be attached to the solid support in a variety of manners. For example, the probe may be attached to the solid support by attachment of the 3' or 5' terminal
nucleotide of the probe to the solid support. In some embodiments, the probe is attached to the solid support by a linker which serves to distance the probe from the solid support. The linker is in many embodiments at least 15-30 atoms in length, or at least 15-50 atoms in length. The required length of the linker will depend on the particular solid support used. For example, a six atom linker is generally sufficient when high cross-linked polystyrene is used as the solid support.
[00209] A wide variety of linkers are known in the art which may be used to attach the oligonucleotide probe to the solid support. The linker may be formed of any compound which does not significantly interfere with the hybridization of the target sequence to the probe attached to the solid support. The linker may be formed of a homopolymeric oligonucleotide which can be readily added on to the linker by automated synthesis. Alternatively, polymers such as functionalized polyethylene glycol can be used as the linker. In some embodiments, polymers such as functionalized polyethylene glycol are used
because they do not significantly interfere with the hybridization of probe to the target oligonucleotide. In some embodiments, the linked is polyethylene glycol.
[00210] The linkages between the solid support, the linker and the probe are normally not cleaved
during removal of base protecting groups under basic conditions at high temperature. Examples of suitable linkages include carbamate and amide linkages.

[00211] Examples of suitable types of solid supports for immobilization of the oligonucleotide probe include controlled pore glass, glass plates, polystyrene, avidin-coated polystyrene beads, cellulose, nylon, acrylamide gel and activated dextran.
[00212] In some embodiments, methods of detecting a level of a target mRNA in a cell will involve amplifying the target nucleic acid, using a pair of nucleic acid primers.
[00213] In general, primers provide for amplification of a target nucleic acid to produce a target nucleic acid amplification product (also referred to as an "amplicon"). Primers will in some embodiments be used in conjunction with a nucleic acid probe. 5' primers generally bind to a region to provide for amplification of the target nucleic, and in many embodiments bind to a 5 ' portion of the target
sequence. 3' primers generally bind to a sequence that is complementary to a 3' portion of the nucleic acid generated by extension from the 5' primer.
[00214] Target nucleotide sequences to which 5' and 3' primers hybridize will be separated from one another by from about 10 nucleotides to about 1000 nucleotides, e.g., from about 10 nucleotides to about 20 nucleotides, from about 20 nucleotides to about 30 nucleotides, from about 30 nucleotides to about 40 nucleotides, from about 40 nucleotides to about 50 nucleotides, from about 50 nucleotides to about 60 nucleotides, from about 60 nucleotides to about 70 nucleotides, from about 70 nucleotides to about 100 nucleotides, from about 100 nucleotides to about 150 nucleotides, from about 150
nucleotides to about 200 nucleotides, from about 200 nucleotides to about 250 nucleotides, from about 250 nucleotides to about 300 nucleotides, from about 300 nucleotides to about 400 nucleotides, from about 400 nucleotides to about 500 nucleotides, or from about 500 nucleotides to about 1000
nucleotides.
[00215] The amplification product will in many embodiments have a length in a range of from about 30 nucleotides (or base pairs, bp) to about 1000 nucleotides (or base pairs), e.g., from about 30 bp to about 50 bp, from about 50 bp to about 60 bp, from about 60 bp to about 70 bp, from about 70 bp to about 80 bp, from about 80 bp to about 90 bp, from about 90 bp to about 100 bp, from about 100 bp to about 150 bp, from about 150 bp to about 200 bp, from about 200 bp to about 250 bp, from about 250 bp to about 300 bp, from about 300 bp to about 350 bp, from about 350 bp to about 400 bp, from about 400 bp to about 500 bp, from about 500 bp to about 600 bp, from about 700 bp, from about 700 bp to about 800 bp, from about 800 bp to about 900 bp, or from about 900 bp to about 1000 bp (e.g., about 1 kb).
[00216] In some embodiments, the primer sequences are in the range of between 10-75 nucleotides in length, such as 10 to 70 nucleotides, 12 to 65 nucleotides, 15 to 60 nucleotides, 20 to 55 nucleotides, 25 to 50 nucleotides, 30 to 45 nucleotides, and the like. In some embodiments, primers are in the range of between 18 to 40, 19 to 35, 20 to 30, 21 to 29, 22 to 28, 23 to 27, 24-25 nucleotides long, and any
length between the stated ranges. Primers of about 20 to 22 nucleotides in length are of particular interest in some embodiments.
[00217] In some embodiments, the first and/or the second primer comprises a detectable label. Suitable labels include fluorochromes, e.g. fluorescein isothiocyanate (FITC), rhodamine, Texas Red, phycoerythrin, allophycocyanin, 6-carboxyfluorescein (6-FAM), 2',7'-dimethoxy-4',5'-dichloro-6- carboxyfluorescein (JOE), 6-carboxy-X-rhodamine (ROX), ό-carboxy^'^'^'^^-hexachlorofluorescein (HEX), 5-carboxyfluorescein (5-FAM) or N,N,N',N'-tetramethyl-6-carboxyrhodamine (TAMRA);
radioactive labels, e.g. 32P, 35S, 3H; etc. The label may be a two stage system, where the amplified DNA is conjugated to biotin, haptens, etc. having a high affinity binding partner, e.g. avidin, specific
antibodies, etc., where the binding partner is conjugated to a detectable label. The label may be
conjugated to one or both of the primers. Alternatively, the pool of nucleotides used in the amplification is labeled, so as to incorporate the label into the amplification product.
Nucleic acid arrays
[00218] In some embodiments, nucleic acid probe that provides for detection of a target nucleic acid is present in an array. A subject nucleic acid array comprises an array of probe nucleic acids immobilized on a solid support surface. Nucleic acid probes are generally oligonucleotides, e.g. oligonucleotides of at least about 12 nucleotides (nt), at least about 15 nt, at least about 18 nt, at least about 20 nt, at least about 25 nt, at least about 30 nt, at least about 40 nt, at least about 50 at least about, at least about 60 nt, or longer. Such an array may comprise a series of oligonucleotides, each of which can specifically hybridize to a different target nucleic acid.
[00219] A variety of different array formats are known in the art, with a wide variety of different probe structures, substrate compositions and attachment technologies. Representative array structures of interest include those described in U.S. Patent Nos.: 6,919,211, 5,143,854; 5,288,644; 5,324,633;
5,432,049; 5,470,710; 5,492,806; 5,503,980; 5,510,270; 5,525,464; 5,547,839; 5,580,732; 5,661,028; 5,800,992; the disclosures of which are herein incorporated by reference; as well as WO 95/21265; WO 96/31622; WO 97/10365; WO 97/27317; EP 373 203; and EP 785 280.
[00220] Essentially, any conceivable substrate for a subject nucleic acid may be employed. The
substrate may be biological, nonbiological, organic, inorganic, or a combination of any of these,
existing as particles, strands, precipitates, gels, sheets, tubing, spheres, containers, capillaries, pads, slices, films, plates, slides, etc. The substrate may have any convenient shape, such as a disc, square, sphere, circle, etc. The substrate is typically flat but may take on a variety of alternative surface
configurations. For example, the substrate may contain raised or depressed regions on which the
synthesis takes place. The substrate and its surface in many embodiments form a rigid support on which to carry out the hybridization reactions described herein. For instance, the substrate may be a
polymerized Langmuir Blodgett film, functionalized glass, Si, Ge, GaAs, GaP, SiO2, SiN4, modified silicon, or any one of a wide variety of gels or polymers such as (poly)tetrafluoroethylene,
(poly)vinylidenedifluoride, polystyrene, polycarbonate, or combinations thereof. Other substrate
materials will be readily apparent to those of skill in the art upon review of this disclosure. In an
exemplary embodiment, the substrate is flat glass or single-crystal silicon with surface relief features of less than 10 μm.

[00221] According to some embodiments, the surface of the substrate is etched using well known
techniques to provide for desired surface features. For example, by way of the formation of trenches, v- grooves, mesa structures, or the like, the synthesis regions may be more closely placed within the focus point of impinging light, be provided with reflective "mirror" structures for maximization of light collection from fluorescent sources, or the like.
[00222] Surfaces on the solid substrate will in many embodiments be composed of the same material as the substrate. Thus, the surface may be composed of any of a wide variety of materials, for example, polymers, plastics, resins, polysaccharides, silica or silica-based materials, carbon, metals, inorganic glasses, membranes, or any of the above-listed substrate materials. In some embodiments the surface may provide for the use of caged binding members which are attached firmly to the surface of the
substrate. In many embodiments, the surface will contain reactive groups, which could be carboxyl, amino, hydroxyl, or the like. In many embodiments, the surface will be optically transparent and will have surface Si-OH functionalities, such as are found on silica surfaces.
[00223] A number of methods are available for creating microarrays of nucleic acids to be used in DNA hybridization assays. Exemplary are PCT Application Serial No. WO95/35505, published December
28, 1995; U.S. patent no. 5,445,934, issued August 29, 1995; and Drmanac etal. (1993) Science
260:1649-1652. Yershov et al. (1996) Genetics 93:4913-4918 describe an alternative construction of an oligonucleotide array. The construction and use of oligonucleotide arrays is reviewed by Ramsay
(1998) supra. Methods of using high density oligonucleotide arrays are known in the art. For example, Milosavljevic et al. (1996) Genomics 37:77-86 describe DNA sequence recognition by hybridization to short oligomers.
[00224] The systems and kits of the subject invention may include the above-described arrays. The systems and kits may further include one or more additional reagents employed in the various methods, such as primers for generating target nucleic acids, dNTPs and/or rNTPs, which may be either premixed or separate, one or more uniquely labeled dNTPs and/or rNTPs, such as biotinylated or Cy3 or Cy5 tagged dNTPs, gold or silver particles with different scattering spectra, or other post synthesis labeling reagent, such as chemically active derivatives of fluorescent dyes, enzymes, such as reverse
transcriptases, DNA polymerases, RNA polymerases, and the like, various buffer mediums, e.g.
hybridization and washing buffers, prefabricated probe arrays, labeled probe purification reagents and components, like spin columns, etc., signal generation and detection reagents, e.g. streptavidin-alkaline phosphatase conjugate, chemifiuorescent or chemiluminescent substrate, and the like.
Internal control nucleic acids
[00225] In certain embodiments, an internal control (IC) or an internal standard is added to serve as a control to show that any negative result is not due to failure of the assay. The use of the IC permits the control of the separation process, the amplification process, and the detection system, and permits the monitoring of assay performance arid quantification for the sample(s). The IC can be included at any suitable point, for example, in the lysis buffer. In one embodiment, the IC comprises phage nucleic acid. Where a solid support is used in the assay, the solid support may additionally include probes
specific to the internal standard (IC probe), thereby facilitating capture when using the IC probe. The IC probe can optionally be coupled with a detectable label that is different from the detectable label for the target sequence. In embodiments where the detectable label is a fluorophore, the IC can be quantified spectrophotometrically and by limit of detection studies.
[00226] In another embodiment, an IC, as described herein, is combined with RNA isolated from the sample according to standard techniques known to those of skill in the art, and described herein. The
RNA is then reverse-transcribed using a reverse transcriptase to provide copy DNA. The cDNA
sequences can be optionally amplified (e.g., by PCR) using labeled primers. The amplification products are separated, typically by electrophoresis, and the amount of radioactivity (proportional to the amount of amplified product) is determined. The amount of mRNA in the sample can then calculated where desired by comparison with the signal produced by the known standards.
Synthesis of primers and probes
[00227] Primers and probes described above are designed based on target sequences and are readily synthesized by standard techniques, e.g., solid phase synthesis via phosphoramidite chemistry, as
disclosed in U.S. Pat. Nos. 4,458,066 and 4,415,732, incorporated herein by reference; Beaucage et al. (1992) Tetrahedron 48:2223-2311; and Applied Biosystems User Bulletin No. 13 (1 Apr. 1987). Other chemical synthesis methods include, for example, the phosphotriester method described by Narang et al., Meth. Enzymol. (1979) 68:90 and the phosphodiester method disclosed by Brown et al., Meth.
Enzymol. (1979) 68:109. PoIy(A) or poly(C), or other non-complementary nucleotide extensions may be incorporated into probes using these same methods. Hexaethylene oxide extensions may be coupled to probes by methods known in the art. Cload et al. (1991) J. Am. Chem. Soc. 113:6324-6326; U.S. Pat. No. 4,914,210 to Levenson et al.; Durand et al. (1990) Nucleic Acids Res. 18:6353-6359; and Horn et al. (1986) Tet. Lett. 27:4705-4708.
Biological assay reagents
[00228] The present invention provides reagents for use in a subject biological assay. For example, as described in more detail below, in some embodiments, a subject method involves contacting a test fibroblast obtained from a patient with a reporter epithelial cell; and determining the effect, if any, of the fibroblast on physical or functional property of the reporter epithelial cell. The present invention provides reagents and systems for carrying out such a biological assay.
[00229] System components can include one or more of a reporter epithelial cell; binding reagents (e.g., antibody reagents) for detecting the presence and/or level of markers present in a reporter epithelial cell; nucleic acid reagents for detecting the presence and/or level of a nucleic acid (e.g., an mRNA, a cDNA copy of an mRNA, etc.) in a reporter epithelial cell; components for assessing mobility of a reporter epithelial cell (e.g., ability to cross a membrane); reagents (e.g., as described above) for
detecting epigenetic modification of a reporter epithelial cell (e.g., histone modification; DNA
hypermethylation; etc.); reagents for detecting secretion or release of molecules from a test fibroblast;

reagents for detecting a phenotypic change in a reporter cell; and reagents for detecting secretion or release from a reporter epithelial cell.
[00230] Suitable reporter epithelial cells include primary epithelial cells and immortalized epithelial cells (e.g., immortalized epithelial cell lines). In some embodiments, a reporter epithelial cell is a
primary mammary epithelial cell, e.g., a primary human mammary epithelial cell. Primary human mammary epithelial cells can be obtained from a suitable source such as reduction mammoplasty.
Reporter epithelial cells can be cultured as described in, e.g., Band and Sager (1989) Proc. Natl. Acad. ScL USA 86:1249-1253; Hammond et al. (1984) Proc. Natl. Acad. Sci. USA 81 :5435; and Romanov et al. (2001) Nature 409:633.
[00231] In some embodiments, a reporter epithelial cell is genetically modified with a nucleic acid comprising a nucleotide sequence encoding a polypeptide that provides a detectable signal.
Polypeptides that provide a detectable signal include fluorescent proteins, chromogenic proteins,
enzymes that catalyze the production of a product that is luminescent, fluorescent, or colored, etc.
Suitable fluorescent proteins include, but are not limited to, a green fluorescent protein (GFP; Chalfie, et al., Science 263(5148):802-805 (Feb 11 , 1994); an enhanced GFP (EGFP), Clontech - Genbank
Accession Number U55762); a blue fluorescent protein (BFP; 1. Quantum Biotechnologies, Inc. 1801 de Maisonneuve Blvd. West, 8th Floor, Montreal (Quebec) Canada H3H 1 J9; 2. Stauber, R. H.
Biotechniques 24(3):462-471 (1998); 3. Heim, R. and Tsien, R. Y. Curr. Biol. 6:178-182 (1996)); an enhanced yellow fluorescent protein (EYFP; Clontech Laboratories, Inc., 1020 East Meadow Circle, Palo Alto, CA 94303); a fluorescent protein as described in, e.g., WO 92/15673, WO 95/07463, WO
98/14605, WO 98/26277, WO 99/49019, U.S. Patent No. 5,292,658, U.S. Patent No. 5,418,155, U.S. Patent No. 5,683,888, U.S. Patent No. 5,741,668, U.S. Patent No. 5,777,079, U.S. Patent No.
5,804,387, U.S. Patent No. 5,874,304, U.S. Patent No. 5,876,995, and U.S. Patent No. 5,925,558; a
GFP from species such as Renilla reniformis, Renϊlla mulleri, or Ptilosarcus guernyi, as described in, e.g., WO 99/49019 and Peelle et al. (2001) J. Protein Chem. 20:507-519; "humanized" recombinant
GFP (hrGFP) (Stratagene); any of a variety of fluorescent and colored proteins from Anthozoan
species, as described in, e.g., Matz et al. (1999) Nature Biotechnol. 17:969-973, U.S. Patent Publication No. 2002/0197676, or U.S. Patent Publication No. 2005/0032085; and the like. Enzymes that catalyze production of a product that provides a detectable signal include, but are not limited to, luciferase, β- galactosidase, horse radish peroxidase, and alkaline phosphatase.
Genetically modified vMEC
[00232] In some embodiments, a reporter epithelial cell is an isolated vMEC (e.g, a CD73+ MEC) that has been genetically modified with a nucleic acid comprising a nucleotide sequence encoding an
oncogene. The present invention thus provides an isolated reporter epithelial cell, where the reporter epithelial cell is a CD73+ MEC that has been genetically modified with an exogenous nucleic acid comprising a nucleotide sequence encoding an oncogene. Suitable oncogenes include, but are not limited to, a ras family oncogene, a src family oncogene, Harvey murine sarcoma virus ras (v-Ha-ras), Kirsten murine sarcoma virus ras (v-Ki-ras), fyn, myc, erbB2, src, yes, sis, and the like.
[00233J In some embodiments, the oncogene is operably linked to a heterologous promoter. Non- limiting examples of suitable eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-I. Selection of the
appropriate vector and promoter is well within the level of ordinary skill in the art. In some
embodiments, the heterologous promoter is a constitutive promoter. In other embodiments, the
heterologous promoter is an inducible promoter. Suitable inducible promoters include, but are not limited to, a tetracycline-inducible promoter, a steroid-inducible promoter (e.g., a glucocorticoid- inducible promoter), and the like. A subject genetically modified, isolated vMEC is immortalized, but has not undergone cancerous transformation. In some embodiments, a subject genetically modified, immortalized vMEC is grown in medium containing 5% serum. In other embodiments, a subject
genetically modified, immortalized vMEC is grown in medium containing 10% serum.
[00234] A subject genetically modified, isolated, immortalized vMEC is useful for detecting stromal components that has the capacity to induce a cancerous transformation of a vMEC, e.g., that has
carcinogenic potential. A subject genetically modified, isolated, immortalized vMEC appears
morphologically normal. Upon contact with a stromal component that has the capacity to induce a cancerous transformation of a vMEC, the genetically modified vMEC undergoes a change that is
indicative of tumor progression. Such changes include, but are not limited to, increased motility;
acquisition of mesenchymal features; increased telomerase activity; phenotypic changes associated with de novo methylation, e.g., methylation of a promoter region; anchorage-independent growth; genomic instability; and capacity for in vivo survival.
[00235] hi some embodiments, a subject genetically modified, immortalized vMEC is further
genetically modified with a nucleic acid comprising a nucleotide sequence encoding a protein that provides for a detectable signal. Suitable proteins include, but are not limited to, fluorescent proteins and enzymes (e.g., β-galactosidase, luciferase, horse radish peroxidase, alkaline phosphatase, etc.).
Polypeptides that provide a detectable signal include fluorescent proteins, chromogenic proteins,
enzymes that catalyze the production of a product that is luminescent, fluorescent, or colored, etc.
Suitable fluorescent proteins are as described above (e.g., including a green fluorescent protein, a red fluorescent protein, a yellow fluorescent protein, etc.).
DETECTION METHODS
[00236] The present invention provides methods of detecting a cell in a mammary tissue that is
precancerous or has an increased likelihood of inducing a cancerous transformation in a neighboring mammary tissue cell. A subject detection method is useful in a variety of clinical applications,
including imaging methods, diagnostic methods, prognostic methods, and monitoring methods, which are also provided.

[00237] A subject detection method generally involves detecting a mammary epithelial cell signature in a biological sample. In some embodiments, a biological sample is a sample that comprises cells, which can include living cells, dead cells, cells that have been treated for histochemical analysis, etc. In other embodiments, a biological sample is a liquid sample that may or may not include living cells, where liquid samples include bodily fluids such as nipple aspirate fluid, urine, blood, serum, plasma, and the like. In other embodiments, a biological sample is a liquid sample that may or may not include living cells, where the liquid sample is a lavage sample, e.g., a ductal lavage sample. In some embodiments, a biological sample has been treated prior to use in a subject detection method, e.g., by enrichment for one or more components (e.g., proteins, nucleic acids, etc.); removal of cells or cell debris; processing for histochemical analysis; and the like.
[00238] In some embodiments, a subject detection method provides for detection of a pre-cancerous mammary epithelial cell. Detection of a pre-cancerous MEC involves detection of an MEC signature, e.g., a signature that is indicative of a pre-cancerous MEC. An "MEC signature" includes, but is not limited to: 1) the presence and/or level of a selected protein or collection of proteins; 2) the presence or absence of a posttranslational modification of a selected protein or collection of proteins; 3) the
presence of a chromatin modification; 4) the level of a selected DNA or collection of DNA; 5) the integrity of a selected DNA or collection of DNA; 6) the methylation status of a selected DNA or collection of DNA; 7) the presence and/or level of a selected mRNA or collection of mRNA; 8) the presence and/or level of a selected microRNA or collection of microRNA; and 9) secretion and/or release of a factor from an MEC.
[00239] As an example, a subject method will in some embodiments involve administering a detectable labeled binding reagent, e.g., a detectably labeled antibody, to an individual; and detecting binding of the antibody reagent to a pre-cancerous mammary epithelial cell in the individual. Detecting binding of the antibody reagent to a pre-cancerous mammary epithelial cell in the individual can be carried out using standard methods, e.g., magnetic resonance imaging, histochemical analysis, and the like. As another example, in some embodiments a subject method will be carried out on a tissue sample
obtained from an individual being tested, e.g., where the tissue sample, will be contacted with a specific binding reagent (e.g., an antibody reagent; a nucleic acid reagent, etc., as described above).
[00240] Detection of a pre-cancerous MEC is useful in a variety of clinical applications, including imaging methods, diagnostic methods, prognostic methods, and monitoring methods. For example, a subject imaging method provides for detection of a pre-cancerous MEC in a female individual, e.g., an individual who presents as "normal," e.g., an individual who would normally undergo a routine
examination or screening procedure that would be carried out on an individual who is not considered at high risk for breast cancer. As another example, detection of a pre-cancerous MEC is useful in a
diagnostic method, e.g., alone or in conjunction with a mammogram, magnetic resonance imaging
(MRI), or other standard diagnostic test, to detect the presence of a pre-cancerous MEC in mammary tissue. As a further example, detection of a pre-cancerous MEC is useful in a prognostic method, e.g., following a procedure such as benign breast biopsy (BBB), to determine the need for a cancer treatment regimen such as chemotherapy. Finally, detection of a pre-cancerous MEC is useful in a monitoring method, e.g., to determine the efficacy of treatment for breast cancer, and/or to determine patient
response to treatment for breast cancer.
[00241] It should be appreciated that a subject detection method can involve one, two, three, or more of the above-mentioned detection methods. In other embodiments, a subject method involves detecting two or more features of an MEC signature, e.g., a subject method can involve detecting two, three, four, five, or more of: 1) the presence and/or level of a selected protein or collection of proteins produced by an MEC; 2) the presence or absence of a posttranslational modification of a selected protein or
collection of proteins in an MEC; 3) the presence of a chromatin modification in an MEC; 4) the level of a selected DNA or collection of DNA in an MEC; 5) the integrity of a selected DNA or collection of DNA in an MEC; 6) the methylation status of a selected DNA or collection of DNA in an MEC; 7) the presence and/or level of a selected mRNA or collection of mRNA in an MEC; 8) the presence and/or level of a selected microRNA or collection of microRNA in an MEC; and 9) secretion and/or release of a factor from an MEC:
Methods for detecting a variant mammary epithelial cell
[00242] Methods for detecting a variant (e.g., pre-cancerous) mammary epithelial cell are provided.
Detection of a pre-cancerous MEC involves detection of an MEC signature, e.g., a signature that is indicative of a pre-cancerous MEC. An "MEC signature" includes, but is not limited to, one or more of the following features: 1) the presence and/or level of a selected protein or collection of proteins; 2) the presence or absence of a posttranslational modification of a selected protein or collection of proteins; 3) the presence of a chromatin modification; 4) the level of a selected DNA or collection of DNA; 5) the integrity of a selected DNA or collection of DNA; 6) the methylation status of a selected DNA or
collection of DNA; 7) the presence and/or level of a selected mRNA or collection of mRNA; 8) the presence and/or level of a selected microRNA or collection of microRNA; and 9) secretion and/or
release of a factor from an MEC.
[00243] In some embodiments, a subject detection method involves detection of a gene product (e.g., polypeptides; nucleic acids) produced by an MEC. In one embodiment, the methods involve contacting a sample with a probe specific for the gene product of interest (e.g., marker polypeptide). "Probe" as used herein in such methods is meant to refer to a molecule that specifically binds a gene product of interest (e.g., the probe binds to the target gene product with a specificity sufficient to distinguish
binding to target over non-specific binding to non-target (background) molecules). "Probes" include, but are not necessarily limited to, antibodies (e.g., antibodies, antibody fragments that retain binding to a target epitope, single chain antibodies, and the like); polynucleotides (e.g., oligonucleotide probes);
and other polypeptide, peptide, or molecule (e.g., receptor ligand) that specifically binds a target gene product of interest.

[002441 Subject detection methods include one or more of: 1) detecting the presence and/or level of a selected protein or collection of proteins in an MEC; 2) detecting the presence of posttranslational modifications of gene expression-controlling proteins in an MEC; 3) detecting the level of a selected
DNA or collection of selected DNA in an MEC; 4) detecting the integrity of a selected DNA in an
MEC; 5) detecting the methylation status of a selected DNA in an MEC; 6) detecting the presence and/or a level of a selected mRNA or collection of mRNA in an MEC; 7) detecting the presence and/or level of a selected microRNA in an MEC; and 8) detecting secretion and/or release of a molecule (e.g.3 a protein, a nucleic acid, an ion, etc.) from an MEC; and 9) detecting a physical, morphological, or functional change in an MEC when contacted with a test fibroblast.
[00245] In some embodiments, the method for detecting the presence or absence of a pre-cancerous epithelial cell in a subject includes detecting a pattern of gene product expression present in a biological sample obtained from a subject; and comparing the pattern of gene product expression from the
biological sample to a library of gene product expression pattern known to be indicative of the presence or absence of a pre-cancerous epithelial cell, wherein the comparing indicates the presence or absence of a pre-cancerous epithelial cell.
[00246] The probe and sample suspected of having the gene product of interest are contacted under conditions suitable for binding of the probe to the gene product. For example, contacting is generally for a time sufficient to allow binding of the probe to the gene product {e.g., from several minutes to a few hours), and at a temperature and conditions of osmolality and the like that provide for binding of the probe to the gene product at a level that is sufficiently distinguishable from background binding of the probe (e.g., under conditions that minimize non-specific binding). Suitable conditions for probe- target gene product binding can be readily determined using controls and other techniques available and known to one of ordinary skill in the art.
[00247] As such, in some embodiments, the pattern of gene product expression will be detected and compared to the library of gene product expression patterns known to be indicative of the presence or absence of a pre-cancerous epithelial cell. Li certain embodiments, the assessment of gene product expression of a single gene product will provide a preliminary result and will be followed up with the assessment of at least a second gene product expression.
[00248] The present invention also provides a method for monitoring progression of a pre-cancerous epithelial cell in a subject by detecting a first pattern of expression of gene products present in a
biological fluid sample obtained from a subject at a first time point, wherein said first pattern is
indicative of a pre-cancerous epithelial cell; detecting a second pattern of expression of gene products present in a biological sample obtained from a subject at a second time point; and comparing the first and second patterns of expression of gene products from the biological samples, wherein the comparing provides for monitoring of the progression of the pre-cancerous epithelial cell from the first time point to the second time point.

[00249] In certain embodiments, the method of monitoring progression of a pre-cancerous epithelial cell in a subject will include detecting a pattern of expression of gene products present in a biological
sample obtained from a subject at more than two time points, such as three or more. In general, the time points for detecting a pattern of expression of gene products can be separated by any amount of time that is desired. For example, the first time point and second time point can be separated by about 3 months, about 6 months, or about 1 year or more, such as about 3 or more years.
[00250] In general, it will be appreciated by one of skill in the art that the duration of time between the first time point and the second time point must be sufficient to provide for a monitoring of the
progression of the pre-cancerous epithelial cell.
[00251] In certain embodiments, a subject detection method provides for monitoring the progression of a pre-cancerous epithelial cell in an individual. In some embodiments, the monitoring of the precancerous epithelial cell in the subject is conducted without concomitant treatment for cancer. In such embodiments, the method of monitoring will provide information as to the status of the pre-cancerous epithelial cell, which information is used to determine whether treatment is warranted, to determine the type of treatment that should be initiated, and/or the treatment regimen. In some embodiments,
monitoring is carried out once a year, every 6 months, every 4 months, every 3 months, or once per month.
[00252] The monitoring of the pre-cancerous epithelial cell in the subject can be conducted in parallel with a preventive approach (e.g., to remove precursors) and/or a treatment regimen for a cancer, e.g., a carcinoma. In such embodiments, the method of monitoring the pre-cancer or cancer during treatment will provide information of whether the treatment is improving the condition, or having no effect or an adverse effect on the condition, hi such embodiments, the first time point may be either just before, concurrent with, or just after the in initiation of a treatment regimen and the second time point may be a time point following a desired treatment period. For example, in such embodiments, the second time point may be about 6 month or more following initiation of treatment, including about 1 year, about 2 years, or more. For example, the detection of the pattern of expression of gene products present in a biological sample obtained from the subject may be determined about once every 6 months to monitor progression of the disease and efficacy of the treatment regimen.
[00253] In general, methods of the invention involving detection of a gene product (e.g., polypeptides or polynucleotides). The probe and sample suspected of having the gene product of interest are
contacted under conditions suitable for binding of the probe to the gene product. For example,
contacting is generally for a time sufficient to allow binding of the probe to the gene product (e.g., from several minutes to a few hours), and at a temperature and conditions of osmolality and the like that provide for binding of the probe to the gene product at a level that is sufficiently distinguishable from background binding of the probe (e.g., under conditions that minimize non-specific binding). Suitable conditions for probe-target gene product binding can be readily determined using controls and other techniques available and known to one of ordinary skill in the art.

[00254] The detection methods can be provided as part of a kit. Thus, the invention further provides kits for detecting the presence/absence and/or a level of expression of a markerjjf the invention, and/or a polypeptide in a human biological sample. The kits of the invention for detecting a marker polypeptide generally comprise a moiety that specifically binds the polypeptide, which may be a specific antibody. The kit may optionally provide additional components that are useful in the procedure, including, but not limited to, buffers, developing reagents, labels, reacting surfaces, means for detection, control
samples, standards, instructions, and interpretive information.
Detecting the presence and/or level of a selected polypeptide or collection of polypeptides
[00255] In some embodiments, a subject detection method involves detecting the presence and/or levels of a selected polypeptide or collection of polypeptides produced by an MEC. The methods generally involve use of a probe to detect the polypeptide(s). In these embodiments, the probe is an antibody or other polypeptide, peptide, or molecule (e.g., receptor ligand) that specifically binds a target
polypeptide of interest.
[00256] In some embodiments, a subject detection method involves detecting the presence and/or level of one or more of the polypeptides listed in Figure 14. In some embodiments, a subject detection
method involves detecting the presence and/or level of one or more of: CD73, CD138, notch receptor-3, CD90, BMI-I, COX-2, Ki67, pi 6, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2. In some embodiments, a
subject detection method involves detecting the presence and/or level of one or more of: CD73, CD 138, notch receptor-3, CD90, BMI-I, and COX-2. In some embodiments, a subject detection method
involves detecting the presence and/or level of CD73, CDl 38, notch receptor-3, CD90, BMI-I5 and
COX-2. In some embodiments, a subject detection method involves detecting the presence and/or level of Ki67 and pl6. In some embodiments, a subject detection method involves detecting the presence and/or level of Ki67 and COX-2. In some embodiments, a subject detection method involves detecting the presence and/or level of Ki67, pi 6, and COX-2.
[00257] The selected polypeptides (also referred to herein as "biomarkers"), or collection of selected polypeptides, can be detected by any suitable method. Detection paradigms that can be employed to this end include enzymatic methods, including immunological-based methods, optical methods,
electrochemical methods (voltametry and amperometry techniques), atomic force microscopy, and
radio frequency methods, e.g., multipolar resonance spectroscopy. It is to be understood that the present invention is not limited to a particular detection method. However, in some embodiments detection is by, for example, fluorescent detection, spectrometric detection, chemiluminescent detection, matrix assisted laser desorption-time-of flight (MALDI-TOF) detection, high pressure liquid chromatographic detection, charge detection, mass detection, radio frequency detection, and light diffraction detection.
Exemplary detection methods that are suitable for use with the subject methods are described herein.
[00258] In some embodiments, detection a selected polypeptide or collection of polypeptides is by use of capture reagents specific to the polypeptides. In some embodiments, the biospecific capture reagent is bound to a solid phase, such as a bead, a plate, a membrane or a chip. Methods of coupling
biomolecules, such as antibodies, to a solid phase are well known in the art. They can employ, for example, bifunctional linking agents, or the solid phase can be derivatized with a reactive group, such as an epoxide or an imidizole, that will bind the molecule on contact. Biospecific capture reagents against different polypeptides can be mixed in the same place, or they can be attached to solid phases in different physical or addressable locations. For example, one can load multiple columns with
derivatized beads, each column able to capture a single polypeptide. Alternatively, one can pack a single column with different beads derivatized with capture reagents against a variety of polypeptides, thereby capturing all the polypeptide analytes in a single place. Accordingly, antibody-derivatized bead-based technologies, such as Multi-Analyte Profiling (xMAP™) technology of Luminex (Austin, Tex.) can be used to detect the polypeptide(s).
[00259] Luminex xMAP™ is based on polystyrene particles (microspheres) that are internally labeled with two different fluorophores. When excited by a 635-nm laser, the fluorophores emit light at
different wavelengths, e.g., 658 and 712 nm. By varying the 658-nm/712-nm emission ratios, the beads are individually classified by the unique Luminex 100 IS analyzer. A third fluorophore coupled to a reporter molecule allows for quantification of the interaction that has occurred on the microsphere surface. The Luminex xMAP™ technology is described, for example, in U.S. Pat. Nos. 5,736,330,
5,981,180, and 6,057,107, all of which are specifically incorporated by reference.
[00260] In yet another embodiment, the surfaces of biochips can be derivatized with the capture
reagents directed against specific polypeptides. Biochips generally comprise solid substrates and have a generally planar surface, to which a capture reagent (also called an adsorbent or affinity reagent) is attached. Frequently, the surface of a biochip comprises a plurality of addressable locations, each of which has the capture reagent bound thereto.
Immunoassays
[00261] Any of a variety of known immunoassay methods can be used for detection, including, but not limited to, immunoassay, using an antibody specific for the polypeptide, e.g., by enzyme-linked
immunosorbent assay (ELISA), radioimmunoassay (RIA), immunohistochemistry; and the like; and functional assays for the encoded polypeptide, e.g., binding activity or enzymatic activity.
[00262] In some embodiments, a subject detection method involves detecting the presence and/or level of one or more of: CD73, CD138, notch receptor-3, CD90, BMI-I, COX-2, Ki67, pl6, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2. In some embodiments, a subject detection method involves detecting the
presence and/or level of one or more of: CD73, CD138, notch receptor-3, CD90, BMI-I, and COX-2. In some embodiments, a subject detection method involves detecting the presence and/or level of
CD73, CDl 38, notch receptor-3, CD90, BMM, and COX-2. In some embodiments, a subject detection method involves detecting the presence and/or level of Ki67 and pl6. In some embodiments, a subject detection method involves detecting the presence and/or level of Ki67 and COX-2. In some embodiments, a subject detection method involves detecting the presence and/or level of Ki67, pi 6, and COX-2.
[00263] For example, an immunofluorescence assay can be easily performed on a biological sample obtained from a patient, e.g., a tissue biopsy. It is also possible to perform such assays in plasma.
[00264] To increase the sensitivity of the assay, the immunocomplex may be further exposed to a
second antibody, which is labeled and binds to the first antibody, which is specific for the encoded polypeptide. Typically, the secondary antibody is detectably labeled, e.g., with a fluorescent marker.
The cells which express the encoded polypeptide will be fluorescently labeled and easily visualized under the microscope. See, for example, Hashido et al. (1992) Biochem. Biophys. Res. Comm.
187:1241-1248.
[00265] As will be readily apparent to the ordinarily skilled artisan upon reading the present
specification, the detection methods and other methods described herein can be varied. Such variations are within the intended scope of the invention. For example, in the above detection scheme, the probe for use in detection can be immobilized on a solid support, and the test sample (e.g., biological sample obtained from a patient) contacted with the immobilized probe. Binding of the test sample to the probe can then be detected in a variety of ways, e.g., by detecting a detectable label bound to the test sample.

[00266] Thus generally the methods comprise: a) contacting a sample comprising an MEC with an antibody specific for one or more of: CD73, CD138, notch receptor-3, CD90, BMI-I, COX-2, Ki67, p 16, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK,
MAPKK, DDR2, TRF2, activin, and MEK1/2; and b) detecting binding between the antibody and molecules of the sample. The level of antibody binding (either qualitative or quantitative) indicates that the MEC is pre-cancerous. For example, where the marker polypeptide is present at a level greater than that associated with a negative control level, the MEC is pre-cancerous, and the patient is susceptible to or at risk of developing breast cancer.
[00267] Suitable controls include a sample known not to contain the marker polypeptide; a sample contacted with an antibody not specific for the marker polypeptide; a sample having a level of
polypeptide that is elevated in a cancerous epithelial cell. A variety of methods to detect specific
antibody-antigen interactions are known in the art and can be used in the method, including, but not limited to, standard immunohistological methods, immunoprecipitation, an enzyme immunoassay, and a radioimmunoassay.
[00268] In general, the specific antibody will be detectably labeled, either directly or indirectly. Direct labels include radioisotopes; enzymes having detectable products (e.g., luciferase, β-galactosidase, and the like); fluorescent labels (e.g., fluorescein isothiocyanate, rhodamine, phycoerythrin, and the like); fluorescence emitting metals, e.g., 152Eu, or others of the lanthanide series, attached to the antibody through metal chelating groups such as EDTA; chemiluminescent compounds, e.g., luminol,
isoluminol, acridinium salts, and the like; bioluminescent compounds, e.g., luciferin, aequorin (green fluorescent protein), and the like. In some embodiments, an antibody reagent comprises, covalently linked to the antibody reagent, a protein that provides for a detectable signal. Suitable proteins include, but are not limited to, fluorescent proteins and enzymes (e.g., β-galactosidase, luciferase, horse radish peroxidase, alkaline phosphatase, etc.). For example, suitable proteins include fluorescent proteins, chromogenic proteins, enzymes that catalyze the production of a product that is luminescent,
fluorescent, or colored, etc.
[00269] Suitable fluorescent proteins include, but are not limited to, a green fluorescent protein (GFP;

Chalfie, et al., Science 263(5148): 802-805 (Feb 11, 1994); an enhanced GFP (EGFP), e.g., Genbank
Accession Number U55762); a blue fluorescent protein; an enhanced yellow fluorescent protein; a fluorescent protein as described in, e.g., WO 92/15673, WO 95/07463, WO 98/14605, WO 98/26277, WO 99/49019, U.S. Patent No. 5,292,658, U.S. Patent No. 5,418,155, U.S. Patent No. 5,683,888, U.S. Patent No. 5,741,668, U.S. Patent No. 5,777,079, U.S. Patent No. 5,804,387, U.S. Patent No.
5,874,304, U.S. Patent No. 5,876,995, and U.S. Patent No. 5,925,558; a GFP from species such as
Renilla reniformis, Renilla mulleri, or Ptilosarcus guernyi, as described in, e.g., WO 99/49019 or Peelle et al. (2001) J. Protein Chem. 20:507-519; any of a variety of fluorescent and colored proteins from
Anthozoan species, as described in, e.g., Matz et al. (1999) Nature Biotechnol. 17:969-973, U.S. Patent Publication No. 2002/0197676, or U.S. Patent Publication No. 2005/0032085; and the like.
[00270] Other suitable detectable labels include fluorescent dyes, e.g., Fluorescein, Rhodamine, Texas

Red, Cy2, Cy3, Cy5, VECTOR Red, ELF™ (Enzyme-Labeled Fluorescence), CyO, CyO.5, CyI, CyI .5, Cy3, Cy3.5, Cy5, Cy7, FluorX, Calcein, Calcein-AM, CRYPTOFLUOR™, Orange (42 kDa),
Tangerine (35 kDa), Gold (31 kDa), Red (42 kDa), Crimson (40 kDa), BHMP, BHDMAP, Br-Oregon, . Lucifer Yellow, Alexa dye family, N-[6-(7-nitrobenz-2-oxa-l, 3-diazol-4-yl)arnino]caproyl] (NBD),
BODIPY™, boron dipyrromethene difluoride, Oregon Green, MITOTRACKER™ Red, DiOC7 (3),
DiICi8, Phycoerythrin, Phycobiliproteins BPE (240 kDa) RPE (240 kDa) CPC (264 kDa) APC (104 kDa), Spectrum Blue, Spectrum Aqua, Spectrum Green, Spectrum Gold, Spectrum Orange, Spectrum
Red, NADH, NADPH, FAD, Infra-Red (IR) Dyes, Cyclic GDP-Ribose (cGDPR), Calcofluor White,
Tyrosine and Tryptophan.
[00271] The antibody may be attached (coupled) to an insoluble support, such as a polystyrene plate or a bead. Indirect labels include second antibodies specific for antibodies specific for the encoded
polypeptide ("first specific antibody"), wherein the second antibody is labeled as described above; and members of specific binding pairs, e.g., biotin-avidin, and the like. The biological sample may be
brought into contact with and immobilized on a solid support or carrier, such as nitrocellulose, that is capable of immobilizing cells, cell particles, or soluble proteins. The support may then be washed with suitable buffers, followed by contacting with a detectably-labeled first specific antibody. Detection methods are known in the art and will be chosen as appropriate to the signal emitted by the detectable label. Detection is generally accomplished in comparison to suitable controls, and to appropriate
standards.

[00272] In some embodiments, a subject detection method involves use of an array of specific binding reagents, e.g., an antibody reagent array. An array can be created by spotting captures agents onto a substrate (e.g., glass, nitrocellulose, etc.) and attaching those capture agents to the substrate. The
antibody reagents can be bound to the substrate by either covalent bonds or by non-specific
interactions, such as hydrophobic interactions. Techniques for constructing arrays and methods of using these arrays are described in, for example, Schena et al. (1996) Proc Natl Acad Sd USA.
93(20): 10614-9; Schena et al. (1995) Science 270(5235) :467-70; Shalon et al. (1996) Genome Res.
6(7):639-45, USPN 5,807,522, EP 799 897; WO 97/29212; WO 97/27317; EP 785 280; WO 97/02357; USPN 5,593,839; USPN 5,578,832; EP 728 520; USPN 5,599,695; EP 721 016; USPN 5,556,752; WO 95/22058; and USPN 5,631,734. The antibody reagents utilized in the arrays can be of varying types and can include, for example, antibodies, including antibody fragments, aptamers, avimers, or
peptidomimetics.
[00273] Common physical substrates for making protein arrays include glass or silicon slides, magnetic particles or other micro beads, functionalized with aldehyde or other chemical groups to help
immobilize proteins. The substrate can also be coated with PLL (polylysine), nitrocellulose, PVDF membranes or modified with specific chemical reagents to adsorb capture agents. The desirable
properties of an ideal surface include: chemical stability before, during, and after the coupling
procedure, suitability for a wide range of capture agents (e.g., hydrophilic and hydrophobic, low MW and high MW), minimal non-specific binding, low or no intrinsic background in detection, presentation of the capture agents in a fully-functional orientation, production of spots with predictable and regular morphology (shape, signal uniformity).
[00274J The variables in the immobilization of proteins include: type of capture agent (e.g., antibody reagent), nature of surface (including any pretreatment prior to use), and the immobilization method.
Both adsorption and covalent attachment have been used for protein arrays. Orientation of the capture agent is very important in presenting it to the ligand or the surface in a functional state. Although
covalent attachment using a variety of chemically activated surfaces (e.g., aldehyde, amino, epoxy) as well as attachment by specific biomolecular interactions (e.g., biotin-streptavidin) provide a stable linkage and good reproducibility, chemical derivatization of the surface may alter the biological activity of the capture agent and/or may result in multi-site attachment.
[00275] In one embodiment, antibody arrays are made with a non-contact deposition printer. The printer uses thermal ink jet heads that can print many solutions simultaneously to produce hundreds of spots of 50-60 μm in diameter with a spacing of 150 μm between spots. The droplet volume ranges between 35 pL to 1.5 nL. The heating element is made out of TaAl or other suitable materials, and is capable of achieving temperatures that can vaporize a sufficient volume of printing buffer to produce a bubble that will push out a precise volume of the antibody solution on the substrate. Selection of printing buffer is important, in that the buffer accomplishes the following: increases printing efficiency (measure of the number of spots that are printed to the total number of spots that are attempted), reduces sample spreading, promotes uniform delivery, stabilizes the capture agents that are being printed, reduces
sample drying, and increases the visibility of the printed spots. In addition to the printing buffer, other variables that affect printing include: size of the drops, the method of washing and drying the print head, and the speed at which the dispensing head moves. Various modifications may be within these conditions.
Immunohistochemical assays
[00276] In some embodiments, a subject detection method is an immunohistochemical assay. See, e.g.,

U.S. Patent No. 6,007,996 for a discussion of various immunohistochemical methods. In general, the method involves contacting a sample comprising an MEC with an antibody specific for a target
polypeptide (e.g., one or more of: CD73, CD138, notch receptor-3, CD90, BMI-I, COX-2, Ki67, pl6, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin Bl , c-kit, STAT3, cyclin Dl , PI3K, MAPK,
MAPKK, DDR2, TRF2, activin, and MEKl /2); and detecting binding, if any, of the antibody to an epitope(s) present in the MEC.
[00277] In general, the specific antibody will be detectably labeled, either directly or indirectly. Direct labels include radioisotopes; enzymes having detectable products (e.g., luciferase, β-galactosidase, and the like); fluorescent labels (e.g., fluorescein isothiocyanate, rhodamine, phycoerythrin, and the like); fluorescence emitting metals, e.g., 152Eu, or others of the lanthanide series, attached to the antibody through metal chelating groups such as EDTA; chemiluminescent compounds, e.g., luminol,
isoluminol, acridinium salts, and the like; bioluminescent compounds, e.g., luciferin, aequorin (green fluorescent protein), and the like. Other suitable detectable labels include fluorescent dyes, e.g.,
Fluorescein, Rhodamine, Texas Red, Cy2, Cy3, Cy5, VECTOR Red, ELF™ (Enzyme-Labeled
Fluorescence), CyO, CyO.5, CyI, CyI .5, Cy3, Cy3.5, Cy5, Cy7, FluorX, Calcein, Calcein-AM,
CRYPTOFLUOR™, Orange (42 kDa), Tangerine (35 kDa), Gold (31 kDa), Red (42 kDa), Crimson (40 kDa), BHMP, BHDMAP, Br-Oregon, Lucifer Yellow, Alexa dye family, N-[6-(7-nitrobenz-2-oxa-l, 3- diazol-4-yl)amino]caproyl] (NBD), BODIPY™, boron dipyrromethene difiuoride, Oregon Green,
MITOTRACKER™ Red, DiOC7 (3), DiIC18, Phycoerythrin, Phycobiliproteins BPE (240 kDa) RPE
(240 kDa) CPC (264 kDa) APC (104 kDa), Spectrum Blue, Spectrum Aqua, Spectrum Green, Spectrum Gold, Spectrum Orange, Spectrum Red, NADH, NADPH, FAD, Infra-Red (IR) Dyes, Cyclic GDP- Ribose (cGDPR), Calcofluor White, Tyrosine and Tryptophan.
[00278] In some embodiments, a sample comprising an MEC is contacted with antibody reagent(s) or other binding reagent(s) specific for one or more of: CD73, CDl 38, notch receptor-3, CD90, BMI-I ,
COX-2, Ki67, pl6, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin B 1 , c-kit, STAT3, cyclin Dl,
PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK 1/2. In some embodiments, a sample
comprising an MEC is contacted with antibody reagent(s) or other binding reagent(s) specific for one or more of: CD73, CDl 38, notch receptor-3, CD90, BMI-I, and COX-2. In some embodiments, a sample comprising an MEC is contacted with antibody reagent(s) or other binding reagent(s) specific for
CD73, CDl 38, notch receptor-3, CD90, BMI-I, and COX-2. In some embodiments, a sample comprising an MEC is contacted with antibody reagent(s) or other binding reagent(s) specific for Ki67 and pl6. In some embodiments, a sample comprising an MEC is contacted with antibody reagent(s) or other binding reagent(s) specific for Ki67 and COX-2. In some embodiments, a sample comprising an MEC is contacted with antibody reagent(s) or other binding reagent(s) specific for Ki67, pi 6, and
COX-2.
[00279] In some embodiments, e.g., where two or more antibodies are used, each antibody being
specific for a different target polypeptide, each of the two or more antibodies is detectably labeled with a different label, where the two or more different labels are distinguishable from one another.
Polypeptide Arrays
[00280] Polypeptide arrays provide a high throughput technique that can assay a large number of
polypeptides in a sample. This technology can be used as a tool to test for expression of a marker
polypeptide and detection of a pre-cancerous epithelial cell. In some embodiments, a subject array comprises a probe for detection of one or more of the polypeptides listed in Figure 14. Of particular interest are arrays which comprise a probe for detection of one or more of the following polypeptides: CD73, CDl 38, notch receptor-3, CD90, BMI-I, COX-2, Ki67, pl6, IGF2, YKL-40, EGF-R, c-jun,
PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and
MEK1/2.
[00281] A variety of methods of producing arrays, as well as variations of these methods, are known in the art and contemplated for use in the invention. For example, arrays can be created by spotting
polypeptide probes onto a substrate (e.g., glass, nitrocellulose, etc.) in a two-dimensional matrix or array having bound probes. The probes can be bound to the substrate by either covalent bonds or by non-specific interactions, such as hydrophobic interactions.
[00282] Samples of polypeptides can be detectably labeled (e.g. , using radioactive or fluorescent labels) and then hybridized to the probes. Alternatively, the polypeptides of the test sample can be immobilized on the array, and the probes detectably labeled and then applied to the immobilized polypeptides. In most embodiments, the "probe" is detectably labeled. In other embodiments, the probe is immobilized on the array and not detectably labeled. In such embodiments, the sample is applied to the polypeptide array and bound gene products (e.g., peptides) are detected using secondary labeled probes.
[00283] Examples of such protein arrays are described in the following patents or published patent applications: U.S. Pat. No. 6,225,047; PCT International Publication No. WO 99/51773; U.S. Pat. No. 6,329,209, PCT International Publication No. WO 00/56934 and U.S. Pat. No. 5,242,828.
Detecting posttranslational modification of a factor
[00284] In some embodiments, a subject detection method involves detecting posttranslational
modification of one or more factors (e.g., polypeptides), present in a MEC, that control gene expression and/or that modulate chromatin, and/or that modulate DNA methylation. In some embodiments, a
subject detection method involves detecting a posttranslational modification of a Polycomb group
(PcG) repressor complex (e.g., modification of a PcG protein such as EED) and/or a posttranslational modification of a histone deacetylase. Posttranslational modifications of chromatin polypeptides
include methylation and acetylation. In some embodiments, a subject detection method involves use of an antibody reagent that specifically binds a chromatin polypeptide, e.g., a chromatin epitope that is susceptible to posttranslational modification or that has been posttranslationally modified. A suitable antibody reagent is contacted with a sample comprising an MEC1 or with a sample comprising MEC proteins, and binding, if any, of the antibody reagent to a chromatin polypeptide in the sample is
detected. For example, in some embodiments, an antibody reagent specifically binds to a chromatin epitope(s) that is not modified, e.g., the antibody reagent binds specifically to a chromatin epitope that comprises only encoded amino acids. In other embodiments, an antibody reagent specifically binds to an acetylated chromatin polypeptide, e.g., the antibody reagents binds specifically to a chromatin
epitope that is acetylated. In other embodiments, an antibody reagent specifically binds to a methylated chromatin polypeptide, e.g., the antibody reagents binds specifically to a chromatin epitope that is methylated. The antibody reagent can be detectably labeled, as described above
Detecting chromatin modifications
[00285] In some embodiments, a subject detection method involves detecting chromatin modification in an MEC. In some embodiments, a subject detection method involves detection of histone acetylation. Suitable detection methods include immunohistochemical methods; and other immunological methods (e.g., immunoprecipitation; protein blot assays; etc.).
Detecting secreted or released molecules
[00286] In some embodiments, a subject detection method involves detecting molecules secreted or released from an MEC. For example, in some embodiments, an MEC is obtained from an individual and is cultured in vitro; and a profile of molecules secreted or released from the cultured MEC is
detected. In other embodiments, a reporter MEC is cultured in vitro in the presence of a fibroblast obtained from an individual; and a profile of molecules secreted or released from the reporter MEC is detected. Molecules secreted or released from an MEC include, but are not limited to, proteins, nucleic acids, and ions.
[00287] Proteins that are secreted or released from an MEC can be detected as described above, using any number of different assay formats, including, e.g., immunological assays, where in some
embodiments, an array of antibody reagents is used to detect two or more proteins secreted or released from an MEC.
[00288] Nucleic acids that are secreted or released from an MEC can be detected as described below, using a nucleic acid probe and/or a nucleic acid primer. For example, in some embodiments, an array of nucleic acid probes is used to detect two or more nucleic acids secreted or released from an MEC.
[00289] Ions that can be detected include, e.g., calcium ions, potassium ions, sodium ions, magnesium ions, chloride ions, hydrogen ions (pH), and the like. Suitable ion-indicating agents include fluorescent calcium indicators, e.g., fura dyes (e.g., fura-2, fura-4F, fura-5F, fura-6F, fura-FF, Fura Red), fluo dyes (e.g., fluo-3, flou-4), indo dyes (e.g., indo-1), rhodamine dyes (e.g., rhod-2, X-rhod-1), Oregon Green 488, Calcium Green, Calcium Crimson, and quin-2; membrane-permeant acetoxymethyl (AM) ester forms of any of the aforementioned fluorescent calcium indicators; membrane-impermeant salt forms of any of the aforementioned fluorescent calcium indicators; fluorescent sodium indicators, e.g.,
benzofuran isophthalate (SBFI), Sodium Green, CoroNa Green; fluorescent potassium indicators, e.g., PBFI, CD222; fluorescent magnesium indicators, e.g., Mag-Fluo-4, Mag-Fura-2, Mag-Fura-5, Mag- Fura-Red, Mag-indo-1, Mag-rho-2, Magnesium Green; fluorescent chloride indicators, e.g., trans-1,2- bis(4-[ 1 '-MQ- 1 "-dimethyl-AQ-xylyl]-pyridinium)ethylene (Bis-DMXPQ), 7-(β-D-ribofuranosylamino)- pyrido[2,l-h]-pteri.din-l l-ium-5-olate (LZQ), Lucigenin, and a variety of 6-methoxyquinolinium
derivatives such as 6-Methoxy-N-(3-sulfopropyl)quinolinium (SPQ), N-(Ethoxycarbonylmethyl)-6- methoxyquinolinium bromide (MQAE) and 6-Methoxy-N-ethylquinolinium iodide (MEQ); and
fluorescent pH indicators, e.g., biscarboxyethyl-carboxyfluorescein (BCECF) and 2',7'-bis-(2- carboxypropyl)-5-(6-)-carboxyfluorescein (BCPCF). Other suitable methods and reagents include those described in, e.g., U.S. Patent Publication No. 2006/0148104.
Detecting the presence and/or level of an mRNA
[00290] In some embodiments, a subject detection method involves detecting the presence and/or level of a selected mRNA, or a collection of selected mRNA, in an MEC. In some embodiments, a cDNA copy of a selected mRNA, or cDNA copies of a collection of selected mRNA, is detected. In some embodiments, a subject detection method will involve nucleic acid hybridization with a nucleic acid probe, nucleic acid amplification with a nucleic acid primer pair, or both. Nucleic acid hybridization and nucleic acid amplification methods are known to those skilled in the art. Exemplary nucleic acid hybridization and nucleic acid amplification methods are discussed in detail below. The following
provides detail of exemplary nucleic acid-based methods for detection, and examples of how such can be adapted for use in the methods of the invention.
[00291] In some embodiments, a subject method for detecting the presence and/or level of an mRNA, a collection of mRNA, in an MEC involves contacting, under stringent hybridization conditions, a subject nucleic acid probe with a target nucleic acid in a sample; and detecting the level of target mRNA in the sample, hi some embodiments, where the detected level of target mRNA indicates that target mRNA is overexpressed or underexpressed in the cell, the cell is considered precancerous. In some embodiments, a cDNA copy of a target mRNA is generated. In some embodiments, the target nucleic acid (mRNA or cDNA copy) is amplified using a nucleic acid primer pair.
[00292] hi some embodiments, a subject method involves detecting, in an MEC (or a nucleic acid
sample obtained from an MEC), the presence and/or level of one or more mRNAs (or a cDNA copy thereof) listed in Figure 14. In some embodiments, & subject method involves detecting, in an MEC (or a nucleic acid sample obtained from an MEC), the presence and/or level of one or more of the
following mRNA (or cDNA copy thereof): CD73, CD138, notch receptor-3, CD90, BMI-I, COX-2,
Ki67, p 16, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K,
MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2.

[00293] In some embodiments, a subject method involves detecting, in an MEC (or a nucleic acid
sample obtained from an MEC), the presence and/or level of two or more (e.g., two, three, four, five, or more) of the following mRNA (or cDNA copy of an mRNA): CD73, CDl 38, notch receptor-3, CD90, BMI-I, COX-2, Ki67, pl6, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEKl /2.
[00294] In some embodiments, a subject method involves detecting, in an MEC (or a nucleic acid
sample obtained from an MEC), the presence and/or level of two, three, four, five, or all of CD73,
CD138, notch receptor-3, CD90, BMI-I, and COX-2 mRNAs (or cDNA copies of same). In some embodiments, a subject method involves detecting, in an MEC (or a nucleic acid sample obtained from an MEC), the presence and/or level of Ki67, COX-2, and pi 6 mRNA (or cDNA copies of same), hi some embodiments, a subject method involves detecting, in an MEC (or a nucleic acid sample obtained from an MEC), the presence and/or level of two, three, four, five, or all of CD73, CD138, notch
receptor-3, CD90, BMI-I, and COX-2 mRNAs (or cDNA copies of same). In some embodiments, a subject method involves detecting, in an MEC (or a nucleic acid sample obtained from an MEC), the presence and/or level of Ki67 and COX-2 mRNA (or cDNA copies of same), hi some embodiments, a subject method involves detecting, in an MEC (or a nucleic acid sample obtained from an MEC), the presence and/or level of Ki67 and pi 6 mRNA (or cDNA copies of same).
[00295] A number of methods are available for analyzing nucleic acids for the presence and/or level of a specific nucleic acid in a cell, or in a sample comprising nucleic acids obtained from a cell (e.g., a cell lysate, etc.). The mRNA can be assayed directly. In some embodiments, an mRNA is detected by
microarray analysis; see, e.g., U.S. Patent Publication No. 2007/0009915.
[00296] In some embodiments, an mRNA is reverse transcribed into cDNA for analysis. The nucleic acid may be amplified by conventional techniques, such as the polymerase chain reaction (PCR), to provide sufficient amounts for analysis. The use of the polymerase chain reaction is described in Saiki, et al. (1985), Science 239:487, and a review of techniques may be found in Sambrook, et al. Molecular Cloning: A Laboratory Manual. CSH Press 1989, pp.14.2-14.33.
[00297] In some embodiments, the method involves contacting the sample under stringent hybridization conditions with a subject nucleic acid probe and detecting binding, if any, of the probe to a target
nucleic acid in the sample. A variety of nucleic acid hybridization methods are well known to those skilled in the art, and any known method can be used, hi many embodiments, the nucleic acid probe will be detectably labeled.
[00298] Where a subject method involves detecting a level of a target nucleic acid in a cell, the method will in some embodiments include amplification of the target nucleic acid, forming a target
amplification product; and can further include a step of hybridizing the target amplification product with a nucleic acid probe.
[00299] In some embodiments, the method involves contacting a sample (e.g., under stringent
hybridization conditions) with a subject nucleic acid primer pair, where the primer pair, under conditions that permit primer-initiated nucleic acid amplification, amplifies any target nucleic acid present in the sample, generating an amplification product (where amplification product is generated when target nucleic acid present in the sample).
[003001 Conditions that permit primer-initiated nucleic acid amplification and catalytic nucleic acid activity are well known to those skilled in the art, and include the presence of a DNA polymerase;
deoxynucleotide triphosphates; and magnesium ions. Suitable reaction conditions are well known to those skilled in the art of nucleic acid amplification. The DNA polymerase is generally one that has high affinity for binding at the 3'-end of an oligonucleotide hybridized to a nucleic acid strand. The
DNA polymerase is generally one that has little or no 5' -→ 3' exonuclease activity so as to minimize degradation of primer, termination or primer extension polynucleotides. The DNA polymerase is
generally one that has little to no proofreading activity. In many embodiments, the DNA polymerase is thermostable, e.g., is catalytically active at temperatures in excess of about 75°C. DNA polymerases that are suitable for use in a subject method include, but are not limited to, DNA polymerases discussed in U.S. Pat. Nos. 5,648,211 and 5744312, which include exo" Vent (New England Biolabs), exo' Deep Vent (New England Biolabs), Bst (BioRad), exo" PfU (Stratagene), Bca (Panvera), sequencing grade
Taq (Promega); thermostable DNA polymerases from Thermoanaerobacter thermohydrosulfuricus; and the like. In some embodiments, the reaction mixture includes an RNAse H.
[00301] Magnesium ions are typically present in the reaction mix in a concentration of from about 1 mM to about 100 mM, e.g., from about 1 mM to about 3 mM, from about 3 mM to about 5 mM, from about 5 mM to about 10 mM, from about 10 mM to about 25 mM, from about 25 mM to about 50 mM, from about 50 mM to about 75 mM, or from about 75 mM to about 100 mM.
[00302] Usually the reaction mixture will comprise four different types of dNTPs corresponding to the four naturally occurring bases are present, i.e. dATP, dTTP, dCTP and dGTP. hi the subject methods, each dNTP will typically be present at a final concentration in the reaction, ranging from about 10 μM to 5000 μM, e.g., from about 10 μM to about 50 μM, from about 50 μM to about 100 μM, from about 100 μM to about 200 μM, from about 200 μM to about 500 μM, from about 500 μM to about 1000 μM, from about 1000 μM to about 2000 μM, from about 2000 μM to about 3000 μM, from about 3000 μM to about 4000 μM, or from about 4000 μM to about 5000 μM. In some embodiments, each dNTP will be present at a final concentration in the reaction of from about 20 μM to 1000 μM, from about 100 μM to about 200 μM, or from about 50 μM to about 200 μM.
[00303] The amplification reaction mixture typically includes an aqueous buffer medium that includes a source of monovalent ions, a source of divalent cations and a buffering agent. Any convenient source of monovalent ions, such as KCl, K-acetate, NHj-acetate, K-glutamate, NH4Cl, ammonium sulfate, and the like may be employed. The divalent cation may be magnesium, manganese, zinc and the like, where the cation will typically be magnesium. Any convenient source of magnesium cation may be employed, including MgCl2, Mg-acetate, and the like. Representative buffering agents or salts that may be present in the buffer include Tris, Tricine, HEPES, MOPS and the like, where the amount of buffering agent will typically range from about 5 to 150 mM, from about 10 to 100 mM, or from about 20 to 50 mM, where in certain embodiments the buffering agent will be present in an amount sufficient to provide a pH ranging from about 6.0 to 9.5, e.g., pH 7.3 at 72 0C. Other agents which may be present in the
buffer medium include chelating agents, such as EDTA, EGTA and the like.
[00304] Each primer nucleic acid is present in the reaction mixture at a concentration of from about 50 nM to about 900 nM, e.g., the 3' primer and the 5' primer nucleic acid are each independently present at a concentration of from about 50 nM to about 75 nM, from about 75 nM to about 100 nM, from
about 100 nM to about 150 nM, from about 150 nM to about 200 nM, from about 200 nM to about 250 nM, from about 250 nM to about 300 nM, from about 300 nM to about 400 nM, from about 400 nM to about 500 nM, from about 500 nM to about 600 nM, from about 600 nM to about 700 nM, from about 700 nM to about 800 nM, or from about 800 nM to about 900 nM.
[00305] A detectable label may be included in an amplification reaction. Suitable labels include
fluorochromes, e.g. fluorescein isothiocyanate (FITC), rhodamine, Texas Red, phycoerythrin,
allophycocyanin, 6-carboxyfluorescein (6-FAM), 2', 7'-dimethoxy-4',5'-dichloro-6-carboxyfluorescein (JOE), 6-carboxy-X-rhodamine (ROX), 6-carboxy-2',4',7\4,7-hexachlorofluorescein (HEX),
5-carboxyfluorescein (5-FAM) orN,N,N',N'-tetramethyl-6-carboxyrhodamine (TAMRA), radioactive labels, e.g. 32P, 35S, 3H; etc. The label may be a two stage system, where the amplified DNA is
conjugated to biotin, haptens, etc. having a high affinity binding partner, e.g. avidin, specific antibodies, etc. , where the binding partner is conjugated to a detectable label. The label may be conjugated to one or both of the primers. Alternatively, the pool of nucleotides used in the amplification is labeled, so as to incorporate the label into the amplification product.
[00306] In one embodiment, a subject method involves amplifying nucleic acids from a sample, which amplifying step follows a reverse transcription step to provide a cDNA template for amplification. In some embodiments, the level of a target mRNA can be indicated, where overexpression or
underexpression of a target mRNA indicates a cancerous or precancerous cell. In general,
amplification-based methods involve reverse transcription of mRNA in a sample and amplifying the resulting cDNA from the sample using a primer and at least one other primer, as described above, and assessing the amplified nucleic acids.
[00307] As is known in the art, an amplified nucleic acid may be assessed by a number of methods, including, for example, determining the presence or absence of the nucleic acid, determining the size of the nucleic acid or determining the abundance of a nucleic acid in relation to another amplified nucleic acid. In most embodiments, an amplified nucleic acid is assessed using gel electrophoresis, nucleic acid hybridization, sequencing, and/or detection of a signal from a label bound to the amplified nucleic acid. Methods of amplifying (e.g., by polymerase chain reaction) nucleic acid, methods of performing
primers extension, and methods of assessing nucleic acids are generally well known in the art (e.g., see Ausubel, et al, Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995 and Sambrook, et al, Molecular Cloning: A Laboratory Manual, Third Edition, (2001) Cold Spring Harbor, N. Y.) and need not be described in any great detail.
[00308] For example, primers and probes described above may be used in polymerase chain reaction
(PCR)-based techniques to detect target nucleic acid (e.g., to detect a level of target mRNA; etc.) in biological samples. PCR is a technique for amplifying a desired target nucleic acid sequence contained in a nucleic acid molecule or mixture of molecules. In PCR, a pair of primers is employed in excess to hybridize to the complementary strands of the target nucleic acid. The primers are each extended by a polymerase using the target nucleic acid as a template. The extension products become target sequences themselves after dissociation from the original target strand. New primers are then hybridized and
extended by a polymerase, and the cycle is repeated to geometrically increase the number of target sequence molecules. The PCR method for amplifying target nucleic acid sequences in a sample is well known in the art and has been described in, e.g., Innis et al. (eds.) PCR Protocols (Academic Press, NY 1990); Taylor (1991) Polymerase chain reaction: basic principles and automation, in PCR: A Practical Approach, McPherson et al. (eds.) IRL Press, Oxford; Saiki et al. (1986) Nature 324:163; as well as in U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,889,818, all incorporated herein by reference in their
entireties.
[00309] In particular, PCR uses relatively short oligonucleotide primers which flank the target
nucleotide sequence to be amplified, oriented such that their 3' ends face each other, each primer
extending toward the other. The polynucleotide sample is extracted and denatured, e.g. by heat, and hybridized with first and second primers which are present in molar excess. Polymerization is catalyzed in the presence of the four deoxyribonucleotide triphosphates (dNTPs-dATP, dGTP, dCTP and dTTP) using a primer- and template-dependent polynucleotide polymerizing agent, such as any enzyme
capable of producing primer extension products, for example, E. coli DNA polymerase I, Klenow
fragment of DNA polymerase I, T4 DNA polymerase, thermostable DNA polymerases isolated from
Thermus aquattcus (Taq), available from a variety of sources (for example, Perkin Elmer), Thermus thermophilus (United States Biochemicals), Bacillus stearothermophilus (Bio-Rad), or Thermococcus litoralis ("Vent" polymerase, New England Biolabs). This results in two "long products" which contain the respective primers at their 5' ends covalently linked to the newly synthesized complements of the original strands.
[00310] The reaction mixture is then returned to polymerizing conditions, e.g., by lowering the
temperature, inactivating a denaturing agent, or adding more polymerase, and a second cycle is
initiated. The second cycle provides the two original strands, the two long products from the first cycle, two new long products replicated from the original strands, and two "short products" replicated from the long products. The short products have the sequence of the target sequence with a primer at each end. On each additional cycle, an additional two long products are produced, and a number of short products equal to the number of long and short products remaining at the end of the previous cycle.

Thus, the number of short products containing the target sequence grows exponentially with each cycle. PCR is typically carried out with a commercially available thermal cycler, e.g., Perkin Elmer.
00311] RNAs encoding a deacylase of interest can be amplified by reverse transcribing the mRNA into cDNA, and then performing PCR (RT-PCR), as described above. Alternatively, a single enzyme may be used for both steps as described in U.S. Pat. No. 5,322,770. mRNA may also be reverse transcribed into cDNA, followed by asymmetric gap ligase chain reaction (RT-AGLCR) as described by Marshall et al. (1994) PCR Meth. App. 4:80-84.
O0312] The fhiorogenic 5' nuclease assay, known as the TAQMAN™ assay (Perkin-Elmer), is a
powerful and versatile PCR-based detection system for nucleic acid targets. For a detailed description of the TAQMAN™ assay, reagents and conditions for use therein, see, e.g., Holland et al., Proc. Natl. Acad. Sci, U.S.A. (1991) 88:7276-7280; U.S. Pat. Nos. 5,538,848, 5,723,591, and 5,876,930, all
incorporated herein by reference in their entireties. Hence, primers and probes derived from regions of a target nucleic acid as described herein can be used in TAQMAN™ analyses to detect a level of target mRNA in a biological sample. Analysis is performed in conjunction with thermal cycling by- monitoring the generation of fluorescence signals. The assay system dispenses with the need for gel electrophoretic analysis, and has the capability to generate quantitative data allowing the determination of, for example, the level of target mRNA (e.g., to detect the presence of a pre-cancerous epithelial cell; etc.).
[00313] The fluorogenic 5' nuclease assay is conveniently performed using, for example, AMPLITAQ
GOLD™ DNA polymerase, which has endogenous 5' nuclease activity, to digest an internal
oligonucleotide probe labeled with both a fluorescent reporter dye and a quencher (see, Holland et al., Proc. Natl. Acad.Sci. USA (1991) 88:7276-7280; and Lee et al., Nucl. Acids Res. (1993) 21:3761- 3766). Assay results are detected by measuring changes in fluorescence that occur during the
amplification cycle as the fluorescent probe is digested, uncoupling the dye and quencher labels and causing an increase in the fluorescent signal that is proportional to the amplification of target nucleic acid.
(00314] The amplification products can be detected in solution or using solid supports. In this method, the TAQMAN™ probe is designed to hybridize to a target sequence within the desired PCR product.
The 5' end of the TAQMAN™ probe contains a fluorescent reporter dye. The 3' end of the probe is blocked to prevent probe extension and contains a dye that will quench the fluorescence of the 51
fluorophore. During subsequent amplification, the 51 fluorescent label is cleaved off if a polymerase with 5' exonuclease activity is present in the reaction. Excision of the 5' fluorophore results in an
increase in fluorescence which can be detected.
[00315] In particular, the oligonucleotide probe is constructed such that the probe exists in at least one single-stranded conformation when unhybridized where the quencher molecule is near enough to the reporter molecule to quench the fluorescence of the reporter molecule. The oligonucleotide probe also exists in at least one conformation when hybridized to a target polynucleotide such that the quencher molecule is not positioned close enough to the reporter molecule to quench the fluorescence of the reporter molecule. By adopting these hybridized and unhybridized conformations, the reporter molecule and quencher molecule on the probe exhibit different fluorescence signal intensities when the probe is hybridized and unhybridized. As a result, it is possible to determine whether the probe is hybridized or unhybridized based on a change in the fluorescence intensity of the reporter molecule, the quencher molecule, or a combination thereof. In addition, because the probe can be designed such that the
quencher molecule quenches the reporter molecule when the probe is not hybridized, the probe can be designed such that the reporter molecule exhibits limited fluorescence unless the probe is either
hybridized or digested.
[00316] Accordingly, the present invention provides methods for amplifying a target nucleotide
sequence using a nucleic acid polymerase having 51 to 3' nuclease activity, one or more primers capable of hybridizing to the target sequence or its extension product, and an oligonucleotide probe capable of hybridizing to the target sequence 3' relative to the primer. During amplification, the polymerase digests the oligonucleotide probe when it is hybridized to the target sequence, thereby separating the reporter molecule from the quencher molecule. As the amplification is conducted, the fluorescence of the
reporter molecule is monitored, with fluorescence corresponding to the occurrence of nucleic acid
amplification. The reporter molecule is in some embodiments a fluorescein dye and the quencher
molecule is in some embodiments a rhodamine dye.
[00317] The target nucleic acids described herein may also be used as a basis for transcription-mediated amplification (TMA) assays. TMA provides a method of identifying target nucleic acids present in very small amounts in a biological sample. Such nucleic acids may be difficult or impossible to detect using direct assay methods. Li particular, TMA is an isothemal, autocatalytic nucleic acid target amplification system that can provide more than a billion RNA copies of a target sequence. The assay can be done qualitatively, to accurately detect the presence or absence of the target sequence in a biological sample. The assay can also provide a quantitative measure of the amount of target sequence over a
concentration range of several orders of magnitude. TMA provides a method for autocatalytically
synthesizing multiple copies of a target nucleic acid sequence without repetitive manipulation of
reaction conditions such as temperature, ionic strength and pH.
[00318] Generally, TMA includes the following steps: (a) isolating nucleic acid from the biological sample of interest (e.g., breast tissue; axillary lymph node tissue; etc.); and (b) combining into a
reaction mixture (i) the isolated nucleic acid, (ii) first and second oligonucleotide primers, the first primer having a complexing sequence sufficiently complementary to the 3' terminal portion of an RNA target sequence, if present (for example the (+) strand), to complex therewith, and the second primer having a complexing sequence sufficiently complementary to the 3' terminal portion of the target
sequence of its complement (for example, the (-) strand) to complex therewith, wherein the first
oligonucleotide further comprises a sequence 5' to the complexing sequence which includes a promoter, (iii) a reverse transcriptase or RNA and DNA dependent DNA polymerases, (iv) an enzyme activity which selectively degrades the KNA strand of an RNA-DNA complex (such as an RNAse H) and (v) an RNA polymerase which recognizes the promoter.
[00319] The components of the reaction mixture may be combined stepwise or at once. The reaction mixture is incubated under conditions whereby an oligonucleotide/target sequence is formed, including DNA priming and nucleic acid synthesizing conditions (including ribonucleotide triphosphates and deoxyribonucleotide triphosphates) for a period of time sufficient to provide multiple copies of the target sequence. The reaction advantageously takes place under conditions suitable for maintaining the stability of reaction components such as the component enzymes and without requiring modification or manipulation of reaction conditions during the course of the amplification reaction. Accordingly, the reaction may take place under conditions that are substantially isothermal and include substantially constant ionic strength and pH. The reaction conveniently does not require a denaturation step to
separate the RNA-DNA complex produced by the first DNA extension reaction.
[00320] Suitable DNA polymerases include reverse transcriptases, such as avian myeloblastosis virus
(AMV) reverse transcriptase (available from, e.g., Seikagaku America, Inc.) and Moloney murine
leukemia virus (MMLV) reverse transcriptase (available from, e.g., Bethesda Research Laboratories).

[00321] Promoters or promoter sequences suitable for incorporation in the primers are nucleic acid sequences (either naturally occurring, produced synthetically or a product of a restriction digest) that are specifically recognized by an RNA polymerase that recognizes and binds to that sequence and
initiates the process of transcription whereby RNA transcripts are produced. The sequence may
optionally include nucleotide bases extending beyond the actual recognition site for the RNA
polymerase which may impart added stability or susceptibility to degradation processes or increased transcription efficiency. Examples of useful promoters include those which are recognized by certain bacteriophage polymerases such as those from bacteriophage T3, T7 or SP6, or a promoter from E. coli. These RNA polymerases are readily available from commercial sources, such as New England Biolabs and Epicentre.
[00322] Some of the reverse transcriptases suitable for use in the methods herein have an RNAse H activity, such as AMV reverse transcriptase. In some embodiments, an exogenous RNAse H, such as E. coli RNAse H, is added, even when AMV reverse transcriptase is used. RNAse H is readily available from, e.g., Bethesda Research Laboratories.
[00323] The RNA transcripts produced by these methods may serve as templates to produce additional copies of the target sequence through the above-described mechanisms. The system is autocatalytic and amplification occurs autocatalytically without the need for repeatedly modifying or changing reaction conditions such as temperature, pH, ionic strength or the like.
[00324] Another method of detection involves use of target sequence-specific oligonucleotide probes, which contain a region of complementarity to the target sequence described above. The probes may be used in hybridization protection assays (HPA). In this embodiment, the probes are conveniently labeled with acridinium ester (AE), a highly chemiluminescent molecule. See, e.g., Nelson et al. (1995) "Detection of Acridiriium Esters by Chemiluminescence" in Nonisotopic Probing, Blotting and
Sequencing, Kricka L. J. (ed) Academic Press, San Diego, Calif.; Nelson et al. (1994) "Application of the Hybridization Protection Assay (HPA) to PCR" in The Polymerase Chain Reaction, Mullis et al.
(eds.) Birkhauser, Boston, Mass.; Weeks et al., Clin. Chem. (1983) 29: 1474-1479; Berry et al., Clin.
Chem. (1988) 34:2087-2090. One AE molecule is directly attached to the probe using a non-nucleotide- based linker arm chemistry that allows placement of the label at any location within the probe. See, e.g., U.S. Pat. Nos. 5,585,481 and 5,185,439. Chemiluminescence is triggered by reaction with alkaline hydrogen peroxide which yields an excited N-methyl acridone that subsequently collapses to ground state with the emission of a photon. Additionally, AE causes ester hydrolysis which yields the
nonchemiluminescent-methyl acridinium carboxylic acid.
[00325] When the AE molecule is covalently attached to a nucleic acid probe, hydrolysis is rapid under mildly alkaline conditions. When the AE-labeled probe is exactly complementary to the target nucleic acid, the rate of AE hydrolysis is greatly reduced. Thus, hybridized and unhybridized AE-labeled probe can be detected directly in solution, without the need for physical separation.
[00326] HPA generally consists of the following steps: (a) the AE-labeled probe is hybridized with the target nucleic acid in solution for about 15 to about 30 minutes. A mild alkaline solution is then added and AE coupled to the unhybridized probe is hydrolyzed. This reaction takes approximately 5 to 10 minutes. The remaining hybrid-associated AE is detected as a measure of the amount of target present. This step takes approximately 2 to 5 seconds. In some embodiments, the differential hydrolysis step is conducted at the same temperature as the hybridization step, typically at 50 to 70 degrees Celsius.
Alternatively, a second differential hydrolysis step may be conducted at room temperature. This allows elevated pHs to be used, for example in the range of IQ-11 , which yields larger differences in the rate of hydrolysis between hybridized and unhybridized AE-labeled probe. HPA is described in detail in, e.g., U.S. Pat. Nos. 6,004,745; 5,948,899; and 5,283,174, the disclosures of which are incorporated by
reference herein in their entireties.
[00327] TMA is described in detail in, e.g., U.S. Pat. No. 5,399,491, the disclosure of which is
incorporated herein by reference in its entirety. In one example of a typical assay, an isolated nucleic acid sample, suspected of containing a deacylase-encoding nucleic acid as described herein, is mixed with a buffer concentrate containing the buffer, salts, magnesium, nucleotide triphosphates, primers, dithiothreitol, and spermidine. The reaction is optionally incubated at about 1000C for approximately two minutes to denature any secondary structure. After cooling to room temperature, reverse
transcriptase, RNA polymerase, and RNAse H are added and the mixture is incubated for two to four hours at 37°C. The reaction can then be assayed by denaturing the product, adding a probe solution, incubating 20 minutes at 600C, adding a solution to selectively hydrolyze the unhybridized probe, incubating the reaction six minutes at 600C, and measuring the remaining chemiluminescence in a luminometer.

00328] Oligonucleotides will in some embodiments be used in nucleic acid sequence-based
amplification (NASBA). This method is a promoter-directed, enzymatic process that induces in vitro continuous, homogeneous and isothermal amplification of a specific nucleic acid to provide RNA
copies of the nucleic acid. The reagents for conducting NASBA include a first DNA primer with a 51 tail comprising a promoter, a second DNA primer, reverse transcriptase, RNAse-H, T7 RNA
polymerase, NTP's and dNTP's. Using NASBA, large amounts of single-stranded RNA are generated from either single-stranded RNA or DNA, or double-stranded DNA. When RNA is to be amplified, the ssRNA serves as a template for the synthesis of a first DNA strand by elongation of a first primer
containing an RNA polymerase recognition site. This DNA strand in turn serves as the template for the synthesis of a second, complementary, DNA strand by elongation of a second primer, resulting in a double-stranded active RNA-polymerase promoter site, and the second DNA strand serves as a
template for the synthesis of large amounts of the first template, the ssRNA, with the aid of a RNA polymerase. The NASBA technique is known in the art and described in, e.g., European Patent
329,822, International Patent Application No. WO 91/02814, and U.S. Pat. Nos. 6,063,603, 5,554,517 and 5,409,818, all of which are incorporated herein in their entireties.
[00329] The target nucleic acids described herein are also useful in nucleic acid hybridization and
amplification techniques that utilize branched DNA molecules. In a basic nucleic acid hybridization assay, single-stranded analyte nucleic acid is hybridized to a labeled single-stranded nucleic acid probe and resulting labeled duplexes are detected. Variations of this basic scheme have been developed to facilitate separation of the duplexes to be detected from extraneous materials and/or to amplify the signal that is detected. One method for amplifying the signal uses amplification multimers that are polynucleotides with a first segment that hybridizes specifically to the analyte nucleic acid or a strand of nucleic acid bound to the analyte and iterations of a second segment that hybridizes specifically to a labeled probe. The amplification is theoretically proportional to the number of iterations of the second segment. The multimers may be either linear or branched. Two general types of branched multimers are useful in these techniques: forked and combed. Methods for making and using branched nucleic acid molecules are known in the art and described in, e.g., U.S. Pat. No. 5,849,481, incorporated herein by reference in its entirety.
[00330] As is readily apparent, design of the assays described herein is subject to a great deal of
variation, and many formats are known in the art. The above descriptions are merely provided as
guidance and one of skill in the art can readily modify the described protocols, using techniques well known in the art.
Detection using nucleic acid arrays
[00331] In some embodiments, a subject method of detecting a target nucleic acid involves detection of the target nucleic acid in a sample of nucleic acids that is labeled with at least a first and a second
distinguishable detectable label. In some embodiments, the method includes the following steps a) contacting a nucleic acid probe for a target nucleic acid with the sample under conditions sufficient for specific binding to occur between the probe and the target nucleic acid; and b) identifying the amount of the first and second labels in the resultant target nucleic acid/probe complex, thereby determining the amount of the target nucleic acid in the sample.
[00332] For example, in some embodiments, the method involves: a) contacting a probe for a target nucleic acid with a sample of nucleic acids under conditions sufficient for duplex nucleic acids to be produced between the probe and the target nucleic acid, and b) identifying the amount of the first and second labels in the resultant duplex nucleic acid.
[00333] In an exemplary microarray assay, a microarray is hybridized with differentially labeled RNA or DNA populations derived from two different samples. For example, RNA (either total RNA or poly A+RNA) is isolated from cells or tissues of interest and is reverse transcribed to yield cDNA. Labeling can be performed during reverse transcription by incorporating a labeled nucleotide in the reaction mixture. Various labels can be used; for example, the nucleotide is conjugated with the fluorescent dyes Cy3 or Cy5. For example, Cy5-dUTP and Cy3-dUTP can be used. cDNA derived from one sample
(representing, for example, a particular cell type, tissue type or growth condition) is labeled with one fluor while cDNA derived from a second sample (representing, for example, a different cell type, tissue type, or growth condition) is labeled with the second fluor. Similar amounts of labeled material from the two samples are cohybridized to the microarray. In the case of a microarray assay in which the samples are labeled with Cy5 (which fluoresces red) and Cy3 (which fluoresces green), the primary data (obtained by scanning the microarray using a detector capable of quantitatively detecting
fluorescence intensity) are ratios of fluorescence intensity (red/green, R/G). These ratios represent the relative concentrations of cDNA molecules that hybridized to the cDNAs represented on the microarray and thus reflect the relative expression levels of the mRNA corresponding to each cDNA/gene
represented on the microarray.
[00334] In certain embodiments, the nucleic acid is extracted from a source (e.g., a cell, group of cells, tissue, culture, etc.) of interest, and includes RNA (e.g., unspliced RNA or mRNA, etc.), or DNA (e.g., genomic DNA of a nucleus or organelle, etc.). In certain embodiments, the sample is a genetic copy of the nucleic acid extracted from a source, such as cDNA, amplified DNA or RNA, or a nucleic acid that contains modified nucleotide residues (e.g., amino-allyl nucleotides). Nucleic acid compositions
suitable for labeling in the subject methods are well known in the art, and their further description may be found in several publications, including Brumbaugh et al (Proc Natl Acad Sci U S A 85, 5610-4,
1988), Hughes et al. (Nat Biotechnol 19, 342-7, 2001), Eberwine et al (Biotechniques. 20:584-91,
1996), Ausubel, et al, (Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995) and
Sambrook, et al, (Molecular Cloning: A Laboratory Manual, Third Edition, (2001) Cold Spring Harbor, N.Y.).
[00335] In some embodiments, the sample contains labeled nucleic acid, where individual nucleic acid molecules within the sample are labeled with at least two, (e.g., two, three, four, five, six, seven or eight or more) detectably distinguishable labels. At least 2, at least about 4, at least about 6, at least about 8, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, or at least about 40 or at least about 50 or more of each distinguishable detectable label may associated with a single nucleic acid molecule.. In certain embodiments, however, particularly those that involve separately labeling two portions of the same sample and mixing the labeled portions together to make a labeled sample, individual nucleic acid molecules within the sample may be labeled with only one type of label.

[00336] Labels of interest include directly detectable and indirectly detectable non-radioactive labels such as fluorescent dyes. Directly detectable labels are those labels that provide a directly detectable signal without interaction with one or more additional chemical agents. Examples of directly detectable labels include fluorescent labels. Indirectly detectable labels are those labels which interact with one or more additional members to provide a detectable signal. In this latter embodiment, the label is a
member of a signal producing system that includes two or more chemical agents that work together to provide the detectable signal. Examples of indirectly detectable labels include biotin or digoxigenin, which can be detected by a suitable antibody coupled to a fluorochrome or enzyme, such as alkaline phosphatase. In some embodiments, the label is a directly detectable label. Directly detectable labels of particular interest include fluorescent labels.
[00337] Suitable fluorescent labels include a fluorophore moiety. Specific fluorescent dyes of interest include: xanthene dyes, e.g. fluorescein and rhodamine dyes, such as fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (commonly known by the abbreviations FAM and F),6-carboxy-2',4\7',4,7- hexachlorofluorescein (HEX), 6-carboxy-4', 5'-dichloro-2', 7'-dimethoxyfiuorescein (JOE or J),
N,N,N',N'-tetramethyl-6-carboxyrhodarrύne (TAMRA or T), 6-carboxy-X-rhodamine (ROX or R),
5-carboxyrhodamine-6G (R6G5 or G5), 6-carboxyrhodamine-6G (R6G6 or G6), and rhodamine 110;
cyanine dyes, e.g. Cy3, Cy5 and Cy7 dyes; coumarins, e.g umbelliferone; benzimide dyes, e.g. Hoechst 33258; phenanthridine dyes, e.g. Texas Red; ethidium dyes; acridine dyes; carbazole dyes; phenoxazine dyes; porphyrin dyes; polymethine dyes, e.g. cyanine dyes such as Cy3, Cy5, etc; BODIPY dyes and quinoline dyes. Specific fϊuorophores of interest that are commonly used in subject applications
include: Pyrene, Coumarin, Diethylaminocoumarin, FAM, Fluorescein Chlorotriazinyl, Fluorescein,
Rl 10, Eosin, JOE, R6G, Tetramethylrhodamine, TAMRA, Lissamine, ROX, Napthofluorescein, Texas Red, Napthofluorescein, Cy3, and Cy5, etc.
[00338] As mentioned above, the labels used in the subject methods are distinguishable, meaning that the labels can be independently detected and measured, even when the labels are mixed. In other words, the amounts of label present (e.g., the amount of fluorescence) for each of the labels are separately determinable, even when the labels are co-located (e.g., in the same tube or in the same duplex
molecule or in the same feature of an array). Suitable distinguishable fluorescent label pairs useful in the subject methods include Cy-3 and Cy-5 (Amersham Inc., Piscataway, NJ), Quasar 570 and Quasar 670 (Biosearch Technology, Novato CA), Alexafluor555 and Alexafluor647 (Molecular Probes,
Eugene, OR), BODIPY V- 1002 and BODIPY V 1005 (Molecular Probes, Eugene, OR), POPO-3 and
TOTO-3 (Molecular Probes, Eugene, OR), and P0PRO3 TOPRO3 (Molecular Probes, Eugene, OR).

Further suitable distinguishable detectable labels may be found in Kricka et al. (Ann Clin Biochem.
39:114-29, 2002).
[00339] In general, at least two distinguishable labels are covalently attached to nucleic acids in a
sample. Means for labeling nucleic acids are generally well known in the art (e.g. Brumbaugh et al Proc Natl Acad Sci U S A 85, 5610-4, 1988; Hughes et al. Nat Biotechnol 19, 342-7, 2001, Eberwine et al Biotechniques. 20:584-91, 1996, Ausubel, et al, Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995 Sambrook, et al, Molecular Cloning: A Laboratory Manual, Third Edition, 2001 Cold
Spring Harbor, N.Y. and DeRisi et al. Science 278:680-686, 1997; Patton WF. Electrophoresis. 2000
21:1123-44; MacBeath G. Nat Genet. 2002 32 Suppl:526-32; and Biotechnol Prog. 1997 13:649-58). These means usually involve either direct chemical modification of the analyte, or a labeled nucleotide that is incorporated into a nucleic acid by nucleic acid replication, e.g., using a polymerase.
[00340] Chemical modification methods for labeling a nucleic acid sample can include incorporation of a reactive nucleotide into a nucleic acid, e.g., an amine-allyl nucleotide derivative such as 5-(3- aminoallyl)-2'-deoxyuridine 5 '-triphosphate, using an RNA-dependent or DNA-dependent DNA or
RNA polymerase, e.g., reverse transcriptase or T7 RNA polymerase, followed by chemical conjugation of the reactive nucleotide to a label, e.g. a N-hydroxysuccinimdyl of a label such as Cy-3 or Cy5 to make a labeled nucleic acids (Brumbaugh et al Proc Natl Acad Sci U S A 85r 5610-4, 1988 and Hughes et al. Nat Biotechnol 19, 342-7, 2001). Such chemical conjugation methods may be combined with
RNA amplification methods (e.g. those of Eberwine et al Biotechniques. 20:584-91, 1996), to produce labeled DNA or RNA.
[00341] Suitable labels may also be incorporated into a sample by means of nucleic acid replication, where modified nucleotides such as modified deoxynucleotides, ribonucleotides, dideoxynucleotides, etc., or closely related analogues thereof, e.g. a deaza analogue thereof, in which a moiety of the
nucleotide, typically the base, has been modified to be bonded to the label. Modified nucleotides are incorporated into a nucleic acid by the actions of a nucleic acid-dependent DNA or RNA polymerases, and a copy of the nucleic acid in the sample is produced that contains the label. Methods of labeling nucleic acids by a variety of methods, e.g., random priming, nick translation, RNA polymerase
transcription, etc., are well generally known in the art (see, e.g., Ausubel, et al, Short Protocols in
Molecular Biology, 3rd ed., Wiley & Sons, 1995 Sambrook, et al, Molecular Cloning: A Laboratory
Manual, Third Edition, 2001 Cold Spring Harbor, N.Y. and DeRisi et al. Science 278:680-686, 1997).

[00342] In some embodiments of the invention, a nucleic acid sample is labeled using a mixture of labels. In other words, two or more distinguishably detectable labels are mixed together, usually in a single vessel or tube, sometimes in equal proportions, in a single labeling reaction for a sample. The two or more labels may be for the same nucleotide e.g. "T" or "U", or a mixture of two, three or four nucleotides. In certain embodiments, however, if the samples are identical (e.g. they are two portions of a sample, or two nucleic acids samples made from the same source), the samples may be labeled
separately and combined to make a labeled sample. As such, the subject methods do not involve labeling two different samples (e.g. samples from two different tissues, times, or conditions), each with distinguishable label, and mixing the samples together.
[00343] Once labeled, the sample is usually applied to a substrate that includes at least one probe, and incubated under conditions suitable for an analyte/probe complex, e.g. a nucleic acid duplex (i.e. a
RNA/RNA, DNA/RNA, or DNA/DNA duplex) to be formed between a probe and a labeled nucleic acid in the sample, if such a labeled nucleic acid is present. In other words, the labeled nucleic acid sample is incubated with a substrate that contains at least one probe under conditions suitable for
binding of the labeled nucleic acid to the probe. In certain embodiments, the substrate that includes the probe is an array of probes, where each probe is contained in a feature of the array, and where an array includes at least about 20, at least about 50, at least about 100, at least about 200, at least about 500, at least about 1,000, at least about 2,000, at least about 5,000, at least about 10,000, at least about 20,000, at least about 50,000, or up to about 100,000 or more features. Arrays used in the subject methods may have known amounts of probes present in a feature of the array. For example, if the concentration of a probe in a solution of probe to be deposited as known, and, the volume of the probe solution that is deposited in a feature is known, an amount of probe present in a feature of an array may be known.
[00344] After incubation, labeled sample that is not bound with a probe is typically washed away from the substrate, and the substrate, now including the labeled nucleic acid/probe duplexes, is scanned. The amount of each label associated with features of the array (each feature containing, e.g., a target nucleic acid/probe complex or a probe if no target nucleic acid is present) is then determined. In most
embodiments, the substrate is scanned in two channels corresponding to the distinguishing features of the probes, such that the amounts of each label associated with each feature is determined
independently (i.e. without interference) from other labels. In certain embodiments, scanning results in two scans, one for each channel, and usually represents a pixilated image of the substrate that reflects the amount of label associated with the features of the substrate. For example, each pixel of the image is accorded a signal level that represents the level of brightness of the label signal. As mentioned above, scanning methods are well known in the art (e.g., DeRisi et al. Science 278:680-686, 1997), and several suitable scanners are commercially available from Perkm-Elmer, Agilent, or Axon Instruments, etc., and are described in U.S. Patent Nos: 5,091,652; 5,760,951, 6,320,196 and 6,355,934), the disclosures of which are herein incorporated by reference.
Detecting the presence and/or levels of a microKNA
[00345] In some embodiments, a subject method involves detecting the presence and/or levels of a microRNA synthesized by an MEC. MicroRNAs that can be detected using a subject method include, but are not limited to, mir 196b (HoxA9), (pl4), 328, 30A-3P, 125b, 30E-3P, 680, 134, 604, 128b,
128a, 331, 520F, 299-3P, 520H, 510, 365, 520G, 9, 324-3P, 351, 125A, 764-5P, 302D, 520D, 652,
520C, 350, 585, 621, 542-5P, 560, 126, and 341.
[00346] MicroRNAs (miRNAs) are encoded by genes, which encode transcripts containing short
double-stranded RNA hairpins. MiRNAs are transcribed as longer precursors, termed pre-miRNAs, which can be 50 to 80 nucleotides in length, and which are sometimes found in clusters and frequently found in introns. Upon transcription, miRNAs undergo nuclear cleavage by an RNase III endonuclease, producing the 60-70-nt stem-loop precursor miRNA (pre-miRNA) with a 5' phosphate and a 2-nt 3 overhang. The pre-miRNAs are cleaved by Dicer about two helical turns away from the ends of the pre- miRNA stem loop, producing double-stranded RNA with strands that are approximately the same
length (21 to 24 nucleotides), and possess the characteristic 5'-phosphate and 3'-hydroxyl termini. One of the strands of this short-lived intermediate accumulates as the mature miRNA and is subsequently incorporated into a ribonucleoprotein complex, the miRNP. MiKNAs interact with target niRNAs at specific sites to induce cleavage of the message or inhibit translation.
[00347J Detection of microRNAs can be carried out using any of a variety of methods. One approach uses stem-loop reverse transcription (RT) followed by TaqMan PCR analysis (Chen et al. Nucleic
Acids Res. 2005;33(20)3 el79). This method includes reverse transcription at low temperature. Another approach is to use a composite primer for reverse transcription which includes a gene-specific portion and a tail sequence used for PCR amplification (Raymond et al. RNA. 2005 Nov.; 11 (11 ):1737-44).
Another approach, described in U.S. Patent Publication No. 2007/0077582) is based on using a target miRNA as a primer for extension by DNA polymerase on a specific oligonucleotide template; the
specific oligonucleotide sequence is longer than the target miRNA sequence and contains at its 3'-end a sequence complementary to target miRNA, and a spacer sequence adjacent to that complementary sequence, which is used in subsequent signal amplification. Also suitable for use is a microarray
analysis method as described in, e.g., U.S. Patent Publication No. 2007/0009915. A quantitative RT- PCR approach that can be used in the mirVana™ method (Ambion).
DNA detection methods
[00348] In some embodiments, a subject detection method involves detecting the levels and/or integrity and/or methylation status and/or packaging of a selected DNA, or collection of DNA, present in an
MEC.
Detecting a level of a selected DNA
[00349] In some embodiments, a subject detection method involves detecting the level of a selected
DNA in an MEC. For example, in some embodiments, a variant MEC (e.g., an MEC that is precancerous) has a deletion of all or part of one or more of chromosome 3p, chromosome 5p,
chromosome 6p, chromosome 8p, chromosome 1 Iq, chromosome 16q, and chromosome 22. In other embodiments, a variant MEC (e.g., an MEC that is pre-cancerous) has an amplification or all or a part of one or more of c-myc, her2/neu, or cyclin Dl .
[00350] Detecting deletion of all or part of a DNA can be carried out using any of a number of well- established methods. In some embodiments, deletion is detected by histochemical analysis. In some embodiments, deletion is detected via metaphase karyotype analysis of the chromosomes present in an MEC. Suitable methods of detecting a DNA deletion include, but are not limited to, array comparative genomic hybridization, fluorescent in situ hybridisation (FISH), quantitative multiplex PCR, Southern blotting, multiplex amplifiable probe hybridization (MAPH), multiplex amplifiable probe hybridization (MLPA), and the like. See, e.g., White et al. (2003) J. Med. Genetics 40:el 13; and Edgley et al. (2002) Nucl. Acids Res. 30:e52;
[00351] In some embodiments, detecting a DNA deletion is carried out by use of restriction
endomicleases that cleave outside of a gene comprising a deletion, e.g., where one restriction
endonuclease cleaves at a site 5' of the deletion and a second restriction endonuclease cleaves 3' of the deletion, such that a restriction fragment is generated that is shorter than the length of a restriction
fragment generated using the same restriction endonucleases, using as a substrate the same gene
without a deletion.
[00352J As another example, amplification using primer pairs spanning the deletion will result in
different sized products corresponding to the deleted and undeleted (e.g., control) gene, which can be distinguished on the basis of size (e.g., by gel electrophoresis). These primer pairs can be used
individually or in a nested PCR experiment. It will also be apparent to one of skill that hybridization methods (e.g., Northern hybridization) or RNAse protection assays using nucleic acid probe specific for the gene (e.g., a control, undeleted gene), or a nucleic acid probe specific for a region flanking the gene, can be used to detect and distinguish undeleted (control) genes and deleted variants.
[00353] Detecting amplification of all or part of a DNA can be carried out using any of a number of well-established methods.
[00354] Representational Oligonucleotide Microarray Analysis (ROMA) detects genomic
amplifications and deletions with boundaries defined at a resolution of ~ 50 kb. See, e.g., Lucito et al. (2003) Genome Res. 13:2291-2305. A ROMA method can be used to detect amplification or deletion of all or a portion of a selected DNA. In another embodiment, a method such as comparative genomic hybridization (CGH) is used. See, e.g., U.S. Patent No. 7,011,949. CGH is a method for detecting
deletions and amplifications in one sample of genomic DNA relative to another individual sample; the method involves comparing the intensity of hybridization of microarray features to each target sample, each labeled with different fluorescent dyes In another embodiment, a method as described in U.S.
Patent Publication No. 2006/0129331 is used.
[00355] In some embodiments, karyotype or other chromosomal analysis using gene-specific nucleic acid probes is carried out to detect amplification (i.e., change in copy number), deletion (including total deletion, partial deletion), insertion, substitution, or changes in the chromosomal location (e.g.,
translocation) of a selected gene. For example, alterations to a selected gene are identified by karyotype analysis, using any of a variety of methods known in the art. One useful technique is in situ
hybridization (ISH). For example, when in situ hybridization techniques are used for karyotype
analysis, a detectable or detectably-labeled probe is hybridized to a chromosomal sample in situ to
locate a selected gene sequence. ISH can comprise one or more of the following steps: (1) fixation of the tissue, cell or other biological structure to be analyzed; (2) prehybridization treatment of the
biological structure to increase accessibility of target DNA (e.g., denaturation with heat or alkali), and to reduce nonspecific binding (e.g., by blocking the hybridization capacity of repetitive sequences, e.g., using human genomic DNA); (3) hybridization of one or more nucleic acid probes (e.g., conventional nucleic acids, PNAs, or other nucleic acid analogs) to the nucleic acid in the biological structure or tissue; (4) posthybridization washes to remove nucleic acid fragments not bound in the hybridization; and, (5) detection of the hybridized nucleic acid fragments. The reagent used in each of these steps and their conditions for use can vary, depending on the particular application. It will be appreciated that these steps can be modified in a variety of ways well known to those of skill in the art.
[00356] In one embodiment of ISH, a gene-specific probe is labeled with a fluorescent label
(fluorescent in situ hybridization; "FISH"). In some embodiments, it is desirable to use dual color
fluorescent in situ hybridization, in which two probes are utilized, each labeled by a different
fluorescent dye. A test probe that hybridizes to the selected sequence of interest is labeled with one dye, and a control probe that hybridizes to a different region is labeled with a second dye. A nucleic acid that hybridizes to a stable portion of the chromosome of interest, such as the centromere region, can be used as the control probe. La this way, one can account for differences between efficiency of hybridization from sample to sample.
Detecting integrity of a selected DNA
[00357] In some embodiments, a subject detection method involves detecting the integrity of a selected

DNA in an MEC, e.g., detecting one or more of: an aneuploidy; telomeric content; a translocation; an aberrant pattern; and the like. Aberrant patterns in DNA include, but are not limited to "firestorms"
(e.g., multiple closely spaced amplicons); "sawtooth" patterns (e.g., characterized by many narrow
segments of duplication and deletion); and the like. See, e.g., Hicks et al. (2006) Genome Res. 16:1465- 1479.
Detecting methylation status of a selected DNA
[00358] In some embodiments, a subject detection method involves detecting the methylation status of a

DNA. For example, in some embodiments, a subject detection method involves detecting the
methylation status of a selected promoter, e.g., a pl6 promoter, e.g., a plδ"^43 promoter.
[00359] Various methods can be used to determine the methylation status of a selected DNA. For
example, indirect methods for DNA methylation pattern determinations at specific loci that have been developed rely on techniques that alter the genomic DNA in a methylation-dependent manner before an amplification event. There- are two primary methods that have been utilized to achieve this
methylation-dependent DNA alteration. The first is digestion by a restriction enzyme that is affected in its activity by 5-methylcytosine in a CpG sequence context. The cleavage, or lack of it, can
subsequently be revealed by Southern blotting or by PCR. The other technique that has received recent widespread use-is the treatment of genomic DNA with sodium bisulfite. Sodium bisulfite treatment converts all unmethylated cytosines in the DNA to uracil by deamination, but leaves the methylated cytosine residues intact. Subsequent PCR amplification replaces the uracil residues with thymines and the 5-methylcytosine residues with cytosines. The resulting sequence difference has been detected using standard DNA sequence detection techniques, primarily PCR.
[00360] An exemplary method involves use of a bisulfite treatment-based method followed by a PCR reaction to analyze specific loci within the genome. There are two principally different ways in which the sequence difference generated by the sodium bisulfite treatment can be revealed. The first is to design PCR primers that uniquely anneal with either methylated or unmethylated converted DNA. This technique is referred to as "methylation specific PCR" or "MSP". See, e.g., U.S. Pat. No. 5,786,146.
The method used by all other bisulfite-based techniques (such as bisulfite genomic sequencing,
COBRA and Ms-SNuPE) is to amplify the bisulfite-converted DNA using primers that anneal at
locations that lack CpG dinucleotides in the original genomic sequence. In this way, the PCR primers can amplify the sequence in between the two primers, regardless of the DNA methylation status of that sequence in the original genomic DNA. This results in a pool of different PCR products, all with the same length and differing in their sequence only at the sites of potential DNA methylation at CpGs located in between the two primers. The difference between these methods of processing the bisulfite- converted sequence is that in MSP, the methylation information is derived from the occurrence or lack of occurrence of a PCR product, whereas in the other techniques a mix of products is always generated and the mixture is subsequently analyzed to yield quantitative information on the relative occurrence of the different methylation states. A method such as described in U.S. Patent No. 7,186,512 is also
suitable for use.
[00361] In some embodiments, the methods involve contacting a genomic sample of DNA with a
modifying agent that modifies unmethylated cytosine (e.g., sodium bisulfite), to produce a converted nucleic acid; (b) amplifying the converted nucleic acid by means of oligonucleotide primers in the presence of one or a plurality of specific oligonucleotide probes, where the one or the plurality of the oligonucleotide primers or the specific probe(s) is/are capable of distinguishing between unmethylated and methylated nucleic acid (e.g., a CpG-specifϊc probe capable of distinguishing between
unmethylated and methylated nucleic acid); and (c) detecting, in real-time during the amplification, the methylated nucleic acid based on amplification-mediated probe displacement. See, e.g., U.S. Patent No. 7,112,404. Amplification and detection can occur simultaneously as measured by fluorescence-based real-time quantitative PCR ("RT-PCR") using specific, dual-labeled dual label TaqMan®
oligonucleotide probes. The displaceable probes can be specifically designed to distinguish between methylated and unmethylated CpG sites present in the original, unmodified nucleic acid sample.
Sodium-bisulfite readily reacts with the 5,6-double bond of cytosine, but not with methylated cytosine, to produce a sulfonated cytosine intermediate that undergoes deamination under alkaline conditions to produce uracil. Because Taq polymerase recognizes uracil as thymine and 5-methylcytidine (m5C) as cytidine, the sequential combination of sodium bisulfite treatment and PCR amplification results in the ultimate conversion of unmethylated cytosine residues to thymine (C- >U— »T) and methylated cytosine residues ("mC") to cytosine (mC→mC→C). Thus, sodium-bisulfite treatment of genomic DNA creates methylation-dependent sequence differences by converting unmethylated cyotsines to uracil, and upon PCR the resultant product contains cytosine only at positions where methylated cytosine occurs in the unmodified nucleic acid.
[00362] In some embodiments, the specific primers are designed to be substantially complementary to each strand of the genomic locus of interest. Typically, one primer is complementary to the negative, (-) strand of the locus (the "lower" strand of a horizontally situated double-stranded DNA molecule) and the other is complementary to the positive (+) strand ("upper" strand). In some embodiments, the
primers are designed to overlap potential sites of DNA methylation (CpG nucleotides) and specifically distinguish modified unmethylated from methylated DNA. This sequence discrimination can be based upon the differential annealing temperatures of perfectly matched, versus mismatched oligonucleotides. In some embodiments, primers are typically designed to overlap from one to several CpG sequences. In other embodiments, e.g., in a quantitative embodiment, the primers do not overlap any CpG sequences. Proteomics analysis
[00363] In some embodiments, a subject detection method involves a proteomics analysis of an MEC.

In some embodiments, an antibody reagent array is used, where the array comprises antibody reagents specific for two or more of the proteins listed in Figure 14. In some embodiments, an antibody reagent array is used, where the array comprises antibody reagents specific for two or more of: CD73, CD138, notch receptor-3, CD90, BMI-I, COX-2, Ki67, pl6, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin Bl , c-kit, STAT3, cyclin Dl , PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2.
[00364] In other embodiments, a polypeptide array is used. Polypeptide arrays provide a high
throughput technique that can assay a large number of polypeptides in a sample. This technology can be used as a tool to test for expression of a marker polypeptide and detection of a pre-cancerous epithelial cell. Of particular interest are arrays which comprise a probe for detection of one or more of the
following polypeptides: CD73, CD138, notch receptor-3, CD90, BMI-I, COX-2, Ki67, pi 6, IGF2,
YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK, MAPKK,
DDR2, TRF2, activin, and MEKl /2.
[00365] A variety of methods of producing arrays, as well as variations of these methods, are known in the art and contemplated for use in the invention. For example, arrays can be created by spotting
polypeptide probes onto a substrate {e.g., glass, nitrocellulose, etc.) in a two-dimensional matrix or array having bound probes. The probes can be bound to the substrate by either covalent bonds or by non-specific interactions, such as hydrophobic interactions.
[00366] Samples of polypeptides can be detectably labeled {e.g. , using radioactive or fluorescent labels) and then hybridized to the probes. Alternatively, the polypeptides of the test sample can be immobilized on the array, and the probes detectably labeled and then applied to the immobilized polypeptides. In most embodiments, the "probe" is detectably labeled. In other embodiments, the probe is immobilized on the array and not detectably labeled. In such embodiments, the sample is applied to the polypeptide array and bound gene products (e.g., peptides) are detected using secondary labeled probes.

[00367] Examples of such protein arrays are described in the following patents or published patent applications: U.S. Pat. No. 6,225,047; PCT International Publication No. WO 99/51773; U.S. Pat. No. 6,329,209, PCT International Publication No. WO 00/56934 and U.S. Pat. No. 5,242,828. Proteomics applications include those described in U.S. Patent Nos.: 4,591,570; 5,171,695; 5,436,170; 5,486,452; 5,532,128 and 6,197,599 as well as published PCT application Nos. WO 99/39210; WO 00/04832; WO 00/04389; WO 00/04390; WO 00/54046; WO 00/63701; WO 01/14425 and WO 01/40803, the
disclosures of which are herein incorporated by reference.
[00368] As noted above, in some embodiments, an antibody reagent array is used to detect proteins produced by an MEC (e.g. a variant MEC), where the array comprises antibody reagents specific for two or more of: CD73, CD138, notch receptor-3, CD90, BMI-I, COX-2, Ki67, pl6, IGF2, YKL-40,
EGF-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2. Thus, e.g., use of an array of a plurality of distinct binding agents ("protein- binding agents" or "protein-binding reagents"), wherein each binding agent includes at least an epitope binding domain of an antibody molecule, is contemplated. The arrays employed in the subject methods can have a plurality of probe spots, each made up of a distinct binding agent (i.e., a plurality of copies of distinct binding agent molecule) stably associated with the surface of a solid support.
[00369] Each probe composition of a protein-binding reagent arrays is made up of multiple copies of a binding agent, where each binding agent includes at least an epitope binding domain of antibody. By epitope binding domain is meant a region or portion of an antibody molecule that specifically binds to an antigen, more particularly a determinant or epitope of a given antigen. As such, in some
embodiments, the protein-binding reagents are antibodies, including specific antigen binding fragments and mimetics thereof. Where antibodies are the binding agent, they may be derived from polyclonal compositions, such that a heterogeneous population is used, where antibodies differing by specificity are each immobilized on the substrate surface; or monoclonal compositions, in which a homogeneous population of identical antibodies that have the same specificity for the target analyte, e.g., protein, are each immobilized on the substrate surface. As such, the binding agent may be either a monoclonal or a polyclonal antibody in certain embodiments.
[00370] In yet other embodiments, the binding agent making up the subject probe compositions is an antibody binding fragment or mimetic, where these fragments and mimetics have the requisite binding affinity for the target analyte, e.g., protein. For example, antibody fragments, such as Fv, F(ab)2 and
Fab may be prepared by cleavage of the intact protein, e.g. by protease or chemical cleavage. Also of interest are recombinantly produced antibody fragments, such as single chain antibodies or scFvs, where such recombinantly produced antibody fragments retain the binding characteristics of the above antibodies, i.e., they include the epitope binding domain (which means the whole domain or a least a functional portion thereof) of an antibody specific for the particular analyte. Such recombinantly
produced antibody fragments generally include at least the VH and VL domains of the subject
antibodies, so as to retain the binding characteristics of the subject antibodies. These recombinantly produced antibody fragments or mimetics of the subject invention may be readily prepared using any convenient methodology, such as the methodology disclosed in U.S. Patent Nos. 5,851,829 and
5,965,371; the disclosures of which are herein incorporated by reference.
[00371] The above described antibodies, fragments and mimetics thereof may be obtained from
commercial sources and/or prepared using any convenient technology, where methods of producing polyclonal antibodies, monoclonal antibodies, fragments and mimetics thereof, including recombinant derivatives thereof, are known to those of the skill in the art. The binding agents typically have a strong affinity for their analyte, where this affinity is at least about 10'6, usually at least about 10"8 and
typically ranges from about 10 s to about 10~13, usually from about 10"9 to about 10"12, where the affinity is the affinity as measured following immobilization of the antibody onto the surface using the binding affinity assay described in Pellequer, J. L., Van Regenmortel, M. H., J Endocrinol, 139, (3) 495-501.
[00372] The probe spots made up of the binding agents as described above and present on the array may be any convenient shape, and can be circular, elliptoid, oval or some other analogously curved shape. The total amount or mass of molecules present in each spot will be sufficient to provide for adequate binding and detection of analytes during the assay in which the array is employed. The total mass of binding agents in each spot can be at least about 10 pg, at least about 100 pg, or at least about 1 ng, where the total mass may be as high as 20 ng or higher. In some embodiments, the total mass of binding agent in each spot does not exceed about 10 ng, or does not exceed about 5 ng. Where the target protein is detectably labeled, the copy number of all of the individual binding agents in a spot will be sufficient to provide enough binding sites for tagged target molecule (e.g., protein being detected) to yield a
detectable signal, and can range from about 100 fluorescence units (FU) to about 65500 FU, or from about 250 FU to about 45000 FU.
[00373] Where the probe spot has an overall circular dimension, the diameter of the spot can range from about 10 to about 5,000 μm, from about 20 to about 1,000 μm, or from about 50 to about 500 μm. The surface area of each spot can be at least about 100 μm2, at least about 200 μm2, or at least about 400 μm2, and may be as great as about 25 mm2 or greater; in some embodiments, the surface area of each spot does not exceed about 5 mm2, or about 1 mm2. The density of binding agents "probe" spots on the array, as well as the overall density of probe and non-probe spots (where the latter are described in greater detail below) may vary greatly. As used herein, the term spot refers to any spot on the array surface that is made up of binding agents, whether control or probe binding agents, and as such includes both probe spots and non-probe spots. The density of the probe spots on the solid surface is at least about 5/cm2 and usually at least about 10/cm2 and may be as high as about 100/cm2, about 200/cm2, about 300/cm2, about 500 /cm2, about 1000/cm2, about 5000/cm2 or higher, but in many embodiments does not exceed about 1000/cm2, and in these embodiments usually does not exceed about 500/cm2 or about 400/cm2 in many embodiments, and in certain embodiments does not exceed about 300/cm2. The spots may be arranged in a spatially defined and physically addressable manner, in any convenient pattern across or over the surface of the array, such as in rows and columns so as to form a grid, in a circular pattern, and the like, where generally the pattern of spots will be present in the form of a grid across the surface of the solid support.
[00374] In the subject arrays, the spots of the pattern are stably associated with or immobilized on the surface of a solid support, where the support may be a flexible or rigid support. By "stably associated" it is meant that the binding agents of the spots maintain their position relative to the solid support under incubation (e.g., binding) and washing conditions, as described below. As such, the individual binding agent members that make up the spots can be non-covalently or covalently stably associated with the support surface based on technologies well known to those of skill in the art. Examples of non-covalent association include non-specific adsorption, binding based on electrostatic (e.g. ion, ion pair
interactions), hydrophobic interactions, hydrogen bonding interactions, specific binding through a
specific binding pair member covalently attached to the support surface, and the like. Examples of covalent binding include covalent bonds formed between the spot binding agents and a functional group present on the surface of the rigid support, where the functional group may be naturally occurring or present as a member of an introduced linking group. In some embodiments, the binding agents making up the spots on the array surface, are covalently bound to the support surface, e.g., through covalent linkages formed between moieties present on the binding agents, e.g., amines, and the substrate surface, etc, as may be present on a glass substrate, e.g., aminated glass. See e.g., the specific covalent
attachment protocol exemplified below.
[00375] As mentioned above, the array is present on either a flexible or rigid substrate. By flexible is meant that the support is capable of being bent, folded or similarly manipulated without breakage.
Examples of solid materials which are flexible solid supports with respect to the present invention
include membranes, flexible plastic films, and the like. By rigid is meant that the support is solid and does not readily bend, i.e. the support is not flexible. As such, the rigid substrates of the subject arrays are sufficient to provide physical support and structure to the polymeric targets present thereon under the assay conditions in which the array is employed, particularly under high throughput handling
conditions. Furthermore, when the rigid supports of the subject invention are bent, they are prone to breakage.
[00376] The solid supports upon which the subject patterns of spots are presented in the subject arrays may take a variety of configurations ranging from simple to complex, depending on the intended use of the array. Thus, the substrate could have an overall slide or plate configuration, such as a rectangular or disc configuration. In many embodiments, the substrate will have a rectangular cross-sectional shape, having a length of from about 10 mm to 200 mm, usually from about 40 to 150 mm and more usually from about 75 to 125 mm and a width of from about 10 mm to 200 mm, usually from about 20 mm to
120 mm and more usually from about 25 to 80 mm, and a thickness of from about 0.01 mm to 5.0 mm, usually from about 0.01 mm to 2 mm and more usually from about 0.01 to 1 mm. Thus, in one
representative embodiment the support may have a micro-titer plate format, having dimensions of approximately 125x85 mm. In another representative embodiment, the support may be a standard
microscope slide with dimensions of from about 25 x 75 mm.
[00377] The substrates of the protein-binding .reagent arrays can be fabricated from a variety of
materials. The materials from which the substrate is fabricated should ideally exhibit a low level of nonspecific binding during binding events. In some embodiments, a material is used that is transparent to visible and/or UV light. For flexible substrates, materials of interest include: nylon, both modified and unmodified, nitrocellulose, polypropylene, and the like. For rigid substrates, specific materials of
interest include: glass; plastics, e.g. polytetrafluoroethylene, polypropylene, polystyrene, polycarbonate, and blends thereof, and the like; metals, e.g. gold, platinum, and the like; etc. Also of interest are
composite materials, such as glass or plastic coated with a membrane, e.g., nylon or nitrocellulose, etc.

[00378J The substrates of the subject arrays comprise at least one surface on which the pattern of spots is present, where the surface may be smooth or substantially planar, or have irregularities, such as
depressions or elevations. The surface on which the pattern of spots is present may be modified with one or more different layers of compounds that serve to modify the properties of the surface in a
desirable manner. Such modification layers, when present, will generally range in thickness from a monomolecular thickness to about 1 mm, usually from a monomolecular thickness to about 0.1 mm and more usually from a monomolecular thickness to about 0.001 mm. Modification layers of interest
include: inorganic and organic layers such as metals, metal oxides, polymers, small organic molecules and the like. Polymeric layers of interest include layers of: peptides, proteins, polynucleic acids or
mimetics thereof, e.g. peptide nucleic acids and the like; polysaccharides, phospholipids, polyurethanes, polyesters, polycarbonates, polyureas, polyamides, polyethyleneamines, polyarylene sulfides,
polysiloxanes, polyimides, polyacetates, polyacrylamides, and the like, where the polymers may be hetero- or homopolymeric, and may or may not have separate functional moieties attached thereto, e.g. conjugated.
[00379] In certain embodiments, e.g., where the binding agent is a whole antibody or analogous
structure, an antibody universal binding layer is present on the substrate surface, e.g., covalently bound to the substrate surface, which layer acts as a linking group or tethering element between the antibody binding agent in the substrate surface and serves to tether the antibody binding agent to the substrate surface. The basic principle is to utilize proteins and ligands with affinity towards antibodies (including but not limited to Protein A, Protein G, Protein L, Protein LA) which are covalently immobilized to a glass, plastic or any other type of surfaces. After the immobilization of the universal binding layer, the antibody binding agents are deposited on the same locations and reversibly immobilized. The universal binding layer of affinity ligands thus forms a layer which protects the consequently bound antibodies from detrimental surface effects. An additional benefit is the directed mode of immobilization as
compared to that of direct covalent attachment of the antibodies to activated surfaces. This results in
100 % availability of the antigen binding sites on the antibodies for consequent detection of antigens. It also provides universal conditions for binding, since the formation of ligand/antibody complex is obtained under mild physiological conditions where as covalent immobilization of proteins is often performed under conditions that might be detrimental to their biological activity.
[00380] The total number of spots on the substrate will vary depending on the number of different probe spots (binding agent probe compositions) one wishes to display on the surface, as well as the number of non probe spots, e.g., control spots, orientation spots, calibrating spots and the like, as may be desired depending on the particular application in which the subject arrays are to be employed. Generally, the pattern present on the surface of the array will comprise at least about 10 distinct spots, usually at least about 20 spots, and more usually at least about 50 distinct spots, where the number of distinct spots may be as high as 10,000 or higher, but will usually not exceed about 5,000 distinct spots, and more usually will not exceed about 3,000 distinct spots and in many instances will not exceed about 2,000 distinct spots. In certain embodiments, each distinct probe spot or probe composition is presented in duplicate, i.e. so that there are two duplicate probe spots displayed on the array for a given target. The number of probe spots present in the array will typically make up a substantial proportion of the total number of spots on the array, where in many embodiments the number of probe spots is at least about 50 number %, usually at least about 80 number % and more usually at least about 90 number % of the total number of spots on the array. As such, in many embodiments the total number of spots on the array ranges from about 10 to about 20,000, usually from about 20 to about 10,000 and more usually from about 100 to 5,000.
[00381] In the arrays of the subject invention (particularly those designed for use in high throughput applications, such as high throughput analysis applications), a single pattern of probe spots may be present on the array or the array may comprise a plurality of different spot patterns, each pattern being as defined above. When a plurality of different spot patterns are present, the patterns may be identical to each other, such that the array comprises two or more identical spot patterns on its surface, or the spot patterns may be different, e.g. in arrays that have two or more different sets of probes present on their surface, e.g., an array that has a pattern of spots corresponding to first population of target analytes and a second pattern of spots corresponding to a second population of analytes . Where a plurality of spot patterns are present on the array, the number of different spot patterns is at least 2, at least 6, or at least 24 or 96, where the number of different patterns will generally not exceed about 384.
[00382] Where the array includes a plurality of spot patterns on its surface, the array can include a plurality of reaction chambers, wherein each chamber has a bottom surface having associated therewith a pattern of spots and at least one wall, usually a plurality of walls surrounding the bottom surface. See e.g. U.S. Patent No. 5,545,531, the disclosure of which is herein incorporated by reference. Of
particular interest in many embodiments are arrays in which the same pattern of spots in reproduced in 24 or 96 different reaction chambers across the surface of the array.
[00383] Within any given pattern of spots on the array, there may be a single spot that corresponds to
(i.e., specifically binds to) a given analyte target or a number of different spots that correspond to the same analyte, where when a plurality of different spots are present that correspond to the same analyte, the probe compositions of each spot that corresponds to the same analyte may be identical or different. In other words, a plurality of different analytes are represented in the pattern of spots, where each
analyte may correspond to a single spot or a plurality of spots, where the probe compositions among the plurality of spots corresponding to the same analyte may be the same or different. Where a plurality of spots (of the same or different composition) corresponding to the same analyte is present on the array, the number of spots in this plurality will be at least about 2 and may be as high as 10; and in some
embodiments will not exceed about 5. In some embodiments, any given analyte is represented by only a single type of probe spot, which may be present only once or multiple times on the array surface, e.g. in duplicate, triplicate etc.
[00384] The number of distinct or different probe spots present on the array, and therefore the number of different analytes represented on the array, is at least about 2, usually at least about 10 and more usually at least about 20, where in many embodiments the number of different analytes represented on the array is at least about 50, or at least about 100. The number of different analytes represented on the array may be as high as 5,000 or higher, and in some embodiments will not exceed about 3,000 or about 2,500. An analyte is considered to be represented on an array if it is able to specifically bind to one or probe compositions on the array.
[00385J The arrays employed in the subject methods may be fabricated using any convenient protocol, where the protocol may vary depending on the nature of the substrate, the nature of any intervening surface layer, e.g., whether or not a universal binding layer is present, and the nature of the binding agents. Where the substrate is a glass substrate or analogous material, typically the surface of the
substrate is first activated to provide for functional groups suitable for use in the covalent bonding, either directly or through a linking group, of the binding agent. For example, glass surfaces may be aminated so as to display amine functional groups via silanization, according to well known surface chemistry protocols. In many embodiments, the binding agent is then immobilized on the functionalized surface, e.g., through direct or indirect covalent bonding, e.g., by non-covalent binding to a covalently bound universal binding layer of molecules, as described above. In some embodiments a surface
activation agent is used, e.g., an agent that provides a linking group capable of forming a covalent linkage between aminated moieties, such as PIDTC and DVS.
[00386] Following surface preparation, e.g., surface activation, a binding agent composition is
immobilized on the substrate surface to produce a spot of the array. The binding agent composition can be an aqueous composition. In some embodiments, the concentration ranges of the deposited binding agent composition is at least about 0.1 mg/mL, or at least about 0.2 mg/mL, where the concentration may be as great as 1 mg/mL or greater. The purity of the binding agent composition typically is at least about 90%, at least about 95%, or at least about 97% pure.
[00387] The binding agent composition is deposited on the array surface using any convenient protocol.

In many embodiments, the binding agent composition is applied using a pin or analogous deposition device. Also of interest are pipette devices, ink jet devices, etc., which are extensively described in the array preparation art. The particular device and protocol employed to spot the subject binding agents is not critical, so long as it results in a functional probe spot, i.e., a probe spot that specifically binds to its target analyte.
(00388] Following deposition of the binding agent compositions to produce the pattern of probe spots on the array, the surface is then contacted with a blocking agent in order to block non-specific binding sites on the array surface. Any convenient blocking agent may be employed, where representative
blocking agents include, but are not limited to, nonfat milk, BSA, gelatin, preimmune serum and the like, where standard blocking protocols may be employed.
[00389] Following preparation and blocking, as described above, the array is typically stored for a
period of time prior to use. The array may be stored in any convenient format, including both dry and wet formats, so long as the activity of the array, i.e., the binding ability of the probe spots on the array for their specific analytes, is not adversely affected. By not adversely affected is meant that the
sensitivity of the array does not change with respect to a given analyte as compared to the array
immediately following blocking by a value that exceeds about 10 fold, and usually does not change by a value that exceeds about 5 fold. In many embodiments, the period of time for which the array is stored prior to use in the subject methods, described in greater detail below, is at least about 2 days, usually at least about 6 months and more usually at least about 9 months and may be as long as about 1 year or longer, where the array is typically not stored for a period that exceeds about 6 months prior to use.
[00390] The sample that is contacted with the substrate surface may vary greatly, depending upon the nature of the assay to be performed. In general, the sample is an aqueous fluid sample. The amount of fluid sample also varies with respect to the nature of the device, the nature of the sample, etc. In many embodiments, the amount of sample that is contacted with the substrate surface ranges from about 1 μl to about 5 ml, e.g., from about 1 μl to about 5 μl, from about 5 μl to about 10 μl, from about 10 μl to about 25 μl, from about 25 μl to about 50 μl, from about 50 μl to about 100 μl, from about 100 μl to about 500 μl, from about 500 μl to about 1 ml, or from about 1 ml to about 5 ml.
[00391] The fluid sample can be a cell lysate; a cell lysate that has been processed by one or more steps, e.g., removal of cellular debris, and the like; a cell fraction; a cell culture supernatant (e.g., the medium in which a cell is cultured in vitro; the fluid surrounding a cell in vivo; and the like. In obtaining the fluid sample, the initial physiological source (e.g., tissue, collection of cells, etc.) may be subjected to a number of different processing steps, where such processing steps might include tissue homogenation, protein extraction and the like, where such processing steps are known to the those of skill in the art. Of particular interest in many embodiments is the use of cellular extracts as the sample.
[00392] In certain embodiments, the initial fluid sample derived from a particular source, e.g., a cell extract, may be subjected to a fractionation protocol that reduces the complexity of the protein
composition of the sample. By reduce the complexity is meant that the total mass of all of the proteins in the sample is reduced by at least about 10 fold, by at least about 100 fold, or at least about 1000 fold.

(00393] In certain embodiments, the fractionation protocol employed is one that reduces the amount of highly abundant proteins in the sample. In this embodiment, a pool of covalently attached antibodies, e.g., one or more columns of antibodies, is employed for enrichment of antigen analytes of interest from an initial sample, e.g., whole cell extracts. After reversible adsorption of the antigens of interest on the multi-antibody column, the non adsorbed material is washed away with washing buffer and the
specifically retarded antigens are eluted and collected for further labeling and incubation with the array containing binding agent spots for the antigen/analytes of interest, e.g., the same antibodies that were used for initial enrichment. In this manner, the initial sample is fractionated so as to reduce the
complexity and enrich the sample for the analytes of interest.
[00394] In some embodiments, the analytes of interest (e.g., proteins) present in the sample are labeled prior to contact with the array. By labeled is meant that the analytes are modified to be joined to, either covalently bonded to or stably but non-covalently bound to, a member of a signal producing system and are thus detectable, either directly or through combined action with one or more additional members of a signal producing system. Examples of directly detectable labels include isotopic and fluorescent moieties. Isotopic moieties or labels of interest include 32P, 33P, 35S, 1251, 3H, and the like. Fluorescent moieties or labels of interest include coumarin and its derivatives, e.g. 7-amino-4-methylcoumarin, aminocoumarin, bodipy dyes, such as Bodipy FL, cascade blue, fluorescein and its derivatives, e.g.
fluorescein isothiocyanate, Oregon green, rhodamine dyes, e.g. texas red, tetramethylrhodamine, eosins and erythrosins, cyanine dyes, e.g. Cy3 and Cy5, macrocyclic chelates of lanthanide ions, e.g. quantum dye™, fluorescent energy transfer dyes, such as thiazole orange-ethidium heterodimer, TOTAB, etc.
Labels may also be members of a signal producing system that act in concert with one or more
additional members of the same system to provide a detectable signal. Illustrative of such labels are members of a specific binding pair, such as ligands, e.g. biotin, fluorescein, digoxigenin, antigen, polyvalent cations, chelator groups and the like, where the members specifically bind to additional members of the signal producing system, where the additional members provide a detectable signal either directly or indirectly, e.g. antibody conjugated to a fluorescent moiety or an enzymatic moiety capable of converting a substrate to a chromogenic product, e.g. alkaline phosphatase conjugate
antibody; and the like.
[00395] The analytes (e.g., proteins produced by an MEC, e.g., a variant MEC) can be labeled
according to any convenient protocol, where the particular protocol employed may vary greatly with respect to the overall assay protocol being practiced and the nature of the specific label. For example, where the analytes are labeled with detectably labeled antibodies, e.g., fluorescently labeled antibodies, the labeling protocol typically comprises contacting the analyte with the labeled antibodies and
incubating the sample under conditions sufficient for the labeled antibody to specifically bind to the analyte in the sample. In these embodiments, the labeled antibodies employed as labeling reagents are specific for an eptitope of the analyte that is available for binding even when the analyte is bound to a probe spot on the array surface.

[00396] The functional moiety of the functionalized labels may vary greatly, and is chosen in view of the functional moiety present on the analytes in the sample, e.g., amine groups on the proteins analytes present in the sample. In other words, the functional moiety present on the functionalized label must be one that reacts with the functional moiety present on the analyte to produce a covalent bond between the analyte and the label. Representative functional moieties that may be present on the label include: amino, sulfhydryl, sulfoxyl, aminosulfhydryl, azido, epoxide, isothiocyanate, isocyanate, anhydride, monochlorotriazine, dichlorotriazine, mono-or dihalogen substituted pyridine, mono- or disubstituted diazine, maleimide, epoxide, aziridine, sulfonyl halide, acid halide, alkyl halide, aryl halide,
alkylsulfonate, N-hydroxysuccinimide ester, imido ester, hydrazine, azidonitrophenyl, azide, 3-(2- pyridyl dithio)-propionamide, glyoxal, aldehyde, iodoacetyl, cyanomethyl ester, p-nitrophenyl ester, o- nitrophenyl ester, hydroxypyridine ester, carbonyl imidazole, and the like.
100397] In certain embodiments where the analytes are labeled prior to contact with the array, the
sample preparation protocol employs a single type of buffer for both the cellular extraction and labeling steps. In other words, a single buffer composition is employed in both the extraction step, where the proteins of the cell are separated from other cellular components/structures, and in the labeling step, where the analytes present in extract are labeled with a detectable label. The single extraction/labeling buffer employed in these embodiments is one that provides for high extraction efficiency, where high extraction efficiency is meant at least about 90% or at about 95 % (by weight) of the proteins are
extracted with the extaction/labeling buffer, as compared to the amount of proteins extracted by SDS boiling. In addition, the buffer is a buffer that extracts proteins from all cellular
compartmentsΛocations. This single cellular extract/labeling buffer can be characterized by including detergents and other components, when present, that are free of primary amines. Representative
detergents employed that may be present in the buffer include, but are not limited to: octyl-β-D- glucopyranoside (ODG), NP-40, Empigen, Pluronic, and the like. The amount of each detergent present in the extraction/labeling buffer may vary, but typically ranges from about 0.01% to about 10%, from about 0.05% to about 5%, or from about 0.1% to about 2%. In addition, the pH of the buffer is selected such that it provides for suitable conditions for both cellular extraction and labeling. As such, the pH can range from about 7 to about 12, or from about 8 to about 10.
[00398] Following sample preparation and any analyte labeling, where desired, the analyte containing fluid sample is contacted with the array of binding agents and contact is maintained under sufficient conditions and for a period of time sufficient for binding of analyte to specific binding pair members on the array surface to occur. For example, the array and analyte containing sample are incubated together for at least about 10 min., usually at least about 20 min., and more usually at least about 30 min., where the incubation time may be as long as about 480 min. or longer, and in some embodiments does not exceed about 60 min. During incubation, the array and sample are maintained at a temperature that typically ranges from about 20 0C to about 28 0C, usually from about 22 0C to about 26 0C. In many embodiments, the array and sample are subjected to mixing or agitation during the incubation step.

[00399] During incubation, the pH of the liquid medium is maintained at a value ranging from about 6.5 to about 8.5, or from about 7.0 to about 8.0. Also present may be one or more buffers, e.g., Tris, sodium citrate and the like; salts, e.g., NaCl, sodium sulfate, and the like; surfactants/surfactants, e.g.,
Pluronics, Tweens, glycerol, ethylene glycol, etc.
[00400] While the contact of the array and analyte containing fluid medium, as well as metal chelating polysaccharide, may be accomplished using any convenient protocol, in many embodiments, the initial sample is first pre-incubated with an incubation buffer that includes the metal ion chelating
polysaccharide to produce a preincubated analyte containing sample, which preincubated sample is then contacted with the array for the incubation period. In these embodiments, the incubation buffer
employed at least includes the metal ion chelating polysaccharide as described above. In addition, the incubation buffer typically includes a number of additional components, including buffering agents, salts, surfactants, etc.
[00401] Following incubation, non-array bound components of the analyte containing medium
contacted with the array surface during incubation are separated or removed from the surface. This separation step can be accomplished using one or more washing steps, in which the array surface is contacted and separated from, including flushed with, one or more different fluid compositions.
[00402] The array surface can subjected to a sequential washing protocol, in which the array surface is washed with a plurality of distinct washing solutions. The number of different washings employed in these embodiments varies, but typically ranges from about 3 to 10, usually from about 5 to 9 and more usually from about 6 to 8, where in certain embodiments, 7 distinct washings are employed, hi these embodiments, the series of different washing mediums employed provides a modulation or change in the nature of the washing medium and components therein, e.g., in order to subject the array surface to a sequential or step-wise change or modulation of conditions, e.g., amount/type of detergent, salt
concentration, buffering agent, additives, etc. In these embodiments, the different washing conditions to which the array is subjected during the sequential wash protocol are ones that provide for a decrease in background and cross-reactivity during detection, and therefore an increase in signal to noise ratio and/or selectivity, so as to provide the sensitive results discussed above. In certain embodiments, the washing conditions are ones that provide for an increase in signal to noise ratio and/or selectivity of at least about 2-fold, at least about 5-fold, or at least about 10 fold and compared to a control assay in which only a single wash step with a wash fluid that is the same as the incubation fluid is performed. In certain embodiments, the sequential wash protocol is characterized by initially employing a high salt wash, e.g., to remove electrostatically bound molecules, followed by sequential use of wash fluids of decreasing detergent composition, and/or a change of buffers, e.g., from Tris to sodium citrate.
[00403] If the analytes in the sample (e.g., proteins produced by an MEC) are not labeled prior to
incubation, as described above, they are labeled at some point prior to detection. As such, the surface bound analytes can be labeled following incubation and an initial wash step, e.g., where the labels are labeled antibodies capable of binding to already surface bound analytes. Alternatively, the labels can be funetionalized to covalently bind to any molecule displaying a corresponding functional group, e.g., a primary amine. In these embodiments, the sample incubated array is contacted with the labeling
composition under conditions sufficient for labeling to occur. An initial signal is then obtained from the array, followed by a washing step to remove bound analytes and other components. A second signal is then obtained. This second signal is then subtracted from the initial signal to obtain a final signal that is representative or related to the amount of analyte bound to the array, which signal is employed as described below to derive the amount of analyte in the sample.
[00404] Following washing, the array surface is read or scanned for the presence of binding complexes between analytes in the assayed sample and binding agents of the probe spots of the array. In other words, analyte/binding agent complexes on the surface of the array are detected.
100405] Any convenient protocol may be employed for detecting the binding agents on the array
surface. Many different protocols for detecting the presence of surface bound binding complexes are known to those of skill in the art, where the detection method may be qualitative or quantitative
depending on the particular application in which the subject method is being performed, where the particular detection protocol employed may or may not use a detectable label. Representative detection protocols that may be employed include those described in WO 00/04389 and WO 00/04382; the
disclosures of which are herein incorporated by reference. Representative non-label protocols include surface plasmon resonance, total internal reflection, Brewster Angle microscopy, optical waveguide light mode spectroscopy, surface charge elements, ellipsitometry, etc., as described in U.S. Patent No. 5,313,264, the disclosure of which is herein incorporated by reference. Alternatively, detectable label based protocols, including protocols that employ a signal producing system, may be employed. The particular protocol employed varies, depending on the nature of the label that is employed. Where fluorescent labels are employed, any convenient fluorescence scanner device, i.e., fluorimeter, may be employed, where numerous such devices and methods for their use are known to those of skill in the art.
[00406] Following detection of the surface bound binding complexes, the presence of any surface
bound binding complexes is then related to the presence of the one or more analytes in the sample. In many embodiments, the signal intensity value obtained for any binding complex is quantitatively
related to the presence of the corresponding analyte in the sample, so as to provide a quantitative
determination of the analyte amount in the sample. This relating step is readily accomplished in that the position on the array at which a particular surface bound complex is located indicates the identity of the analyte or protein, since the binding agent for the protein is attached to a known specific location on the array. Thus, this relating step merely comprises determining the location on the array on which a
binding complex is present, comparing that location to a reference that provides information regarding the correlation of each location to a particular analyte and thereby deriving the identity of the analyte in the sample. In sum, the location of the surface bound binding complexes is used to determine the
identity of the one or more analytes of interest in the sample.

[00407] By way of further illustration, the following representative protein assay is summarized. Where one is interested in assaying a sample for the presence of 100 different proteins, an array displaying a collection of 100 different antibody binding agents is prepared, where each different antibody binding agents in the collection specifically binds to a different protein member of the 100 different proteins being assayed. The array is then contacted with the sample being assayed under conditions sufficient for binding complexes to be produced between the probe binding agent spots and their corresponding target proteins in the sample. Any resultant binding complexes on the surface of the array are then
detected and the location of the detected binding complexes is used to determine which of the 100
proteins of interest is present in the sample.
[00408] In certain embodiments, two or more physiological sources, e.g., cell extracts (e.g., MEC cell extracts, variant MEC cell extracts, etc.), are assayed according to the above protocols in order to
generate analyte profiles for the two or more sources that may be compared. In such embodiments, analyte containing sample may be separately contacted to identical arrays or together to the same array under binding conditions, depending on whether a means for distinguishing the patterns generated by the different populations of analytes is employed, e.g. distinguishable labels, such as two or more
different emission wavelength fluorescent dyes, such as Cy3 and Cy5, two or more isotopes with
different energy of emission, such as 32P and 33P, gold or silver particles with different scattering
spectra, labels which generate signals under different treatment conditions, like temperature, pH,
treatment by additional chemical agents, etc., or generate signals at different time points after treatment. Biological assays
[00409] In some embodiments, a subject detection method is a biological assay, to detect one or more of a morphological, physiological, or functional characteristic of an MEC. Biological assays include, e.g., an assay involving contacting a reporter epithelial cell with a test fibroblast obtained from a patient; and determining the effect, if any, of the test fibroblast on the reporter epithelial cell.
[00410] A biological assay includes an assay that detects one or more of: 1) the presence and/or level of markers present in a reporter epithelial cell; 2) the presence and/or level of a nucleic acid (e.g., an
mRNA, a cDNA copy of an mRNA, etc.) in a reporter epithelial cell; 3) mobility of a reporter epithelial cell (e.g., ability to cross a membrane); 4) epigenetic modification of a reporter epithelial cell (e.g., histone modification; DNA hypermethylation; etc.); 5) secretion or release of molecules from a test fibroblast; 6) secretion or release of molecules from a reporter epithelial cell; and 7) phenotypic
changes.
[00411] The present invention provides a method of detecting an effect of a component of stroma on tumor progression in a variant human mammary epithelial cell (vMEC). The method generally
involves: a) contacting a test stomal component with a vMEC in vitro; and b) determining the effect, if any, of the test stromal component on a cell characteristic of the vMEC, wherein a test stromal
component that induces a cell characteristic change in the vMEC that is indicative of tumor progression indicates that the test stromal component has carcinogenic potential.

[00412] In some embodiments, a variant (pre-cancerous) HMEC is immortalized by genetically
modifying the cell in vitro with a construct encoding a constitutively active oncogene, e.g.,
constitutively active Ha-Ras Vl 2, to generate an immortalized variant HMEC. The variant HMEC is contacted in vitro with a test fibroblast or other component of the stroma. The effect, if any, of the fibroblast on a cell characteristic of the immortalized vHMEC is determined. Where the immortalized vMEC exhibits an altered cell characteristic in the presence of the test fibroblast, the test fibroblast is considered to be pre-cancerous or cancerous, or to have carcinogenic potential. Cell characteristics include, but are not limited to, increased motility; acquisition of mesenchymal features; increased
telomerase activity; phenotypic changes associated with de novo methylation, e.g., methylation of a promoter region; anchorage-independent growth; genomic instability; and capacity for in vivo survival.

[00413] In some embodiments, the cell characteristic is acquisition of mesenchymal features, e.g., the reporter epithelial cell undergoes an epithelial-to-mesenchymal transition (EMT). Features that are characteristic of EMT include down-regulation of genes such as those encoding cellular adhesion
molecules, and up-regulation of mesenchymal markers. Gene products that are down-regulated (e.g., are present, if at all, at reduced levels) include, but are not limited to, E-cadherin, βl-integrin, and
cytokeratin. Gene products that are up-regulated include, but are not limited to, N-cadherin, fibronectin, and twist. Changes in the level of a gene product can be detected as described above, e.g., using an above-described method for detecting a change in protein level and/or using an above-described method for detecting a change in an mRNA level.
[00414] In other embodiments, the cell characteristic is a morphological change. For example, the
reporter epithelial cell can acquire a spindle shaped morphology. In other embodiments, the cell
characteristic is increased motility of the reporter epithelial cell. Motility can be assessed using any known assay, e.g., an assay as described in Valster et al. (2005) Methods 37:208. For example, a
transwell migration assay can be used. The transwell migration assay has been amply described in the art; see, e.g., McKinnon et al. (2001) J. Clin. Endocrinol. Metab. 86:3665; Redmond et al. (1999)
Thromb. Haemost. 81:293; and Seton-Rogers et al. (2004) Proc. Natl. Acad. Sd. USA 101 :1257.
[00415] Suitable reporter epithelial cells include primary epithelial cells and immortalized epithelial cells (e.g., immortalized epithelial cell lines). In some embodiments, a reporter epithelial cell is a
primary mammary epithelial cell, e.g., a primary human mammary epithelial cell. Primary human
mammary epithelial cells can be obtained from a suitable source such as reduction mammoplasty.
Reporter epithelial cells can be cultured as described in, e.g., Band and Sager (1989) Proc. Natl. Acad. ScI USA 86:1249-1253; Hammond et al. (1984) Proc. Natl. Acad. Sci. USA 81 :5435; and Romanov et al. (2001) Nature 409:633. In some embodiments, the reporter epithelial cell is a subject immortalized vHMEC, as described above.
[00416] In some embodiments, a reporter epithelial cell is genetically modified with a nucleic acid comprising a nucleotide sequence encoding a polypeptide that provides a detectable signal.
Polypeptides that provide a detectable signal include fluorescent proteins, chromogenic proteins, enzymes that catalyze the production of a product that is luminescent, fluorescent, or colored, etc.
Suitable fluorescent proteins include, but are not limited to, a green fluorescent protein (GFP; Chalfie, et al., Science 263(5148):802-805 (Feb 11, 1994); an enhanced GFP (EGFP), Clontech - Genbank
Accession Number U55762); a blue fluorescent protein (BFP; 1. Quantum Biotechnologies, Inc. 1801 de Maisonneuve Blvd. West, 8th Floor, Montreal (Quebec) Canada H3H 1 J9; 2. Stauber, R. H.
Biotechniques 24(3):462-471 (1998); 3. Heim, R. and Tsien, R. Y. Curr. Biol. 6:178-182 (1996)); an enhanced yellow fluorescent protein (EYFP; Clontech Laboratories, Inc., 1020 East Meadow Circle, Palo Alto, CA 94303); a fluorescent protein as described in, e.g., WO 92/15673, WO 95/07463, WO
98/14605, WO 98/26277, WO 99/49019, U.S. Patent No. 5,292,658, U.S. Patent No. 5,418,155, U.S. Patent No. 5,683,888, U.S. Patent No. 5,741,668, U.S. Patent No. 5,777,079, U.S. Patent No.
5,804,387, U.S. Patent No. 5,874,304, U.S. Patent No. 5,876,995, and U.S. Patent No. 5,925,558; a
GFP from species such as Renilla reniformis, Renilla mulleri, or Ptilosarcus guernyi, as described in, e.g., WO 99/49019 and Peelle et al. (2001) J. Protein Chem. 20:507-519; "humanized" recombinant
GFP (hrGFP) (Stratagene); any of a variety of fluorescent and colored proteins from Anthozoan
species, as described in, e.g., Matz et al. (1999) Nature Biotechnol. 17:969-973, U.S. Patent Publication No. 2002/0197676, or U.S. Patent Publication No. 2005/0032085; and the like. Enzymes that catalyze production of a product that provides a detectable signal include, but are not limited to, luciferase, β- galactosidase, horse radish peroxidase, and alkaline phosphatase.
Detecting altered metabolism
[00417] In some embodiments, a subject method of detecting a pre-cancerous MEC involves use of a method that detects a cell with altered metabolism (e.g., altered glucose metabolism; altered protein synthesis, e.g., incorporation of amino acids into proteins; altered nucleic acid synthesis, e.g., altered incorporation of nucleotides into nucleic acids; etc.). It has been found that a pre-cancerous MEC (e.g., a vHMEC) exhibits altered metabolism, e.g., an altered metabolism characteristic of a cancer cell. For example, a pre-cancerous MEC exhibits increased glucose metabolism, compared to a normal, noncancerous MEC. In some embodiments, the methods involve administering to in individual being tested an agent that is selectively taken up by a pre-cancerous MEC, compared to a normal, non-cancerous
MEC. For example, the agent is taken up by a pre-cancerous MEC, and is substantially not taken up by a normal, non-cancerous MEC. The agent can be imaged using, e.g., Positron Emission Tomography
(PET), computer-assisted tomography (CT), magnetic resonance imaging (MRI), and the like.
[00418] In some embodiments, a subject method involves imaging an individual for the presence of an agent that selectively labels cells with altered (e.g., increased) glucose metabolism, where a precancerous MEC selectively takes up the agent. An example of such an agent is the positron-emitting
18F-labeled fluorodeoxyglucose (FDG), or a glucose derivative as described in U.S. Patent No.
5,904,915, e.g., a halogenated glucose derivative, where the halogen is a radioisotope of a halogen atom.

[00419] In other embodiments, a subject method involves imaging an individual for the presence of an agent that selectively labels cells with altered (e.g., increased) protein synthesis, where a pre-cancerous MEC selectively takes up the agent. An aexample of such an agent is "C-methionine.
[00420] In other embodiments, a subject method involves imaging an individual for the presence of an agent that selectively labels cells with altered (e.g., increased) DNA synthesis, where a pre-cancerous
MEC selectively takes up the agent. An aexample of such an agent is 18F-thymidine.
IMAGING METHODS
[00421] As noted above, a subject detection method is useful in an imaging method. For example,
detection (e.g., detection of an MEC signature) can be carried out in the context of risk assessment, where the analysis can be carried out on a woman who is considered to be at low risk of developing breast cancer, or on a woman who is considered at greater risk of developing breast cancer.
[00422] In some embodiments, a biological sample from a patient is subjected to an above-described detection method. Detection of an MEC signature that is indicative of a pre-cancerous MEC provides an indication of an increased risk of breast cancer. For example, in some embodiments, detection of an MEC signature that is indicative of a pre-cancerous MEC provides an indication that the individual from whom the biological sample was obtained has an at least about 25%, at least about 50%, at least about 75%, at least about 2-fold, at least about 5-fold, or at least about 10-fold, or higher, increased risk of developing breast cancer within the next year, within the next 5 years, or within the next 10 years, compared to the risk of developing breast cancer in an individual not having the MEC signature.
[00423] In some embodiments, a biological sample is a sample that comprises cells, which can include living cells, dead cells, cells that have been treated for histochemical analysis, etc. In other
embodiments, a biological sample is a liquid sample that may or may not include living cells, where liquid samples include bodily fluids such as nipple aspirate fluid, urine, blood, serum, plasma, and the like. In other embodiments, a biological sample is a liquid sample that may or may not include living cells, where the liquid sample is a lavage sample, e.g., a ductal lavage sample. In some embodiments, a biological sample has been treated prior to use in a subject detection method, e.g., by enrichment for one or more components (e.g., proteins, nucleic acids, etc.); removal of cells or cell debris; processing for histochemical analysis; and the like.
[00424] In some embodiments, where an MEC signature indicative of a pre-cancerous MEC is detected, monitoring of the individual on a regular basis will be recommended. For example, where an MEC signature indicative of a pre-cancerous MEC is detected, the individual will be monitored yearly, twice yearly, three times per year, or four times per year, where the monitoring will include one or more of carrying out a subject detection method, MRI, and the like.
DIAGNOSTIC METHODS
[00425] As noted above, a subject detection method is useful in a diagnostic method. For example, detection (e.g., detection of an MEC signature) can be carried out following, or in conjunction with, another diagnostic assay, such mammography, magnetic resonance imaging (MRI) of breast tissue and/or axillary lymph node tissue, etc.
[00426] In some embodiments, a subject detection method is carried out on a woman who is considered to be at high risk of developing breast cancer. In other embodiments, a subject detection method is carried out on a woman who has undergone mammography or MRI, where the mammogram indicates the presence, or the possible presence, of cancerous breast tissue.
PROGNOSTIC METHODS
[00427] As noted above, a subject detection method is useful in a prognostic method. In some
embodiments, a subject prognostic method is carried out on an individual who has undergone a benign breast biopsy. In some embodiments, a subject prognostic method is carried out on an individual who has been diagnosed with ductal carcinoma in situ. The methods generally involve carrying out a subject detection method on such individuals. In these embodiments, a subject detection method can provide for a determination of the likelihood that an individual will go on to develop a malignant breast cancer. If such a determination is made, then treatment for cancer may be recommended, or further monitoring may be recommended.
[00428] In some embodiments, subject method provides for determination of the likelihood that an individual diagnosed with ductal carcinoma in situ (DCIS) will develop a malignant breast cancer. In some embodiments, the methods involve detecting an MEC signature, e.g., detecting a gene product produced by an MEC, e.g., detecting one or more of the gene products listed in Figure 14, e.g.,
detecting one or more of CD73, CD138, notch receptor-3, CD90, BMI-I, COX-2, Ki67, pl6, IGF2,
YKL-40, EGR-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK, MAPKK,
DDR2, TRF2, activin, and MEK1/2 gene products, as described in detail above. In some embodiments, the methods involve detecting an MEC signature, e.g., detecting one or more of the following proteins: CD73, CDl 38, notch receptor-3, CD90, BMI-I, COX-2, Ki67, pl6, IGF2, YKL-40, EGR-R, c-jun,
PCNA, jnk, cyclin B 1 , c-kit, STAT3 , cyclin D 1 , PI3K, MAPK, MAPKK, DDR2, TRF2, activin and
MEK1/2. In some embodiments, the methods involve detecting one or more of CD73, CDl 38, notch receptor-3, CD90, BMI-I, and COX-2 polypeptides. In some embodiments, the methods involve
detecting one or more of COX-2, Ki67, and pl6 polypeptides.
[00429] In some embodiments, subject method provides for determination of the likelihood that an individual with a benign breast biopsy (BBB) will develop a malignant breast cancer. In some
embodiments, the methods involve detecting an MEC signature, e.g., detecting a gene product produced by an MEC, e.g., detecting one or more of CD73, CDl 38, notch receptor-3, CD90, BMI-I, COX-2,
Ki67, p 16, IGF2, YKL-40, EGR-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K,
MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2 gene products, as described in detail above. In some embodiments, the methods involve detecting an MEC signature, e.g., detecting one or more of the following proteins: CD73, CD138, notch receρtor-3, CD90, BMI-I, COX-2, Ki67, ρl6, IGF2, YKL-40, EGR-R, c-jun, PCNA, jnk, cyclin Bl, c-kit, STAT3, cyclin Dl, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2. In some embodiments, the methods involve detecting one or more of CD73,
CD138, notch receptor-3, CD90, BMI-I, and COX-2 polypeptides. In some embodiments, the methods involve detecting one or more of COX-2, Ki67, and pi 6 polypeptides.
MONITORING METHOD
[00430] As noted above, a subject detection method is useful in a monitoring method, e.g., monitoring efficacy of a breast cancer treatment; monitoring patient response to a breast cancer treatment; etc. In some embodiments, a subject monitoring method involves carrying out a subject detection method on an individual who has undergone, or is undergoing, one or more treatments for breast cancer, where the treatments include, e.g., cancer chemotherapy, radiation therapy, a biological therapy (e.g., antibody treatments, etc.), and surgery (e.g., mastectomy, lumpectomy, etc.). A subject monitoring method can be carried out before the beginning of any such treatment and/or during the course of a treatment
regimen, and/or following a treatment regimen. For example, a subject monitoring method can be
carried out at the end of a treatment regimen, and at various time intervals thereafter, to monitor patient response to the treatment, and/or to monitor the efficacy of the treatment.
CARCINOMAS
[00431] The methods are useful for detecting, and/or staging, and/or grading a wide variety of cancers, including carcinomas. Carcinomas that can be detected using a subject method include, but are not limited to, esophageal carcinoma, hepatocellular carcinoma, basal cell carcinoma (a form of skin
cancer), squamous cell carcinoma (various tissues), bladder carcinoma, including transitional cell
carcinoma (a malignant neoplasm of the bladder), bronchogenic carcinoma, colon carcinoma, colorectal carcinoma, gastric carcinoma, lung carcinoma, including small cell carcinoma and non-small cell
carcinoma of the lung, adrenocortical carcinoma, thyroid carcinoma, pancreatic carcinoma, breast
carcinoma, ovarian carcinoma, prostate carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinoma, cystadenocarcinoma, medullary
carcinoma, renal cell carcinoma, ductal carcinoma in situ or bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, WiIm' s tumor, cervical carcinoma, uterine carcinoma, testicular carcinoma, osteogenic carcinoma, epithelial carcinoma, and nasopharyngeal carcinoma, etc.
COMPUTER-BASED SYSTEMS AND METHODS
[00432] The invention also provides a variety of computer-related embodiments. Specifically, the
automated means for performing the methods described above may be controlled using computer- readable instructions, i.e., programming. Accordingly, in some embodiments the invention provides computer programming for analyzing and comparing a pattern of gene product expression present in a biological sample obtained from a subject to a library of gene product expression patterns known to be indicative of the presence or absence of a pre-cancerous epithelial cell, wherein the comparing indicates the presence or absence of a pre-cancerous epithelial cell.
[00433] hi another embodiment, the invention provides computer programming for analyzing and
comparing a first and a second pattern of expression of gene products from biological samples takes from a subject in at least two different time points, wherein the first pattern is indicative of a precancerous epithelial cell, and/or progression from a pre-cancerous epithelial cell to a cancerous
epithelial cell. In such embodiments, the comparing provides for monitoring of the progression of the pre-cancerous epithelial cell or for monitoring progression of a carcinoma from the first time point to the second time point.
[00434] In yet another embodiment, the invention provides computer programming for analyzing and comparing a pattern of gene product expression from a biological sample to a library of gene product expression patterns known to be indicative of the presence or absence of a carcinoma, wherein the
comparing providing a differential diagnosis between a benign carcinoma, and an aggressive
carcinoma, e.g., the gene product expression pattern provides for staging and/or grading of a carcinoma.

[00435] The methods and systems described herein can be implemented in numerous ways. In one
embodiment of particular interest, the methods involve use of a communications infrastructure, for example the internet. Several embodiments of the invention are discussed below. It is also to be
understood that the present invention may be implemented in various forms of hardware, software, firmware, processors, or a combination thereof. The methods and systems described herein can be
implemented as a combination of hardware and software. The software can be implemented as an
application program tangibly embodied on a program storage device, or different portions of the
software implemented in the user's computing environment (e.g., as an applet) and on the reviewer's computing environment, where the reviewer may be located at a remote site (e.g., at a service provider's facility).
[00436] For example, during or after data input by the user, portions of the data processing can be
performed in the user-side computing environment. For example, the user-side computing environment can be programmed to provide for defined test codes to denote platform, carrier/diagnostic test, or both; processing of data using defined flags, and/or generation of flag configurations, where the responses are transmitted as processed or partially processed responses to the reviewer's computing environment in the form of test code and flag configurations for subsequent execution of one or more algorithms to provide a results and/or generate a report in the reviewer's computing environment.
[00437] The application program for executing the algorithms described herein may be uploaded to, and executed by, a machine comprising any suitable architecture. In general, the machine involves a
computer platform having hardware such as one or more central processing units (CPU), a random
access memory (RAM), and input/output (I/O) interface(s). The computer platform also includes an operating system and microinstruction code. The various processes and functions described herein may either be part of the microinstruction code or part of the application program (or a combination thereof) which is executed via the operating system. In addition, various other peripheral devices may be
connected to the computer platform such as an additional data storage device and a printing device.
[00438] As a computer system, the system generally includes a processor unit. The processor unit
operates to receive information, which generally includes test data (e.g., specific gene products assayed), and test result data (e.g., the pattern of gene product expression for a sample). This
information received can be stored at least temporarily in a database, and data analyzed in comparison to a library of gene product expression patterns known to be indicative of the presence or absence of a pre-cancerous epithelial cell, or known to be indicative of a stage and/or grade of a carcinoma.
[00439] Part or all of the input and output data can also be sent electronically; certain output data (e.g., reports) can be sent electronically or telephonically (e.g., by facsimile, e.g., using devices such as fax back). Exemplary output receiving devices can include a display element, a printer, a facsimile device and the like. Electronic forms of transmission and/or display can include email, interactive television, and the like. In an embodiment of particular interest, all or a portion of the input data and/or all or a portion of the output data (e.g., usually at least the library of gene product expression patterns known to be indicative of the presence or absence of a pre-cancerous epithelial cell) are maintained on a server for access, e.g., confidential access. The results may be accessed or sent to professionals as desired.
[00440] A system for use in the methods described herein generally includes at least one computer processor (e.g., where the method is carried out in its entirety at a single site) or at least two networked computer processors (e.g., where gene product expression data for a biological sample obtained from a subject is to be input by a user (e.g., a technician or someone performing the activity assays)) and
transmitted to a remote site to a second computer processor for analysis (e.g., where the pattern of gene expression is compared to a library of gene product expression patterns known to be indicative of the presence or absence of a pre-cancerous epithelial cell), where the first and second computer processors are connected by a network, e.g., via an intranet or internet). The system can also include a user
component(s) for input; and a reviewer component(s) for review of data, and generation of reports, including detection of a pre-cancerous epithelial cell, staging and/or grading of a carcinoma, or
monitoring the progression of a pre-cancerous epithelial cell or a carcinoma. Additional components of the system can include a server component(s); and a database(s) for storing data (e.g., as in a database of report elements, e.g., a library of gene product expression patterns known to be indicative of the presence or absence of a pre-cancerous cell and/or known to be indicative of a grade and/or a stage of a carcinoma, or a relational database (RDB) which can include data input by the user and data output.
The computer processors can be processors that are typically found in personal desktop computers (e.g., EBM, Dell, Macintosh), portable computers, mainframes, minicomputers, or other computing devices.

[00441] The networked client/server architecture can be selected as desired, and can be, for example, a classic two or three tier client server model. A relational database management system (RDMS), either as part of an application server component or as a separate component (RDB machine) provides the interface to the database.
[00442] In one embodiment, the architecture is provided as a database-centric user/server architecture, in which the user application generally requests services from the application server which makes
requests to the database (or the database server) to populate the activity assay report with the various report elements as required, especially the assay results for each activity assay. The server(s) (e.g., either as part of the application server machine or a separate RDB/relational database machine)
responds to the user's requests.
[00443] The input components can be complete, stand-alone personal computers offering a full range of power and features to run applications. The user component usually operates under any desired
operating system and includes a communication element (e.g., a modem or other hardware for
connecting to a network), one or more input devices (e.g., a keyboard, mouse, keypad, or other device used to transfer information or commands), a storage element (e.g., a hard drive or other computer- readable, computer-writable storage medium), and a display element (e.g., a monitor, television, LCD, LED, or other display device that conveys information to the user). The user enters input commands into the computer processor through an input device. Generally, the user interface is a graphical user interface (GUI) written for web browser applications.
[00444] The server component(s) can be a personal computer, a minicomputer, or a mainframe and offers data management, information sharing between clients, network administration and security. The application and any databases used can be on the same or different servers.
[00445] Other computing arrangements for the user and server(s), including processing on a single machine such as a mainframe, a collection of machines, or other suitable configuration are
contemplated. In general, the user and server machines work together to accomplish the processing of the present invention.
[00446] Where used, the database(s) is usually connected to the database server component and can be any device which will hold data. For example, the database can be any magnetic or optical storing device for a computer (e.g., CDROM, internal hard drive, tape drive). The database can be located remote to the server component (with access via a network, modem, etc.) or locally to the server
component.
[00447] Where used in the system and methods, the database can be a relational database that is
organized and accessed according to relationships between data items. The relational database is
generally composed of a plurality of tables (entities). The rows of a table represent records (collections of information about separate items) and the columns represent fields (particular attributes of a record). In its simplest conception, the relational database is a collection of data entries that "relate" to each other through at least one common field.
[00448] Additional workstations equipped with computers and printers may be used at point of service to enter data and, in some embodiments, generate appropriate reports, if desired. The computer(s) can have a shortcut (e.g., on the desktop) to launch the application to facilitate initiation of data entry, transmission, analysis, report receipt, etc. as desired.
COMPUTER-READABLE STORAGE MEDIA
[00449] The invention also contemplates a computer-readable storage medium (e.g. CD-ROM, memory key, flash memory card, diskette, etc.) having stored thereon a program which, when executed in a computing environment, provides for implementation of algorithms to carry out all or a portion of the methods described herein, including detection of a pre-cancerous epithelial cell, staging and/or grading of a carcinoma, or monitoring the progression of a pre-cancerous epithelial cell or a carcinoma. Where the computer-readable medium contains a complete program for carrying out the methods described herein, the program includes program instructions for collecting, analyzing and comparing a pattern of gene product expression patterns from a biological sample (e.g., a biopsy sample) obtained from a
subject to a library of gene product expression patterns known to be indicative of the presence or
absence of a pre-cancerous epithelial cell, and generally includes computer readable code devices for interacting with a user as described herein, processing that data in conjunction with analytical
information, and generating unique printed or electronic media for that user.
[00450] Where the storage medium provides a program which provides for implementation of a portion of the methods described herein (e.g., the user-side aspect of the methods (e.g., data input, report receipt capabilities, etc.)), the program provides for transmission of data input by the user (e.g., via the internet, via an intranet, etc.) to a computing environment at a remote site. Processing or completion of
processing of the data may be carried out at the remote site to provide for detection of a pre-cancerous epithelial cell, staging and/or grading of a carcinoma, or monitoring the progression of a pre-cancerous epithelial cell or a carcinoma. The computer-readable storage medium can also be provided in
combination with one or more reagents for carrying out one or more of the activity assays (e.g., control compounds, cells, probes, arrays, or other activity assay test kit components).
KITS AND SYSTEMS
[00451] Also provided by the subject invention are kits for practicing the subject methods, as described above, including detection of a cancerous or pre-cancerous epithelial cell, differential diagnosis
malignant versus benign cancer, or monitoring the progression of a cancer. The subject kits include at least one or more of: a probe or primer for detection of a marker polynucleotide, a marker polypeptide, or an anti-marker polypeptide antibody. Other optional components of the kit include: restriction
enzymes, control primers and plasmids; nucleic acid or polypeptide standards; buffers; reaction
mixtures (e.g., for carrying out the assay); enzymes (e.g., DNA polymerase, reverse transcriptase, and the like); cells; and the like. The various components of the kit may be present in separate containers or certain compatible components may be precombined into a single container, as desired.
Kits for detecting a target nucleic acid
[00452] A subject kit comprises a pair of nucleic acids (primer pairs), one or more nucleic acid probes, or both, where the primer pairs and probes are suitable for use in a subject method, as described above. The nucleic acids will in some embodiments be present in a suitable storage medium, e.g., buffered solution, typically in a suitable container. The kit includes the primers and/or probes, and may further include a buffer; reagents (e.g., for polymerase chain reaction (e.g., deoxynucleotide triphosphates
(dATP, dTTP, dCTP, and dGTP), a thermostable DNA polymerase, a buffer suitable for polymerase chain reaction, a solution containing Mg2+ ions (e.g., MgCl2), and other components well known to those skilled in the art for carrying out a polymerase chain reaction)). The kit may further include instructions for use of the kit, which instructions may be provided in a variety of forms, e.g., as printed information, on a compact disc, and the like. The kit may further include reagents necessary for
extraction of DNA (or mRNA) from a biological sample (e.g., breast biopsy, axillary lymph node
biopsy, etc.) from an individual. The kit may further include reagents necessary for reverse transcription of an mRNA, to make a cDNA copy of the mRNA.
[00453] The kit may further include positive and negative controls. An example of a positive control is a target nucleic acid that includes a region that will be amplified by primer pairs included in the kit. An example of a negative control is a nucleic acid (e.g., an albumin-encoding nucleic acid) that will not be amplified by nucleic acid primers included in the kit. The kits are useful in diagnostic applications, as described in detail above. A subject kit is useful to determine whether a target mRNA is present at higher or lower than normal levels in an epithelial cell.
[00454] A kit will in some embodiments provide a standard for normalization of a level of a target polynucleotide to a standard, e.g., a level of a glucose-6-phosphate dehydrogenase polynucleotide (e.g, a G6PDH mRNA or cDNA copy of a G6PDH mRNA).
[00455] Exemplary kits include at least one primer, at least two primers (a 5' and a 3' primer), or at least two primers and a probe, as described above. Also included in the subject kits may be buffers, dNTPs, and controls, (e.g., positive and negative control nucleic acids) for performing the subject
methods. Primers in the subject kits may be detectably labeled or unlabeled).
Kits for detecting a target polypeptide
[00456] A subject kit for detecting a target polypeptide comprises one or more anti-target polypeptide antibody reagents. For example, a subject kit will include antibody reagent(s) specific for a polypeptide that is included in an MEC signature (e.g., a variant MEC signature). In some embodiments, the
antibody will comprise a detectable label, hi some embodiments, the antibody will be bound to an
insoluble support, e.g., a bead (e.g., a polystyrene bead, a magnetic bead, etc.); a plastic surface (e.g., the well of an ELISA plate); a membrane (e.g., a test strip; a polyvinylpyrrolidone membrane; a
nitrocellulose membrane; etc.); and the like.
[00457] A subject kit can further include, if desired, one or more of various conventional components, such as, for example, containers with one or more buffers (e.g., wash buffers), detection reagents or antibodies. Printed instructions, either as inserts or as labels, indicating quantities of the components to be used and guidelines for their use, can also be included in the kit. hi the present disclosure it should be understood that the specified materials and conditions are important in practicing the invention but that unspecified materials and conditions are not excluded so long as they do not prevent the benefits of the invention from being realized.
[00458] A kit will in some embodiments provide a standard for normalization of a level of a target polypeptide to a standard, e.g., a level of an actin polypeptide, a level of a GAPDH polypeptide, etc. A kit will in some embodiments further include negative controls, e.g., antibodies specific for a non-target polypeptide; and the like.

[00459] Kits may also include components for conducting western blots (e.g., pre-made gels,
membranes, transfer systems, etc.); components for carrying out ELISAs (e.g., 96-well plates; plates containing wells in multiples of 96); components for conducting immunohistochemical analysis of a tissue sample; and the like.
Additional components
[00460] In addition to above-mentioned components, the subject kits typically further include
instructions for using the components of the kit to practice the subject methods. The instructions for practicing the subject methods are generally recorded on a suitable recording medium. For example, the instructions may be printed on a substrate, such as paper or plastic, etc. As such, the instructions may be present in the kits as a package insert, in the labeling of the container of the kit or components thereof (i.e., associated with the packaging or subpackaging) etc. In other embodiments, the instructions are present as an electronic storage data file present on a suitable computer readable storage medium, e.g. CD-ROM, diskette, etc. In yet other embodiments, the actual instructions are not present in the kit, but means for obtaining the instructions from a remote source, e.g. via the internet, are provided. An
example of this embodiment is a kit that includes a web address where the instructions can be viewed
.and/or from which the instructions can be downloaded. As with the instructions, this means for
obtaining the instructions is recorded on a suitable substrate.
METHODS FOR ISOLATING VMEC
[00461] The present invention provides methods for isolating vMEC, e.g., a human vMEC (vHMEC), from a sample that comprises, in addition to vMEC, one or more other cell types, e.g., one or more of MEC, fibroblasts, and the like. The methods generally involve contacting the sample comprising a mixed cell population comprising a vMEC with a specific binding reagent that binds specifically to
CD73, where the specific binding reagent binds CD73 present on the cell surface of a vMEC present in the sample, forming a complex between the specific binding reagent and the vMEC; and separating the complex from the sample. In some embodiments, the specific binding reagent is immobilized on an insoluble support.
[00462] In some embodiments, the specific binding reagent is an antibody specific for CD73. In these embodiments, the method generally involves contacting a sample comprising a mixed cell population comprising a vMEC with an antibody specific for CD73, where the anti-CD73 antibody binds CD73 present on the cell surface of a vMEC present in the sample, forming a complex between the specific binding reagent and the vMEC; and separating the complex from the sample. In some embodiments, the anti-CD73 antibody is immobilized on an insoluble support.
[00463] Suitable insoluble supports include, but are not limited to, beads (e.g., polystyrene beads, magnetic beads, and the like); plastic surfaces (e.g., polystyrene or polycarbonate multi-well plates typically used in an enzyme-linked immunosorbent assay (ELISA) or radioimmunoassay (RIA), and the like); sheets, e.g., nylon, nitrocellulose, and the like; and chips, e.g., SiC>2 chips such as those used in microarrays.

100464] The separation step is carried out in any of a varied of ways, depending in part on the nature of the insoluble support to which the anti-CD73 antibody is bound. In some embodiments, an anti-CD73 antibody is immobilized on the surface of a magnetic bead, and the separation step comprises applying a magnetic field to the sample comprising a complex formed between the anti-CD73 antibody and a vMEC. In other embodiments, an anti-CD73 antibody is immobilized on the surface of a plastic bead, and the separation step comprises low-speed centrifugation.
[00465] A subject method of isolating a vMEC from a mixed cell population comprising a vMEC can include one or more washing steps. For example, a washing step can be included after the formation of a complex between an anti-CD73 antibody and a vMEC, and before and/or after the separation step.
[00466] A subject method of isolating a vMEC from a mixed cell population yields a substantially pure vMEC cell population, e.g, a cell population comprising at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, or at least about 99% vMEC.
The vMEC are CD73+, and are morphologically normal (e.g., do not exhibit a cancerous morphology).

[00467] The present invention further provides a CD73 binding reagent, e.g., a reagent that specifically binds CD73, immobilized on the surface of an insoluble support. A subject immobilized CD73 binding reagent is useful for isolating a vMEC from a mixed population of cells comprising a vMEC. In some embodiments, the CD73 binding reagent is an antibody that binds specifically to CD73.
[00468] Suitable insoluble supports include, but are not limited to, beads (e.g., polystyrene beads,
magnetic beads, and the like); plastic surfaces (e.g., polystyrene or polycarbonate multi-well plates typically used in an enzyme-linked immunosorbent assay (ELISA) or radioimmunoassay (RIA), and the like); sheets, e.g., nylon, nitrocellulose, and the like; and chips, e.g., SiO chips such as those used in microarrays.

EXAMPLES
[00469] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight,
molecular weight is weight average molecular weight, temperature is in degrees Celsius, and pressure is at or near atmospheric. Standard abbreviations may be used, e.g., bp, base pair(s); kb, kilobase(s); pi, picoliter(s); s or sec, second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); kb, kilobase(s); bp, base pair(s); nt, nucleotide(s); i.m., intramuscular(ly); i.p., intraperitoneal(ly); s.c, subcutaneous(ly);
and the like.

Example 1 : Markers associated with pre-cancerous ("variant") mammary epithelial cells
[00470] Breast cancer affects one out of eight women in the U.S., and it is the second leading cause of cancer deaths in U.S. women. This work focused on understanding the early events of breast cancer development; specifically, events that can cause normal cells to transition to cancer cells. A model culture system of growing normal mammary epithelial cells (HMEC) was employed to identify
molecular events leading to early transformation. When normal human mammary epithelial cells
(HMEC) are grown in serum-free conditions in vitro, majority of the cells enter a growth arrest after 10 to 20 population doublings. However, a subpopulation of the cells, "variant" HMEC (vHMEC),
continues to grow for an additional 30 to 50 population doublings when the bulk of the normal HMEC are arrested (Figure 1). All vHMEC grown from women of various ages, parities, and genetic
backgrounds share silencing of plό""1013 expression via promoter-hypermethylation. pi 6"1^43 is a key cyclin-dependent kinase (CDK) inhibitor that inhibits CDK4/6-cyclinD activity, and which activity is needed to phosphorylate RB thereby allowing cells to pass through the Gl /S phase of the cell cycle.
Loss of plό"^4" activity has been found in 31 percent of all human breast cancers and loss of plό1*"013 confers many characteristics associated with malignancy in vHMEC. p\6MKAa loss in vHMEC is
sufficient to induce centrosome dysfunction leading to genomic abnormalities and it also results in hypermethylation OΪH0XA9 transcriptional regulatory region and silencing of HOXA9 expression which may be preventing vHMEC from undergoing normal differentiation. Moreover, vHMEC contain a subpopulation of cells that express high levels of cyclooxgenase-2 (COX-2). The presence of COX-2 provides several "hallmarks" of cancers to vHMEC, such as resistance to apoptosis, increase chemo- attraction, motility, and invasion that may lead to initiation of angiogenesis. COX-2 overexpression has been shown to be sufficient to induce mammary tumors in mice. Cells with silenced pl6INK4A via promoter hypermethylation exist in normal mammary tissue and that COX-2 overexpressing cells
overlap in areas of tissues containing pi 6INK4a-silenced cells.
[00471] It was hypothesized that vHMEC exist in normal mammary tissue and that these cells are likely candidates to be breast cancer precursors in vivo. To test this hypothesis, expression micro-array
analysis comparing vHMEC vs. HMEC was performed. From the micro-array analysis, 26 potential cell surface markers were screened that may distinguish vHMEC from normal HMEC via fluorescent
activated cell sorting (FACS). Markers were identified that facilitate the prospective isolation of a
subpopulation of cells from normal mammary reduction tissues having extended growth characteristics which phenocopies cultured vHMEC.
[00472] Figure 2. Marker expression on vHMEC and HMEC A) FACS analysis profiles of CD73,
CD90, CD138, and Notch receptor-3 expression on vHMEC (blue) and HMEC (green) is shown.
Cultured vHMEC and HMEC from mammary reductions were trypsinized to single cells incubated with anti-CD73-PE, -CD90-APC, CD138-FITC, and -notch receptor-3 -FITC antibodies and analyzed by
FACS. Immunocytochemistry of vHMEC and HMEC with anti-CD73 and anti-CD90 antibodies. Cells were grown on coverslips, fixed and stained with anti-CD73 and -CD90 antibodies followed by anti- mouse-FITC secondary antibodies and fluorescent signal was visualized by confocal microsopy. Cell nuclei were stained with Hoechst dye (blue) and CD73 and CD90 expression shown in green. Cell distribution of vHMEC (blue) and HMEC (green) co-stained with anti-CD73 and -CD90 antibodies.
Cultured vHMEC and HMEC from mammary reductions were trypsinized to single cells, incubated with anti-CD73-PE and -CD90-APC antibodies and analyzed by FACS.
[00473] Figure 3. pl6mκ4a-promotermethylation specific PCR (pl6 MSP) indicated that cells in the
CD73+CD90" (vHMEC) population exhibited plβ1*"013 promoter hypermethylation, whereas plβ1™"" promoter methylation was not detected in the CD73"CD90+ (vHMEC-depleted) or unsorted population. Cells that were sorted as indicated previously were cultured for 10 to 22 days, trypsinized, and frozen as pellets. Genomic DNA was extracted from cells, bisulfate treated, and subjected to pl6 MSP. M
represents a PCR reaction using pl6-promoter-methylation specific PCR primers, and U represents a
PCR reaction using unmethylated promoter PCR primers.
[00474] Figure 4. Isolation of vHMEC from disease-free mammary reduction tissues: Mammary
reduction tissues were digested to single cells and cells were incubated with anti-CD73-PE and -CD90- APC antibodies and subjected to FACS. Scatter plot representing total cell population and the gates used to isolate the designated subpopulations are shown. Cells were first gated for small cells based on forward and side scatter, and small cells were further separated by designated gates as shown.
Percentage of cells sorted from each population is as indicated. Cells exhibited extended growth resided in CD73+CD90" (vHMEC), whereas CD73"CD90+ population (vHMEC-depleted) entered a
proliferation plateau within a short period of time.
[00475] Figure 5. Cells that were sorted based on the gates as shown in Figure 4 were grown in culture, and growth curves of the sorted cells are shown. Total population doublings were determined after every passage of the cells. Phase contrast pictures of sorted CD73+CD90" and CD73~CD90+ cells are shown. After 16 days of culturing CD73+CD90" cells remained small shiny and continued to grow, whereas CD73'CD90+ cells were large, flat, vacuolated, and appeared senescent.
Figure 6. CD73 positive cells are predominantly located at the basal region. Paraffin-embedded sections of normal mammary tissue were stained with anti-CD73 antibody. Cells expressing CD73 are brown, whereas CD73 negative cells are light blue. Arrows indicate sample areas that contain CD73 positive cells. The right panel is a magnified area of the same tissue section as the left panel.
[00477] The data indicate that: 1) variant HMEC (vHMEC) can be distinguished by markers CD73high,

CDl 38hi8h, Notch Receptor-3high, and CD90low; 2) CD73+CD9(T cell population isolated from normal mammary reduction tissues have vHMEC growth characteristics, whereas CD73~CD90+ population is devoid of vHMEC; and 3) normal HMEC can acquire vHMEC growth characteristics by reducing pi 6 expression.

Example 2: Abrogated stress response distinguishes basal-like tumors and DCIS with worse prognosis

MATERIAL AlNfD METHODS
[00478] Cells and cell culture. Human mammary epithelial cells (HMEC) and variant HMEC
(vHMEC) were isolated from reduction mammoplasties (RM) of multiple individuals RM 13, RM 15, RMl 6, RMl 8, RM21. Cells were propagated in modified MCBC 170 media (MEGM, BioWhittaker) as previously described ((Hammond, Ham et al. 1984; Romanov, Kozakiewicz et al. 2001)). All
experiments were conducted with exponentially growing HMEC between population doublings 7 to 10, and exponentially growing mid-passage vHMEC between population doublings 20 to 34. Non- tumorigenic immortalized 184Al breast cells were a kind gift from M.Stampfer (Lawrence Berkeley
National Laboratories). Breast cancer cell lines T47D, SKBr3, BT549 and MDA-MB-231 were
obtained from the ATCC.
[00479] DNA constructs. DNA constructs used in this study are as follows: pMSCV, pMSCV-shpl 6
(G. Hannon and S. Lowe, Cold Spring Harbor Laboratories); pLXSN, pLXSN-HPV16 E7
(D.Galloway, Fred Hutchinson Cancer Center); pMKO, pMKO-shRb (W. Hahn, Harvard Medical
School and Dana-Farber Cancer Institute), pBabe; pBabe-cycIinDl (O. Tetsu, UCSF Cancer Center), pBabe, pBabe-hTert (K.Collins, UC-Berkeley); LXSP and LXSP-COX-2 (D.Dixon, Vanderbilt
University Medical Center). All constructs were packaged in Phoenix A cells for viral propagation. To generate stable cell lines we exposed HMEC, vHMEC or breast cell lines to viral supernatant
containing 8 μg/ml Polybrene (Sigma). Cells containing stable DNA integration were selected in
medium containing 4 μg/ml puromycin (pMSCV, pMKO, and LXSP constructs), 50 μg/ml G418
(LXSN constructs) or 20 μg/ml hygromycin (pBabe). Where indicated, cell lines were imaged using a standard phase contrast microscopy.
[00480] Western Blot. Total protein (15 - 20 μg) lysates were electrophoretically separated by SDS- PAGE and transferred onto polyvinylidene difiuoride (PVDF) membranes according to standard
procedures. Antisera against COX-2 (160107; Cayman Chemical, MI), Rb (554136, BD Pharmingen), pl6 (16P07 Neomarkers), E2F1 (sc-251 Santa Cruz), cyclmDl (2926, Cell Signaling), p53 (sc-126,
Santa Cruz), p21 (SC-6246 Santa Cruz) were used according to manufacturers protocols.
[00481] Tumor samples. The primary gene expression analyses were performed on a cohort of 130 primary breast cancers from UC San Francisco and California Pacific Medical Center. Details of this cohort have been previously described. (Chin, DeVries et al. 2006) Raw microarray data and additional sample information is available (e.g., available on the Internet at http:// followed by
cancer.lbl.gov/breastcancer/data.php). Paraffin-embedded tumor samples corresponding to 61 of the
130 cases were obtained with Institutional Review Board approval and analyzed by
immunohistochemistry.
[00482] Gene expression profiling analyses The 130 UCSF/CPMC CEL files were background
adjusted and normalized using RMA Express (available on the Internet at http:// followed by rmaexpress.bmbolstad.com/). Nearest centroid determination was performed using BRB Arraytools
(available on the Internet at http:// followed by linus.nci.nih.gov/BRB-ArrayTools.html). Hierarchical clustering analyses were performed using Cluster 3.0 (available on the Internet at http:// followed by bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm) on median-centered log expression values using Pearson correlation and centroid linkage. Clustered data was visualized using Java
Treeview (on the Internet at http:// followed byjtreereview.sourceforge.net/).
[00483] Derivation of molecular subtypes The recently defined 1300-gene "Intrinsic/UNC" gene set, derived from Agilent Human oligonucleotide platform data was cross-referenced to Affymetrix Ul 33 A to derive an intrinsic set for these studies. A subset of 1090 genes from the intrinsic/UNC genes
represented on the Ul 33 A platform were additionally filtered for top 20% of variability within the 130 tumor set. This analysis resulted in 589 unique genes that are intrinsically variable and available for this analysis. Hierarchical clustering utilizing this set of 589 genes is shown in Table 7, below.
[00484] Molecular subtype classification was also determined through a nearest centroid based
classifier. Hu et. al. derived a subset of 306 intrinsic genes that are conserved across microarray
platforms. 297 of these genes are represented on the U133A platform. Based upon the 297-subset of training data available on the Internet (at http:// followed by genome.unc.edu/pubsup/breasttumor) a nearest centroid class prediction analysis was performed on the 130 tumor samples with leave-one-out cross validation and probability calculated using the Bayesian Analog of Compound Covariate
Predictor.
[00485] Pre-malignant samples. We analyzed a series of archival paraffin-embedded normal breast tissue specimens from reduction mammoplasties (n=47), tissue containing atypical ductal hyperplasia (n=33) and ductal carcinoma in situ (n= 70). The DCIS samples comprise a subset of a large
population-based cohort study among women in the San Francisco Bay Area diagnosed with DCIS and treated by lumpectomy alone between 1983 and 1996. This patient population was followed for an average of 12.4 years. All tissue was acquired with Institutional Review Board approval from the
surgical pathology laboratory of the University of California, San Francisco and California Pacific
Medical Center. Patients were identified through anonymous reference numbers in accordance with federal guidelines.
[00486] Tissue Preparation and Imiminobistochemistry. Five-micron sections cut from formalin- fixed paraffin embedded tissue blocks were deparaffinized and rehydrated following standard protocol. After incubation with hydrogen peroxide, slides were microwaved in ImM EDTA, pH8, for antigen retrieval. Nonspecific protein binding was blocked with horse serum (Vectstain Elite ABC kit, Vector Labs). Sections were incubated with antisera against COX-2 (Dako M3617, 1/200), pi 6 (Neomarkers MS218, 1/150), Ki67 (Dako M7250, 1/80) overnight at 40C. Antigen-antibody complexes were labelled using the Vectastain Elite ABC and following standard protocol (Vector Laboratories, CA) and
visualised using 2.5% 3-amino-9-ethyl-carbazole in 5OmM acetate buffer pH5, with 0.05% hydrogen peroxide. Sections were counterstained in Mayers hematoxylin mounted in Crystal Mount (BMM02, American Mastertech). Once dry the sections were permanently mounted with a glass coverslip using clearmount (MMCLEl, American Mastertech).
[00487] Evaluation of immunohistochemistry staining. All staining was evaluated by light
microscopy after examination of the entire slide and without knowledge of the patients' clinical
information. Estimation of COX-2 protein expression was determined by COX-2 staining intensity on a 0, I7 2, 3 scale (0 - no staining, 1 - weak; 2 - moderate; 3 - strong staining), pi 6 immunostaining was also scored on a 0, 1, 2, 3 scale based on the extent of immunopositive cells (0 - no staining; 1 - < 25% nuclear and/or cytoplasmic staining; 2 — 26 — 80% nuclear and/or cytoplasmic staining; 3 - > 80%
nuclear and/or cytoplasmic staining). Where indicated for both COX-2 and pi 6, high immunostaining reflects specimens that have a score of > 2. Ki67 immunostaining was determined by manually
counting immunopositive nuclei among a minimum of 1000 total nuclei in an average of three fields of view. Where indicated high Ki67 immunopositivity reflects specimens that contain a minimum of 10% of nuclei positive for Ki67.
[00488] Statistical analysis. Chi-square tests were used to test for associations between pi 6, COX-2,

Ki67, nuclear grade and combinations therein with subsequent tumor development among women with DCIS. JMP-In statistical package (SAS Institute) was used for all analyses.
[00489] A Cox Proportional Hazards Model stratified by year of diagnosis was used to study the ability of four markers (grade and expression of Cox2, pi 6 and Ki67) to predict recurrence during follow-up. Controls were matched to cases by year of diagnosis. There were too few cases and controls for several of the years of diagnosis, so years were grouped as shown in Table 1 for the stratified analyses. First we analyzed that biomarkers separately and then in combinations of two factors. There were too few cases to warrant finer breakdowns of combinations of factors. Results are expressed as Hazard Ratios, which take time to recurrence, for cases, and follow-up time for controls into account.
Table 1
Years of recurrent diagnosis were grouped
to stratify analysis
year ofdx non-recur recur group
1983 1 1
1984 3 1 1
1985 6 1 1
1986 3 2 2
1987 5 4 2
1988 3 5 3
1989 4 3 3
1990 10 5 4
1991 3 8 5
1992 2 1 6
1993 1 3 6
1994 1 1 6
1995 1 6
1996 3 2 6 RESULTS
Determination of risk for subsequent tumor events in women diagnosed with DCIS and treated with lumpectomy alone.
[00490] Our goal has been to evaluate potential predictive characteristics and their association with- outcome in a population-based cohort of women in the San Francisco Bay Area diagnosed with DCIS between 1983 and 1996 and treated by lumpectomy alone. Similar to rates reported by others (Fisher et alSemOncol2001; Cornfield et al.2004 Cancer;Bijker et al 2006.JCO ), -25% of these women exhibited a subsequent tumor event within 10 years after surgical lumpectomy without additional therapy. In this study, a subsequent tumor event (also termed disease recurrence) was defined as a subsequent DCIS lesion or invasive cancer lesion diagnosed in the ipsilateral breast at least 6 months following the initial diagnosis of DCIS. In our previous study, we found 3 characteristics of DCIS lesions that were each associated with a higher risk for subsequent tumor development (Kerlikowske et al, 2003). These DCIS lesions were (1) detected in younger women (<50 years of age) (2) detected by palpation or (3)
exhibited positive surgical margins. None of these characteristics provided a positive predictive value of more than 60%.
[00491] In the present study we used a subset of this population-based cohort (38 controls and 32
cases), followed for an average 12.4 years, to evaluate novel pathways that identify women that have an increased risk of developing subsequent tumor events (both DCIS and invasive cancer). These samples are a representative subset of the larger DCIS cohort previously described (Kerlikowske et al, 2003). In this study, we sought to understand the biological features that characterize DCIS lesions that portend a better or worse prognosis and improve the predictive power of defined biomarkers.
[00492] Histologic markers, such as nuclear grade, were the first to be examined in this cohort. Similar to our previous findings and that of others (Silverstein et al. 1995 Lancet; Barnes et al, 2000JP; Bijker et al, 2001 BrjC; Kerlikowske et al. 2003; Millis et al BJC2004), DCIS of high nuclear grade
significantly increases the risk of developing a subsequent tumor event and inversely correlates with recurrence-free survival (HR 5.6, 95% CI 1.2 to 25.5, P=0.025 for high grade DCIS. However, although nuclear grade statistically stratifies a subpopulation of women with increased risk for a subsequent tumor event, a substantial fraction of women with high nuclear grade DCIS (36 %, 9/25) do not develop subsequent disease. Likewise, 25 % of women with low grade DCIS (3/12) experience subsequent disease. In other words, high nuclear grade has a positive predictive value of 64% and low nuclear grade has a negative predictive value of 75 %.
[00493] To date, few molecular markers have been found that adequately predict which of the women initially diagnosed with DCIS have an increased risk of developing a subsequent tumor event. One of the first molecular markers that were considered in this study for risk stratification is a marker for proliferative index, Ki67. The level of Ki67 immunostaining was determined by manually counting immunopositive nuclei in a minimum of 1000 nuclei in an average of three fields of view. High Ki67 immunopositivity reflects specimens that contain a minimum of 10% of nuclei positive for Ki67.
Similar to previous findings (Ringberg et al 2001; Barnes et al 2005; ClinCancerR.es; Wilson et al 2006 BrJCancer;) examining the role of Ki67 measured as a single variable in modifying risk, we find that high Ki67 significantly stratifies women that develop a subsequent tumor (DCIS and invasive
combined; P=OOl 1 ; Table 2) and predicts a reduced recurrence-free survival (HR.3.3, 95% CI 1.4 to 8.0, P=007; Fig. 7C) as compared to those that do not. However, a high proliferative index has a
positive predictive value of 65% and a low proliferative index (Ki67 in less than 10% of nuclei) has a negative predictive value of 65%.
Table 2
Marker n Control Case P -value
p16 70
High 50% (9/18) 50% (9/18) 0.672
Low 56% (29/52) 46% (23/52)
p16 High 18
Ki67 High 0 % (0/8) 100% (8/8) <0.001
K67 Low 90% (9/10) 10% (1/10)
p1β Low 52
Ki67 High 50% (9/18) 50% (9/18) 0.542
Ki67 Low 59% (20/34) 41% (14/34)
Kl 67 70
High 35% (9/26) 65% (17/26) 0.011
Low 66% (29/44) 34% (15/44)
pi 6 staining intensity with a score > 2 is considered positive, IG67 positive case* exhibited
>10% nuclei immunopoiitivity P*αrues were determined using Pearson Qτi-qusre test.

Deregulation of pl6/Rb increases the risk of subsequent tumor events among women diagnosed with DCIS.
[00494] A well-recognized barrier to carcinogenesis is the induction of a senescent cellular response.

Activated pi 6 signalling is a hallmark of the senescent cellular response pathway that induces a growth arrest in response to various cellular stressors such as genotoxic, oxidative, oncogenic or metabolic stress (see Mooi & Peeper, 2006; Schmitt, 2003; Collado & Serrano, 2005; Campisi, 2005). This response is believed to be a crucial mechanism for controlling unchecked proliferation by limiting the propagation of damaged cells. One would predict that DCIS lesions expressing markers that are
activated during a senescent cellular response, such as increased pi 6 expression, would be associated with fewer subsequent tumor events.
[00495] To determine if expression of this tumor suppressor pathway in DCIS lesions provides
mechanistic insight about subsequent tumor events, we stained 70 samples of DCIS for pi 6 expression by immunohistochemistry, Immunostaining was scored on a 0, 1, 2, 3 scale where a score of 0 or 1 was considered low staining and a score of 2 or 3 was considered high. We find 26% (18/70) of DCIS
lesions show high pi 6 staining (Figure 7A, Table 3). This pi 6 immunopositivity is not associated with any clinicopathological variables such as nuclear grade or hormone receptor status (Table 3). Cases positive for pl6 staining displayed moderate to intense plό staining in the epithelium with varying degrees of lobular heterogeneity. At one extreme, a minority of cases, 28% (5/18) exhibited intense pi 6 staining in virtually all epithelial cells. The remaining pi 6 positive cases (13/18) exhibited
heterogeneous immunopositivity in 26% to 80% of epithelial cells. The surrounding stromal
compartment in a fraction of cases (10%) also exhibited pi 6 staining, primarily confined to fibroblasts surrounding cystic ducts. We would predict that high pi 6 expression induces a cellular growth arrest, and thus DCIS lesions overexpressing pi 6 would represent lesions that do not develop a subsequent recurrent disease. This prediction was not substantiated. We find that high pi 6 expression does not significantly stratify women at increased risk for developing a subsequent tumor event (DCIS and invasive cancer combined; Fig.7A, Table 3). Furthermore, high pl6 expression demonstrated no
correlation with nuclear grade (Table 3).
Table 3
n p16+ COX-2+ Ki67+ p16+/KiG7+ COX-2+/KI67+ p16+/COX-2+/KI67+
ALL DCIS 26% (18/70) 56% (39/70) 37% (26/70) 11% (β/70) 26% (18/70) 9% (6/70)
Nuclear Grade
Low 12 25% (3/12) 67% (8/12) D% (0/12) 0% (0/12) 0% (Q/12) 0% (0/12)
Intermediate 32 22% (7/32) 34% (11/32) 25% (8/32) 6% (2/32) 13% (4/32) 6% (2/32)
High 26 31% (8/26) 77% (20/26)) 69% (18/26) 23% (6/26) 54% (14/26) 15% (4/26)
P-value 0.742 0.004 <0.001 0.046 0.003 0.013
p16 and COX-2 staining Intensity with B icon > 2 fa considered pβiitive, K67 positive cans exhibited >10% nudd Inxronopostivtty.
P-nrfra were deteπnincd using PeiπonChrqu-π: test.
[00496] Paradoxically, overexpression of pl6 can represent two different biological processes; a
response to cellular stress (Mooi & Peeper, 2006; Schmitt, 2003; Collado & Serrano, 2005; Campisi, 2005)) or abrogation of functional Rb signalling (Serrano et al 1993; Nature; Bates S et al 1994
Oncogene; Parry et al 1995 EMBO;). Interestingly, inactivation of key Rb members leads to the
upregulation of pl6 due to unobstructed negative feedback regulation. The presence of proliferation can distinguish between these two situations. A cell that has maintained functional pl6/Rb signalling will experience stress-induced overexpression of pi 6 that will cause a proliferative arrest characteristic of cellular senescence. On the other hand, a cell that has compromised the pRb pathway will experience a regulatory-induced over expression of pi 6 and can disregard the many stress signals that induce
senescence and cellular arrest thereby allowing unimpeded proliferation and bypass of senescence.
[00497] Since high pi 6 expression can reflect two opposing phenotypes that can be distinguished by proliferation, we stained serial sections for Ki67. We found that 37% (26/70) and 63% (44/70) of the lesions within this cohort express high and low Ki67, respectively. Almost half (8/18) of DCIS lesions exhibiting high pi 6 levels also show high Ki67 index labelling (Table 2). We determined if this
phenotype, representing deregulated pl6/Rb signaling, identifies DCIS with worse prognosis. Our analysis demonstrated that all women with DCIS that show high pi 6 and high Ki67 develop a
subsequent tumor (Table 2) and thus Ki67 significantly stratifies high pi 6 expressing lesions in women who develop a subsequent breast cancer (Wilcox on rank test; i*=0.001, Fig.7B) as compared to those that do not. Consequently, we calculate that women with DCIS that exhibit high pi 6 and high RL67 have a substantially increased risk of developing a subsequent tumor (HR = 21.8, 95% CI, 2.6 to 180; /MhOOOl; Fig.7B) as compared to women with lesions that show high pi 6 and low Ki67 labelling. In fact, DCIS lesions that show high plό and low Ki67 index labelling identify benign lesions (90%, 9/10 are non-recurrent samples; Table 2). Therefore, proliferation is an obligate qualifier of pi 6 because the presence or absence of high Ki67 in lesions that show high pi 6 expression dictates their risk for
developing subsequent disease (Wilcoxon rank test; P=0.426; Fig.7D, Table 2). Moreover, women with DCIS that exhibit low pi 6 irrespective of Ki67 do not have a differential risk of developing
recurrent disease (HR = 1.1, 95% CI, 0.4 to 3.4; P=0.85). The high Ki67/high pl6 phenotype is
weighed toward higher grade lesions, such that 75% (6/8) are high grade DCIS and the remaining 25%
(2/8) are intermediate grade (Table 3). Strikingly, lesions expressing high Ki67/high pi 6 phenotype exhibit a positive predictive value of 100% and lesions expressing a low Ki67/high pl6 phenotype have a negative predictive value of 90%.
[00498] Figure 7A-D. pi 6 overexpression coupled with proliferation increases the risk of subsequent tumor events among women with DCIS. A) High pi 6 staining (immunopositivity score of >2) fails to stratify women with DCIS that develop subsequent disease (case versus control). Kaplan-Meier
estimates of recurrence-free survival demonstrate that women with DCIS staining high or low for pl6 immunopositivity develop subsequent disease at the same rate. Box plots and corresponding P-values were determined using Wilcoxon/Kruskal-Wallis rank of sums test. B) DCIS lesions high for plό
immunostaining and elevated Ki67 significantly stratify women that develop subsequent breast cancer from those that do not develop recurrent disease. Recurrence-free survival among women with DCIS that exhibit high pi 6 and high Ki67 (>10% of nuclei positive for Ki67) is significantly reduced
compared to lesions that are high pl6/low Ki67. C) Active proliferation measured by elevated Ki67 index labeling significantly stratifies women with DCIS that develop recurrent disease. DCIS with
elevated Ki67 identifies women with decreased recurrence-free survival and increased risk for
developing a subsequent tumor. Ki67 positivity was determined by counting a minimum of 1000 nuclei, with a score of >10% Ki67 nuclear staining considered positive. D) DCIS lesions with low pi 6
immunostaining irrespective of Ki67 labelling do not have a differential risk of developing subsequent disease. E) Immunohistochemistry staining for pi 6. Staining was scored on a 0, 1, 2, 3 scale with a score of >2 considered positive.
[00499] These data demonstrate that high pi 6 expression stratifies DCIS into two clinically significant populations. One population shows high pi 6 expression in presence of active proliferation, indicating deregulated pl6/Rb signalling, and identifies DCIS lesions with worse prognosis. The second
population shows highplό in the absence of proliferation, indicating functional pl6/Rb signaling, and identifies DCIS lesion with good prognosis. Interestingly, the tumor events that develop subsequent to DCIS with high pi 6 and high Ki67 are more often diagnosed as invasive breast cancer (62%). These data predict that the association of high pl6 levels with a high Ki67 index will be well-represented in invasive tumors and that the association of high pi 6 levels with a low Ki67 index will be
underrepresented in invasive tumors (since this phenotype is postulated to be a barrier to
carcinogenesis). To test this prediction, we examined invasive tumors for the distribution of pl6
overexpression and high Ki67 as a coupled phenotype.
High pl6 mRNA levels defines the basal-Iike subtype of invasive tumors
[00500] Previous reports have demonstrated that ipsilateral tumors that develop subsequent to DCIS share many histological and genetic alternations with the primary lesion (Millis et al. 2004 BrJCancer; Bijker et al 2001 BrJCancer;). For example, primary high grade DCIS is associated with the
development of recurrent high grade DCIS or high grade invasive carcinoma. High concordance of genetic alterations demonstrated by loss of heterozygosity or comparative genomic hybridization
between primary DCIS and subsequent recurrences also suggest a clonal relationship ((Lininger, Park et al. 1998; Waldman, DeVries et al. 2000). Given our finding that all DCIS lesions expressing high pl6 and a high Ki67 index are followed by subsequent tumor formation and that these lesions are weighed toward invasive disease, one might predict that this phenotype would be reflected in invasive
carcinomas.
[00501] To explore the subtype distribution of pl6 overexpression, we examined gene expression
profiles of 130 primary invasive breast tumors using Affymetrix Ul 33 A derived oligonucleotide
microarray data generated at our institution (Chin et al, 2006). Recent studies have defined distinct molecular subtypes that display an intrinsic heterogeneity with prognostic significance for invasive tumors. Molecular subtypes were derived based upon a nearest centroid approach using molecular subtype training data as previously defined (see Materials and Methods) (Hu, Fan et al. 2006).
Unsupervised clustering of these 130 samples with a set of intrinsically variable genes identifies
luminal A, luminal B, normal-like, ERBB2 positive and basal-like clusters.
[00502] It was found that increased pi 6 mRNA preferentially characterizes the highly proliferative basal-like tumor subtype. The expression of the pl6 gene is increased in the majority of basal-like
tumors with 81% of basal-like samples showing pl6 mRNA levels greater than 1.5-fold above the
median. In addition, it was found that high pi 6 expression falls within a gene cluster comprised of many well-established basal-like genes, such as keratin 5, 17, SFRP5, and MMP-7. In keeping with the expected biology, the basal-like sample cluster that expresses high pi 6 mRNA is enriched for tumors with relatively low levels of Rb and cyclin Dl mRNA. Increased cyclin Dl levels were found to be most consistently elevated in the luminal B subtype.
[00503] To confirm the reproducibility of the observed differential subtype specificity of pi 6/Rb/Cyclin

Dl , we analyzed gene expression levels in four publicly available datasets from three different
platforms. In each case, tumors with overexpression of pi 6 were consistently found to be classified as basal-like tumors. The low transcript levels of both Rb and cyclinDl were also enriched in the basal- like tumor subtype.
I l l [00504] These data demonstrate that transcriptional upregulation of pi 6 is a characteristic feature of highly proliferative basal-like tumors. Taken together with the observation that Rb transcript levels are among the lowest in this subgroup this suggests that loss of functional pl6/Rb signalling may play a defining role in the biology of basal-like tumors. Overexpression of pl6 does not simply reflect
proliferating tumor cells since highly proliferating Luminal B tumors do not exhibit plθ levels above the median. Instead, the Luminal B subgroup of tumors commonly overexpresses cyclin Dl . We
demonstrate that deregulation of pl6/Rb signalling, exemplified by overexpression of pl6 in actively proliferating cells, define basal-like tumors and identify DCIS lesions with worse prognosis.
High COX-2 mRNA levels are enriched in basal-like tumors
[00505 J To further analyze pi 6 and explore gene expression interactions, hierarchical clustering was performed on top variable genes in 130 tumors. To select for genes with variable expression, we filtered those with >1.5 fold change from the median in at least 10% of samples and with a log intensity
variation p<0.001, resulting in 6000 unique genes. To classify the 6000-gene clustering into molecular subtypes, rumors were grouped according to the sample clustering using the 589 intrinsic gene set.
Members of the pl6/Rb/cyclinDl pathway did show variable expression, as well as many members of the E2F family. This analysis also demonstrates that among the variable genes, overexpression of COX- 2 falls within the basal gene cluster along with the overexpression of pi 6. Our finding that COX-2 mRNA expression is enriched in basal-like tumors was exciting and of particular interest because we have previous shown that COX-2 is overexpressed in mammary epithelial cells with deregulated
p 16/Rb signalling (Crawford et al, Gauthier et al).
[00506] COX-2 mRNA levels were > 1.5 fold above the median in 18% of the tumors analyzed with
COX-2 overexpression distributed in two major subtype classes of tumors, basal-like and normal-like. We find that 50% (16/32) of basal-like and 33% (4/12) of normal-like tumors overexpress the COX-2 transcript. The basal and normal-like subtypes are known to share high levels of basal genes. Consistent with the subtype distribution of increased COX-2 mRNA, unsupervised hierarchical clustering
demonstrates that COX-2 clusters with basal-like genes. In contrast, luminal tumors and ERBB2
positive tumors tend to express COX-2 mRNA levels below the median.
[00507] To determine if the prevalence of COX-2 overexpression in basal and normal-like tumors is unique to this tumor set, we analyzed four independent published microarray data sets across 3 different platforms. In each independent series, the highest levels of COX-2 mRNA were found within the basal- like tumors. Similar to the distribution in our original set of invasive tumors, the independent datasets also exhibited increased COX-2 in normal-like samples and lower levels of COX-2 gene expression in the majority of luminal and ERBB2 subtypes.
Concordance between pl6 or COX-2 mRNA and protein expression in tumors
[00508] The low levels of COX-2 mRNA expression in ERBB2 positive tumors was perplexing because previous studies had demonstrated that, when assessed with immunohistochemistry, COX-2 protein levels were enriched in ERBB2 amplified tumors (Ristimaki et al,2002 CancerRes 62:632; cho et al.

2005. Breast; Boland et al. 2004,BrJCancer 90:423;). Notably, microarray analyses of human tumor samples are typically average measurements of numerous cell types that often represent arbitrary units relative to a median value and fail to address post-transcriptional and post-translational regulation. Any one these reasons could underlie the discordance between mRNA levels and protein expression as
determined by immunohistochemistry. To interpret the biological significance of microarray based measurements of mRNA expression in vivo, it is critical to relate thresholds of detection of mRNA by microarray to levels of protein expression as measured by immunohistochemistry. Further, it is
important to determine the contributions of distinct cell types to overall levels of gene expression and the relative locations within different cellular compartments. To address these issues and to better
understand p!6 and COX-2 regulation in vivo, we performed pi 6 and COX-2 immunohistochemistry on paraffin-embedded tumor blocks representing 54 of the 130 tumors analyzed by microarray (Figure 8A-D). These samples were chosen to represent all 5 molecular subtypes and span a continuum from the lowest to the highest levels of pi 6 and COX-2 microarray gene expression.
[00509] hi samples of invasive tumors that showed elevated pi 6 via microarray analysis,
immunopositivity was predominantly found in carcinoma cells. To a lesser extent, heterogeneous foci exhibiting pi 6 staining were detectable in the morphologically normal epithelial cells within or adjacent to the invasive tumor. Occasional pi 6 positivity was also observed in fibroblasts, predominantly those within desmoplastic appearing stroma. Cases with elevated COX-2 showed abundant staining within the carcinoma cells as well as in the morphologically normal epithelial, hi rare cases, we found intense COX-2 staining in macrophages infiltrating and surrounding the invasive tumors. COX-2 staining was not observed in mesenchymal cells.
[00510] For pi 6, we observe a significant correlation (Wilcoxon rank of sums, PO.0001) between
mRNA levels by microarray and protein expression by IHC among all tumors analyzed (Figure 8A).
Basal tumors that express the highest levels of pi 6 mRNA showed intense pi 6 protein staining by
immunohistochemistry (score 3+, Figure 8B). We did observe a small fraction of ERBB2 positive tumors (2/8) that showed intense plό staining despite having low levels of mRNA expression. This overall concordance between mRNA and protein suggests that pi 6 protein levels are primarily
regulated at the transcriptional level and that pi 6 protein levels reflect the subtype specificity.
[00511] In contrast, evaluation of COX-2 demonstrated poor correlation (Wilcoxon rank of sums,
P=O.161) between mRNA levels determined by microarray and protein levels determined by EHC
among the tumors analyzed (Figure 8C). In examining those cases with the highest levels of COX-2 mRNA, as defined by a greater than 2-fold increase over the median value, there is complete
concordance as all showed high COX-2 imrnunoreactivity (Figure 8D). Ten of the 54 invasive tumors show COX-2 mRNA levels greater than 2-fold above the median, eight of these cases are basal and the remaining two are classified as normal-like. In remaining cases (44/54), 10 of them exhibited relatively low mRNA detected by microarray analysis and were discordant with the elevated protein expression as measured by HiC (Figures 8D). We found that 80% of the discordant samples were in the ErBB2 subtype.
[00512] The observation of high COX-2 protein expression by IHC in the absence of high COX-2
mRNA by microarray has a number of possible explanations including technical (i.e. inconsistent sampling of tumor tissue in microarray samples) and biological (i.e. post-transcriptional or post- translational regulation of COX-2). Inconsistent sampling of tumor tissue in microarray samples
appears an unlikely explanation as all of the samples exhibiting low COX-2 mRNA still showed robust basal-like tumor microarray signatures (Figure 8B,C). Furthermore, a number of the samples
discordant for COX-2 showed concordant IHC and microarray elevations in pi 6. A biological
explanation for the discrepant protein/HC and mENA/microarray levels for COX-2 is most likely given the particularly striking discordance in the ERBB2 positive tumors. The majority of ERRB2 tumors (75%, 6/8) showed high COX-2 immunoreactivity, yet none of these tumors showed elevated
COX-2 mRNA (Figure 8D). Many in vitro studies have demonstrated that COX-2 in addition to being regulated through de novo transcription is also often regulated by mRNA stabilization (Dixon, Kaplan et al. 2000; Ramsay, Ciznadija et al. 2003). While both these methods of regulation would be reflected in our gene expression analysis, post-translational regulation of COX-2 would not. These results
suggest that ERBB2 positive invasive tumors target protein stabilization of COX-2 as a distinct and important mechanism of achieving COX-2 protein overeexpression.
[00513] Figure 8A-D. Concordance between pi 6 or COX-2 mRNA and protein expression in tumors.

A) There is good concordance between pl6 mRNA expression determined by gene expression profiling and protein levels determined by immunohistochemistry. The correlation between the mRNA levels
(expressed as log median centered) and high or low pl6 imrnunostaining was determined using
Wilcoxon rank of sums analysis. B) We determined the level of concordance among invasive tumor subtypes. The log median centered mRNA level of pi 6 for each sample analyzed is plotted as a
continuous variable (red triangles) distributed by breast cancer subtype. The corresponding protein levels of pl6 are plotted as immunohistochemistry scores 0,1, 2, or 3 (black squares). C) There is poor concordance between COX-2 mRNA and protein levels. The correlation between the mRNA levels
(expressed as log median centered) and high or low COX-2 immunostaining was determined using
Wilcoxon rank of sums analysis. D) We analyzed the discordance of mRNA (red triangles) and protein (black squares) levels of COX-2 in invasive tumors within different molecular subtypes determined by hierarchical clustering. The log median centered mRNA level of COX-2 for each sample analyzed is plotted as a continuous variable (red triangles) distributed by breast cancer subtype. The corresponding protein levels of COX-2 are plotted as immunohistochemistry scores 0,1, 2, or 3 (black squares).
COX-2 overexpression coupled with proliferation increases the risk of subsequent tumor events among women with DCIS.
[00514] Our findings that COX-2 mRNA levels are enriched in basal-like tumors and that COX-2
protein levels are elevated in both basal and ERBB2 positive tumors, led us to determine if elevated COX-2 protein expression in DCIS also portends a worse prognosis. In the 70 cases previous analyzed for pi 6 and Ki67, we stained serial sections for COX-2 for evaluation by immunohistochemistry. We determined the level of COX-2 staining on a 0,1,2,3 scale of immunopositivity. Representative COX-2 staining is illustrated in Figure 9C). We considered a score of 0 or 1 to represent low staining and a score of 2 or 3 to be high immunostaining. We find that 56% (39/70) of DCIS lesions show high COX- 2 protein levels (Table 3). To determine if expression of COX-2 in DCIS is clinically significant, we determined if cases with high COX-2 staining stratifies risk for developing subsequent disease. We find that high COX-2 immunopositivity by itself does not stratify risk for subsequent tumor formation and, similar to pi 6 overexpression by itself, is equally distributed among women that develop subsequent
DCIS or invasive cancer (case) and those that do not (control; HR=I .0, 95% CI, 0.5 to 2.2, P=0.99;
Table 4; Figure 9A).
Table 4

Marker π Control Case P -value
COX-2 70
Htgh 56% (22/39) 44% (17/39) 0.689
Low 52% (16/31) 4B% (15/31)
COX-2 High 39
Ki67 High 27% (5/18) 72% (13/1B) <0.001
K67 L.OW 81% (17/21) 19% (4/21)
COX-2 Low 31
Ki67 High 50% (4/8) 50% (4/8) 0.916
Ki67 Low 52% (12/23) 48% (11/23)
K167 70
High 35% (9Λ26) 65% (17/26) 0.011
Low 66% (29/44) 34% (15/44)
COX-2 staining intensity with a score > 2 Ii α-raldmed po-ttivnKifi7 positive oases exhibited
>10K nuclei immunopositivity P-vafuu were determined using Peanon Chj-quare test
[00515] Since COX-2 expression in invasive tumors is found in actively proliferating cells, we
determined the fraction of DCIS expressing high COX-2 and high Ki67. Almost half (18/39) of DCIS lesions showing high COX-2 also exhibit high Ki67 and is weighed toward higher grade lesions (Table 3). We determined if this phenotype (high COX-2 coupled with high Ki67) identifies DCIS lesions with worse prognosis. Indeed, stratifying high and low COX-2 DCIS lesions by proliferation identifies women with differential risk for recurrent disease. Figure 6B demonstrates a significantly higher
fraction of women (13 of 18) with DCIS showing high COX-2 and high Ki67 develop a subsequent tumor (Wilcoxon rank test; P=0.0002). We calculate a significant increased risk of developing a
subsequent breast cancer and decreased recurrence-free survival when the primary DCIS lesion exhibits high COX-2 and high Ki67 labelling as compared to lesions that show high COX-2 and low Ki67 (HR = 4.72, 95% CI, 1.0 to 22.1, P=0.0004; Figure 9B, Table 4). Similar to our findings for pi 6,
proliferation is an obligate qualifier of COX-2 because high Ki67 does not stratify low COX-2
expressing lesions (Wilcoxon rank test; P=0.925). Correspondingly, we do not observe a differential risk for recurrent disease in women that exhibit low COX-2 expressing DCIS irrespective of Ki67 (HR
= 0.86, 95% CI, 0.2 to 3.3, P=0.79). In examining the lesions that develop subsequent to DCIS that are immunopositive for both COX-2 and Ki67, we find that 8 of the 13 cases recur as invasive breast
"cancer. These data suggest that COX-2 and Ki67 immunopositive cells may identify an aggressive
cellular phenotype.
[00516J Figure 9A-C. COX-2 overexpression coupled with proliferation increases the risk of
subsequent tumor events among women with DCIS. A) COX-2 staining intensity (score 0, 1 , 2, or 3) fails to stratify women with DCIS that have a differential risk of developing recurrent disease.
Recurrence-free survival is not different in women with DCIS that exhibits high or low for COX-2 immunopositivity (score of >2 was considered high). Box plots and corresponding P-values were
determined using Wilcoxon/Kruskal-Wallis rank of sums test. B) DCIS lesions high for COX-2
immunostaining and elevated Ki67 significantly stratify women that develop subsequent breast cancer from those that do not develop subsequent disease. Recurrence-free survival among women with DCIS that exhibit high COX-2/high Ki67 is significantly reduced compared to lesions that are high COX- 2/Low Ki67. C) DCIS lesions with low COX-2 immunostaining irrespective of Ki67 labelling do not have a differential risk of developing recurrent disease. D) Immunohistochemistry staining for COX-2. Staining was scored on a 0, 1, 2, 3 scale with a score of >2 considered positive.
Predicting invasive tumor formation using molecular markers
[00517] These findings with COX-2 and Ki67 parallel our observations in examining the expression of p 16 and Ki67. Given that 12% (8/65) of the DCIS lesions we examined from the UCSF cohort show high pl6/high Ki67 and 25% (16/65) show high COX-2/high Ki67 (Table 3), we determined if one phenotype is enriched for the other. We find that 75% (6/8) of high 16/high Ki67 DCIS exhibits
overexpression of COX-2, and 38% (6/16) of high COX-2/high Ki67 lesions show high pl6 expression (Figure 10). Strikingly, expression of all three markers, high pi 6, high COX-2, high Ki67, provides the first signature that is strong in predicting a subsequent invasive event over a non-invasive (DCIS) event. Since invasive lesions have the potential to invade and seed metastatic foci, this distinction is clinically relevant. Of the 6 DCIS lesion that overexpress all three markers, all develop a subsequent tumor event, 5 develop invasive breast cancer.
[00518] Figure 10. Diagram representing DCIS lesions expressing combinations of pi 6, COX-2 and
Ki67. High COX-2 and/or high pi 6 classifies two clinically different populations of cells in DCIS that can be stratified by proliferation. One population overexpresses COX-2 and/or pi 6 in the presence of proliferation and identifies women that develop subsequent DCIS (black circles) or invasive breast cancer (red circles). The second population overexpresses COX-2 and/or pi 6 in the absence of
proliferation and identifies women that do not develop subsequent disease (open circles).
[00519] Similar to our observations that elevated pi 6 in the absence of proliferation identifies more benign lesions (Table 2), 81% (17/21) of women with high COX-2 and low Ki 67 expressing lesions do not develop a subsequent tumor event (Table 4). Therefore, elevated levels of either pi 6 or COX-2 in the absence of proliferation suggest stress activation and identify a phenotype with more favourable prognosis. Equally intriguing, expression of high pi 6, high COX and low Ki67 marks a low risk of developing subsequent disease. We observe 7 DCIS lesions exhibiting high COX-2/high pi 6 and low
Ki67, of which 6 do not develop a subsequent tumor event. The one sample that developed subsequent disease recurred as DCIS. These observations suggest high COX-2 and high pi 6 classifies two
clinically different populations of cells in DCIS that can be stratified by proliferation. One population overexpresses COX-2 and/or pi 6 in the presence of proliferation and identifies lesions with poor
prognosis. The second population overexpresses COX-2 and/or pi 6 absence of proliferation and
identifies DCIS lesions with good prognosis (Figure 10).
COX-2 overexpression causes cell cycle arrest in cells that maintain functional pl6/Rb signaling.

[00520] It is well appreciated that in vitro, cell cycle checkpoints are essential to preserve genomic stability. Overexpression of pl6 in normal cells, induced by exogenous stressors or genetic
manipulation, causes an irreversible cell cycle arrest and morphological changes characteristic of
cellular senescence. It has been speculated that inactivation of this critical checkpoint in vivo would allow cells to propagate under unfavourable conditions that promote genomic instability and accelerate tumorigenesis. Our observations that abrogation of this checkpoint, reflected by high plό/high Ki67 expressing lesions in DCIS, portends a worse prognosis support this hypothesis.
[00521] These observations parallel our findings with COX-2 expression and elevated Ki67. We
observe high COX-2 expressing DCIS lesions identify two distinct populations of cells, one that is quiescent and the other that is actively proliferating, that have different prognoses. These data prompted us to determine the cellular context that governs COX-2 and if it is associated with quiescence or
proliferation. We investigated the S-phase fraction in a continuum of cell populations from normal to malignant engineered to constitutively overexpress COX-2 compared to vector control populations. S- phase fraction was determined following a 4h pulse of BrdU incorporation and flow cytometric
analysis.
[00522] It was found that in normal cells, COX-2 inhibits cell proliferation while, in pre-malignant and malignant cells, overexpression of COX-2 subsists in the presence of ongoing proliferation. COX-2 expression was increased in normal human mammary epithelial cells (HMEC) generated from
reduction mammoplasty tissue from 3 different individuals via expression of an exogenous COX-2 construct; it was found that sustained COX-2 overexpression significantly reduces the number of
cycling cells (Figure HA). The diminished S-phase fraction of HMEC-COX-2 cells limits the
proliferative capacity and reduces the lifespan of these cells in culture. These data parallel the finding when pi 6 was overexpressed in HMEC. In contrast, in non-tumorigenic cells that exhibit pre-malignant characteristics, both mortal (variant HMEC, vHMEC) and immortal (vHMEC-hTert and 184A1) as well as tumorigenic breast cancer cell lines (T47D, SKBr3, BT549 and MDA-MB-231), COX-2
overexpression neither induces nor diminishes proliferation (Figure HA). Functional pl6/Rb signaling is one of the distinguishing features of normal cells compared to all other cells we examined. Therefore, it is hypothesized that COX-2 overexpression resulting in a cell cycle arrest is only observed in normal breast epithelial cells that retain functional pl6/Rb signalling. All other cells that were examined have compromised pl6/Rb signalling through diverse mechanisms including pl6 hypermethylation
(vHMEC, vHMEC-hTert, T47D), pl6 deletion (MDA-MB -231), or Rb deletion (BT549). These
analyses suggest cells with compromised plό/Rb signalling support COX-2 expression and its ensuing phenotypes in actively proliferating cells.
[00523] To extend this analysis, the differential response to COX-2 overexpression in HMEC versus a subpopulation of HMEC that have lost pi 6 expression through promoter hypermethylation (variant
HMEC) was further explored. Constitutive expression of COX-2 in HMEC produced enlarged flattened cells that are growth arrested compared to vector control cells (Figure HB). In contrast, overexpression of COX-2 in cells lacking pi 6 (vHMEC) continued to proliferate without morphologic change (Figure HB). To characterize the molecular changes underlying the differential phenotypic response to COX-2 overexpression, cell lysates were probed for cell cycle regulatory proteins by immunoblotting. HMEC overexpressing COX-2 exhibited elevated protein levels of pl6, p53 and p21 (Figure HC). This is in contrast to vHMEC where overexpression COX-2 did not alter the level of p53 or p21. Thus, COX-2 induces a cell-cycle arrest in pi 6 expressing cells while pl6-silenced cells are refractive to COX-2- induced growth inhibition. This phenotype is also observed in cells that have abrogated all Rb family members. Targeted degradation of Rb, plO7 and pl30 (all three Rb family members) by HPV16-E7 in HMEC results in ongoing proliferation in the presence of COX-2 overexpression (Figure HB). Thus, COX-2 overexpression in cells with functional pl6/Rb signalling induces a pl6-dependent growth arrest, while cells with disrupted pl6/Rb signalling continue to proliferate in the presence of COX-2 overexpression.
[00524] Figure HA-C. Overexpression of COX-2 in the absence or presence of proliferation is
dependent on p!6/Rb dysfunction. A) Cell populations with varying malignancy were retrovirally infected with a constitutive COX-2 expressing construct (COX-2) or an empty vector control (LXSP). Cells were pulsed for 4 h with BrdU and analyzed by flow cytometry following propidium iodide
staining. The S-phase fraction of COX-2 expressing cells were compared to vector control cells and represented as fold increase of controls. B) Phase contrast micrographs of primary human mammary epithelial cells (HMEC), variant HMEC (vHMEC) lacking pi 6 expression and HMEC expressing
HPVl 6-E7 retrovirally infected with a constitutive COX-2 expressing construct (COX-2) or an empty vector control (LXSP). C) We determined the molecular changes underlying the differential phenotypic response to COX-2 by probing cell lysates from COX-2 overexpressing and vector control HMEC and vHMEC for COX-2, pi 6, p53 and p21.
Deregulation of pl6/Rb signalling causes COX-2 overexpression.
[00525] The finding that the majority of high pl6/high Ki67 DCIS lesions overexpress COX-2 suggests that deregulation of pl6/Rb may drive COX-2 expression. To test this hypothesis, specific members of the p 16/Rb pathway were genetically modulated, and the levels of COX-2 protein expression compared to HMEC that maintain pi 6 expression were determined. First, basal and induced COX-2 protein levels in HMEC lacking pl6 activity were compared. Sequence specific silencing of pl6 by retroviral
infection of HMEC with a short hairpin RNA (shplό) downregulated pi 6 protein levels leading to the upregulation of both Rb and E2F1 compared to control HMEC infected with an empty pMSCV vector (Figure 12A and Zhang et al. 2006). Basal levels of COX-2 expression did not change with the removal of pl6 activity. However, exogenous induction of COX-2 by exposure to inducing stimuli (for example TGF-β) resulted in COX-2 upregulation in pi 6 silenced cells while vector control cells remain
unresponsive. These results were observed in two independent reduction mammoplasties and three independent determinations after exposure to TGF-β. These findings demonstrate that while the basal levels of COX-2 protein remained unchanged with the removal of pi 6 activity, the genetic silencing of pi 6 sensitizes cells to exogenous COX-2 induction and demonstrates that a secondary event is
necessary for COX-2 overexpression.
[00S26] To extend this analysis, we determined how other alterations within this pathway, mutations common in cancer, affect COX-2 expression. We modulated the pl6/Rb pathway by three additional methods, cyclin Dl overexpression, pRb downregulation, and expression of a viral oncoprotein,
HPVl 6-E7 and determined the effect on basal and exogenously-induced COX-2 protein levels. To determine if cyclin Dl induces and/or sensitizes cells to COX-2 induction, we measured COX-2 protein levels in HMEC engineered to stably express cyclin Dl under the regulation of an independent,
constitutively active promoter. Cyclin Dl was introduced into cells generated from three different
reduction mammoplasties and resulted in cyclin Dl protein overproduction similar in level to that
measured in tumor cells. Overexpression of cyclin Dl alone did not cause hyperphosphorylation of Rb3 and instead lead to a slight reduction in overall Rb protein levels (Figure 12B). These results are
consistent with previous findings (Lundberg et al, 1998) that overexpression of cyclin Dl is not
sufficient for Rb inactivation. The absence of E2F1 upregulation following cyclin Dl overexpression supports our finding that Rb remains active. We demonstrate that overexpression of cyclin Dl did not induce basal COX-2 expression and failed to render cells sensitive to exogenous induction by TGF-β
(Figure 12B). These data suggest that cyclin Dl overexpression does not modulate Rb activity, does not alter basal levels of COX-2 expression or render cells sensitive to exogenous COX-2 induction. To determine if inactivation of Rb is sufficient for the upregulation of COX-2, we infected HMEC with a retrovirus containing a short hairpin RNA against Rb (shRb) and determined COX-2 protein levels in cells from two independent experiments. As anticipated, sequence specific silencing of Rb
downregulated Rb protein levels and caused the upregulation of E2F1 compared to control HMEC
infected with an empty pMKO vector (Figure 12C). Viral transduction with shRb was integrated In these cells, both basal levels and exogenously induced levels of COX-2 protein were increased (Figure 12C) supporting a central role for the loss of Rb in driving COX-2 overexpression. Similar to results obtained with Rb genetic silencing, expression of the human papilloma virus 16-E7 (HPV16-E7)
elevated both basal and induced levels of COX-2 protein (Figure 12D). Stable expression of HPVl 6- E7 was performed in cells generated from three independent reduction mammoplasties. Mammary epithelial cells expressing HPV16-E7 show downregulation of Rb and thus inactivation of Rb and consequently upregulation of E2F1 (Figure 12D). HPVl 6-E7 is well characterized for its role as a transforming oncoprotein through targeted degradation of all three members of Rb family (Rb, pi 07 and p 130) and driving E2F-dependent transactivation.
[00527J Figure 12A-E. Deregulation of distinct members of the pl6/cyclin Dl/Rb pathway
differentially regulate COX-2. A) To determine if pl6 is necessary for the upregulation of COX-2,
HMEC were retrovirally infected with a construct encoding a short hair-pin RNA against pl6 (shplθ) or an empty vector control construct (pMSCV). Cell lysates were probed by western blot for COX-2, pi 6, Rb and E2F1. To determine if genetic downregulation of pi 6 in HMEC are sensitive to the
upregulate COX-2 in response to exogenous induction, cell lysates were probed for COX-2 by
imrnunoblotting following 24 h exposure to lng/ml TGF-β. B) To determine if cyclin Dl is necessary for COX-2 upregulation, HMEC were retrovirally infected with a constitutely expressing cyclin Dl construct (cycDl) or an empty vector control construct (pBabe). Cell lysates were probed by western blot for COX-2, cyclin Dl, pl6, Rb and E2F1. To determine if genetic upregulation of cyclin Dl in
HMEC are sensitive to the upregulate COX-2 in response to exogenous induction, cell lysates were probed for COX-2 by immunoblotting following 24 h exposure to lng/ml TGF-β. C) To determine if Rb is necessary for COX-2 upregulation, HMEC were retrovirally infected with a construct encoding a short hair-pin RNA against Rb (shRb) or an empty vector control construct (pMKO). Cell lysates were probed by western blot for COX-2, Rb, pi 6 and E2F1. To determine if genetic downregulation of Rb in HMEC are sensitive to the upregulate COX-2 in response to exogenous induction, cell lysates were probed for COX-2 by immunoblotting following 24 h exposure to lng/ml TGF-β. D) To determine if Rb family members (Rb, plO7 and pl30) are necessary for the upregulation of COX-2, HMEC were retrovirally infected with HPV16-E7 or an empty vector control construct (pLSXN). Cell lysates were probed by western blot for COX-2, Rb. pi 6 and E2F1. To determine if genetic downregulation of all Rb family members in HMEC are sensitive to the upregulate COX-2 in response to exogenous
induction, cell lysates were probed for COX-2 by immunoblotting following 24 h exposure to lng/ml TGF-β. E) Diagram representing the connection between pl6/Rb pathway and COX-2.
[00528] These data demonstrate that abrogation of pl6/Rb signalling through genetic silencing of pi 6,

Rb and Rb family members sensitizes cells to COX-2 upregulation. Thus, the propensity of COX-2 overexpression in DCIS lesions that exhibit high pi 6/high Ki67 may be a consequence of deregulation of the p 16/Rb pathway.
pl6 and COX-2 overexpression can be found in a subset of epithelial cells in normal breast tissue and atypical ductal hyperplasias.
[00529] We have described two cellular phenotypes that define a subset of invasive tumors and DCIS with worse prognosis. These findings prompted us to determine the prevalence of these phenotypes in normal breast tissue and in tissue biopsies diagnosed with atypical ductal hyperplasia (no DCIS present). We characterized pl6 and COX-2 expression and proliferation index in normal breast biopsies (n = 40) and atypical ductal hyperplasias (ADH; n = 20). Representative pi 6 immunostaining in normal and ADH biopsies is shown in Figure 13). We find that the majority of disease-free breast tissues
exhibited low levels or were devoid of pi 6 expression while 7.5% of the cases displayed heterogeneous 16 staining in 25%-85% of the morphologically normal epithelium (Table 5). In examining a series of ADH lesions, we find 27% of cases showed heterogeneous pi 6 immunostaining, an increase as
compared to disease-free tissue that did not reach statistical significance (Table 5; Pearson chi-square test P=O.394). Similar to our findings in DCIS, the surrounding stromal compartment in a fraction of cases (10%), both in normal tissue and tissue containing ADH also exhibited pl6 staining in fibroblasts surrounding cystic ducts. For COX-2, we have previously demonstrated and illustrate here that
approximately 20%-30% of tissue from disease-free women exhibit foci of cells with heterogeneous
COX-2 staining in normal epithelium (Fig.13; Crawford et al, 2004; Gauthier et al.2005) and others have confirmed this observation (Boland et al. 2005).
[00530] Figure 13A and 13B. pl6 and COX-2 overexpression identify a subset of epithelial cells in normal breast tissue and atypical ductal hyperplasias that may provide risk stratification. A)
Representative of pi 6, COX-2 and Ki 67 immunostaining in normal disease-free breast tissue, atypical ductal hyperplasia (ADH) and DCIS are illustrated. The bar graph demonstrates the percent positive cases for each biomarker. pi 6 and COX-2 staining intensity with a score > 2 is considered positive.
Ki67 mmunostaining is considered positive in cases exhibiting more that 10% nuclei immunopositivity. B)To determine if pl6 and/or COX-2 is correlated with proliferation, we evaluated pi 6 and COX-2 immunopositive staining (score of >2 was considered high) with the percent Ki67 nuclear positivity expressed as a continuous variable in normal , ADH and DCIS. Box plots and corresponding P-values were determined using Wilcoxon/Kruskal-Wallis rank of sums test.
100531] In ADH lesions, we find 65% of lesions (13/20) stain positive for COX-2 (Table 5) a
significant increase as compared to disease-free breast tissue, p=0.01). In examining the relationship between pl6 and COX-2, we observe concomitant overexpression in 2.5% (1/40) of normal tissue devoid of disease (Table 6). In ADH and DCIS, we observe -10% (2/20) and 19% (13/70) lesions overexpress both pi 6 and COX-2, respectively (Table 6).
Table 5
Epithelium p16+ COX-2* KΪS7+ P16+/KIG7+ COX-2+/KJ67+ p16+/COX-2+/Kiβ7+
Normal 7.5% 93/40) 30% (12/40) 0% (0/40) 0% (0/40) 0% (0/40) 0% (0/40)
ADH 20% (4/20) 65% (13/20) 5% (1/20) 5% (1/20) 0% (0/20) 0% (0/2O)
DClS 26% (18/70) 56% (39/70) 37% (26/70) 11% (8/70) 26% OBfTO) 9% (6/70)
p16 and COX-2 staining intensity with a score > 2 a considered positive, Ktδ7 positive easel exhibited > 10% nuclei immunopodtivity,
P-values were determined using Pearson CN-quarα test.

Table 6
Epithelium piβ High p16 LOW p. value
Normal
COX-2 high 2.5% (1/40) 27.5% (11/40) 0.605
COX-2 low 5% (2/40) 65% (26/40)
ADH COX-2 high 10% (2/20) 55% (11/20) 0.481
COX-2 low 10% (2/20) 25% (5/20)
DCIS

COX-2 high 19% (13/70) 37% (26/70) 0.101
COX-2 low 7% (5/70) 37% (26/70)
piG oπd GQX-2 staining intensity with o score > 2 b considered positive.
P-valua were determined using Pearson ChNjuw e test.
[00532] In our analysis of DCIS, we demonstrated that proliferation was an obligate qualifier for pi 6 and COX-2 in determining which lesions have worse prognosis. In ADH, we observe only 1 case of 20 that exhibits coupled high Ki67 and high pi 6 staining (Table 5). There were no examples of high
Ki67/high COX-2 staining in ADH lesions. However, it remains to be determined if elevated levels of coincident overexpression of pl6 and COX-2 (2.5% in isolated normal lobules and 10% of ADH cases) may facilitate genomic instability and provide a selection pressure for clonal outgrowth. If these cells manifest the same tumorigenic proclivity as those that overexpress COX-2 and pi 6 in DCIS, we would predict that women from which these types of biopsies are obtained would exhibit subsequent disease.

[00533] As discussed above, the recently defined 1300-gene "Intrinsic/UNC" gene set, derived from
Agilent Human oligonucleotide platform data was cross-referenced to Affymetrix U133A to derive a intrinsic set for these studies. A subset of 1090 genes from the intrinsic/UNC genes represented on the Ul 33A platform were additionally filtered for top 20% of variability within the 130 tumor set. This analysis resulted in 589 unique genes that are intrinsically variable and available for this analysis.
Hierarchical clustering utilizing this set of 589 genes is shown in Figure 14. The genes listed in Figure 14 are differentially expressed in vHMECs, and allow one to distinguish HMEC (e.g., normal, or non- pre-cancerous HMEC) from vHMEC.
Example 3: Extracellular signaling and intracellular Ras activation cooperate to modulate endothelial- to-mesenchymal transition (EMT) and de novo methylation in human mammary epithelial cells
[00534] Over fifty percent of human breast carcinomas express elevated levels of normal Ha-Ras 3, and expression of oncogenic Ras is one of the components required for transformation of HMEC 2. As described in Example 1, a subpopulation of HMEC that display tumorigenic phenotypes was isolated from disease-free women; these "variant HMEC" appear to have engaged the process of malignant transformation. Stable expression of constitutively active Ha-Ras Vl 2 into these cells led to their
immortalization. These immortalized variant HMEC (vHMEC) are a valuable model of pre-malignant mammary epithelia to study the effects of stromal components on mammary tumor progression.

[00535] In order to examine the effect of oncogenic stress on the behavior of vHMECs, vHMECs were transduced with a retroviral construct encoding constitutively active Ha-Ras V12. Unlike normal cells, vHMEC expressing oncogenic ras failed to undergo a proliferative arrest. Since the microenvironment can modulate characteristics of epithelial cells, the possibility that extracellular signaling might
cooperate with intracellular Ras activation in altering the phenotypes of vHMEC was tested. To mimic secretory aspects of the extracellular environment, both vHMEC carrying control vector and vHMEC expressing Ha-Ras V12 were exposed at agonesence to media containing 0.5% serum. It was found that extracellular stimulation resulting from the presence of 0.5% serum was sufficient to cause
immortalization of vHMEC expressing Ha-Ras but not control vHMEC.
[00536] It was observed that HMEC-Ras cells undergo a morphological change, and acquire
mesenchymal features, when co-cultured with carcinoma-associated fibroblasts, as well as with certain BRCAl mutant fibroblasts. In contrast, this morphological change was not observed when HMEC-Ras are co-cultured with normal fibroblasts. Since HMEC-Ras cells respond differentially to normal and cancer stroma, they can be used as a reporter cell line for the sensing of stromal signals.
vHMEC are resistant to Ha-ras-induced proliferative arrest and display chromosomal
abnormalities.
[00537] To test the effect of oncogenic stress on primary HMEC and vHMEC exhibiting pi 6 promoter hypermethylation, cells were retrovirally transduced with constitutively active Ha-rasV12. Expression of Ha-rasV12 was confirmed by immunoblot analysis (Fig. 15A). Despite oncogenic ras expression, vHMEC failed to undergo a proliferative arrest as seen normal HMEC (Fig. 15B), and previously
shown in normal fibroblasts. Instead, they continued to grow, and did so until entering agonescence, a period of heightened growth and apoptosis.
[00538] In order to determine whether the resistance to ras-induced proliferative arrest was associated with alterations in genomic integrity, a chromosomal analysis of vHMEC expressing Ha-rasV12 or the control vector was performed. The results indicate that upon continued propagation, vHMEC-ras cells became increasingly genomically unstable as evidenced by the accumulation of a number of
chromosomal abnormalities, including structural abnormalities, telomeric associations and alterations in ploidy (Fig. 15C). These chromosomal abnormalities do not appear to be due to centrosome
dysfunction as no differences in centrosome number were detected between the cell populations.
[00539] Figures 15A-C. vHMEC are resistant to Ha-ras-induced proliferative arrest and display
chromosomal abnormalities. A. Immunoblot analysis demonstrating Ha-rasV12 expression in HMEC and vHMEC following retroviral transduction with pLXSP3-Ha-rasV12 (r) or the control pLXSP3 vector (v). Constructs were expressed in HMEC and vHMEC derived from five different individuals. A representative blot is shown along with actin as a loading control. B. Cell cycle analysis and
corresponding growth curves of HMEC and vHMEC expressing Ha-rasV12 or control vector
demonstrating that the number of cells in S-phase dropped from 33.8% to 8.8% following Ha-rasV12 expression in HMEC, but remained the same in vHMEC. HMEC underwent a proliferative arrest in response to oncogenic ras, while vHMEC continued to proliferate. C. Chromosomal analysis of
vHMEC-vector and vHMEC-ras cells. Control vHMEC (vector) and vHMEC expressing oncogenic
Ha-RasV12 (ras) were harvested at different passages, as indicated, and processed for metaphase
analysis. Standard G-banding karyotypic analysis was performed on at least fifty metaphase spreads for each cell population. The number of abnormalities observed are presented as percentages. "Total" refers to all structural abnormalities and telomeric associations, not including numerical abnormalities.
"Structural" refers to all deletions, duplications, rings, marker chromosomes, chromatid exchanges and translocations. "TAS" refers to telomeric associations. "Aneuploidy" refers to additions or deletions of whole chromosomes.
Combined serum-induced extracellular signaling and intracellular ras activation leads to
immortalization of vHMEC and upregulation of telomerase activity.
[005401 Since the microenvironment can modulate the characteristics of epithelial cells, we tested the possibility that extracellular signaling might cooperate with intracellular ras activation in altering the behavior of vHMEC. Studies have shown that the gene expression pattern of cultured primary
fibroblasts in response to serum exposure resembles that of a wounding response, and that this wound- response signature is strongly predictive of metastasis and progression for a variety of carcinomas.
Chang et al. (2004) PLoS Biol. 2:E7. Studies were initiated by exposing both vHMEC carrying control vector (vHMEC-vector) and vHMEC expressing Ha-rasV12 (vHMEC-ras) at agonesence to media containing 0.5% or 10% serum. It was found that extracellular stimulation resulting from the presence of either 0.5% serum (vHMEC-rasO.5) or 10% serum (vHMEC-raslO) was sufficient to cause
immortalization of vHMEC-ras but not control vHMEC (Fig. 16A, left graph).
[00541] To address whether constitutive extracellular stimulation resulting from the exposure to serum is required for the continued proliferation of vHMEC-rasO.5 and vHMEC-raslO, serum stimulation was withdrawn by placing these cells into mammary epithelial growth media (MEGM) without serum. It was found that both cell populations were capable of continued proliferation under these conditions, indicating that once immortalization is initiated by extracellular serum stimulation, the proliferation is independent of continued serum stimulation (Fig. 16A, middle and right graphs). Consistent with this, once immortalized, vHMEC expressing Ha-rasV12 displayed an increase in telomerase activity (Fig.
16B).
[00542] Figures 16A and 16B. Serum-induced extracellular signaling and intracellular ras activation leads to immortalization of vHMEC and increased telomerase activity. A. Growth curves of vHMEC expressing Ha-rasV 12 or control vector in the absence or presence of 0.5% or 10% serum. Arrow
indicates time at which serum was added (day 150). vHMEC cultured in the presence of both 0.5%
(vHMEC-rasO.5) and 10% (vHMEC-raslO) serum resumed proliferation and began being passaged again after 93 and 129 days, respectively (left graph). Both vHMEC-rasO.5 and vHMEC-raslO
continued to proliferate in the absence of serum (vHMEC-ras0.5->0; middle graph) and vHMEC-raslO- >0; right graph) once they were immortalized B. Telomerase activity assay. Telomerase activity was measured using the Quantitative Telomerase Detection Kit from Allied Biotech and is represented as the amount of telomerase activity in 1 μg of Iy sate compared to the TDA standard provided in the kit. Each sample was analyzed in triplicate. A no template control, heat inactivated sample, and cell
lysates from telomerase positive (MDA MB231) and telomerase negative (U2OS) cells were included with each experiment.
Extracellular signaling and intracellular ras activation cooperate to induce EMT.
[00543] Although vHMEC expressing oncogenic ras upregulated telomerase activity and became
immortalized in the presence of both 0.5% and 10% serum, the cells grown in 10% serum underwent a distinguishing change in morphology that was not observed in the presence of 0.5% serum (Fig. 17A, first panel). In the presence of 10% serum, the cells assumed a mesenchymal appearance suggestive of an epithelial to mesenchymal transition (EMT). This mesenchymal phenotype did not require
constitutive extracellular serum stimulation, as it was maintained upon serum withdrawal (Fig. 17A,
second panel). The epithelial phenotype of ras-expressing vHMEC grown in 0.5% serum (vHMEC- rasθ.5), and the mesenchymal phenotype of the same cells grown in 10% serum (vHMEC-raslO), were manifested both on plastic (2D) and in matrigel (3D). The epithelial vHMEC-rasO.5 formed
mammospheres, while the mesenchymal vHMEC-raslO retained their spindle morphology when
cultured alone in matrigel (Fig 17A, third panel). In addition, when the epithelial vHMEC-rasO.5 were co-cultured in 3D with normal human mammary fibroblasts derived from reduction mammoplasties, they were capable of forming ductal structures reminiscent of breast ducts in vivo. In contrast, the mesenchymal vHMEC-raslO retained their spindle morphology under the same co-culture conditions
(Fig. 17A, fourth panel).
EMT occurs de nόvo and is accompanied by molecular alterations and epigenetic modifications at the E-cadherin locus.
[00544J EMT is characterized by a downregulation of cellular adhesion molecules, and an upregulation of mesenchymal markers. Since E-cadherin is a critical mediator of cell-cell contacts, loss of its
expression is a characteristic feature of EMT. In addition, studies have shown that cell lines in which E-cadherin is irreversibly suppressed as a result of promoter methylation appear mesenchymal.
Lombaerts et al. (2006) Br. J. Cancer 94:661. Since the mesenchymal appearance of vHMEC-raslO appears to be irreversible (as it is maintained in the absence of extracellular serum stimulation), the hypothesis that epigenetic alterations may be involved in downregulating the expression of epithelial markers in these cells was tested.
[00545] Epigenetic modifications in the promoter region of E-cadherin were tested using both direct sequencing and methylation-specifϊc PCR. MCF7 and MDA-MB-231 cells were used as negative and positive controls for methylation of E-cadherin, respectively. Consistent with the morphological
appearance of the cells, methylation of the E-cadherin promoter was observed in the mesenchymal vHMEC-raslO, but not in the epithelial vHMEC-rasO.5 cells (Fig. 17B, lanes 1-4). This methylation pattern was also maintained after the cells were switched to no (0.5->0) or low (10->0.5) serum growth conditions (Fig. 17B, lanes 5-8), consistent with the maintenance of their morphology under those
conditions. Interestingly, the E-cadherin promoter was unmethylated in early passage vHMEC-raslO despite the fact that these cells appeared mesenchymal (Fig. 17B, lanes 11-14). This suggests that the emergence of vHMEC-ras exhibiting mesenchymal characteristics is unlikely due to the selection of a rare pre-existing population of vHMEC. Rather, the acquisition of mesenchymal features is likely to be the consequence of an active molecular process within vHMEC-raslO.
[00546] The protein 14-3-3σ is another mammary epithelial-specific marker that is often downregulated in breast cancer and methylated in fibroblasts, but unmethylated and expressed and in epithelial cells.
Moreira et al. (2005) MoI. Cell. Proteomics 4:555; and Sato et al. (2006) Cancer Lett. 236:105.
Consistent with the fact that all the cells are of epithelial origin, the promoter region of this gene
remained unmethylated as detected by methylation-specific PCR (Fig. 17B). hi addition, since E- cadherin is not methylated in human mammary fibroblasts (Fig. 17D), vHMEC-raslO cells that have acquired a mesenchymal phenotype can be distinguished from fibroblasts on the basis of their E- cadherin methylation. Thus, together the data suggest that the mesenchymal appearing vHMEC-raslO originated from mammary epithelial cells, not contaminating mammary fibroblasts.
[00547] To directly test the hypothesis that EMT is the result of an active process within vHMEC-raslO, two independent clones of vHMEC-rasO.5 (clonel and clone2) were isolated, and the clones were
exposed to media containing 10% serum. Both clones initially appeared epithelial in morphology (Fig. 17C) and expressed E-cadherin (Fig. 17D), as did all the vHMEC exhibiting an epithelial morphology, namely the parental vHMEC, vHMEC-vector, vHEMC-ras and vHMEC-rasO.5 from which the clones were isolated (Fig. 17D). However, after continued exposure to media containing 10% serum, both clones gradually acquired a mesenchymal morphology, their E-cadherin promoter became methylated
(Fig. 17C), and E-cadherin expression was lost (Fig. 17D). Coincident with the loss of E-cadherin
expression, the acquisition of mesenchymal morphology was associated with upregulation of the
mesenchymal marker, N-cadherin as well as upregulation of fibronectin, demonstrating a functional consequence of the acquisition of a mesenchymal phenotype (Fig. 17D). In contrast, all vHMEC
exhibiting an epithelial morphology expressed E-cadherin, but only very low levels of N-cadherin and fibronectin (Fig. 17D). This demonstrates that the changes in cellular morphology and methylation observed in vHMEC-ras exposed to 10% serum are the result of an EMT and occur de novo.
[00548] Figures 17A-D. Extracellular signaling and intracellular ras activation cooperate to modulate cellular morphology and methylation. A. Photomicrographs of vHMEC-ras grown in 0.5% serum
(rasθ.5), top panel, or 10% serum (raslO), bottom panel, both in 2D and 3D. Photos of 2D cultures represent the cells grown in their original concentration of serum (0.5% and 10%), as well as after they were switched to no serum (0.5->0 and 10->0). Photos of 3D cultures represent the cells grown alone or in combination with normal fibroblasts derived from a reduction mammoplasty (+RMF). Photos were taken at 10x magnification after 7 days in culture. B. Methylation-specific PCR (MSP) analysis of E- cadherin and 14-3-3σ on PCR products from bisulfite-modified DNA isolated from vHMEC-ras cells grown in 0.5%, 10%, 0.5->0%, or 10->0.5% serum as well as early passage vHMEC-rasO.5 (E0.5) and two early passage vHMEC-raslO cells (ElO). Bisulfite-modified DNA from MCF7 and MDA-MB-231 cells was used as unmethylated and methylated control templates, respectively for E-cadherin, while bisulfite-modified DNA from MDA-MB-231 and MDA-MB-435 served as unmethylated and
methylated controls for 14-3-3σ. Also included is a water control (no template). Product sizes from methylated or unmethylated sequences of E-cadherin were 116bp and 97bp, respectively, while product sizes for the methylated and unmethylated sequences of 14-3 -3s were 107bp. Molecular weight markers are indicated on the left in base pairs. C. MSP analysis of E-cadherin and 14-3-3σ on two early (Cl-E and C2-E) and late (Cl-L and C2-L) passage clones isolated from vHMEC-rasO.5. Human mammary fibroblasts (HMF) were used as a positive control for methylation of 14-3-3σ. Photomicrographs of the early and late passage (P) clones analyzed for methylation are shown below the gel and depict the early epithelial and late mesenchymal morphology of the cells. Cells were photographed at 10x
magnification. D. Immunoblot analysis of molecular markers associated with EMT, including
fibronectin (Fn), N-cadherin (N-cad), and E-cadherin (E-cad) was performed on cell lysates prepared from parental vHMEC (par), vHMEC-vector (vec), vHMEC-ras (ras), vHMEC-rasO.5 (0.5), early and late passage vHMEC-raslO (1OE and 10L), early and late passage clone 1 (Cl-E and Cl-L), and early and late passage clone 2 (C2-E and C2-L). Actin is shown as a loading control.
TGFβ cooperates with oncogenic ras to induce EMT in immortalized vHMEC.
[00549] Having observed that extracellular signaling induced by 10% serum can cooperate with
intracellular ras activation to induce EMT in vHMEC, it was then asked whether appropriate growth factor stimulation could induce EMT in the immortalized vHMEC-rasO.5 cells which had maintained their epithelial morphology. TGFβ has been shown to play a critical role in the induction of EMT.
Thiery et al. (2003) Curr. Opinion Cell. Biol. 15:740; and Zavadil et al. (2005) Oncogene 24:5764.
vHMEC-rasO.5 cells were treated with TGFβ and the expression of molecular markers associated with EMT was assessed by immunofluorescence, flow cytometry, and immunoblot analysis. Within 48h of treatment, the cells began to undergo a morphological change, which became clearly manifested by
72h. This morphological change was associated with a diminution in cytokeratin expression and
disruption of both cell-cell and cell-matrix contacts, as evidenced by the loss of E-cadherin and βl- integrin expression, respectively (Fig. 18A). Coincident with the loss of epithelial marker expression was an upregulation in the expression of the mesenchymal markers, twist (Fig. 18B), N-cadherin, and fibronectin (Fig. 18C). Vimentin is another molecular marker often upregulated following EMT.
Although immunofluorescence staining indicated that it is endogenously expressed in vHMEC, its expression pattern following TGFβ treatment clearly reflects the reorganization of the epithelial cell morphology into a mesenchymal one (Fig. 18A).
[00550] Unlike the EMT observed in cells exposed to 10% serum, TGFβ-induced EMT is reversible.
Consistent with that, methylation of the E-cadherin promoter in these cells following TGFβ treatment was not observed; however, methylation of the E-cadherin promoter was observed in MDA-MB-231 cells, which were used as a positive control (Fig. 18D). As expected, the promoter of the epithelial marker 14-3-3σ remained unmethylated in all the epithelial cells, and methylated in the human
mammary fibroblasts, which were used as a positive control (Fig. 18D).
[00551] Figures 18A-D. TGFβ induces EMT in vHMEC-rasO.5 cells without modulating methylation of E-cadherin. A. Immunofluorescence analysis. Cells were treated with 2 ng/ml TGFβ for 72h, and immunostained for pancytokeratin, E-cadherin, βl-integrin, and vimentin. B. Flow cytometric analysis of twist expression before (green curve) and after (purple curve) treatment with 2 ng/ml TGFβ for 72h. C. Immunoblot analysis of the mesenchymal markers fϊbronectin (Fn) and N-cadherin (N-cad) was performed on cell lysates prepared from vHMEC-rasO.5 that were either untreated (-) or treated (+) with 2 ng/ml TGFβ for 72h. Cell lystates prepared from human mammary fibroblasts were used as a
positive control (C) and actin is shown as a loading control. D. MSP analysis of E-cadherin and 14-3- 3σ was conducted on the PCR products of bisulfite-treated DNA isolated from vHMEC-rasO.5
untreated (-TGF) or treated (+TGF) with 2 ng/ml TGFβ for 96h as described in Fig. 3B and C.
Bisulfϊte-modifϊed DNA from MCF7 and MDA-MB-231 cells was used as unmethylated and
methylated control templates, respectively for E-cadherin, while bisulfite-modified DNA from MDA- MB-231 and human mammary fibroblasts (HMF) served as unmethylated and methylated controls for 14-3-3s. Also included is a water control (no template).
TGFβ-induced EMT is associated with enhanced motility in vHMEC-rasO.5 cells.
[00552] To determine whether the morphological change in vHMEC-rasO.5 following TGFβ treatment was associated with increased motility, confluent cell monolayers were scratched with a pipet tip, and the ability of the cells to migrate into the denuded area was assessed using time-lapse microscopy. It was found that although vHMEC-rasO.5 cells were very motile, the mesenchymal phenotype induced by TGFβ treatment led to an increase in directed migration, which allowed these cells to fill in the denuded area faster than untreated cells.
[00553] A transwell invasion assay was used to examine the invasive behavior of vHMEC-control, non- immortalized vHMEC-ras, vHMEC-rasO.5, vHMEC-raslO in response to serum. It was found that regardless of the stimulus, vHMEC-raslO were significantly more invasive than all other vHMEC.
These data suggest that extracellular stimulation provided by either serum can initiate EMT in
immortalized vHMEC and that acquisition of this mesenchymal phenotype is associated with increased invasive ability.
Immortalized vHMEC expressing oncogenic ras are capable of anchorage- independent growth and can survive and proliferate in vivo.
[00554] Since the immortalized vHMEC expressing oncogenic ras exhibited phenotypic and functional changes associated with targeted DNA methylation that are typically observed during tumor
progression, it was asked if these cells had any tumorigenic potential. Anchorage-independent growth is the best in vitro correlate of tumorigenicity, therefore, it was first examined whether vHMEC
expressing oncogenic ras could grow in soft agar. As shown in Fig. 19, the parental, vector control, and non-immortalized vHMEC-ras cells failed to grow in soft agar. In contrast, the immortalized vHMEC- rasθ.5 and vHMEC-raslO as well as the two clones isolated from vHMEC-rasO.5 cells displayed some, albeit weak, capacity for anchorage-independent growth, suggesting that they may have some
tumorigenic potential.
[00555] Figure 19. vHMEC immortalized with Ha-ras are capable of anchorage independent growth. Soft agar colony assay. Parental vHMEC (par), vHMEC-vector (vec), vHMEC-ras (ras), vHMEC-rasO.5 (rasθ.5), vHMEC-raslO (raslO), clone 1 (Cl), and clone 2 (C2) were plated in 35 mm dishes at a concentration of 50 000 cells per dish, in triplicate. After 14 days, colonies were counted manually in eight different fields. The data are presented as the average of the sum of 8 different fields counted.
Example 4: Overexpression of TRF2 results in activin A-depeπdent induction of COX-2 in vitro and in vivo
MATERIALS AND METHODS
[00556] Tissue Samples: High (n=7) and low (n=8) grade + one unknown non-recurrent ductal
carcinoma in situ (DCIS) specimens were obtained with institutional review board approval from the surgical pathology laboratory at the University of California, San Francisco. Patients were identified through anonymous reference numbers in accordance with federal guidelines.
[00557] Telomere Content Determination: A 5 μm tissue section was stained with hematoxylin and eosin and cellular morphology was evaluated. This reference slide was used to guide microdissection of 6 x 25 μm sections. Microdissection was performed using a Leica AS-LMD microdissection
microscope on slides stained with methyl-green following standard procedures. DNA was purified from populations enriched for DCIS using proteinase K and chloroform/phenol. DNA was quantitated using Picogreen dye following the manufacturer's protocol (Invitrogen). Telomere content was
determined as described previously (Fordyce et al, 2005). Briefly, DNA was denatured and fixed to positively charged membrane using a vacuum apparatus and then hybridized to a labeled telomere- specific probe (TTAGGG)4 (IDT). The tagged probe was detected using an antibody conjugated to alkaline phosphatase and a chemiluminescent substrate, CDP-STAR (New England Biolabs). Blots were exposed to film, and the intensity of each spot was determined using Image Quant software
(Molecular Dynamics). Samples were analyzed in triplicate. Data is expressed as a percentage of placental DNA.
[00558] Tissue Preparation and Immunohistochemistry (including evaluation): Five-micron
sections were cut form paraffin-embedded tissue blocks adjacent to sections used for telomere content determination. Tissue sections were deparaffmized and rehydrated using standard protocols.
Microwave antigen retrieval was accomplished using 0.00 IM EDTA, pH=8 for COX-2, 0.01 M citrate for γH2AX and Antigen Unmasking Solution (Vector Laboratories) for TRF2. Antiserum against COX- 2 (1:200, Dako), γH2AX (1:150, Upstate) and TRF2 (1:20, Imgenex) was incubated on tissue sections for ~16 hrs at 4°C. Antigen-antibody complexes were labeled using the Vectastain Elite ABC
following standard protocols (Vector Laboratories, CA) and visualized using 2.5% 3-amino-9-ethyl- carbazole in 5OmM acetate buffer pH5, with 0.05% hydrogen peroxide. Sections were counterstained in Mayers hematoxylin mounted in Crystal Mount (BMM02, American Mastertech). Once dry, the
sections were permanently mounted with a glass coverslip using clearmount (MMCLEl, American
Mastertech). A blocking step (0.01% Triton X 1000 for 1 hr) was added to this protocol prior to
addition of the primary antibody for the TRF2 staining.
[00559J The degree of γH2AX, COX-2 or TRF2 staining intensity was evaluated in a blinded fashion.

For COX-2, staining intensity was examined by light microscopy and was scored as low to absent (1), moderate (2) or strong (3) in the majority of either DCIS or adjacent normal tissue. For the purpose of the study, COX-2 expression scored as 2 or 3 was considered high. TRF2 and γH2AX expression was evaluated by counting the number of positive nuclei in a minimum of 500 cells. The mean level of positive cells for either TRF2 (29%) or γH2AX (27%) was used to stratify the tissues into high and low groups.
[00560] Cell Culture: Human mammary epithelial cells (vHMEC) were isolated from reduction
mammoplasty (RM) of four individuals RM9, RM15, RM16 and RM18. HMEC undergo a spontaneous proliferation barrier between 8 and 12 population doublings. Variant human mammary epithelial cells (vHMEC) escape this growth barrier and have silenced pi 6 through promoter methylation. Cells were propagated in 2D cultures in modified MCBD 170 media (MEGM, Lonza) as previously described
(Romanov et al, 2001; Hammond et al 1984). All experiments were performed on exponentionally growing early passage vHMEC (between 13 to 20 population doublings); RM9, 15, 16 and 18 cease to expand in cell number at population doublings 45, 60, 50 and 53, respectively. Activin A (Sigma) and the p38 inhibitor, SB203580, (Sigma) were added to culture media for 48 and 24 hours (respectively) prior to harvest at the doses shown in figures 3 and 4. The same amount of solvent for each molecule was added to the culture media for controls.
[00561] Wound Closure Assay: Wound closure assays were performed as previously described
(Dumont et al, 2003 JBC). Cells were plated in duplicate wells of a 6-well plate at 2 x 105 each and allowed to proliferate until confluent. Confluent cell monolayers were wounded by manually scrapping the cells with a pipette tip and an ocular ruler was used to verify the widths of the resulting wounds.
Media was replaced and wound closure was monitored by microscopy.
[00562] Expression of TRF2: The TRF2 gene was excised from the pLPC construct using Hind III and

EcoRI and inserted into the pWPl lenti viral expression vector. The TRF2-pWP construct was
packaged in 293T cells for viral propagation. Lenti-viral supernatant was diluted 1:1 with MEGM
media containing polybrene (8μg/ml; Sigma) and added to vHMEC for 4 to 6 hrs. Infection efficiency was monitored using GFP expression, which was driven from the same promoter via an IRES sequence.

[00563] Quantitative PCR: Total RNA was isolated from cells and cDNA synthesized using standard methods. cDNA was subsequently used for quantitative real-time PCR using the standard curve
method. Primer-probe sets for COX-2 (Hs00153133), TRF2 (Hs00194619) and activin A
(HsOOl 70103) were obtained from ABI (location). The expression of GUSB (IDT), an external control, was used to normalize for variances in input cDNA.
[00564] Western Blotting, ELISA and Immunofluorescence: Cell pellets were lysed in T-PER buffer

(Pierce). Cell lysates were fractioned in gradient polyacrylamide gels (4-20%) and transferred to
Hybond-P (Amersham Biosciences) membranes using standard procedures. Antibodies against COX-2 (1:200, Cayman), phospho-p38, (1:200, Cell Signaling) were used according to manufacturers'
protocols. Activin A protein levels were measured using the Duo-Set Activin ELISA kit (R&D
Systems) following the manufacturer's directions. Parental vHMEC or cells over expresing vector or TRF2 were plated in 6-well dishes at 1 x 10s in duplicate. Media was replaced the following day and allowed to condition for 72 hours prior to analysis. Levels of activin A were determined in cells from all four donors. For immunocytochemistry, 5 x 104 cells were seeded directly onto glass cover slips and fixed in 4% paraformaldehye (PFA) for 15 minutes at room temperature and stored in 0.01% PFA at
40C. Cover slips were treated with anti-TRF2 antibody (1 :100, Imgenex) or anti-γH2AX (1 :1000,
Upstate) following the manufacturer's protocols. Nuclei were counterstained using Dapi (Molecular probes, location) and visualized using a LSM450 Zeiss confocal microscope. The mean fluorescent intensity of γH2AX signal (voxels) in each nucleus was determined with the Volocity 4.0.0 software package (Improvision) on Z-stacks.
[00565] Statistical Methods: ANOVA was used to test the relationship between gene expression or activin protein levels in the vHMEC treatment groups (parent, vector and TRF2 over-expressing cells). The relationship between telomere content and COX-2, γH2AX and TRF2 staining intensity was
examined using a T-test. Chi-Square test was used to evaluate the relationship between staining
intensity for TRF2 and COX-2 and γH2AX. The Jmp statistical package (SAS Institute) was used for all analyses.
RESULTS
[00566] Telomere Content is Inversely Associated with γH2AX, TRF2 and COX-2 Expression in

DCIS. Fifteen high and low grade non-recurrent DCIS lesions ductal carcinoma in situ (DCIS) lesions were microdissected and used for DNA purification. Telomere content, a proxy for telomere length, was measured in the nine lesions from which sufficient DNA was obtained. Telomere content ranged from 39 to 417% of the placental standard. Telomere content was not associated with patient age at surgery, ethnicity, menopausal status, DCIS grade or tumor size. To determine if the reduced telomere content measured in this cohort was associated with a DNA damage response, we evaluated the levels of γH2AX, a DNA damage marker, with immunohistochemistry on serial sections of the DCIS lesions.

As shown in Figure 20, telomere content was inversely associated with the proportion of γH2AX
positive nuclei in the DCIS lesion (T-test, p=0.001).
[00567] Exogenous expression of the telomere binding protein, TRF2, results in progressive telomere shortening. De Lange (2002) Oncogene 21:532; de Lange (2005) Genes Dev. 19:2100; Smogorzewska et al. (2000) MoI. Cell. Biol. 20:1659; and Oh et al. (2005) Am. J. Pathol. 166:73. It was determined if there was an association between telomere content and TRF2 in our DCIS cohort. The proportion of
TRF2 positive nuclei in DCIS lesions was evaluated in 14 of 15 cases. Telomere content was measured in 8 of these cases. As shown in Figure 20, TRF2 expression was higher in the in DCIS lesions with low telomere content than in lesions with high telomere content (T-test, p=0.001). TRF2 expression was associated with the proportion of cells in the DCIS lesion expressing γH2AX (X2, p=0.005).
[00568] The observation that increases in COX-2 expression coincides with telomere loss and genomic instability in primary variant human mammary epithelial cells (vHMEC) in vitro, suggested that there might be a relationship between loss of telomere homeostatsis and COX-2. It was postulated that the increase in γH2AX positive nuclei in DCIS lesions with reduced telomeres is indicative of loss of
telomere homeostasis. The levels of COX-2 expression were evaluated, using immunohistochemistry in the DCIS cohort. Strikingly, there was a significant relationship between telomere content and the degree of COX-2 staining in the DCIS lesion (T-test, p=0.004). The degree of COX-2 and γH2AX
expression were directly associated with each other (X2, p<0.0001). Likewise, there was a statistically significant relationship between TRF2 expression and COX-2 (X2, p=0.005). None of COX-2, γH2AX, and TRF2 were associated with any of the other parameters evaluated in this study. These data show that the reduced telomere content observed in the DCIS lesions is inversely associated with the
induction of a DNA damage response, and the expression of TRF2 and COX-2.
[00569] Figure 20: Telomere Content is Associated with COX-2 Expression. COX-2 and γH2AX
levels were evaluated using immunohistochemistry. For COX-2, lesions were scored as low to absent (1 ), moderate (2) or strong (3) in the majority of either DCIS or adjacent normal tissue. For the purpose of the study, COX-2 expression scored as 2 or 3 was considered high. The number of γH2AX positive nuclei were manually counted and expressed as a percentage of the total number of nuclei within a region of DCIS. The mean percentage of γH2AX positive nuclei (27%) was used to stratify lesions.
Telomere content, a proxy for telomere length was measured in DCIS following microdissection and is expressed as percentage of placental control. Box plots show the relationship between telomere content and either γH2AX (right) or COX-2 (left) when DCIS lesions are stratified into two groups (high or low staining intensity).
[00570] Exogenous Expression of TRF2 in vHMEC. To more directly access if changes in telomere length or structure can induce COX-2, an in vitro model system was used. The observation that TRF2 expression is associated with telomere content in this DCIS cohort is consistent with previous reports showing that exogenous expression of TRF2 results in telomere loss (de Lange supra; Smogorzewska et al. supra; Oh et al, 2005, supra). TRF2 is also an integral component of multiple protein complexes localized to the telomere and is important for the formation of the unique DNA loop at the extreme ends of the telomere (de Lange, supra). Exponentially growing early-passage (PD<15) variant human
mammary epithelial cells (vHMEC) purified from four donors were mock infected or infected with lenti virus containing vector alone (pWP) or vector plus the TRF2 gene. Infection efficiency was monitored using GFP expression driven by an IRES sequence. TRF2 mRNA (ANOVA, p=0.0002) and protein levels were significantly up regulated in vHMEC infected with TRF2 containing lenti virus when
compared to parent and vector controls. Over expression of proteins can result in altered localization. It was verified that TRF2 was confined to the nucleus using immunofluorescence. The rates of
proliferation and number of population doublings for parent, vector and TRF2 over expressing cells from all four donors were evaluated using growth curve analysis. Consistent with previous reports, cells expressing TRF2 underwent slightly fewer population doublings than vector and parental controls, but had similar rates of cell replication, particularly at early passages. Flow cytometry for BrDu and propidium iodide was used to evaluate the proportion of cells in each phase of the cell cycle in cells over expressing TRF2 and parent and vector controls. There was no change in the proportion of cells Ln any phase of the cell cycle in parental vHMEC compared to cells infected with vector alone or over expressing TRF2.
[00571] Previous reports have shown that over expression of TRF2 leads to a preferential enrichment of single strand breaks at the telomeres and increased telomere loss. It was postulated that over expression of TRF2 would result in accumulation of the DNA damage marker γH2AX in vitro. vHMEC over expressing either TRF2wt or vector and parental controls were grown on glass cover slips, fixed and treated with antiserum against γH2AX. The mean fluorescent intensity of γH2AX in vHMEC with or without TRF2wt was determined. As shown in Figure 21, there was a statistically significant increase in the mean number of γH2AX voxels in cells over expressing TRF2 (ANOVA, p<0.0001). Thus, exogenous expression of TRF2 up-regulates γH2AX in vHMEC and recapitulates the increase in
γH2AX observed in DCIS with reduced telomeres.
[00572] Figure 21 : γH2AX is Up Regulated in vHMEC Expressing TRF2. Levels of γH2AX were determined using immuofluorescence with an anti-γH2AX antibody (Upstate). ELevels of γH2AX
expression were determined using Z-stacks obtained on a confocal microscope. The mean intensity of γH2AX voxels/nucleus were determined using Volocity software (company) in vHMEC from two
donors.
[00573] COX-2 is Up Regulated in vHMEC expressing TRF2 in a Phospho-p38 Dependent
Manner. Since COX-2 levels were associated with both telomere content and the levels of γH2AX expression in the DCIS cohort, the level of COX-2 in vHMEC over expressing TRF2 was evaluated.
COX-2 mRNA and protein levels were evaluated using Q-PCR and immunoblotting, respectively.
COX-2 mRNA levels were increased approximately two fold in vHMEC over expressing TRF2 (ANOVA, p=0.002, Figure 22a). Likewise, COX-2 protein levels were increased in vHMEC over expressing TRF2 when compared to parental and vector controls. Next, it was determined if the
increase in COX-2 observed in TRF2 over expressing vHMEC was able to induce a phenotype
associated with COX-2 expression. Previous reports have shown that COX-2 expression enhances cell motility. A cell wounding assay was used to evaluate the motility of vHMEC over expressing TRF2 compared to vector and parental controls from two donors. Confluent monolayers in duplicate wells were manually wounded with a sterile pipette tip. After ensuring that the width of the wounds was similar, cells were monitored with microscopy for 12 hours. Cells over expressing TRF2 were able to fill the wound in 8 hours, while parent and vector controls required approximately 12 hours (Figure
22c), demonstrating a modest, but consistent increase in cell motility.
[00574] It has previously been shown that the increase of COX-2 observed in late-passage vHMEC is dependent on the MAPK, p38. Here it is shown that the activated phospho-p38 is up-regulated in early passage vHMEC cells over expressing TRF2 (Figure 22b). To determine if phospho-p38 is necessary for the induction of COX-2 in response to TRF2, early passage parent, vector, and TRF2 over
expressing vHMEC were treated with the phospho-p38 inhibitor SB203580. As shown in Figures 22A and 22B, inhibition of phospho-p38 lead to a marked decrease in COX-2 mRNA (ANOVA, p=0.002) and protein levels in cells expressing TRF2. This finding demonstrates that expression of TRF2 is able to induce COX-2 in a phospho-p38 dependent manner in vHMEC.
[00575] Figures 22A-C: COX-2 is Induced in vHMEC Over Expressing TRF2 and is Dependent on p38. A, Box plot showing the levels of COX-2 mRNA as measured with Q-PCR in untreated parental vHMEC or vHMEC over expressing either vector (pWP) or TRF2, or treated with the phospho-p38 inhibitor SB203580 for 24 hrs at the indicated doses. Inset is p-value comparing either parent, vector and TRF2 cells or cells treated with SB203580 to untreated controls. B, Representative immunoblot showing COX-2, phospho-p38 and actin (loading control) for the conditions described in A. C,
Representative example of wounding assay showing parent vHMEC and vHMEC over expressing
vector or TRF2 at 0, 4 and 8 hrs following wounding.
[00576] Activin A Induces COX-2 Up-regulation in vHMEC. A variety of signal transduction
pathways can lead to the activation (and phosphorylation) of p38. To further elucidate the mechanisms by which TRP2 induces COX-2 in vHMEC, microarrays were used to screen for modulators of p38 activity. Activin A, a member of the TGF-β superfamily, was up regulated in vHMEC over expressing TRP2 when compared to parent and vector controls. Previous reports have demonstrated that binding of activin A to its receptor can lead to the phosphorylation and activation of p38. Activin A is a
homodimer of the activin βA subunits. The activin βA monomer can also form a heterodimer with inhibin α, to produce the activin A antagonist, inhibin A. Microarray analysis demonstrated that
inhibin α was not differentially expressed in vHMEC over expressing TRP2 when compared to
controls. The results of the microarray analysis were validated using Q-PCR. As shown in Figure 23a, activin βA was significantly up regulated in cells over expressing TRP2 (ANOVA, p=0.03).

[00577] Activin A protein levels were measured using ELISA (Figure 23b). Mean levels of activin A protein in condition media from parental vHMEC or vector controls was 1.3 ng/ml and 1.7 ng/ml, respectively. In contrast, the mean level of activin A in conditioned media from vHMEC expressing
TRF2 was 4.4 ng/ml, an approximately 5-fold increase (pO.0001, ANOVA). These data demonstrate that activin A is up regulated in vHMEC over expressing TRF2.
[00578] To determine if activin A was sufficient to induce COX-2 expression we treated vHMEC from two donors in duplicate experiments with exogenous activin A. As shown in Figure 23c, exogenous activin A induced an approximately two-fold increase in COX-2 mRNA (ANOVA, p=0.001) and
protein. Treatment with exogenous activin A also caused an increase in the levels of phospho-p38
(Figure 23d). Since activin A is a secreted protein, it was reasoned that conditioned media from cells over expressing TRF2 should be able to induce COX-2 expression in vHMEC. Conditioned media from parent, vector and vHMEC over expressing TRF2 was collected from two donors and used to treat uninfected vHMEC obtained from three donors. COX-2 mRNA and protein were increased
approximately two fold when vHMEC were treated with conditioned media from cells over expressing TRF2. Likewise, phospho-p38 levels were increased in vHMEC treated with conditioned media from cells over expressing TRF2. Taken together these data suggest that the induction of COX-2 expression observed in early-passage vHMEC over expressing TRF2 is driven by activin A.
[00579] Figures 23 A-D: Activin A is Up Regulated in vHMEC and Induces COX-2. A. Box plot
showing the levels of activin A mRNA measured using Q-PCR in parental vHMEC, or vHMEC over expressing vector (pWP) or TRF2 from 4 donors, p-value was calculated using ANOVA and is shown in the inset. B, Box plot showing the levels of activin A protein measured using ELISA in parental vHMEC or vHMEC over expressing vector (pWP) or TRF2 from 4 donors. Inset shows p-value
calculated using ANOVA. C, vHMEC from 2 donors were treated with exogenous activin A for 48 hrs at the indicated doses. Box plot shows the levels of COX-2 mRNA as measured by Q-PCR. Inset shows p-values for untreated cells compared to the two highest doses of activin A. The experiment was performed in quadruplicate. D, Representative immunoblots showing the levels of COX-2, phospho- p38 and actin (loading control) for cells and treatments described in C.
Example 5: Cell surface markers that identify cancer cell precursors
METHOD & MATERIALS
Screening of markers
[00580] HMEC were trypsinized, washed, spun down, and counted. Cells were incubated in MEGM +

2% FBS for 2 hours to regenerate cell surface markers. Cells were spun down, and incubated with anti- CD73-phycoerythrin (anti-CD73-PE; PE-conjugated antibody to CD73) (12μL per 1x106 cells) for 30 min. Then cells were spun down and incubated with anti-CD90-allophycocyanin (anti-CD90-APC;
APC-conjugated antibody to CD90) (1 μL per 1x106 cells). Following staining, cells were washed 3X with PBS and subjected by flow cytometry. Flow cytometry profiles were analyzed by Flowjo
software.

Flow sorting of cells and culturing of cells
[00581] Human mammary tissue were digested as described (Romanov et al. (2001 ) Nature 409:633-7), and further digested to single cells as described (Liu et al. (2004) Proc Natl Acad Sci USA 101 :4158- 63). Cells were counted and incubated in MEGM + 2% FBS for 2 hours. Cells were spun down, and incubated with CD73-PE (12μL per IxIO6 cells) for 30 min. Then cells were spun down and incubated with CD90-APC (IuL per IxIO6 cells) and anti-epithelial-specific antigen-fluorescein isothiocyanate
(anti-ESA-FITC; FITC-conjugated antibody to ESA) (2μL per IxIO6 cells). Following staining, cells were washed 3X with PBS and subjected to flow cytometry. Cells were sorted by BD FAC Aria. Once cells were isolated, they were plated in a 12-well plate with 1 mL of MEGM. Cells were passaged once reached ~70% confluency, counted and population doublings (PD) was determined.
Methylation-specifϊc PCR (MSP)
[00582] Cells were sorted and mixed with O.5xlO5 HeLa carrier cells. Genomic DNA was prepared, bisulfate treated, and subjected to methylation specific PCR.
Immunoblot
[00583] Cells were lysed by 1% SDS and 1 % b-mecaptoethanol, and cell lysate was subjected to
immunoblot analysis as described (Liu et al. (2003) Oncogene 22:9243-53). Anti-Bmi-1 antibody was purchased from Upstate Cell Technology.
RESULTS
[00584] Based on microarray experiments, potential candidate markers were identified that are
important for distinguishing cancer precursor cells from bulk epithelial cells. 19 cell surface markers were screened via flow cytometry. It was found that the markers CD73, CD138, CD90, CD133, and
Notch receptor-3 clearly distinguished cultured vHMEC from HMEC. Expression of CD73, CD 138, and Notch Receptor-3 in the vHMEC was increased by —12-fold, ~5-fold, and ~6-fold respectively, as compared to HMEC (median vHMEC vs. HMEC; Fig. 24A), whereas expression of CD90 and CDl 33 in the vHMEC was decreased by ~7-fold, and ~3-fold respective relative to HMEC.
[00585] Immunocytochemical analysis of vHMEC and HMEC with anti-CD73 and anti-CD90
antibodies also showed results consistent with FACs analysis (Fig. 24B). Detectable levels of CD73 were seen in vHMEC but not in HMEC, and the localization of CD73 was predominantly on the cell surface. Likewise, only cell surface expression of CD90 was detected in HMEC, and not in vHMEC
(Fig. 24B). When anti-CD73 and anti-CD90 antibodies were combined, the vHMEC population was easily distinguishable from the HMEC population; vHMEC were CD73+ (Figure 24C).
[00586] Figures 24A-C: (A) Histogram of flow cytometric analysis of CD73, CD90, CDl 38, Notch receptor-3, and pi 6 expression on vHMEC and HMEC is shown. Cultured vHMEC and HMEC from matched mammary reduction individual were trypsinized to single cells, incubated with anti-CD73, - CD90-APC, -CD138-FITC, Notch receptor-3-FITC, or-pl6-PE antibodies, and analyzed by flow
cytometry. (B) Immunocytochemistry of vHMEC and HMEC with anti-CD73 and anti-CD90
antibodies. Cells were grown on coverslips, fixed, and stained with anti-CD73 and -CD90 antibodies followed by anti-mouse-FITC secondary antibodies, and fluorescent signal was visualized by confocal microscopy. Cell nuclei were stained with Hoechst dye; and CD73 and CD90 expression was detected using antibodies. (C) Cell distribution of vHMEC and HMEC co-stained with anti-CD73 and -CD90 antibodies. Cultured vHMEC and HMEC from matched mammary reduction individual were
trypsinized to single cells, incubated with anti-CD73-PE and -CD90-APC antibodies, and analyzed by flow cytometry.
[00587] Since the markers CD73 and CD90 distinguish the variant population in cultured cells, the markers were applied to mammary tissues that have not subjected to culturing conditions. Mammary tissue from five individuals were processed as described in (1) and further digested to single cells.
Cells were incubated with antibodies to ESA (to identify epithelial cells), CD73, and CD90; and sorted by flow cytometry. Cells were gated as indicated and isolated.
[00588] To determine whether the isolated cells contained the distinguishing characteristic of vHMEC, methylation of the pi 6 promoter, methylation-specific PCR was performed on the various gated cells. 10,000 cells were isolated from each CD73CD90 fraction and diluted the cells into 5x105 carrier cells, HeLa cells. Genomic DNA was prepared, bisulfate converted, and subjected to methylation specific
PCR. Methylation of the pl6 promoter was detected in cell fractions with CD73+ epithelial cells, but not in bulk epithelial cell populations.
[00589] To determine if gated populations proliferated in a manner similar to that of vHMEC or
HMEC, different sorted fractions were subjected to culturing. CD73+ cells grew for an extended time under conditions where the bulk population encountered a proliferative arrest. This evaluation was conducted with cells from 4 individuals.

[00590] While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and
equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.