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1. WO2011008746 - SERUM MARKERS ASSOCIATED WITH EARLY AND OTHER STAGES OF BREAST CANCER

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[ EN ]

What is Claimed:

I. An isolated breast cancer complex selected from the group consisting of Stage 0 Complexes, Stage I Complexes, Stage II Complexes, Stage III Complexes and Stage IV Complexes.

s 2. The isolated breast cancer complex of claim 1, comprising a cancer peptide

fragment, wherein the cancer peptide fragment comprises a cancer peptide motif having an amino acid sequence selected from SEQ ID NOs: 1-122.

3. The isolated breast cancer complex of claim 2, wherein the cancer peptide

fragment is the cancer peptide motif.

o 4. The isolated breast cancer complex of claim 2, wherein the cancer peptide motif has an amino acid sequence of SEQ ID NO: 44 or 46.

5. An isolated polypeptide comprising a cancer peptide motif having a n amino acid sequence selected from SEQ ID NOs: 1-122.

6. The isolated polypeptide of claim 5, wherein the cancer peptide motif has an 5 amino acid sequence of SEQ ID NO: 44 or 46.

7. A method of producing antibodies, comprising (a) administering an effective amount of a polypeptide to an immunologically competent host, wherein the polypeptide comprises a cancer peptide motif having an amino acid sequence selected from SEQ ID NOs: 1-122, and (b) recovering antibodies from the host. 0 8. The method of claim 7, wherein the cancer peptide motif has an amino acid

sequence of SEQ ID NO: 44 or 46.

9. An isolated antibody that binds specifically to a cancer polypeptide comprising a cancer peptide motif having an amino acid sequence selected from SEQ ID NOs:

1-122.

5 10. An isolated antibody that binds specifically to a cancer peptide motif having an amino acid sequence of SEQ ID NO: 44 or 46.

II. A method of inhibiting the growth of a cancer cell, comprising applying an

antibody to the cell, wherein the antibody binds specifically to a cancer polypeptide comprising a cancer peptide motif having an amino acid sequence 0 selected from SEQ ID NOs: 1-122, whereby the growth of the cancer cell is

inhibited.

12. The method of Claim 11, wherein the cancer cell is a breast cancer cell or a

glioma cell.

13. The method of claim 11, wherein the antibody binds specifically a cancer 5 polypeptide having an amino acid sequence of SEQ ID NO: 44 or 127.

14. An array, comprising a plurality of antibodies, wherein each antibody binds specifically to a cancer polypeptide comprising a cancer peptide motif having an amino acid sequence selected from SEQ ID NOs: 1-122.

15. The array of claim 14, wherein at least one antibody binds specifically to a cancer 5 polypeptide having an amino acid sequence selected from SEQ ID NOs: 44 and

123-127.

16. The array of claim 15, wherein the cancer polypeptide has an amino acid

sequence selected from SEQ ID NOs: 44 and 127.

17. An array, comprising a plurality of antibodies, wherein each antibody binds o specifically a cancer polypeptide comprising a cancer peptide motif, wherein each cancer peptide motif is present in a breast cancer complex selected from the group consisting of Stage 0 Complexes, Stage I Complexes, Stage II Complexes, Stage III Complexes and Stage IV Complexes.

18. A method of detecting a low copy number polypeptide in a biological sample, s comprising

(a) obtaining the biological sample comprising a plurality of serum albumin complexes;

(b) separating the serum albumin complexes on a membrane by a two- dimensional membrane electrophoresis;

o (c) digesting at least one separated serum albumin complex on the membrane with a protease; and

(d) detecting the polypeptide in the digested complex.

19. The method of claim 18, wherein the polypeptide comprises a cancer peptide motif having an amino acid sequence selected from SEQ ID NOs: 1-122.

5 20. The method of claim 18, further comprising determining the amino acid sequence of the detected polypeptide.

21. A kit for detecting a low copy number polypeptide in a biological sample,

comprising a membrane suitable for two-dimensional membrane electrophoresis, a protease, and instructions for using the kit in the method of claim 18. 0 22. The kit of claim 21, further comprising an agent that detects a disease-specific marker.

23. A method of identifying a disease-specific marker, comprising:

(a) obtaining a biological sample comprising a plurality of serum albumin complexes from a reference subject;

5 (b) obtaining a biological sample comprising a plurality of serum albumin complexes from a diseased subject;

(c) separating the serum albumin complexes in step (a) by a two-dimensional membrane electrophoresis to generate a reference separation profile;

(d) separating the serum albumin complexes in step (b) by a two-dimensional membrane electrophoresis to generate a disease separation profile ;

5 (5) comparing the reference separation profile with the disease separation profile to determine whether there is a difference in the number, distribution or both number and distribution of the separated serum albumin complexes between the reference separation profile and the disease separation profile, wherein the difference represents a disease-specific marker.

io 24. A method of diagnosing a disease in a test subject, comprising

(a) obtaining a biological sample comprising a plurality of serum albumin complexes from the test subject;

(b) separating the serum albumin complexes by a two-dimensional membrane electrophoresis to generate a test separation profile;

I5 (c) providing a reference separation profile representing the disease; and

(d) comparing the test separation profile with the reference separation profile to determine whether there is a substantial similarity between the test separation profile and the reference separation profile, wherein the substantial similarity indicates that the test subject has the disease.

20 25. A method of staging cancer in a test subject, comprising

(a) obtaining a biological sample comprising a plurality of serum albumin complexes from the test subject;

(b) separating the serum albumin complexes by a two-dimensional membrane electrophoresis to generate a test separation profile;

5 (c) providing a plurality of stage -specific reference separation profiles

representing the cancer; and

(d) comparing the test separation profile with the stage-specific reference separation profiles to determine whether there is a substantial similarity between the test separation profile and one of the stage-specific reference separation 30 profiles, wherein the substantial similarity indicates that the test subject has the specific stage of cancer represented by the one of the stage-specific reference separation profiles.

26. The method of claim 18, 23, 24 or 25, wherein at least one of the serum albumin complexes is a breast cancer complex selected from the group consisting of Stage 35 0 Complexes, Stage I Complexes, Stage II Complexes, Stage III Complexes and

Stage IV Complexes.

27. The method of claim 26, wherein the breast cancer complex comprises a cancer polypeptide comprising a cancer peptide motif having an amino acid sequence selected from SEQ ID NOs: 1-122.

28. The method of claim 23 or 24, wherein the disease is selected from the group consisting of cancer, a neurological disease, an autoimmune disease, and a heart disease.

29. The method of claim 25 or 28, wherein the cancer is selected from the group

consisting of adenocarcinoma of rectum, bladder cancer, breast cancer, colon cancer, endometrial carcinoma, esophagus squamous cell carcinoma, glioma, hepatocellular carcinoma, infiltrating ductal breast carcinoma, larynx cancer, lung squamous cell carcinoma, melanoma, mucinous cystadenocarcinoma of ovary, pancreatic cancer, prostate cancer, renal cell carcinoma, small bowel malignant stromal tumor, and stomach adenocarcinoma.

30. The method of claim 28, wherein the neurological disease is selected from the group consisting of Alzheimer's disease, multiple sclerosis, Parkinson's disease, and migraine headaches.

31. The method of claim 23, 24 or 25, wherein the comparing step is performed on a computer.

32. The method of claim 24 or 25, further comprising treating the test subject having the disease or the specific stage of cancer with a therapy suitable for treating the disease or the specific stage of cancer.

33. The method of claim 32, wherein the therapy comprises administering to the test subject a biomolecule having high affinity for a cancer polypeptide comprising a cancer peptide motif having an amino acid sequence selected from SEQ ID NOs: 1- 122.

34. The method of claim 33, wherein the biomolecule is an antibody.

35. The method of claim 29, wherein the cancer is breast cancer.

36. The method of claim 25, wherein the stage-specific reference separation profiles comprise first, second, third and fourth stage-specific reference separation profiles representing stages I, II, III and IV of breast cancer, respectively.

37. A method for detecting an antigen in a biological sample, comprising

(a) incubating the antibody of claim 9 or 10 with the biological sample under conditions to permit formation of an antigen-antibody complex,

(b) detecting the presence of the antigen-antibody complex, wherein the presence of the antigen-antibody complex indicates the presence of the antigen in the biological sample.

38. The method of claim 37, further comprising

(a) separating the antigen-antibody complex on a membrane by electrophoresis to generate an antigen-antibody complex spot on the membrane, and

(b) quantifying the antigen in the antigen-antibody complex spot. s 39. The method of claim 37, wherein the antigen is a cancer peptide motif.

40. The method of claim 37, wherein the electrophoresis is one-dimensional or two- dimensional membrane electrophoresis.

41. A method for detecting an antigen in a biological sample, comprising

(a) incubating the biological sample with an antibody to permit formation of o an antigen-antibody complex,

(b) separating the antigen-antibody complex on a membrane by electrophoresis to generate an antigen-antibody complex spot on the membrane, and

(c) detecting the presence of the antigen-antibody complex, wherein the s presence of the antigen-antibody complex indicates the presence of the antigen in the biological sample.

42. The method of claim 41, wherein the electrophoresis is one-dimensional or two- dimensional membrane electrophoresis.

43. The method of claim 41, further comprising quantifying the antigen in the 0 antigen-antibody complex spot.