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1. WO2020223576 - FRATAXIN-SENSITIVE MARKERS FOR DETERMINING EFFECTIVENESS OF FRATAXIN REPLACEMENT THERAPY


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INTERNATIONAL SEARCH REPORT (ISR)
Part 1:  1  2  3  4  5  6          Part 2:  A  B  C  D  E 
International application No. Applicant's or agent's file reference
PCT/US2020/030884 130197-00320
International filing date (day/month/year) (Earliest) Priority Date (day/month/year)
30 April 2020 30 April 2019
Applicant
CHONDRIAL THERAPEUTICS, INC.
FOR FURTHER ACTION: See Form PCT/ISA/220 as well as, where applicable, item 5 below.
This international search report has been prepared by this International Searching Authority and is transmitted to the applicant according to Article 18. A copy is being transmitted to the International Bureau.
It is also accompanied by a copy of each prior art document cited in this report.
1. Basis of the report
a. With regard to the language, the international search was carried out on the basis of:
the international application in the language in which it was filed.
a translation of the international application into                                          which is the language of a translation furnished for the purposes of international search (Rules 12.3(a) and 23.1(b)).
b.
This international search report has been established taking into account the rectification of an obvious mistake authorized by or notified to this Authority under Rule 91 (Rule 43.6bis(a)).
c.
1. With regard to any nucleotide and/or amino acid sequence disclosed in the international application, the international search was carried out on the basis of a sequence listing:
a. forming part of the international application as filed:
in the form of an Annex C/ST.25 text file.
on paper or in the form of an image file.
b. furnished together with the international application under PCT Rule 13ter.1(a) for the purposes of international search only in the form of an Annex C/ST.25 text file.
c. furnished subsequent to the international filing date for the purposes of international search only:
in the form of an Annex C/ST.25 text file (Rule 13ter.1(a)).
on paper or in the form of an image file (Rule 13ter.1(b) and Administrative Instructions, Section 713).
2.
In addition, in the case that more than one version or copy of a sequence listing has been filed or furnished, the required statements that the information in the subsequent or additional copies is identical to that forming part of the application as filed or does not go beyond the application as filed, as appropriate, were furnished.
3.
Additional comments:
2. Certain claims were found unsearchable
3. Unity of invention is lacking
This International Searching Authority found multiple inventions in this international application, as follows:
1. claims: 6, 50, 55, 72, 77, 82(completely); 1-5, 7, 13, 19, 20, 22-49, 51-54, 56, 62, 68-71, 73-76, 78-81, 83(partially)
Methods for evaluating effectiveness of Frataxin (FXN) replacement therapy comprising: (a) determining an FXN replacement expression profile for at least FXN-sensitive genomic marker (FSGMs) CYR61 in a sample from an FXN deficient patient following treatment with FXN replacement therapy; (b) comparing the patient FXN replacement expression profile with a baseline FXN(-) expression profile; and (c) using the comparison to determine effectiveness of the FXN replacement therapy. Compositions, panels, kits thereto.
2. claims: 1-5, 7-49, 51-54, 56-71, 73-76, 78-81, 83(all partially)
Methods for evaluating effectiveness of Frataxin (FXN) replacement therapy wherein invention 2 is defined by the first marker as depicted in Table 2, namely ABCE1. Compositions, panels, kits thereto.
3-85. claims: 1-5, 7-49, 51-54, 56-71, 73-76, 78-81, 83(all partially)
concerns methods for evaluating effectiveness of Frataxin (FXN) replacement therapy wherein inventions 3-85 are defined by the markers as depicted consecutively in Table 2 (with the exception of CYR61 which is sorted to the first invention), namely marker ADAMTS1 for invention 3, ADNP marker for invention 4 and so on until marker TMEM126a for invention 85. Compositions, kits, panels thereto.
1.
As all required additional search fees were timely paid by the applicant, this international search report covers all searchable claims.
2.
As all searchable claims could be searched without effort justifying additional fees, this Authority did not invite payment of additional fees.
3.
As only some of the required additional search fees were timely paid by the applicant, this international search report covers only those claims for which fees were paid, specifically claims Nos.:
4.
No required additional search fees were timely paid by the applicant. Consequently, this international search report is restricted to the invention first mentioned in the claims; it is covered by claims Nos.: 6, 50, 55, 72, 77, 82(completely); 1-5, 7, 13, 19, 20, 22-49, 51-54, 56, 62, 68-71, 73-76, 78-81, 83(partially)
Remark on Protest
The additional search fees were accompanied by the applicant’s protest and, where applicable, the payment of a protest fee.
The additional search fees were accompanied by the applicant’s protest but the applicable protest fee was not paid within the time limit specified in the invitation.
No protest accompanied the payment of additional search fees.
4. Title of the invention
The text is approved as submitted by the applicant.
The text has been established by this Authority to read as follows:
5. Abstract
The text is approved as submitted by the applicant.
The text has been established, according to Rule 38.2, by this Authority as it appears in Box No. IV. The applicant may, within one month from the date of mailing of this international search report, submit comments to this Authority.
6. Drawings
a.
The figure of the drawings to be published with the abstract is Figure No. ____________
as suggested by the applicant.
as selected by this Authority, because the applicant failed to suggest a figure.
as selected by this Authority, because this figure better characterizes the invention.
b.
none of the figures is to be published with the abstract.

A. CLASSIFICATION OF SUBJECT MATTER

     C12Q 1/6809 (2018.01)i; C12Q 1/6883 (2018.01)i
According to International Patent Classification (IPC) or to both national classification and IPC

B. FIELDS SEARCHED

Minimum documentation searched (classification system followed by classification symbols):
     C12Q
Documentation searched other than minimum documentation to the extent that such documents are included in the fields searched:
Electronic data base consulted during the international search (name of data base and, where practicable, search terms used):
EPO-Internal, BIOSIS, EMBASE, WPI Data

C. DOCUMENTS CONSIDERED TO BE RELEVANT

Category* Citation of document, with indication, where appropriate, of the relevant passages Relevant to claim No.
(1)
X
VIJAYENDRAN CHANDRAN ET AL, "Inducible and reversible phenotypes in a novel mouse model of Friedreich's Ataxia", ELIFE,Vol. 6, 19 December 2017 (2017-12-19),
XP055715118
1-7,13,19,20,22-56,62,68
page 18; figures 7a, 7b (and supplements 1-6) 8 (with supplement 1)
page 21 - page 24
(2)
X
HUMMERT C ET AL, "Creation and Comparison of Different Chip Definition Files for Affymetrix Microarrays", 2011 INTERNATIONAL CONFERENCE ON BIOINFORMATICS & COMPUTATIONAL BIOLOGY. BIOCOMP 2011, 18-21 JULY 2011, LAS VEGAS NV, USA,,Vol. 1, 01 January 2011 (2011-01-01), page 16-22,
XP009186218
ISBN: 9781601321701
69-83
abstract
(3)
X
PILARKSY CHRISTIAN P ET AL, "Expression of the extracellular matrix signalling molecule Cyr61 is downregulated in prostate cancer", PROSTATE, WILEY-LISS, NEW YORK, NY, US,Vol. 36, No. 2, 01 July 1998 (1998-07-01), page 85-91,
XP009521728
69-83
abstract
(4)
X
SAKAMOTO S ET AL, "Increased expression of CYR61, an extra cellular matrix signaling protein, in human benign prostatic hyperplasia and its regulation by lysophosphatidic acid", ENDOCRINOLOGY, THE ENDOCRINE SOCIETY, US,Vol. 45, No. 6, 01 June 2004 (2004-06-01), page 2929-2940,
XP002981701
69-83
abstract
(5)
A
JIUN-I LAI ET AL, "Transcriptional profiling of isogenic Friedreich ataxia neurons and effect of an HDAC inhibitor on disease signatures", JOURNAL OF BIOLOGICAL CHEMISTRY,Vol. 294, No. 6, 08 February 2019 (2019-02-08), page 1846-1859,
XP055715112
1-7,13,19,20,22-56,62,68
abstract
page 1853 - page 1854
(6)
A
JILL SERGESKETTER NAPIERALA ET AL, "Comprehensive analysis of gene expression patterns in Friedreich's ataxia fibroblasts by RNA sequencing reveals altered levels of protein synthesis factors and solute carriers", DISEASE MODELS & MECHANISMS,Vol. 10, No. 11, 01 November 2017 (2017-11-01), page 1353-1369,
XP055715105
1-7,13,19,20,22-56,62,68
abstract
(7)
A
NAPIERALA J ET AL, "Upregulation of mitochondrial aldehyde dehydrogenase activity inhibits lipid peroxidation in friedreich's ataxia cells", 22 April 2018 (2018-04-22), Vol. 90, No. 15, Supplement 1,
XP009521707
[retrieved on  2018-04-09]
1-7,13,19,20,22-56,62,68
the whole document
(8)
A
ABRAHAO AGESSANDRO ET AL, "Gene Expression Profile in Peripheral Blood Cells of Friedreich Ataxia Patients", 15 July 2015 (2015-07-15), Vol. 15, No. 3, page 306-313,
XP035959447
[retrieved on  2015-07-15]
1-7,13,19,20,22-56,62,68
abstract
*
Special categories of cited documents:
"A"
document defining the general state of the art which is not considered to be of particular relevance
"D"
document cited by the applicant in the international application
"E"
earlier application or patent but published on or after the international filing date
"L"
document which may throw doubts on priority claim(s) or which is cited to establish the publication date of another citation or other special reason (as specified)
"O"
document referring to an oral disclosure, use, exhibition or other means
"P"
document published prior to the international filing date but later than the priority date claimed
"T"
later document published after the international filing date or priority date and not in conflict with the application but cited to understand the principle or theory underlying the invention
"X"
document of particular relevance; the claimed invention cannot be considered novel or cannot be considered to involve an inventive step when the document is taken alone
"Y"
document of particular relevance; the claimed invention cannot be considered to involve an inventive step when the document is combined with one or more other such documents, such combination being obvious to a person skilled in the art
"&"
document member of the same patent family
Name and mailing address of the ISA/:
European Patent Office
P.B. 5818, Patentlaan 2, 2280 HV Rijswijk,
Netherlands
Telephone No. (+31-70)340-2040
Facsimile No. (+31-70)340-3016
Date of the actual completion of the international search:
17 July 2020
Date of mailing of the international search report:
14 September 2020
Authorized officer:
Costa Roldán, Nuria
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