GENOMIC CLASSIFIER THAT PREDICTS RESPONSE TO MULTI-KINASE INHIBITOR TREATMENT INTRODUCTION

• US 20170342499A1
• Filed: 12/18/2015
• Published: 11/30/2017
• Est. Priority Date: 12/19/2014
• Status: Abandoned Application

• Current Assignee: Centre Leon Berard
• Original Assignee: Centre Leon Berard
• Inventors: BLAY, Jean-Yves, JIANG, Xiaojun, TREDAN, Olivier, RAY COQUARD, Isabelle
• Application Number:
  US15/537,263
• Publication Number:
  US 20170342499A1
• Time in Patent Office: Days
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6832 Enhancement of hybridisation reaction
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2539/115 Comparative genomic hybridisation [CGH]
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The method for predicting the anti-tumor response in a human or animal having a tumor to multiple kinase inhibitors, using any multiple kinase inhibitor, comprises selection of genes encoding for protein kinases targeted by the said tyrosine kinase inhibitor, for each one of these genes, providing at least one nucleic acid probe which hybridizes to said gene under stringent conditions, thus providing an array of nucleic acid probes, having a biological sample containing cancer cells from said human or animal, extracting DNA from the sample, fragmenting into DNA fragments, optionally labeling the DNA fragments, submitting the optionally labeled DNA fragments to hybridization with the array of nucleic acid probes, recovering and quantifying for all the genes the gains or losses in gene copy numbers, wherein gains and losses of gene copy numbers of each selected gene are used to determine whether the tumor is sensitive or not to said kinase inhibitor.

Claims

1. A method for predicting the anti-tumor response in a human or animal having a tumor to multiple kinase inhibitors, using any multiple kinase inhibitor, comprising:

selection of genes encoding for protein kinases targeted by the said tyrosine kinase inhibitor,

for each one of these genes, providing at least one nucleic acid probe which hybridizes to said gene under stringent conditions, thus providing an array of nucleic acid probes,

having a biological sample containing cancer cells from said human or animal,

extracting DNA from the sample, fragmenting into DNA fragments, optionally labeling the DNA fragments,

submitting the optionally labeled DNA fragments to hybridization with the array of nucleic acid probes, and

recovering and quantifying for all the genes the gains and losses in gene copy numbers,

wherein gains and losses of gene copy numbers of each selected gene are used to determine whether the tumor is sensitive or not to said kinase inhibitor.

2. The method of claim 1, wherein the array of nucleic acid probes is an array of oligonucleotides.

3. The method of claim 1, comprising mixing the optionally labeled DNA fragments with optionally labelled non-tumoral reference DNA and subjecting the mixture to Comparative Genomic Hybridization (CGH).

4. The method of claim 3, wherein CGH is performed using a human whole-genome oligonucleotide array.

5. The method of claim 1, wherein:

the sum TTC of the copy-number gains of all selected genes encoding for protein kinases targeted by said kinase inhibitor is calculated, and

the sum TTL of the copy-number losses of all selected genes encoding for protein kinases targeted by said kinase inhibitor is calculated,

wherein a sum of the copy-number gains greater than the sum of copy-number losses is indicative that the tumor is sensitive to the kinase inhibitor.

6. The method of claim 5, wherein:

a TTC≧

4 and TTC≧

TTL is indicative that the tumor is sensitive to the kinase inhibitor;

a TTC≧

4 and TTC<

TTL is indicative that the tumor is resistant to the kinase inhibitor;

a TTC such as 1<

TTC<

4 combined to TTC>

TTL is indicative that the tumor is sensitive to the kinase inhibitor;

a TTC such as 1<

TTC<

4 combined to TTC≦

TTL is indicative that the tumor is resistant to the kinase inhibitor; and

/or

a TTC≦

1 is indicative that the tumor is resistant to the kinase inhibitor.

7. The method of claim 5, wherein the following algorithm is used:

8. The method of claim 1, wherein CGH is an array comparative genomic hybridization.

9. The method of claim 1, wherein the kinase inhibitor is regorafenib, imatinib, sorafenib, pazopanib, axitinib, cabozantinib or vandetanib.

10. The method of claim 9, wherein the kinase inhibitor is regorafenib and the genes are selected from the group consisting of ieRET, (VEGFR1(FLT1), VEGFR2(KDR), VEGFR3(FLT4), KIT, PDGFRα

, PDGFRβ

, FGFR1, FGFR2, angiopoietin-1 receptor(TEK), DDR2, High affinity nerve growth factor receptor(NTRK1), EPHA2, RAF1, BRAF, MAPK11, FRK and ABL1.

13. The inhibitor for the use of claim 12, wherein the human or animal that has been predicted as sensitive to the multi-kinase inhibitor by the method according to claim 1.

11. A multi-kinase inhibitor for use in treating a cancer in a human or animal that has been predicted as sensitive to the multi-kinase inhibitor.

12. The inhibitor for the use of claim 11, wherein the human or animal that has been predicted as sensitive to the multi-kinase inhibitor by Comparative Genomic Hybridization (CGH).

14. The inhibitor for the use of claim 12, wherein the human or animal that has been predicted as sensitive to the multi-kinase inhibitor by Comparative Genomic Hybridization (CGH) and use of the following algorithm: