US 2019/0316203 A1 · GENE SIGNATURE FOR IMMUNE THERAPIES IN CANCER

Gene signature for immune therapies in cancer

AssigneeAlmac Diagnostics Limited

InventorsTimothy Davison, Jude O'Donnell, Max Bylesjo, Fionnuala Patterson, Steve Deharo, Laura A. Hill, Katherine E. Keating, Vitali Proutski, Denis Paul Harkin, Richard Kennedy, Nicolas Goffard, Steven Walker, Laura Taggart, Eileen Parkes

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Abstract

An immune response subtype of cancer is associated with DNA damage which allows subjects to be stratified for particular therapies including immune therapies which may be combined with DNA damage therapeutics. A method for predicting responsiveness to an antagonist of an inhibitory immune checkpoint and/or an agonist of a stimulatory immune checkpoint comprises determining the expression level of at least one gene selected from Table 2B, 2A or 1 in a sample from the subject. The determined expression level is used to predict responsiveness to an antagonist of an inhibitory immune checkpoint and/or an agonist of a stimulatory immune checkpoint.

Claims25

Dependent claims

1-60. (canceled)

A method of treating cancer in a subject comprising:

(a) obtaining a biological sample of the cancer from the subject;
(b) measuring an expression level of at least one biomarker in the biological sample, wherein the at least one biomarker is CXCL10, MX1, IDO1, IF144L, CD2, GBP5, PRAME, ITGAL, LRP4, APOL3, CDR1, FYB, TSPAN7, RAC2, KLHDC7B, GRB14, AC138128.1, KIF26A, CD274, CD109, ETV7, MFAP5, OLFM4, PI15, FOSB, FAM19A5, NLRC5, PRICKLE1, EGR1, CLDN10, ADAMTS4, SP140L, ANXA1, RSAD2, ESR1, IKZF3, OR2I1P, EGFR, NAT1, LATS2, CYP2B6, PTPRC, PPP1R1A, AL137218.1, TERFIP1, ABCA12, ALDH3B2, APOBEC3G, APOC1, APOL6, ARHGAP9, BAMBI, BIK, BIRC3, BTN3A3, C12orf48, C17orf28, C1orf162, C1orf64, C1QA, C21orf70, C22orf32, C6orf211, CACNG4, CCDC69, CCL5, CCNB2, CCND1, CCR7, CD163, CD22, CD24, CD3D, CD3E, CD52, CD53, CD79A, CDH1, CDKN3, CECR1, CHEK1, CKMT1B, CMPK2, CNTNAP2, COX16, CRIP1, CXCL9, CYBB, DDX58, DDX60L, ERBB2, FADS2, FAM26F, FAM46C, FASN, FBP1, FBXO2, FKBP4, FLJ40330, GBP1, GBP4, GIMAP4, GLRX, GLUL, GVIN1, H2AFJ, HGD, HIST1H2BK, HIST3H2A, HLA-DOA, HLA-DPB1, HMGB2, HMGB3, HSP90AA1, IF127, IFI44, IF16, IFIH1, IGJ, IKZF1, IL10RA, IL2RG, IL7R, IMPAD1, IQGAP3, IRF1, ISG15, KIAA1467, KIF20A, KITLG, KLRK1, KRT19, LAIR1, LCP1, LOC100289702, LOC100294459, LOC150519, LOC4APOL39949, LYZ, MAL2, MGC29506, MIAT, MS4A1, NAPSB, NCKAP1L, NEK2, NLRC3, NPNT, NQO1, OAS2, OAS3, PAQR4, PARP14, PARP9, PIK3CG, PIM2, PLEK, POU2AF1, PP14571, PPP2R2C, PSMB9, RAMP1, RARA, RASSF7, RTP4, SAMD9, SAMD9L, SASH3, SCD, SELL, SIX1, SLAMF7, SLC12A2, SLC9A3R1, SPOCK2, SQLE, ST20, ST6GALNAC2, STAT1, STRA13, SUSD4, SYT12, TAP1, TBC1D10C, TNFRSF13B, TNFSF10, TOB1, TOM1L1, TRIM22, UBD, UBE2T, UCK2, USP18, VNN2, XAF1, ZWINT, or any biomarker corresponding to SEQ ID NO:
1-50.
(c) determining a test score derived from the measured expression level of the at least one biomarker;
(c) providing a pre-determined threshold score;
(d) comparing the test score and the pre-determined threshold score;
and
(e) treating the subject if the test score is equal to or greater than the pre-determined threshold score with (i) at least one antagonist of an inhibitory immune check point and/or (ii) at least one agonist of a stimulatory immune check point.

5 more elements

A method of treating cancer in a subject comprising:

(a) obtaining a biological sample of the cancer from the subject;
(b) measuring an expression level of at least one biomarker in the biological sample, wherein the at least one biomarker is selected from the group consisting of CXCL10, MX1, IDO1, IF144L, CD2, GBP5, PRAME, ITGAL, LRP4, APOL3, CDR1, FYB, TSPAN7, RAC2, KLHDC7B, GRB14, AC138128.1, KIF26A, CD274, CD109, ETV7, MFAP5, OLFM4, PI15, FOSB, FAM19A5, NLRC5, PRICKLE1, EGR1, CLDN10, ADAMTS4, SP140L, ANXA1, RSAD2, ESR1, IKZF3, OR2I1P, EGFR, NAT1, LATS2, CYP2B6, PTPRC, PPP1R1A, and AL137218.1;
(c) determining a test score derived from the measured expression level of the at least one biomarker;
(c) providing a pre-determined threshold score;
(d) comparing the test score and the pre-determined threshold score;
and
(e) treating the subject with at least one antagonist of an inhibitory immune check point if the combined test score is equal to or greater than the pre-determined threshold score.

4 more elements

A method of treating cancer in a subject comprising:

(a) obtaining a biological sample of the cancer from the subject;
(b) measuring an expression level of at least one biomarker in the biological sample, wherein the at least one biomarker is selected from the group consisting of CXCL10, MX1, IDO1, IF144L, CD2, GBP5, PRAME, ITGAL, LRP4, APOL3, CDR1, FYB, TSPAN7, RAC2, KLHDC7B, GRB14, AC138128.1, KIF26A, CD274, CD109, ETV7, MFAP5, OLFM4, PI15, FOSB, FAM19A5, NLRC5, PRICKLE1, EGR1, CLDN10, ADAMTS4, SP140L, ANXA1, RSAD2, ESR1, IKZF3, OR2I1P, EGFR, NAT1, LATS2, CYP2B6, PTPRC, PPP1R1A, and AL137218.1;
(c) determining a test score derived from the measured expression level of the at least one biomarker;
(c) providing a pre-determined threshold score;
(d) comparing the test score and the pre-determined threshold score;
and
(e) treating the subject with at least one agonist of a stimulatory immune check point if the combined test score is equal to or greater than the pre-determined threshold score.

4 more elements

Dependencies are inferred from the claim text.

Facts

Application

15/746,097Filed 21 Jul 2016

Priority

GB 1512869.721 Jul 2015

Published

17 Oct 2019

Term ends

Not estimatedThe source records don’t support an estimate.

Classification6 codes

C12Q 1/6886
For diseases caused by alterations of genetic material: for cancer
G16H 50/30
ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or…: for…
C12Q 2600/106
Oligonucleotides characterized by their use: pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
C12Q 2600/158
Oligonucleotides characterized by their use: expression markers