SG11201901432YA - Immunotherapy markers and uses therefor - Google Patents

Immunotherapy markers and uses therefor

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Publication number
SG11201901432YA
SG11201901432YA SG11201901432YA SG11201901432YA SG11201901432YA SG 11201901432Y A SG11201901432Y A SG 11201901432YA SG 11201901432Y A SG11201901432Y A SG 11201901432YA SG 11201901432Y A SG11201901432Y A SG 11201901432YA SG 11201901432Y A SG11201901432Y A SG 11201901432YA
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SG
Singapore
Prior art keywords
immune checkpoint
immunotherapy
immune
expressed
international
Prior art date
Application number
SG11201901432YA
Inventor
Andrew Nguyen
John Zachary Sanborn
Shahrooz Rabizadeh
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Nantomics Llc
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Publication date
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Publication of SG11201901432YA publication Critical patent/SG11201901432YA/en

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    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
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    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
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    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
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    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
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    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
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    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/20—Heterogeneous data integration
    • G—PHYSICS
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    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
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    • C12Q2600/00—Oligonucleotides characterized by their use
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2570/00—Omics, e.g. proteomics, glycomics or lipidomics; Methods of analysis focusing on the entire complement of classes of biological molecules or subsets thereof, i.e. focusing on proteomes, glycomes or lipidomes
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
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  • Health & Medical Sciences (AREA)
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Abstract

APOBECPOLE Mutation Signature of 3 Significant POLE/APOBEC Signatures found. Yes Mutation Rate 3.71 per Megabase coding DNA Yes Immune Checkpoint Expression 5 of 9 immune checkpoint related genes over-expressed Yes Checkpoint Gene IDO1 HAVCR2 Common Name IDO TIM3 Immunotherapy Related Gene Expression Function Immune Escape Signal Immune Checkpoint Immune Checkpoint Immune Checkpoint Ligand Immune Checkpoint Ligand Status TPM Normal 55.05 Normal 27.57 24.82 Over-expressed 22.58 Over-expressed 20.18 Over-expressed 16.42 LAG3 LAG3 PDCD1LG2 PDL2 CD274 PDL1 CD40 CD40 Immune Escape Signal Normal CTLA4 CTLA4 Immune Checkpoint Over-expressed 8.39 PDCD1 PD1 Immune Checkpoint Over-expressed 5.61 I L2 IL2 Immune Stimulatory Normal 0.21 Signal FIG. 1 N O cc O O (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 01 March 2018 (01.03.2018) W I PO I PCT omit VIII °nolo III i oiloo Imo oimIE (10) International Publication Number WO 2018/039567 Al (51) International Patent Classification: G06F 19/18 (2011.01) G06F 19/22 (2011.01) G06F 19/00 (2011.01) (21) International Application Number: PCT/US2017/048629 (22) International Filing Date: 25 August 2017 (25.08.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/379,700 25 August 2016 (25.08.2016) US (71) Applicant: NANTOMICS, LLC [US/US]; 9920 Jefferson Boulevard, Culver City, California 90232 (US). (72) Inventors: NGUYEN, Andrew; 9920 Jefferson Boule- vard, Culver City, California 90232 (US). SANBORN, John Zachary; 9920 Jefferson Boulevard, Culver City, California 90232 (US). RABIZADEH, Shahrooz; 9920 Jefferson Boulevard, Culver City, California 90232 (US). (74) Agent: FESSENMAIER, Martin et al.; UMBERG ZIPSER LLP, 1920 Main Street, Suite 750, Irvine, Califor- nia 92614 (US). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, (54) Title: IMMUNOTHERAPY MARKERS AND USES THEREFOR Immunotherapy Markers This analysis examines the contribution of MSI status, POLE/APOBEC, mutation rate and mutational signatures and immune checkpoint expression for sensitivity towards an immunotherapy approach. This sample contains 3 of 4 indicators that suggests sensitivity to immunotherapy. Immunotherapy Sensitivity Markers Marker Status Immunotherapy Permissive MSI Status Microsatellite Stable. No (57) : Systems and methods for prediction of the treatment outcome for immune therapy are presented in which omics data of a patient tumor sample are used. Most typically, the omics data are processed to identify mutational signatures (especially APOBEC/POLE signatures), immune checkpoint expression, and MSI status as leading indicators to predict the treatment outcome for immune therapy. Such prediction advantageously integrates various parameters that would otherwise, when individually considered, skew prediction outcome. [Continued on next page] WO 2018/039567 Al MIDEDIMOMMIDIREIHNIMIINIMEHOHMEMON TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Published: with international search report (Art. 21(3)) before the expiration of the time limit for amending the claims and to be republished in the event of receipt of amendments (Rule 48.2(h))
SG11201901432YA 2016-08-25 2017-08-25 Immunotherapy markers and uses therefor SG11201901432YA (en)

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US201662379700P 2016-08-25 2016-08-25
PCT/US2017/048629 WO2018039567A1 (en) 2016-08-25 2017-08-25 Immunotherapy markers and uses therefor

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EP (1) EP3500966B1 (en)
JP (1) JP6995842B2 (en)
KR (2) KR20200003294A (en)
CN (1) CN109937452B (en)
AU (1) AU2017315468B2 (en)
CA (1) CA3034771C (en)
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WO (1) WO2018039567A1 (en)

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AU2017315468A1 (en) 2019-03-28
KR20200003294A (en) 2020-01-08
US20190237196A1 (en) 2019-08-01
JP6995842B2 (en) 2022-01-17
US20240079089A1 (en) 2024-03-07
CA3034771A1 (en) 2018-03-01
WO2018039567A1 (en) 2018-03-01
JP2019534685A (en) 2019-12-05
CA3034771C (en) 2021-10-26
AU2017315468B2 (en) 2020-02-13
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