[go: up one dir, main page]

WO2025093579A1 - Signature génétique pour prédire une réponse à une thérapie par inhibiteur de point de contrôle immunitaire - Google Patents

Signature génétique pour prédire une réponse à une thérapie par inhibiteur de point de contrôle immunitaire Download PDF

Info

Publication number
WO2025093579A1
WO2025093579A1 PCT/EP2024/080633 EP2024080633W WO2025093579A1 WO 2025093579 A1 WO2025093579 A1 WO 2025093579A1 EP 2024080633 W EP2024080633 W EP 2024080633W WO 2025093579 A1 WO2025093579 A1 WO 2025093579A1
Authority
WO
WIPO (PCT)
Prior art keywords
hla
cancer
havcr2
vsir
tumor
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
PCT/EP2024/080633
Other languages
English (en)
Inventor
Abhishek Garg
Isaure VANMEERBEEK
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Katholieke Universiteit Leuven
Original Assignee
Katholieke Universiteit Leuven
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Katholieke Universiteit Leuven filed Critical Katholieke Universiteit Leuven
Publication of WO2025093579A1 publication Critical patent/WO2025093579A1/fr
Pending legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • 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
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present invention relates to methods to predict the response to immunotherapy of a cancer patient and its use in a method of treating cancer.
  • Immune -checkpoint signaling involving interactions between immune-inhibitory receptors and their cognate ligands, is used by tumors to suppress anticancer immunity. Accordingly, immune-checkpoint blockers (ICBs) targeting T cell-associated ‘classical’ immune-inhibitory receptors (like PD-1) or their ligands (like PD-L1) have revolutionized treatment of various cancer patients. Regrettably, several cancer types or patient sub-groups remain unresponsive to PD-(L)1 blockade. Non -immunogenic or low antigenic tumors with sparse T cells that enrich tumor-associated macrophages (TAM) are particularly resistant to ICBs.
  • TAM tumor-associated macrophages
  • some of the most dominant immunoresistance mechanisms include defects in antigen presentation/availability, TAM-based immunosuppression, dysregulated interferon (IFN)-y signaling, and/or, enrichment of alternative immune-inhibitory receptors.
  • IFN dysregulated interferon
  • TAM-specific immune-inhibitory receptor signaling enriched exclusively in tumors resistant to PD-(L)1 blockade, and its therapeutic or clinical impact remains unexplored. It is not clear which classical or alternative immune-inhibitory receptors are preferentially exploited by TAM to support immune subversion.
  • the inventors have found that the enrichment of HAVCR2(+)VSIR(+) TAM within the tumors is predictive of shorter patient survival and resistance to unimodal ICB targeting PD-1, PD-L1, CTLA-4, HAVcr-2 and/or VISTA. Moreover the inventors have studied the impact of the HAVCR2(+)VSIR(+) TAM on patient’s response to therapy combining an immunogenic cell death (ICD) inducer with ICB (multimodal ICD therapy) and found that the enrichment of HAVCR2(+)VSIR(+) TAM is indicative of susceptibility to anti- HAVcr-2 and/or anti- VISTA multimodal ICD therapy.
  • ICD immunogenic cell death
  • HAVCR2(+)VSIR(+) TAM a method to identify patient bearing tumors enriched in HAVCR2(+)VSIR(+) TAM has been developed by identifying a genetic signature associated with the HAVCR2(+)VSIR(+) TAM niche.
  • This signature comprises genes, the expression of which is positively associated with the presence of HAVCR2(+)VSIR(+) TAM and may be used on easily accessible bulk protein and/or RNA extracts.
  • the present invention relates to a method for predicting the response to cancer immunotherapy of a cancer patient and/or prognosing the survival of a cancer patient and/or quantifying tumor-associated macrophages expressing both HAVCR2 and VSIR in a tumor sample from a cancer patient and/or quantifying tumor-associated macrophages expressing CSF1R, HAVCR2 and VSIR in a tumor sample from a cancer patient, comprising the steps of: a. measuring in a tumor sample from said patient the expression of at least 10, preferably at least 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
  • said method is for predicting the response to cancer immunotherapy of a cancer patient and comprises the steps of: a. measuring in a tumor sample from said patient the expression of at least 10, preferably at least 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85 or 86 genes selected from the group consisting of VSIR, TYROBP, HAVCR2, B2M, GRN, LAPTM5, CD74, HLA-C, PSAP, NPC2, TMEM176B, VAMP
  • said method is for quantifying tumor-associated macrophages expressing both HAVCR2 and VSIR in a tumor sample from a cancer patient and/or quantifying tumor-associated macrophages expressing CSF1R, HAVCR2 and VSIR in a tumor sample from a cancer patient, comprising the steps of: a.
  • said measuring step (a) comprises measuring in a tumor sample from said patient the expression of at least 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85 or 86 genes selected from the group consisting of VSIR, TYROBP, HAVCR2, B2M, GRN, LAPTM5, CD74, HLA-C, PSAP, NPC2, TMEM176B, VAMP8, HLA-A, HLA-DMB, HLA- DPA1, GPX1, CD68, HLA-DMA, TMSB4X, OAZ1, HLA-
  • said measuring step (a) comprises measuring in a tumor sample from said patient the expression of at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85 or 86 genes selected from the group consisting of VSIR, TYROBP, HAVCR2, B2M, GRN, LAPTM5, CD74, HLA-C, PSAP, NPC2, TMEM176B, VAMP8, HLA-A, HLA- DMB, HLA-DPA1, GPX1, CD68, HLA-DMA, TMSB4X, OAZ1, HLA-E, CFL1, ARPC1B, FCGRT, ITM2B, C1QC, PFN1, HLA-B, HLA-DPB1, H
  • said measuring step (a) comprises measuring in a tumor sample from said patient the expression of VSIR, HAVCR2 and CSF1R.
  • said measuring step (a) comprises measuring in a tumor sample from said patient the expression of VSIR, HAVCR2, CSF1R, HLA-DMA, ARHGDIB, ITGB2, AIF1, CAPZB, SYNGR2, and BST2
  • said measuring step (a) comprises measuring in a tumor sample from said patient the expression of the following genes: VSIR, TYROBP, HAVCR2, B2M, GRN, LAPTM5, CD74, HLA-C, PSAP, NPC2, TMEM176B, VAMP8, HLA-A, HLA-DMB, HLA-DPA1, GPX1, CD68, HLA-DMA, TMSB4X, OAZ1, HLA-E, CFL1, ARPC1B, FCGRT, ITM2B, C1QC, PFN1, HLA-B, HLA-DPB1, HLA-DRA, CST3, ARHGDIB, CYBA, TMSB10, CTSB, HLA-DQB1, ITGB2, ACTG1, CAPG, ARPC3, S100A11, RPL15, CTSS, C1QB, ATP6V0B, CTSA, RPS2, YBX1, CTSC, PTMA, SRP14, AIF1, C1QA, P
  • said cancer immunotherapy comprises administration of a blocking agent targeting the human protein, Programmed cell death protein 1 (PD-1), Programmed cell death 1 ligand 1 (PD-L1), Cytotoxic T-lymphocyte protein 4 (CTLA-4), Hepatitis A virus cellular receptor 2 (HAVcr-2) and/or V-type immunoglobulin domain-containing suppressor of T-cell activation (VISTA).
  • said cancer immunotherapy comprises administration of a blocking agent targeting the human protein PD-1, PD-L1, CTLA-4, HAVcr-2 and/or VISTA in combination with an immunogenic cell death (ICD)-inducing therapy.
  • ICD immunogenic cell death
  • said cancer immunotherapy comprises administration of a blocking agent targeting the human proteins HAVcr-2 and/or VISTA in combination with ICD- inducing therapy.
  • said immunogenic cell death (ICD)-inducing therapy comprises administration of paclitaxel, docetaxel, Epothilones A to F, anthracy clines, in particular doxorubicin, epirubicin, idarubicin and mitoxantrone, cyclophosphamide, oxaliplatin, bortezomib, carfilzomib, PARP inhibitors, therapeutic oncolytic virus, LTX-315, LTX- 401, crizotinib, cetuximab, dinaciclib, ibrutinib, spautin-1, bleomycin, LB-100, shikonin, and/or capsaicin; and/or treatment with ionizing radiation, extracorporeal photochemotherapy, hypericin-based photodynamic therapy and/or near-infrared photoimmunotherapy .
  • anthracy clines in particular doxorubicin, epirubicin,
  • said measuring is done by measuring RNA and/or protein level in bulk RNA and/or bulk protein extract(s).
  • said cancer is selected form the group consisting of lung cancer, colorectal cancer, skin cancer, uterine cancer, kidney cancer, liver cancer, lymphoma, head and neck cancer, stomach cancer, breast cancer, pancreas cancer, bladder cancer, brain cancer, adrenal glands cancer, cervical cancer, bile duct cancer, esophageal cancer, mesothelioma, ovarian cancer, extra-adrenal paragangliomas, prostate cancer, sarcoma, testicular cancer, thyroid cancer and eye cancer.
  • said cancer is selected form the group consisting of lung cancer, colorectal cancer, skin cancer, uterine cancer, kidney cancer, liver cancer, lymphoma, head and neck cancer, stomach cancer, breast cancer and pancreas cancer.
  • RNA and/or bulk protein extract is used herein in reference to RNA or protein extract on pooled cell populations (e.g. tissue sample) and is thus defined in contrast with transcriptome or proteome analyses done on single cells.
  • “Cancer immunotherapy”, “checkpoint inhibitor therapy”, “immune checkpoint inhibitor therapy”, “immune checkpoint blockade (ICB)”, “ICB” or “immune checkpoint blockade therapy” are used herein interchangeably in reference to therapy comprising the administration of a blocking agent (or combination thereof), generally an antibody, that blocks, or inhibits, an inhibitory immune checkpoint protein to avoid dampening of the immune response, classically T-cell -mediated response, against cancer cells.
  • a blocking agent or combination thereof
  • an antibody that blocks, or inhibits, an inhibitory immune checkpoint protein to avoid dampening of the immune response, classically T-cell -mediated response, against cancer cells.
  • the terms also include administration of such a blocking agent, in combination with another therapeutic agent.
  • inhibitory immune checkpoint protein relevant in the context of the invention includes, without being limited to, the following human proteins: Programmed cell death protein 1 (PD-1, UniProtKB reference Q15116), Programmed cell death 1 ligand 1 (PD-L1, UniProtKB reference Q9NZQ7), Cytotoxic T-lymphocyte protein 4 (CTLA-4, UniProtKB reference P16410), Hepatitis A virus cellular receptor 2 (HAVcr-2, UniProtKB reference Q8TDQ0, alternatively known as T-cell immunoglobulin mucin receptor 3 or TIM-3) and V-type immunoglobulin domaincontaining suppressor of T-cell activation (VISTA, UniProtKB reference Q9H7M9, encoded by the VSIR gene).
  • PD-1 Programmed cell death protein 1
  • PD-L1 Programmed cell death 1 ligand 1
  • CTL-4 Cytotoxic T-lymphocyte protein 4
  • HAVcr-2 Hepatitis A virus cellular receptor 2
  • TIM-3 V-type immuno
  • Cancer immunotherapy may be referred to by the combination of the term “anti” in front of the name of the inhibitory immune checkpoint protein.
  • anti-PD-1 cancer immunotherapy designate the administration of a PD-1 blocking agent, such as a PD-1 blocking antibody.
  • references herein to “one embodiment” or “an embodiment” means that a particular feature, structure, or characteristic described in connection with the embodiment is included in at least one embodiment of the present invention.
  • appearances of the phrases “in one embodiment” or “in an embodiment” in various places throughout this specification are not necessarily all referring to the same embodiment, but may.
  • the particular features, structures or characteristics may be combined in any suitable manner, as would be apparent to a person skilled in the art from this disclosure, in one or more embodiments.
  • expression or “expressing” when used herein in reference to a gene refers to transcription and/or translation of said gene.
  • the measure of the expression of a gene hence refers to the measure of the quantity of (m)RNA and/or protein produced by said gene.
  • ICD-inducing therapy or “ICD-inducing therapy” are used interchangeably in reference a therapy that induces ICD, a form of regulated cell death that is sufficient to activate an adaptive immune response in immunocompetent syngeneic hosts.
  • Methods to identify ICD and thus ICD-inducing therapy are well-known in the art, for example by following the “Consensus guidelines for the definition, detection and interpretation of immunogenic cell death” published by Galluzzi et al. (J Immunother Cancer. 2020; 8(1): e000337).
  • ICD is notably characterized by secretion and/or exposure on the dying cell surface of damage-associated molecular patterns (DAMP) that are necessary for the recruitment and maturation of antigen-presenting cells, including, without being limited to, ANXA1, CALR, adenosine triphosphate, CCL2, CXCL1, CXCL10, cytosolic RNA, cytosolic DNA, ERp57, Extracellular DNA, F-actin, HMGB1, HSP70, HSP90, TFAM and Type I IFN. It is thus within the reach of the skilled artisan to identify therapies inducing ICD.
  • DAMP damage-associated molecular patterns
  • Example of such therapies include, without being limited to therapy comprising (i) administration of chemotherapeutics such as paclitaxel (CAS number 33069-62-4), docetaxel (CAS number 114977-28-5), Epothilones A to F (CAS numbers 152044-53-6, 152044-54-7, 186692-73-9, 189453-10-9, 201049-37-8 and 208518-52-9) anthracyclines, in particular doxorubicin (CAS numbers 23214-92-8 and 25316-40-9), epirubicin (CAS number 56420-45-2), idarubicin (CAS number 58957-92- 9) and mitoxantrone (CAS number 65271-80-9), cyclophosphamide (CAS number 50- 18-0), oxaliplatin (CAS number 61825-94-3), bortezomib (CAS number 179324-69-7) and carfilzomib (CAS number 868540-17-4) and PARP inhibitors; (ii)
  • a “therapeutically effective amount” means herein an amount that is sufficient to achieve the effect for which it is indicated, herein the treatment of cancer.
  • the amount of the therapeutic agent(s) to be administered can be determined by standard procedures well known by those of ordinary skill in the art. Physiological data of the patient (e.g. age, size, and weight), the routes of administration and the disease to be treated have to be taken into account to determine the appropriate dosage. The amount may also vary according to other aspect of a treatment protocol (e.g. administration of other medicaments and the like).
  • the present invention relates to a method for (i) predicting the response to cancer immunotherapy of a cancer patient and/or (ii) prognosing the survival of a cancer patient and/or (iii) quantifying tumor-associated macrophages expressing both HAVCR2 and VSIR in a tumor sample from a cancer patient and/or (iv) quantifying tumor-associated macrophages expressing CSF1R, HAVCR2 and VSIR in a tumor sample from a cancer patient.
  • the cancer immunotherapy comprises administration of a blocking agent, preferably of a blocking antibody, targeting an inhibitory immune checkpoint protein.
  • the cancer immunotherapy comprises administration of a blocking agent, preferably of a blocking antibody, targeting the human protein, Programmed cell death protein 1 (PD-1), Programmed cell death 1 ligand 1 (PD-L1), Cytotoxic T-lymphocyte protein 4 (CTLA-4), Hepatitis A virus cellular receptor 2 (HAVcr-2) and/or V-type immunoglobulin domain-containing suppressor of T-cell activation (VISTA).
  • PD-1 Programmed cell death protein 1
  • PD-L1 Programmed cell death 1 ligand 1
  • CLA-4 Cytotoxic T-lymphocyte protein 4
  • HAVcr-2 Hepatitis A virus cellular receptor 2
  • VISTA V-type immunoglobulin domain-containing suppressor of T-cell activation
  • the cancer immunotherapy comprises administration of a blocking agent, preferably of a blocking antibody, targeting the human protein, PD-1, PD-L1, CTLA-4, HAVcr-2 and/or VISTA in combination with an Immunogenic Cell Death (ICD) -inducing therapy.
  • the cancer immunotherapy comprises administration of a blocking agent, preferably of a blocking antibody, targeting the human protein, PD-1, PD-L1, HAVcr-2 and/or VISTA in combination with an ICD)-inducing therapy.
  • the cancer immunotherapy comprises administration of a blocking agent, preferably of a blocking antibody, targeting the human protein, HAVcr- 2 and/or VISTA in combination with an ICD -inducing therapy.
  • the immunogenic cell death (ICD)-inducing therapy comprises administration of paclitaxel, docetaxel, epothilones A to F, anthracy clines, in particular doxorubicin, epirubicin, idarubicin and mitoxantrone, cyclophosphamide, oxaliplatin, bortezomib, carfilzomib, PARP inhibitors, therapeutic oncolytic viruses, LTX-315, LTX- 401, crizotinib, cetuximab, dinaciclib, ibrutinib, spautin-1, bleomycin, LB-100, shikonin, and/or capsaicin; and/or treatment with ionizing radiation, extracorporeal photochemotherapy, hypericin-based photodynamic therapy and/or near-infrared photoimmunotherapy.
  • anthracy clines in particular doxorubicin, epirubicin,
  • the immunogenic cell death (ICD)-inducing therapy comprises administration of paclitaxel, docetaxel, epothilones A to F, anthracyclines, in particular doxorubicin, epirubicin, idarubicin and mitoxantrone, cyclophosphamide, oxaliplatin, bortezomib, carfilzomib, crizotinib, cetuximab, dinaciclib, ibrutinib, spautin-1, bleomycin, LB-100, shikonin, and/or capsaicin; and/or treatment with ionizing radiation, extracorporeal photochemotherapy, hypericin-based photodynamic therapy and/or near-infrared photoimmunotherapy.
  • the immunogenic cell death (ICD) -inducing therapy comprises administration of paclitaxel.
  • the method of the invention comprise a step of measuring in a tumor sample from said patient the expression of at least 1, 2, 3, 4, 5, 6, 7, 8 or 9, preferably at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29, more preferably at least 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49, even more preferably at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85 or 86 genes selected from the group consisting of VSIR, TYROBP, HAVCR2, B2M, GRN, LAPTM5, CD74, HLA-C, PSAP, NPC2, TM
  • VSIR TYROBP
  • HAVCR2, B2M GRN, LAPTM5, CD74, HLA-C, PSAP, NPC2, TMEM176B, VAMP8, HLA-A, HLA-DMB, HLA-DPA1, GPX1, CD68, HLA- DMA, TMSB4X, OAZ1, HLA-E, CFL1, ARPC1B, FCGRT, ITM2B, C1QC, PFN1, HLA-B, HLA-DPB1, HLA-DRA, CST3, ARHGDIB, CYBA, TMSB10, CTSB, HLA-DQB1, ITGB2, ACTG1, CAPG, ARPC3, S100A11, RPL15, CTSS, C1QB, ATP6V0B, CTSA, RPS2, YBX1, CTSC, PTMA, SRP14, AIF1, C1QA, PPT1, CTSH, CALM2, CSF1R, YWHAH, RPL28, CAPZB,
  • the method of the invention comprise a step of measuring in a tumor sample from said patient the expression of VSIR, TYROBP, HAVCR2, B2M, GRN, LAPTM5, CD74, HLA-C, PSAP, NPC2, TMEM176B, VAMP8, HLA-A, HLA- DMB, HLA-DPA1, GPX1, CD68, HLA-DMA, TMSB4X, OAZ1, HLA-E, CFL1, ARPC1B, FCGRT, ITM2B, C1QC, PFN1, HLA-B, HLA-DPB1, HLA-DRA, CST3, ARHGDIB, CYBA, TMSB10, CTSB, HLA-DQB1, ITGB2, ACTG1, CAPG, ARPC3, S100A11, RPL15, CTSS, C1QB, ATP6V0B, CTSA
  • the measuring step of the invention comprises measuring the expression of VSIR, HAVCR2, CD68, FCGRT, C1QC, C1QB, C1QA, CSF1R and FCER1G .
  • the method of the invention comprise a step of measuring in a tumor sample from said patient the expression of VSIR, HAVCR2, CD68, FCGRT, C1QC, C1QB, C1QA, CSF1R and FCER1G and optionally, of at least 1, 2, 3, 4, 5, 6, 7, 8 or 9, preferably at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29, more preferably at least 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49, even more preferably at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,
  • the measuring step of the invention comprises measuring the expression of VSIR, HAVCR2 and CSF1R.
  • the method of the invention comprise a step of measuring in a tumor sample from said patient the expression of VSIR, HAVCR2 and CSF1R and optionally, of at least 1, 2, 3, 4, 5, 6, 7, 8 or 9, preferably at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29, more preferably at least 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49, even more preferably at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82 or 83 genes selected from the group consisting of
  • the measuring step of the invention comprises measuring the expression of VSIR, HAVCR2, CSF1R, HLA-DMA, ARHGDIB, ITGB2, AIF1, CAPZB, SYNGR2, and BST2.
  • the method of the invention comprise a step of measuring in a tumor sample from said patient the expression of VSIR, HAVCR2, CSF1R, HLA-DMA, ARHGDIB, ITGB2, AIF1, CAPZB, SYNGR2, and BST2, and, optionally, of at least 1, 2, 3, 4, 5, 6, 7, 8 or 9, preferably at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29, more preferably at least 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49, even more preferably at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62,
  • the measuring step of the invention comprises measuring the expression of EEF1A1, RPSA, GPX1, ITM2B, ACTG1, RPL13A, ARPC3, ACTB, PPIA, PTMA, TMSB4X and CTSC.
  • the method of the invention comprise a step of measuring in a tumor sample from said patient the expression of EEF1A1, RPSA, GPX1, ITM2B, ACTG1, RPL13A, ARPC3, ACTB, PPIA, PTMA, TMSB4X and CTSC, and optionally, of at least 1, 2, 3, 4, 5, 6, 7, 8 or 9, preferably at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29, more preferably at least 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49, even more preferably at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, or 74 genes selected from the group consisting of VSIR, TYROBP, HAVCR2, B2M
  • the step of measuring of gene expression in the tumor sample from the cancer patient may be done by measuring RNA and/or protein level.
  • Techniques to measure RNA level include, without being limited to quantitative RT-PCR, RNA sequencing, DNA microarrays northern blot, in-situ hybridization and the like.
  • Techniques to measure protein level include, without being limited to, immunoassays such as ELISA, western blot and immunohistochemistry, mass spectrometry-based assays and the like.
  • the inventors have found that the method of the invention can, despite relating to the detection of a distinct tumor-associated macrophages population within the tumor sample, be applied on pooled tumor cell population. This is advantageous in particular to simplify sample preparation.
  • the step of measuring of gene expression in the tumor sample from the cancer patient is done by measuring RNA and/or protein level in bulk RNA and/or bulk protein extract(s).
  • the method of the invention comprises a step of comparing the measured gene expression (in the tumor sample from the cancer patient) to a reference gene expression level.
  • the term “reference gene expression level” refers to a measure of gene expression for a given control subjects or for a given population of control subject, of know outcome in respect to response to cancer immunotherapy and/or survival prognosis and/or of know amount, or proportion, of tumor-associated macrophages expressing both HAVCR2 and VSIR and/or of know amount, or proportion, of tumor-associated macrophages expressing both CSF1R, HAVCR2 and VSIR. It is within the reach of the skilled artisan to select for the reference gene expression level the most appropriate data set representation, such as for example and without limitation, raw values, means, medians, or any form of mathematical or graphical representation.
  • the reference gene expression level comprises information on the level of expression of the same gene that are considered in the measuring step. Therefore, embodiments relating to selection of genes considered in the measuring step may apply to the determination of the reference gene expression level.
  • the reference gene expression level corresponds to a cancer immunotherapy response group and/or to patient survival prognosis group and/or to an amount, or proportion, of HAVCR2 and VSIR-expressing tumor-associated macrophages group and/or to an amount, or proportion of, CSF1R, HAVCR2 and VSIR-expressing tumor-associated macrophages group.
  • Example of response to cancer immunotherapy include, without being limited to, clinical responses such as duration of survival, time to disease progression, response rate (e.g. complete or partial response), length of progression-free survival, treatment of the cancer, inhibition of tumor growth, occurrence of relapse or metastasis.
  • expression of the genes in Table 1 is higher in patients that do not respond to cancer immunotherapy, in particular to anti-PD-1, anti-PD-Ll, anti- CTLA-4, anti-HAVcr-2 and/or anti-VISTA therapy when said cancer immunotherapy is not combined with an Immunogenic Cell Death-inducing therapy than in responders to said therapy; (ii) expression of the genes in Table 1 is higher in patients that do respond to anti-VISTA and/or anti-HAVcr-2 therapy combined with an Immunogenic Cell Deathinducing therapy than in non-responder to said therapy (iii) expression of the genes in Table 1 increases with the amount of HAVCR2(+)VSIR(+) tumor associated macrophages present within the tumor sample; (iv) expression of the genes in Table 1 increases with the amount of HAVCR2(+)VSIR(+)CSFR1(+) tumor associated macrophages (i.e., TAM expressing HAVCR2, VSIR and CSFR1) present within the tumor sample and
  • control subject(s) to establish a reference gene expression level corresponding to a cancer immunotherapy response group and/or to patient survival prognosis group and/or to an amount, or proportion, of HAVCR2 and VSIR-expressing tumor-associated macrophages group and/or to an amount, or proportion of, CSF1R, HAVCR2 and VSIR-expressing tumor-associated macrophages group, notably accounting for parameters such as for instance, and without limitation, the targeted sensitivity or specificity or the number of groups to be defined.
  • the cancer immunotherapy response group corresponds to responders to said cancer immunotherapy.
  • a responder to cancer immunotherapy refers to a cancer patient showing a positive outcome (e.g., longer survival, treatment, remission or slowing-down of the progression, of the cancer) following said cancer immunotherapy.
  • the cancer immunotherapy response group corresponds to responders to a cancer immunotherapy comprising administration of a blocking agent, preferably a blocking antibody, targeting the human proteins HAVcr-2 and/or VISTA in combination with a immunogenic cell death inducer.
  • the method of the invention comprises a step of assigning on the basis of the comparison between the measured gene expression level and the reference gene expression level, the cancer patient to a cancer immunotherapy response group and/or to patient survival prognosis group and/or to an amount, or proportion, of HAVCR2 and VSIR-expressing tumor-associated macrophages group and/or to an amount, or proportion of, CSF1R, HAVCR2 and VSIR-expressing tumor-associated macrophages group.
  • This step thereby allows i) predicting the response to cancer immunotherapy of a cancer patient and/or (ii) prognosing the survival of a cancer patient and/or (iii) quantifying tumor-associated macrophages expressing both HAVCR2 and VSIR in a tumor sample from a cancer patient and/or (iv) quantifying tumor-associated macrophages expressing CSF1R, HAVCR2 and VSIR in a tumor sample from a cancer patient.
  • patient(s) refers to human subject(s).
  • cancer patient(s) refers to patient(s) affected with cancer.
  • the cancer is selected from the group consisting of lung cancer (in particular, lung adenocarcinoma , lung squamous cell carcinoma and non-small cell lung cancer), colorectal cancer (in particular colon adenocarcinoma, rectum adenocarcinoma and colorectal adenocarcinoma), skin cancer (in particular skin subcutaneous melanoma and basal cell carcinoma), uterine cancer (in particular, uterine corpus endometrial carcinoma, uterine carcinosarcoma and endometrial adenocarcinoma), kidney cancer (in particular kidney renal papillary cell carcinoma and renal clear cell carcinoma), liver cancer (in particular, hepatocellular carcinoma), lymphoma, head and neck cancer (in particular, head and neck squamous cell carcinoma and nasopharyngeal cancer), stomach cancer (in particular stomach adenocarcinoma), breast cancer (in particular breast invasive carcinoma), pancreas cancer (in particular pancreatic a
  • the cancer is selected from the group consisting of lung cancer (in particular, lung adenocarcinoma and non-small cell lung cancer), colorectal cancer (in particular colorectal adenocarcinoma), skin cancer (in particular, skin subcutaneous melanoma and basal cell carcinoma), uterine cancer (in particular endometrial adenocarcinoma), kidney cancer (in particular renal clear cell carcinoma), liver cancer (in particular hepatocellular carcinoma), lymphoma, head and neck cancer (in particular nasopharyngeal cancer), stomach cancer (in particular stomach adenocarcinoma), breast cancer (in particular breast invasive carcinoma), pancreas cancer (pancreatic adenocarcinoma), bladder cancer (bladder urothelial carcinoma) and brain cancer (in particular glioblastoma.
  • lung cancer in particular, lung adenocarcinoma and non-small cell lung cancer
  • colorectal cancer in particular colorectal adenocarcinoma
  • the cancer is selected from the group consisting of lung cancer (in particular, lung adenocarcinoma and non-small cell lung cancer), colorectal cancer (in particular colorectal adenocarcinoma), skin cancer (in particular, skin subcutaneous melanoma and basal cell carcinoma), uterine cancer (in particular endometrial adenocarcinoma), kidney cancer (in particular renal clear cell carcinoma), liver cancer (in particular hepatocellular carcinoma), lymphoma, head and neck cancer (in particular nasopharyngeal cancer), stomach cancer (in particular stomach adenocarcinoma), breast cancer (in particular breast invasive carcinoma) and pancreas cancer (pancreatic adenocarcinoma).
  • lung cancer in particular, lung adenocarcinoma and non-small cell lung cancer
  • colorectal cancer in particular colorectal adenocarcinoma
  • skin cancer in particular, skin subcutaneous melanoma and basal cell carcinoma
  • uterine cancer in
  • the cancer is selected from the group consisting of colorectal cancer, skin cancer (in particular skin subcutaneous melanoma), uterine cancer (in particular endometrial adenocarcinoma), kidney cancer (in particular renal clear cell carcinoma), stomach cancer (in particular stomach adenocarcinoma) breast cancer (in particular breast invasive carcinoma) and pancreas cancer (pancreatic adenocarcinoma).
  • skin cancer in particular skin subcutaneous melanoma
  • uterine cancer in particular endometrial adenocarcinoma
  • kidney cancer in particular renal clear cell carcinoma
  • stomach cancer in particular stomach adenocarcinoma
  • breast cancer in particular breast invasive carcinoma
  • pancreas cancer pancreatic adenocarcinoma
  • the cancer is lung cancer. In one embodiment, the cancer is lung adenocarcinoma or non-small cell lung cancer.
  • the sample is a tumor sample.
  • the sample is a cancerous tumor sample.
  • a sample can be a solid sample (e.g., solid biopsy, or part of a surgically excised or removed tumor) or a fluid sample (e.g. a liquid biopsy, such as non-invasive liquid biopsy or non-invasive sample).
  • the (cancerous) tumor sample can be a sample comprising cell-free genetic material shed from the tumor, and/or can be a sample comprising circulating tumor cells
  • the method of the invention comprises a step of providing a (tumor or cancerous tumor) sample from the cancer patient.
  • the sample was previously taken from the cancer patient.
  • the method of the invention does not comprise a step of collecting the sample from the subject (In other words, the method of the invention is an in vitro method).
  • the method of the invention is for predicting the response to cancer immunotherapy of a cancer patient and comprises the steps of: a. measuring in a tumor sample from said patient the expression of at least at least 1, 2, 3, 4, 5, 6, 7, 8 or 9, preferably at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29, more preferably at least 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49, even more preferably at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85 or 86 genes selected from the group consisting of VSIR, TYROBP, HAVCR2, B2M, GRN
  • the method of the invention is for prognosing the survival of a cancer patient and comprises the steps of: a. measuring in a tumor sample from said patient the expression of at least at least 1, 2, 3, 4, 5, 6, 7, 8 or 9, preferably at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29, more preferably at least 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49, even more preferably at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85 or 86 genes selected from the group consisting of VSIR, TYROBP, HAVCR2, B2M, GRN, L
  • the method of the invention is for prognosing the survival of a cancer patient and comprises the steps of: a. measuring in a tumor sample from said patient the expression of at least at least 1, 2, 3, 4, 5, 6, 7, 8 or 9, preferably at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29, more preferably at least 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48 or 49, even more preferably at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85 or 86 genes selected from the group consisting of VSIR, TYROBP, HAVCR2, B2M, GRN, L
  • the present invention further relates to a method of treating cancer in a cancer patient comprising the steps of: a. predicting the response to cancer immunotherapy of said patient using the method of the invention for predicting the response to cancer immunotherapy; and, b. administering (a therapeutically effective amount of) said cancer immunotherapy to said patient, preferably administering said cancer immunotherapy to said patient identified as a responder to said cancer immunotherapy at step (a).
  • the method of treatment of the invention comprises the steps of: a. predicting the response to cancer immunotherapy of said patient using the method of the invention for predicting the response to cancer immunotherapy; b. administering (a therapeutically effective amount of) said cancer immunotherapy to said patient, preferably administering (a therapeutically effective amount of) said cancer immunotherapy to said patient identified a responder to said cancer immunotherapy at step (a), wherein said cancer immunotherapy comprises administration of (a therapeutically effective amount of) a blocking agent, preferably of a blocking antibody, targeting the human protein, HAVcr-2 and/or VISTA in combination with an Immunogenic Cell Death (ICD) -inducing therapy.
  • a blocking agent preferably of a blocking antibody, targeting the human protein, HAVcr-2 and/or VISTA in combination with an Immunogenic Cell Death (ICD) -inducing therapy.
  • the present invention further also relates to a method of treating cancer in a cancer patient comprising the steps of: a. quantifying using the method of the invention tumor-associated macrophages expressing both HAVCR2 and VSIR, and/or tumor-associated macrophages expressing CSF1R, HAVCR2 and VSIR, in a tumor sample from said cancer patient; and, b. administering (a therapeutically effective amount of) ICB therapy to said patient, preferably administering ICB therapy to said patient when macrophages expressing both HAVCR2 and VSIR and/or macrophages expressing CSF1R, HAVCR2 and VSIR are detected in said tumor sample.
  • the method of treatment of the invention comprises the steps of: a. quantifying using the method of the invention tumor-associated macrophages expressing both HAVCR2 and VSIR, and/or tumor-associated macrophages expressing CSF1R, HAVCR2 and VSIR, in a tumor sample from said cancer patient; and, b.
  • ICB therapy comprises administering (a therapeutically effective amount of) ICB therapy to said patient, preferably administering ICB therapy to said patient when macrophages expressing both HAVCR2 and VSIR and/or macrophages expressing CSF1R, HAVCR2 and VSIR are detected in said tumor sample, wherein said ICB therapy comprises administration of a (therapeutically effective amount of) blocking agent, preferably of a blocking antibody, targeting the human protein, HAVcr-2 and/or VISTA, preferably in combination with an Immunogenic Cell Death (ICD) -inducing therapy.
  • a (therapeutically effective amount of) blocking agent preferably of a blocking antibody, targeting the human protein, HAVcr-2 and/or VISTA, preferably in combination with an Immunogenic Cell Death (ICD) -inducing therapy.
  • ICD Immunogenic Cell Death
  • Figure 7 Tumor volume curve of wild-type MC38 tumor-bearing mice treated with anti 250pg -TIM3 antibody (aTIM3), 250pg anti-VISTA antibody (a- VISTA) or PBS on day
  • FIG. 8 Tumor volume curve of wild-type LLC tumor-bearing mice treated with 250
  • ig anti-PDl antibody (a-PDl) and/or combination with 250pg anti-TIM3 antibody (a- TIM3) or 250pg anti-VISTA antibody (a- VISTA) or PBS on day 11, 14 and 18 after tumor injection. (n 4).
  • a-TIM3 anti-TIM3 antibody
  • a-VISTA 250pg anti-VISTA antibody
  • a-TIM3 anti-TIM3 antibody
  • a-VISTA 250pg anti-VISTA antibody
  • a-TIM3 anti-TIM3 antibody
  • a-VISTA 250pg anti-VISTA antibody
  • PTX paclitaxel
  • PBS 250 pg anti-TIM3 antibody
  • a-VISTA 250 pg anti-VISTA antibody
  • Wild type C57BL/6j were obtained from the KU Leuven breeding facility. All subcutaneous tumor experiments were done using 7- to 12-week-old female/male mice, maintained in the conventional mouse facility. Mouse Experiments were approved by the animal ethics committee at KU Leuven (project Pl 14/2019 and pl 95/2020) following the European directive 2010/63/EU as amended by the Regulation (EU) 2019/1010 and the Flemish government decree of 17 February 2017.
  • the pre-existing scRNAseq dataset of subcutaneous murine Lewis lung carcinoma (LLC)-tumors [7] was uploaded into the same workflow and further analyzed to maintain uniformity. This workflow was used for generating density plots, or dot plots, as applicable. Cellular annotations either pre-existed on the level of author-derived annotations or were based on automated annotations available within the above work-flow.
  • LLC subcutaneous murine Lewis lung carcinoma
  • HAVCR2(+)VSIR(+) Tumor Associated Macrophages TAM
  • CRC ColoRectal Cancer
  • DGE differential gene-enrichment
  • RRCTOME co-dependent pathway enrichment analyses
  • an alternative name for VSIR was C10orf54.
  • VSIR, HAVCR2, CD68, FCGRT, C1QC, C1QB, C1QA, CSF1R and FCER1G therein are major TAM genes.
  • Table 1 List of positively enriched genes in HAVCR2(+)VSIR(+) TAM.
  • HGNC HUGO Gene Nomenclature Committee
  • EBL-EBI European Bioinformatics Institute
  • Wellcome Genome Campus Hinxton, Cambridge CB10 1SD, United Kingdom www.genenames.org. Data retrieved July, 2023.
  • HAVCR2(+)VSIR(+) TAM HAVCR2 and VSIR expression > 0
  • the hits were filtered at a Jaccard’s index threshold of 0.7.
  • the TCGA dataset described above was used for a prognostic analysis, in which the effect of the expression of the HAVCR2 - VSIR metagene (mean expression of all genes in signature of Table 1) was associated with the overall survival, using a Cox regression as implemented in lifelines [15] 0.26.3 with default settings.
  • Adrenocortical carcinoma 76
  • Bladder Urothelial Carcinoma BLCA
  • BRCA Breast invasive carcinoma
  • CECD Cervical squamous cell carcinoma and endocervical adenocarcinoma
  • Cholangiocarcinoma CHOL
  • COAD Colon adenocarcinoma
  • EGF Esophageal carcinoma
  • GBM Glioblastoma multiforme
  • HNSC Kidney Chromophobe
  • KICH Kidney renal clear cell carcinoma
  • KIRC Kidney renal papillary cell carcinoma
  • LIHC Liver hepatocellular carcinoma
  • mice Seven to twelve-week-old female/male C57BL/6J mice were subcutaneously (s.c) injected with IxlO 6 LLC, MC38 cells. In the case of chemotherapy, mice were treated with 8mg/kg of Cisplatin (Sigma #p4394) or Paclitaxel (Sigma #T1912) on day 10, 13 and 17 via intraperitoneal (i.p.) injections.
  • Cisplatin Sigma #p4394
  • Paclitaxel Sigma #T1912
  • mice When applicable, mice were treated or cotreated with 250 g of anti-mouse PD-L1 (clone MIH5; Polpharma Biologies), antimouse CTLA-4 (clone 4F10; Polpharma Biologies), anti- mPD-l(RMPl-14; Polpharma Biologies), anti-mouse HAVcr-2 (clone B8.2C12; BioXCell), or anti- mouse VISTA (clone 13F3; BioXCell), on day 11, 14 and 18 via i.p. injections. Mice were monitored and weighed every other day and tumor volume was determined by height x width x length.
  • TILs Murine tumor infiltrating leukocytes
  • Tumors were isolated at day 24 after tumor injection. A single cell suspension was made, using the tumor dissociation kit (Miltenyi #130-096-730). TILs were isolated through magnetic bead separation via CD45 (Miltenyi #130-110-618). Isolated TILs were maintained in RPMI supplemented with 100 u/mL penicillin, 100 pg/L streptomycin, 2.5% Hepes Ph7.5, 10% heat-inactivated fetal bovine serum (FBS).
  • FBS heat-inactivated fetal bovine serum
  • F4/80 (clone T45-2342), CDl lb (clone ICRF44), HAVcr-2 (cloneB8.2C12) and VISTA (cloneMH5A).
  • FC receptor of all samples were blocked using TruStain FcX (Biolegend #101320) for 15min. Cells were further stained with the indicated antibodies above, diluted in 0.5% BSA, for lh and fixed with cytofix (BD Bioscience #554655). After fixation, cells were maintained in 0.5% BSA. Flow cytometry was performed on FACSCanto (BD Bioscience) or the ID7000 (SONY). Cell doublets were excluded based on FSC-A/FSC-H. Flow cytometry data was analysed using Flow Jo.
  • the scRNAseq atlas generated in [25] was used to obtain the minimal gene list.
  • Talk2Data’s co-expression function was used to calculate the absolute Jaccard scores amongst genes of HAVCR2(+)VSIR(+)TAMs signature indicated in Table 1, guided by VSIR and CSF1R.
  • VSIR and CSF1R had the highest Jaccard index (0.53) and were therefore used to guide the search for the minimal gene list.
  • TAM Tumor Associated Macrophages
  • Proportion of cells (number of cells expressing the gene to total amount of cells - %) and expression levels (Z-score) of indicated genes. This heightened (co-)expression of HAVCR2 and VSIR was unique for TAM compartment since it was not seen in other broad T or B cell subsets and dendritic cells (DCs) as shown in Table 4.
  • HAVCR2(+)VSIR(+) phenotype was strongly associated with anti-inflammatory SPP1(+)TAM in primarily MSS-CRC , rather than pro -inflammatory TAMs or MSI-CRC (Table 7).
  • Table 7 scRNAseq data from 23 primary colorectal cancer (CRC) patients (4 microsatellite instable high (MSI-H) and 19 microsatellite stable (MSS)) including 10 matched normal adjacent tissues.
  • HAVCR2(+)VSIR(+) vs. HAVCR2(-)VSIR(-)TAM showed that HAVCR2(+)VSIR(+)TAM enriched for phagocytosis, pattern-recognition receptor (PRR) signaling relevant for danger sensing (e.g., nucleic acids), and anti-inflammatory signaling (Table 8).
  • PRR pattern-recognition receptor
  • Table 8 aggregated scores for representative pathway terms based on a broader differential pathway-enrichment analysis between HAVCR2(+)VSIR(+)TAM vs. HAVCR2 NEG VSIR NEG TAMS in CRC patient dataset from Table 7.
  • HAVCR2(+)VSIR(+)TAM signature was used as a guide to find similar immune populations in a massive database of -300 publicly- available scRNAseq datasets spanning >60 normal or diseased tissues [6]. Strikingly, the alignment between HAVCR2(+)VSIR(+)TAM signature and macrophages was a dominant characteristic of multiple human tumors (especially of epithelial -origin), rather than other healthy/diseased tissues.
  • HAVCR2(+)VSIR(+)TAM niche is preferentially enriched in immuno-resistant human tumors and allowed us to extract a signature for HAVCR2(+)VSIR(+)TAM which included all genes positively enriched when HAVCR2(+)VSIR(+)TAM are present in the tumor (Table 1).
  • HAVCR2(+)VSIR(+) TAM embed in the human pan-cancer immune- landscape and how they prognostically or predictively associate with patient survival we pursued a high-powered bulk-tumor transcriptome and high resolution scRNAseq mapping.
  • HAVCR2(+)VSIR(+)TAM signature associated with increased hazard ratio (HR>1) implying shorter overall survival (OS) in all the pan-cancer immune-landscape classes, except the immunogenic IFNy-dominant tumors (Table 9).
  • HAVCR2(+)VSIR(+) TAM niche we selected following representative, epithelial-origin, tumor models syngeneic for C57BL/6 mice: non-immunogenic LLC (macrophage HIGH IFNy-signalling LOW ) versus immunogenic MC38 (macrophage LOW IFNy-signalling HIGH ).
  • ICD immunogenic cell death
  • PTX paclitaxel
  • Apoptotic ICD is well-established to propagate danger signaling and create immunogenic phagocytic interface [22], [23].
  • CDDP cisplatin
  • HAVcr-2 or VISTA blockade synergized with only PTX (but not CDDP) to cause significant tumor regression (figures 10 and 12).
  • Such synergism was absent in MC38-tumours (figures 11 and 13).
  • the triple combination of PTX-treatment with HAVcr-2 and VISTA co-blockade was not significantly different from doublet combinations thereby indicating that HAVcr-2 or VISTA performed redundant, rather than separate, immune functions (figure 14).
  • HAVcr-2 or VISTA blockade synergizes with ICD-inducing chemotherapy to re-polarize Havcr2(+)Vsir(+) TAM toward pro -inflammatory phenotype, which associated with regression of non- immunogenic LLC -tumors.
  • EEF1A1, RPSA, GPX1, ITM2B, ACTG1, RPL13A, ARPC3, ACTB, PPIA, PTMA, TMSB4X and CTSC had an increased hazard ratio (HR>1) implying shorter overall survival (OS) and negative prognostic impact (Table 10).
  • Table 10 Gene expression of all 86 genes of HAVCR2+VSIR+ tumor associated macrophage/TAM signature and their Hazard ratio (HR) for the impact on overall survival (OS) and p-value.
  • Table 11 Jaccard index per gene for VSIR, HAVCR2 and CSF1R.
  • sensitivity to VISTA or HAVcr-2 multimodal ICD therapy z.e. therapy combining HAVcr-2 and/or VISTA blockade with an ICD inducer.

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • Wood Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Hospice & Palliative Care (AREA)
  • Biophysics (AREA)
  • Oncology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

La présente invention concerne un procédé de prédiction de la réponse à l'immunothérapie anticancéreuse d'un patient cancéreux et/ou de pronostic de la survie d'un patient cancéreux et/ou de quantification de macrophages associés à une tumeur exprimant à la fois HAVCR2 et VSIR dans un échantillon tumoral provenant d'un patient cancéreux et/ou de quantification de macrophages associés à une tumeur exprimant CSF1R, HAVCR2 et VSIR dans un échantillon tumoral provenant d'un patient cancéreux par mesure de l'expression de gènes sélectionnés. La présente invention concerne en outre l'utilisation du procédé de l'invention pour prédire la réponse à l'immunothérapie anticancéreuse d'un patient cancéreux, dans une méthode de traitement du cancer.
PCT/EP2024/080633 2023-10-30 2024-10-30 Signature génétique pour prédire une réponse à une thérapie par inhibiteur de point de contrôle immunitaire Pending WO2025093579A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
EP23206642.3 2023-10-30
EP23206642 2023-10-30

Publications (1)

Publication Number Publication Date
WO2025093579A1 true WO2025093579A1 (fr) 2025-05-08

Family

ID=88600173

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/EP2024/080633 Pending WO2025093579A1 (fr) 2023-10-30 2024-10-30 Signature génétique pour prédire une réponse à une thérapie par inhibiteur de point de contrôle immunitaire

Country Status (1)

Country Link
WO (1) WO2025093579A1 (fr)

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2019070755A1 (fr) * 2017-10-02 2019-04-11 The Broad Institute, Inc. Procédés et compositions pour détecter et moduler une signature génétique de résistance à l'immunothérapie dans un cancer
WO2019232542A2 (fr) * 2018-06-01 2019-12-05 Massachusetts Institute Of Technology Procédés et compositions pour détecter et moduler des signatures géniques micro-environnementales à partir du lcr de patients présentant des métastases
WO2022012420A1 (fr) * 2020-07-17 2022-01-20 信达生物制药(苏州)有限公司 Combinaison de nucléotides et son utilisation
WO2023081117A1 (fr) * 2021-11-02 2023-05-11 The Regents Of The University Of California Ciblage d'immunothérapie

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2019070755A1 (fr) * 2017-10-02 2019-04-11 The Broad Institute, Inc. Procédés et compositions pour détecter et moduler une signature génétique de résistance à l'immunothérapie dans un cancer
WO2019232542A2 (fr) * 2018-06-01 2019-12-05 Massachusetts Institute Of Technology Procédés et compositions pour détecter et moduler des signatures géniques micro-environnementales à partir du lcr de patients présentant des métastases
WO2022012420A1 (fr) * 2020-07-17 2022-01-20 信达生物制药(苏州)有限公司 Combinaison de nucléotides et son utilisation
WO2023081117A1 (fr) * 2021-11-02 2023-05-11 The Regents Of The University Of California Ciblage d'immunothérapie

Non-Patent Citations (30)

* Cited by examiner, † Cited by third party
Title
A. D. GARG ET AL.: "Pathogen response-like recruitment and activation of neutrophils by sterile immunogenic dying cells drives neutrophil-mediated residual cell killing", CELL DEATH DIFFER., vol. 24, 2017, pages 832 - 843
A. D. GARG, E. ROMANO, N. RUFO, P. AGOSTINIS: "Immunogenic versus tolerogenic phagocytosis during anticancer therapy: mechanisms and clinical translation", DEATH DIFFER., vol. 23, 2016, pages 938 - 951
A. LÁNCZKYB. GYORFFY: "Web-Based Survival Analysis Tool Tailored for Medical Research (KMplot): Development and Implementation", J. MED. INTERNET RES., vol. 23, 2021, pages e27633
A. MANTOVANIP. ALLAVENAF. MARCHESIC. GARLANDA: "Macrophages as tools and targets in cancer therapy", NAT. REV. DRUG DISCOV., vol. 21, 2022, pages 799 - 820, XP093113995, DOI: 10.1038/s41573-022-00520-5
A. MAYNARD ET AL.: "Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing", CELL, vol. 182, 2020, pages 1232 - 1251
A. MURGASKI ET AL.: "Efficacy of CD40 agonists is mediated by distinct cdc subsets and subverted by suppressive macrophages", CANCER RES., vol. 82, 2022, pages 3785 - 3801
AUSBACHER ET AL., BIOCHIM BIOPHYS ACTA, vol. 1818, 2012, pages 2917 - 2925
CITING LIFELINES - LIFELINES 0.27.4 DOCUMENTATION, Retrieved from the Internet <URL:https://lifelines.readthedocs.io/en/stable/Citing%20lifelines.html>
COULTON ET AL.: "Using a pan-cancer atlas to investigate tumour associated macrophages as regulators of immunotherapy response", NAT. COMMUN., vol. 15, no. 1, 6 July 2024 (2024-07-06), pages 5665
F. FINOTELLO ET AL.: "Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data", GENOME MED, vol. 11, 2019, pages 34, XP055779315, DOI: 10.1186/s13073-019-0638-6
G. CURIGLIANO ET AL.: "Phase I/Ib Clinical Trial of Sabatolimab, an Anti-TIM-3 Antibody, Alone and in Combination with Spartalizumab, an Anti-PD-1 Antibody, in Advanced Solid Tumors", CLIN. CANCER RES., vol. 27, 2021, pages 3620 - 3629, XP093005120, DOI: 10.1158/1078-0432.CCR-20-4746
G. KROEMERC. GALASSIL. ZITVOGELL. GALLUZZI: "Immunogenic cell stress and death", NAT. IMMUNOL., vol. 23, 2022, pages 487 - 500
GALLUZZI ET AL.: "Consensus guidelines for the definition, detection and interpretation of immunogenic cell death", J IMMUNOTHER CANCER, vol. 8, no. 1, 2020, pages e000337
H.-O. LEE ET AL.: "Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer", NAT. GENET., vol. 52, 2020, pages 594 - 603, XP037156945, DOI: 10.1038/s41588-020-0636-z
HAUG ET AL., JOURNAL OF MEDICINAL CHEMISTRY, vol. 59, no. 868540-17-4, 2016, pages 2918 - 2927
I. VANMEERBEEK ET AL.: "Trial watch: chemotherapy-induced immunogenic cell death in immuno-oncology", ONCOIMMUNOLOGY, vol. 9, 2020, pages 1703449
J. SPROOTEN: "Peripherally-driven myeloid NFkB and IFN/ISG responses predict malignancy risk, survival, and immunotherapy regime in ovarian cancer", J. IMMUNOTHER. CANCER., vol. 9, 2021
J. VIVIAN ET AL.: "Toil enables reproducible, open source, big biomedical data analyses", NAT. BIOTECHNOL., vol. 35, 2017, pages 314 - 316
K. MULDER ET AL.: "Cross-tissue single-cell landscape of human monocytes and macrophages in health and disease", IMMUNITY, vol. 54, 2021, pages 1883 - 1900
M. J. GOLDMAN ET AL.: "Visualizing and interpreting cancer genomics data via the Xena platform", NAT. BIOTECHNOL., vol. 38, 2020, pages 675 - 678, XP037167652, DOI: 10.1038/s41587-020-0546-8
M. SADE-FELDMAN ET AL.: "Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma", CELL, vol. 175, no. 1632032-53-1, 2018, pages 998 - 1013
P. LIU ET AL.: "Crizotinib-induced immunogenic cell death in non-small cell lung cancer", NAT. COMMUN., vol. 10, 2019, pages 1486, XP055735534, DOI: 10.1038/s41467-019-09415-3
PETTY AMY J. ET AL: "Targeting Tumor-Associated Macrophages in Cancer Immunotherapy", CANCERS, vol. 13, no. 21, 22 October 2021 (2021-10-22), CH, pages 5318, XP093147442, ISSN: 2072-6694, DOI: 10.3390/cancers13215318 *
S. A. KOVÁCSB. GYORFFY: "Transcriptomic datasets of cancer patients treated with immune-checkpoint inhibitors: a systematic review", J. TRANSL. MED., vol. 20, 2022, pages 249
S. NAULAERTS ET AL., BIORXIV
SCIPY - CITING SCIPY, Retrieved from the Internet <URL:https://scipy.org/citing-scipy>
T. D. WU ET AL.: "Peripheral T cell expansion predicts tumour infiltration and clinical response", NATURE, vol. 579, 2020, pages 274 - 278, XP037060242, DOI: 10.1038/s41586-020-2056-8
T. LE ET AL.: "BBrowser: Making single-cell data easily accessible", BIORXIV, 2020
V. THORSSON ET AL.: "The immune landscape of cancer", IMMUNITY, vol. 48, 2018, pages 812 - 830
XIE XIAOXUE ET AL: "The Expression Pattern and Clinical Significance of the Immune Checkpoint Regulator VISTA in Human Breast Cancer", FRONTIERS IN IMMUNOLOGY, vol. 11, 29 October 2020 (2020-10-29), Lausanne, CH, XP093147165, ISSN: 1664-3224, DOI: 10.3389/fimmu.2020.563044 *

Similar Documents

Publication Publication Date Title
Camidge et al. Comparing and contrasting predictive biomarkers for immunotherapy and targeted therapy of NSCLC
JP7401710B2 (ja) 正規化バイオマーカースコアからがん治療を特定するためのシステム及び方法
Figueiredo et al. Loss of BAP1 expression is associated with an immunosuppressive microenvironment in uveal melanoma, with implications for immunotherapy development
Park et al. Future prospects of immune checkpoint blockade in cancer: from response prediction to overcoming resistance
Karasaki et al. An immunogram for the cancer-immunity cycle: towards personalized immunotherapy of lung cancer
Kasikova et al. Calreticulin exposure correlates with robust adaptive antitumor immunity and favorable prognosis in ovarian carcinoma patients
JP6630742B2 (ja) ファルネシルトランスフェラーゼ阻害剤を用いて癌患者を治療する方法
Catacchio et al. Immune prophets of lung cancer: the prognostic and predictive landscape of cellular and molecular immune markers
Parra et al. Immunohistochemical and image analysis-based study shows that several immune checkpoints are co-expressed in non–small cell lung carcinoma tumors
US11473150B2 (en) Methods for the detection and treatment of classes of hepatocellular carcinoma responsive to immunotherapy
US20150218649A1 (en) Biomarker associated with risk of melanoma reoccurrence
Alame et al. The immune contexture of primary central nervous system diffuse large B cell lymphoma associates with patient survival and specific cell signaling
Zhang et al. Differential expression of PD-L1 and IDO1 in association with the immune microenvironment in resected lung adenocarcinomas
KR20220022050A (ko) 지속적인 임상 이익을 위한 암 바이오마커
CN112567052A (zh) 预后和治疗响应预测方法
Shinohara et al. New evaluation of the tumor immune microenvironment of non-small cell lung cancer and its association with prognosis
US20190284640A1 (en) Methods and Systems for Predicting Response to Immunotherapies for Treatment of Cancer
JP2024521124A (ja) がん治療に対する応答を予測するｍｉｒｎａ
WO2017042815A1 (fr) Structures lymphoïdes ectopiques utilisées en tant que cibles pour la détection du cancer du foie, pour la prédiction de risques et la thérapie
Willmes et al. SERPINB1 expression is predictive for sensitivity and outcome of cisplatin-based chemotherapy in melanoma
WO2025093579A1 (fr) Signature génétique pour prédire une réponse à une thérapie par inhibiteur de point de contrôle immunitaire
US20230323468A1 (en) Immune gene signatures in muscle invasive bladder cancer
WO2023282749A1 (fr) Classificateur génique pour les phénotypes immunitaires spatiaux du cancer
JP2024508856A (ja) 卵巣がんの診断方法及び処置方法
JP2023538783A (ja) 前立腺がんの放射線治療用線量の選択

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 24799210

Country of ref document: EP

Kind code of ref document: A1