A Pan-Cancer Clinical Platform to Predict Immunotherapy Outcomes and Prioritize Immuno-Oncology Combinations in Early-Phase Trials

Immunotherapy (IO) is effective in multiple tumor types but current biomarkers for patient selection have proven modest sensitivity and their clinical utility is often limited by the need for complex profiling assays. Here, we developed VIGex, an optimized gene signature based on the expression level of 12 genes involved in immune response and T-cell exhaustion with RNA-seq. To achieve clinical utility and scalability, we implemented and validated VIGex using the nCounter platform (Nanostring) on a large clinical cohort encompassing 909 tumor samples across 45 tumor types. VIGex was developed as a continuous variable, with cutoffs selected to detect 3 main categories (Hot, Intermediate-Cold and Cold) based on the different inflammatory status of the tumor microenvironment as assessed by systematic clustering analysis. Hot tumors had the highest VIGex scores and exhibited an increased abundance of tumor-infiltrating lymphocytes as compared to the Intermediate-Cold and Cold. VIGex scores varied depending on tumor origin and anatomic site of metastases, with liver metastases showing an immunosuppressive tumor microenvironment. The predictive power of VIGex-Hot was validated in a cohort of 98 refractory solid tumor from patients treated in early phase IO trials and its clinical performance was confirmed through an extensive metanalysis across 13 clinically-annotated gene expression datasets from 877 patients treated with IO agents. Lastly, we generated a pan-cancer biomarker platform that integrates VIGex categories with the expression levels of IO targets under development in early phase clinical trials. Applying this clinical platform, we provide a biology-informed prioritization of IO combination regimens to guide clinical treatment decisions. Our results support the clinical utility of VIGex as a tool to aid clinicians for patient selection and personalized IO interventions. Funding Information: This research has been funded by the Comprehensive Program of Cancer Immunotherapy & Immunology II (CAIMI-II) supported by the BBVA Foundation (grant 53/2021). A. Hernando-Calvo would like to acknowledge fellowship funding from the Spanish Society of Medical Oncology (SEOM) and CRIS Cancer Foundation and Hold´em For Life Oncology Fellowship. Declaration of Interests: A. Hernando-Calvo reports financial Interests, Personal, Other, Travel, Accommodations, Expenses: Merk Serono and Kyowa Kirin International. I. Brana reports research funding for the present manuscript from Incyte, Merck Sharp & Dohme (MSD), Cellex Foundation, La Caixa Foundation, BBVA Foundation Comprehensive Program of Cancer Immunotherapy and Immunology (CAIMI) - (grant 89/2017). Other research funding as principal investigator: Astrazeneca, Bicycle therapeutics, Boehringer Ingellheim, Bristol Myers Squibb, Celgene, Dragonfly, GlaxoSmithkline, Gliknik, Immutep, ISA Pharmaceuticals, Janssen Oncology, Kura, Merck Serono, Nanobiotics, Novartis, Northern Biologics, Orion Pharma, Odonate Therapeutics, Regeneron, Pfizer, Sanofi, Pharmamar, Seattle Genetics, Shattuck Labs and VCN Biosciences. Consulting fees: Achilles Therapeutics, Bristol Myers Squibb, Cancer Expert Now, eTheRNA immunotherapies, Merck Serono, Merck Sharp & Dohme (MSD), Rakuten pharma, Boehringer Ingellheim and PCI biotech. Payment or honoraria: Bristol Myers Squibb, Merck Serono, Merck Sharp & Dohme (MSD). Support for attending meetings and/or travel: Merck Sharp &Dohme (MSD) and Merck Serono. Leadership or fiduciary role in other board, society, committee or advocacy group, paid or unpaid: ESMO Head and Neck track, EORTC Head and Neck group and Cancer Core Europe Clinical Taskforce. Other financial or non-financial interests: Bristol Myers Squibb educational grant. J. Stagg- Advisory Board, Personal: Surface Oncology, Tarus Therapeutics. Stocks/Shares, Personal: Surface Oncology. Research Grant, Institutional, Financial interest: Surface Oncology. BHK co-Founder of the MAQC (Massive Analysis and Quality Control) Society. BHK SAB of: Consortium de recherche biopharmaceutique (CQDM), Quebec; Canada Break Through Cancer; Commonwealth Cancer Consortium, United States; Canadian Institute of Health Research - Institute of Genetics, Canada; IONIQ Sciences, US. BHK: Executive Committee of the Terry Fox Digital Health and Discovery Platform, Canada, and Board of Directors of AACR International - Canada, The American Association for Cancer Research, United States. BHK consultant for Code Ocean Inc, United States. C. Valverde reports financial interest as advisory board, personal: Bayer, Boehringer Ingelheim, GSK, Lilly, Mundipharma, PharmaMar. Invited speaker, personal: Roche. Local PI, Institutional, Financial interest, clinical trial: Adaptimmune, Ayala Therapeutics, Bayer (coordinating PI), Foghorn Therapeutics, Inhibrx, Karyopharm and Lilly. Non-financial interest: GEIS-Spanish Sarcoma Group for Research, Member of Board of Directors. President since 2018.E. Muñoz-Couselo - Advisory board: Amgen, Bristol-Myers Squibb, Merck Sharp & Dohme, Novartis, Pierre Fabre, Roche, Sanofi. Honoraria:Amgen, Bristol-Myers Squibb, Merck Sharp & Dohme, Novartis, Pierre Fabre, Roche. Clinical trial participation (principal investigator): Bristol-Myers Squibb, GlaxoSmithKline, Merck Sharp & Dohme, Novartis, Pierre Fabre, Roche. C. Suarez Invited Speaker, Personal: Astellas pharma, Bristol Myers Sqquib (Inst), Hoffmann-La Roche LTD, Ipsen, Pfizer S.L.U. Advisory board, personal: Astellas pharma, Bayer, Bristol Myers Sqquib (Inst), Hoffmann-La Roche LTD, Ipsen, Merck Sharp Dohme, Pfizer S.L.U, Sanofi-Aventis. E. Élez Advisory Board, Personal: Amgen, Bayer, Hoffman LA-Roche, Merck Serono, MSD, Pierre Fabre, Sanofi, Servier. Invited Speaker, personal: Novartis, Organon. Funding, Institutional, Financial interest: Amgen Inc, Array Biopharma Inc, AstraZeneca Pharmaceuticals LP, BeiGene, Boehringer Ingelheim, Bristol-Myers Squibb International Corporation, Celgene International SARL, Debiopharm International SA, Genentech Inc, HalioDX SAS, Foffmann-La Roche Ltd, Hutchison MediPharma International, Janssen-Cilag SA, Medimmune, Menarini, Merck Health KGAA, Merck Sharp & Dohme de España SA, Merus NVS, Mirati, Novartis Farmaceútica SA, Pfizer, PharmaMar SA, Sanofi Aventis Recherche & Développement, Servier and Taiho Pharma USA Inc. Non Financial Interest: American Society of Clinical Oncology (ASCO), Other ,Volunteer member of the ASCO Annual Meeting Scientific Program Committee: Developmental Therapeutics – Immunotherapy; European Society for Medical Oncology (ESMO), Other , Speaker of the ESMO Academy; Sociedad Española de Oncología Médica (SEOM), Other: Coordinator of the SEOM +MIR Section of Residents and Young Assistants. Other (travel accomodations, expenses): Amgen, Array BioPharma, Bristo-Myers Squibb, Merck Serono, Roche, Sanofi and Servier. J. Capdevila Personal conflicts of interest:Scientific consultancy role (Speaker and advisory roles) from Novartis, Pfizer, Ipsen, Exelixis, Bayer, Eisai, Advanced Accelerator Applications, Amgen, Sanofi, Lilly, Huchinson Pharma, ITM, Advanz, Merck Serono, Esteve, Roche. Research support: Research grants from Novartis, Pfizer, Astrazeneca, Advanced Accelerator Applications, Eisai, Amgen and Bayer. A. Oaknin has served on advisory boards for Agenus, AstraZeceneca. Clovis Oncology, Inc., Corcept Therapeutics, Deciphera Pharmaceutical, Eisai Europe Limited, EMD Serono, Inc., F. Hoffmann-La Roche, GlaxoSmithKline, GOG, Immunogen, Medison Pharma, Merck Sharp & Dohme de España, Mersana Therapeutics, Novocure GmbH, Pharma Mar, prIME Oncology, ROCHE FARMA, Sattucklabs, Sutro Biopharma, Inc, and and received support for travel or accommodation from Roche, AstraZeneca, PharmaMar and GSK. Clovis. C.Saura has served as consultant, participated in advisory boards or received travel grants from: AstraZeneca, AX'Consulting, Byondis B.V, Daiichi Sankyo, Eisai, Exact Sciences, Exeter Pharma, F.Hoffmann-La Roche Ltd, ISSECAM, MediTech, Merck Sharp & Dohme, Novartis, Pfizer, Philips, Pierre Fabre, PintPharma, Puma Biotechnology, SeaGen, and Zymeworks. Dr. Macarullas hs received honoraria for consultancy from: Ability Pharmaceuticals, Amgen, AstraZeneca, Basilea Pharma, Baxter, BioLineRX Ltd, Celgene, Eisai, Ellipses, Esteve, Pharmaceuticals, Incyte, Ipsen Bioscience, Inc, Janssen, Lilly, MDS Medscape, Novocure, QED Therapeutics, Roche Farma, Sanofi-Aventis, Servier, and Zymeworks. Travel expenses from Servier, AstraZeneca, Sanofi and Incyte. Advisory Board, Personal: Astellas Pharma, AstraZeneca,Bayer, Johnson & Johnson, MSD Oncology, Novartis (AAA), Roche, Sanofi. Local PI, Institutional, No financial interest: Janssen-Cilag International NV. Lilly, S.A, Medimmune, Novartis Farmacéutica S.A, Sanofi-Aventis S.A. Advisory board: Amgen, Astra Zeneca, Bayer, Bristol-Myers Squibb, Daichi Sankyo, Eli Lilly, F. Hoffmann-La Roche, Glaxo Smith Kline, Janssen, Merck Sharp & Dohme, Merck Serono, Novartis, Peptomyc, Pfizer, Sanofi, Takeda. Invited speaker: Amgen, Astra Zeneca, Bristol-Myers Squibb, Eli Lilly, F. Hoffmann-La Roche, Janssen, Medscape, Merck Sharp & Dohme, Peervoice, Pfizer, Medical Trends, Merck Serono, Sanofi, Takeda, TouchOncology. Research funding:Merck Healthcare KGAa, Fundación Merck Salud. Independent member of the Board: Grífols. RD declares advisory role for Roche, Boehringer Ingelheim, received a speaker’s fee from Roche, Boehringer Ingelheim, Ipsen, Amgen, Servier, Sanofi, Libbs, Merck Sharp & Dohme, Lilly and AstraZeneca and research grants from Merck and Pierre Fabre. P. Bedard Local PI, Institutional: Amgen, AstraZeneca, Bicara, BMS, Genentech/Roche, Lilly, Merck, Nektar Therapeutics, Novartis, Pfizer, Sanofi, SeaGen and Zymeworks. Research Grant, Institutional: Pfizer. Funding, institutional: Servier. P. Nuciforo Advisory board, personal> Bayer, MSD Oncology. Invited speaker, personal: Novartis. Other, personal, consultant:Targos Molecular Pathology GmbH. J Seoane Memmber of Board of Directors, personal: Northern Biologics Inc. Ownership interest, Personal, Co-Founder: Mosaic Biomedicals. Research Grant, Institutional, No financial interest: Astra Zeneca, Hoffmann-La Roche LTD, Isarna Therapeutics, Mosaic Biomedicals SL, Northern Biologics INC, Ridgeline Therapeutics and Roche Glycart AG. Non-financial interests: Asociación Española contra el cancer (Member of Board of Directors), European Association for Cancer Research (ECR) (Member of Board of Directors, Secretary General). J.Tabernero reports personal financial interest in form of scientific consultancy role for Array Biopharma, AstraZeneca, Bayer, Boehringer Ingelheim, Chugai, Daiichi Sankyo, F. Hoffmann-La Roche Ltd, Genentech Inc, HalioDX SAS, Hutchison MediPharma International, Ikena Oncology, Inspirna Inc, IQVIA, Lilly, Menarini, Merck Serono, Merus, MSD, Mirati, Neophore, Novartis, Ona Therapeutics, Orion Biotechnology, Peptomyc, Pfizer, Pierre Fabre, Samsung Bioepis, Sanofi, Scandion Oncology, Scorpion Therapeutics, Seattle Genetics, Servier, Sotio Biotech, Taiho, Tessa Therapeutics and TheraMyc. Stocks: Oniria Therapeutics and also educational collaboration with Imedex/HMP, Medscape Education, MJH Life Sciences, PeerView Institute for Medical Education and Physicians Education Resource (PER). E Garralda Consulting or advisory role: Roche, Ellipses pharma, Neomed Therapeutics, Janssen, Boehringer Ingelheim. Seattle Genetics. TFS. Alkermes. Thermo Fisher Scientific. Bristol-Myers Squibb. MabDiscovery. Anaveon. F-Star Therapeutics. Speakers Bureau MSD, Roche, Thermo Fisher Scientific and Lilly. Research funding (recipient institution): Novartis. Roche. Thermo Fisher Scientific, AstraZeneca/MEdImmune, Taiho Oncology, BeiGene. Other relationship (recipient institution): Affimed Gmbh, Amgen SA, Anaveon AG, AstraZeneca AB, Biontech Gmbh, Catalym Gmbh, CytomX Therapeutics. F.Hoffmann La Roche Ltd, F-Satar Beta Limited, Genentech Inc, Genmab B.v, Hutchison MEdipharma Limited, Imcheck Therapeutics, Immunoscore Ltd, Janssen-Cilag SA, Medimmune Llc, Merck kgga, Novartis Farmaceutica, S.a, peptomyc, Ribon Therapeutics, Roche Farma SA, Seattle Genetics Inc, Symphogen A/S, Taiho Pharma Usa Inc. A Vivancos Advisory Board, personal: Bayer, Bristol Meyers Squibb, Guardant Health, Incyte, Roche. Stocks or Shares: Reveal Genomics. Research Grant, institutional, financial interest, preclinical research grant: Incyte and Roche. All others have nothing to declare. Ethics Approval Statement: Patients enrolled in the VHIO prescreening program had their tumors profiled by means of RNA-seq or Nanostring technology. This study received REB approval at Vall D’Hebron University Hospital.