A pan-cancer clinical platform to predict immunotherapy outcomes and prioritize immuno-oncology combinations in early-phase trials
Alberto Hernando‐Calvo, María Vila-Casadesús, Yacine Barèche, Alberto González‐Medina, Farnoosh Abbas‐Aghababazadeh, Deborah Lo Giacco, Ágatha Martín, Omar Saavedra, Irene Braña, María Vieito, Roberta Fasani, John Stagg, Francesco M. Mancuso, Benjamin Haibe‐Kains, Ming Han, Roger Berché, Trevor J. Pugh, Oriol Mirallas, José Jimenez, N. Saoudi Gonzalez, Claudia Valverde, Eva Muñoz‐Couselo, Cristina Suárez, Marc Díez, Elena Élez, Jaume Capdevila, Ana Oaknin, Cristina Saura, Teresa Macarulla, Joan Carles, Enriqueta Felip, Rodrigo Dienstmann, Philippe L. Bédard, Paolo Nucíforo, Joan Seoane, Josep Tabernero, Elena Garralda, Ana Vivancos
Abstract
BACKGROUND: Immunotherapy is effective, but current biomarkers for patient selection have proven modest sensitivity. Here, we developed VIGex, an optimized gene signature based on the expression level of 12 genes involved in immune response with RNA sequencing. METHODS: We implemented 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 three main categories (hot, intermediate-cold and cold) based on the different inflammatory status of the tumor microenvironment. FINDINGS: Hot tumors had the highest VIGex scores and exhibited an increased abundance of tumor-infiltrating lymphocytes as compared with 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 observed in a cohort of 98 refractory solid tumor from patients treated in early-phase immunotherapy trials and its clinical performance was confirmed through an extensive metanalysis across 13 clinically annotated gene expression datasets from 877 patients treated with immunotherapy agents. Last, we generated a pan-cancer biomarker platform that integrates VIGex categories with the expression levels of immunotherapy targets under development in early-phase clinical trials. CONCLUSIONS: Our results support the clinical utility of VIGex as a tool to aid clinicians for patient selection and personalized immunotherapy interventions. FUNDING: BBVA Foundation; 202-2021 Division of Medical Oncology and Hematology Fellowship award; Princess Margaret Cancer Center.