IMMUNOMARK · Omics integration for precision cancer immunotherapy

Omics integration for precision cancer immunotherapy

Checkpoint inhibitor therapy constitutes a promising cancer treatment strategy that targets the immune checkpoints to re-activate silenced T cell cytotoxicity. Immune checkpoint blockade (ICB) demonstrated durable responses and acceptable toxicity. However, up to ~85% of patients present with innate or acquired resistance to ICB, limiting its clinical utility. Current response biomarker candidates, including DNA mutation and neoantigen load, immune profiles, as well as programmed death-ligand 1 (PD-L1) expression, are only weak predictors of ICB response. Thus, identification of novel, more predictive biomarkers constitutes one of the most important areas of immunotherapy research. In IMMUNOMARK, we proposed a multilayer integrative omics analysis to identify biomarkers of clinical response to immunotherapy amenable to be used in liquid biopsies, and therefore contribute to reach the Horizon 2020 Research & Innovation goal: “to improve our ability to monitor health and to prevent, detect, treat and manage disease”. The specific scientific goal was to identify definite biomarkers predictive of the response to anti-PD-1, anti-PD-L1, and anti-CTLA4 therapy in patients with metastatic melanoma and advanced Non–Small-Cell Lung Cancer (NSCLC). Our research strategy, implemented in two Work Packages, consisted of the multidimensional exploration of putative players in the innate and acquired resistance scenarios. On one hand, we hypothesized that the phenotypic changes associated to the resistance to ICB are not only related to genetic variants but also to epigenetic differences among individuals. Other dimension integrated in the study was the stroma, which has resulted vital for deciphering which cells of the inflammatory infiltrate are the most important for determining a good response to ICB. Finally, we considered not only solid biopsies but also liquid biopsies in order to search for non-invasive biomarkers of response that could give a real-time information of the treatment efficacy. The most important conclusions derived from the results of this study are two: 1) The most significant mechanisms of response to ICB in both metastatic melanoma and NSCLC patients are driven by a differential activity of specific cells of the immune system. - In NSCLC, the EPIMMUNE CpG signature, specifically the unmethylated status of a CpG site of FOXP1, a gene related to quiescent naïve CD4+ T-cells, is associated with favorable outcome of ICB treated patients. - In metastatic melanoma, a transcriptomic signature of 140 genes defines the innate response to ICB, and 58 out of them are associated with overall survival, constituting new putative predictors of outcome. Importantly, the differential expression signature has unmasked a major contribution of the B lymphocytes in the response to ICB in melanoma patients, which has been validated in single cell RNA-seq datasets. Moreover, we have identified the plasmablast-like B lymphocytes as the specific subtype enriched in the patients that respond well to ICB; overall, this opens a completely new avenue for disentangling the immune-suppressor role of B cells in cancer. 2) Direct Fluorescence-activated cell-based quantification of specific lymphocyte and myeloid cell populations in peripheral blood from patients from metastatic melanoma and NSCLC provides non-invasive biomarkers of outcome to ICB treatment. In addition, their combination with specific clinicopathological variables in logistic regression prediction model increases the ability to predict response with high specificity and sensitivity.

Data: CORDIS, © European Union