Abstract 2006: Comprehensive multiparametric analysis of non-small cell lung cancer describes novel genotype-immunophenotype relationships and provides putative biomarker signatures of response to checkpoint blockade
Authors: Javier Ramos-Paradas, David Gomez-Sanchez, Aranzazu Rosado, Irene Ferrer, Nuria Carrizo, Ana B. Enguita, Maria T. Muñoz, Urbicio Perez-Gonzalez, Ivan Martinez, Luis Paz-Ares, Eva M. Garrido-Martin
Journal: Cancer Research (2020)

Abstract Lung cancer leads cancer mortality, being Non-Small-Cell Lung Cancer (NSCLC) the most prevalent subtype. Immunotherapy with checkpoint inhibitors has shown promising results in NSCLC, yet this benefit is restricted to a subset of patients. Robust predictive biomarkers of response are lacking. We seek a multiparametric biomarker signature. We hypothesize that specific molecular alterations of NSCLC tumor cells have a deep impact on the immune microenvironment. Describing this relationship is critical to predict response to immunotherapy. We evaluated 178 samples from a retrospective cohort of clinically annotated early stage NSCLC patients. We analyzed their immune profile by immunohistochemistry and a RNAseq immune panel. In parallel, we defined their molecular aberrations and Tumor Mutational Burden by Next Generation Sequencing. We integrated our multiparametric data with Multi-Omics Factor Analysis. Adenocarcinomas (N=80) cluster in 4 groups with two main immunophenotypes. Key factors of this clustering are TOP2A, MKI67, CCNB2, CDK1, JCHAIN, VEGFA, PCLAF, KRT7, FOXM1, BUB1. The proimmune tumors upregulate genes related to immune activation (CD40LG, CD28, MS4A1), signaling (CD79B), chemoattraction (CXCR2), antigen presentation (CD1C, HLA-DQA2), inflammatory cytokines (IL2, IL1B), and immune cells (CD19). Oppositely, the protumoral samples overexpress genes involved in cell cycle (CCNB2, FOXM1, CDKN2A, CDKN3), immune inhibition (CD276), angiogenesis (VEGFA) and proliferation (AKT1, EGFR, PIK3CA, MTOR, MKI67). Regarding molecular characterization, KRAS mutation is enriched in the proimmune subset, while the protumoral one gathers mutations in ARID1A and ALK. Squamous cell carcinomas (N=98) cluster in 4 groups with two main immunophenotypes. Critical factors of this clustering are TRIM29, FOXM1, KRT5, TOP2A, MKI67, TFRC, CCNB2, CD44, EGFR, KREMEN1. The proimmune tumors upregulate genes involved in immune signaling (CD3D, CD3E, CD3G, CD79A, CD79B), activation (CD40LG, CD27, MS4A1), chemoattraction (CXCR5, CXCL13), antigen presentation (CD1C, HLA-DMA/DPB1/DRA/DMB/DOB), inflammatory cytokines (IFNG, IL17F, IL21), immune cells (CD8A, CD19) and immunomodulation (ICOS). Contrarily, the protumoral samples upregulate genes related to cell cycle (FOXM1, BUB1, CCNB2, CDK1), immune cells (FOXP3), angiogenesis (VEGFA), apoptosis (BCL2), immunomodulation (PD-L1) and proliferation (AKT1, MTOR, MYC, PIK3CA, MKI67). Of note, the proimmune subset has higher infiltration of CD8+, CD4+ and B cells. The protumoral one accrues mutations in TFRC, PIK3CA, PIK3CB, FGF3, FGF10. In conclusion, we performed a comprehensive description of novel NSCLC subgroups based on multiparametric data that will improve prediction of response to immunotherapy. Citation Format: Javier Ramos-Paradas, David Gomez-Sanchez, Aranzazu Rosado, Irene Ferrer, Nuria Carrizo, Ana B. Enguita, Maria T. Muñoz, Urbicio Perez-Gonzalez, Ivan Martinez, Luis Paz-Ares, Eva M. Garrido-Martin. Comprehensive multiparametric analysis of non-small cell lung cancer describes novel genotype-immunophenotype relationships and provides putative biomarker signatures of response to checkpoint blockade [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2006.