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Germline features associated with immune infiltration in solid tumors

By Sahar Shahamatdar, Meng Xiao He, Matthew Reyna, Alexander Gusev, Saud H AlDubayan, Eliezer M Van Allen, Sohini Ramachandran

Posted 24 Mar 2019
bioRxiv DOI: 10.1101/586081

Given the clinical success of immune checkpoint blockade (ICB) across a diverse set of solid tumors, and the emerging role for different immune infiltrates in contributing to response to ICB, a comprehensive assessment of the properties that dictate immune infiltrations may reveal new biological insights and inform the development of new effective therapies. Multiple studies have examined somatic and functional immune properties associated with different tumor infiltrates; however, germline features that associate with specific immune infiltrates in cancers have been incompletely characterized. Here, we analyzed over 7 million autosomal germline variants in the TCGA cohort (5788 European-ancestry samples across 30 cancer types) and tested for pan-cancer association with established immune-related phenotypes that describe the tumor immune microenvironment. We identified: one SNP associated with the fraction of follicular helper T cells in bulk tumor; 77 unique candidate genes, some of which are involved in cytokine-mediated signaling (e.g. CNTF and TRIM34) and cancer pathogenesis (e.g. ATR and AKAP9); and subnetworks with genes that are part of DNA repair (RAD51 and XPC) and transcription elongation (CCNT2) pathways. We found a positive association between polygenic risk for rheumatoid arthritis and absolute fraction of infiltrating CD8 T cells. Overall, we identified multiple germline genetic features associated with specific tumor-immune phenotypes across cancer, and developed a framework for probing inherited features that contribute to variation in immune infiltration.

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