Tumor genomic subtypes orthogonal to mutation burden predict the efficacy of immune checkpoint therapy [article]

Shiro Takamatsu, Junzo Hamanishi, J.B. Brown, Ken Yamaguchi, Koji Yamanoi, Kosuke Murakami, Osamu Gotoh, Seiichi Mori, Masaki Mandai, Noriomi Matsumura
2021 medRxiv   pre-print
AbstractBackgroundIn cancer therapy, precise tumor-agnostic biomarkers that predict response to immune checkpoint inhibitors (ICIs) are needed. To explain treatment response differences among tumor types, the application of mutational signatures, patterns of genomic alterations that reflect differences in distinct underlying carcinogenic processes, holds promise but has not been extensively integrated into prediction methodologies.MethodsBased on mutational signature analysis, we developed a
more » ... atification for all solid tumors in The Cancer Genome Atlas (TCGA). Then, we developed the Tumor Genomic Subtype Analyzer (TGSA) to classify tumors submitted to whole-exome sequencing. Using existing data from 938 pan-cancer ICI-treated cases with outcomes, we evaluated the subtype-response predictive performance.ResultsSystematic analysis on TCGA samples identified eight tumor genomic subtypes, which were characterized by features represented by smoking exposure, ultraviolet light exposure, APOBEC enzyme activity, POLE mutation, mismatch repair deficiency, homologous recombination deficiency, genomic stability, and aging. The former five subtypes were presumed to form an immune-responsive group acting as candidates for ICI therapy because of their high expression of immune-related genes and enrichment in cancer types with FDA approval for ICI monotherapy. In the validation cohort, the samples assigned by TGSA to the immune-reactive subtypes were significantly related to ICI response independent of cancer type and high TMB status.ConclusionMutational signature-based tumor subtyping can serve as a tumor-agnostic biomarker for ICI response prediction. The results indicate that the mutational process underlying carcinogenesis affects tumor immunogenicity, and thus sensitivity to ICI.
doi:10.1101/2021.10.03.21264330 fatcat:fqjpx4ask5erzlomkudlacbzqa