Convergent mutations in tissue-specific regulatory regions reveal novel cancer drivers

Abstract

Although much effort has been devoted to identifying coding mutations across cancer types, regulatory mutations remain poorly characterized. Here, we describe a framework to identify non-coding drivers by aggregating mutations in cell-type specific regulatory regions for each gene. Application of this approach to 2,634 patients across 11 human cancer types identified 60 pan-cancer, 22 pan-breast and 192 cancer specific candidate driver genes that were enriched for expression changes. Analysis of high-throughput CRISPR knockout screens revealed large, cancer specific growth effects for these genes, on par with coding mutations and exceeding that for promoter mutations. Amongst the five candidate drivers selected for further analysis, four (IPO9, MED8, PLEKHA6, and OXNAD1) were associated with survival across multiple cancer types. These studies demonstrate the power of our cell-type aware, convergent regulatory framework to define novel tissue specific cancer driver genes, considerably expanding evidence of functional non-coding mutations in cancer.