Pan-cancer evolution signatures link clonal expansion to dynamic changes in the tumour immune microenvironment

Abstract

Cancer is an evolutionary process characterised by profound intra-tumour heterogeneity. Intra-tumour heterogeneity can be quantified using in silico estimates of cancer cell fractions of tumour-specific somatic mutations. Here we demonstrate a data-driven approach that uses cancer cell fraction distributions to identify 4 robust pan-cancer evolutionary signatures from an analysis of 4,146 individual tumour samples (TCGA) representing 17 distinct cancer types. Evolutionary signatures defined a continuum of cancer cell fractions representing neutral evolution, clonal expansion and fixation. Correlation of evolutionary signatures with programs representing distinct mutational and biological processes demonstrated that individual tumours enriched for clonal expansions and fixations were associated with immune evasion and distinct changes in the tumour immune microenvironment. We observed a dynamic switch between adaptive and innate immune processes as tumours undergo clonal fixation and escape immune surveillance. We also identify mutational processes underpinning different modes of tumour evolution and demonstrate that switching between adaptive and innate immune cell populations is accompanied by the clonal expansion of driver genes that modulate tumour-stroma interactions.