Widespread perturbation of ETS factor binding sites in cancer [SCREEN_HOOK_SIGGERS_v2]

Although >90% of somatic mutations reside in non-coding regions, few have been reported as cancer drivers. To predict driver non-coding variants (NCVs), we present a novel transcription factor (TF)-aware burden test (TFA-BT) based on a model of coherent TF function in promoters. We applied our TFA-BT to NCVs from the Pan-Cancer Analysis of Whole Genomes cohort and predicted 2,555 driver NCVs in the promoters of 813 genes across 20 cancer-types. These genes are enriched in cancer-related gene ontologies, essential genes, and genes associated with cancer prognosis. We found that 765 candidate driver NCVs alter transcriptional activity, 510 lead to differential binding of TF-cofactor regulatory complexes, and that they primarily impact the binding of ETS factors. Finally, we show that different NCVs within a promoter often affect transcriptional activity through shared mechanisms. Our integrated computational and experimental approach shows that cancer NCVs are widespread and that ETS factors are commonly disrupted. Differential Cofactor (COF) recruitment screen to cancer non-coding variants (NCVs) (ID: 086310) – These experiments profiled recruitment of a panel of six COFs (SRC1/NCOA1, BRD4, KAT8/MOF, NCOR1, RBBP5, TBL1XR1) to 2,956 pairs of reference and alternate alleles predicted by our transcription factor-aware burden test (TFA-BT). COF recruitment was profiled using nuclear extracts from SK-MEL-28 and Jurkat cells. Technical replicates were performed (REP1 and REP2) for each COF screened. NCV CASCADE (ID: 086772) – These experiments use the CASCADE approach to characterize COF recruitment motifs for target loci by profiling recruitment to all single-nucleotide variants across each locus. Motifs were determined for 395 NCV loci identified as differentially bound between reference and alternate alleles in our initial screen. COF recruitment was profiled using the same six COFs and nuclear extracts from Jurkat cells. Technical replicates were performed for each COF screened.