Widespread perturbation of ETS factor binding sites in cancer

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. Overall design: The study consists of a single MPRA experiment testing somatic variants identified in cancers. Variants for screening were selected using a transcription factor aware burden test (TFA-BT). For each library we processed independent transfections in three unique cell lines; in total we completed 5 replicates of Jurkat (lymphoma), SK-MEL-28 (melanoma), and HT-29 (colorectal) cell lines. Raw data is provided as Illumina reads of the 20 bp barcode from the RNA extracted 24 hours post transfection as well as from the plasmid library used for transfection. We also provide Illumina paired-end reads used to link oligo/barcode combinations from the ?gfp vector. Processed count files are unnormalized counts for each oligo reported per barcode (uncollapsed).