Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes

Recent studies have shown that mutations at non-coding elements, such as promoters and enhancers, can act as cancer drivers. However, an important class of non-coding elements, namely CTCF insulators, has been overlooked in the previous driver analyses. We used insulator annotations from CTCF and cohesin ChIA-PET and analyzed somatic mutations in 1,962 whole genomes from 21 cancer types. Using the heterogeneous patterns of transcription-factor-motif disruption, functional impact, and recurrence of mutations, we developed a computational method that revealed 21 insulators showing signals of positive selection. In particular, mutations in an insulator in multiple cancer types, including 16% of melanoma samples, are associated with TGFB1 up-regulation. Using CRISPR-Cas9, we find that alterations at two of the most frequently mutated regions in this insulator increase cell growth by 40%–50%, supporting the role of this boundary element as a cancer driver. Thus, our study reveals several CTCF insulators as putative cancer drivers. [Display omitted] •Enrichment of CTCF motif-disrupting mutations is associated with neutral signatures•Novel computational method predicts 21 insulator drivers•A predicted driver on chr19 is associated with TGFB1 up-regulation•CTCF ChIP-seq, 3C, and CRISPR-Cas9 support the computational predictions We developed a computational method that combines recurrence and functional impact of mutations to identify cancer drivers. Application of the method on 1,962 cancer whole genomes reveals putative drivers at CTCF insulators. In particular, mutations in an insulator on chr19 are associated with TGFB1 up-regulation and may point to a novel mechanism of TGF-β signaling modulation in multiple cancer types.