Functional analyses of super-enhancer dysregulation in colorectal carcinoma patient samples.

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PROJECT SUMMARY Colorectal carcinoma (CRC) represents a malignancy that is among the highest in both cancer incidence and mortality in men and women in the United States, yet disease remains dependent on cytotoxic therapies as standard of care, highlighting a need for the identification of novel targets. We and other groups have demonstrated extensive enhancer reprogramming in CRC; however, their biological impact on disease progression remains unknown. Using a tissue ChIP-seq and RNA-seq approach on human CRC tumors and matched normal epithelium, I found that enhancer reprogramming in CRC extends to the super-enhancer (SE) landscape. The inclusion of an equal number of patient-matched normal colorectal crypt epithelium controls identifies de novo formation of aberrant, tumor-specific super-enhancers as well as frequent loss of physiologic normal-specific SEs with high recurrence across my cohort of samples. Super-enhancers are well-described to selectively regulate key cell identity genes including proto-oncogenes in malignant cells—their profiling is an established framework in target discovery in many difficult to treat cancers through leveraging epigenomic dysregulation. Thus, our preliminary findings have unique implications for CRC biology. In this proposal, I seek to elucidate a function for top recurrently gained and lost super-enhancers in CRC tumors. I will test the hypothesis that perturbing both SEs and putative regulated genes will affect proliferation and invasion in CRC using in vitro and colon organoid driven in vivo models. Findings from the proposed project will advance knowledge in the field of how the active regulatory landscape in CRC tumors contributes to tumorigenesis, promoting novel avenues of investigation and therapeutic targeting.