Uncovering cancerous enhancers of prostate and breast cancers

More than 95% of the human genome is not used for coding of proteins; named also the “dark matter” of the genome. It has become increasingly clear in recent years that this non-protein-coding DNA in fact plays a crucial role in the regulation of genes. In these regions there are approximately 500,000 'enhancer' elements. Enhancers are genomic regions that contain a unique set of epigenetic composition of histone marks and harbor specific binding sites for transcription factors. Enhancers function by activating target genes through DNA looping across large genomic distances. Recent studies indicated that dysfunctional enhancers contribute to cancer progression. This includes cancer-predisposing single-nucleotide polymorphisms, large-scale genomic rearrangements, and somatic mutations. Though current genomic tool allow the identification of enhancers, we lack unbiased methods to systematically interrogate the functions of enhancers. Towards this goal, we recently published a proof-of-concept paper demonstrating the possibility to perform screens of enhancers using the CRISPR-Cas9 genome editing technology. We showed that both positive selection and drop out types of screens could be used, as well as a tiling approach to uncover novel functional elements within enhancers. We propose here to identify enhancer regions that are essential for the function of ESR1 and AR, two ligand-activated transcription factors linked to breast and prostate cancer, respectively. We hypothesize that deregulated activity of these enhancers in cancer will increase risk and will drive acquired drug resistance. Therefore, following the identification of the functional enhancers, we will sequence the identified enhancer regions in hundreds of tumors to assign single nucleotide polymorphisms and somatic mutations as drivers of cancer as well as of resistance to anti-hormonal therapy. This information will be used for diagnosis and improved cancer therapy.