Functionally Characterizing the Enhancer Cistrome in Advanced Human Kidney Cancer

The mechanism by which genes are turned "on" is driven by proteins called transcription factors (TFs) binding to certain locations in the human genome called regulatory elements. TFs recognize and bind to specific regulatory elements (i.e., stretches of specific DNA sequences) and this interaction can result in a gene being turned on. These regulatory elements are proving to be important in cancer biology. Regulatory elements are located throughout the 98 percent of the human genome that does not code for genes. Due to the lack of tools available for studying the noncoding region, until recently it was difficult to identify, to functionally characterize, and to therapeutically target there 'non-genic' genomic regions. Advances are enabling the systematic identification and testing of relevant regulatory elements as well as the ability to target their associated TFs, which were once considered 'undruggable'. The ultimate goals of our proposal are to identify and characterize critical regulatory elements that contribute to advanced kidney cancer. Aim 1 will utilize a method called chromatin immunoprecipitation followed by sequencing (ChIP-seq) in clinically relevant patient samples to characterize the regulatory landscape during progression to metastatic disease. We will also use a novel technique called HiChIP to create a 3D model of the kidney cancer genome to determine which regions communicate with each other. Gene regulation often occurs when distal enhancers come into contact with target genes in 3D space. Finally, using an innovative technology termed genome editing, Aim2 will identify candidate regulatory elements that are functionally relevant for mediating resistance to therapy. By focusing on epigenetics and the non-coding portions of the genome, our proposal takes a decidedly innovative approach to identifying functionally important gene regulatory elements. These regions have been understudied compared with the protein coding genome.