PBRM1 bromodomain missense mutations in ccRCC vascular signaling

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PROJECT SUMMARY Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma. Although outcomes are favorable with early detection and surgery, approximately 30% of patients present with metastatic disease. This highlights the need for an improved biochemical understanding of and targeted therapeutic options for ccRCC. ccRCC is a uniquely vascular cancer due to mutations in the von Hippel-Lindau (VHL) gene, which encodes the substrate recognition subunit of a ubiquitin ligase that degrades hypoxia- inducible factor-α (HIF-α) transcription factors in normoxia. VHL loss results in nuclear HIF-α accumulation and aberrant expression of downstream pro-angiogenic gene targets in a likely HIF-2α-biased manner. Thus, ccRCC tumors are uniquely susceptible to anti-angiogenic therapies, which though effective, are associated with substantial undesirable toxicities for patients. Recent clinical trials have demonstrated that mutations in Polybromo-1 (PBRM1), an epigenetic acetyl-lysine reader protein commonly mutated in ccRCC, correlate with improved outcomes for anti-angiogenic therapies. However, these studies presume that all PBRM1 mutations are loss-of-function and neglect to consider that ~15% of ccRCC-related PBRM1 mutations are missense mutations, generating full-length proteins with a spectrum of undetermined structural and functional impacts. ccRCC-associated PBRM1 missense mutations cluster in bromodomains (BDs), the functional domains of PBRM1 that bind acetyl-lysine residues in histones and other nuclear proteins and nucleic acids. Therefore, a better knowledge of the biochemical impacts of PBRM1 BD missense mutations in ccRCC is critical to promote PBRM1 as a predictive biomarker for patient response to anti-antiangiogenic therapies, so that non-responding patients can avoid unnecessary therapeutic toxicity and seek alternative treatments. This fellowship will elucidate the biochemical impacts of ccRCC-associated PBRM1 BD missense mutations on protein stability and acetylated histone binding function and determine the role of PBRM1 in the regulation of the HIF-2α and angiogenesis pathways. Aim 1 will identify which PBRM1 BD missense mutations are biochemically benign or deleterious for protein structure and function by integrating computational prediction with biophysical assay validation. Aim 2 will determine the effects of PBRM1 BD missense mutations on HIF-2α and angiogenesis pathway regulation by assessing HIF-2α transcriptional output, HIF-2α promoter accessibility, and angiogenic potential in ccRCC cellular assays. This fellowship addresses knowledge gaps in the biochemical basis of ccRCC pathogenesis with the overall goal to promote the most effective use of standard ccRCC treatment modalities. Successful completion of this fellowship will further precision medicine approaches for the treatment of ccRCC by advancing PBRM1 mutational status as a nuanced and predictive biomarker to prevent unnecessary patient drug exposures.