Synthetic Lethal Targeting of SETD2 in Renal Cell Carcinoma

ABSTRACT Clear cell renal cell carcinoma (ccRCC) accounts for ~75% of kidney cancers and is the 8th leading cause of cancer death in the United States. After completion of The Cancer Genome Atlas (TCGA) Project, clinically actionable mutations were identified in virtually every solid tumor. One major exception, however, is RCC, where the current standard of care, checkpoint inhibitor and anti-VEGF therapy, does not take into account that ~50% of RCCs have mutations in chromatin regulators. After first-line therapy, response rates are 20% and there are no FDA-approved therapies that target chromatin regulators, highlighting the need to identify how loss-of-function genotypes can be therapeutically targeted. The epigenome is profoundly disrupted in cancers including ccRCC. Aside from the near ubiquitous loss of VHL, the mutational landscape of ccRCC is dominated by loss-of-function mutations in epigenetic regulators, including SETD2, BAP1, and PBRM1. SETD2 loss has now been firmly linked to poor outcome and metastasis. The molecular phenotype of H3K36me3 deregulation in SETD2-mutant ccRCC makes this an ideal scenario to study from the angle of synthetic lethality because it induces global epigenetic changes that must be compensated for, creating unique vulnerabilities. Targeting factors that exhibit genetic epistasis with known cancer mutations to drive a synthetic lethal phenotype is a proven therapeutic approach. We performed an unbiased CRISPR/Cas9 screen to identify factors that exhibit synthetic lethality with SETD2 loss-of-function. The epigenetic factor NSD1, a writer of H3K36me1/2 acting through the H3K36 pathway, was identified. Based on these findings, we hypothesize that suppression of the H3K36 axis in the form of its epigenetic writers (NSD1 in a SETD2 loss context) drives a synthetic lethal phenotype mediated by distinct enhancer remodeling accompanied by expression defects incompatible with cell viability. Identification of NSD1, which is part of a larger family of three related proteins (NSD1/2/3) within the H3K36 signaling axis in turn, will lead to novel approaches for individualized therapeutics to target SETD2 loss-of-function, classically defined as ‘undruggable’. We will address this hypothesis with three aims. In aim 1 we functionally characterize the synthetic lethal phenotypes associated with H3K36 writers NSD1, NSD2, and NSD3 in isogenic SETD2 ccRCC cell lines. In aim 2 we demonstrate the utility of pharmacologic inhibitors of H3K36 signaling in driving synthetic lethality in SETD2-mutant cells and elucidate their biological underpinnings. Finally, in aim 3 we validate the efficacy and specificity of genetic and pharmacologic targeting of the H3K36 signaling axis to induce SETD2-mutant synthetic lethality in vivo using mouse models. Our studies will shed new light on how epigenetic regulators and the H3K36 axis specifically, drive cancer and metastasis when deregulated. This is expected to positively affect human health by generating preclinical evidence for new ways to treat SETD2-mutant ccRCC that will minimize off-target side effects, and enhance survival for patients with ccRCC, particularly those with more aggressive/metastatic disease.