SETD2 loss-of-function uniquely sensitizes cells to epigenetic targeting of NSD1-directed H3K36 methylation [RNA-seq]

SETD2 is the sole epigenetic factor responsible for catalyzing histone 3, lysine 36, tri-methylation (H3K36me3) in mammals. Its role in regulating diverse cellular processes such as RNA splicing, DNA repair, and spurious transcription underlie its broader tumor suppressor function, which has been detailed in a multitude of cancer types. SETD2 mutation, and by extension loss of H3K36me3, promotes the epithelial-mesenchymal transition (EMT) and is clinically associated with adverse outcomes highlighting a therapeutic need to develop targeted therapies against this dangerous mutation. To this end we employed an unbiased genome-wide synthetic lethal screen, which identified another H3K36me writer, NSD1, as a synthetic lethal modifier in SETD2-mutant cells. Confirmation of this synthetic lethal interaction was performed via modeling in isogenic clear cell renal cell carcinoma (ccRCC ) cell lines. Depletion of NSD1 using a CRISPRi targeting approach promoted the loss of SETD2-mutant cells coincident with elevated DNA damage and apoptosis. Surprisingly, only suppression of NSD1, and not the related H3K36-methyltransferases NSD2 or NSD3, promoted synthetic lethality (SL) in these models. Further investigation of H3K36me2 targeting by NSD1 and NSD2 respectively highlight the independent functions of these epigenetic writers. Furthermore, as a proof-of-principle we demonstrate the therapeutic feasibility of targeting this synthetic lethal interaction by recapitulating the phenotype using a first-of-its kind pharmacologic inhibitor against NSD1 (BT5). Notably, these findings unify unbiased genome-wide screening approaches with the latest genetic and pharmacologic modeling methodologies to reveal an entirely novel epigenetic approach in the advancement of individualized therapies for the treatment of SETD2-mutant cancer.