BMAL1-HIF2α heterodimers contribute to ccRCC

Circadian disruption enhances cancer risk, and many tumors exhibit disordered circadian gene expression. We show rhythmic gene expression is unexpectedly robust in clear cell renal cell carcinoma (ccRCC). Furthermore, the clock gene BMAL1 is higher in ccRCC than in healthy kidneys, unlike in other tumor types. BMAL1 is closely related to ARNT and we show that BMAL1-HIF2α regulates a subset of HIF2α target genes in ccRCC cells. Depletion of BMAL1 reprograms HIF2α chromatin association and target gene expression and reduces ccRCC growth in culture and in xenografts. Analysis of pre-existing data reveals higher BMAL1 in patient-derived xenografts that are sensitive to growth suppression by HIF2α antagonists. We show that increasing BMAL1 sensitizes ccRCC-derived A498 cells to growth inhibition by PT2399. Together, these findings indicate that an alternate HIF2α heterodimer containing the circadian partner BMAL1 contributes to HIF2α activity, growth, and sensitivity to HIF2α antagonist drugs in ccRCC cells. To characterize the localizations of endogenous BMAL1 and HIF2α in native chromatin, we sequenced genomic DNA associated with BMAL1 or HIF2α in A498 cells. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) were performed using CUT&RUN assay kit (CST #86652) following the manufacturer protocol. 100,000 A498 cells infected with lentivirus expressing shRNA targeting “scramble” or BMAL1 were used for each reaction.