Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma

Immune checkpoint inhibitors targeting the programmed cell death 1 receptor (PD-1) improve survival in a subset of patients with clear cell renal cell carcinoma (ccRCC). To identify genomic alterations in ccRCC that correlate with response to anti-PD-1 monotherapy, we performed whole-exome sequencing of metastatic ccRCC from 35 patients. We found that clinical benefit was associated with loss-of-function mutations in the <i>PBRM1</i> gene (<i>P</i> = 0.012), which encodes a subunit of the PBAF switch-sucrose nonfermentable (SWI/SNF) chromatin remodeling complex. We confirmed this finding in an independent validation cohort of 63 ccRCC patients treated with PD-1 or PD-L1 (PD-1 ligand) blockade therapy alone or in combination with anti-CTLA-4 (cytotoxic T lymphocyte-associated protein 4) therapies (<i>P</i> = 0.0071). Gene-expression analysis of PBAF-deficient ccRCC cell lines and <i>PBRM1</i>-deficient tumors revealed altered transcriptional output in JAK-STAT (Janus kinase-signal transducers and activators of transcription), hypoxia, and immune signaling pathways. <i>PBRM1</i> loss in ccRCC may alter global tumor-cell expression profiles to influence responsiveness to immune checkpoint therapy.