Molecular Subtypes Based on Genomic and Transcriptomic Features Correlate with the Responsiveness to Immune Checkpoint Inhibitors in Metastatic Clear Cell Renal Cell Carcinoma

SIMPLE SUMMARY: Immune checkpoint inhibitors (ICIs), such as programmed cell death protein 1 (PD-1) blockade, have proven to be the most effective agents for the management of many cancer types. Although ICIs are the current standard of care for treating metastatic clear cell renal cell carcinoma (ccRCC), 40–60% of patients still have intrinsic resistance to ICIs across multiple clinical trials. Therefore, identifying optimal biomarkers that can predict either responders or non-responders to ICIs has been of tremendous importance. Here, we generated targeted sequencing and whole transcriptomic sequencing of 60 patients with metastatic ccRCC treated with ICIs. Moreover, transcriptomic analysis was integrated to identify molecular subtypes using a total of 177 tumor samples by merging our data and published data derived from the CheckMate 025 trial. Our results show that these molecular subtypes are associated with specific genomic alterations, distinct molecular pathways, and differential clinical outcomes in patients with metastatic ccRCC treated with ICIs. ABSTRACT: Clear cell renal cell carcinoma (ccRCC) has been reported to be highly immune to and infiltrated by T cells and has angiogenesis features, but the effect of given features on clinical outcomes followed by immune checkpoint inhibitors (ICIs) in ccRCC has not been fully characterized. Currently, loss of function mutation in PBRM1, a PBAF-complex gene frequently mutated in ccRCC, is associated with clinical benefit from ICIs, and is considered as a predictive biomarker for response to anti-PD-1 therapy. However, functional mechanisms of PBRM1 mutation regarding immunotherapy responsiveness are still poorly understood. Here, we performed targeted sequencing (n = 60) and whole transcriptomic sequencing (WTS) (n = 61) of patients with metastatic ccRCC treated by ICIs. By integrating WTS data from the CheckMate 025 trial, we obtained WTS data of 177 tumors and finally identified three molecular subtypes that are characterized by distinct molecular phenotypes and frequency of PBRM1 mutations. Patient clustered subtypes 1 and 3 demonstrated worse responses and survival after ICIs treatment, with a low proportion of PBRM1 mutation and angiogenesis-poor, but were immune-rich and cell-cycle enriched. Notably, patients clustered in the subtype 2 showed a better response and survival after ICIs treatment, with enrichment of PBRM1 mutation and metabolic programs and a low exhausted immune phenotype. Further analysis of the subtype 2 population demonstrated that GATM (glycine amidinotransferase), as a novel gene associated with PBRM1 mutation, plays a pivotal role in ccRCC by using a cell culture model, revealing tumor, suppressive-like features in reducing proliferation and migration. In summary, we identified that metastatic ccRCC treated by ICIs have distinct genomic and transcriptomic features that may account for their responsiveness to ICIs. We also revealed that the novel gene GATM can be a potential tumor suppressor and/or can be associated with therapeutic efficacy in metastatic ccRCC treated by ICIs.