Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer

Genomic and transcriptomic analysis of 393 non-small cell lung cancer patients treated with checkpoint inhibitors identifies molecular features associated with response. Anti-PD-1/PD-L1 agents have transformed the treatment landscape of advanced non-small cell lung cancer (NSCLC). To expand our understanding of the molecular features underlying response to checkpoint inhibitors in NSCLC, we describe here the first joint analysis of the Stand Up To Cancer-Mark Foundation cohort, a resource of whole exome and/or RNA sequencing from 393 patients with NSCLC treated with anti-PD-(L)1 therapy, along with matched clinical response annotation. We identify a number of associations between molecular features and outcome, including (1) favorable (for example, ATM altered) and unfavorable (for example, TERT amplified) genomic subgroups, (2) a prominent association between expression of inducible components of the immunoproteasome and response and (3) a dedifferentiated tumor-intrinsic subtype with enhanced response to checkpoint blockade. Taken together, results from this cohort demonstrate the complexity of biological determinants underlying immunotherapy outcomes and reinforce the discovery potential of integrative analysis within large, well-curated, cancer-specific cohorts.

Automated summary

Genomic and transcriptomic analysis of 393 non-small cell lung cancer patients treated with checkpoint inhibitors reveals molecular features associated with treatment response. The study analyzes data from the Stand Up To Cancer-Mark Foundation cohort, including whole exome and/or RNA sequencing, and identifies associations between molecular features and outcome, such as genomic subgroups, expression of immunoproteasome components, and tumor-intrinsic subtype. The findings demonstrate the complexity of immunotherapy outcomes and highlight the discovery potential of integrative analysis in well-curated cancer-specific cohorts.