Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification

Immunotherapy is a mainstay of non-small cell lung cancer (NSCLC) management. While tumor mutational burden (TMB) correlates with response to immunotherapy, little is known about the relationship between the baseline immune response and tumor genotype. Using single-cell RNA sequencing, we profiled 361,929 cells from 35 early-stage NSCLC lesions. We identified a cellular module consisting of PDCD1+CXCL13+ activated T cells, IgG+ plasma cells, and SPP1+ macrophages, referred to as the lung cancer activation module (LCAMhi). We confirmed LCAMhi enrichment in multiple NSCLC cohorts, and paired CITE-seq established an antibody panel to identify LCAMhi lesions. LCAM presence was found to be independent of overall immune cell content and correlated with TMB, cancer testis antigens, and TP53 mutations. High baseline LCAM scores correlated with enhanced NSCLC response to immunotherapy even in patients with above median TMB, suggesting that immune cell composition, while correlated with TMB, may be a nonredundant biomarker of response to immunotherapy. [Display omitted] •scRNA-seq of immune cells in 35 NSCLCs reveals activation module (LCAM)•CITE-seq validates and extends scRNA-seq-based cell annotations•LCAM is associated with tumor mutational burden, ectopic antigens, and driver mutations•LCAM confers prognostic benefit in anti-PD-L1 treatment but not chemotherapy Leader et al. provide the largest NSCLC cohort analyzed by scRNA-seq and CITE-seq, demonstrating shared and variable elements of the treatment-naive immune response and identifying independent immune-modifying effects of tumor mutational burden and TP53 mutation, resulting in a refined model of how neoantigens, driver mutations, and immune state combine to drive immunotherapeutic response.