Immune checkpoint blockade (ICB) is widely used to treat non-small cell lung cancer (NSCLC) patients and works by inhibiting the PD-1/PDL1 axis to reinvigorate exhausted T cells. In the prevailing model, the primary mechanism for direct tumor cell killing occurs through cytotoxic CD8+ T cells.

Here, we use single-cell multi-omic profiling (a combination of single-cell RNA sequencing, TCR sequencing, and surface protein profiling) in 10 NSCLC patients to identify a population of CD4+ T cells that are tumor-infiltrating, clonally expanded, and express a cytotoxic gene program.

Concordantly, we found in the same patients a subpopulation of tumor cells with elevated HLA class II expression, suggesting a mechanism for tumor-mediated antigen presentation to CD4+ T cells. Finally, we show that a cytotoxic CD4 gene signature is associated with improved progression-free survival in a cohort of 180 NSCLC patients treated with ICB regimens, including those with loss of heterozygosity at the HLA class I locus.

Overall, these results suggest a model where cytotoxic CD4+ T cells can perform direct tumor cell killing in a class II restricted manner and that their presence is associated with favorable ICB outcomes in NSCLC.

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