Different tumour-resident memory T-cell subsets regulate responses to anti-PD-1 and anti-CTLA-4 cancer immunotherapies

The involvement of tumour-resident memory T (TRM) cells in responses to immune checkpoint inhibitors remains unclear. Here, we show that while CD103+CD8 TRM cells are involved in response to PD-1 blockade, CD49a+CD4 TRM cells are required for the response to anti-CTLA-4. Using preclinical mouse models, we demonstrate that the benefits of anti-PD-1 treatment are compromised in animals challenged with anti-CD8 and anti-CD103 blocking antibodies. By contrast, the benefits of anti-CTLA-4 are decreased by anti-CD4 and anti-CD49a neutralizing antibodies. Single-cell RNA sequencing on tumour-infiltrating T-lymphocytes (TIL) reveals a CD49a+CD4 TRM signature, enriched in Ctla-4 transcripts, exacerbated upon anti-CTLA-4. CTLA-4 blockade expands CD49a+CD4 TRM cells and increases tumour-specific CD4-TIL-mediated cytotoxicity. A CD49a+CD4 TRM signature enriched in CTLA-4 and cytotoxicity-linked transcripts is also identified in human TILs. Multiplex immunohistochemistry in a cohort of anti-CTLA-4-plus-anti-PD-1-treated melanomas reveals an increase in CD49a+CD4 T-cell density in pre-treatment tumours, which correlates with higher rates of patient progression-free survival. Thus, CD49a+CD4 TRM cells may correspond to a predictive biomarker of response to combined immunotherapy.