Single cell transcriptomics reveals colonic lymphocyte remodelling and emergence of polyfunctional, cytolytic lymphocyte responses in CPI-induced colitis

Immune checkpoint inhibitors (CPIs) have revolutionised cancer treatment, with previously untreatable disease now amenable to potential cure. Combination regimens of anti-CTLA-4 and anti-PD-1 show enhanced efficacy but are prone to off-target immune-mediated tissue injury, particularly at the barrier surfaces. To probe the impact of immune checkpoints on intestinal homeostasis, mice were challenged with anti-CTLA-4 and anti-PD-1 immunotherapy and manipulation of the intestinal microbiota. Single-cell RNA-sequencing revealed remodelling of mucosal lymphocytes with induction of polyfunctional lymphocyte responses characterized by increased expression of Ifng, other pro-inflammatory cytokines/chemokines (Il22, Il17a Ccl3, Ccl4 and Ccl9), cytotoxicity molecules (Gzmb, Gzma, Prf1, Nkg7) and the chemokine receptor Cxcr6. In comparison with mucosal lymphocytes in the steady state, polyfunctional lymphocytes from both CD4+ and CD8+ lineages upregulated costimulatory molecules and checkpoint molecules in CPI-colitis, indicating that these cells are tightly regulated. Single cell RNA-sequencing study of CD45+ lymphocytes from the colons of mice with CPI-colitis and healthy controls.