Clonally expanded effector CD4 ⁺ cytotoxic T lymphocytes are associated with severe neurological adverse events after immune checkpoint inhibitor therapy

Background Immune checkpoint inhibitor (ICI) therapies present a pillar of modern cancer therapy but can cause neurological immune-related adverse events (n-irAEs), of which up to 35% are severe or even fatal. However, the detailed immunological mechanisms and risk factors underlying n-irAEs remain largely unknown. Here, we leveraged single-cell genomics to dissect immune cell type, state, and clonal heterogeneity associated with n-irAEs. Methods We performed coupled single-cell RNA sequencing and T cell receptor (TCR) profiling on peripheral blood cells of 17 patients with cancer receiving ICI therapy, including 8 patients with acute neurotoxicity. This approach enabled integrated analyses of immune cell states and T cell clonality linked to ICI-induced n-irAEs. Results We profiled 186 435 immune cells and conducted pseudotime analyses, revealing that patients with n-irAEs, compared with controls, present with clonally expanded CD4 + cytotoxic T lymphocytes (CD4 + CTLs) with an n-irAE-specific effector gene expression profile. These T cells predominantly belong to a select set of expanded clonal families and express genes linked to antigen-induced activation, cell lysis, and neuroinflammation. Moreover, they highly express CXCR3 (FC=2.03 compared with control CD4 + CTLs, with a false discovery rate=7.7×10⁻⁴), encoding the chemokine receptor of CXCL10, previously nominated as a biomarker for severe ICI therapy-induced n-irAEs with concomitant multiple organ system toxicity. Conclusions Overall, our study highlights the expansion and activation of CD4 + CTLs in ICI-induced neurotoxicity, proposing these cells as potential targets for developing new biomarkers and therapeutic strategies to improve patient outcomes.