Single‐Cell Profiling Reveals Clonally Expanded CX3CR1 + T Cells in Anti‐NMDA Receptor Encephalitis

ABSTRACT Anti‐ N‐methyl‐D‐aspartate receptor encephalitis (NMDAR‐E) is a prevalent autoimmune neurological disorder, yet T cell‐driven immunopathology and its contributions to therapeutic resistance and fulminant neuroinflammation remain poorly defined. Integrative single‐cell multi‐omic profiling, combining single‐cell RNA sequencing, single‐cell T cell receptor (TCR) sequencing, and cellular indexing of transcriptomes and epitopes by sequencing, is applied to systematically map peripheral and cerebrospinal fluid (CSF) immune landscapes in treatment‐naïve NMDAR‐E patients, with orthogonal validation conducted across independent cohorts via multiparameter flow cytometry and ex vivo NR1 peptide stimulation. Clonally expanded CX3CR1‐expressing CD4 + and CD8 + T cells are identified as a core disease‐associated effector population, characterized by high predicted affinity for the pathogenic GluN1 N368/G369 epitope, robust proinflammatory and cytotoxic transcriptional programs, and enhanced intercellular crosstalk with activated B cells through major histocompatibility complex (MHC), CD99, and macrophage migration inhibitory factor signaling axes. Preferentially enriched in patient CSF, these cells produce elevated interferon‐γ (IFN‐γ) and tumor necrosis factor‐α (TNF‐α) upon antigen‐specific stimulation, collectively highlighting a disease‐associated inflammatory T cell state linked to peripheral immune activation and CNS immune remodeling, with potential translational relevance for future biomarker and therapeutic investigation.