A new clustering method identifies multiple sclerosis‐specific T‐cell receptors

OBJECTIVE: To characterize T‐cell receptors (TCRs) and identify target epitopes in multiple sclerosis (MS). METHODS: Peripheral blood mononuclear cells were obtained from 39 MS patients and 19 healthy controls (HCs). TCR repertoires for α/β/δ/γ chains, TCR diversity, and V/J usage were determined by next‐generation sequencing. TCR β chain repertoires were compared with affectation status using a novel clustering method, Grouping of Lymphocyte Interactions by Paratope Hotspots (GLIPH). Cytomegalovirus (CMV)‐IgG was measured in an additional 113 MS patients and 93 HCs. Regulatory T cells (Tregs) were measured by flow cytometry. RESULTS: TCR diversity for all four chains decreased with age. TCRα and TCRβ diversity was higher in MS patients (P = 0.0015 and 0.024, respectively), even after age correction. TRAJ56 and TRBV4‐3 were more prevalent in MS patients than in HCs (p(corr) = 0.027 and 0.040, respectively). GLIPH consolidated 208,674 TCR clones from MS patients into 1,294 clusters, among which two candidate clusters were identified. The TRBV4‐3 cluster was shared by HLA‐DRB1*04:05‐positive patients (87.5%) and predicted to recognize CMV peptides (CMV‐TCR). MS Severity Score (MSSS) was lower in patients with CMV‐TCR than in those without (P = 0.037). CMV‐IgG‐positivity was associated with lower MSSS in HLA‐DRB1*04:05 carriers (P = 0.0053). HLA‐DRB1*04:05‐positive individuals demonstrated higher CMV‐IgG titers than HLA‐DRB1*04:05‐negative individuals (P = 0.017). CMV‐IgG‐positive patients had more Tregs than CMV‐IgG‐negative patients (P = 0.054). INTERPRETATION: High TCRα/TCRβ diversity, regardless of age, is characteristic of MS. Association of a CMV‐recognizing TCR with mild disability indicates CMV’s protective role in HLA‐DRB1*04:05‐positive MS.