Discrete TCR repertoires and CDR3 features distinguish effector and Foxp3+ regulatory T lymphocytes in myelin oligodendrocyte glycoprotein-induced experimental allergic encephalomyelitis.

Regulatory T lymphocytes (Tregs) expressing the Foxp3 transcription factor are critical modulators of autoimmunity. Foxp3(+) Tregs may develop in the thymus as a population distinct from conventional Foxp3(-) αβ T cells (Tconvs). Alternatively, plasticity in Foxp3 expression may allow for the interconversion of mature Tregs and Tconvs. We examined >160,000 TCR sequences from Foxp3(+) or Foxp3(-) populations in the spleens or CNS of wild-type mice with experimental allergic encephalomyelitis to determine their relatedness and identify distinguishing TCR features. Our results indicate that the CNS-infiltrating Tregs and Tconvs arise predominantly from distinct sources. The repertoires of CNS Treg or Tconv TCRs showed limited overlap with heterologous populations in both the CNS and the spleen, indicating that they are largely unrelated. Indeed, Treg and Tconv TCRs in the CNS were significantly less related than those populations in the spleen. In contrast, CNS Treg and Tconv repertoires strongly intersected those of the homologous cell type in the spleen. High-frequency sequences more likely to be disease associated showed similar results, and some public TCRs demonstrated Treg- or Tconv-specific motifs. Different charge characteristics and amino acid use preferences were identified in the CDR3β of Tregs and Tconvs infiltrating the CNS, further indicating that their repertoires are qualitatively distinct. Therefore, discrete populations of Tregs and Tconvs that do not substantially interconvert respond during experimental allergic encephalomyelitis. Differences in sequence and physical characteristics distinguish Treg and Tconv TCRs and imply dissimilar Ag recognition properties.