T-cell receptor repertoire of mice with organ-specific autoimmunity resulting from a partial defect in T cell negative selection and dendritic cell enhancement

Abstract Previously, we reported a new genetic model of spontaneous autoimmune disease in which mice with a hypomorphic mutation of Aire (AireGW/+) combined with deletion of Lyn in dendritic cells develop autoimmune uveitis with a 50% penetrance. Here we demonstrate that a key autoantigen in this model is interphotoreceptor retinoid-binding protein (IRBP) as AireGW/+ Lyn−/− IRBP−/− mice failed to develop uveitis. The expansion of CD4+ T cells recognizing amino acids 271–290 (“P2”) of IRBP correlated strongly with autoimmune disease in mice with intact IRBP. To study the role of these T cells, we did single-cell RNA-seq with TCR sequencing for P2-specific CD4+ T cells isolated from eye-draining lymph nodes (LN) of AireGW/+ Lyn−/− mice with and without uveitis. Both mice showed an expansion of these T cells in eye-draining LNs, but it was greater in mice with disease. A remarkable clonal diversity of TCRs was seen, with some sharing of TCR Vα or Vβ sequences. Expansions of particular T cell clonotypes were more evident in LN of mice with disease, and even greater in the retinas of mice with disease. We reconstituted several P2–specific TCR clonotypes in a T cell hybridoma line and verified their specificity. One of the TCR clonotypes was expressed in developing thymocytes by retroviral transduction of bone marrow stem cells from Rag2−/− mice and transplanted into WT or AireGW/+ recipient mice. Remarkably, the small residual expression of IRBP in the thymus of AireGW/+ mice was sufficient to induce substantial negative selection of thymocytes with this TCR clonotype. Thus, deficiency of negative selection of P2 tetramer–specific TCR promotes the development of uveitis in AireGW/+ Lyn−/− mice, even if negative selection is only partly compromised.