Transcriptomic, clonal, and functional analyses reveal Liver tissue-imprinted immuno-profile of circulating autoreactive CD4 T cells in autoimmune liver diseases

Autoimmune liver diseases (AILD) are immune-mediated disorders in which CD4 T cells may play a central role. However, self-antigen-specific CD4 T cells are mainly characterized in the bloodstream, and the link with the immune response in the targeted tissue is a difficult and under-studied task in AILD. We hypothesize that circulating self-antigen-specific CD4 T cells contain dominant hepatic CD4 T cell clonotypes and represent liver-derived autoreactive CD4 T cells. Single cell transcriptomic analysis of circulating self-antigen-specific CD4 T cells reveal a specific B-helper and immuno-exhausted transcriptional profile, which is conserved for different autoantigens, but distinct from several other types of foreign antigen specificities. The dominant hepatic CD4 T cell clones shared a similar transcriptomic signature and were enriched in the circulating PD1+ TIGIT+ HLA-DR+ CD4 T cell subset. In liver biopsy, PD1+ CD4 T cells were present in tertiary lymphoid structure, reinforcing the hypothesis of a pathogenic role of these cells. Using a mouse model, we demonstrated antigen-specific CD4 T cells acquired the immuno-exhausted transcriptional profile when they accumulated in the liver after local antigen reactivity. Inhibition of immune checkpoint molecules contributed to increased hepatic damages in a CD4 T cell dependent manner. This study reveals the origin of liver-autoreactive CD4 T cells in the blood of AILD patients that are imprinted by the liver environment and recirculate from the damaged tissue during the active phase of the disease. In addition, this study also shows how immune checkpoint molecules contribute to local antigen-specific tolerance in the liver, which may be dysregulated in AILD and immunotherapy-induced acute hepatitis. Finally, our study enables tracking and isolating liver autoreactive CD4 T cells in future diagnostic and therapeutic purposes.