Integrative molecular profiling of autoreactive CD4 T cells in autoimmune hepatitis.

In most autoimmune disorders, crosstalk of B cells and CD4 T cells results in the accumulation of autoantibodies. In autoimmune hepatitis (AIH), the presence of anti-Soluble Liver Antigen (SLA) autoantibodies is associated with reduced overall survival, but the associated autoreactive CD4 T cells have not been characterized yet. Here we isolated and deeply characterized SLA-specific CD4 T cells in AIH patients.We used brief ex vivo re-stimulation with overlapping SLA peptides to isolate and phenotype circulating SLA-specific CD4 T cells, and integrative single-cell RNA-seq (scRNA-seq) to characterize their transcriptome and T cell receptor (TCR) repertoire. Autoreactive TCRs were cloned and used to identify dominant SLA-derived epitopes. SLA-specific CD4 T cells were tracked in peripheral blood through TCR sequencing, to identify their phenotypic niche. We further characterized disease-associated peripheral blood T cells by high content flow cytometry in n=42 AIH patients and n=17 non-alcoholic steatohepatitis controls.Autoreactive SLA-specific CD4 T cells were only detected in patients with anti-SLA autoantibodies and had a memory PD-1+CXCR5-CCR6-CD27+ phenotype. ScRNA-seq revealed their pro-inflammatory/B-Helper profile. SLA81-100 and SLA177-204 contain dominant Tcell epitopes. Autoreactive TCR clonotypes were predominantly found in the memory PD-1+CXCR5-CD4 T cells which were significantly increased in the blood of AIH patients and supported B cell differentiation through IL-21. Finally, we identified specific T cell phenotypes linked to disease activity and IgG level during AIH.This work provides a deep characterization of rare circulating autoreactive CD4 T cells and the identification of their peripheral reservoir in AIH. We also propose generic phenotype of autoreactive T cells related to AIH disease activity which will be essential to track, delineate and potentially target those pathogenic cells.

Click here to read the full article @ Journal of Hepatology