Integrative molecular profiling of autoreactive CD4 T cells in autoimmune hepatitis

J Hepatol. 2020 Dec;73(6):1379-1390. doi: 10.1016/j.jhep.2020.05.053. Epub 2020 Jul 8.


Background & aims: 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 yet been characterised. Herein, we isolated and deeply characterised SLA-specific CD4 T cells in patients with AIH.

Methods: We used brief ex vivo restimulation with overlapping SLA peptides to isolate and phenotype circulating SLA-specific CD4 T cells, and integrative single-cell RNA-seq (scRNA-seq) to characterise 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 characterised disease-associated peripheral blood T cells by high-content flow cytometry in 42 patients with AIH and 17 controls with non-alcoholic steatohepatitis.

Results: 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 T-cell epitopes. Autoreactive TCR clonotypes were predominantly found in the memory PD-1+CXCR5-CD4 T cells, which were significantly increased in the blood of patients with AIH and supported B-cell differentiation through IL-21. Finally, we identified specific T-cell phenotypes linked to disease activity and IgG level during AIH.

Conclusions: We provide a deep characterisation of rare circulating autoreactive CD4 T cells and identify their peripheral reservoir in AIH. We also propose a specific phenotype of autoreactive T cells related to AIH disease activity, which will be essential to track, delineate, and potentially target these pathogenic cells.

Lay summary: One principal characteristic of autoimmune hepatitis (AIH), like for many other autoimmune diseases, is the accumulation of autoantibodies produced by B lymphocytes following their interaction with autoreactive CD4 T lymphocytes. In this study, we identified and characterised with high resolution these CD4 T cells. This will be essential to track, delineate, and potentially target them during AIH.

Keywords: Autoimmune hepatitis; Autoreactive CD4 T cells; Autoreactive TCR clonotypes; Single-cell RNA-seq; Soluble liver antigen.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Autoantibodies / immunology
  • Autoantigens / immunology*
  • B-Lymphocytes / immunology
  • CD4-Positive T-Lymphocytes / immunology*
  • Epitopes, T-Lymphocyte / analysis
  • Female
  • Hepatitis, Autoimmune* / blood
  • Hepatitis, Autoimmune* / immunology
  • Hepatitis, Autoimmune* / pathology
  • Humans
  • Immunologic Memory
  • Male
  • Middle Aged
  • Programmed Cell Death 1 Receptor / genetics
  • Receptors, Antigen, T-Cell / genetics
  • Receptors, CXCR5 / genetics
  • Sequence Analysis, RNA
  • Tumor Necrosis Factor Receptor Superfamily, Member 7 / genetics


  • Autoantibodies
  • Autoantigens
  • CXCR5 protein, human
  • Epitopes, T-Lymphocyte
  • PDCD1 protein, human
  • Programmed Cell Death 1 Receptor
  • Receptors, Antigen, T-Cell
  • Receptors, CXCR5
  • Tumor Necrosis Factor Receptor Superfamily, Member 7
  • liver antigen LA-1