Objective : Deciphering the transcriptomic signature of self-antigen-specific CD4 T cells is challenging but crucial to open new therapeutic perspectives in autoimmune diseases (AD). However, whether this signature is conserved among multiple self-antigen reactivities remains unknown. To answer this question, we isolated reactive CD4 T cells specific for three distinct liver self-antigens from the blood of patients with an autoimmune liver diseases (AILD), and compared their transcriptome to that of CD4 T cells specific for three foreign antigens.
Methods : After a short ex vivo reactivation, we isolated single CD4 T cells specific for SLA, CYP2D6 and PDCE2 antigens from the blood of 7 AILD patients with anti-SLA autoantibodies, 3 AILD patients with anti-LKM1 autoantibodies (targeting CYP2D6) and 6 AILD patients with anti-Type-2-mitochondria autoantibodies (targeting PDCE2), respectively. For comparison, we isolated CD4 T cells specific for MP65 (Candida albicans), MP1 (H1N1), and Spike (SARS-Cov2) from the same patients. We analyzed those cells by FACS-based 5-prime end single-cell RNA-seq (FB5P-seq) for integrative single-cell analysis of transcriptome and antigen receptor repertoire (TCR).
Results : Based on the scRNA-seq reads, we reconstructed TCR sequences. For each antigen reactivity more than 50% of specific CD4 T cells were part of expanded clonotypes, consistent with in vivo antigen-specific clonal expansion. Clustering of the gene expression profiles revealed distinct transcriptomic signatures between the three foreign antigen specificities. By contrast, the three liver self-antigen reactivities tended to cluster together and presented a conserved transcriptomic signature characterized by TIGIT, CTLA4 and CXCL13 expression.
Conclusion : Our results reveal that human autoreactive CD4 T cells have a conserved target tissue-specific transcriptomic signature, clearly distinct from that of foreign antigen-specific CD4 T cells, at least in AILD patients. These findings open new prospects for a generalized treatment targeting liver-specific autoreactive T cells.