TCRβ repertoire of memory T cell reveals potential role for Escherichia coli in the pathogenesis of primary biliary cholangitis

Background Primary biliary cholangitis (PBC) is an organ-specific, T cell-mediated autoimmune disease which is characterized by the breakdown of self-tolerance to the highly conserved pyruvate dehydrogenase complex, especially the pyruvate dehydrogenase E2 complex (PDC-E2). However, the molecular mechanism of breakdown of self-tolerance is still unclear. Methods A combination of multiplex-PCR and immune repertoire sequencing (IR-seq) was used for a standardized analysis of memory T cell receptor (TCR) beta-chain repertoire of PBC patient and healthy volunteers. In vitro induction and expansion of human PDC-E2(163-176) (human PDC-E2)-specific T cells and E coli PDC-E2(31-44/134-147/235-248) (E coli PDC-E2)-specific T cells, and identified the human (and E coli) PDC-E2-specific TCR beta repertoire by IR-seq. Results Primary biliary cholangitis patients have shorter complementarity-determining region 3s (CDR3s), and higher degree of sequence overlap in the TCR beta repertoire of memory T cell. Moreover, altered insertion patterns and skewed TRBV segment usage were observed in PBC patients. With regard to the pathogenesis, the concentration of E coli was higher in PBC patients' faecal. The frequency of E coli (and human)-specific TCRs was higher in the memory TCR beta repertoire of PBC patients compared with healthy controls. Importantly, the TCR beta repertoire characteristics were almost identical between E coli PDC-E2-related TCRs and human PDC-E2-related TCRs, including the patterns of TRBV usage, CDR3 length and amino acid composition. Conclusion Our findings comprehensively revealed the TCR beta repertoire characterization of PBC patients, and provided a TCR molecular basis to understand the mechanism of cross-recognition between human PDC-E2 and E coli PDC-E2, and the imbalance of immune tolerance in PBC.