Identification of a novel PDC-E2 epitope in Primary Biliary Cholangitis and application for engineered Treg therapy

Background and Aims: Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease, characterized by progressive destruction of small intrahepatic bile ducts and portal inflammation. Treatment options are limited with reliance on liver transplantation in advanced cases. The adaptive immune response is implicated in disease pathogenesis by both the presence of anti-mitochondrial antibodies targeting the E2 subunit of the pyruvate dehydrogenase complex (PDC-E2), in 90-95% of patients, and T cells infiltrating the portal tracts in affected individuals. Here, we examined T cell responses to peptides derived from PDC-E2, with a focus on CD4 T cell responses restricted to HLA Class II DRB4*0101, an allele found in 62% of PBC patients, to uncover PDC-E2 epitopes that could be used for Engineered Treg therapy. Approach and Results: Using an Activation Induced Marker assay and single cell RNA-sequencing, we found clonal expansion of CD4 T cells reactive to PDC-E2 epitopes in both conventional (Tconv) and regulatory T (Treg) cells. The TCR repertoires were non-overlapping and private and included TCRs specific for a novel PDC-E2 epitope restricted to DRB4*0101. CD4 Tconv cells from healthy and PBC subjects that responded to the PDC-E2 novel epitope showed phenotypic heterogeneity skewed towards T follicular helper cell subset. Using a TCR specific for this novel PDC-E2 epitope, we created an engineered Treg that suppressed PDC-E2 specific polyclonal CD4 Tconv cells from PBC patients. Conclusions: This study advances the knowledge of PDC-E2 specific T cell responses and introduces a novel PDC-E2 epitope recognized by reactive Tconv and Treg cells. Generation of engineered Treg specific for this epitope with effective suppressive activity provides therapeutic potential as Treg therapy targeting PDC-E2 in PBC.