The role of MAIT cells in a variety of autoimmune diseases has been analyzed, and in some they provide a pathogenic role, while in others they participate in tissue healing or there is no consensus. We are analyzing T cells for their role in the pathogenesis of primary biliary cholangitis (PBC), an autoimmune disease of the bile ducts that occurs predominantly in women. PBC was selected for deeply probing the role of MAIT cells in autoimmune disease because of the frequency of MAIT cells in the liver, and MAIT cell reactivity to one more bile acids. Furthermore, genetic studies support this connection. The Data base of Immune Cell eQTLs, Expression and Epigenomics (DICE) project (https://dice-database.org/) has identified many genetic loci that affect gene expression in MAIT cells. Some of these loci have been implicated by genome wide association studies (GWAS) in the pathogenesis of an autoimmune disease, and PBC stands out in provided examples of such a MAIT cell-autoimmunity connection. We are carrying out scRNA-seq analysis of T cells from PBC patients and controls, including intrahepatic MAIT and their counterparts from peripheral blood. The studies indicate that liver MAIT cells are clonally expanded, and they have a more activated and potentially inflammatory gene expression signature compared to MAIT cells in the blood. MAIT cells are also being compared to gd T cells and CD4 and CD8 T lymphocytes.