mRNA profiles of DNT cells in primary biliary cholangitis patients

Primary biliary cholangitis (PBC) is an autoimmune liver disease of unknown pathogenesis. We find a decreased number and immunosupressive function of double nagative T (DNT) cells in PBC patients. To further unveil the mechanism by which suppressive function and quantity of DNT cells in PBC patients was impaired, we performed a whole-transcriptome analysis on DNT cells isolated from 13 PBC patients and 6 HCs. Total RNA of DNT cells from HCs and PBC patients were isolated and assessed. Transcriptome sequencing libraries were then generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and sequenced on an Illumina Hiseq platform (Illumina, San Diego, CA). Differentially expressed genes with a fold change of >=2.0 and p < 0.05 between HC and PBC patients were submitted to GO and KEGG enrichment analysis. Thie biologic processes of GO enrichment analysis showed that cell co-stimulations, cell migration, apoptotic process, cell activation and cell cytotoxicity were enriched, which helped to explain the alterations in number and suppressive function of DNT cells between HCs and patients from a mRNA level. Meanwhile, we observed that T cell receptor signaling pathway was enriched in DEGS and all identified genes with GSEA. Additionally the leading-edge genes of this pathway exhibited downregulation in PBC patients, subsequently supported by real-time PCR. PIK3R1 and MAP3K8 exhibited more significant reduction in DNT cells from PBC patients. Overall design: mRNA profiles of DNT cells from 6 healthy controls and 13 PBC patients were generated by deep sequencing with Illumina Hiseq platform.