Transcriptomic analysis of thymic epithelial cells and extra thymic epithelial cells

Regulation of MHC I expression has been studied almost exclusively in hematolymphoid cells. We report that thymic epithelial cells (TECs), particularly in the medulla (mTECs), constitutively express up to 100-fold more cell surface MHC I proteins than epithelial cells (ECs) from the skin, colon and lung. Differential abundance of cell surface MHC I in primary ECs is regulated via transcription of MHC I and of genes implicated in the generation of MHC I-binding peptides. Superior MHC I expression in TECs is unaffected by deletion of Ifnar1 or Ifngr1, but is lessened by deletion of Aire, Ifnlr1, Stat1 or Nlrc5, and is driven mainly by type III IFN produced by mTECs. Ifnlr1−/− mice show impaired negative selection of CD8 thymocytes, and at 9 months of age, present autoimmune manifestations. Our study shows unanticipated variation in MHC I expression by ECs from various sites and provides compelling evidence that superior expression of MHC I in TECs is crucial for proper thymocyte education. We performed RNA-sequencing in triplicate from different types of primary epithelial cells (ECs) isolated from thymus, skin, lung and colon in order to identify the mechanisms involved in differential expression level of MHC I molecules on these different sources of ECs. Each replicate contained a pool of FACS-sorted ECs isolated from 5 mice.