GSE107536
RNA-sequencing of cTECs, mTECs, and thymocyte maturation subsets SM, M1 and M2 from the CD4 and CD8 lineages from WT and Psmb11-deficient mice [DSP405]
Purpose: Cortical thymic epithelial cells (cTECs) contain a unique type of proteasomes, thymoproteasomes. Indirect evidence suggests that the key role of PSMB11, a catalytic subunit of thymoproteasomes specific to cTECs, is to generate a unique repertoire of MHC I peptides. Notably, PSMB11-deficient mice display defective development of CD8 thymocytes. The objective of this study was to characterize the impact of PSMB11 on cTECs and thymocyte development. Since different types of proteasomes have non-redundant effects on gene expression, we hypothesized that thymoproteasomes should have a distinct impact on the transcriptome and thereby the function of cTECs. Results: We report that PSMB11 in cortical thymic epithelial cells has dramatic effects on cTECs on both CD4 and CD8 thymocyte populations. PSMB11 modulates the expression of 850 genes in cTECs, 582 in CD4 thymocytes and 284 in CD8 thymocytes. PSMB11-regulated cTEC genes are involved mainly in cell-cell adhesion, extracellular matric organization and thymocyte chemotaxis. PSMB11-deficient cTECs acquire features of mTECs and perturb thymocyte development. Deletion of PSMB11 causes a major cell stress in both CD4 and CD8 thymocyte populations. Of note, PSMB11-deficiency had no impact on medullary thymic epithelial cells (mTECs), which originate from progenitors that express PSMB11 early in ontogeny. Conclusion: We conclude that PSMB11 has pervasive effects on both CD4 and CD8 thymocytes via regulation of gene expression in cTECs. Overall design: We performed RNA-sequencing in triplicate on cTECs, mTECs, and SM, M1 and M2 thymocytes from the CD4 and CD8 lineages, in order to identify differential gene expression between WT and Psmb11-deficient mice.