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Mus

ABSTRACT: Identification of novel subsets of medullary thymic epithelial cells

PROVIDER: PRJDB5700 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR090726.fastq.gz	Fastqsanger.gz
	DRR090727.fastq.gz	Fastqsanger.gz
	DRR139979.fastq.gz	Fastqsanger.gz
	DRR139980.fastq.gz	Fastqsanger.gz

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Comparison of ectopic gene expression in Cdx1+/+ and Cdx1-/- thymic medullary epithelial cells

Project description:We have found that Cdx1 can promote ectopic gene expression in thymic epithelial cells. We isolated MHCIIhi CD80hi medullary thymic epithelial cells from Cdx1-/- and Cdx1+/+ and compare gene expression between the two subsets, also in the context of Cdx1-mediated changes in intestinal epithelial cells.

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Rat thymic epithelium-free areas are specialized medullary niches enriched for mature thymocytes and distinct stromal subsets

Project description:The rat thymic medulla provides the microenvironment for negative selection, late thymocyte maturation, and thymocyte egress, and is generally characterized by widespread distribution of medullary thymic epithelial cells (mTECs). In contrast, rat thymic medulla contains medullary epithelium-free areas (mEFAs), but the cellular composition and functional significance of these regions remain unclear. Here, we combined spatial transcriptomics, scRNA-seq, and robust cell-type decomposition (RCTD) to characterize mEFAs in Lewis rat thymus. These analyses revealed that mature single-positive thymocytes, including CD4SP, CD8SP, and regulatory T-cell-lineage cells, were preferentially localized in mEFAs, whereas immature SP subsets were enriched in medullary epithelium-containing areas. Rat thymic mesenchymal cell-3 and -4 (TMC3 and TMC4) subsets were also enriched in mEFAs. These subsets were broadly similar to mouse medullary fibroblasts but displayed distinct predicted interactions with SP thymocytes, including costimulatory molecule–receptor, chemokine–receptor, and ECM–integrin axes. In addition, the venous endothelial cells (vECs) expressing portal endothelial cell markers were accumulated in mEFAs. The S1P transporter gene Spns2 was preferentially expressed in both TMC4 and vEC subsets, suggesting increased local concentration in mEFAs. These findings indicate that rat mEFAs are specialized medullary niches linking stromal organization, thymocyte maturation, and thymic egress.

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Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells [scRNA-seq]

Project description:We profiled medullary thymic epithelial cell subsets from a variety of conditions by scRNA-seq to investigate mechanisms of T-cell tolerance.

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Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells [RNA-seq]

Project description:We profiled medullary thymic epithelial cell subsets and peripheral cell types by bulk RNA-seq to investigate mechanisms of T-cell tolerance.

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Project description:Thymic epithelial cells govern thymic T lymphocyte differentiation and selection. Medullary TECs (mTECs) facilitate the negative selection of self-reactive thymocytes and the differentiation of FOXP3+ regulatory T cells. Medullary TECs are also distinctive for their “promiscuous” gene expression, transcribing thousands of peripheral tissue genes (PTG) that are otherwise only expressed highly in one or two other organs. Much of this PTG expression by mTECs is controlled by the autoimmune regulator, AIRE. To probe the mechanism by which KAT7 promotes AIRE function, we performed ATAC-seq to compare chromatin accessibility in MHCII-high medullary thymic epithelial cells from Kat7-knockout and wildtype mice.

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Project description:RNA-seq libraries were generated on thymic epithelial cell (TEC) subsets from thymic samples (11 days to 3 months of age). Cells were sorted to isolate cortical TEC (cTEC), MHC low medullary TEC (mTEClo) and MHC high medullary TEC (mTEChi). Between 7,575 and 50,000 cells were isolated for each sample. TEC were isolated using CD45 MACS depletion followed by the sorting protocol described in Stoeckler et al. J Vis Exp 2013 (PMID 24084687; doi: 10.3791/50951). The study has been granted ethical approval and is publicly listed (IRAS ID 156910, CPMS 19587).

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