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Tracking regulatory T cell development in the thymus using scRNA-Seq/TCR-Seq

ABSTRACT: Tracking regulatory T cell development in the thymus using scRNA-Seq/TCR-Seq

PROVIDER: PRJNA837576 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19178250_1.fastq.gz	Fastqsanger.gz
	SRR19178250_2.fastq.gz	Fastqsanger.gz
	SRR19178251_1.fastq.gz	Fastqsanger.gz
	SRR19178251_2.fastq.gz	Fastqsanger.gz
	SRR19178252_1.fastq.gz	Fastqsanger.gz

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Tracking regulatory T cell development in the thymus using scRNA-Seq/TCR-Seq

Project description:Recent studies have demonstrated that mature regulatory T cells ( Tregs) develop in the thymus via two pathways involving distinct Treg progenitors (TregP) - CD25+FOXP3- (CD25+ TregP) and CD25-FOXP3lo (FOXP3lo TregP) Treg progenitors. To examine this process in more detail we carried out single-cell RNA-Seq and TCR-Seq on sorted CD4+CD8+ double-positive (DP) thymocytes, CD4+ Ssingle -positive (CD4SP)P thymocytes, CD25+ TregP, FOXP3lo TregP, mature CD25+FOXP3+ Tregs and recirculating/long-term resident Tregs (RT-Tregs). Sorted populations were individually hashtagged and then combined into one scRNA-Seq/TCR-Seq library before sequencing and subsequent analysis. We found that both CD25+ TregP and FOXP3lo TregP arise via an initial agonist activated state that gives rise to a second transitional stage before differentiating into mature Tregs. Using both scRNA-Seq and bulk RNA-Seq on sorted thymocyte subsets we demonstrate that CD25+Foxp3- TregP are significantly enriched for Il2 production, suggesting that they are the major source of IL-2 needed to convert TregP into mature Tregs. Using TCR-Seq we found that several TCRs were clearly biased in favor of the conventional or Treg lineages, but that a large fraction of TCRs were found in both these lineages. Finally, we found that recirculating/resident Tregs in the thymus are not monomorphic, but are composed of multiple distinct subsets and that these RT-Tregs express the most diverse TCR repertoire of all CD4SP thymcocytes. Thus, our studies define multiple stages of Treg differentiation within the thymus, and serve as a resource for future studies on CD4+ thymocyte development and Treg differentiation.

2022-06-30 | GSE202871 | GEO

scRNA-seq of human fetal thymus

Project description:scRNA-seq of human fetal thymus

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Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation

Project description:we compare the TCR repertoires of MAIT1 and MAIT17 cells from the mouse thymus using 5’ scRNAseq and scTCRseq of MR1:5-OP-RU tetramer positive thymocytes. A thorough analysis of TCR features between MAIT sub-populations did not show any difference between the repertoires of MAIT1 and MAIT17 subsets. Quantitative simulation of clonotype distributions of MAIT1 and MAIT17 cells allowed us to investigate the role of TCR characteristics in MAIT fate choice, and to pinpoint the stage at which lineage commitment occurs. Our results indicate that the TCR characteristics are not instructive in MAIT lineage choice and that MAIT1/17 commitment takes place during MAIT cell proliferation in the thymus. Finally, we performed analogous analysis of a published scRNA-seq and scTCR-seq dataset of iNKT from mouse thymus and demonstrated that our conclusions are also relevant for iNKT1 vs iNKT17 fate commitment.

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scRNA-seq of human fetal thymus

Project description:To investigate the gene regulatory mechanisms driving T cell development, we generated single-cell transcriptomics and chromatin accessibility data from a human fetal thymus sample at 10 weeks of gestation.

2021-11-30 | E-MTAB-9840 | biostudies-arrayexpress

TCR signal strength controls thymic differentiation of discrete proinflammatory Î³Î´T cell subsetsistinct TCR signal strength requirements in the thymus

Project description:The murine thymus produces discrete Î³Î´ T cell subsets making either IFN-Î³ or IL-17, but the role of the TCR in this developmental process remains controversial. Here we generated a non-transgenic and polyclonal model of reduced TCR expression and signal strength selectively on Î³Î´ T cells. Mice haploinsufficient for both CD3Î³ and CD3Î´ (CD3DH) showed normal Î±Î² thymocyte subsets but specific defects in Î³Î´ T cell development, namely impaired differentiation of IL-17-producing embryonic VÎ³6+ (but not adult VÎ³4+) Î³Î´ T cells and a marked depletion of IFN-Î³-producing CD122+ NK1.1+ (VÎ³1-biased) Î³Î´ T cells throughout life. As result, adult CD3DH mice showed defective peripheral IFN-Î³ responses and were resistant to experimental cerebral malaria. Thus, strong TCR signaling is required within specific developmental windows with distinct VÎ³ usage and differential cytokine production by effector Î³Î´ T cell subsets. We investigated the transcriptional changes associated with reduced TCRÎ³Î´ signaling in the CD3DH model. Transcriptome-wide analysis of FACS-purified CD3DH or WT Î³Î´ thymocytes from E18 or 6-week was carried looking for patterns of gene expression during ontogeny

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Investigating human T cell development in the human pediatric thymus using scRNA-seq

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Investigating human T cell development in the human pediatric thymus using scRNA-seq

Project description:To study human T cell development at the single cell level we profiled thymocytes from 3 pediatric donors using scRNA-seq. The data was subsequently used in the construction of a cell atlas of human thymic development across the life span. This allowed the identification of over 50 cell states in the human thymus and helped map the developmental trajectories of conventional and unconventional T cells throughout development.

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