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Single Cell Transcriptome Mapping of Human Thymopoiesis Reveals a Continuum of Cell States During T-Lineage Specification and Commitment

ABSTRACT: Single Cell Transcriptome Mapping of Human Thymopoiesis Reveals a Continuum of Cell States During T-Lineage Specification and Commitment

PROVIDER: PRJNA578128 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10302342_1.fastq.gz	Fastqsanger.gz
	SRR10302342_2.fastq.gz	Fastqsanger.gz
	SRR10302343_1.fastq.gz	Fastqsanger.gz
	SRR10302343_2.fastq.gz	Fastqsanger.gz
	SRR10302344_1.fastq.gz	Fastqsanger.gz

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Single Cell Transcriptome Mapping of Human Thymopoiesis Reveals a Continuum of Cell States During T-Lineage Specification and Commitment

Project description:Single cell studies elucidating the transcriptional continuum underpinning lineage commitment in the human bone marrow (BM) have advanced the understanding of hematopoiesis beyond the classic hierarchical model. However, T-lineage commitment, which occurs in the thymus remains incompletely defined. We mapped single cell transcriptomes spanning post-natal human thymopoiesis including the earliest progenitors. Instead of previously described discrete populations, transcriptional and lineage assay data resolved a continuum of novel cell states within CD34+ thymic progenitor cells. The initial stages of thymopoiesis involve multilineage priming of single cells followed by a gradual transition to T-commitment, a continuum previously undescribed outside the BM. Early progenitors express a hematopoietic stem cell (HSC) like profile but unlike HSC show initiation of T-priming. Species related differences exist in the earliest progenitor cells.

2020-06-12 | GSE139042 | GEO

GATA3 induces human T cell commitment following Notch-induced T-lineage specification (expression)

Project description:Here, we show that GATA3 induces T-lineage commitment following Notch-induced T-lineage specification through direct regulation of at least 3 distinct processes: repression of NK-cell fate, activation of T-lineage genes to promote further differentiation, and down modulation of Notch signalling activity. Gene expression was measured in RPMI8402 cells after transduction with control, shGATA3 or shTCF1 and culture for 48h. Cells were collected 48h after transduction and sorted for EGFP+. This was performed for 2 replicates.

2016-04-06 | E-GEOD-76348 | biostudies-arrayexpress

Single-Cell RNA-Seq Mapping of Human Thymopoiesis Reveals Lineage Specification Trajectories and a Commitment Spectrum in T Cell Development.

Project description:The challenges in recapitulating in vivo human T cell development in laboratory models have posed a barrier to understanding human thymopoiesis. Here, we used single-cell RNA sequencing (sRNA-seq) to interrogate the rare CD34+ progenitor and the more differentiated CD34- fractions in the human postnatal thymus. CD34+ thymic progenitors were comprised of a spectrum of specification and commitment states characterized by multilineage priming followed by gradual T cell commitment. The earliest progenitors in the differentiation trajectory were CD7- and expressed a stem-cell-like transcriptional profile, but had also initiated T cell priming. Clustering analysis identified a CD34+ subpopulation primed for the plasmacytoid dendritic lineage, suggesting an intrathymic dendritic specification pathway. CD2 expression defined T cell commitment stages where loss of B cell potential preceded that of myeloid potential. These datasets delineate gene expression profiles spanning key differentiation events in human thymopoiesis and provide a resource for the further study of human T cell development.

| S-EPMC7388724 | biostudies-literature

GATA3 induces human T cell commitment following Notch-induced T-lineage specification (expression)

2016-04-06 | GSE76348 | GEO

GATA3 restrains Notch signaling activity and represses NK cell development to induce human T cell commitment following Notch-induced T-lineage specification (ChIP-Seq)

Project description:The stepwise conversion of multipotent precursors into committed T-cell progenitors depends on several transcriptional regulators, but the interplay between these factors is still obscure. This is particularly true in human since the core early Notch signalling pathway also supports NK cell development and requires tight regulation for efficient T-lineage commitment and differentiation. Here, we show that GATA3, in contrast to TCF1, induces T-lineage commitment following NOTCH1-induced T-lineage specification through direct regulation of at least 3 distinct processes: repression of NK-cell fate, activation of T-lineage genes to promote further differentiation, and downmodulation of Notch signalling activity. GATA3-mediated repression of the NOTCH1 target gene DTX1 hereby is essential to induce T-lineage commitment at the expense of NK cell differentiation. Thus, human T-lineage commitment is dependent on the precise collaboration of several transcriptional regulators that integrate through both positive and negative regulatory loops. ChIP-sequencing data was generated for GATA3 in human thymocytes

2016-04-06 | E-GEOD-71751 | biostudies-arrayexpress

GATA3 restrains Notch signaling activity and represses NK cell development to induce human T cell commitment following Notch-induced T-lineage specification (expression)

Project description:The stepwise conversion of multipotent precursors into committed T-cell progenitors depends on several transcriptional regulators, but the interplay between these factors is still obscure. This is particularly true in human since the core early Notch signalling pathway also supports NK cell development and requires tight regulation for efficient T-lineage commitment and differentiation. Here, we show that GATA3, in contrast to TCF1, induces T-lineage commitment following NOTCH1-induced T-lineage specification through direct regulation of at least 3 distinct processes: repression of NK-cell fate, activation of T-lineage genes to promote further differentiation, and downmodulation of Notch signalling activity. GATA3-mediated repression of the NOTCH1 target gene DTX1 hereby is essential to induce T-lineage commitment at the expense of NK cell differentiation. Thus, human T-lineage commitment is dependent on the precise collaboration of several transcriptional regulators that integrate through both positive and negative regulatory loops. Gene expression was profiled in CT CD34+ cells after transduction with control or GATA3 and coculture on OP9-DL1 for 48h. Cells were collected 48h after coculture and sorted for CD45+EGFP+. 3 independent experiments were performed on 3 different thymus donors.

2016-04-06 | E-GEOD-71752 | biostudies-arrayexpress

Distinct Chromatin States Define a Program Of Mesenchymal Stem Cell Commitment To Osteogenesis

Project description:Multipotent mesenchymal stromal cells (MSCs) from bone marrow are critical for regeneration and homeostasis of multiple tissues. As epigenetic mechanisms are a fundamental regulator of lineage specification and cell fate, we examined histone modification changes in MSCs at distinct stages osteogenic differentiation, including: proliferation, early commitment, matrix deposition, and mineralization. Temporal changes of multiple histone modifications along with several transcriptional regulators were assessed and correlated to gene expression, which revealed distinct epigenetic mechanisms that regulate transcriptional programs necessary for commitment and tissue-specific phenotype development. Patterns of stage-specific enrichment of histone modifications revealed distinct modes of repression and activation of gene expression that would not be detected using single endpoint analysis. In addition, we have defined dynamic enhancer regions that control tissue-specific genes. Our work provides a cornerstone to understand the epigenetic regulation of transcriptional programs that are important for MSC commitment, as well as insights to facilitate MSC-based therapeutic interventions.

2017-05-05 | GSE76074 | GEO

Recapitulation of murine thymopoiesis in vitro from single hematopoietic stem cells

Project description:We report a serum-free, 3-D murine artificial thymic organoid (ATO) system that mimics normal murine thymopoiesis from four different mouse strains with the production of all T cell populations, from early thymic progenitors to functional single positive (CD8SP and CD4SP) TCRaband TCRyd cells. RNA sequencing aligned ATO-derived populations with phenotypically identical primary thymocytes. ATOs initiated with Rag1-/- marrow produced the same differentiation block as seen in the endogenous thymus, and Notch signaling patterns in ATOs mirrored primary thymopoiesis. ATOs initiated with defined hematopoietic stem cells (HSCs) and progenitors from marrow and thymus recapitulated subsequent stages and the normal kinetics of T cell differentiation. Remarkably, a single HSC deposited into ATOs generated a complete trajectory of T cell differentiation producing a similar diverse TCR repertoire across clones. ATOs represent a technically simple, highly reproducible and powerful experimental platform for the study of clonal thymopoiesis from HSCs.

2020-12-15 | GSE146224 | GEO

GATA3 restrains Notch signaling activity and represses NK cell development to induce human T cell commitment following Notch-induced T-lineage specification (expression)

2016-04-06 | GSE71752 | GEO

A continuum of cell states spans pluripotency and lineage commitment in human embryonic stem cells.

Project description:BackgroundCommitment in embryonic stem cells is often depicted as a binary choice between alternate cell states, pluripotency and specification to a particular germ layer or extraembryonic lineage. However, close examination of human ES cell cultures has revealed significant heterogeneity in the stem cell compartment.Methodology/principal findingsWe isolated subpopulations of embryonic stem cells using surface markers, then examined their expression of pluripotency genes and lineage specific transcription factors at the single cell level, and tested their ability to regenerate colonies of stem cells. Transcript analysis of single embryonic stem cells showed that there is a gradient and a hierarchy of expression of pluripotency genes in the population. Even cells at the top of the hierarchy generally express only a subset of the stem cell genes studied. Many cells co-express pluripotency and lineage specific genes. Cells along the continuum show a progressively decreasing likelihood of self renewal as their expression of stem cell surface markers and pluripotency genes wanes. Most cells that are positive for stem cell surface markers express Oct-4, but only those towards the top of the hierarchy express the nodal receptor TDGF-1 and the growth factor GDF3.SignificanceThese findings on gene expression in single embryonic stem cells are in concert with recent studies of early mammalian development, which reveal molecular heterogeneity and a stochasticity of gene expression in blastomeres. Our work indicates that only a small fraction of the population resides at the top of the hierarchy, that lineage priming (co-expression of stem cell and lineage specific genes) characterizes pluripotent stem cell populations, and that extrinsic signaling pathways are upstream of transcription factor networks that control pluripotency.

| S-EPMC2768791 | biostudies-literature

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