Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression analysis of FOXN1+ thymic endoderm cells derived from the in vitro differentiation of human embryonic stem cells

ABSTRACT: The goal of this study was to document the gene expression profile of FOXN1+ thymic endoderm cells derived from the in vitro differentiation of human pluripotent stem cells. Thymic epithelial cells (TECs) play a critical role in T-cell maturation and tolerance induction. The generation of TECs from in vitro differentiation of human pluripotent stem cells (PSCs) would provide a platform for studying the mechanisms of this interaction and have implications for immune reconstitution. To facilitate analysis of PSC-derived TECs, we generated human embryonic stem cell (hESC) reporter lines in which sequences encoding GFP were targeted to FOXN1, a gene required for TEC development. Using this FOXN1GFP/w line as a read out, we developed a reproducible protocol for generating FOXN1-GFP+ thymic endoderm cells. Transcriptional profiling and flow cytometry identified Integrin-β4 (ITGB4, CD104) and HLA-DR as markers that could be used in combination with EpCAM to selectively purify FOXN1+ TEC progenitors from differentiating cultures of unmanipulated PSCs. Human FOXN1+ TEC progenitors generated from PSCs will facilitate the study of thymus biology and are a valuable resource for future applications in regenerative medicine

ORGANISM(S): Homo sapiens

PROVIDER: GSE56373 | GEO | 2014/05/01

SECONDARY ACCESSION(S): PRJNA243062

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene expression analysis of FOXN1+ thymic endoderm cells derived from the in vitro differentiation of human embryonic stem cells

Project description:The goal of this study was to document the gene expression profile of FOXN1+ thymic endoderm cells derived from the in vitro differentiation of human pluripotent stem cells. Thymic epithelial cells (TECs) play a critical role in T-cell maturation and tolerance induction. The generation of TECs from in vitro differentiation of human pluripotent stem cells (PSCs) would provide a platform for studying the mechanisms of this interaction and have implications for immune reconstitution. To facilitate analysis of PSC-derived TECs, we generated human embryonic stem cell (hESC) reporter lines in which sequences encoding GFP were targeted to FOXN1, a gene required for TEC development. Using this FOXN1GFP/w line as a read out, we developed a reproducible protocol for generating FOXN1-GFP+ thymic endoderm cells. Transcriptional profiling and flow cytometry identified Integrin-β4 (ITGB4, CD104) and HLA-DR as markers that could be used in combination with EpCAM to selectively purify FOXN1+ TEC progenitors from differentiating cultures of unmanipulated PSCs. Human FOXN1+ TEC progenitors generated from PSCs will facilitate the study of thymus biology and are a valuable resource for future applications in regenerative medicine Human embryonic stem cells were differentiated for 30 days using the protocol described by Soh et al, 2014. The hESCs used in this protocol had been genetically modified by targeting sequences encoding GFP to the FOXN1 locus, thus enabling FOXN1 expressing cells to be identified on the basis of GFP expression. At differentiation day 30, differentiating cells were separated into three fractions using FACS. These fractions were the FOXN1+(GFP+)EpCAM+, FOXN1-(GFP-)EpCAM+, FOXN1-(GFP-)EpCAM-.

2014-05-01 | E-GEOD-56373 | biostudies-arrayexpress

Transcriptional regulation of the thymus master regulator Foxn1 [ATAC-Seq]

Project description:FOXN1 is a transcription factor critical for the development of both thymic epithelial cell (TEC) and hair follicle cell (HFC) compartments. However, mechanisms controlling its expression remain poorly understood. To address this question, we performed thorough analyses of the conservation and chromatin status of the Foxn1 locus in different tissues and states, and identified several putative cis-regulatory regions unique to TEC vs. HFC. Furthermore, experiments using genetically modified mice with specific deletions in the Foxn1 locus and additional bioinformatic analyses helped us identify key regions and transcription factors involved in either positive or negative regulation of Foxn1 in both TEC and HFC. Specifically, we identified SIX1 and FOXN1 itself, as key factors inducing Foxn1 expression in embryonic and neonatal TECs. Together, our data provide important mechanistic insights into the transcriptional regulation of the Foxn1 gene in TEC vs. HFC and highlight the role of FOXN1 in its autoregulation

2022-08-03 | GSE192873 | GEO

Transcriptional regulation of the thymus master regulator Foxn1 [RNAseq_AR3_vs_nude]

2022-08-03 | GSE192872 | GEO

Transcriptional regulation of the thymus master regulator Foxn1 [RNAseq_dev_HFC]

2022-08-03 | GSE192871 | GEO

Transcriptional regulation of the thymus master regulator Foxn1 [WGBS]

2022-08-03 | GSE198591 | GEO

Transcriptional regulation of the thymus master regulator Foxn1 [ChIP-seq]

2022-08-03 | GSE204741 | GEO

microRNA expression in thymic epithelial cells

Project description:Thymic epithelial cells (TECs) support T cell development in the thymus. Cortical thymic epithelial cells (cTECs) facilitate positive selection of developing thymocytes whereas medullary thymic epithelial cells (mTECs) facilitate the deletion of self-reactive thymocytes in order to prevent autoimmunity. The mTEC compartment is highly dynamic with continuous maturation and turnover, but the genetic regulation of these processes remains poorly understood. MicroRNAs (miRNAs) are important regulators of TEC genetic programs since miRNA-deficient TECs are severely defective. However, the individual miRNAs important for TEC maintenance and function and their mechanisms of action remain unknown. Here, we demonstrate that miR-205 is highly and preferentially expressed in mTECs during both thymic ontogeny and in the postnatal thymus. This distinct expression is suggestive of functional importance for TEC biology. Genetic ablation of miR-205 in TECs, however, neither revealed a role for miR-205 in TEC function during homeostatic conditions nor during recovery from thymic stress conditions. Thus, despite its distinct expression, miR-205 on its own is largely dispensable for mTEC biology. In order to identify miRNAs differentially expressed in mTECs, we purified cortical thymic epithelial cells (cTECs), mTECs and CD45+ cells as three distinct populations and prepared RNA for microarray analysis. Thymic subsets were FACS-purified from 4-week old NOD wildtype mice. Thymi from 10-12 female mice were pooled together for stromal cell isolation for a total of 3 CD45+, 2 cTEC and 3 mTEC biologic replicates.

2015-07-28 | E-GEOD-68674 | biostudies-arrayexpress

microRNA expression in thymic epithelial cells

2015-07-28 | GSE68674 | GEO

A FOXN1 mutation competitively displaces wild-type FOXN1 from higher-order nuclear condensates to cause immunodeficiency

Project description:The transcription factor FOXN1 is a master regulator of thymic epithelial cell development and function. Here we demonstrate that FOXN1 expression is differentially regulated during organogenesis and participates in multi-molecular nuclear condensates essential for the factor's transcriptional activity. FOXN1's C-terminal sequence regulates the diffusion velocity within these aggregates and modulates the binding to proximal gene regulatory regions. These dynamics are significantly altered in a patient's FOXN1 mutant modified in its C-terminal sequence. This mutant is transcriptionally inactive and acts as a dominant negative factor displacing wild-type FOXN1 from condensates and causing athymia and severe lymphopenia in heterozygotes. Expression of the mutated mouse ortholog, Foxn1, selectively impairs mouse thymic epithelial cell (TEC) differentiation, revealing a gene dose dependency for individual TEC subtypes. We have therefore identified the cause for a primary immunodeficiency disease and determined the mechanism by which this FOXN1 gain-of-function mutant mediates its dominant negative effect.

2021-10-29 | PXD025552 | Pride

CD90 marks a mesenchymal program in human thymic epithelial cells in vitro and in vivo

Project description:Thymic epithelium is critical for the structural integrity of the thymus and for T cell development. Within the fully formed thymus, large numbers of hematopoietic cells shape the thymic epithelium into a scaffold-like structure which bears little similarity to classical epithelial layers, such as those observed in the skin, intestine or pancreas. Here, we show that human thymic epithelial cells (TECs) possess an epithelial identity that also incorporates the expression of mesenchymal cell associated genes, whose expression levels vary between medullary and cortical TECs (m/cTECs). Using pluripotent stem cell (PSC) differentiation systems, we identified a unique population of cells that co-expressed the master TEC transcription factor FOXN1, as well as the epithelial associated marker EPCAM and the mesenchymal associated gene CD90. Using the same serum free culture conditions, we also observed co-expression of EPCAM and CD90 on cultured TECs derived from neonatal human thymus in vitro. Single cell RNA-sequencing revealed these cultured TECs possessed an immature mTEC phenotype and expressed epithelial and mesenchymal associated genes, such as EPCAM, CLDN4, CD90 and COL1A1. Importantly, flow cytometry and single cell RNA-sequencing analysis further confirmed the presence of an EPCAM+CD90+ population in the CD45- fraction of neonatal human thymic stromal cells in vivo. Using the human thymus cell atlas, we found that cTECs displayed more pronounced mesenchymal characteristics than mTECs during embryonic development. Collectively, these results suggest human TECs possess a hybrid gene expression program comprising both epithelial and mesenchymal elements, and provide a basis for the further exploration of thymus development from primary tissues and from the in vitro differentiation of PSCs.

2022-02-28 | GSE196005 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data