Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide transcriptome analysis of integrin β1 inhibited primed and naïve human induced pluripotent stem cells.

ABSTRACT: Cell states are governed by cell-intrinsic properties and external cues that regulate cell shape and signaling via cell-cell junctions or adhesions. Integrin β1-mediated adhesion is dispensable in early mouse embryogenesis at pre-implantation but becomes indispensable post-implantation. This implies distinct roles for β1-integrins in the naïve pre-implantation and primed post-implantation pluripotent stem cells (PSC). These, however, remain poorly understood. We investigated β1-integrin control of naïve-like and primed human induced PSC (hiPSC). We find that integrin β1 is active in naïve and primed hiPSCs and the degree of activity varies in vitro on different ECMs. Inhibition of integrin β1 in primed hiPSCs induces naïve-like colony features, reduces actomyosin contraction and ERK activity and alters gene expression, indicative of more naïve-like features. Integrin β1 inhibition supports epigenetic reversion of primed PSC to a naïve-like status, which involves dramatic reorganization of colony morphology, actin and adhesions. Furthermore, continued β1 integrin inhibition facilitates the maintenance of a naïve-like state through gene expression. These data reveal unprecedented integrin-dependent regulation of PSC states and demonstrate how integrin inhibitors may help to fine-tune hiPSC function and properties in vitro.

ORGANISM(S): Homo sapiens

PROVIDER: GSE205423 | GEO | 2025/06/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Inhibition of integrin β1 activity support a naïve-like state in human induced pluripotent stem cells

Project description:Cell states are governed by cell-intrinsic properties and external cues that regulate cell shape and signaling via cell-cell junctions or adhesions. Integrin β1-mediated adhesion is dispensable in early mouse embryogenesis at pre-implantation but becomes indispensable post-implantation. This implies distinct roles for β1-integrins in the naïve pre-implantation and primed post-implantation pluripotent stem cells (PSC). These, however, remain poorly understood. We investigated integrin β1 control of naïve-like and primed human induced PSC (hiPSC) states. We find that integrin β1 is active in naïve and primed hiPSCs and the degree of activity varies in vitro on different extracellular matrices (ECMs). Integrin β1 inhibition in primed hiPSCs induces naïve-like colony features, reduces actomyosin contraction and ERK activity and alters gene expression, indicative of more naïve-like features. Reverting the primed state of pluripotency to naïve involves dramatic reorganization of colony morphology, actin and adhesions. Importantly, functional and single-cell transcriptomics analyses demonstrate that integrin β1 inhibition attenuates colony morphology transitions in cells exiting naïve pluripotency. These data reveal unprecedented integrin-dependent regulation of PSC states and demonstrate how integrin inhibitors may help to fine-tune hiPSC function and properties in vitro.

2025-05-19 | GSE282224 | GEO

DNA methylation in marmoset primed and naive pluripotent stem cells, and trophoblast stem cells

Project description:Bisulfite sequencing on bulk populations of marmoset naïve pluripotent stem cells (PSC), primed PSC, and trophoblsat stem cells.

2024-11-21 | E-MTAB-12453 | biostudies-arrayexpress

Formative transition of human naïve pluripotent stem cells

Project description:Human naïve pluripotent stem cells (PSC) share features with pre-implantation epiblast. They thus provide an unmatched opportunity for characterising the developmental programme of pluripotency in Homo sapiens. Here we confirm that naïve PSC do not respond directly to germ layer induction, but must first acquire competence. Capacitation for multi-lineage differentiation occurs without exogenous growth factor stimulation and is facilitated by inhibition of Wnt signalling. Whole transcriptome profiling during this formative transition highlights dynamic changes in gene expression, affecting many cellular properties, including metabolism and epithelialisation. Notably, naïve pluripotency factors are exchanged for post-implantation factors, but competent cells remain devoid of lineage primed transcription. The gradual pace of transition for human naïve PSC is consistent with the timespan of primate development from blastocyst to gastrulation. Transcriptome trajectory during in vitro capacitation of human naïve cells tracks the progression of epiblast during embryogenesis in Macaca fascicularis, but shows greater divergence from mouse development. Thus the formative transition of naïve PSC in a simple culture system may recapitulate essential and specific features of pluripotency dynamics during an inaccessible period of human embryogenesis.

2019-03-07 | GSE123055 | GEO

3D ECM-rich environment sustains the identity of naïve human iPSCs [Naive_3Dvs2D_p6]

Project description:The establishment of in vitro naïve human pluripotent stem cell cultures opened new perspectives for the study of early events in human development. The role of several transcription factors and signaling pathways during maintenance of human naïve pluripotency has been characterized. However, little is known about the role exerted by the extracellular matrix and its three-dimensional organization. Here, using an unbiased and integrated approach combining transcriptional, proteomic and secretome analyses, we found that naïve, but not primed, hiPSC colonies are characterized by a self-organized extracellular matrix (ECM)-rich microenvironment. Based on this, we developed a 3D culture system that supports robust long-term feeder-free self-renewal of naïve hiPSCs, and also allows direct and timely developmental morphogenesis simply by modulating the signalling environment. Our study opens new perspectives for future applications of naïve hiPSCs to study critical stages of human development in 3D starting from a single cell

2022-10-01 | GSE196157 | GEO

3D ECM-rich environment sustains the identity of naïve human iPSCs

Project description:The establishment of in vitro naïve human pluripotent stem cell cultures opened new perspectives for the study of early events in human development. The role of several transcription factors and signalling pathways during maintenance of human naïve pluripotency have been characterized. However, little is known about the role exerted by the extracellular matrix (ECM) and its three-dimensional (3D) organization. Here, using an unbiased and integrated approach combining transcriptional, proteomic and secretome analyses, we found that naïve, but not primed, hiPSC colonies are characterized by a self-organized ECM-rich microenvironment. Based on this, we developed a 3D culture system that supports robust long-term feeder-free self-renewal of naïve hiPSCs, and also allows direct and timely developmental morphogenesis simply by modulating the signalling environment. Our study opens new perspectives for future applications of naïve hiPSCs to study critical stages of human development in 3D starting from a single cell.

2023-02-20 | GSE213024 | GEO

3D ECM-rich environment sustains the identity of naïve human iPSCs II

2022-10-01 | GSE196050 | GEO

Establishment of Bovine Induced Pluripotent Stem Cells

Project description:Pluripotent stem cells (PSCs) have been successfully developed in many species. However, generating bovine induced pluripotent stem cells (biPSCs) has been challenging. Here we report the generation of biPSCs by overexpression of lysine-specific demethylase 4A (KDM4A) and repro-gramming factors OCT4, SOX2, KLF4, cMYC, LIN28, and NANOG (KdOSKMLN). These biPSCs exhibited silenced transgene expression at passage 10, and had prolonged self-renewal capacity for over 70 passages. The biPSCs have flat, primed-like PSC colony morphology in combined me-dia of knockout serum replacement (KSR) and mTeSR, but switched to dome-shaped, naïve-like PSC colony morphology in mTeSR medium and 2i/LIF with single cell colonization capacity. These cells have comparable proliferation rate to the reported primed- or naïve-state human PSCs, with three-germ layer differentiation capacity and normal karyotype. Transcriptome analysis revealed a high similarity of biPSCs to reported bovine embryonic stem cells (ESCs) and embryos. The naïve-like biPSCs can be incorporated into mouse embryos, with the extended capacity of in-tegration into extra-embryonic tissues. Finally, 24.6% cloning efficiency could be achieved in nu-clear transfer (NT) experiment using late passage biPSCs as nuclear donors. Our report represents a significant advance in the establishment of bovine PSCs.

2021-09-27 | GSE180931 | GEO

3D ECM-rich environment sustains the identity of naïve human iPSCs [Bulk RNA-seq in triplicate after 1, 4, and 7 days of culture]

Project description:The establishment of in vitro naïve human pluripotent stem cell cultures opened new perspectives for the study of early events in human development. In the last 5 years the signalling environment promoting human naïve pluripotency has been extensively investigated. However, little is known about the role exerted by the extracellular matrix and three-dimensional organization in naïve maintenance. Here, by using an unbiased and integrated approach we found that naïve, but not primed, hiPSC colonies are characterized by an extracellular matrix-rich microenvironment, and by a specific extracellular matrix fingerprint at transcriptional, proteomic and secretome levels. Based on this, we developed a 3D culture system which supports robust long-term feeder-free expansion of naïve hiPSCs. In this same 3D ECM-rich environment, we can recapitulate timely developmental morphogenesis simply by modulating the signalling environment. Our study opens new perspectives for future applications of naïve hiPSCs to study critical stages of human development in three-dimensions starting from a single cell.

2021-11-11 | GSE161717 | GEO

3D ECM-rich environment sustains the identity of naïve human iPSCs

2021-11-11 | GSE161371 | GEO

Derivation of Human Naïve Pluripotent Stem Cells by Activation of YAP

Project description:Expression profiling of Naïve and Primed hESCs using Illumina HT-12 v.4 expression BeadChip We report that over-expression of the transcription factor YAP in male and female human ESCs and iPSCs promotes the generation of naïve PSCs. YAP-induced naïve PSCs have a naïve-specific dome-like colony morphology, rapid clonal growth rate for more than 70 passages, normal karyotype, expression of pluripotency markers and ability to form teratomas. Lysophosphatidic acid (LPA) can substitute for YAP to generated transgene-free human naïve PSCs. We performed microarray analyses on hESCs and hIPSCs in primed and naïve ESC media and show that YAP overexpressing cells in naïve media (Ying et al 2008, Ludwig et al 2006, Theunnissen 2014) display a distinct naïve-like transcriptional profile and other hallmarks of the naïve state. These results uncover an unexpected role for YAP in the transition to the human naïve state, and provide a platform in which to further dissect this transition and probe early human embryology.

2016-02-03 | GSE69200 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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