scholarly journals Activin/Nodal Signaling Controls Divergent Transcriptional Networks in Human Embryonic Stem Cells and in Endoderm Progenitors

Stem Cells ◽  
2011 ◽  
Vol 29 (8) ◽  
pp. 1176-1185 ◽  
Author(s):  
Stephanie Brown ◽  
Adrian Teo ◽  
Siim Pauklin ◽  
Nicholas Hannan ◽  
Candy H.-H. Cho ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Transcriptional Networks ◽  
Nodal Signaling

scholarly journals Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells

2014 ◽  
Author(s):  
Virginie Mournetas ◽  
Quentin M. Nunes ◽  
Patricia A. Murray ◽  
Christopher M. Sanderson ◽  
David G. Fernig
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Human Embryonic Stem Cells ◽  
Inner Cell Mass ◽  
Meta Analysis ◽  
Cell Mass ◽  
Embryonic Stem ◽  
Interaction Network ◽  
Transcriptional Networks

Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for regenerative medicine, but at present, little is known about the mechanisms that regulate hESC stemness; in particular, the role of cell-cell and cell-extracellular matrix interactions remain relatively unexplored. Methods and results. In this study we have performed an in silico analysis of cell-microenvironment interactions to identify novel proteins that may be responsible for the maintenance of hESC stemness. A hESC transcriptome of 8,934 mRNAs was assembled using a meta-analysis approach combining the analysis of microarrays and the use of databases for annotation. The STRING database was utilised to construct a protein-protein interaction network focused on extracellular and transcription factor components contained within the assembled transcriptome. This interactome was structurally studied and filtered to identify a short list of 92 candidate proteins, which may regulate hESC stemness. Conclusion. We hypothesise that this list of proteins, either connecting extracellular components with transcriptional networks, or with hub or bottleneck properties, may contain proteins likely to be involved in determining stemness.

scholarly journals Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells

2014 ◽  
Author(s):  
Virginie Mournetas ◽  
Quentin M. Nunes ◽  
Patricia A. Murray ◽  
Christopher M. Sanderson ◽  
David G. Fernig
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Human Embryonic Stem Cells ◽  
Inner Cell Mass ◽  
Meta Analysis ◽  
Cell Mass ◽  
Embryonic Stem ◽  
Interaction Network ◽  
Transcriptional Networks

Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for regenerative medicine, but at present, little is known about the mechanisms that regulate hESC stemness; in particular, the role of cell-cell and cell-extracellular matrix interactions remain relatively unexplored. Methods and results. In this study we have performed an in silico analysis of cell-microenvironment interactions to identify novel proteins that may be responsible for the maintenance of hESC stemness. A hESC transcriptome of 8,934 mRNAs was assembled using a meta-analysis approach combining the analysis of microarrays and the use of databases for annotation. The STRING database was utilised to construct a protein-protein interaction network focused on extracellular and transcription factor components contained within the assembled transcriptome. This interactome was structurally studied and filtered to identify a short list of 92 candidate proteins, which may regulate hESC stemness. Conclusion. We hypothesise that this list of proteins, either connecting extracellular components with transcriptional networks, or with hub or bottleneck properties, may contain proteins likely to be involved in determining stemness.

scholarly journals Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells

2014 ◽  
Author(s):  
Virginie Mournetas ◽  
Quentin M. Nunes ◽  
Patricia A. Murray ◽  
Christopher M. Sanderson ◽  
David G. Fernig
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Human Embryonic Stem Cells ◽  
Inner Cell Mass ◽  
Meta Analysis ◽  
Cell Mass ◽  
Embryonic Stem ◽  
Interaction Network ◽  
Transcriptional Networks

Background. Human embryonic stem cells (hESCs) are pluripotent cells derived from the inner cell mass of in vitro fertilised blastocysts, which can either be maintained in an undifferentiated state or committed into lineages under determined culture conditions. These cells offer great potential for regenerative medicine, but at present, little is known about the mechanisms that regulate hESC stemness; in particular, the role of cell-cell and cell-extracellular matrix interactions remain relatively unexplored. Methods and results. In this study we have performed an in silico analysis of cell-microenvironment interactions to identify novel proteins that may be responsible for the maintenance of hESC stemness. A hESC transcriptome of 8,934 mRNAs was assembled using a meta-analysis approach combining the analysis of microarrays and the use of databases for annotation. The STRING database was utilised to construct a protein-protein interaction network focused on extracellular and transcription factor components contained within the assembled transcriptome. This interactome was structurally studied and filtered to identify a short list of 92 candidate proteins, which may regulate hESC stemness. Conclusion. We hypothesise that this list of proteins, either connecting extracellular components with transcriptional networks, or with hub or bottleneck properties, may contain proteins likely to be involved in determining stemness.

scholarly journals Analysis of Oct4-Dependent Transcriptional Networks Regulating Self-Renewal and Pluripotency in Human Embryonic Stem Cells

Stem Cells ◽  
2007 ◽  
Vol 25 (2) ◽  
pp. 500-510 ◽  
Author(s):  
Yasmin Babaie ◽  
Ralf Herwig ◽  
Boris Greber ◽  
Thore C. Brink ◽  
Wasco Wruck ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Transcriptional Networks ◽  
Self Renewal

scholarly journals Inhibition of Activin/Nodal signaling promotes specification of human embryonic stem cells into neuroectoderm

2008 ◽  
Vol 313 (1) ◽  
pp. 107-117 ◽  
Author(s):  
Joseph R. Smith ◽  
Ludovic Vallier ◽  
Giuseppe Lupo ◽  
Morgan Alexander ◽  
William A. Harris ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Nodal Signaling

scholarly journals Rapid changes in morphogen concentration control self-organized patterning in human embryonic stem cells

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Idse Heemskerk ◽  
Kari Burt ◽  
Matthew Miller ◽  
Sapna Chhabra ◽  
M Cecilia Guerra ◽  
...  
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Embryonic Stem Cells ◽  
Cell Fate ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Nodal Signaling ◽  
Cell Fate Decisions ◽  
Self Organized ◽  
Rapid Changes

During embryonic development, diffusible signaling molecules called morphogens are thought to determine cell fates in a concentration-dependent way. Yet, in mammalian embryos, concentrations change rapidly compared to the time for making cell fate decisions. Here, we use human embryonic stem cells (hESCs) to address how changing morphogen levels influence differentiation, focusing on how BMP4 and Nodal signaling govern the cell-fate decisions associated with gastrulation. We show that BMP4 response is concentration dependent, but that expression of many Nodal targets depends on rate of concentration change. Moreover, in a self-organized stem cell model for human gastrulation, expression of these genes follows rapid changes in endogenous Nodal signaling. Our study shows a striking contrast between the specific ways ligand dynamics are interpreted by two closely related signaling pathways, highlighting both the subtlety and importance of morphogen dynamics for understanding mammalian embryogenesis and designing optimized protocols for directed stem cell differentiation.Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see <xref ref-type="decision-letter" rid="SA1">decision letter</xref>).

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