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Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences

Mathew, S and Jaramillo, M and Zhang, X and Zhang, LA and Soto-Gutiérrez, A and Banerjee, I (2012) Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences. BMC Systems Biology, 6.

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Abstract

Background: Lineage specific differentiation of human embryonic stem cells (hESCs) is largely mediated by specific growth factors and extracellular matrix molecules. Growth factors initiate a cascade of signals which control gene transcription and cell fate specification. There is a lot of interest in inducing hESCs to an endoderm fate which serves as a pathway towards more functional cell types like the pancreatic cells. Research over the past decade has established several robust pathways for deriving endoderm from hESCs, with the capability of further maturation. However, in our experience, the functional maturity of these endoderm derivatives, specifically to pancreatic lineage, largely depends on specific pathway of endoderm induction. Hence it will be of interest to understand the underlying mechanism mediating such induction and how it is translated to further maturation. In this work we analyze the regulatory interactions mediating different pathways of endoderm induction by identifying co-regulated transcription factors.Results: hESCs were induced towards endoderm using activin A and 4 different growth factors (FGF2 (F), BMP4 (B), PI3KI (P), and WNT3A (W)) and their combinations thereof, resulting in 15 total experimental conditions. At the end of differentiation each condition was analyzed by qRT-PCR for 12 relevant endoderm related transcription factors (TFs). As a first approach, we used hierarchical clustering to identify which growth factor combinations favor up-regulation of different genes. In the next step we identified sets of co-regulated transcription factors using a biclustering algorithm. The high variability of experimental data was addressed by integrating the biclustering formulation with bootstrap re-sampling to identify robust networks of co-regulated transcription factors. Our results show that the transition from early to late endoderm is favored by FGF2 as well as WNT3A treatments under high activin. However, induction of late endoderm markers is relatively favored by WNT3A under high activin.Conclusions: Use of FGF2, WNT3A or PI3K inhibition with high activin A may serve well in definitive endoderm induction followed by WNT3A specific signaling to direct the definitive endoderm into late endodermal lineages. Other combinations, though still feasible for endoderm induction, appear less promising for pancreatic endoderm specification in our experiments. © 2012 Mathew et al.; licensee BioMed Central Ltd.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Mathew, S
Jaramillo, M
Zhang, X
Zhang, LA
Soto-Gutiérrez, A
Banerjee, Iipb1@pitt.eduIPB1
Centers: Other Centers, Institutes, or Units > McGowan Institute for Regenerative Medicine
Date: 15 December 2012
Date Type: Publication
Journal or Publication Title: BMC Systems Biology
Volume: 6
DOI or Unique Handle: 10.1186/1752-0509-6-154
Schools and Programs: Swanson School of Engineering > Chemical Engineering
Refereed: Yes
MeSH Headings: Bone Morphogenetic Protein 4--pharmacology; Cell Differentiation--drug effects; Cell Lineage--drug effects; Cluster Analysis; Embryonic Stem Cells--cytology; Embryonic Stem Cells--drug effects; Embryonic Stem Cells--metabolism; Endoderm--cytology; Endoderm--drug effects; Fibroblast Growth Factor 2--pharmacology; Gene Expression Regulation, Developmental--drug effects; Humans; Models, Biological; Pancreas--cytology; Protein Kinase Inhibitors--pharmacology; Signal Transduction--drug effects; Time Factors; Transcription Factors--metabolism; Wnt3A Protein--pharmacology
Other ID: NLM PMC3547704
PubMed Central ID: PMC3547704
PubMed ID: 23241383
Date Deposited: 04 Mar 2014 19:41
Last Modified: 03 Feb 2019 07:55
URI: http://d-scholarship.pitt.edu/id/eprint/20666

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