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Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences
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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3547704/ https://www.ncbi.nlm.nih.gov/pubmed/23241383 http://dx.doi.org/10.1186/1752-0509-6-154 |
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author | Mathew, Shibin Jaramillo, Maria Zhang, Xinan Zhang, Li Ang Soto-Gutiérrez, Alejandro Banerjee, Ipsita |
author_facet | Mathew, Shibin Jaramillo, Maria Zhang, Xinan Zhang, Li Ang Soto-Gutiérrez, Alejandro Banerjee, Ipsita |
author_sort | Mathew, Shibin |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3547704 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35477042013-01-23 Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences Mathew, Shibin Jaramillo, Maria Zhang, Xinan Zhang, Li Ang Soto-Gutiérrez, Alejandro Banerjee, Ipsita BMC Syst Biol Research Article 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. BioMed Central 2012-12-15 /pmc/articles/PMC3547704/ /pubmed/23241383 http://dx.doi.org/10.1186/1752-0509-6-154 Text en Copyright ©2012 Mathew et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Mathew, Shibin Jaramillo, Maria Zhang, Xinan Zhang, Li Ang Soto-Gutiérrez, Alejandro Banerjee, Ipsita Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences |
title | Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences |
title_full | Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences |
title_fullStr | Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences |
title_full_unstemmed | Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences |
title_short | Analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences |
title_sort | analysis of alternative signaling pathways of endoderm induction of human embryonic stem cells identifies context specific differences |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3547704/ https://www.ncbi.nlm.nih.gov/pubmed/23241383 http://dx.doi.org/10.1186/1752-0509-6-154 |
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