Dataset Information

Comparison of the gene expression profile of undifferentiated human embryonic stem cell lines and differentiating embryoid bodies.

ABSTRACT:

Background

The identification of molecular pathways of differentiation of embryonic stem cells (hESC) is critical for the development of stem cell based medical therapies. In order to identify biomarkers and potential regulators of the process of differentiation, a high quality microarray containing 16,659 seventy base pair oligonucleotides was used to compare gene expression profiles of undifferentiated hESC lines and differentiating embryoid bodies.

Results

Previously identified "stemness" genes in undifferentiated hESC lines showed down modulation in differentiated cells while expression of several genes was induced as cells differentiated. In addition, a subset of 194 genes showed overexpression of greater than > or = 3 folds in human embryoid bodies (hEB). These included 37 novel and 157 known genes. Gene expression was validated by a variety of techniques including another large scale array, reverse transcription polymerase chain reaction, focused cDNA microarrays, massively parallel signature sequencing (MPSS) analysis and immunocytochemisty. Several novel hEB specific expressed sequence tags (ESTs) were mapped to the human genome database and their expression profile characterized. A hierarchical clustering analysis clearly depicted a distinct difference in gene expression profile among undifferentiated and differentiated hESC and confirmed that microarray analysis could readily distinguish them.

Conclusion

These results present a detailed characterization of a unique set of genes, which can be used to assess the hESC differentiation.

SUBMITTER: Bhattacharya B

PROVIDER: S-EPMC1260016 | biostudies-literature | 2005 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparison of the gene expression profile of undifferentiated human embryonic stem cell lines and differentiating embryoid bodies.

Bhattacharya Bhaskar B Cai Jingli J Luo Youngquan Y Miura Takumi T Mejido Josef J Brimble Sandii N SN Zeng Xianmin X Schulz Thomas C TC Rao Mahendra S MS Puri Raj K RK

BMC developmental biology 20051005

<h4>Background</h4>The identification of molecular pathways of differentiation of embryonic stem cells (hESC) is critical for the development of stem cell based medical therapies. In order to identify biomarkers and potential regulators of the process of differentiation, a high quality microarray containing 16,659 seventy base pair oligonucleotides was used to compare gene expression profiles of undifferentiated hESC lines and differentiating embryoid bodies.<h4>Results</h4>Previously identified ...[more]

PMID: 16207381

Similar Datasets

Project description:BackgroundDifferentiation of embryonic stem cells (ESCs) into specific cell types with minimal risk of teratoma formation could be efficiently directed by first reducing the differentiation potential of ESCs through the generation of clonal, self-renewing lineage-restricted stem cell lines. Efforts to isolate these stem cells are, however, mired in an impasse where the lack of purified lineage-restricted stem cells has hindered the identification of defining markers for these rare stem cells and, in turn, their isolation.Methodology/principal findingsWe describe here a method for the isolation of clonal lineage-restricted cell lines with endothelial potential from ESCs through a combination of empirical and rational evidence-based methods. Using an empirical protocol that we have previously developed to generate embryo-derived RoSH lines with endothelial potential, we first generated E-RoSH lines from mouse ESC-derived embryoid bodies (EBs). Despite originating from different mouse strains, RoSH and E- RoSH lines have similar gene expression profiles (r(2) = 0.93) while that between E-RoSH and ESCs was 0.83. In silico gene expression analysis predicted that like RoSH cells, E-RoSH cells have an increased propensity to differentiate into vasculature. Unlike their parental ESCs, E-RoSH cells did not form teratomas and differentiate efficiently into endothelial-like cells in vivo and in vitro. Gene expression and FACS analysis revealed that RoSH and E-RoSH cells are CD9(hi), SSEA-1(-) while ESCs are CD9(lo), SSEA-1(+). Isolation of CD9(hi), SSEA-1(-) cells that constituted 1%-10% of EB-derived cultures generated an E-RoSH-like culture with an identical E-RoSH-like gene expression profile (r(2) = 0.95) and a propensity to differentiate into endothelial-like cells.ConclusionsBy combining empirical and rational evidence-based methods, we identified definitive selectable surface antigens for the isolation and propagation of lineage-restricted stem cells with endothelial-like potential from mouse ESCs.

Project description:Pluripotent embryonic stem cells (ESCs) are capable of differentiating into all mesoderm-derived cell lineages, including endothelial, hematopoietic, and cardiac cell types. Common strategies to direct mesoderm differentiation of ESCs rely on exposing the cells to a series of biochemical and biophysical cues at different stages of differentiation to promote maturation toward specific cell phenotypes. Shear forces that mimic cardiovascular physiological forces can evoke a myriad of responses in somatic and stem cell populations, and have, thus, been studied as a means to direct stem cell differentiation. However, elucidating the effects of shear pre-conditioning on the subsequent vascular differentiation and morphogenesis of ESCs has yet to be examined. In this study, ESC monolayers were subjected to physiological shear (5 dyn/cm(2)) or static conditions for 2 days on collagen IV-coated substrates before initiating embryoid body (EB) differentiation. Immediately after the pre-conditioning period, shear pre-conditioned and statically cultured ESCs exhibited similar morphologies and largely retained a pluripotent phenotype; however, ESCs exposed to fluid shear expressed increased levels of endothelial marker genes Flk-1 (∼3-fold), VE-cadherin (∼3-fold), and PECAM (∼2-fold), compared with statically cultured ESCs. After 7 days of EB culture, ∼70% of EBs formed from shear pre-conditioned ESCs expressed significantly higher levels of endothelial marker genes compared with EBs formed from statically cultured ESCs. Interestingly, unlike EBs formed from statically cultured ESCs, EBs formed from fluid shear stress pre-conditioned ESCs exhibited a centrally localized region of VE-cadherin(+) cells that persisted for at least 10 days of differentiation. These results demonstrate that fluid shear stress pre-conditioning not only promotes ESC endothelial gene expression but also subsequently impacts the organization of endothelial cells within EBs. Together, these studies highlight a novel approach to promote in vitro morphogenesis of developmental vasculogenic models and potentially promote pre-vascularization of tissue-engineered constructs derived from pluripotent stem cells.

Dataset Information

Comparison of the gene expression profile of undifferentiated human embryonic stem cell lines and differentiating embryoid bodies.

Background

Results

Conclusion

Publications

Comparison of the gene expression profile of undifferentiated human embryonic stem cell lines and differentiating embryoid bodies.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets