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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression profiles of induced pluripotent mesenchymal stromal cells [Affymetrix]

ABSTRACT: Reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is an epigenetic phenomenon. We have reprogrammed mesenchymal stromal cells (MSC) from human bone marrow by retrovirus-mediated overexpression of OCT-3/4, SOX2, c-MYC, and KLF4. This series summarizes gene expression profiles of eight iP-MSC clones derived from three different donors. These datasets were subsequently used for PluriTest analysis (Muller FJ, Schuldt B et al., Nat. Methods 2011; 8: 315-317) demonstrating that all iP-MSC clones were clearly associated with pluripotent cells. Eight iP-MSC clones derived from three different donors.

ORGANISM(S): Homo sapiens

SUBMITTER: Wolfgang Wagner

PROVIDER: E-GEOD-38806 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profiles of induced pluripotent mesenchymal stromal cells [Affymetrix]

Project description:Reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is an epigenetic phenomenon. We have reprogrammed mesenchymal stromal cells (MSC) from human bone marrow by retrovirus-mediated overexpression of OCT-3/4, SOX2, c-MYC, and KLF4. This series summarizes gene expression profiles of eight iP-MSC clones derived from three different donors. These datasets were subsequently used for PluriTest analysis (Muller FJ, Schuldt B et al., Nat. Methods 2011; 8: 315-317) demonstrating that all iP-MSC clones were clearly associated with pluripotent cells.

2012-09-24 | GSE38806 | GEO

Induced Pluripotent Mesenchymal Stromal Cell Clones Retain Donor-Derived Differences in DNA Methylation Profiles

Project description:Reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is an epigenetic phenomenon. It has been suggested that iPSC retain some tissue-specific memory whereas little is known about inter-individual epigenetic variation of iPSC clones. In this study we have reprogrammed mesenchymal stromal cells (MSC) from human bone marrow by retrovirus-mediated overexpression of OCT-3/4, SOX2, c-MYC, and KLF4. Global DNA-methylation profiles of the initial MSC, MSC-derived iPSC (iP-MSC) and embryonic stem cells (ESC) were then compared using a high density DNA-methylation array covering more than 450,000 CpG sites. Overall, DNA-methylation patterns of iP-MSC and ESC were similar whereas some CpG sites revealed highly significant differences, which were not related to parental MSC. Furthermore, hypermethylation in iP-MSC versus ESC was particularly enriched in developmental genes as well as shore regions next to CpG islands indicating that these differences are not due to tissue-specific memory or random de novo methylation. Subsequently, we searched for CpG sites with donor-specific variation in MSC preparations. These “epigenetic fingerprints” were highly enriched in non-promoter regions and outside of CpG islands – and they were maintained upon reprogramming into iP-MSC. In conclusion, DNA methylation profiles of iP-MSC clones from the same donor were closely related despite heterogeneity of MSC. On the other hand, iP-MSC maintain donor-derived epigenetic differences. In the absence of isogenic controls for disease modeling applications, it would therefore be more appropriate to compare iPSC from different donors rather than a high number of different clones from the same patient. 16 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

2013-01-09 | E-GEOD-34688 | biostudies-arrayexpress

Induced Pluripotent Mesenchymal Stromal Cell Clones Retain Donor-Derived Differences in DNA Methylation Profiles

2013-01-09 | GSE34688 | GEO

Pluripotent Stem Cells Escape From Senescence-Associated DNA Methylation Changes

Project description:This SuperSeries is composed of the following subset Series: GSE37065: Long-term culture associated gene expression changes in MSC [Affymetrix] GSE37066: Pluripotent Stem Cells Escape From Senescence-Associated DNA Methylation Changes [Illumina] GSE38806: Gene expression profiles of induced pluripotent mesenchymal stromal cells [Affymetrix] Refer to individual Series

2012-09-24 | E-GEOD-37067 | biostudies-arrayexpress

Long-term culture associated gene expression changes in MSC [Affymetrix]

Project description:Mesenchymal stromal cells (MSC) were isolated from human bone marrow. Here, we have compared gene expression profiles of MSC at early and late passages. Long-term culture associated gene expression changes were then correlated with DNA-methylation profiles. The goal of this study was to determine if senescence-associated DNA-methylation (SA-DNAm) changes are reflected by differential gene expression. Overall, genes with SA-DNAm changes (particularly with SA-hypomethylation) were detected at low level and seemed to be scarcely expressed at early and late passages. MSC were isolated from three different donors and culture expanded until replicative senescence. Gene expression profiles were compared at early and late passage using GeneChip Humang Gene 1.0 ST arrays (Affymetrix). Six hybridizations are included in this series.

2012-09-24 | E-GEOD-37065 | biostudies-arrayexpress

CD146 expression in mesenchymal stem cells is associated with vascular smooth muscle commitment

Project description:Bone-marrow mesenchymal stem cells (MSCs) are plastic adherent cells that can differentiate into various tissue lineages, including osteoblasts, adipocytes and chondrocytes. However, this progenitor property is not shared by all cells within the MSC population. In addition, MSCs vary in their proliferation capacities and expression of markers. Because of heterogeneity of CD146 expression in the MSC population, we compared CD146-/Low and CD146High cells under clonal and non-clonal (sorted MSCs) conditions to determine whether this expression is associated with specific functions. CD146-/Low and CD146High MSCs did not differ in colony-forming unit-fibroblast number, osteogenic and adipogenic differentiation or in vitro hematopoietic supportive activity. However, CD146-/Low clones proliferated slightly but significantly faster than did CD146High clones. In addition, a strong expression of CD146 molecule was associated with a commitment towards a vascular smooth muscle cell lineage with upregulation of calponin-1 expression. Thus, within a bone-marrow MSC population, certain subpopulations characterized by high expression of CD146, are committed toward a vascular smooth muscle cell lineage. Clonal MSC were selected on the basis of CD146 level at their surface (CD146Low and CD146 High) and non-clonal MSC were compared from 4 different donors.

2013-07-04 | E-GEOD-48540 | biostudies-arrayexpress

Functional Evaluation of Mesenchymal Stem Cells Derived from Canine Induced Pluripotent Stem Cells

Project description:Comparison of gene expression profiles of canine induced pluripotent stem cells (iPSC) and iPS derived mesenchymal stem cells (iMSC) by microarray Mesenchymal stem cells (MSCs) exhibit broad immune modulatory activity in vivo and can suppress T cell and dendritic cell activation in vitro. Currently, most MSC for clinical usage are derived from adipose or bone marrow tissues from younger donors, in part due to ease of procurement and to the superior immune modulatory activity of young MSC. However, use of MSC from multiple unrelated donors makes it difficult to standardize MSC cellular products with uniform immune modulatory properties. One solution to this problem is the use of MSC derived from induced pluripotent stem cells (iPSC), as iPSC-derived MSC have nearly unlimited proliferative potential and exhibit in vitro phenotypic stability. Given the value of dogs as a spontaneous disease model for pre-clinical evaluation of stem cell therapeutics, we investigated the functional properties of canine iPSC-derived MSC (iMSC), including their immune modulatory properties and their potential for teratoma formation. We found that canine iMSC downregulated expression of pluripotency genes and appeared morphologically similar to conventional MSC. Importantly, iMSC retained a stable phenotype even after multiple passages, did not form teratomas when inoculated in immune deficient mice, and did not induce tumor formation in purpose-bred dogs following systemic injection. The immune potency of iMSC was similar to that of adipose and bone-marrow derived MSC with respect to suppression of T cell and DC activation. We concluded therefore that iMSC were phenotypically stable, immunologically potent, and safe with respect to tumor formation, and represented an important new source of cells for therapeutic modulation of inflammatory disorders.

2017-01-26 | GSE94081 | GEO

Long-term culture associated gene expression changes in MSC (TGFb treatment)

Project description:Mesenchymal stromal cells (MSC) were isolated from human bone marrow. Here, we have compared gene expression profiles of MSC at early and late passages and upon stimulation with transforming growth factor beta 1 (TGF-b1). Stimulation was performed with 1ng/mL TGF-b1 for 1, 4, or 12 hours as indicated. The goal of this study was to determine if senescence-associated gene expression changes and TGF-b1 induced gene expression changes are related. 24 samples were hybridized GeneChip Human Gene 1.0 ST Arrays (Affymetrix)

2014-02-05 | E-GEOD-46019 | biostudies-arrayexpress

miRNOME of healthy donor and myelodysplastic bone marrow mesenchymal stromal cells (MSC)

Project description:We have demonstrated that DICER1 (a key enzyme of miRNA biogenesis) was underexpressed in myelodysplastic syndrome MSC. We hypothesize that those MSC harbored a deregulated pattern of miRNA versus healthy donors MSC.

2020-10-04 | GSE139471 | GEO

Gene expression data of human dermal pilla cells, human induced pluripotent stem cell-derived CD271+CD90+ mesenchymal stem cells before and after the induction toward dermal papilla cells

Project description:To assess if human induced pluripotent stem cell-derived mesenchymal stem cells (hiPSC-MSCs) could be induce to acquire dermal papilla (DP) properties (especially hair inductive capacity), hiPSCs were initially programmed in serum-free MSC medium with FGF, TGFbeta and PDGF. Subsequently, hiMSCs were exposed to retinoic acid and activators of WNT, BMP and FGF signaling pathways. Global gene expression profiles were compared among primarily cultured human DP cells, hiPSC-MSCs before and after induction. Human dermal papillae were microdissected and cultured from different donors. Induction from hiPSCs to MSCs and subsequent sorting of CD271+CD90+ subpopulation and thier induction to DP was performed using WD39 hiPSC lines in two independent experimentations to generate hiPSC-MSC-1,hiPSC-MSC-2 ipDPSC-1 and ipDPSC-2. Funding: The Human Stem Cells Informatization Project of the Ministry of Health, Labour and Welfare, Japan

2015-01-01 | E-GEOD-61511 | biostudies-arrayexpress

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