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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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE38806 | GEO | 2012/09/24

SECONDARY ACCESSION(S): PRJNA168982

REPOSITORIES: GEO

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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. Eight iP-MSC clones derived from three different donors.

2012-09-24 | E-GEOD-38806 | biostudies-arrayexpress

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

microRNA expression in facet cartilage degeneration

Project description:Osteoarthritis (OA) of spine (facet joints; FJ) is one of the major causes of severe low back pain and disability worldwide. The degeneration of facet cartilage is a hallmark of FJ OA. However, endogenous mechanisms that initiate degeneration of facet cartilage are unknown and there are no disease-modifying therapies to stop FJ OA. In this study we performed microRNA array analysis to identify differentially expressed microRNAs in facet cartilage from patients with FJ OA compared to facet cartilage from patients with lumbar disc herniation (LDH).

2016-03-15 | GSE79258 | GEO

Assessing the developmental potential of human pluripotent stem cells using Pluritest

Project description:The International Stem Cell Initiative compared three common approaches for assessing pluripotent stem cells (PSC). The formation of teratomas in vivo, or embryoid bodies (EB) in vitro, provide direct tests of differentiation, whereas PluriTest predicts pluripotency through bioinformatic analysis of transcriptomes of undifferentiated cells. Here we studied the starting poulations of pluripotent stem cells using an Illumina HumanHT-12 V4.0 expression beadchip assays

2017-06-20 | GSE97884 | GEO

Homo sapiens

Project description:Assessing the developmental potential of human pluripotent stem cells using Pluritest

| PRJNA383140 | ENA

HTT-OMNI: A Web-based Platform for Huntingtin Interaction Exploration and Multi-omics Data Integration

Project description:We have developed a web-based platform for HTT PPI visualization, exploration, and multi-omic integration called HTT-OMNI. We demonstrate the utility of this platform not only for exploring and filtering existing huntingtin (HTT) PPIs, but also for investigating user-generated omics datasets. For example, we demonstrate the comparison of a published HTT IP-MS experiment, performed in the striatum brain region of a mouse HD model, to unpublished HTT IP-MS experiments in the cortex brain region. Overall, HTT-OMNI summarizes and integrates known HTT PPIs with polyQ-dependent transcriptome and proteome measurements, providing an all-in-one exploratory platform that facilitates the prioritization of target genes that may contribute to HD pathogenesis.

2022-08-15 | PXD034158 | Pride

Secretome analysis of human bone marrow derived mesenchymal stromal cells

Project description:As an essential cellular component of the bone marrow (BM) microenvironment mesenchymal stromal cells (MSC) play a pivotal role for the physiological regulation of hematopoiesis, in particular through the secretion of cytokines and chemokines. Mass spectrometry (MS) facilitates the identification and quantification of a large amount of secreted proteins (secretome), but can be hampered by the false-positive identification of contaminating proteins released from dead cells or derived from cell medium. To reduce the likelihood of contaminations we applied an approach combining secretome and proteome analysis to characterize the physiological secretome of BM derived human MSC. Our analysis revealed a secretome consisting of 315 proteins. Pathway analyses of these proteins revealed a high abundance of proteins related to cell growth and/or maintenance, signal transduction and cell communication thereby representing key biological functions of BM derived MSC on protein level. Within the MSC secretome we identified several cytokines and growth factors such as VEGFC, TGF-β1, TGF-β2 and GDF6 which are known to be involved in the physiological regulation of hematopoiesis. By comparing the peptide patterns of secretomes and cell lysates 17 proteins were identified as candidates for proteolytic processing. Taken together, our combined MS work-flow reduced the likelihood of contaminations and enabled us to carve out a specific overview about the composition of the secretome from human BM derived MSC. This methodological approach and the specific secretome signature of BM derived MSC may serve as basis foffuture comparative analyses of the interplay of MSC and HSPC in patients with hematological malignancies.

2019-02-12 | PXD011643 | Pride

Gene array comparison of highly and poorly chondrogenic clones of adult human mesenchymal stem cells (MSCs)

Project description:MSCs are a heterogeneous population of cells with different capacities for lineage differentiation. MSC clones were prepared from a single adult human bone marrow sample and screened for their chondrogenic capacity using cartilage tissue engineering (measured by type II collagen content). The aim was to compare genes expressed by highly and poorly chondrogenic clones to identify genes associated with those MSCs with an enhanced capacity for cartilage formation. The 4 most highly chondrogenic and the 4 least chondrogenic MSC clones identified following screening by cartilage tissue engineering were selected for gene array comparison using Affymetrix microarrays.

2015-04-30 | E-GEOD-54684 | biostudies-arrayexpress

Characterization and therapeautic application of mesenchymal stem cells with neuromesodermal origin from human pluripotent stem cells

Project description:Here, human pluripotent stem cells (including hiPSC and hESC) were induced to differentiate to mesenchymal stem cells (MSC) through the intermediate stage of neuromesoderm (NMP). We sequenced mRNA samples at different stages during NMP-MSC differentiation of human pluripotent stem cells to generate the gene expression profiles of these cells.

2019-05-17 | GSE120420 | GEO

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