Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Molecular signatures of human iPSCs highlight sex differences and cancer genes

ABSTRACT: We compared human female hiPSC lines (all derived from IMR-90 fibroblasts) that were XIST RNA-positive and XIST RNA-negative. We also examined the gene expression patterns for 2 female hIPSCs (derived from different disease model fibroblasts) that were also negative for XIST RNA. hiPS 12D-1 is derived from Huntington's Disease patient and 6C-1 is derived from a Type I Diabetes Mellitus patient (Park et al Nature 2008). hiPSCs (undifferentiated) were cultured to confluency then RNA was isolated using TriZOL (MEFs were removed using trypsin). cDNA was converted using NuGEN then hybridized to Affymetrix 3' arrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Ruslan Sadreyev

PROVIDER: E-GEOD-36233 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Molecular signatures of human induced pluripotent stem cells highlight sex differences and cancer genes.

Anguera Montserrat C MC Sadreyev Ruslan R Zhang Zhaoqing Z Szanto Attila A Payer Bernhard B Sheridan Steven D SD Kwok Showming S Haggarty Stephen J SJ Sur Mriganka M Alvarez Jason J Gimelbrant Alexander A Mitalipova Maisam M Kirby James E JE Lee Jeannie T JT

Cell stem cell 20120701 1

Although human induced pluripotent stem cells (hiPSCs) have enormous potential in regenerative medicine, their epigenetic variability suggests that some lines may not be suitable for human therapy. There are currently few benchmarks for assessing quality. Here we show that X-inactivation markers can be used to separate hiPSC lines into distinct epigenetic classes and that the classes are phenotypically distinct. Loss of XIST expression is strongly correlated with upregulation of X-linked oncogen ...[more]

PMID: 22770242

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Project description:Human ES cells (hESCs) and human induced pluripotent stem cells (hiPSCs) are usually generated and maintained on living feeder cells like mouse embryonic fibroblasts or on a cell-free substrate like Matrigel. For clinical applications, a quality-controlled, xenobiotic-free culture system is required to minimize risks from contaminating animal-derived pathogens and immunogens. We previously reported that the pericellular matrix of decidua-derived mesenchymal cells (PCM-DM) is an ideal human-derived substrate on which to maintain hiPSCs/hESCs. In this study, we examined whether PCM-DM could be used for the generation and long-term stable maintenance of hiPSCs. Decidua-derived mesenchymal cells (DMCs) were reprogrammed by the retroviral transduction of four factors (OCT4, SOX2, KLF4, c-MYC) and cultured on PCM-DM. The established hiPSC clones expressed alkaline phosphatase, hESC-specific genes and cell-surface markers, and differentiated into three germ layers in vitro and in vivo. At over 20 passages, the hiPSCs cultured on PCM-DM held the same cellular properties with genome integrity as those at early passages. Global gene expression analysis showed that the GDF3, FGF4, UTF1, and XIST expression levels varied during culture, and GATA6 was highly expressed under our culture conditions; however, these gene expressions did not affect the cellsM-bM-^@M-^Y pluripotency. PCM-DM can be conveniently prepared from DMCs, which have a high proliferative potential. Our findings indicate that PCM-DM is a versatile and practical human-derived substrate that can be used for the feeder-cell-free generation and long-term stable maintenance of hiPSCs. Keywords: Induced pluripotent stem cells; Extracellular matrix; Decidua; Mesenchymal cells The microarray study was carried out using Affymetrix Human Genome U133 Plus 2.0 gene expression arrays. Total RNA was extracted from cells with RNeasy (Qiagen), and 100ng of total RNA was used to synthesize aRNA using the 3M-bM-^@M-^Y IVT Express Kit, according to the manufacturerM-bM-^@M-^Ys instructions (Affymetrix Inc., Santa Clara, CA). After aRNA purification, 15 M-NM-<g of aRNA was fragmented and hybridized with a pre-equilibrated GeneChip array (Human Genome U133 Plus 2.0 gene expression array, Affymetrix) at 45M-BM-0C for 16 hours. The GeneChip array was then washed, stained, and scanned according to the manufacturerM-bM-^@M-^Ys instructions. The gene expression data were extracted using Affymetrix Expression Console software.

Dataset Information

Molecular signatures of human iPSCs highlight sex differences and cancer genes

Publications

Molecular signatures of human induced pluripotent stem cells highlight sex differences and cancer genes.

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