Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide analysis of the isogenic embryonic and induced pluripotent stem cell lines revealed no traces of parental cell type or reprogramming process and provided the approach for the best clone selection [methylation]

ABSTRACT: Genome wide DNA methylation profiling of two parental human embryonic stem cell (ESC) lines (hESM01 and n5), three n5-derived somatic cell lines (N-neurons, F-fibroblasts, R-retinal pigment epithelium), and three pairs of induced pluripotent stem cell (iPSC) clones (iN, iF, iR). All lines are isogenic. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. For each line there are a biological (different passages) or technical (same passage) replicate.

ORGANISM(S): Homo sapiens

SUBMITTER: Maria Shutova

PROVIDER: E-GEOD-70737 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Previously we have shown that extravillous cytotrophoblast (EVT) outgrowth and migration on a collagen gel explant model were restricted by exposure to decidual natural killer cells (dNK). This study investigates the molecular causes behind this phenomenon. Genome wide DNA methylation of exposed and unexposed EVT was assessed using the Illumina Infinium HumanMethylation450 BeadChip array (450K array). The array identified 444 differentially methylated CpG loci in dNK-treated EVT compared to medium control (P<0.05). The represented genes from these loci had critical biological roles in cellular development, cellular organization and maintenance by Ingenuity Pathway Analysis (IPA). Furthermore, 23 mobility-related genes were identified by IPA from dNK-treated EVT. Among these genes, CLDN4 (encoding claudin-4) and FUT4 (encoding fucosyltranferase IV) were chosen for follow-up studies because of the biological relevance found in the research on tumor cells. The results showed that the mRNA and protein expressions of both CLDN4 and FUT4 in dNK-treated EVT were significantly reduced, and were inversely correlated with DNA methylation. Knocking down CLDN4 and FUT4 by siRNA reduced trophoblast invasion, possibly through the altered MMP-2 and/or MMP-9 expression and activity. Taken together, dNK alter EVT mobility at least partially in association with an alteration of DNA methylation profile. Hypermethylation of CLDN4 and FUT4 reduce protein expressions. CLDN4 and FUT4 are representative genes that participate in modulating trophoblast mobility. This studied analyzed 17 samples of placental villous explant cultre exposed to different growth conditions. 6 Control samples (biological replicates) were cultured and unexposed to any other cells. 5 samples (biological replicates and from the same placentas as the controls) were cultured and exposed to conditions containing decidua natural killer cells trapped inside hollow fibres (thus only the factors secreted by the cells could interact with the explant culture and not the cells themselves. 6 samples (biological replicates and from the same placentas as the controls) were cultured and exposed to media containing IL-15. The DNA from the villous explants was isolated, bisulfite converted and run on the array.

Dataset Information

Genome-wide analysis of the isogenic embryonic and induced pluripotent stem cell lines revealed no traces of parental cell type or reprogramming process and provided the approach for the best clone selection [methylation]

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