Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Nuclear Matrix Association in Proliferative and Invasive Cytotrophoblasts

ABSTRACT: Abnormal trophoblast invasion is associated with the most common and most severe complications of human pregnancy. The biology of invasion, as well as the etiology of abnormal invasion remains poorly understood. The aim of this study was to characterize the transcriptome of the HTR-8/SVneo human cytotrophoblast cell line which displays well characterized invasive and non-invasive behaviors, and to correlate the activity of the transcriptome with nuclear matrix attachment and cell phenotype. Interestingly comparison of the transcriptome did not reveal an obvious significant difference between the transcriptomes of invasive and non-invasive HTR cells. In contrast, comparison of the MARs on chromosomes 14-18 revealed an increased number of MARs associated with an invasive phenotype. These attachment areas were more likely to be associated with silent (rather than actively transcribed) genes. DNA extraction with a 2 M NaCl solution followed by restriction digestion with EcoR1 facilitates the separation of matrix bound DNA from non matrix bound DNA. Genomic CGH arrays were used to map the relative differences between attached (scaffold/matrix) and non-attached (loop) portions of the genome in non-invasive (proliferative) and invasive trophoblasts. The matrix association was assessed relative to gene expression measured on Illumina expression beadchips.

ORGANISM(S): Homo sapiens

SUBMITTER: Stephen Krawetz

PROVIDER: E-GEOD-17501 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Nuclear matrix association: switching to the invasive cytotrophoblast.

Drennan K J KJ Linnemann A K AK Platts A E AE Heng H H HH Armant D R DR Krawetz S A SA

Placenta 20100325 5

Abnormal trophoblast invasion is associated with the most common and most severe complications of human pregnancy. The biology of invasion, as well as the etiology of abnormal invasion remains poorly understood. The aim of this study was to characterize the transcriptome of the HTR-8/SVneo human cytotrophoblast cell line which displays well characterized invasive and non-invasive behavior, and to correlate the activity of the transcriptome with nuclear matrix attachment and cell phenotype. Compa ...[more]

PMID: 20346505

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Project description:Intestinal fibrosis is a well-known complication of inflammatory bowel disease (IBD) and has important clinical implications for both forms of IBD, Crohn's disease (CD) and ulcerative colitis (UC). In addition to mesenchymal cells, endothelial cell contribute to organ fibrosis through the process of endothelial-to-mesenchymal transition (EndoMT). Our aim was to investigate if human intestinal microvascular endothelial cells (HIMEC) can undergo EndoMT, produce extracellular matrix, and contribute to fibrosis in both forms of IBD. Cellular transformation is a highly complex event involving drastic changes in multiple gene expression levels. To assess global genomic changes accompanying HIMEC transformation, we performed microarray analysis comparing transformed to non-transformed/untreated HIMEC. Consistent with the morphological, phenotypic and functional findings, transformed HIMEC downregulated the expression levels of genes typically expressed in endothelial cells and upregulated several genes of ECM molecules known to be increased in intestinal fibrosis. Thus, it is evident that inflammatory stimuli induce transdifferentiation of HIMEC into matrix-producing mesenchymal cells. Because the conditions inducing transformation in vitro reproduce those found in vivo during active gut inflammation, the microvasculature may contribute to IBD-associated fibrosis through the novel process of EndoMT. This series includes all untreated or CONTROL HIMEC samples (4). Surgically resected specimens were used for isolation of human intestinal microvascular endothelial cells (HIMEC). HIMEC monolayers derived from intestinal mucosa of four different subjects – 2 controls, 1 ulcerative colitis, and 1 crohns were cultured in 75cm2 tissue culture flasks coated with fibronectin. Cells were left untreated (unstimulated/non-transformed) or exposed to the combination of IL-1b 100 U/ml, TNF-a 100 U/ml and TGF-b1, 5ng/ml (TGFTNFIL1) for six days. HIMEC medium was changed every 3 days. Total ribonucleic acid (RNA) was extracted using a commercially available kit (Qiagen®). RNA was reverse transcribed into cRNA which was then hybridized to the Illumina HumanRef-8 v2 Expression BeadChip. The raw gene expression datasets were processed to remove outliers, log2 transformed and quantile normalized using R lumi software. Those genes that satisfied the FDR p-value threshold of < 0.05 or raw p-value of <0.001 were identified as significant for the functional pathway and network analysis.

Project description:Intestinal fibrosis is a well-known complication of inflammatory bowel disease (IBD) and has important clinical implications for both forms of IBD, Crohn's disease (CD) and ulcerative colitis (UC). In addition to mesenchymal cells, endothelial cell contribute to organ fibrosis through the process of endothelial-to-mesenchymal transition (EndoMT). Our aim was to investigate if human intestinal microvascular endothelial cells (HIMEC) can undergo EndoMT, produce extracellular matrix, and contribute to fibrosis in both forms of IBD. Cellular transformation is a highly complex event involving drastic changes in multiple gene expression levels. To assess global genomic changes accompanying HIMEC transformation, we performed microarray analysis comparing transformed to non-transformed/untreated HIMEC. Consistent with the morphological, phenotypic and functional findings, transformed HIMEC downregulated the expression levels of genes typically expressed in endothelial cells and upregulated several genes of ECM molecules known to be increased in intestinal fibrosis. Thus, it is evident that inflammatory stimuli induce transdifferentiation of HIMEC into matrix-producing mesenchymal cells. Because the conditions inducing transformation in vitro reproduce those found in vivo during active gut inflammation, the microvasculature may contribute to IBD-associated fibrosis through the novel process of EndoMT. This series includes all treated or TRANSFORMED HIMEC samples (4). Surgically resected specimens were used for isolation of human intestinal microvascular endothelial cells (HIMEC). HIMEC monolayers derived from intestinal mucosa of four different subjects – 2 controls, 1 ulcerative colitis, and 1 crohns were cultured in 75cm2 tissue culture flasks coated with fibronectin. Cells were left untreated (unstimulated/non-transformed) or exposed to the combination of IL-1b 100 U/ml, TNF-a 100 U/ml and TGF-b1, 5ng/ml (TGFTNFIL1) for six days. HIMEC medium was changed every 3 days. Total ribonucleic acid (RNA) was extracted using a commercially available kit (Qiagen®). RNA was reverse transcribed into cRNA which was then hybridized to the Illumina HumanRef-8 v2 Expression BeadChip. The raw gene expression datasets were processed to remove outliers, log2 transformed and quantile normalized using R lumi software. Those genes that satisfied the FDR p-value threshold of < 0.05 or raw p-value of <0.001 were identified as significant for the functional pathway and network analysis.

Dataset Information

Nuclear Matrix Association in Proliferative and Invasive Cytotrophoblasts

Publications

Nuclear matrix association: switching to the invasive cytotrophoblast.

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