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Transcription profiling of human fat biopsies from subcutaneous adipose tissue from unrelated individuals - a systems genetics approach implicates USF1, FADS3 and other causal candidate genes for familial combined hyperlipidemia

ABSTRACT: Assessment of mRNA expression levels in fat biopsies from subcutaneous adipose tissue from unrelated individuals. Experiment Overall Design: Subcutaneous adipose tissue from 70 unrelated individuals.

ORGANISM(S): Homo sapiens

SUBMITTER: Christopher Plaisier

PROVIDER: E-GEOD-17170 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia.

Plaisier Christopher L CL Horvath Steve S Huertas-Vazquez Adriana A Cruz-Bautista Ivette I Herrera Miguel F MF Tusie-Luna Teresa T Aguilar-Salinas Carlos C Pajukanta Päivi P

PLoS genetics 20090911 9

We hypothesized that a common SNP in the 3' untranslated region of the upstream transcription factor 1 (USF1), rs3737787, may affect lipid traits by influencing gene expression levels, and we investigated this possibility utilizing the Mexican population, which has a high predisposition to dyslipidemia. We first associated rs3737787 genotypes in Mexican Familial Combined Hyperlipidemia (FCHL) case/control fat biopsies, with global expression patterns. To identify sets of co-expressed genes co-re ...[more]

PMID: 19750004

Similar Datasets

A systems genetics approach implicates USF1, FADS3 and other causal candidate genes for familial combined hyperlipidemia

Project description:Assessment of mRNA expression levels in fat biopsies from subcutaneous adipose tissue from unrelated individuals. Keywords: Subcutaneous adipose tissue.

2009-09-14 | GSE17170 | GEO

Overexpression of USF1 in HEK293T cells

Project description:Overexpression of USF1 in HEK293T cells in vitro to ascertain the genes downstream of USF1. Will identify direct targets as well as indirect targets of USF1. Keywords: Overexpression of transcription factor to determine downstream targets. Cloned USF1 from cDNA and transiently transfected into HEK293T cells. Total RNA collected 48 hours after transfection. Empty vector used as control. Expression of USF1 was validated using western blot, and qRT-PCR was used to validate differential expression.

2009-09-14 | E-GEOD-17300 | biostudies-arrayexpress

Transcription profiling of human biopsies from subcutaneous adipose tissue from unrelated individuals reveals galanin preproprotein is associated with elevated plasma triglycerides

Project description:Assessment of mRNA expression levels in fat biopsies from subcutaneous adipose tissue from unrelated individuals. Experiment Overall Design: Subcutaneous adipose tissue from 49 unrelated individuals.

2009-01-17 | E-GEOD-13506 | biostudies-arrayexpress

Galanin preproprotein is associated with elevated plasma triglycerides

Project description:Assessment of mRNA expression levels in fat biopsies from subcutaneous adipose tissue from unrelated individuals. Keywords: Subcutaneous adipose tissue.

2009-01-13 | GSE13506 | GEO

A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia.

Project description:We hypothesized that a common SNP in the 3' untranslated region of the upstream transcription factor 1 (USF1), rs3737787, may affect lipid traits by influencing gene expression levels, and we investigated this possibility utilizing the Mexican population, which has a high predisposition to dyslipidemia. We first associated rs3737787 genotypes in Mexican Familial Combined Hyperlipidemia (FCHL) case/control fat biopsies, with global expression patterns. To identify sets of co-expressed genes co-regulated by similar factors such as transcription factors, genetic variants, or environmental effects, we utilized weighted gene co-expression network analysis (WGCNA). Through WGCNA in the Mexican FCHL fat biopsies we identified two significant Triglyceride (TG)-associated co-expression modules. One of these modules was also associated with FCHL, the other FCHL component traits, and rs3737787 genotypes. This USF1-regulated FCHL-associated (URFA) module was enriched for genes involved in lipid metabolic processes. Using systems genetics procedures we identified 18 causal candidate genes in the URFA module. The FCHL causal candidate gene fatty acid desaturase 3 (FADS3) was associated with TGs in a recent Caucasian genome-wide significant association study and we replicated this association in Mexican FCHL families. Based on a USF1-regulated FCHL-associated co-expression module and SNP rs3737787, we identify a set of causal candidate genes for FCHL-related traits. We then provide evidence from two independent datasets supporting FADS3 as a causal gene for FCHL and elevated TGs in Mexicans.

| S-EPMC2730565 | biostudies-literature

Expression data of human coronary artery perivascular adipocytes and subcutaneous adipocytes

Project description:Inflammatory crosstalk between perivascular adipose tissue and and blood vessel wall may contribute to atherosclerosis pathogenesis, and exhibits more pro-inflammatory than adipogenic phenotype than subcutaneous adipocytes. To identify a genomic basis for biologic differences, we performed genome-wide expression to identiy expression genes differentially regulated between perivascular and subcutaneous adipocytes.for biologic differences. We performed global gene expression analyses on in vitro differentiated adipocytes from human left coronary artery perivascular adipose tissue and subcutaneous adipose tissues derived from unrelated donors who were non-obese and did not have any known metabolic or atherosclerotic disease.

2013-03-15 | E-GEOD-45169 | biostudies-arrayexpress

Transcription profiling of human cell lines and tissues - Luscombe re-analysis of GNF/Novartis data

Project description:The expression data utilized in this analysis derives from the raw data published by Su et al. 2004 (also known as GNF/Novartis dataset or E-AFMX-5 in ArrayExpress, GSE1133 and GDS596 in GEO). The data contains 79 different human tissues and cell types with 2 replicates per tissue/cell type. The data reprocessed using GCRMA and PANP packages from Bioconductor.

2008-02-23 | E-TABM-145 | biostudies-arrayexpress

Homo sapiens

Project description:Deep subcutaneous adipose tissue (dSAT) vs. superficial subcutaneous adipose (sSAT)

| PRJNA143827 | ENA

Gene expression of genetically related and unrelated human embryonic stem cell lines

Project description:Gene expression of sibling human ES cell lines are more similar to each other than unrelated cell lines. Undifferentiated human embryonic stem cells were used for analysis. We sought to determine whether genetic differences underly variations between different human ES cell lines. Sibling cell lines that are genetically closer than non-sibling cell provided the opportunity to determine this. We found that sibling cell lines are more similar in their gene expression patterns than unrelated cell lines.

2009-03-20 | GSE15294 | GEO

Bulk RNA sequencing of subcutaneous, abdominal and perivascular adipose derived stem cells

Project description:Previous publications demonstrated that there were anatomical, physiological, cellular, clinical and prognostic differences among adipose tissue present in subcutaneous areas, abdominal cavity and outside adventitial layer of artery. Thus, we wondered whether ASCs from subcutaneous adipose tissue, abdominal adipose tissue and perivascular adipose tissue were also different in gene expression. Here we performed bulk RNA-Seq assay for subcutaneous, abdominal and perivascular adipose derived stem cells.

2021-04-13 | GSE171946 | GEO

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