Project description:Bulk RNAseq data from abdominal subcutaneous sampling of a racially diverse sample of healthy premenopausal women and men with a range of BMI.
Project description:Over the past two decades, studies have identified distinct transcriptional signatures between ABD and GF-adipose tissues and between both body shapes. Remarkably, a significant fraction of these depot specific gene expression patterns and more recently the differential chromatin structure profiles have been shown to be conserved during the culture and in vitro differentiation of the precursor cells into mature adipocytes. Our team and others have also shown distinct DNA methylation levels between ABD and GF-AT, that are preserved in isolated ADSCs cultured in vitro. Altogether, these data suggest that depot specific epigenomic profiles contribute significantly to the unique transcriptional profiles of ABD vs GF adipose tissues depots. To extend these earlier studies and to determine how the differential gene expression patterns in different adipose depots may be significantly influenced by chromatin landscape we performed H3K4me3, H3K4me2, H3K27me3, H3K9me3 and CTCF ChIP-seq and ATAC-seq on chromatin isolated from ABD and GF-ADSCs. We paired this with highly differentially expressed genes between ABD and GF-ADSCs. Then, to evaluate the potential role for long range chromatin interactions we utilized an H3K27Ac Hi-ChIP approach to capture putative regulatory loops with at least one anchor being marked by this enhancer associated histone mark. This in-depth analysis of the chromatin structure and organization of ABD and GF-ADSCs provides a better understanding of the intrinsic genomic regulatory features that help define the functionally distinct phenotypes of different subcutaneous adipose tissue depots and how they influence fat distribution in women.
Project description:Individualized analysis through expression profiling of 20,000 probes in 28 tissue samples evaluated in subcutaneous and omental adipose tissue obtained during surgical intervention in non-obese and obese patients. Patients consisted of men and women of varying body size (lean to severely obese). Samples were collected at the time of operation in the fasting state. Samples consisted of subcutaneous and omental adipose tissue as well as a blood sample from lean and obese men and women removed in the fasting state at the time of surgery.
Project description:Obesity has considerable effects on morbidity and mortality, and the prevalence of obesity has been increasing rapidly worldwide during the past two decades. Even if obesity affects the entire individual, adipose tissue plays a central role in the development of obesity. Expression profiling of adipose tissue may give insights into the mechanisms contributing to obesity and obesity-related disorders. The Swedish Obese Subjects (SOS) Sib-Pair Study consists of 154 nuclear families with BMI-discordant sib pairs (BMI difference more than 10 kg/m2) resulting in a study population consisting of 732 subjects. The full SOS Sib-Pair study offspring cohort consists of 425 subjects. Microarray expression analysis in subcutaneous adipose tissue was performed in 375 subjects (262 women and 113 men) of the SOS Sib-Pair offspring cohort. Microarray expression analysis in subcutaneous adipose tissue was performed in women (n=262) and men (n=113) of the SOS Sib-Pair offspring cohort.
Project description:Human adipose serived stem cells (ASC) isolated from A and GF adipose tissue obtained from premenopausal women were used to perform assess accessible chromatin regions by ATAC-seq, chromatin marks, CTCF and RNAPII identification by chIP-seq
Project description:To evaluate wether miRNA expression patterns contributes to obesity total RNA were purified from subcutaneous adipose tissue (SAT)and used in miRNA microarrays. Platform contain LNA-modified probes for all human miRNAs present in release 8.2 of the miRBase microRNA Registry. Two RNA pools from 3 non obese men (CM) and from 5 non obese women (CW) were used as controls. Expression profiling revealed that a large set of miRNAs is expressed in SAT. Forty two miRNAs changed by at least 1.5 folds in 17/20 obese subjects versus non obese control pool. Particularly, 21/42 were up-regulated and 21/42 were down-regulated. Among the differentially expressed miRNA, miR-519d, miR-498 and miR-150 were up-regulated, miR-659 and miR-371-3p_MM2 were down-regulated consistently in 20/20 obese subjects. To search for miRNAs eventually associated with obesity we used a microarray to evaluate the expression of 1458 different miRNAs in 10 obese women (OBW) and 10 obese men (OBM). Two RNA pools from 3 non obese men (CM) and from 5 non obese women (CW) were used as controls.
Project description:Individualized analysis through expression profiling of 20,000 probes in 28 tissue samples evaluated in subcutaneous and omental adipose tissue obtained during surgical intervention in non-obese and obese patients. Patients consisted of men and women of varying body size (lean to severely obese). Samples were collected at the time of operation in the fasting state.
Project description:Human adipose serived stem cells (ASC) isolated from A and GF adipose tissue obtained from premenopausal women were used to overexpress and downregulate HOTAIR (respectively). RNA-seq was used to study the transcriptome of control and treated cells.
