Genome-wide maps of chromatin state in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GF) subcutaneous adipose tissue
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PROVIDER: PRJNA793019 | ENA |
REPOSITORIES: ENA
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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.
2024-01-02 | GSE224777 | GEO
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.
2024-01-02 | GSE224770 | GEO
Project description:To identify genes differentially expressed in abdominal and gluteal adipose tissue, we determined the mRNA transcription profile of 10 abdominal and 10 gluteal female adipose tissue sections using Agilent Whole Human Genome Microarrays. RNA of 10 subcutaneous abdominal and 10 subcutaneous gluteal fat depot samples was processed by Miltenyi Biotech GmbH (Bergisch Gladbach, Germany) and loaded on single-color Whole Human Genome 4x44K microarrays (G4112F) from Agilent Technologies.
2013-11-15 | E-GEOD-47511 | biostudies-arrayexpress
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
Project description:In humans, adipose tissue is distributed in subcutaneous abdominal and subcutaneous gluteal depots that comprise a variety of functional differences. Whereas energy storage in gluteal adipose tissue has been shown to mediate a protective effect, an increase of abdominal adipose tissue is associated with metabolic disorders. However, the molecular basis of depot-specific characteristics is not completely understood yet. Using array-based analyses of transcription profiles, we identified a specific set of genes that was differentially expressed between subcutaneous abdominal and gluteal adipose tissue. To investigate the role of epigenetic regulation in depot-specific gene expression, we additionally analyzed genome-wide DNA methylation patterns in abdominal and gluteal depots. By combining both data sets, we identified a highly significant set of depot-specifically expressed genes that appear to be epigenetically regulated. Interestingly, the majority of these genes form part of the homeobox gene family. Moreover, genes involved in fatty acid metabolism were also differentially expressed. Therefore we suppose that changes in gene expression profiles might account for depot-specific differences in lipid composition. Indeed, triglycerides and fatty acids of abdominal adipose tissue were more saturated compared to triglycerides and fatty acids in gluteal adipose tissue. Taken together, our results uncover clear differences between abdominal and gluteal adipose tissue on the gene expression and DNA methylation level as well as in fatty acid composition. Therefore, a detailed molecular characterization of adipose tissue depots will be essential to develop new treatment strategies for metabolic syndrome associated complications. DNA methylation profiles of abdominal adipose tissue (6 samples) and gluteal adipose tissue (6 samples) were generated using Infinium methylation 450K BeadChips from Illumina (Illumina, San Diego, USA).
2013-11-15 | E-GEOD-47512 | biostudies-arrayexpress
Project description:In humans, adipose tissue is distributed in subcutaneous abdominal and subcutaneous gluteal depots that comprise a variety of functional differences. Whereas energy storage in gluteal adipose tissue has been shown to mediate a protective effect, an increase of abdominal adipose tissue is associated with metabolic disorders. However, the molecular basis of depot-specific characteristics is not completely understood yet. Using array-based analyses of transcription profiles, we identified a specific set of genes that was differentially expressed between subcutaneous abdominal and gluteal adipose tissue. To investigate the role of epigenetic regulation in depot-specific gene expression, we additionally analyzed genome-wide DNA methylation patterns in abdominal and gluteal depots. By combining both data sets, we identified a highly significant set of depot-specifically expressed genes that appear to be epigenetically regulated. Interestingly, the majority of these genes form part of the homeobox gene family. Moreover, genes involved in fatty acid metabolism were also differentially expressed. Therefore we suppose that changes in gene expression profiles might account for depot-specific differences in lipid composition. Indeed, triglycerides and fatty acids of abdominal adipose tissue were more saturated compared to triglycerides and fatty acids in gluteal adipose tissue. Taken together, our results uncover clear differences between abdominal and gluteal adipose tissue on the gene expression and DNA methylation level as well as in fatty acid composition. Therefore, a detailed molecular characterization of adipose tissue depots will be essential to develop new treatment strategies for metabolic syndrome associated complications.
2013-11-15 | GSE47512 | GEO
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
2022-05-31 | GSE192749 | GEO
Project description:SVF was isolated from ABD and GF-adipose tissue biopsies by collagenase digestion and centrifugation, from 5 healthy women (38yo ±4.4; 31.8kg/m-2 ±3.12; WHR 0.86 ±0.05). After isolation, cells were counted with a Countess II automated cell counter (Thermofisher Scientific). Single cell suspension (56K/mL) was distributed into eight wells of a 384-well source plate (Takara Bio USA, San Jose, CA) and dispensed onto a iCELL8 350v Chip (Takara Bio USA) using an iCELL8 MultiSample NanoDispenser (Takara Bio USA). We distributed the ABD and GF-SVF of each subject on the same chip. The method used was described in [6]. In brief, mRNA from single cells were isolated, converted to full-length cDNA prior to unbiased amplification of 3’ and 5’ ends using SMART-Seq® ICELL8® Application Kit (Takara Bio, USA). Multiplexed sequencing libraries were generated from cDNA using the Illumina Nextera XT protocol and 150bp paired-end sequencing was performed on an Novogene HiSeqX instrument.
2024-02-23 | GSE255996 | GEO
Project description:Background and objective: Combination antiretroviral therapy (cART) is associated with lipodystrophy i.e. loss of subcutaneous adipose tissue in abdomen, limbs and face and its accumulation intra-abdominally. No fat is lost dorsocervically and it can even accumulates in this region (“buffalo hump”). It is unknown how preserved dorsocervical fat differs from abdominal subcutaneous fat in HIV-1-infected cART-treated patients with (cART+LD+) and without (cART+LD-) lipodystrophy. Results: Albeit dorsocervical adipose tissue in cART+LD+ seems spared from lipoatrophy, its mitochondrial DNA (mtDNA, copies/cell) content was significantly lower (by 62%) than that of the corresponding tissue in cART+LD-. Expression of CD68 mRNA, a marker of macrophages, and numerous inflammatory genes in microarray were significantly lower in dorsocervical vs. abdominal subcutaneous adipose tissue. Genes with the greatest difference in expression between the two depots were those involved in regulation of transcription and regionalization (homeobox genes), irrespective of lipodystrophy status. There was negligible mRNA expression of uncoupling protein 1, a gene characteristic of brown adipose tissue, in either depot. Conclusions: As mtDNA is depleted even in the non-atrophic dorsocervical adipose tissue, it is unlikely that the cause of lipoatrophy is loss of mtDNA. Dorsocervical adipose tissue is less inflamed than lipoatrophic adipose tissue. It does not resemble brown adipose tissue. The greatest difference in gene expression between dorsocervical and abdominal s.c. adipose tissue is in expression of homeobox genes. We used histology, microarray, polymerase chain reaction and magnetic resonance imaging to compare dorsocervical and abdominal subcutaneous adipose tissue in cART+LD+ (n=21) and cART+LD- (n=11). The study consists of 17 patients on antiretroviral treatment who have developed lipodystrophy and 11 patients that are on similar treatment but have not developped lipodystrophy. All patients are HIV+ and have 2 adipose tissue samples taken from them (dorsocervical+abdominal).
2011-09-14 | E-GEOD-28073 | biostudies-arrayexpress
Project description:To identify genes differentially expressed in abdominal and gluteal adipose tissue, we determined the mRNA transcription profile of 10 abdominal and 10 gluteal female adipose tissue sections using Agilent Whole Human Genome Microarrays.
2013-11-15 | GSE47511 | GEO