Transcriptomic and Metabolomic Analyses Reveal Distinctive Metabolic Characteristics of Superficial and Deep Subcutaneous Adipose Tissues
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ABSTRACT:
PROVIDER: PRJNA895419 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22084533_1.fastq.gz | Fastqsanger.gz | |||
| SRR22084533_2.fastq.gz | Fastqsanger.gz | |||
| SRR22084534_1.fastq.gz | Fastqsanger.gz | |||
| SRR22084534_2.fastq.gz | Fastqsanger.gz | |||
| SRR22084535_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: The purpose of the study was to find out the molecular and metabolic characteristics of human superficial (SSAT) and deep subcutaneous adipose tissue (DSAT) by performing transcriptomics and metabolomics analysis Methods: We conducted RNA-sequencing and metabolome analysis of SSAT and DSAT in a 48-year-old female patient with a BMI of 27.6 kg/m2. Six samples for each group were collected during a deep inferior epigastric perforator flap breast reconstruction. The calculated transcripts per million values were processed for unsupervised hierarchically clustered heat map generation, and Gene set enrichment analysis. For metabolomics analysis, the samples were analyzed in two modes for cationic and anionic metabolites by Capillary Electrophoresis Time-of-Flight Mass Spectrometry (CE-TOFMS). The metabolome was processed for principal component analysis (PCA) and heat map generation. For indirect metabolic flux analyses, primary adipocytes obtained from SSAT and DSAT were analyzed with Seahorse® extracellular flux analyzer. Results: PCA and heat map data revealed global differences in the transcriptome and metabolome of SSAT and DSAT. The top up-regulated gene sets in the SSAT were related to adipogenesis (FDR q < 0.0001), oxidative phosphorylation (FDR q < 0.0001), fatty acid metabolism (FDR q < 0.0001) and glycolysis (FDR q = 0.001), while inflammatory response (FDR q < 0.05) was the top up-regulated gene set in DSAT. Consequently, the metabolites related to glycolysis were abundant in SSAT, while the metabolites related to fatty acid metabolism and oxidative phosphorylation were abundant in DSAT. In cellular flux analysis, SSAT showed higher level of glycolysis and spare oxidative phosphorylation capacities. Conclusion: The global transcriptome and metabolome difference suggest that human superficial and deep subcutaneous adipose tissue are metabolically distinguishable subcompartments.
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Project description:In addition to total body fat, the regional distribution and inflammatory status of enlarged adipose tissue are strongly linked to metabolic and cardiovascular complications of obesity. We recently showed that the severity of liver non-alcoholic histopathology in obese subjects increased with the amounts of macrophages in visceral adipose tissue (VAT), while no relation was found with the subcutaneous adipose tissue (SAT). In the abdominal region, SAT is anatomically divided into superficial (sSAT) and deep (dSAT) layers. The aim of the present study was to test the hypothesis that these distinct compartments differentially contribute to hepatic alteration in obesity.
2011-09-01 | GSE30133 | GEO
Project description:In addition to total body fat, the regional distribution and inflammatory status of enlarged adipose tissue are strongly linked to metabolic and cardiovascular complications of obesity. We recently showed that the severity of liver non-alcoholic histopathology in obese subjects increased with the amounts of macrophages in visceral adipose tissue (VAT), while no relation was found with the subcutaneous adipose tissue (SAT). In the abdominal region, SAT is anatomically divided into superficial (sSAT) and deep (dSAT) layers. The aim of the present study was to test the hypothesis that these distinct compartments differentially contribute to hepatic alteration in obesity. Total RNA was isolated from two different strata of human adipose tissue of 8 subjects.
2011-08-31 | E-GEOD-30133 | biostudies-arrayexpress
Project description:We profiled total mRNA of laser captured microdissected hippocampal deep and superficial CA1 subfields from adult male (45-50 days) Wistar rats (Rattus norvegicus) (180-200g) subjected to kainic acid-induced status epilepticus (chronic epileptic phase) and control animals.
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Project description:PurposeTo develop and evaluate an automated segmentation method for accurate quantification of abdominal adipose tissue (AAT) depots (superficial subcutaneous adipose tissue [SSAT], deep subcutaneous adipose tissue [DSAT], and visceral adipose tissue [VAT]) in neonates and young children.Materials and methodsThis was a secondary analysis of prospectively collected data, which used abdominal MRI data from Growing Up in Singapore Towards healthy Outcomes, or GUSTO, a longitudinal mother-offspring cohort, to train and evaluate a convolutional neural network for volumetric AAT segmentation. The data comprised imaging volumes of 333 neonates obtained at early infancy (age ≤2 weeks, 180 male neonates) and 755 children aged either 4.5 years (n = 316, 150 male children) or 6 years (n = 439, 219 male children). The network was trained on images of 761 randomly selected volumes (neonates and children combined) and evaluated on 100 neonatal volumes and 227 child volumes by using 10-fold validation. Automated segmentations were compared with expert-generated manual segmentation. Segmentation performance was assessed using Dice scores.ResultsWhen the model was tested on the test datasets across the 10 folds, the model had strong agreement with the ground truth for all testing sets, with mean Dice similarity scores for SSAT, DSAT, and VAT, respectively, of 0.960, 0.909, and 0.872 in neonates and 0.944, 0.851, and 0.960 in children. The model generalized well to different body sizes and ages and to all abdominal levels.ConclusionThe proposed segmentation approach provided accurate automated volumetric assessment of AAT compartments on MR images of neonates and children.Keywords Pediatrics, Deep Learning, Convolutional Neural Networks, Water-Fat MRI, Image Segmentation, Deep and Superficial Subcutaneous Adipose Tissue, Visceral Adipose TissueClinical trial registration no. NCT01174875 Supplemental material is available for this article. © RSNA, 2021.
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Project description:Although multiple gene and protein expression have been extensively profiled in human pulmonary arterial hypertension (PAH), the mechanism for the development and progression of pulmonary hypertension remains elusive. Analysis of the global metabolomic heterogeneity within the pulmonary vascular system leads to a better understanding of disease progression. Using a combination of high-throughput liquid-and-gas-chromatography-based mass spectrometry, we showed unbiased metabolomic profiles of disrupted glycolysis, increased TCA cycle, and fatty acid metabolites with altered oxidation pathways in the severe human PAH lung. The results suggest that PAH has specific metabolic pathways contributing to increased ATP synthesis for the vascular remodeling process in severe pulmonary hypertension. These identified metabolites may serve as potential biomarkers for the diagnosis of severe PAH. By profiling metabolomic alterations of the PAH lung, we reveal new pathogenic mechanisms of PAH in its later stage, which may differ from the earlier stage of PAH, opening an avenue of exploration for therapeutics that target metabolic pathway alterations in the progression of PAH. Global profiles were determined in human lung tissue and compared across 11 normal and 12 severe pulmonary arterial hypertension patients. Using a combination of microarray and high-throughput liquid-and-gas-chromatography-based mass spectrometry, we showed unbiased metabolomic profiles of disrupted glycolysis, increased TCA cycle, and fatty acid metabolites with altered oxidation pathways in the severe human PAH lung.
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Project description:The low temperature normally applied to prevent fruit decay during the storage of apples, can also triggers the onset of a chilling injury disorder known as superficial scald. In this work, the etiology of this disorder and the mechanism of action of two preventing strategies, such as the application of 1-MCP and storage at low oxygen concentration in ‘Granny Smith’ and ‘Ladina’ apple cultivars was investigated. The metabolite assessment highlighted a reorganization of specific secondary metabolites, in particular flavan-3-ols (catechin, epicatechin and procyanidin B) and unsaturated fatty acids (oleic acid, linoleic acid and linolenic acid), while the genome-wide transcriptomic analysis grouped the DEGs into four functional clusters. The KEGG pathway, GO enrichment analysis, together with the gene-metabolite profiling interactome, showed as the treatment with 1-MCP prevented the development of superficial scald by actively promoting the production of unsaturated fatty acids, especially in ‘Granny Smith’. ‘Ladina’ was instead more susceptible to superficial scald, and characterized by a higher accumulation of very long chain fatty acids (VLCFAs). Storage at low oxygen concentration stimulated a higher accumulation of ethanol and acetaldehyde together with the expression of genes involved in anaerobic respiration, such as malate and alcohol dehydrogenase and pyruvate decarboxylase in both cultivars. Moreover, in ‘Granny Smith’ apple, the expression of three members of the VII subgroups of ERF genes, encoding for elements coordinating the acclimation process to hypoxia in plants was observed. The global RNA-Seq pattern also elucidated a specific transcriptomic signature between the two cultivars, validating the effect of the different genetic background in the control of this disorder.
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