Whole blood expression profiling of obese diet-sensitive, obese diet-resistant and lean human subjects
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE18897 | GEO | 2009/11/05
SECONDARY ACCESSION(S): PRJNA121301
REPOSITORIES: GEO
Similar Datasets
Project description:We have carried out whole-genome expression profiling of whole blood from obese subjects, defined as obese diet-sensitive and obese diet-resistant, and well matched lean individuals. The diet-sensitive or diet-resistant status refers to the different rates of weight loss observed in the two groups on a low-calorie diet regimen. Bioinformatic analysis revealed alterations in transcription in key pathways that are consistent with impaired capacity for fatty acid oxidation driven mitochondrial ATP synthesis in obese subjects who are resistant to weight loss. A total of 80 samples are analyzed. This consists of 20 lean subjects studied at one timepoint and 20 obese subjects (10 diet-sensitive and 10 diet-resistant) studied at 3 timepoints during caloric restriction (day of entry into program, week 3 into the program and week 6 into the program)
2009-11-04 | E-GEOD-18897 | biostudies-arrayexpress
Project description:Skeletal muscle (rectus femoris) gene expression was analyzed from diet-resistant and diet-sensitive obese women undergoing clinically supervised weight-loss at a weight management clinic The goal of the study was to characterize global gene expression profiles in skeletal muscle from obese women, prior to their participation in a clinically supervised, low-calorie diet, weight management program. Following entry into the weight-loss program, subjects can be categorized as being 'diet-sensitive' or 'diet-resistant' depending on the rates of weight loss achieved. In the current study, we selected an equal number of diet-sensitive and diet-resistant subjects for comparative expression profiling
2009-07-29 | GSE17371 | GEO
Project description:To investigate the transcriptional profiles of adipocytes and stromal vascular cells from mouse visceral adipose tissue(vWAT) in lean (Low fat diet, LFD fed), obese (high fat diet, HFD fed) and formerly obese (diet switch (SW) from 9 weeks HFD, to 3 weeks LFD) to induce weight loss.
2022-08-04 | GSE210014 | GEO
Project description:Adipose tissue stromal cells contribute to the regulation of adipose tissue in lean and obese states. Myeloid cells such as adipose tissue macrophages (ATMs) and dendritic cells (ATDCs) undergo both quantitative and qualitative changes with obesity. Due to similarity in markers the identify of adipose tissue dendritic cells and macrophages has been elusive. We have refined prior protocols to unambiguously discern ATM and ATDC in mice. We used microarrays to compare the profiles of ATMs and ATDC from gonadal adipose tissue from lean, obese, and formerly obese mice. We also isolated preadipocytes (PA) from lean and obese mice for comparison. Male C57Bl/6 mice were fed normal diet (ND) or high fat diet (HFD) for 16 weeks. Weight loss (WL) mice were switched from the HFD to ND for 8 weeks. RNA was purified from FACS sorted cell populations (live cells only) obtained from gonadal/epididymal adipose tissue depots. ATMs were defined as CD11c+ (CD45+CD64+ CD11c+) or CD11c- (CD45+CD64+ CD11c-) ATMs. ATDC were defined as CD64- CD11c+. PA were defined as CD31- CD45- Sca1+ PDGFRA+.
2016-09-01 | GSE85846 | GEO
Project description:The prevalence of obesity has been increasing rapidly worldwide during the past two decades. This is alarming, since obesity has considerable effects on morbidity and mortality. The majority of gene expression studies about the effect of obesity and weight loss have been performed using the adipose tissue for mRNA extraction. However, also the liver plays a central role in maintaining energy balance. To our knowledge, no overall analysis of hepatic gene expression in response to changes in nutritional status has been made in humans Therefore, it is important to investigate how a short-time hypocaloric diet affects overall hepatic gene expression and the metabolic profile in a group of overweight and obese women. The subjects (n=31) were middle-aged, overweight (BMI>25 kg/m2) women with gallstone disease scheduled for an elective gallbladder operation. The intervention subjects were placed on a hypocaloric AHA step I diet with a recommended daily energy intake of 5.0 MJ. The objective was to reduce 0.5 kg of body weight per week. The control subjects were instructed to continue their habitual diet and not to lose weight. Basic clinical measurements and laboratory analyses were performed twice at baseline and at two week intervals during the weight reduction period. Surgical liver biopsies were obtained at the end of the weight reduction period. RNA samples of 4 individuals from the intervention group and 4 individuals from the control group were selected for the microarray analysis. The results from the microarray analysis were fairly surprising. Only one gene was up-regulated and the rest 142 down-regulated in the diet intervention group compared to the control group when a minimum of 2-fold change was set as the limit. The global decrease in hepatic gene expression was unexpected but the results are interesting, with several genes not previously linked to weight reduction. The decrease in triglyceride and fasting plasma insulin concentrations observed in our study is in accordance with results from many previous weight-loss trials. Keywords: Overall hepatic gene expression associated with obesity and moderate weight loss in a group of overweight and obese middle-aged women.
2008-07-23 | GSE7117 | GEO
Project description:Patients had low calorie diet weight reduction run in prior to the day of surgery. The human liver and subcutaneous fat tissue samples were obtained from 12 obese subjects undergoing bariatric surgery and then used for the mRNA expression analyses.
2016-06-15 | GSE83322 | GEO
Project description:The obese people with abnormal BMI are predisposed to insulin resistance and diabetes. At the same time, human subjects with obesity and high BMI that are otherwise insulin sensitive are an interesting group to study the underlying gene expression patterns which provide them with such protective phenotype. Objective: Insulin resistance (IR) is one of the earliest predictors of type 2 diabetes. However, diagnosis of IR is limited. High fat fed mouse models provide key insights into IR. We hypothesized that early features of IR are associated with persistent changes in gene expression (GE) and endeavoured to (a) develop novel methods for improving signal:noise in analysis of human GE using mouse models; (b) identify a GE motif that accurately diagnoses IR in humans; and (c) identify novel biology associated with IR in humans. Methods: We integrated human muscle GE data with longitudinal mouse GE data and developed an unbiased three-level cross-species analysis platform (single-gene, gene-set and networks) to generate a gene expression motif (GEM) indicative of IR. A logistic regression classification model validated GEM in 3 independent human datasets (n =115). Results: This GEM of 93 genes substantially improved diagnosis of IR compared to routine clinical measures across multiple independent datasets. Individuals misclassified by GEM possessed other metabolic features raising the possibility that they represent a separate metabolic subclass. The GEM was enriched in pathways previously implicated in insulin action and revealed novel associations between β-catenin and Jak1 and IR. Functional analyses using small molecule inhibitors showed an important role for these proteins in insulin action. Conclusions: This study shows that systems approaches for identifying molecular signatures provides a powerful way to stratify individuals into discrete metabolic groups. Moreover, we speculate that the β-catenin pathway may represent a novel biomarker for IR in humans that warrant future investigation. Gene expression from muscle biopsies of Lean, Obese insulin sensitive (OIS), Obese insulin resistant (OIR) and obese T2D patients (T2D) were compared for differential expression between the groups (n=7 in each group)
2015-12-15 | E-GEOD-73034 | biostudies-arrayexpress
Project description:Obtaining adipose tissue samples are paramount to the understanding of human obesity. We have examined the impact of needle-aspirated and surgical biopsy techniques on the study of subcutaneous adipose tissue (scAT) gene expression in both obese and lean subjects. Biopsy sampling methods have a significant impact on data interpretation and revealed that gene expression profiles derived from surgical tissue biopsies better capture the significant changes in molecular pathways associated with obesity. We hypothesize that this is because needle biopsies do not aspirate the fibrotic fraction of scAT; which subsequently results in an under-representation of the inflammatory and metabolic changes that coincide with obesity. This analysis revealed that the biopsy technique influences the gene expression underlying the biological themes commonly discussed in obesity (e.g. inflammation, extracellular matrix, metabolism, etc), and is therefore a caveat to consider when designing microarray experiments. These results have crucial implications for the clinical and physiopathological understanding of human obesity and therapeutic approaches. Keywords: subject and tissue biopsy technique comparison Tissue samples from lean and obese subjects were analyzed: total of 36 hybridizations. The goal was to compare the effect of biopsy sampling methods on global subcutaneous adipose tissue gene expression analyses. The following subject groups were used for the analysis: 9 lean subjects: needle biopsy 9 lean subjects: surgical biopsy 9 obese subjects: needle biopsy 9 obese subjects: surgical biopsy
2008-12-22 | E-GEOD-12050 | biostudies-arrayexpress
Project description:OBJECTIVE Diet intervention in obese adults is the first strategy to induce weight loss and to improve insulin sensitivity. We hypothesized that improvements in insulin sensitivity after weight loss from a short-term dietary intervention tracks with alterations in expression of metabolic genes and abundance of specific lipid species. RESEARCH DESIGN AND METHODS Eight obese, insulin resistant, non-diabetic adults were recruited to participate in a three-week low calorie diet intervention study (1000 kcal/day). Fasting blood samples and vastus lateralis skeletal muscle biopsies were obtained before and after the dietary intervention. Clinical chemistry and measures of insulin sensitivity were determined. Unbiased microarray gene expression and targeted lipidomic analysis of skeletal muscle was performed. RESULTS Body weight was reduced, insulin sensitivity (HOMA-IR) was enhanced, and serum insulin concentration and blood lipid (triglyceride, cholesterol, LDL and HDL) levels were improved after dietary intervention. Gene set enrichment analysis of skeletal muscle revealed that oxidative phosphorylation and inflammatory processes were among the most enriched KEGG-pathways identified after dietary intervention. mRNA expression of PDK4 and MLYCD increased, while SCD decreased in skeletal muscle after dietary intervention. Dietary intervention altered the intramuscular lipid profile of skeletal muscle, with changes in content of phosphatidylcholine and triglyceride species among the pronounced. CONCLUSIONS Short-term diet intervention and weight loss in obese adults alters metabolic gene expression and reduces specific phosphatidylcholine and triglyceride species in skeletal muscle, concomitant with improvements in clinical outcomes and enhanced insulin sensitivity.
2019-02-05 | GSE103682 | GEO
Project description:Whole blood expression profiling of obese diet-sensitive, obese diet-resistant and lean human subjects
| PRJNA121301 | ENA