Next Generation Sequencing Methylation Profiling in Skeletal Muscle from Lean and Obese Subjects [Microarray expression]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Samantha Day
PROVIDER: E-GEOD-73078 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Obesity is a metabolic disease caused by environmental, genetic, and epigenetic factors. However, the epigenetic mechanisms of obesity are incompletely understood. The aim of our study was to identify skeletal muscle DNA methylation patterns in obesity. Muscle biopsies were obtained basally from lean (n=11) and obese (n=9) participants in combination with euglycemic hyperinsulinemic clamps to assess insulin sensitivity. We performed reduced representation bisulfite sequencing next generation methylation analysis on DNA isolated from vastus lateralis muscle biopsies.
2015-11-01 | E-GEOD-73303 | biostudies-arrayexpress
Project description:This study was undertaken to test the hypothesis that short term exposure (4 hours) to physiologic hyperinsulinemia in normal, healthy subjects without a family history of diabetes would induce a low grade inflammatory response, independently of glycemic status. We performed euglycemic hyperinsulinemic (80 mU/m2/min) clamps in 12 healthy, insulin sensitive subjects with no family history of diabetes followed by biopsies of the vastus lateralis muscle taken basally and after 30 and 240 minutes of insulin infusion. Gene expression profiles were generated using Affymetrix HG-U133A arrays. No probe sets had significantly altered expression at 30 minutes of the insulin clamp, but 121 probe sets (117 upregulated and 4 downregulated) were significantly altered after 240 minutes. Hyperinsulinemia in normal, healthy human subjects increased the mRNAs for a number of inflammatory genes and transcription factors. Microarray and quantitative RT-PCR revealed the upregulation of chemokine, cc motif, ligand 2 (CCL2), CCL8, thrombomodulin (THBD), ras-related associated with diabetes (RRAD), metallothionein (MT), and serum/glucocorticoid regulated kinase (SGK), and downregulation of CITED2 (a CREB-binding protein-interacting transactivator), a known coactivator of PPAR-alpha. Interestingly, SGK and CITED2 are located at chromosome 6q23, where we previously detected strong linkage to hyperinsulinemia. A control saline infusion performed on 3 normal, healthy subjects without a family history of diabetes demonstrated that the genes altered following the euglycemic-hyperinsulinemic clamp were due to insulin and independent of biopsy removal. This study demonstrates that insulin acutely regulates the expression of genes involved in inflammation and transcription, and identifies several candidate genes/pathways for further investigation. Experiment Overall Design: Twelve subjects received a vastus lateralis muscle biopsy followed by a 180-min euglycemic, hyperinsulinemic (80 mU/m2.min) clamp. Muscle biopsies from each subject were homogenized in RNAStat solution (Tel-Test Inc., Friendswood, TX), using a Polytron homogenizer (Brinkmann Instruments Westbury, NY). Total RNA was purified with RNeasy and DNase I treatment (Qiagen, Chatsworth, CA). RNA was prepared for hybridization to Affymetrix (Santa Clara, CA) HG-U133A arrays according to the manufacturerâs instructions.
2008-06-16 | E-GEOD-9105 | biostudies-arrayexpress
Project description:Obesity-related insulin resistance (OIR) is one of the main contributors to type 2 diabetes and other metabolic diseases. Protein kinases are implicated in key signaling steps including insulin signaling and glucose metabolism. Molecular mechanisms underlying OIR involving global active kinases remain less understood. Herein, we report findings from an in vivo active kinase profiling study in skeletal muscle from lean control (Lean) and OIR human participants, which identified the 1st active kinome comprised of 54 active protein kinases in human skeletal muscle. The activities of 23 kinases were different in OIR compared to Lean muscle (11 hyper- and 12 hypo-active), while their protein abundance was the same between the two groups. The activities of multiple kinases involved in AMPK and p38 signaling were lower in OIR compared to Lean. On the contrary, multiple kinases in JNK signaling pathway exhibited higher activity in OIR vs. Lean muscle. The kinase-substrate-prediction based on experimental data further confirmed a potential down-regulation of insulin signaling (e.g., inhibited phosphorylation of insulin receptor substrate-1 and AKT1/2). These findings provide a global view of the active kinome in OIR and Lean muscle, pinpoint novel specific impairment in kinase activities in multiple signaling pathways important for skeletal muscle insulin resistance, and provide potential drug targets (i.e., abnormal active kinase) to prevent and/or reverse skeletal muscle insulin resistance in humans.
2020-01-23 | PXD011909 | Pride
Project description:The purpose of this experiment was to determine what gene expression changes are induced by acute exercise in humans, and how those changes relate to insulin sensitivity 14 subjects had muscle biopsies at rest and 30 minutes after a single exercise bout for measurement of mRNA changes. Glucose clamps were used to assess insulin sensitivity.
2013-01-01 | E-GEOD-43219 | biostudies-arrayexpress
Project description:A single bout of exercise followed by intake of carbohydrates leads to glycogen supercompensation in the prior exercised muscle. The molecular mechanisms underlying this well-known phenomenon remain elusive. Here we report that a single bout of exercise induces marked activation of glycogen synthase (GS) and AMP-activated protein kinase (AMPK) for several days beyond normalized muscle glycogen content in man. Acute muscle specific deletion of AMPK activity in mouse muscle abrogated the ability for glycogen supercompensation, providing genetic evidence that AMPK serves as essential driver for glycogen supercompensation. Muscle proteomic analyses revealed elevated glucose uptake capacity in the prior exercised muscle while key proteins in fat oxidation and glycolysis largely remained unchanged. The temporal order of these sustained cellular alterations induced by a single bout of exercise provide a mechanism to offset the otherwise tight feedback inhibition of glycogen synthesis and glucose uptake by glycogen, ultimately leading to muscle glycogen supercompensation.
2018-08-30 | PXD009196 | Pride
Project description:Purpose. Insulin resistant muscle is resistant to gene expression changes induced by acute exercise. This study was undertaken to identify transcription factors that differentially respond to exercise in insulin resistance. Candidate transcription factors were identified from analysis of 5’-untranslated regions (5’-UTRs) of exercise responsive genes and from analysis of the 5’-UTRs of genes coding for proteins that differ in abundance in insulin resistance. Research design and methods. Muscle biopsies were obtained from lean and obese subjects before and after a single exercise bout. Euglycemic glucose clamps assessed insulin sensitivity. Global proteomics analysis identified differentially abundant proteins. The 5’-UTRs of genes coding for significant proteins were subjected to transcription factor enrichment analysis to identify candidate transcription factors. Q-rt-PCR to determine expression of candidate transcription factors was performed on RNA from resting and post-exercise muscle biopsies; immunoblots quantified protein abundance. Results. Obese subjects were insulin resistant compared to lean but performed exercise at the same intensity. Proteins involved in mitochondrial function, protein targeting and translation, and metabolism were among those significantly different between the groups. Transcription factor enrichment analysis of genes coding for these proteins revealed new candidate transcription factors. Q-rt-PCR analysis of RNA and immunoblot analysis from pre- and post-exercise muscle biopsies revealed several transcription and growth factors that had altered responses to exercise in insulin resistant subjects. Conclusions. These results confirm findings of an association between insulin sensitivity and transcription factor mRNA response to exercise and extend these results to show that obesity also may be a sufficient prerequisite for exercise resistance. Analysis of the muscle proteome together with determination of effects of exercise on expression of transcription factors suggests that abnormal responses of transcription factors to exercise may be responsible for differences in protein abundances in insulin resistant muscle.
2021-09-09 | PXD023354 | Pride
Project description:This study aimed to determine skeletal muscle DNA methylation changes in a cohort of volunteers with a range of insulin sensitivities following 8-weeks of supervised exercise training. We studied 13 sedentary participants (5M/8F, 34.6 ± 3.1 years) and performed euglycemic hyperinsulinemic clamps with vastus lateralis muscle biopsies and peak aerobic activity (VO2 peak) tests before and after training. We extracted DNA from the muscle biopsies and performed global methylation using Illumina's Methylation EPIC 850K BeadChip.
2022-03-01 | E-MTAB-11282 | biostudies-arrayexpress
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2015-11-01 | E-GEOD-73304 | biostudies-arrayexpress
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2014-02-02 | E-MTAB-2141 | biostudies-arrayexpress
Project description:Myofibrillar myopathy (MFM) in horses is a late onset disease that affects performance and athleticism. It is characterized by myofibrillar disarray and protein aggregation with no known cause. The objective of this study was to elucidate the molecular drivers of MFM in Warmblood (WB) horses by proteomic profiling (5 MFM WB, 4 non-MFM WB) of gluteal muscle. MFM horses used in this study had a chronic history of poor performance and exercise intolerance as well as accumulation of desmin aggregates in > 4 myofibers per muscle sample. The Equine Neuromuscular Diagnostic Laboratory database at Michigan State University was queried to identify WB horses with snap frozen gluteus medius biopsies available for analysis. Non-MFM control horses were defined as horses with no history of exercise intolerance and no evidence of desmin accumulation or other histopathology in muscle biopsies. Muscle biopsy samples were obtained at rest from horses that had not undertaken strenuous exercise in the preceding 48 hours.
2021-09-09 | PXD019187 | Pride