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Nobrega M, Farris K, Andersen E, Donkin I, Versteyhe S, Kristiansen VB, Simpson S, Barres R. Splicing across adipocyte differentiation is highly dynamic and impacted by metabolic phenotype. RESEARCH SQUARE 2023:rs.3.rs-3487148. [PMID: 37961160 PMCID: PMC10635361 DOI: 10.21203/rs.3.rs-3487148/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Adipose tissue dysfunction underlies many of the metabolic complications associated with obesity. A better understanding of the gene regulation differences present in metabolically unhealthy adipose tissue can provide insights into the mechanisms underlying adipose tissue dysfunction. Here, we used RNA-seq data collected from a differentiation time course of lean, obese, and obese with type 2 diabetes (T2D) individuals to characterize the role of alterative splicing in adipocyte differentiation and function. We found that splicing was highly dynamic across adipocyte differentiation in all three cohorts, and that the dynamics of splicing were significantly impacted by metabolic phenotype. We also found that there was very little overlap between genes that were differentially spliced in adipocyte differentiation and those that were differentially expressed, positioning alternative splicing as a largely independent gene regulatory mechanism whose impact would be missed when looking at gene expression changes alone. To assess the impact of alternative splicing across adipocyte differentiation on genetic risk for metabolic diseases, we integrated the differential splicing results generated here with genome-wide association study results for body mass index and T2D, and found that variants associated with T2D were enriched in regions that were differentially spliced in early differentiation. These findings provide insight into the role of alternative splicing in adipocyte differentiation and can serve as a resource to guide future variant-to-function studies.
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Borup A, Donkin I, Boon M, Frydland M, Martinez-Tellez B, Loft A, Keller S, Kjaer A, Kjaergaard J, Hassager C, Barres R, Rensen P, Christoffersen C. ASsociation of the apolipoprotein M and sphingosine-1-phosphate complex with brown adipose tissue after cold exposure in humans. Atherosclerosis 2021. [DOI: 10.1016/j.atherosclerosis.2021.06.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Williams K, Carrasquilla GD, Ingerslev LR, Hochreuter MY, Hansson S, Pillon NJ, Donkin I, Versteyhe S, Zierath JR, Kilpeläinen TO, Barrès R. Epigenetic rewiring of skeletal muscle enhancers after exercise training supports a role in whole-body function and human health. Mol Metab 2021; 53:101290. [PMID: 34252634 PMCID: PMC8355925 DOI: 10.1016/j.molmet.2021.101290] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 12/13/2022] Open
Abstract
Objectives Regular physical exercise improves health by reducing the risk of a plethora of chronic disorders. We hypothesized that endurance exercise training remodels the activity of gene enhancers in skeletal muscle and that this remodeling contributes to the beneficial effects of exercise on human health. Methods and results By studying changes in histone modifications, we mapped the genome-wide positions and activities of enhancers in skeletal muscle biopsies collected from young sedentary men before and after 6 weeks of endurance exercise. We identified extensive remodeling of enhancer activities after exercise training, with a large subset of the remodeled enhancers located in the proximity of genes transcriptionally regulated after exercise. By overlapping the position of enhancers with genetic variants, we identified an enrichment of disease-associated genetic variants within the exercise-remodeled enhancers. Conclusion Our data provide evidence of a functional link between epigenetic rewiring of enhancers to control their activity after exercise training and the modulation of disease risk in humans.
Exercise training changes in skeletal muscle gene expression is enriched for secreted factors. The activity of skeletal muscle enhancers undergoes substantial remodeling after exercise training. Skeletal muscle enhancer activity and gene transcription are strongly associated. Exercise training-remodeled enhancer regions are enriched for GWAS SNPs associated with human traits and diseases.
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Fabre O, Ingerslev LR, Garde C, Donkin I, Simar D, Barrès R. Exercise training alters the genomic response to acute exercise in human adipose tissue. Epigenomics 2018; 10:1033-1050. [PMID: 29671347 PMCID: PMC6190185 DOI: 10.2217/epi-2018-0039] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aim: To determine the genomic mechanisms by which adipose tissue responds to acute and chronic exercise. Methods: We profiled the transcriptomic and epigenetic response to acute exercise in human adipose tissue collected before and after endurance training. Results: Although acute exercises were performed at same relative intensities, the magnitude of transcriptomic changes after acute exercise was reduced by endurance training. DNA methylation remodeling induced by acute exercise was more prominent in trained versus untrained state. We found an overlap between gene expression and DNA methylation changes after acute exercise for 32 genes pre-training and six post-training, notably at adipocyte-specific genes. Conclusion: Training status differentially affects the epigenetic and transcriptomic response to acute exercise in human adipose tissue.
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Ingerslev LR, Donkin I, Fabre O, Versteyhe S, Mechta M, Pattamaprapanont P, Mortensen B, Krarup NT, Barrès R. Endurance training remodels sperm-borne small RNA expression and methylation at neurological gene hotspots. Clin Epigenetics 2018; 10:12. [PMID: 29416570 PMCID: PMC5785820 DOI: 10.1186/s13148-018-0446-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/18/2018] [Indexed: 01/03/2023] Open
Abstract
Remodeling of the sperm epigenome by lifestyle factors before conception could account for altered metabolism in the next generation offspring. Here, we hypothesized that endurance training changes the epigenome of human spermatozoa. Using small RNA (sRNA) sequencing and reduced representation bisulfite sequencing (RRBS), we, respectively, investigated sRNA expression and DNA methylation in pure fractions of motile spermatozoa collected from young healthy individuals before, after 6 weeks of endurance training and after 3 months without exercise. Expression of 8 PIWI interacting RNA were changed by exercise training. RRBS analysis revealed 330 differentially methylated regions (DMRs) after training and 303 DMRs after the detraining period, which were, in both conditions, enriched at close vicinity of transcription start sites. Ontology analysis of genes located at proximity of DMRs returned terms related to neurological function at the trained state and, to a much lesser extent, at the detrained state. Our study reveal that short-term endurance training induces marked remodeling of the sperm epigenome, and identify genes related to the development of the central nervous system as potential hot spots for epigenetic variation upon environmental stress.
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Raghuraman S, Donkin I, Versteyhe S, Barrès R, Simar D. The Emerging Role of Epigenetics in Inflammation and Immunometabolism. Trends Endocrinol Metab 2016; 27:782-795. [PMID: 27444065 DOI: 10.1016/j.tem.2016.06.008] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/15/2016] [Accepted: 06/20/2016] [Indexed: 12/12/2022]
Abstract
Recent research developments have shed light on the risk factors contributing to metabolic complications, implicating both genetic and environmental factors, potentially integrated by epigenetic mechanisms. Distinct epigenetic changes in immune cells are frequently observed in obesity and type 2 diabetes mellitus, and these are associated with alterations in the phenotype, function, and trafficking patterns of these cells. The first step in the development of effective therapeutic strategies is the identification of distinct epigenetic signatures associated with metabolic disorders. In this review we provide an overview of the epigenetic mechanisms influencing immune cell phenotype and function, summarize current knowledge about epigenetic changes affecting immune functions in the context of metabolic diseases, and discuss the therapeutic options currently available to counteract epigenetically driven metabolic complications.
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Donkin I, Barrès R, Pinborg A. [Epigenetic influence on embryonic development]. Ugeskr Laeger 2016; 178:V02160132. [PMID: 27649584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The epigenome is sensitive to environmental changes and can sustainably alter gene expression, notably during embryonic development. New research indicates that epigenetic factors are heritable, which is why paternal lifestyle may affect fetal development and risk of disease. Children conceived by assisted reproduction technology (ART) have an increased risk of peri- and postnatal complications, and as specific ART protocols associate with specific risk profiles, the procedures themselves may cause epigenetic changes contributing to the altered outcomes of the 5,000 Danish children annually conceived by ART.
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Donkin I, Versteyhe S, Ingerslev LR, Qian K, Mechta M, Nordkap L, Mortensen B, Appel EVR, Jørgensen N, Kristiansen VB, Hansen T, Workman CT, Zierath JR, Barrès R. Obesity and Bariatric Surgery Drive Epigenetic Variation of Spermatozoa in Humans. Cell Metab 2016; 23:369-78. [PMID: 26669700 DOI: 10.1016/j.cmet.2015.11.004] [Citation(s) in RCA: 339] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 08/27/2015] [Accepted: 11/04/2015] [Indexed: 02/06/2023]
Abstract
Obesity is a heritable disorder, with children of obese fathers at higher risk of developing obesity. Environmental factors epigenetically influence somatic tissues, but the contribution of these factors to the establishment of epigenetic patterns in human gametes is unknown. Here, we hypothesized that weight loss remodels the epigenetic signature of spermatozoa in human obesity. Comprehensive profiling of the epigenome of sperm from lean and obese men showed similar histone positioning, but small non-coding RNA expression and DNA methylation patterns were markedly different. In a separate cohort of morbidly obese men, surgery-induced weight loss was associated with a dramatic remodeling of sperm DNA methylation, notably at genetic locations implicated in the central control of appetite. Our data provide evidence that the epigenome of human spermatozoa dynamically changes under environmental pressure and offers insight into how obesity may propagate metabolic dysfunction to the next generation.
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de Castro Barbosa T, Ingerslev LR, Alm PS, Versteyhe S, Massart J, Rasmussen M, Donkin I, Sjögren R, Mudry JM, Vetterli L, Gupta S, Krook A, Zierath JR, Barrès R. High-fat diet reprograms the epigenome of rat spermatozoa and transgenerationally affects metabolism of the offspring. Mol Metab 2015; 5:184-197. [PMID: 26977389 PMCID: PMC4770269 DOI: 10.1016/j.molmet.2015.12.002] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/08/2015] [Accepted: 12/18/2015] [Indexed: 11/17/2022] Open
Abstract
Objectives Chronic and high consumption of fat constitutes an environmental stress that leads to metabolic diseases. We hypothesized that high-fat diet (HFD) transgenerationally remodels the epigenome of spermatozoa and metabolism of the offspring. Methods F0-male rats fed either HFD or chow diet for 12 weeks were mated with chow-fed dams to generate F1 and F2 offspring. Motile spermatozoa were isolated from F0 and F1 breeders to determine DNA methylation and small non-coding RNA (sncRNA) expression pattern by deep sequencing. Results Newborn offspring of HFD-fed fathers had reduced body weight and pancreatic beta-cell mass. Adult female, but not male, offspring of HFD-fed fathers were glucose intolerant and resistant to HFD-induced weight gain. This phenotype was perpetuated in the F2 progeny, indicating transgenerational epigenetic inheritance. The epigenome of spermatozoa from HFD-fed F0 and their F1 male offspring showed common DNA methylation and small non-coding RNA expression signatures. Altered expression of sperm miRNA let-7c was passed down to metabolic tissues of the offspring, inducing a transcriptomic shift of the let-7c predicted targets. Conclusion Our results provide insight into mechanisms by which HFD transgenerationally reprograms the epigenome of sperm cells, thereby affecting metabolic tissues of offspring throughout two generations.
Body weight and glucose metabolism are altered in F1 and F2 offspring of F0-HFD fathers. High-fat diet reprograms the epigenome of sperm cells. Spermatozoa from F0-HFD fathers and F1 offspring share common epigenetic signatures. Expression of let-7c is changed in sperm of founders and in the adipose tissue of the offspring.
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Johannesen HH, Löfgren J, Donkin I, Hansen AE, Loft A, Højgaard L, Kjær A. Identification and characterization of human brown adipose tissue (BAT) content and metabolism in adults using [(18)F]-FDG PET/MR - a pilot study. EJNMMI Phys 2015; 1:A68. [PMID: 26501658 PMCID: PMC4546015 DOI: 10.1186/2197-7364-1-s1-a68] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Simar D, Versteyhe S, Donkin I, Liu J, Hesson L, Nylander V, Fossum A, Barrès R. DNA methylation is altered in B and NK lymphocytes in obese and type 2 diabetic human. Metabolism 2014; 63:1188-97. [PMID: 24996265 DOI: 10.1016/j.metabol.2014.05.014] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 05/17/2014] [Accepted: 05/29/2014] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Obesity is associated with low-grade inflammation and the infiltration of immune cells in insulin-sensitive tissues, leading to metabolic impairment. Epigenetic mechanisms control immune cell lineage determination, function and migration and are implicated in obesity and type 2 diabetes (T2D). The aim of this study was to determine the global DNA methylation profile of immune cells in obese and T2D individuals in a cell type-specific manner. MATERIAL AND METHODS Fourteen obese subjects and 11 age-matched lean subjects, as well as 12 T2D obese subjects and 7 age-matched lean subjects were recruited. Global DNA methylation levels were measured in a cell type-specific manner by flow cytometry. We validated the assay against mass spectrometry measures of the total 5-methylcytosine content in cultured cells treated with the hypomethylation agent decitabine (r=0.97, p<0.001). RESULTS Global DNA methylation in peripheral blood mononuclear cells, monocytes, lymphocytes or T cells was not altered in obese or T2D subjects. However, analysis of blood fractions from lean, obese, and T2D subjects showed increased methylation levels in B cells from obese and T2D subjects and in natural killer cells from T2D patients. In these cell types, DNA methylation levels were positively correlated with insulin resistance, suggesting an association between DNA methylation changes, immune function and metabolic dysfunction. CONCLUSIONS Both obesity and T2D are associated with an altered epigenetic signature of the immune system in a cell type-specific manner. These changes could contribute to the altered immune functions associated with obesity and insulin resistance.
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