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Farris KM, Senior AM, Sobreira DR, Mitchell RM, Weber ZT, Ingerslev LR, Barrès R, Simpson SJ, Crean AJ, Nobrega MA. Dietary macronutrient composition impacts gene regulation in adipose tissue. Commun Biol 2024; 7:194. [PMID: 38365885 PMCID: PMC10873408 DOI: 10.1038/s42003-024-05876-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Diet is a key lifestyle component that influences metabolic health through several factors, including total energy intake and macronutrient composition. While the impact of caloric intake on gene expression and physiological phenomena in various tissues is well described, the influence of dietary macronutrient composition on these parameters is less well studied. Here, we use the Nutritional Geometry framework to investigate the role of macronutrient composition on metabolic function and gene regulation in adipose tissue. Using ten isocaloric diets that vary systematically in their proportion of energy from fat, protein, and carbohydrates, we find that gene expression and splicing are highly responsive to macronutrient composition, with distinct sets of genes regulated by different macronutrient interactions. Specifically, the expression of many genes associated with Bardet-Biedl syndrome is responsive to dietary fat content. Splicing and expression changes occur in largely separate gene sets, highlighting distinct mechanisms by which dietary composition influences the transcriptome and emphasizing the importance of considering splicing changes to more fully capture the gene regulation response to environmental changes such as diet. Our study provides insight into the gene regulation plasticity of adipose tissue in response to macronutrient composition, beyond the already well-characterized response to caloric intake.
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Affiliation(s)
- Kathryn M Farris
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Alistair M Senior
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Débora R Sobreira
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Robert M Mitchell
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Zachary T Weber
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Lars R Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, DK-2200, Copenhagen, Denmark.
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur & Centre National pour la Recherche Scientifique (CNRS), Valbonne, 06560, France.
| | - Stephen J Simpson
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Angela J Crean
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
| | - Marcelo A Nobrega
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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2
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Basse AL, Nielsen KN, Karavaeva I, Ingerslev LR, Ma T, Havelund JF, Nielsen TS, Frost M, Peics J, Dalbram E, Dall M, Zierath JR, Barrès R, Færgeman NJ, Treebak JT, Gerhart-Hines Z. NAMPT-dependent NAD + biosynthesis controls circadian metabolism in a tissue-specific manner. Proc Natl Acad Sci U S A 2023; 120:e2220102120. [PMID: 36996103 PMCID: PMC10083581 DOI: 10.1073/pnas.2220102120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
Molecular clocks in the periphery coordinate tissue-specific daily biorhythms by integrating input from the hypothalamic master clock and intracellular metabolic signals. One such key metabolic signal is the cellular concentration of NAD+, which oscillates along with its biosynthetic enzyme, nicotinamide phosphoribosyltransferase (NAMPT). NAD+ levels feed back into the clock to influence rhythmicity of biological functions, yet whether this metabolic fine-tuning occurs ubiquitously across cell types and is a core clock feature is unknown. Here, we show that NAMPT-dependent control over the molecular clock varies substantially between tissues. Brown adipose tissue (BAT) requires NAMPT to sustain the amplitude of the core clock, whereas rhythmicity in white adipose tissue (WAT) is only moderately dependent on NAD+ biosynthesis, and the skeletal muscle clock is completely refractory to loss of NAMPT. In BAT and WAT, NAMPT differentially orchestrates oscillation of clock-controlled gene networks and the diurnality of metabolite levels. NAMPT coordinates the rhythmicity of TCA cycle intermediates in BAT, but not in WAT, and loss of NAD+ abolishes these oscillations similarly to high-fat diet-induced circadian disruption. Moreover, adipose NAMPT depletion improved the ability of animals to defend body temperature during cold stress but in a time-of-day-independent manner. Thus, our findings reveal that peripheral molecular clocks and metabolic biorhythms are shaped in a highly tissue-specific manner by NAMPT-dependent NAD+ synthesis.
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Affiliation(s)
- Astrid L Basse
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Karen N Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Iuliia Karavaeva
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Lars R Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Tao Ma
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jesper F Havelund
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Thomas S Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Mikkel Frost
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Julia Peics
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Emilie Dalbram
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Morten Dall
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Juleen R Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur and CNRS, 06560 Valbonne, France
| | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Zachary Gerhart-Hines
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
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3
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Moharrek F, Ingerslev LR, Altıntaş A, Lundell L, Hansen AN, Small L, Workman CT, Barrès R. Comparative analysis of sperm DNA methylation supports evolutionary acquired epigenetic plasticity for organ speciation. Epigenomics 2022; 14:1305-1324. [PMID: 36420698 DOI: 10.2217/epi-2022-0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Aim: To perform a comparative epigenomic analysis of DNA methylation in spermatozoa from humans, mice, rats and mini-pigs. Materials & methods: Genome-wide DNA methylation analysis was used to compare the methylation profiles of orthologous CpG sites. Transcription profiles of early embryo development were analyzed to provide insight into the association between sperm methylation and gene expression programming. Results: We identified DNA methylation variation near genes related to the central nervous system and signal transduction. Gene expression dynamics at different time points of preimplantation stages were modestly associated with spermatozoal DNA methylation at the nearest promoters. Conclusion: Conserved genomic regions subject to epigenetic variation across different species were associated with specific organ functions, suggesting their potential contribution to organ speciation and long-term adaptation to the environment.
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Affiliation(s)
- Farideh Moharrek
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Lars R Ingerslev
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Ali Altıntaş
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Leonidas Lundell
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Ann N Hansen
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Lewin Small
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Christopher T Workman
- Department of Biotechnology & Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Romain Barrès
- The Novo Nordisk Foundation Centre for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark.,Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur & Centre National pour la Recherche Scientifique (CNRS), Valbonne, 06560, France
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4
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Andersen E, Juhl CR, Kjøller ET, Lundgren JR, Janus C, Saupstad M, Ingerslev LR, Jensen SBK, Holst JJ, Stallknecht BM, Madsbad S, Torekov SS, Barrès R. O-018 Sperm count is increased by diet-induced weight loss and maintained by exercise or GLP-1 analogue treatment: a randomised controlled trial. Hum Reprod 2022. [DOI: 10.1093/humrep/deac104.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Study question
Does diet-induced weight loss improve semen parameters, and are these possible improvements maintained with sustained weight loss?
Summary answer
An 8-week low-calorie diet-induced weight loss was associated with improved sperm count, which was maintained after one year in men who maintained weight loss.
What is known already
Obesity is associated with impaired semen parameters. Weight loss improves metabolic health in obesity, but there is a lack of knowledge on the acute and long-term effects of weight loss on semen parameters.
Study design, size, duration
This is a substudy of men with obesity enrolled in a randomised, controlled, double-blinded trial (the S-LITE trial). The trial was conducted between August 2016 and November 2019. A total of 56 men was included in the study and assigned to an initial 8-week low-calorie diet (800 kcal/day) followed by randomisation to 52 weeks of either: placebo, exercise training, and placebo (exercise), the GLP-1 analogue liraglutide (liraglutide) or liraglutide in combination with exercise training (combination).
Participants/materials, setting, methods
Inclusion criteria were men who delivered semen samples, 18 to 65 years of age and a body mass index between 32 to 43 kg/m2, but otherwise healthy. The study was carried out at Hvidovre Hospital and at the University of Copenhagen, and the participants were from the Greater Copenhagen Area. We assessed semen parameters, anthropometrics and collected blood samples before (T0) and after the 8-week low-calorie dietary intervention (T1) and after 52 weeks (T2).
Main results and the role of chance
The men lost on average 16.5 kg (95% CI: 15.2-17.8) bodyweight during the low-calorie diet, which increased sperm concentration 1.49 fold (95% CI: 1.18-1.88, P<0.01) and sperm count 1.41 fold (95% CI: 1.07-1.87, P<0.01). These improvements were maintained for 52 weeks in men who maintained the weight loss but not in men who regained weight. Semen volume, sperm motility and motile sperm count did not change.
Limitations, reasons for caution
The S-LITE trial was a randomised controlled trial of weight loss maintenance. Analysis of semen was preregistered to explore the effects of weight loss and weight loss maintenance on semen parameters. Due to the small sample size, definite inferences cannot be made.
Wider implications of the findings
This study shows that sperm concentration and sperm count were improved after a diet-induced weight loss in men with obesity. Our findings indicate that both liraglutide and exercise as weight maintenance strategies may be used to maintain the improvements in sperm concentration and count.
Trial registration number
H-16027082
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Affiliation(s)
- E Andersen
- Novo Nordisk Foundation Center for Basic Metabolic Research- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen , Denmark
| | - C R Juhl
- Department of Biomedical Sciences- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen , Denmark
| | - E T Kjøller
- Novo Nordisk Foundation Center for Basic Metabolic Research- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen , Denmark
| | - J R Lundgren
- Department of Biomedical Sciences- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen , Denmark
| | - C Janus
- Department of Biomedical Sciences- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen , Denmark
| | - M Saupstad
- Novo Nordisk Foundation Center for Basic Metabolic Research- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen , Denmark
| | - L R Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen , Denmark
| | - S B K Jensen
- Department of Biomedical Sciences- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen , Denmark
| | - J J Holst
- Department of Biomedical Sciences- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen , Denmark
| | - B M Stallknecht
- Department of Biomedical Sciences- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen , Denmark
| | - S Madsbad
- Department of Endocrinology, Copenhagen University Hospital Hvidovre, Hvidovre , Denmark
| | - S S Torekov
- Department of Biomedical Sciences- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen , Denmark
| | - R Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen , Denmark
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5
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Andersen E, Juhl CR, Kjøller ET, Lundgren JR, Janus C, Dehestani Y, Saupstad M, Ingerslev LR, Duun OM, Jensen SBK, Holst JJ, Stallknecht BM, Madsbad S, Torekov SS, Barrès R. Sperm count is increased by diet-induced weight loss and maintained by exercise or GLP-1 analogue treatment: a randomized controlled trial. Hum Reprod 2022; 37:1414-1422. [PMID: 35580859 PMCID: PMC9247415 DOI: 10.1093/humrep/deac096] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/25/2022] [Indexed: 01/11/2023] Open
Abstract
STUDY QUESTION Does diet-induced weight loss improve semen parameters, and are these possible improvements maintained with sustained weight loss? SUMMARY ANSWER An 8-week low-calorie diet-induced weight loss was associated with improved sperm concentration and sperm count, which were maintained after 1 year in men who maintained weight loss. WHAT IS KNOWN ALREADY Obesity is associated with impaired semen quality. Weight loss improves metabolic health in obesity, but there is a lack of knowledge on the acute and long-term effects of weight loss on semen parameters. STUDY DESIGN, SIZE, DURATION This is a substudy of men with obesity enrolled in a randomized, controlled, double-blinded trial (the S-LITE trial). The trial was conducted between August 2016 and November 2019. A total of 56 men were included in the study and assigned to an initial 8-week low-calorie diet (800 kcal/day) followed by randomization to 52 weeks of either: placebo and habitual activity (placebo), exercise training and placebo (exercise), the Glucagon Like Peptide 1 (GLP-1) analogue liraglutide and habitual activity (liraglutide) or liraglutide in combination with exercise training (combination). PARTICIPANTS/MATERIALS, SETTING, METHODS Inclusion criteria were men who delivered semen samples, 18 to 65 years of age, and a body mass index between 32 and 43 kg/m2, but otherwise healthy. The study was carried out at Hvidovre Hospital and at the University of Copenhagen, and the participants were from the Greater Copenhagen Area. We assessed semen parameters and anthropometrics and collected blood samples before (T0), after the 8-week low-calorie dietary intervention (T1), and after 52 weeks (T2). MAIN RESULTS AND THE ROLE OF CHANCE The men lost on average 16.5 kg (95% CI: 15.2-17.8) body weight during the low-calorie diet, which increased sperm concentration 1.49-fold (95% CI: 1.18-1.88, P < 0.01) and sperm count 1.41-fold (95% CI: 1.07-1.87, P < 0.01). These improvements were maintained for 52 weeks in men who maintained the weight loss, but not in men who regained weight. Semen volume, sperm motility and motile sperm count did not change. LIMITATIONS, REASONS FOR CAUTION The S-LITE trial was a randomized controlled trial of weight loss maintenance. Analysis of semen was preregistered to explore the effects of weight loss and weight loss maintenance on semen parameters, but definite inferences cannot be made. WIDER IMPLICATIONS OF THE FINDINGS This study shows that sperm concentration and sperm count were improved after a diet-induced weight loss in men with obesity. Our findings indicate that either or both liraglutide and exercise as weight maintenance strategies may be used to maintain the improvements in sperm concentration and count. STUDY FUNDING/COMPETING INTEREST(S) This work is supported by an excellence grant from the Novo Nordisk Foundation (NNF16OC0019968), a Challenge Programme Grant from the Novo Nordisk Foundation (NNF18OC0033754) and a grant from Helsefonden. The Novo Nordisk Foundation Center for Basic Metabolic Research is an independent research centre at the University of Copenhagen, partially funded by an unrestricted donation from the Novo Nordisk Foundation (NNF18CC0034900). Saxenda (liraglutide) and placebo pens were provided by Novo Nordisk. Cambridge Weight Plan diet products for the 8-week low-calorie diet were provided by Cambridge Weight Plan. E.A.: shareholder, employee of ExSeed Health Ltd. Grant Recipient from ExSeed Health Ltd and listed on Patents planned, issued or pending with ExSeed Health Ltd; J.J.H.: consultant for Eli Lilly A/S and Novo Nordisk A/S. Lecture fees for Novo Nordisk A/S. Listed on Patents planned, issued or pending with the University of Copenhagen, Advocacy group for Antag Therapeutics and Bainan Biotech; S.M.: lecture fees for Novo Nordisk A/S. Recipient of Support for attending meetings from Novo Nordisk A/S. Advisory boards of Novo Nordisk A/S; Sanofi Aventis and Merck Sharp & Dohme. S.S.T.: research grant recipient Novo Nordisk. The remaining authors have no conflicts of interest to declare. TRIAL REGISTRATION NUMBER The trial was approved by the Ethical Committee of the Capital Region of Denmark (H-16027082) and the Danish Medicines Agency (EudraCT Number: 2015-005585-32). ClinicalTrials.gov identifier (NCT number): NCT04122716. TRIAL REGISTRATION DATE 11 May 2016. DATE OF FIRST PATIENT’S ENROLMENT August 2016.
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Affiliation(s)
| | | | - Emma T Kjøller
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julie R Lundgren
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Janus
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yasmin Dehestani
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marte Saupstad
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars R Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Olivia M Duun
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simon B K Jensen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens J Holst
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bente M Stallknecht
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sten Madsbad
- Department of Endocrinology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Signe S Torekov
- Correspondence address. Mærsk Tower 7.7, Blegdamsvej 3B, 2200 Copenhagen N, Denmark. Tel: +45-35-33-72-88; E-mail: (R.B.); Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Panum 12.4.08, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark. Tel: +45-22-98-38-27; E-mail: (S.S.T.)
| | - Romain Barrès
- Correspondence address. Mærsk Tower 7.7, Blegdamsvej 3B, 2200 Copenhagen N, Denmark. Tel: +45-35-33-72-88; E-mail: (R.B.); Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Panum 12.4.08, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark. Tel: +45-22-98-38-27; E-mail: (S.S.T.)
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6
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Dall M, Hassing AS, Niu L, Nielsen TS, Ingerslev LR, Sulek K, Trammell SAJ, Gillum MP, Barrès R, Larsen S, Poulsen SS, Mann M, Ørskov C, Treebak JT. Hepatocyte-specific perturbation of NAD + biosynthetic pathways in mice induces reversible nonalcoholic steatohepatitis-like phenotypes. J Biol Chem 2021; 297:101388. [PMID: 34762911 PMCID: PMC8648833 DOI: 10.1016/j.jbc.2021.101388] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/25/2021] [Accepted: 11/04/2021] [Indexed: 12/12/2022] Open
Abstract
Nicotinamide phosphoribosyltransferase (NAMPT) converts nicotinamide to NAD+. As low hepatic NAD+ levels have been linked to the development of nonalcoholic fatty liver disease, we hypothesized that ablation of hepatic Nampt would affect susceptibility to liver injury in response to diet-induced metabolic stress. Following 3 weeks on a low-methionine and choline-free 60% high-fat diet, hepatocyte-specific Nampt knockout (HNKO) mice accumulated less triglyceride than WT littermates but had increased histological scores for liver inflammation, necrosis, and fibrosis. Surprisingly, liver injury was also observed in HNKO mice on the purified control diet. This HNKO phenotype was associated with decreased abundance of mitochondrial proteins, especially proteins involved in oxidoreductase activity. High-resolution respirometry revealed lower respiratory capacity in purified control diet-fed HNKO liver. In addition, fibrotic area in HNKO liver sections correlated negatively with hepatic NAD+, and liver injury was prevented by supplementation with NAD+ precursors nicotinamide riboside and nicotinic acid. MS-based proteomic analysis revealed that nicotinamide riboside supplementation rescued hepatic levels of oxidoreductase and OXPHOS proteins. Finally, single-nucleus RNA-Seq showed that transcriptional changes in the HNKO liver mainly occurred in hepatocytes, and changes in the hepatocyte transcriptome were associated with liver necrosis. In conclusion, HNKO livers have reduced respiratory capacity, decreased abundance of mitochondrial proteins, and are susceptible to fibrosis because of low NAD+ levels. Our data suggest a critical threshold level of hepatic NAD+ that determines the predisposition to liver injury and supports that NAD+ precursor supplementation can prevent liver injury and nonalcoholic fatty liver disease progression.
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Affiliation(s)
- Morten Dall
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Anna S Hassing
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Lili Niu
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Thomas S Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Lars R Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Karolina Sulek
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Samuel A J Trammell
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark; Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthew P Gillum
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Steen Larsen
- Department of Biomedical Sciences, Xlab, Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark; Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Steen S Poulsen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Cathrine Ørskov
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
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7
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Small L, Ingerslev LR, Manitta E, Laker RC, Hansen AN, Deeney B, Carrié A, Couvert P, Barrès R. Ablation of DNA-methyltransferase 3A in skeletal muscle does not affect energy metabolism or exercise capacity. PLoS Genet 2021; 17:e1009325. [PMID: 33513138 PMCID: PMC7875352 DOI: 10.1371/journal.pgen.1009325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 02/10/2021] [Accepted: 01/04/2021] [Indexed: 02/03/2023] Open
Abstract
In response to physical exercise and diet, skeletal muscle adapts to energetic demands through large transcriptional changes. This remodelling is associated with changes in skeletal muscle DNA methylation which may participate in the metabolic adaptation to extracellular stimuli. Yet, the mechanisms by which muscle-borne DNA methylation machinery responds to diet and exercise and impacts muscle function are unknown. Here, we investigated the function of de novo DNA methylation in fully differentiated skeletal muscle. We generated muscle-specific DNA methyltransferase 3A (DNMT3A) knockout mice (mD3AKO) and investigated the impact of DNMT3A ablation on skeletal muscle DNA methylation, exercise capacity and energy metabolism. Loss of DNMT3A reduced DNA methylation in skeletal muscle over multiple genomic contexts and altered the transcription of genes known to be influenced by DNA methylation, but did not affect exercise capacity and whole-body energy metabolism compared to wild type mice. Loss of DNMT3A did not alter skeletal muscle mitochondrial function or the transcriptional response to exercise however did influence the expression of genes involved in muscle development. These data suggest that DNMT3A does not have a large role in the function of mature skeletal muscle although a role in muscle development and differentiation is likely. Skeletal muscle is a plastic tissue able to adapt to environmental stimuli such as exercise and diet in order to respond to energetic demand. One of the ways in which skeletal muscle can rapidly react to these stimuli is DNA methylation. This is when chemical groups are attached to DNA, potentially influencing the transcription of genes. We investigated the function of DNA methylation in skeletal muscle by generating mice that lacked one of the main enzymes responsible for de novo DNA methylation, DNA methyltransferase 3A (DNMT3A), specifically in muscle. We found that loss of DNMT3A reduced DNA methylation in muscle however this did not lead to differences in exercise capacity or energy metabolism. This suggests that DNMT3a is not involved in the adaptation of skeletal muscle to diet or exercise.
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Affiliation(s)
- Lewin Small
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars R. Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eleonora Manitta
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rhianna C. Laker
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ann N. Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Brendan Deeney
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alain Carrié
- Sorbonne Université-INSERM UMR_S 1166 ICAN, Pitié-Salpêtrière Hospital, Paris, France
| | - Philippe Couvert
- Sorbonne Université-INSERM UMR_S 1166 ICAN, Pitié-Salpêtrière Hospital, Paris, France
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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8
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Nicolaisen TS, Klein AB, Dmytriyeva O, Lund J, Ingerslev LR, Fritzen AM, Carl CS, Lundsgaard AM, Frost M, Ma T, Schjerling P, Gerhart-Hines Z, Flamant F, Gauthier K, Larsen S, Richter EA, Kiens B, Clemmensen C. Thyroid hormone receptor α in skeletal muscle is essential for T3-mediated increase in energy expenditure. FASEB J 2020; 34:15480-15491. [PMID: 32969079 PMCID: PMC7702122 DOI: 10.1096/fj.202001258rr] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 09/01/2020] [Accepted: 09/11/2020] [Indexed: 12/18/2022]
Abstract
Thyroid hormones are important for homeostatic control of energy metabolism and body temperature. Although skeletal muscle is considered a key site for thyroid action, the contribution of thyroid hormone receptor signaling in muscle to whole‐body energy metabolism and body temperature has not been resolved. Here, we show that T3‐induced increase in energy expenditure requires thyroid hormone receptor alpha 1 (TRα1) in skeletal muscle, but that T3‐mediated elevation in body temperature is achieved in the absence of muscle‐TRα1. In slow‐twitch soleus muscle, loss‐of‐function of TRα1 (TRαHSACre) alters the fiber‐type composition toward a more oxidative phenotype. The change in fiber‐type composition, however, does not influence the running capacity or motivation to run. RNA‐sequencing of soleus muscle from WT mice and TRαHSACre mice revealed differentiated transcriptional regulation of genes associated with muscle thermogenesis, such as sarcolipin and UCP3, providing molecular clues pertaining to the mechanistic underpinnings of TRα1‐linked control of whole‐body metabolic rate. Together, this work establishes a fundamental role for skeletal muscle in T3‐stimulated increase in whole‐body energy expenditure.
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Affiliation(s)
- Trine S Nicolaisen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Anders B Klein
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oksana Dmytriyeva
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Lund
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars R Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andreas M Fritzen
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Christian S Carl
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Anne-Marie Lundsgaard
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Frost
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tao Ma
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peter Schjerling
- Institute of Sports Medicine Copenhagen, Department of Orthopedic Surgery, Bispebjerg-Frederiksberg Hospital and Center for Healthy Aging, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zachary Gerhart-Hines
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frederic Flamant
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, INRA USC 1370, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Karine Gauthier
- Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Lyon 1, CNRS UMR 5242, INRA USC 1370, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Steen Larsen
- Xlab, Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Erik A Richter
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Bente Kiens
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Christoffer Clemmensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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9
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Lundell LS, Parr EB, Devlin BL, Ingerslev LR, Altıntaş A, Sato S, Sassone-Corsi P, Barrès R, Zierath JR, Hawley JA. Time-restricted feeding alters lipid and amino acid metabolite rhythmicity without perturbing clock gene expression. Nat Commun 2020; 11:4643. [PMID: 32938935 PMCID: PMC7495469 DOI: 10.1038/s41467-020-18412-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/16/2020] [Indexed: 12/20/2022] Open
Abstract
Time-restricted feeding (TRF) improves metabolism independent of dietary macronutrient composition or energy restriction. To elucidate mechanisms underpinning the effects of short-term TRF, we investigated skeletal muscle and serum metabolic and transcriptomic profiles from 11 men with overweight/obesity after TRF (8 h day-1) and extended feeding (EXF, 15 h day-1) in a randomised cross-over design (trial registration: ACTRN12617000165381). Here we show that muscle core clock gene expression was similar after both interventions. TRF increases the amplitude of oscillating muscle transcripts, but not muscle or serum metabolites. In muscle, TRF induces rhythmicity of several amino acid transporter genes and metabolites. In serum, lipids are the largest class of periodic metabolites, while the majority of phase-shifted metabolites are amino acid related. In conclusion, short-term TRF in overweight men affects the rhythmicity of serum and muscle metabolites and regulates the rhythmicity of genes controlling amino acid transport, without perturbing core clock gene expression.
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Affiliation(s)
- Leonidas S Lundell
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Evelyn B Parr
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Fitzroy, VIC, 3000, Australia
| | - Brooke L Devlin
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Fitzroy, VIC, 3000, Australia
| | - Lars R Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ali Altıntaş
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Shogo Sato
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, INSERM U1233, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juleen R Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
| | - John A Hawley
- Exercise and Nutrition Research Program, Mary MacKillop Institute for Health Research, Australian Catholic University, Fitzroy, VIC, 3000, Australia.
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10
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Daniel S, Nylander V, Ingerslev LR, Zhong L, Fabre O, Clifford B, Johnston K, Cohn RJ, Barres R, Simar D. T cell epigenetic remodeling and accelerated epigenetic aging are linked to long-term immune alterations in childhood cancer survivors. Clin Epigenetics 2018; 10:138. [PMID: 30400990 PMCID: PMC6219017 DOI: 10.1186/s13148-018-0561-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 10/07/2018] [Indexed: 01/08/2023] Open
Abstract
Background Cancer treatments have substantially improved childhood cancer survival but are accompanied by long-term complications, notably chronic inflammatory diseases. We hypothesize that cancer treatments could lead to long-term epigenetic changes in immune cells, resulting in increased prevalence of inflammatory diseases in cancer survivors. Results To test this hypothesis, we established the epigenetic and transcriptomic profiles of immune cells from 44 childhood cancer survivors (CCS, > 16 years old) on full remission (> 5 years) who had received chemotherapy alone or in combination with total body irradiation (TBI) and hematopoietic stem cell transplant (HSCT). We found that more than 10 years post-treatment, CCS treated with TBI/HSCT showed an altered DNA methylation signature in T cell, particularly at genes controlling immune and inflammatory processes and oxidative stress. DNA methylation remodeling in T cell was partially associated with chronic expression changes of nearby genes, increased frequency of type 1 cytokine-producing T cell, elevated systemic levels of these cytokines, and over-activation of related signaling pathways. Survivors exposed to TBI/HSCT were further characterized by an Epigenetic-Aging-Signature of T cell consistent with accelerated epigenetic aging. To investigate the potential contribution of irradiation to these changes, we established two cell culture models. We identified that radiation partially recapitulated the immune changes observed in survivors through a bystander effect that could be mediated by circulating factors. Conclusion Cancer treatments, in particular TBI/HSCT, are associated with long-term immune disturbances. We propose that epigenetic remodeling of immune cells following cancer therapy augments inflammatory- and age-related diseases, including metabolic complications, in childhood cancer survivors. Electronic supplementary material The online version of this article (10.1186/s13148-018-0561-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Daniel
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Wallace Wurth Building East Room 420, Sydney, NSW, 2052, Australia
| | - Vibe Nylander
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Lars R Ingerslev
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, Australia
| | - Odile Fabre
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Briana Clifford
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Wallace Wurth Building East Room 420, Sydney, NSW, 2052, Australia
| | - Karen Johnston
- School of Women's and Children's Health, UNSW Sydney and Kids Cancer Centre, Sydney Children's Hospital Network, Randwick, Australia
| | - Richard J Cohn
- School of Women's and Children's Health, UNSW Sydney and Kids Cancer Centre, Sydney Children's Hospital Network, Randwick, Australia
| | - Romain Barres
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Wallace Wurth Building East Room 420, Sydney, NSW, 2052, Australia. .,The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark.
| | - David Simar
- Mechanisms of Disease and Translational Research, School of Medical Sciences, UNSW Sydney, Wallace Wurth Building East Room 420, Sydney, NSW, 2052, Australia. .,The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, Panum, University of Copenhagen, 2200, Copenhagen N, Denmark.
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11
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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: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- Odile Fabre
- Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars R Ingerslev
- Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Garde
- Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Donkin
- Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David Simar
- Mechanisms of Disease & Translational Research, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Romain Barrès
- Integrative Physiology, The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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12
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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: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- Lars R. Ingerslev
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ida Donkin
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Odile Fabre
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Soetkin Versteyhe
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Mie Mechta
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Pattarawan Pattamaprapanont
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Brynjulf Mortensen
- Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Nikolaj Thure Krarup
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Romain Barrès
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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13
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Abstract
Methylation of nuclear genes encoding mitochondrial proteins participates in the regulation of mitochondria function. The existence of cytosine methylation in the mitochondrial genome is debated. To investigate whether mitochondrial DNA (mtDNA) is methylated, we used both targeted- and whole mitochondrial genome bisulfite sequencing in cell lines and muscle tissue from mouse and human origin. While unconverted cytosines were detected in some portion of the mitochondrial genome, their abundance was inversely associated to the sequencing depth, indicating that sequencing analysis can bias the estimation of mtDNA methylation levels. In intact mtDNA, few cytosines remained 100% unconverted. However, removal of supercoiled structures of mtDNA with the restriction enzyme BamHI prior to bisulfite sequencing decreased cytosine unconversion rate to <1.5% at all the investigated regions: D-loop, tRNA-F+12S, 16S, ND5 and CYTB, suggesting that mtDNA supercoiled structure blocks the access to bisulfite conversion. Here, we identified an artifact of mtDNA bisulfite sequencing that can lead to an overestimation of mtDNA methylation levels. Our study supports that cytosine methylation is virtually absent in mtDNA.
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Affiliation(s)
- Mie Mechta
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars R Ingerslev
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Odile Fabre
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Picard
- Department of Psychiatry and Neurology, Division of Behavioral Medicine, Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Medical Center, New York, NY, United States
| | - Romain Barrès
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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14
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Nylander V, Ingerslev LR, Andersen E, Fabre O, Garde C, Rasmussen M, Citirikkaya K, Bæk J, Christensen GL, Aznar M, Specht L, Simar D, Barrès R. Ionizing Radiation Potentiates High-Fat Diet-Induced Insulin Resistance and Reprograms Skeletal Muscle and Adipose Progenitor Cells. Diabetes 2016; 65:3573-3584. [PMID: 27650856 DOI: 10.2337/db16-0364] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 09/14/2016] [Indexed: 11/13/2022]
Abstract
Exposure to ionizing radiation increases the risk of chronic metabolic disorders such as insulin resistance and type 2 diabetes later in life. We hypothesized that irradiation reprograms the epigenome of metabolic progenitor cells, which could account for impaired metabolism after cancer treatment. C57Bl/6 mice were treated with a single dose of irradiation and subjected to high-fat diet (HFD). RNA sequencing and reduced representation bisulfite sequencing were used to create transcriptomic and epigenomic profiles of preadipocytes and skeletal muscle satellite cells collected from irradiated mice. Mice subjected to total body irradiation showed alterations in glucose metabolism and, when challenged with HFD, marked hyperinsulinemia. Insulin signaling was chronically disrupted in skeletal muscle and adipose progenitor cells collected from irradiated mice and differentiated in culture. Epigenomic profiling of skeletal muscle and adipose progenitor cells from irradiated animals revealed substantial DNA methylation changes, notably for genes regulating the cell cycle, glucose/lipid metabolism, and expression of epigenetic modifiers. Our results show that total body irradiation alters intracellular signaling and epigenetic pathways regulating cell proliferation and differentiation of skeletal muscle and adipose progenitor cells and provide a possible mechanism by which irradiation used in cancer treatment increases the risk for metabolic disease later in life.
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Affiliation(s)
- Vibe Nylander
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Lars R Ingerslev
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Emil Andersen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Odile Fabre
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Christian Garde
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rasmussen
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Kiymet Citirikkaya
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Josephine Bæk
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Gitte L Christensen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Aznar
- Department of Oncology, Section of Radiotherapy, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lena Specht
- Department of Oncology, Section of Radiotherapy, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Hematology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - David Simar
- Inflammation and Infection Research, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Romain Barrès
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
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15
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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: 313] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- Ida Donkin
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Soetkin Versteyhe
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Lars R Ingerslev
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Kui Qian
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Mie Mechta
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Loa Nordkap
- University Department of Growth and Reproduction, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Brynjulf Mortensen
- Steno Diabetes Center, Gentofte 2810, Denmark; Center for Diabetes Research, University of Copenhagen, Gentofte Hospital, Hellerup 2900, Denmark
| | - Emil Vincent R Appel
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Niels Jørgensen
- University Department of Growth and Reproduction, Copenhagen University Hospital, Copenhagen 2100, Denmark
| | - Viggo B Kristiansen
- Department of Surgical Gastroenterology, Hvidovre Hospital, Hvidovre 2650, Denmark
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Christopher T Workman
- Department of Systems Biology, Technical University of Denmark, Lyngby 2800, Denmark; Center for non-coding RNA in Technology and Health, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg 1870, Denmark
| | - Juleen R Zierath
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Romain Barrès
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.
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16
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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: 237] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Affiliation(s)
- Thais de Castro Barbosa
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Lars R Ingerslev
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Petter S Alm
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Soetkin Versteyhe
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Julie Massart
- Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Morten Rasmussen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ida Donkin
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rasmus Sjögren
- Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Jonathan M Mudry
- Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Laurène Vetterli
- Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Shashank Gupta
- Department of Veterinary Disease Biology, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Anna Krook
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Juleen R Zierath
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Romain Barrès
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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