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Espino-Gonzalez E, Dalbram E, Mounier R, Gondin J, Farup J, Jessen N, Treebak JT. Impaired skeletal muscle regeneration in diabetes: From cellular and molecular mechanisms to novel treatments. Cell Metab 2024; 36:1204-1236. [PMID: 38490209 DOI: 10.1016/j.cmet.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/10/2024] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
Diabetes represents a major public health concern with a considerable impact on human life and healthcare expenditures. It is now well established that diabetes is characterized by a severe skeletal muscle pathology that limits functional capacity and quality of life. Increasing evidence indicates that diabetes is also one of the most prevalent disorders characterized by impaired skeletal muscle regeneration, yet underlying mechanisms and therapeutic treatments remain poorly established. In this review, we describe the cellular and molecular alterations currently known to occur during skeletal muscle regeneration in people with diabetes and animal models of diabetes, including its associated comorbidities, e.g., obesity, hyperinsulinemia, and insulin resistance. We describe the role of myogenic and non-myogenic cell types on muscle regeneration in conditions with or without diabetes. Therapies for skeletal muscle regeneration and gaps in our knowledge are also discussed, while proposing future directions for the field.
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Affiliation(s)
- Ever Espino-Gonzalez
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Emilie Dalbram
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Rémi Mounier
- Institut NeuroMyoGène, Unité Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS UMR 5261, Inserm U1315, Univ Lyon, Lyon, France
| | - Julien Gondin
- Institut NeuroMyoGène, Unité Physiopathologie et Génétique du Neurone et du Muscle, Université Claude Bernard Lyon 1, CNRS UMR 5261, Inserm U1315, Univ Lyon, Lyon, France
| | - Jean Farup
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Niels Jessen
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus 8200, Denmark; Department of Clinical Pharmacology, Aarhus University Hospital, Aarhus 8200, Denmark
| | - Jonas T Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.
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Ouni M, Kovac L, Gancheva S, Jähnert M, Zuljan E, Gottmann P, Kahl S, de Angelis MH, Roden M, Schürmann A. Novel markers and networks related to restored skeletal muscle transcriptome after bariatric surgery. Obesity (Silver Spring) 2024; 32:363-375. [PMID: 38086776 DOI: 10.1002/oby.23954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 01/26/2024]
Abstract
OBJECTIVE The aim of this study was to discover novel markers underlying the improvement of skeletal muscle metabolism after bariatric surgery. METHODS Skeletal muscle transcriptome data of lean people and people with obesity, before and 1 year after bariatric surgery, were subjected to weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression. Results of LASSO were confirmed in a replication cohort. RESULTS The expression levels of 440 genes differing between individuals with and without obesity were no longer different 1 year after surgery, indicating restoration. WGCNA clustered 116 genes with normalized expression in one major module, particularly correlating to weight loss and decreased plasma free fatty acids (FFA), 44 of which showed an obesity-related phenotype upon deletion in mice. Among the genes of the major module, 105 represented prominent markers for reduced FFA concentration, including 55 marker genes for decreased BMI in both the discovery and replication cohorts. CONCLUSIONS Previously unknown gene networks and marker genes underlined the important role of FFA in restoring muscle gene expression after bariatric surgery and further suggest novel therapeutic targets for obesity.
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Affiliation(s)
- Meriem Ouni
- German Institute of Human Nutrition, Department of Experimental Diabetology, Potsdam, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Leona Kovac
- German Institute of Human Nutrition, Department of Experimental Diabetology, Potsdam, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Sofiya Gancheva
- German Center for Diabetes Research (DZD), Munich, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University, Düsseldorf, Germany
| | - Markus Jähnert
- German Institute of Human Nutrition, Department of Experimental Diabetology, Potsdam, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Erika Zuljan
- German Institute of Human Nutrition, Department of Experimental Diabetology, Potsdam, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Pascal Gottmann
- German Institute of Human Nutrition, Department of Experimental Diabetology, Potsdam, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Sabine Kahl
- German Center for Diabetes Research (DZD), Munich, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
| | - Martin Hrabĕ de Angelis
- German Center for Diabetes Research (DZD), Munich, Germany
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- School of Life Sciences, Technical University Munich, Freising, Germany
| | - Michael Roden
- German Center for Diabetes Research (DZD), Munich, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital, Heinrich Heine University, Düsseldorf, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research, Heinrich Heine University, Düsseldorf, Germany
| | - Annette Schürmann
- German Institute of Human Nutrition, Department of Experimental Diabetology, Potsdam, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
- Institute of Nutritional Sciences, University of Potsdam, Nuthetal, Germany
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Romero MA, Pyle AD. 'Enhancing' skeletal muscle and stem cells in three-dimensions: genome regulation of skeletal muscle in development and disease. Curr Opin Genet Dev 2023; 83:102133. [PMID: 37951138 PMCID: PMC10872784 DOI: 10.1016/j.gde.2023.102133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/09/2023] [Accepted: 10/14/2023] [Indexed: 11/13/2023]
Abstract
The noncoding genome imparts important regulatory control over gene expression. In particular, gene enhancers represent a critical layer of control that integrates developmental and differentiation signals outside the cell into transcriptional outputs inside the cell. Recently, there has been an explosion in genomic techniques to probe enhancer control, function, and regulation. How enhancers are regulated and integrate signals in stem cell development and differentiation is largely an open question. In this review, we focus on the role gene enhancers play in muscle stem cell specification, differentiation, and progression. We pay specific attention toward the identification of muscle-specific enhancers, the binding of transcription factors to these enhancers, and how enhancers communicate to their target genes via three-dimensional looping.
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Affiliation(s)
- Matthew A Romero
- Department of Microbiology, Immunology and Molecular Genetics, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA
| | - April D Pyle
- Department of Microbiology, Immunology and Molecular Genetics, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, USA.
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4
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Bustos-Aibar M, Aguilera CM, Alcalá-Fdez J, Ruiz-Ojeda FJ, Plaza-Díaz J, Plaza-Florido A, Tofe I, Gil-Campos M, Gacto MJ, Anguita-Ruiz A. Shared gene expression signatures between visceral adipose and skeletal muscle tissues are associated with cardiometabolic traits in children with obesity. Comput Biol Med 2023; 163:107085. [PMID: 37399741 DOI: 10.1016/j.compbiomed.2023.107085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 04/28/2023] [Accepted: 05/27/2023] [Indexed: 07/05/2023]
Abstract
Obesity in children is related to the development of cardiometabolic complications later in life, where molecular changes of visceral adipose tissue (VAT) and skeletal muscle tissue (SMT) have been proven to be fundamental. The aim of this study is to unveil the gene expression architecture of both tissues in a cohort of Spanish boys with obesity, using a clustering method known as weighted gene co-expression network analysis. For this purpose, we have followed a multi-objective analytic pipeline consisting of three main approaches; identification of gene co-expression clusters associated with childhood obesity, individually in VAT and SMT (intra-tissue, approach I); identification of gene co-expression clusters associated with obesity-metabolic alterations, individually in VAT and SMT (intra-tissue, approach II); and identification of gene co-expression clusters associated with obesity-metabolic alterations simultaneously in VAT and SMT (inter-tissue, approach III). In both tissues, we identified independent and inter-tissue gene co-expression signatures associated with obesity and cardiovascular risk, some of which exceeded multiple-test correction filters. In these signatures, we could identify some central hub genes (e.g., NDUFB8, GUCY1B1, KCNMA1, NPR2, PPP3CC) participating in relevant metabolic pathways exceeding multiple-testing correction filters. We identified the central hub genes PIK3R2, PPP3C and PTPN5 associated with MAPK signaling and insulin resistance terms. This is the first time that these genes have been associated with childhood obesity in both tissues. Therefore, they could be potential novel molecular targets for drugs and health interventions, opening new lines of research on the personalized care in this pathology. This work generates interesting hypotheses about the transcriptomics alterations underlying metabolic health alterations in obesity in the pediatric population.
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Affiliation(s)
- Mireia Bustos-Aibar
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain.
| | - Concepción M Aguilera
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain; Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition, Carlos III Health Institute, 28029, Madrid, Spain.
| | - Jesús Alcalá-Fdez
- Department of Computer Science and Artificial Intelligence, Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI), University of Granada, 18071, Granada, Spain.
| | - Francisco J Ruiz-Ojeda
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain; RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center at the Helmholtz Zentrum München, Neuherberg, 85764, Munich, Germany.
| | - Julio Plaza-Díaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain; Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Ontario, Canada.
| | - Abel Plaza-Florido
- PROmoting FITness and Health through physical activity research group, Sport and Health University Research Institute, Department of Physical Education and Sports, University of Granada, 18071, Granada, Spain; Pediatric Exercise and Genomics Research Center, Department of Pediatrics, School of Medicine, University of California at Irvine, Irvine, 92617, CA, United States.
| | - Inés Tofe
- Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition, Carlos III Health Institute, 28029, Madrid, Spain; University Clinical Hospital, Institute Maimónides of Biomedicine Investigation of Córdoba, University of Córdoba, 14004, Córdoba, Spain.
| | - Mercedes Gil-Campos
- Biomedical Research Networking Center for Physiopathology of Obesity and Nutrition, Carlos III Health Institute, 28029, Madrid, Spain; University Clinical Hospital, Institute Maimónides of Biomedicine Investigation of Córdoba, University of Córdoba, 14004, Córdoba, Spain.
| | - María J Gacto
- Department of Software Engineering, University of Granada, 18071, Granada, Spain.
| | - Augusto Anguita-Ruiz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071, Granada, Spain; Barcelona Institute for Global Health, ISGlobal, 08003, Barcelona, Spain.
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Duan YY, Chen XF, Zhu RJ, Jia YY, Huang XT, Zhang M, Yang N, Dong SS, Zeng M, Feng Z, Zhu DL, Wu H, Jiang F, Shi W, Hu WX, Ke X, Chen H, Liu Y, Jing RH, Guo Y, Li M, Yang TL. High-throughput functional dissection of noncoding SNPs with biased allelic enhancer activity for insulin resistance-relevant phenotypes. Am J Hum Genet 2023; 110:1266-1288. [PMID: 37506691 PMCID: PMC10432149 DOI: 10.1016/j.ajhg.2023.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Most of the single-nucleotide polymorphisms (SNPs) associated with insulin resistance (IR)-relevant phenotypes by genome-wide association studies (GWASs) are located in noncoding regions, complicating their functional interpretation. Here, we utilized an adapted STARR-seq to evaluate the regulatory activities of 5,987 noncoding SNPs associated with IR-relevant phenotypes. We identified 876 SNPs with biased allelic enhancer activity effects (baaSNPs) across 133 loci in three IR-relevant cell lines (HepG2, preadipocyte, and A673), which showed pervasive cell specificity and significant enrichment for cell-specific open chromatin regions or enhancer-indicative markers (H3K4me1, H3K27ac). Further functional characterization suggested several transcription factors (TFs) with preferential allelic binding to baaSNPs. We also incorporated multi-omics data to prioritize 102 candidate regulatory target genes for baaSNPs and revealed prevalent long-range regulatory effects and cell-specific IR-relevant biological functional enrichment on them. Specifically, we experimentally verified the distal regulatory mechanism at IRS1 locus, in which rs952227-A reinforces IRS1 expression by long-range chromatin interaction and preferential binding to the transcription factor HOXC6 to augment the enhancer activity. Finally, based on our STARR-seq screening data, we predicted the enhancer activity of 227,343 noncoding SNPs associated with IR-relevant phenotypes (fasting insulin adjusted for BMI, HDL cholesterol, and triglycerides) from the largest available GWAS summary statistics. We further provided an open resource (http://www.bigc.online/fnSNP-IR) for better understanding genetic regulatory mechanisms of IR-relevant phenotypes.
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Affiliation(s)
- Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Ren-Jie Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Ying-Ying Jia
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Xiao-Ting Huang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Meng Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Ning Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Mengqi Zeng
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Zhihui Feng
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Wei Shi
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Wei-Xin Hu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Xin Ke
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Rui-Hua Jing
- Department of Ophthalmology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710000, China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China
| | - Meng Li
- Department of Orthopedics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, China; Department of Orthopedics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China.
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6
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Cheng J, Cao X, Wang X, Wang J, Yue B, Sun W, Huang Y, Lan X, Ren G, Lei C, Chen H. Dynamic chromatin architectures provide insights into the genetics of cattle myogenesis. J Anim Sci Biotechnol 2023; 14:59. [PMID: 37055796 PMCID: PMC10103417 DOI: 10.1186/s40104-023-00855-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 02/16/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Sharply increased beef consumption is propelling the genetic improvement projects of beef cattle in China. Three-dimensional genome structure is confirmed to be an important layer of transcription regulation. Although genome-wide interaction data of several livestock species have already been produced, the genome structure states and its regulatory rules in cattle muscle are still limited. RESULTS Here we present the first 3D genome data in Longissimus dorsi muscle of fetal and adult cattle (Bos taurus). We showed that compartments, topologically associating domains (TADs), and loop undergo re-organization and the structure dynamics were consistent with transcriptomic divergence during muscle development. Furthermore, we annotated cis-regulatory elements in cattle genome during myogenesis and demonstrated the enrichments of promoter and enhancer in selection sweeps. We further validated the regulatory function of one HMGA2 intronic enhancer near a strong sweep region on primary bovine myoblast proliferation. CONCLUSIONS Our data provide key insights of the regulatory function of high order chromatin structure and cattle myogenic biology, which will benefit the progress of genetic improvement of beef cattle.
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Affiliation(s)
- Jie Cheng
- College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling district, Yangling, Shaanxi province, 712100, China
| | - Xiukai Cao
- College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling district, Yangling, Shaanxi province, 712100, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Xiaogang Wang
- College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling district, Yangling, Shaanxi province, 712100, China
| | - Jian Wang
- College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling district, Yangling, Shaanxi province, 712100, China
| | - Binglin Yue
- College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling district, Yangling, Shaanxi province, 712100, China
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Southwest Minzu University, Chengdu, 610225, China
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling district, Yangling, Shaanxi province, 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling district, Yangling, Shaanxi province, 712100, China
| | - Gang Ren
- College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling district, Yangling, Shaanxi province, 712100, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling district, Yangling, Shaanxi province, 712100, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling district, Yangling, Shaanxi province, 712100, China.
- College of Animal Science, Xinjiang Agricultural University, Urumqi, 830052, China.
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7
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Promoter-Adjacent DNA Hypermethylation Can Downmodulate Gene Expression: TBX15 in the Muscle Lineage. EPIGENOMES 2022; 6:epigenomes6040043. [PMID: 36547252 PMCID: PMC9778270 DOI: 10.3390/epigenomes6040043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
TBX15, which encodes a differentiation-related transcription factor, displays promoter-adjacent DNA hypermethylation in myoblasts and skeletal muscle (psoas) that is absent from non-expressing cells in other lineages. By whole-genome bisulfite sequencing (WGBS) and enzymatic methyl-seq (EM-seq), these hypermethylated regions were found to border both sides of a constitutively unmethylated promoter. To understand the functionality of this DNA hypermethylation, we cloned the differentially methylated sequences (DMRs) in CpG-free reporter vectors and tested them for promoter or enhancer activity upon transient transfection. These cloned regions exhibited strong promoter activity and, when placed upstream of a weak promoter, strong enhancer activity specifically in myoblast host cells. In vitro CpG methylation targeted to the DMR sequences in the plasmids resulted in 86−100% loss of promoter or enhancer activity, depending on the insert sequence. These results as well as chromatin epigenetic and transcription profiles for this gene in various cell types support the hypothesis that DNA hypermethylation immediately upstream and downstream of the unmethylated promoter region suppresses enhancer/extended promoter activity, thereby downmodulating, but not silencing, expression in myoblasts and certain kinds of skeletal muscle. This promoter-border hypermethylation was not found in cell types with a silent TBX15 gene, and these cells, instead, exhibit repressive chromatin in and around the promoter. TBX18, TBX2, TBX3 and TBX1 display TBX15-like hypermethylated DMRs at their promoter borders and preferential expression in myoblasts. Therefore, promoter-adjacent DNA hypermethylation for downmodulating transcription to prevent overexpression may be used more frequently for transcription regulation than currently appreciated.
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Pillon NJ, Sardón Puig L, Altıntaş A, Kamble PG, Casaní-Galdón S, Gabriel BM, Barrès R, Conesa A, Chibalin AV, Näslund E, Krook A, Zierath JR. Palmitate impairs circadian transcriptomics in muscle cells through histone modification of enhancers. Life Sci Alliance 2022; 6:6/1/e202201598. [PMID: 36302651 PMCID: PMC9614702 DOI: 10.26508/lsa.202201598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 12/10/2022] Open
Abstract
Obesity and elevated circulating lipids may impair metabolism by disrupting the molecular circadian clock. We tested the hypothesis that lipid overload may interact with the circadian clock and alter the rhythmicity of gene expression through epigenomic mechanisms in skeletal muscle. Palmitate reprogrammed the circadian transcriptome in myotubes without altering the rhythmic mRNA expression of core clock genes. Genes with enhanced cycling in response to palmitate were associated with post-translational modification of histones. The cycling of histone 3 lysine 27 acetylation (H3K27ac), a marker of active gene enhancers, was modified by palmitate treatment. Chromatin immunoprecipitation and sequencing confirmed that palmitate exposure altered the cycling of DNA regions associated with H3K27ac. The overlap between mRNA and DNA regions associated with H3K27ac and the pharmacological inhibition of histone acetyltransferases revealed novel cycling genes associated with lipid exposure of primary human myotubes. Palmitate exposure disrupts transcriptomic rhythmicity and modifies enhancers through changes in histone H3K27 acetylation in a circadian manner. Thus, histone acetylation is responsive to lipid overload and may redirect the circadian chromatin landscape, leading to the reprogramming of circadian genes and pathways involved in lipid biosynthesis in skeletal muscle.
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Affiliation(s)
- Nicolas J Pillon
- Department of Physiology and Pharmacology, Section of Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Sardón Puig
- Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Ali Altıntaş
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Prasad G Kamble
- Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | | | - Brendan M Gabriel
- Department of Physiology and Pharmacology, Section of Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Ana Conesa
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Alexander V Chibalin
- Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Erik Näslund
- Division of Surgery, Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Anna Krook
- Department of Physiology and Pharmacology, Section of Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Juleen R Zierath
- Department of Physiology and Pharmacology, Section of Integrative Physiology, Karolinska Institutet, Stockholm, Sweden .,Department of Molecular Medicine and Surgery, Section of Integrative Physiology, Karolinska Institutet, Stockholm, Sweden.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
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9
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Pervjakova N, Moen GH, Borges MC, Ferreira T, Cook JP, Allard C, Beaumont RN, Canouil M, Hatem G, Heiskala A, Joensuu A, Karhunen V, Kwak SH, Lin FTJ, Liu J, Rifas-Shiman S, Tam CH, Tam WH, Thorleifsson G, Andrew T, Auvinen J, Bhowmik B, Bonnefond A, Delahaye F, Demirkan A, Froguel P, Haller-Kikkatalo K, Hardardottir H, Hummel S, Hussain A, Kajantie E, Keikkala E, Khamis A, Lahti J, Lekva T, Mustaniemi S, Sommer C, Tagoma A, Tzala E, Uibo R, Vääräsmäki M, Villa PM, Birkeland KI, Bouchard L, Duijn CM, Finer S, Groop L, Hämäläinen E, Hayes GM, Hitman GA, Jang HC, Järvelin MR, Jenum AK, Laivuori H, Ma RC, Melander O, Oken E, Park KS, Perron P, Prasad RB, Qvigstad E, Sebert S, Stefansson K, Steinthorsdottir V, Tuomi T, Hivert MF, Franks PW, McCarthy MI, Lindgren CM, Freathy RM, Lawlor DA, Morris AP, Mägi R. Multi-ancestry genome-wide association study of gestational diabetes mellitus highlights genetic links with type 2 diabetes. Hum Mol Genet 2022; 31:3377-3391. [PMID: 35220425 PMCID: PMC9523562 DOI: 10.1093/hmg/ddac050] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/09/2022] [Accepted: 02/23/2022] [Indexed: 11/12/2022] Open
Abstract
Gestational diabetes mellitus (GDM) is associated with increased risk of pregnancy complications and adverse perinatal outcomes. GDM often reoccurs and is associated with increased risk of subsequent diagnosis of type 2 diabetes (T2D). To improve our understanding of the aetiological factors and molecular processes driving the occurrence of GDM, including the extent to which these overlap with T2D pathophysiology, the GENetics of Diabetes In Pregnancy Consortium assembled genome-wide association studies of diverse ancestry in a total of 5485 women with GDM and 347 856 without GDM. Through multi-ancestry meta-analysis, we identified five loci with genome-wide significant association (P < 5 × 10-8) with GDM, mapping to/near MTNR1B (P = 4.3 × 10-54), TCF7L2 (P = 4.0 × 10-16), CDKAL1 (P = 1.6 × 10-14), CDKN2A-CDKN2B (P = 4.1 × 10-9) and HKDC1 (P = 2.9 × 10-8). Multiple lines of evidence pointed to the shared pathophysiology of GDM and T2D: (i) four of the five GDM loci (not HKDC1) have been previously reported at genome-wide significance for T2D; (ii) significant enrichment for associations with GDM at previously reported T2D loci; (iii) strong genetic correlation between GDM and T2D and (iv) enrichment of GDM associations mapping to genomic annotations in diabetes-relevant tissues and transcription factor binding sites. Mendelian randomization analyses demonstrated significant causal association (5% false discovery rate) of higher body mass index on increased GDM risk. Our results provide support for the hypothesis that GDM and T2D are part of the same underlying pathology but that, as exemplified by the HKDC1 locus, there are genetic determinants of GDM that are specific to glucose regulation in pregnancy.
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Affiliation(s)
- Natalia Pervjakova
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Gunn-Helen Moen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Diamantina Institute, The University of Queensland, Woolloongabba QLD 4102, Australia
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
| | - Maria-Carolina Borges
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Teresa Ferreira
- Big Data Institute, Li Ka Shing Center for Health for Health Information and Discovery, Oxford University, Oxford, UK
| | - James P Cook
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Universite de Sherbrooke, Quebec, Canada
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Mickaël Canouil
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille F-59000, France
- University of Lille, Lille University Hospital, Lille F-59000, France
| | - Gad Hatem
- Department of Clinical Sciences, Lund University, Skåne University Hospital, Lund University Diabetes Centre, Malmö SE-20502, Sweden
| | - Anni Heiskala
- Centre for Life-Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Anni Joensuu
- Department of Public Health Solutions, Finnish Institute for Health and Welfare, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ville Karhunen
- Centre for Life-Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St Mary's Hospital, London, UK
| | - Soo Heon Kwak
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Frederick T J Lin
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jun Liu
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Sheryl Rifas-Shiman
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Claudia H Tam
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, The People's Republic of China
| | - Wing Hung Tam
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, The People's Republic of China
| | | | - Toby Andrew
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille F-59000, France
- University of Lille, Lille University Hospital, Lille F-59000, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Juha Auvinen
- Centre for Life-Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Bishwajit Bhowmik
- Centre of Global Health Research, Diabetic Association of Bangladesh, Dhaka, Bangladesh
| | - Amélie Bonnefond
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille F-59000, France
- University of Lille, Lille University Hospital, Lille F-59000, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Fabien Delahaye
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille F-59000, France
- University of Lille, Lille University Hospital, Lille F-59000, France
| | - Ayse Demirkan
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Section of Statistical Multi-omics, Department of Clinical and Experimental Research, University of Surrey, Surrey, UK
| | - Philippe Froguel
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille F-59000, France
- University of Lille, Lille University Hospital, Lille F-59000, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Kadri Haller-Kikkatalo
- Department of Immunology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Hildur Hardardottir
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Livio Reykjavik, Reykjavik, Iceland
| | - Sandra Hummel
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany
| | - Akhtar Hussain
- Centre of Global Health Research, Diabetic Association of Bangladesh, Dhaka, Bangladesh
- Faculty of Health Sciences, Nord University, Bodø, Norway
| | - Eero Kajantie
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Elina Keikkala
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Amna Khamis
- Inserm U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille F-59000, France
- University of Lille, Lille University Hospital, Lille F-59000, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jari Lahti
- Department of Psychology and Logopedics, University of Helsinki, Helsinki, Finland
| | - Tove Lekva
- Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway
| | - Sanna Mustaniemi
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Christine Sommer
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
| | - Aili Tagoma
- Department of Immunology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Evangelia Tzala
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St Mary's Hospital, London, UK
| | - Raivo Uibo
- Department of Immunology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Marja Vääräsmäki
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Finland
| | - Pia M Villa
- Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Hyvinkää Hospital, Helsinki and Uusimaa Hospital District, Hyvinkää, Finland
| | - Kåre I Birkeland
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Universite de Sherbrooke, Quebec, Canada
- Department of Medical Biology, Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay–Lac-St-Jean – Hôpital de Chicoutimi, Québec, Canada
| | - Cornelia M Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Sarah Finer
- Centre for Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Leif Groop
- Department of Clinical Sciences, Lund University, Skåne University Hospital, Lund University Diabetes Centre, Malmö SE-20502, Sweden
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Esa Hämäläinen
- Department of Clinical Chemistry, University of Eastern Finland, Kuopio, Finland
| | - Geoffrey M Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA
| | - Graham A Hitman
- Centre for Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Hak C Jang
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Marjo-Riitta Järvelin
- Centre for Life-Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- School of Public Health, Department of Epidemiology and Biostatistics, Imperial College London, St Mary's Hospital, London, UK
| | - Anne Karen Jenum
- General Practice Research Unit (AFE), Department of General Practice, Institute of Health and Society, Faculty of Medicine, University of Oslo, Post Box 1130 Blindern, Oslo 0318, Norway
| | - Hannele Laivuori
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Department of Obstetrics and Gynecology, Tampere University, Hospital and Faculty of Medicine and Health Technology, Center for Child, Adolescent, and Maternal Health, Tampere University, Tampere, Finland
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ronald C Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, The People's Republic of China
- Laboratory for Molecular Epidemiology in Diabetes, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, The People's Republic of China
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Hong Kong SAR, The People's Republic of China
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Skåne University Hospital, Lund University Diabetes Centre, Malmö SE-20502, Sweden
| | - Emily Oken
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Kyong Soo Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Universite de Sherbrooke, Quebec, Canada
- Department of Medicine, Faculty of Medicine and Health Sciences, University of Sherbrook, Québec, Canada
| | - Rashmi B Prasad
- Department of Clinical Sciences, Lund University, Skåne University Hospital, Lund University Diabetes Centre, Malmö SE-20502, Sweden
| | - Elisabeth Qvigstad
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sylvain Sebert
- Centre for Life-Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Kari Stefansson
- deCODE Genetics/Amgen, Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Department of Clinical Sciences, Lund University, Skåne University Hospital, Lund University Diabetes Centre, Malmö SE-20502, Sweden
- Department of Endocrinology, Abdominal Centre, Helsinki University Hospital, Helsinki, Finland
- Folkhalsan Research Center, Helsinki, Finland
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Department of Medicine, Faculty of Medicine and Health Sciences, University of Sherbrook, Québec, Canada
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Paul W Franks
- Department of Clinical Sciences, Lund University, Malmö, Sweden
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Cecilia M Lindgren
- Big Data Institute, Li Ka Shing Center for Health for Health Information and Discovery, Oxford University, Oxford, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Program in Medical and Population Genetics, Broad Institute, Boston, MA, USA
| | - Rachel M Freathy
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Deborah A Lawlor
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, University of Manchester, Manchester, UK
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
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10
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Aerobic Exercise Prevents Chronic Inflammation and Insulin Resistance in Skeletal Muscle of High-Fat Diet Mice. Nutrients 2022; 14:nu14183730. [PMID: 36145106 PMCID: PMC9503887 DOI: 10.3390/nu14183730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/21/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Obesity is commonly accompanied by chronic tissue inflammation and leads to insulin resistance. Aerobic exercise is an essential treatment for insulin resistance and has anti-inflammatory effects. However, the molecular mechanisms of exercise on obesity-associated inflammation and insulin resistance remain largely unknown. Here, we evaluated the effects of aerobic exercise on inflammation and insulin resistance in skeletal muscles of high-fat diet (HFD) mice. Male C57BL/6J mice were fed a high-fat diet or a normal diet for 12 weeks, and then aerobic training was performed on a treadmill for 8 weeks. Body weight, fasting blood glucose, food intake levels, and glucose and insulin tolerance were evaluated. The levels of cytokines, skeletal muscle insulin resistance, and inflammation were also analyzed. Eight weeks of aerobic exercise attenuated HFD-induced weight gain and glucose intolerance, and improved insulin sensitivity. This was accompanied by enhanced insulin signaling. Exercise directly resulted in a significant reduction of lipid content, inflammation, and macrophage infiltration in skeletal muscles. Moreover, exercise alleviated HFD-mediated inflammation by suppressing the activation of the NF-κB pathway within skeletal muscles. These results revealed that aerobic exercise could lead to an anti-inflammatory phenotype with protection from skeletal muscle insulin resistance in HFD-induced mice.
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11
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Sheng CY, Son YH, Jang J, Park SJ. In vitro skeletal muscle models for type 2 diabetes. BIOPHYSICS REVIEWS 2022; 3:031306. [PMID: 36124295 PMCID: PMC9478902 DOI: 10.1063/5.0096420] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Type 2 diabetes mellitus, a metabolic disorder characterized by abnormally elevated blood sugar, poses a growing social, economic, and medical burden worldwide. The skeletal muscle is the largest metabolic organ responsible for glucose homeostasis in the body, and its inability to properly uptake sugar often precedes type 2 diabetes. Although exercise is known to have preventative and therapeutic effects on type 2 diabetes, the underlying mechanism of these beneficial effects is largely unknown. Animal studies have been conducted to better understand the pathophysiology of type 2 diabetes and the positive effects of exercise on type 2 diabetes. However, the complexity of in vivo systems and the inability of animal models to fully capture human type 2 diabetes genetics and pathophysiology are two major limitations in these animal studies. Fortunately, in vitro models capable of recapitulating human genetics and physiology provide promising avenues to overcome these obstacles. This review summarizes current in vitro type 2 diabetes models with focuses on the skeletal muscle, interorgan crosstalk, and exercise. We discuss diabetes, its pathophysiology, common in vitro type 2 diabetes skeletal muscle models, interorgan crosstalk type 2 diabetes models, exercise benefits on type 2 diabetes, and in vitro type 2 diabetes models with exercise.
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Affiliation(s)
- Christina Y. Sheng
- Biohybrid Systems Group, Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Young Hoon Son
- Biohybrid Systems Group, Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | | | - Sung-Jin Park
- Biohybrid Systems Group, Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University School of Medicine, Atlanta, Georgia 30322, USA
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12
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Barutcu AR, Elizalde G, Gonzalez AE, Soni K, Rinn JL, Wagers AJ, Almada AE. Prolonged FOS activity disrupts a global myogenic transcriptional program by altering 3D chromatin architecture in primary muscle progenitor cells. Skelet Muscle 2022; 12:20. [PMID: 35971133 PMCID: PMC9377060 DOI: 10.1186/s13395-022-00303-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The AP-1 transcription factor, FBJ osteosarcoma oncogene (FOS), is induced in adult muscle satellite cells (SCs) within hours following muscle damage and is required for effective stem cell activation and muscle repair. However, why FOS is rapidly downregulated before SCs enter cell cycle as progenitor cells (i.e., transiently expressed) remains unclear. Further, whether boosting FOS levels in the proliferating progeny of SCs can enhance their myogenic properties needs further evaluation. METHODS We established an inducible, FOS expression system to evaluate the impact of persistent FOS activity in muscle progenitor cells ex vivo. We performed various assays to measure cellular proliferation and differentiation, as well as uncover changes in RNA levels and three-dimensional (3D) chromatin interactions. RESULTS Persistent FOS activity in primary muscle progenitor cells severely antagonizes their ability to differentiate and form myotubes within the first 2 weeks in culture. RNA-seq analysis revealed that ectopic FOS activity in muscle progenitor cells suppressed a global pro-myogenic transcriptional program, while activating a stress-induced, mitogen-activated protein kinase (MAPK) transcriptional signature. Additionally, we observed various FOS-dependent, chromosomal re-organization events in A/B compartments, topologically associated domains (TADs), and genomic loops near FOS-regulated genes. CONCLUSIONS Our results suggest that elevated FOS activity in recently activated muscle progenitor cells perturbs cellular differentiation by altering the 3D chromosome organization near critical pro-myogenic genes. This work highlights the crucial importance of tightly controlling FOS expression in the muscle lineage and suggests that in states of chronic stress or disease, persistent FOS activity in muscle precursor cells may disrupt the muscle-forming process.
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Affiliation(s)
- A Rasim Barutcu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Present address: Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Gabriel Elizalde
- Department of Orthopaedic Surgery, University of Southern California, Los Angeles, CA, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alfredo E Gonzalez
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Kartik Soni
- Department of Orthopaedic Surgery, University of Southern California, Los Angeles, CA, USA
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Present address: BioFrontiers and Department of Biochemistry, University of Colorado Boulder, Boulder, CO, 80303, USA
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Albert E Almada
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Department of Orthopaedic Surgery, University of Southern California, Los Angeles, CA, USA.
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, USA.
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13
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Wohlwend M, Laurila PP, Williams K, Romani M, Lima T, Pattawaran P, Benegiamo G, Salonen M, Schneider BL, Lahti J, Eriksson JG, Barrès R, Wisløff U, Moreira JBN, Auwerx J. The exercise-induced long noncoding RNA CYTOR promotes fast-twitch myogenesis in aging. Sci Transl Med 2021; 13:eabc7367. [PMID: 34878822 DOI: 10.1126/scitranslmed.abc7367] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Martin Wohlwend
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway.,Clinic of Cardiology, St. Olavs Hospital, Torgarden, NO-3250 Trondheim, Norway
| | - Pirkka-Pekka Laurila
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Kristine Williams
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Mario Romani
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Tanes Lima
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Pattamaprapanont Pattawaran
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Giorgia Benegiamo
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Minna Salonen
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, FI-00271 Helsinki, Finland
| | - Bernard L Schneider
- Bertarelli Foundation Gene Therapy Platform, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1202 Geneva, Switzerland
| | - Jari Lahti
- Turku Institute for Advanced Studies, University of Turku, FI-20014 Turku, Finland.,Department of Psychology and Logopedics, University of Helsinki, FI-00014 Helsinki, Finland
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland.,Folkhälsan Research Center, University of Helsinki, FI-00014 Helsinki, Finland.,Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, SG-119228 Singapore, Singapore.,Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research, SG-117609 Singapore, Singapore
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Ulrik Wisløff
- Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - José B N Moreira
- Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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14
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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: 3] [Impact Index Per Article: 1.0] [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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Affiliation(s)
- Kristine Williams
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Germán D Carrasquilla
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Lars Roed Ingerslev
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Mette Yde Hochreuter
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Svenja Hansson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Nicolas J Pillon
- Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Ida Donkin
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Soetkin Versteyhe
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Juleen R Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark; Department of Physiology and Pharmacology, Karolinska Institutet, 171 77, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska University Hospital, 171 76, Stockholm, Sweden
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark.
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15
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Zhang R, Wang J, Xiao Z, Zou C, An Q, Li H, Zhou X, Wu Z, Shi D, Deng Y, Yang S, Wei Y. The Expression Profiles of mRNAs and lncRNAs in Buffalo Muscle Stem Cells Driving Myogenic Differentiation. Front Genet 2021; 12:643497. [PMID: 34306003 PMCID: PMC8294193 DOI: 10.3389/fgene.2021.643497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Buffalo breeding has become an important branch of the beef cattle industry. Hence, it is of great significance to study buffalo meat production and meat quality. However, the expression profiles of mRNA and long non-coding RNAs (lncRNA) molecules in muscle stem cells (MuSCs) development in buffalo have not been explored fully. We, therefore, performed mRNA and lncRNA expression profiling analysis during the proliferation and differentiation phases of MuSCs in buffalo. The results showed that there were 4,820 differentially expressed genes as well as 12,227 mRNAs and 1,352 lncRNAs. These genes were shown to be enriched in essential biological processes such as cell cycle, p53 signaling pathway, RNA transport and calcium signaling pathway. We also identified a number of functionally important genes, such as MCMC4, SERDINE1, ISLR, LOC102394806, and LOC102403551, and found that interference with MYLPF expression significantly inhibited the differentiation of MuSCs. In conclusion, our research revealed the characteristics of mRNA and lncRNA expression during the differentiation of buffalo MuSCs. This study can be used as an important reference for the study of RNA regulation during muscle development in buffalo.
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Affiliation(s)
- Ruimen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Jinling Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Zhengzhong Xiao
- The Animal Husbandry Research Institute of Guangxi Autonomous, Nanning, China
| | - Chaoxia Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Qiang An
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Xiaoqing Zhou
- The Animal Husbandry Research Institute of Guangxi Autonomous, Nanning, China
| | - Zhuyue Wu
- The Animal Husbandry Research Institute of Guangxi Autonomous, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Yanfei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Sufang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China.,International Zhuang Medical Hospital Affiliated to Guangxi University Chinese Medicine, Nanning, China
| | - Yingming Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
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16
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Rovito D, Rerra AI, Ueberschlag-Pitiot V, Joshi S, Karasu N, Dacleu-Siewe V, Rayana KB, Ghaibour K, Parisotto M, Ferry A, Jelinsky SA, Laverny G, Klaholz BP, Sexton T, Billas IML, Duteil D, Metzger D. Myod1 and GR coordinate myofiber-specific transcriptional enhancers. Nucleic Acids Res 2021; 49:4472-4492. [PMID: 33836079 PMCID: PMC8096230 DOI: 10.1093/nar/gkab226] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 03/12/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle is a dynamic tissue the size of which can be remodeled through the concerted actions of various cues. Here, we investigated the skeletal muscle transcriptional program and identified key tissue-specific regulatory genetic elements. Our results show that Myod1 is bound to numerous skeletal muscle enhancers in collaboration with the glucocorticoid receptor (GR) to control gene expression. Remarkably, transcriptional activation controlled by these factors occurs through direct contacts with the promoter region of target genes, via the CpG-bound transcription factor Nrf1, and the formation of Ctcf-anchored chromatin loops, in a myofiber-specific manner. Moreover, we demonstrate that GR negatively controls muscle mass and strength in mice by down-regulating anabolic pathways. Taken together, our data establish Myod1, GR and Nrf1 as key players of muscle-specific enhancer-promoter communication that orchestrate myofiber size regulation.
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Affiliation(s)
- Daniela Rovito
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | - Anna-Isavella Rerra
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | | | - Shilpy Joshi
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | - Nezih Karasu
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | - Vanessa Dacleu-Siewe
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | - Khalil Ben Rayana
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | - Kamar Ghaibour
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | - Maxime Parisotto
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | - Arnaud Ferry
- Centre de Recherche en Myologie, UMRS974-Sorbonne Université-INSERM U974-Association Institut de Myologie, France
| | - Scott A Jelinsky
- Department of Inflammation and Immunology, Pfizer Research, Cambridge, MA, USA
| | - Gilles Laverny
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | - Bruno P Klaholz
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | - Tom Sexton
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | - Isabelle M L Billas
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | - Delphine Duteil
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
| | - Daniel Metzger
- Université de Strasbourg, CNRS UMR7104, INSERM U1258, IGBMC, F-67400 Illkirch, France
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17
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Batista TM, Haider N, Kahn CR. Defining the underlying defect in insulin action in type 2 diabetes. Diabetologia 2021; 64:994-1006. [PMID: 33730188 PMCID: PMC8916220 DOI: 10.1007/s00125-021-05415-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 01/29/2021] [Indexed: 01/08/2023]
Abstract
Insulin resistance is one of the earliest defects in the pathogenesis of type 2 diabetes. Over the past 50 years, elucidation of the insulin signalling network has provided important mechanistic insights into the abnormalities of glucose, lipid and protein metabolism that underlie insulin resistance. In classical target tissues (liver, muscle and adipose tissue), insulin binding to its receptor initiates a broad signalling cascade mediated by changes in phosphorylation, gene expression and vesicular trafficking that result in increased nutrient utilisation and storage, and suppression of catabolic processes. Insulin receptors are also expressed in non-classical targets, such as the brain and endothelial cells, where it helps regulate appetite, energy expenditure, reproductive hormones, mood/behaviour and vascular function. Recent progress in cell biology and unbiased molecular profiling by mass spectrometry and DNA/RNA-sequencing has provided a unique opportunity to dissect the determinants of insulin resistance in type 2 diabetes and the metabolic syndrome; best studied are extrinsic factors, such as circulating lipids, amino acids and other metabolites and exosomal microRNAs. More challenging has been defining the cell-intrinsic factors programmed by genetics and epigenetics that underlie insulin resistance. In this regard, studies using human induced pluripotent stem cells and tissues point to cell-autonomous alterations in signalling super-networks, involving changes in phosphorylation and gene expression both inside and outside the canonical insulin signalling pathway. Understanding how these multi-layered molecular networks modulate insulin action and metabolism in different tissues will open new avenues for therapy and prevention of type 2 diabetes and its associated pathologies.
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Affiliation(s)
- Thiago M Batista
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Nida Haider
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - C Ronald Kahn
- Section of Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA.
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18
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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] [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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19
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Small L, Altıntaş A, Laker RC, Ehrlich A, Pattamaprapanont P, Villarroel J, Pillon NJ, Zierath JR, Barrès R. Contraction influences Per2 gene expression in skeletal muscle through a calcium-dependent pathway. J Physiol 2020; 598:5739-5752. [PMID: 32939754 PMCID: PMC7756801 DOI: 10.1113/jp280428] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
KEY POINTS Exercising at different times of day elicits different effects on exercise performance and metabolic health. However, the specific signals driving the observed time-of-day specific effects of exercise have not been fully identified. Exercise influences the skeletal muscle circadian clock, although the relative contribution of muscle contraction and extracellular signals is unknown. Here, we show that contraction acutely increases the expression of the core circadian clock gene Period Circadian Regulator 2 (Per2) and phase-shifts Per2 rhythmicity in muscle cells. This contraction effect on core clock genes is mediated through a calcium-dependant mechanism; The results obtained in the present study suggest that a proportion of the ability of exercise to entrain the skeletal muscle clock is driven directly by muscle contraction. Contraction interventions may be used to mimic some time-of-day specific effects of exercise on metabolism and muscle performance. ABSTRACT Exercise entrains the central and peripheral circadian clocks, although the mechanism by which exercise modulates expression of skeletal muscle clock genes is unclear. The present study aimed to determine whether skeletal muscle contraction alone could directly influence circadian rhythmicity and uncover the underlying mechanism by which contraction modulates clock gene expression. We investigated the expression of core clock genes in human skeletal muscle after acute exercise, as well as following in vitro contraction in mouse soleus muscle and cultured C2C12 skeletal muscle myotubes. Additionally, we interrogated the molecular pathways by which skeletal muscle contraction could influence clock gene expression. Contraction acutely increased the expression of the core circadian clock gene Period Circadian Regulator 2 (Per2) and phase-shifted Per2 rhythmicity in C2C12 myotubes in vitro. Further investigation revealed that pharmacologically increasing cytosolic calcium concentrations by ionomycin treatment mimicked the effect of contraction on Per2 expression. Similarly, treatment with a calcium channel blocker, nifedipine, blocked the effect of electric pulse stimulation-induced contraction on Per2 expression. Increased calcium influx from contraction lead to binding of the phosphorylated form of cAMP response element-binding protein (CREB) to the Per2 promoter, suggesting a role of CREB in contraction-induced Per2 transcription. Thus, by dissociating the effect of muscle contraction alone from the whole effect of exercise, our investigations indicate that a proportion of the ability of exercise to entrain the skeletal muscle clock is driven directly by contraction.
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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
| | - Ali Altıntaş
- 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
| | - Amy Ehrlich
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Pattarawan Pattamaprapanont
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julia Villarroel
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicolas J Pillon
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Juleen R Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Romain Barrès
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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