1
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Li Y, Faiz A, Moshage H, Schilling L, Kamps JAAM. Responses of retinal and brain microvasculature to streptozotocin induced diabetes revealed by global expression profiling. Diab Vasc Dis Res 2023; 20:14791641221147533. [PMID: 36606460 PMCID: PMC9982389 DOI: 10.1177/14791641221147533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
This study aims to determine the effects of diabetes in the retinal and brain microvasculature through gene expression profiling. Twelve male Wistar rats were randomly divided into two groups: streptozotocin-induced diabetic rats and time-matched nondiabetic rats. The retinal microvessels (RMVs) and brain microvessels (BMVs) were mechanically isolated from individual rats. Differentially expressed genes (DEGs) in diabetic and nondiabetic microvessels were identified by cDNA microarrays analysis. In RMVs, we identified 43 DEGs, of which 20 were upregulated while 23 were downregulated by diabetes. In BMVs, 35 genes DEGs were identified, of which 22 were upregulated and 13 were downregulated by diabetes. Altered expression of the Nars, Gars, Mars, Iars, Yars, Bcl2, Nqo1, NR4A3, Gpd1, Stc1, Tsc22d3, Tnfrsf21 mRNA as observed in the microarray analyses, was confirmed by quantitative RT-PCR. The aminoacyl-tRNA synthetases (aaRSs) pathway in RMVs was significantly overrepresented as compared to BMVs. Our study demonstrates for the first time that in the brain microvasculature multiple compensatory mechanisms exists, serving to protect brain tissue from diabetic insults, whereas these mechanisms are not activated in the retinal microvasculature. This provides new insights as to why brain microvasculature is less susceptible to diabetes.
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Affiliation(s)
- Youhai Li
- Division of Neurosurgical Research, Heidelberg University, Mannheim, Germany; European Center of Angioscience, Medical
Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Pathology and Medical
Biology, University Medical Center
Groningen, Groningen, The Netherlands
| | - Alen Faiz
- Department of Pathology and Medical
Biology, University Medical Center
Groningen, Groningen, The Netherlands
| | - Han Moshage
- Department of Gastroenterology and
Hepatology, University Medical Center
Groningen, Groningen, The Netherlands
| | - Lothar Schilling
- Division of Neurosurgical Research, Heidelberg University, Mannheim, Germany; European Center of Angioscience, Medical
Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jan AAM Kamps
- Department of Pathology and Medical
Biology, University Medical Center
Groningen, Groningen, The Netherlands
- Jan AAM Kamps, Department of Pathology and
Medical Biology, University of Groningen, University Medical Center Groningen,
Hanzeplein 1 (EA11), 9713GZ Groningen, The Netherlands.
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2
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George MN, Leavens KF, Gadue P. Genome Editing Human Pluripotent Stem Cells to Model β-Cell Disease and Unmask Novel Genetic Modifiers. Front Endocrinol (Lausanne) 2021; 12:682625. [PMID: 34149620 PMCID: PMC8206553 DOI: 10.3389/fendo.2021.682625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/13/2021] [Indexed: 01/21/2023] Open
Abstract
A mechanistic understanding of the genetic basis of complex diseases such as diabetes mellitus remain elusive due in large part to the activity of genetic disease modifiers that impact the penetrance and/or presentation of disease phenotypes. In the face of such complexity, rare forms of diabetes that result from single-gene mutations (monogenic diabetes) can be used to model the contribution of individual genetic factors to pancreatic β-cell dysfunction and the breakdown of glucose homeostasis. Here we review the contribution of protein coding and non-protein coding genetic disease modifiers to the pathogenesis of diabetes subtypes, as well as how recent technological advances in the generation, differentiation, and genome editing of human pluripotent stem cells (hPSC) enable the development of cell-based disease models. Finally, we describe a disease modifier discovery platform that utilizes these technologies to identify novel genetic modifiers using induced pluripotent stem cells (iPSC) derived from patients with monogenic diabetes caused by heterozygous mutations.
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Affiliation(s)
- Matthew N. George
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Karla F. Leavens
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Division of Endocrinology and Diabetes, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Paul Gadue
- Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
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3
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Zhong JY, Cui XJ, Zhan JK, Wang YJ, Li S, Lin X, Xiang QY, Ni YQ, Liu L, Liu YS. LncRNA-ES3 inhibition by Bhlhe40 is involved in high glucose-induced calcification/senescence of vascular smooth muscle cells. Ann N Y Acad Sci 2020; 1474:61-72. [PMID: 32483833 DOI: 10.1111/nyas.14381] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/28/2020] [Accepted: 05/08/2020] [Indexed: 12/29/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been investigated as novel regulatory molecules involved in diverse biological processes. Our previous study demonstrated that lncRNA-ES3 is associated with the high glucose-induced calcification/senescence of human aortic vascular smooth muscle cells (HA-VSMCs). However, the mechanism of lncRNA-ES3 in vascular calcification/aging remained largely unknown. Here, we report that the expression of basic helix-loop-helix family member e40 (Bhlhe40) was decreased significantly in HA-VSMCs treated with high glucose, whereas the expression of basic leucine zipper transcription factor (BATF) was increased. Overexpression of Bhlhe40 and inhibition of BATF alleviated calcification/senescence of HA-VSMCs, as confirmed by Alizarin Red S staining and the presence of senescence-associated β-galactosidase-positive cells. Moreover, we identified that Bhlhe40 regulates lncRNA-ES3 in HA-VSMCs by binding to the promoter region of the lncRNA-ES3 gene (LINC00458). Upregulation or inhibition of lncRNA-ES3 expression significantly promoted or reduced calcification/senescence of HA-VSMCs, respectively. Additionally, we identified that lncRNA-ES3 functions in this process by suppressing the expression of miR-95-5p, miR-6776-5p, miR-3620-5p, and miR-4747-5p. The results demonstrate that lncRNA-ES3 triggers gene silencing of multiple miRNAs by binding to Bhlhe40, leading to calcification/senescence of VSMCs. Our findings suggest that pharmacological interventions targeting lncRNA-ES3 may be therapeutically beneficial in ameliorating vascular calcification/aging.
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Affiliation(s)
- Jia-Yu Zhong
- Department of Geriatrics, The Second Xiangya Hospital, Institute of Aging and Age-Related Disease Research, Central South University, Changsha, Hunan, People's Republic of China
| | - Xing-Jun Cui
- Department of Geriatrics, The Second Xiangya Hospital, Institute of Aging and Age-Related Disease Research, Central South University, Changsha, Hunan, People's Republic of China
| | - Jun-Kun Zhan
- Department of Geriatrics, The Second Xiangya Hospital, Institute of Aging and Age-Related Disease Research, Central South University, Changsha, Hunan, People's Republic of China
| | - Yan-Jiao Wang
- Department of Geriatrics, The Second Xiangya Hospital, Institute of Aging and Age-Related Disease Research, Central South University, Changsha, Hunan, People's Republic of China
| | - Shuang Li
- Department of Geriatrics, The Second Xiangya Hospital, Institute of Aging and Age-Related Disease Research, Central South University, Changsha, Hunan, People's Republic of China
| | - Xiao Lin
- Department of Geriatrics, The Second Xiangya Hospital, Institute of Aging and Age-Related Disease Research, Central South University, Changsha, Hunan, People's Republic of China
| | - Qun-Yan Xiang
- Department of Geriatrics, The Second Xiangya Hospital, Institute of Aging and Age-Related Disease Research, Central South University, Changsha, Hunan, People's Republic of China
| | - Yu-Qing Ni
- Department of Geriatrics, The Second Xiangya Hospital, Institute of Aging and Age-Related Disease Research, Central South University, Changsha, Hunan, People's Republic of China
| | - Le Liu
- Department of Geriatrics, The Second Xiangya Hospital, Institute of Aging and Age-Related Disease Research, Central South University, Changsha, Hunan, People's Republic of China
| | - You-Shuo Liu
- Department of Geriatrics, The Second Xiangya Hospital, Institute of Aging and Age-Related Disease Research, Central South University, Changsha, Hunan, People's Republic of China
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4
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Aguirre M, Rivas MA, Priest J. Phenome-wide Burden of Copy-Number Variation in the UK Biobank. Am J Hum Genet 2019; 105:373-383. [PMID: 31353025 PMCID: PMC6699064 DOI: 10.1016/j.ajhg.2019.07.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/28/2019] [Indexed: 10/26/2022] Open
Abstract
Copy-number variations (CNVs) represent a significant proportion of the genetic differences between individuals and many CNVs associate causally with syndromic disease and clinical outcomes. Here, we characterize the landscape of copy-number variation and their phenome-wide effects in a sample of 472,228 array-genotyped individuals from the UK Biobank. In addition to population-level selection effects against genic loci conferring high mortality, we describe genetic burden from potentially pathogenic and previously uncharacterized CNV loci across more than 3,000 quantitative and dichotomous traits, with separate analyses for common and rare classes of variation. Specifically, we highlight the effects of CNVs at two well-known syndromic loci 16p11.2 and 22q11.2, previously uncharacterized variation at 9p23, and several genic associations in the context of acute coronary artery disease and high body mass index. Our data constitute a deeply contextualized portrait of population-wide burden of copy-number variation, as well as a series of dosage-mediated genic associations across the medical phenome.
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Affiliation(s)
- Matthew Aguirre
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Manuel A Rivas
- Department of Biomedical Data Science, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - James Priest
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94035, USA.
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5
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Chang HC, Kao CH, Chung SY, Chen WC, Aninda LP, Chen YH, Juan YA, Chen SL. Bhlhe40 differentially regulates the function and number of peroxisomes and mitochondria in myogenic cells. Redox Biol 2018; 20:321-333. [PMID: 30391825 PMCID: PMC6218633 DOI: 10.1016/j.redox.2018.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/11/2018] [Accepted: 10/13/2018] [Indexed: 12/26/2022] Open
Abstract
PGC-1α is a key regulator of oxidative metabolism facilitating the expression of genes critical for the function and biogenesis of the two key oxidative organelles, mitochondria and peroxisomes, in skeletal muscle (SKM) and other organs. Our recent studies have found that the transcription factor Bhlhe40 negatively regulates PGC-1α gene expression and its coactivational activity, therefore, this factor should have profound influence on the biogenesis and metabolic activity of mitochondria and peroxisomes. Here we found that both the number and activity of peroxisomes were increased upon knockdown of Bhlhe40 expression but were repressed by its over-expression. Mitochondrial efficiency was significantly reduced by Bhlhe40 knockdown, resulting in the burst of ROS. Over-expression of a constitutively active PGC-1α-interactive domain (named as VBH135) of Bhlhe40 mimicked the effects of its knockdown on peroxisomes but simultaneously reduced ROS level. Furthermore, the efficiency, but not the number, of mitochondria was also increased by VBH135, suggesting differential regulation of peroxisomes and mitochondria by Bhlhe40. Unsaturated fatty acid oxidation, insulin response, and oxidative respiration were highly enhanced in Bhlhe40 knockdown or VBH135 over-expressed cells, suggesting the importance of Bhlhe40 in the regulation of unsaturated fatty acid and glucose oxidative metabolism. Expression profiling of genes important for either organelle also supports differential regulation of peroxisomes and mitochondria by Bhlhe40. These observations have established the important role of Bhlhe40 in SKM oxidative metabolism as the critical regulator of peroxisome and mitochondrion biogenesis and functions, and thus should provide a novel route for developing drugs targeting SKM metabolic diseases. Knockout of Bhlhe40 increased ROS but over-expression of Bhlhe40 reduced ROS. Peroxisome number was increased by Bhlhe40 knockout or VBH135 overexpression. Mitochondrial efficiency was reduced by Bhlhe40 knockout but increased by VBH135. Oxidative respiration was enhanced by Bhlhe40 knockdown or VBH135 overexpression. Bhlhe40 repressed PGC-1α coactivation of nuclear gene expression.
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Affiliation(s)
- Hsuan Chia Chang
- Department of Life Sciences, National Central University, Jhongli, Taiwan, ROC
| | - Chien Han Kao
- Department of Life Sciences, National Central University, Jhongli, Taiwan, ROC
| | - Shih Ying Chung
- Department of Life Sciences, National Central University, Jhongli, Taiwan, ROC
| | - Wei Cheng Chen
- Department of Life Sciences, National Central University, Jhongli, Taiwan, ROC
| | - Lulus Putri Aninda
- Department of Life Sciences, National Central University, Jhongli, Taiwan, ROC
| | - Yi Huan Chen
- Department of Life Sciences, National Central University, Jhongli, Taiwan, ROC
| | - Yi An Juan
- Department of Life Sciences, National Central University, Jhongli, Taiwan, ROC
| | - Shen Liang Chen
- Department of Life Sciences, National Central University, Jhongli, Taiwan, ROC.
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6
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Ramos-Lopez O, Samblas M, Milagro FI, Riezu-Boj JI, Crujeiras A, Martinez JA, Project MENA. Circadian gene methylation profiles are associated with obesity, metabolic disturbances and carbohydrate intake. Chronobiol Int 2018; 35:969-981. [PMID: 29580070 DOI: 10.1080/07420528.2018.1446021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Omar Ramos-Lopez
- Department of Nutrition, Food Science and Physiology, and Center for Nutrition Research, University of Navarra, Pamplona, Spain
| | - Mirian Samblas
- Department of Nutrition, Food Science and Physiology, and Center for Nutrition Research, University of Navarra, Pamplona, Spain
| | - Fermin I. Milagro
- Department of Nutrition, Food Science and Physiology, and Center for Nutrition Research, University of Navarra, Pamplona, Spain
- CIBERobn, Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición, Carlos III Health INstitute, Madrid, Spain
| | - Jose I. Riezu-Boj
- Department of Nutrition, Food Science and Physiology, and Center for Nutrition Research, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - A.B. Crujeiras
- CIBERobn, Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición, Carlos III Health INstitute, Madrid, Spain
- Laboratory of Molecular and Cellular Endocrinology, Instituto de Investigación Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain
| | - J. Alfredo Martinez
- Department of Nutrition, Food Science and Physiology, and Center for Nutrition Research, University of Navarra, Pamplona, Spain
- CIBERobn, Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y Nutrición, Carlos III Health INstitute, Madrid, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- IMDEA Food, Research Institute on Food & Health Sciences, Madrid, Spain
| | - MENA Project
- Other Members of the MENA Project in Alphabetical Order Are: Abete I, Cuervo M, Goni L, Marti A, Martinez-Gonzalez MA, Moreno-Aliaga MJ, Navas-Carretero S, San-Cristobal R, Santos JL and Zulet MA
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7
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Lim D, Strucken EM, Choi BH, Chai HH, Cho YM, Jang GW, Kim TH, Gondro C, Lee SH. Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea. PLoS One 2016; 11:e0151324. [PMID: 27023061 PMCID: PMC4811422 DOI: 10.1371/journal.pone.0151324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 02/26/2016] [Indexed: 01/01/2023] Open
Abstract
Korean Hanwoo cattle have been subjected to intensive artificial selection over the past four decades to improve meat production traits. Another three cattle varieties very closely related to Hanwoo reside in Korea (Jeju Black and Brindle) and in China (Yanbian). These breeds have not been part of a breeding scheme to improve production traits. Here, we compare the selected Hanwoo against these similar but presumed to be unselected populations to identify genomic regions that have been under recent selection pressure due to the breeding program. Rsb statistics were used to contrast the genomes of Hanwoo versus a pooled sample of the three unselected population (UN). We identified 37 significant SNPs (FDR corrected) in the HW/UN comparison and 21 known protein coding genes were within 1 MB to the identified SNPs. These genes were previously reported to affect traits important for meat production (14 genes), reproduction including mammary gland development (3 genes), coat color (2 genes), and genes affecting behavioral traits in a broader sense (2 genes). We subsequently sequenced (Illumina HiSeq 2000 platform) 10 individuals of the brown Hanwoo and the Chinese Yanbian to identify SNPs within the candidate genomic regions. Based on allele frequency differences, haplotype structures, and literature research, we singled out one non-synonymous SNP in the APP gene (APP: c.569C>T, Ala199Val) and predicted the mutational effect on the protein structure. We found that protein-protein interactions might be impaired due to increased exposed hydrophobic surfaces of the mutated protein. The APP gene has also been reported to affect meat tenderness in pigs and obesity in humans. Meat tenderness has been linked to intramuscular fat content, which is one of the main breeding goals for brown Hanwoo, potentially supporting a causal influence of the herein described nsSNP in the APP gene.
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Affiliation(s)
- Dajeong Lim
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Eva M. Strucken
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
| | - Bong Hwan Choi
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Han Ha Chai
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Yong Min Cho
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Gul Won Jang
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Tae-Hun Kim
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 565–851, Republic of Korea
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chung Nam National University, Daejeon 305–764, Republic of Korea
- * E-mail:
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Yazdi FT, Clee SM, Meyre D. Obesity genetics in mouse and human: back and forth, and back again. PeerJ 2015; 3:e856. [PMID: 25825681 PMCID: PMC4375971 DOI: 10.7717/peerj.856] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Accepted: 03/05/2015] [Indexed: 12/19/2022] Open
Abstract
Obesity is a major public health concern. This condition results from a constant and complex interplay between predisposing genes and environmental stimuli. Current attempts to manage obesity have been moderately effective and a better understanding of the etiology of obesity is required for the development of more successful and personalized prevention and treatment options. To that effect, mouse models have been an essential tool in expanding our understanding of obesity, due to the availability of their complete genome sequence, genetically identified and defined strains, various tools for genetic manipulation and the accessibility of target tissues for obesity that are not easily attainable from humans. Our knowledge of monogenic obesity in humans greatly benefited from the mouse obesity genetics field. Genes underlying highly penetrant forms of monogenic obesity are part of the leptin-melanocortin pathway in the hypothalamus. Recently, hypothesis-generating genome-wide association studies for polygenic obesity traits in humans have led to the identification of 119 common gene variants with modest effect, most of them having an unknown function. These discoveries have led to novel animal models and have illuminated new biologic pathways. Integrated mouse-human genetic approaches have firmly established new obesity candidate genes. Innovative strategies recently developed by scientists are described in this review to accelerate the identification of causal genes and deepen our understanding of obesity etiology. An exhaustive dissection of the molecular roots of obesity may ultimately help to tackle the growing obesity epidemic worldwide.
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Affiliation(s)
- Fereshteh T. Yazdi
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada
| | - Susanne M. Clee
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - David Meyre
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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Byrne K, McWilliam S, Vuocolo T, Gondro C, Cockett NE, Tellam RL. Genomic architecture of histone 3 lysine 27 trimethylation during late ovine skeletal muscle development. Anim Genet 2014; 45:427-38. [PMID: 24673416 PMCID: PMC4286725 DOI: 10.1111/age.12145] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2014] [Indexed: 12/21/2022]
Abstract
The ruminant developmental transition from late foetus to lamb is associated with marked changes in skeletal muscle structure and function that reflect programming for new physiological demands following birth. To determine whether epigenetic changes are involved in this transition, we investigated the genomic architecture of the chromatin modification, histone 3 lysine 27 trimethylation (H3K27me3), which typically regulates early life developmental processes; however, its role in later life processes is unclear. Chromatin immunoprecipitation coupled with next‐generation sequencing was used to map H3K27me3 nucleosomes in ovine longissimus lumborum skeletal muscle at 100 days of gestation and 12 weeks post‐partum. In both states, H3K27me3 modification was associated with genes, transcription start sites and CpG islands and with transcriptional silencing. The H3K27me3 peaks consisted of two major categories, promoter specific and regional, with the latter the dominant feature. Genes encoding homeobox transcription factors regulating early life development and genes involved in neural functions, particularly gated ion channels, were strongly modified by H3K27me3. Gene promoters differentially modified by H3K27me3 in the foetus and lamb were enriched for gated ion channels, which may reflect changes in neuromuscular function. However, most modified genes showed no changes, indicating that H3K27me3 does not have a large role in late muscle maturation. Notably, promyogenic transcription factors were strongly modified with H3K27me3 but showed no differences between the late gestation foetus and lamb, likely reflecting their lack of involvement in the myofibre fusion process occurring in this transition. H3K27me3 is a major architectural feature of the epigenetic landscape of ruminant skeletal muscle, and it comments on gene transcription and gene function in the context of late skeletal muscle development.
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Affiliation(s)
- K Byrne
- CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, QLD, 4067, Australia
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Schwenk RW, Vogel H, Schürmann A. Genetic and epigenetic control of metabolic health. Mol Metab 2013; 2:337-47. [PMID: 24327950 PMCID: PMC3854991 DOI: 10.1016/j.molmet.2013.09.002] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 09/09/2013] [Accepted: 09/13/2013] [Indexed: 02/06/2023] Open
Abstract
Obesity is characterized as an excess accumulation of body fat resulting from a positive energy balance. It is the major risk factor for type 2 diabetes (T2D). The evidence for familial aggregation of obesity and its associated metabolic diseases is substantial. To date, about 150 genetic loci identified in genome-wide association studies (GWAS) are linked with obesity and T2D, each accounting for only a small proportion of the predicted heritability. However, the percentage of overall trait variance explained by these associated loci is modest (~5-10% for T2D, ~2% for BMI). The lack of powerful genetic associations suggests that heritability is not entirely attributable to gene variations. Some of the familial aggregation as well as many of the effects of environmental exposures, may reflect epigenetic processes. This review summarizes our current knowledge on the genetic basis to individual risk of obesity and T2D, and explores the potential role of epigenetic contribution.
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Key Words
- ADCY3, adenylate cyclase 3
- AQP9, aquaporin 9
- BDNF, brain-derived neurotrophic factor
- CDKAL1, CDK5 regulatory subunit associated protein 1-like 1
- CPEB4, cytoplasmic polyadenylation element binding protein 4
- DUSP22, dual specificity phosphatase 22
- DUSP8, dual specificity phosphatase 8
- Epigenetics
- GALNT10, UDP-N-acetyl-alpha-d-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)
- GIPR, gastric inhibitory polypeptide receptor
- GNPDA2, glucosamine-6-phosphate deaminase 2
- GP2, glycoprotein 2 (zymogen granule membrane)
- GWAS
- HIPK3, homeodomain interacting protein kinase 3
- IFI16, interferon, gamma-inducible protein 16
- KCNQ1, potassium voltage-gated channel, KQT-like subfamily, member 1
- KLHL32, kelch-like family member 32
- LEPR, leptin receptor
- MAP2K4, mitogen-activated protein kinase kinase 4
- MAP2K5, mitogen-activated protein kinase kinase 5
- MIR148A, microRNA 148a
- MMP9, matrix metallopeptidase 9 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV collagenase)
- MNDA, myeloid cell nuclear differentiation antigen
- NFE2L3, nuclear factor, erythroid 2-like 3
- Obesity
- PACS1, phosphofurin acidic cluster sorting protein 1
- PAX6, paired box gene 6
- PCSK1, proprotein convertase subtilisin/kexin type 1
- PGC1α, peroxisome proliferative activated receptor, gamma, coactivator 1 alpha, PM2OD1
- PRKCH, protein kinase C, eta
- PRKD1, protein kinase D1
- PRKG1, protein kinase, cGMP-dependent, type I
- Positional cloning
- QPCTL, glutaminyl-peptide cyclotransferase-like
- RBJ, DnaJ (Hsp40) homolog, subfamily C, member 27
- RFC5, replication factor C (activator 1) 5
- RMST, rhabdomyosarcoma 2 associated transcript (non-protein coding)
- SEC16B, SEC16 homolog B
- TFAP2B, transcription factor AP-2 beta (activating enhancer binding protein 2 beta)
- TNNI3, troponin I type 3 (cardiac)
- TNNT1, troponin T type 1 (skeletal, slow)
- Type 2 diabetes
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Affiliation(s)
| | | | - Annette Schürmann
- Corresponding author. Tel.: +49 33200 882368; fax: +49 33200 882334.
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