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de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MR, Williams RW, Li JZ, Chen H. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats. CELL GENOMICS 2024; 4:100527. [PMID: 38537634 PMCID: PMC11019364 DOI: 10.1016/j.xgen.2024.100527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 02/29/2024] [Indexed: 04/09/2024]
Abstract
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
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Affiliation(s)
- Tristan V de Jong
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yanchao Pan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Chris Benner
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - William Chow
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Wendy M Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Peter A Doris
- The Brown Foundation Institute of Molecular Medicine, Center for Human Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hakan M Gunturkun
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victor Guryev
- Genome Structure and Ageing, University of Groningen, UMC, Groningen, the Netherlands
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Jun Huang
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA
| | - Panjun Kim
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ling Li
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Pejman Mohammadi
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jennifer R Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hongyang Wang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Burt M Sharp
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Francesca Telese
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
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Rahman MA, Cai C, Bo N, McNamara DM, Ding Y, Cooper GF, Lu X, Liu J. An individualized Bayesian method for estimating genomic variants of hypertension. BMC Genomics 2023; 23:863. [PMID: 37936055 PMCID: PMC10631115 DOI: 10.1186/s12864-023-09757-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 10/19/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Genomic variants of the disease are often discovered nowadays through population-based genome-wide association studies (GWAS). Identifying genomic variations potentially underlying a phenotype, such as hypertension, in an individual is important for designing personalized treatment; however, population-level models, such as GWAS, may not capture all the important, individualized factors well. In addition, GWAS typically requires a large sample size to detect the association of low-frequency genomic variants with sufficient power. Here, we report an individualized Bayesian inference (IBI) algorithm for estimating the genomic variants that influence complex traits, such as hypertension, at the level of an individual (e.g., a patient). By modeling at the level of the individual, IBI seeks to find genomic variants observed in the individual's genome that provide a strong explanation of the phenotype observed in this individual. RESULTS We applied the IBI algorithm to the data from the Framingham Heart Study to explore the genomic influences of hypertension. Among the top-ranking variants identified by IBI and GWAS, there is a significant number of shared variants (intersection); the unique variants identified only by IBI tend to have relatively lower minor allele frequency than those identified by GWAS. In addition, IBI discovered more individualized and diverse variants that explain hypertension patients better than GWAS. Furthermore, IBI found several well-known low-frequency variants as well as genes related to blood pressure that GWAS missed in the same cohort. Finally, IBI identified top-ranked variants that predicted hypertension better than GWAS, according to the area under the ROC curve. CONCLUSIONS The results support IBI as a promising approach for complementing GWAS, especially in detecting low-frequency genomic variants as well as learning personalized genomic variants of clinical traits and disease, such as the complex trait of hypertension, to help advance precision medicine.
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Affiliation(s)
- Md Asad Rahman
- Department of Engineering Management and Systems Engineering, Missouri University of Science and Technology, Rolla, MO, USA
| | - Chunhui Cai
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Na Bo
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dennis M McNamara
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gregory F Cooper
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xinghua Lu
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jinling Liu
- Department of Engineering Management and Systems Engineering, Missouri University of Science and Technology, Rolla, MO, USA.
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO, USA.
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA.
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Olivera S, Graham D. Sex differences in preclinical models of hypertension. J Hum Hypertens 2023; 37:619-625. [PMID: 36335169 PMCID: PMC10403342 DOI: 10.1038/s41371-022-00770-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 10/03/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Abstract
Hypertension remains the primary contributor in the development of cardiovascular disease which is rapidly increasing worldwide. High blood pressure affects men and women differently and understanding these sex differences is the ultimate unmet need for researchers in this field. Due to the inherent differences in hypertension prevalence, control and outcomes between men and women, novel research needs to be carried out to tackle these disparities and improve targeted treatment. Animal models of hypertension have provided valuable insights into the sexual dimorphism of blood pressure mechanisms. The availability of genetic and non-genetic hypertensive strains allows the opportunity to study diverse environmental and genetic factors that affect blood pressure, therefore presenting a valuable tool for researchers. Sex differences are present before birth and throughout life, which presents a challenge for the study of disease development in humans, but these complexities can be resolved with the use of in vivo models that display similarities to human disease. The aim of the present review is to provide an overview of the different available animal models of hypertension that present sexual dimorphisms and to discuss their relevance to humans.
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Affiliation(s)
- Sol Olivera
- School of Cardiovascular and Metabolic Health, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK
| | - Delyth Graham
- School of Cardiovascular and Metabolic Health, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK.
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4
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Silhavy J, Mlejnek P, Šimáková M, Marková I, Malínská H, Hüttl M, Kazdová L, Kazantsev D, Mancini M, Novotný J, Pravenec M. CD36 regulates substrates utilisation in brown adipose tissue of spontaneously hypertensive rats: In vitro study. PLoS One 2023; 18:e0283276. [PMID: 37053180 PMCID: PMC10101526 DOI: 10.1371/journal.pone.0283276] [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: 10/26/2022] [Accepted: 03/06/2023] [Indexed: 04/14/2023] Open
Abstract
Thermogenesis in brown adipose tissue (BAT) uses intracellular triglycerides, circulating free fatty acids and glucose as the main substrates. The objective of the current study was to analyse the role of CD36 fatty acid translocase in regulation of glucose and fatty acid utilisation in BAT. BAT isolated from spontaneously hypertensive rat (SHR) with mutant Cd36 gene and SHR-Cd36 transgenic rats with wild type variant was incubated in media containing labeled glucose and palmitate to measure substrate incorporation and oxidation. SHR-Cd36 versus SHR rats showed significantly increased glucose incorporation into intracellular lipids associated with reduced glycogen synthase kinase 3β (GSK-3β) protein expression and phosphorylation and increased oxidation of exogenous palmitate. It can be concluded that CD36 enhances glucose transport for lipogenesis in BAT by suppressing GSK-3β and promotes direct palmitate oxidation.
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Affiliation(s)
- Jan Silhavy
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Mlejnek
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Miroslava Šimáková
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Irena Marková
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Hana Malínská
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Martina Hüttl
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Ludmila Kazdová
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Dmitry Kazantsev
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
- 1st Faculty of Medicine, Institute of Pathological Physiology, Charles University, Prague, Czech Republic
| | - Massimiliano Mancini
- Division of Morphologic and Molecular Pathology, S. Andrea Hospital, Sapienza, University of Rome, Rome, Italy
| | - Jiří Novotný
- Department of Physiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
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5
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Kuramoto T. Positional cloning of rat mutant genes reveals new functions of these genes. Exp Anim 2023; 72:1-8. [PMID: 36058846 PMCID: PMC9978133 DOI: 10.1538/expanim.22-0089] [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] [Indexed: 11/04/2022] Open
Abstract
The laboratory rat (Rattus norvegicus) is a key model organism for biomedical research. Rats can be subjected to strict genetic and environmental controls. The rat's large body size is suitable for both surgical operations and repeated measurements of physiological parameters. These advantages have led to the development of numerous rat models for genetic diseases. Forward genetics is a proven approach for identifying the causative genes of these disease models but requires genome resources including genetic markers and genome sequences. Over the last few decades, rat genome resources have been developed and deposited in bioresource centers, which have enabled us to perform positional cloning in rats. To date, more than 100 disease-related genes have been identified by positional cloning. Since some disease models are more accessible in rats than mice, the identification of causative genes in these models has sometimes led to the discovery of novel functions of genes. As before, various mutant rats are also expected to be discovered and developed as disease models in the future. Thus, the forward genetics continues to be an important approach to find genes involved in disease phenotypes in rats. In this review, I provide an overview the development of rat genome resources and describe examples of positional cloning in rats in which novel gene functions have been identified.
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Affiliation(s)
- Takashi Kuramoto
- Laboratory of Animal Nutrition, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa 243-0034, Japan
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6
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Tahir UA, Katz DH, Avila-Pachecho J, Bick AG, Pampana A, Robbins JM, Yu Z, Chen ZZ, Benson MD, Cruz DE, Ngo D, Deng S, Shi X, Zheng S, Eisman AS, Farrell L, Hall ME, Correa A, Tracy RP, Durda P, Taylor KD, Liu Y, Johnson WC, Guo X, Yao J, Chen YDI, Manichaikul AW, Ruberg FL, Blaner WS, Jain D, Bouchard C, Sarzynski MA, Rich SS, Rotter JI, Wang TJ, Wilson JG, Clish CB, Natarajan P, Gerszten RE. Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals. Nat Commun 2022; 13:4923. [PMID: 35995766 PMCID: PMC9395431 DOI: 10.1038/s41467-022-32275-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 07/25/2022] [Indexed: 01/27/2023] Open
Abstract
Integrating genetic information with metabolomics has provided new insights into genes affecting human metabolism. However, gene-metabolite integration has been primarily studied in individuals of European Ancestry, limiting the opportunity to leverage genomic diversity for discovery. In addition, these analyses have principally involved known metabolites, with the majority of the profiled peaks left unannotated. Here, we perform a whole genome association study of 2,291 metabolite peaks (known and unknown features) in 2,466 Black individuals from the Jackson Heart Study. We identify 519 locus-metabolite associations for 427 metabolite peaks and validate our findings in two multi-ethnic cohorts. A significant proportion of these associations are in ancestry specific alleles including findings in APOE, TTR and CD36. We leverage tandem mass spectrometry to annotate unknown metabolites, providing new insight into hereditary diseases including transthyretin amyloidosis and sickle cell disease. Our integrative omics approach leverages genomic diversity to provide novel insights into diverse cardiometabolic diseases.
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Affiliation(s)
- Usman A Tahir
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | - Daniel H Katz
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | | | | | - Akhil Pampana
- Broad Institute of Harvard and MIT, Cambridge, MA, US
| | - Jeremy M Robbins
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | - Zhi Yu
- Broad Institute of Harvard and MIT, Cambridge, MA, US
| | - Zsu-Zsu Chen
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | - Mark D Benson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | - Daniel E Cruz
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | - Debby Ngo
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | - Shuliang Deng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | - Xu Shi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | - Shuning Zheng
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | - Aaron S Eisman
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | - Laurie Farrell
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | - Michael E Hall
- University of Mississippi Medical Center, Jackson, MS, US
| | - Adolfo Correa
- University of Mississippi Medical Center, Jackson, MS, US
| | - Russell P Tracy
- Department of Pathology Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, US
| | - Peter Durda
- Department of Pathology Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, US
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, US
| | - Yongmei Liu
- Department of Medicine, Division of Cardiology, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, US
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, US
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, US
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, US
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, US
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, US
- Division of Biostatistics and Epidemiology, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, US
| | - Frederick L Ruberg
- Section of Cardiovascular Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, US
| | | | - Deepti Jain
- University of Washington, Seattle, Washington, US
| | - Claude Bouchard
- Human Genomic Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA, US
| | - Mark A Sarzynski
- Department of Exercise Science, University of South Carolina, Columbia, SC, US
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, US
- Division of Biostatistics and Epidemiology, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, US
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor UCLA Medical Center, Torrance, CA, US
| | - Thomas J Wang
- Department of Medicine, UT Southwestern Medical Center, Dallas, TX, US
| | - James G Wilson
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US
| | - Clary B Clish
- Broad Institute of Harvard and MIT, Cambridge, MA, US
| | - Pradeep Natarajan
- Broad Institute of Harvard and MIT, Cambridge, MA, US
- Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, US
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, US.
- Broad Institute of Harvard and MIT, Cambridge, MA, US.
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7
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A systematic review and meta-analysis on the association between CD36 rs1761667 polymorphism and cardiometabolic risk factors in adults. Sci Rep 2022; 12:5916. [PMID: 35396566 PMCID: PMC8993862 DOI: 10.1038/s41598-022-09908-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/21/2022] [Indexed: 12/04/2022] Open
Abstract
The cluster of differentiation 36 (CD36) is one of the main receptors implicated in the pathogenesis of the cardiovascular disease. This study aimed to assess the association between CD36 rs1761667 polymorphism and cardiometabolic risk factors including body mass index (BMI), waist circumference (WC), total cholesterol (TC), triglyceride, HDL-C, LDL-C, blood pressure and fasting blood glucose (FBG). PubMed, EMBASE, Scopus, web of science, and Google Scholar were searched up to December 2021. Subgroup and meta-regression analyses were conducted to explore sources of heterogeneity. Eighteen eligible studies (6317 participants) were included in the study. In the overall analysis, a significant association was found between rs1761667 polymorphism of CD36 and TG in allelic (p < 0.001), recessive (p = 0.001) and homozygous (p = 0.006) models. A relationship between this polymorphism and HDL-C and FBG level was observed in the recessive genetic model. In the subgroup analysis, the A allele was associated with impaired lipid profiles (TC, LDL-C and HDL-C) in the Asian population. The influences of health status, design of the study, confounders, and other sources of heterogeneity should be considered when interpreting present findings. Cohort studies with large sample size and in different ethnicities are needed to confirm the relationship between rs1761667 SNP and cardiometabolic risk factors.
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8
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Senko AN, Overall RW, Silhavy J, Mlejnek P, Malínská H, Hüttl M, Marková I, Fabel KS, Lu L, Stuchlik A, Williams RW, Pravenec M, Kempermann G. Systems genetics in the rat HXB/BXH family identifies Tti2 as a pleiotropic quantitative trait gene for adult hippocampal neurogenesis and serum glucose. PLoS Genet 2022; 18:e1009638. [PMID: 35377872 PMCID: PMC9060359 DOI: 10.1371/journal.pgen.1009638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 05/02/2022] [Accepted: 03/07/2022] [Indexed: 11/19/2022] Open
Abstract
Neurogenesis in the adult hippocampus contributes to learning and memory in the healthy brain but is dysregulated in metabolic and neurodegenerative diseases. The molecular relationships between neural stem cell activity, adult neurogenesis, and global metabolism are largely unknown. Here we applied unbiased systems genetics methods to quantify genetic covariation among adult neurogenesis and metabolic phenotypes in peripheral tissues of a genetically diverse family of rat strains, derived from a cross between the spontaneously hypertensive (SHR/OlaIpcv) strain and Brown Norway (BN-Lx/Cub). The HXB/BXH family is a very well established model to dissect genetic variants that modulate metabolic and cardiovascular diseases and we have accumulated deep phenome and transcriptome data in a FAIR-compliant resource for systematic and integrative analyses. Here we measured rates of precursor cell proliferation, survival of new neurons, and gene expression in the hippocampus of the entire HXB/BXH family, including both parents. These data were combined with published metabolic phenotypes to detect a neurometabolic quantitative trait locus (QTL) for serum glucose and neuronal survival on Chromosome 16: 62.1-66.3 Mb. We subsequently fine-mapped the key phenotype to a locus that includes the Telo2-interacting protein 2 gene (Tti2)-a chaperone that modulates the activity and stability of PIKK kinases. To verify the hypothesis that differences in neurogenesis and glucose levels are caused by a polymorphism in Tti2, we generated a targeted frameshift mutation on the SHR/OlaIpcv background. Heterozygous SHR-Tti2+/- mutants had lower rates of hippocampal neurogenesis and hallmarks of dysglycemia compared to wild-type littermates. Our findings highlight Tti2 as a causal genetic link between glucose metabolism and structural brain plasticity. In humans, more than 800 genomic variants are linked to TTI2 expression, seven of which have associations to protein and blood stem cell factor concentrations, blood pressure and frontotemporal dementia.
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Affiliation(s)
- Anna N. Senko
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Rupert W. Overall
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Jan Silhavy
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Mlejnek
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Malínská
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Martina Hüttl
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Irena Marková
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Klaus S. Fabel
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Ales Stuchlik
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Gerd Kempermann
- German Center for Neurodegenerative Diseases (DZNE) Dresden, Germany
- CRTD–Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany
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9
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Pravenec M, Šilhavý J, Mlejnek P, Šimáková M, Mráček T, Pecinová A, Tauchmannová K, Hütl M, Malínská H, Kazdová L, Neckář J, Kolář F, Žurmanová J, Novotný J, Houštěk J. Conplastic strains for identification of retrograde effects of mitochondrial dna variation on cardiometabolic traits in the spontaneously hypertensive rat. Physiol Res 2021; 70:S471-S484. [DOI: 10.33549/physiolres.934740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial retrograde signaling is a pathway of communication from mitochondria to the nucleus. Recently, natural mitochondrial genome (mtDNA) polymorphisms (haplogroups) received increasing attention in the pathophysiology of human common diseases. However, retrograde effects of mtDNA variants on such traits are difficult to study in humans. The conplastic strains represent key animal models to elucidate regulatory roles of mtDNA haplogroups on defined nuclear genome background. To analyze the relationship between mtDNA variants and cardiometabolic traits, we derived a set of rat conplastic strains (SHR-mtBN, SHR-mtF344 and SHR-mtLEW), harboring all major mtDNA haplotypes present in common inbred strains on the nuclear background of the spontaneously hypertensive rat (SHR). The BN, F344 and LEW mtDNA differ from the SHR in multiple amino acid substitutions in protein coding genes and also in variants of tRNA and rRNA genes. Different mtDNA haplotypes were found to predispose to various sets of cardiometabolic phenotypes which provided evidence for significant retrograde effects of mtDNA in the SHR. In the future, these animals could be used to decipher individual biochemical components involved in the retrograde signaling.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - J Houštěk
- Institute of Physiology, Czech Academy of Sciences, Vídeňská 1083, 14220 Prague, Czech Republic. ,
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10
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Witte F, Ruiz-Orera J, Mattioli CC, Blachut S, Adami E, Schulz JF, Schneider-Lunitz V, Hummel O, Patone G, Mücke MB, Šilhavý J, Heinig M, Bottolo L, Sanchis D, Vingron M, Chekulaeva M, Pravenec M, Hubner N, van Heesch S. A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion. Genome Biol 2021; 22:191. [PMID: 34183069 PMCID: PMC8240307 DOI: 10.1186/s13059-021-02397-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 06/02/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Little is known about the impact of trans-acting genetic variation on the rates with which proteins are synthesized by ribosomes. Here, we investigate the influence of such distant genetic loci on the efficiency of mRNA translation and define their contribution to the development of complex disease phenotypes within a panel of rat recombinant inbred lines. RESULTS We identify several tissue-specific master regulatory hotspots that each control the translation rates of multiple proteins. One of these loci is restricted to hypertrophic hearts, where it drives a translatome-wide and protein length-dependent change in translational efficiency, altering the stoichiometric translation rates of sarcomere proteins. Mechanistic dissection of this locus across multiple congenic lines points to a translation machinery defect, characterized by marked differences in polysome profiles and misregulation of the small nucleolar RNA SNORA48. Strikingly, from yeast to humans, we observe reproducible protein length-dependent shifts in translational efficiency as a conserved hallmark of translation machinery mutants, including those that cause ribosomopathies. Depending on the factor mutated, a pre-existing negative correlation between protein length and translation rates could either be enhanced or reduced, which we propose to result from mRNA-specific imbalances in canonical translation initiation and reinitiation rates. CONCLUSIONS We show that distant genetic control of mRNA translation is abundant in mammalian tissues, exemplified by a single genomic locus that triggers a translation-driven molecular mechanism. Our work illustrates the complexity through which genetic variation can drive phenotypic variability between individuals and thereby contribute to complex disease.
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Affiliation(s)
- Franziska Witte
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: NUVISAN ICB GmbH, Lead Discovery-Structrual Biology, 13353, Berlin, Germany
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Camilla Ciolli Mattioli
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
- Present Address: Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - Jana Felicitas Schulz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Valentin Schneider-Lunitz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Oliver Hummel
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Michael Benedikt Mücke
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
| | - Jan Šilhavý
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Matthias Heinig
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg, Munich, Germany
- Department of Informatics, Technische Universitaet Muenchen (TUM), Boltzmannstr. 3, 85748 Garching, Munich, Germany
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Daniel Sanchis
- Institut de Recerca Biomedica de Lleida (IRBLLEIDA), Universitat de Lleida, Edifici Biomedicina-I. Av. Rovira Roure, 80, 25198, Lleida, Spain
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany.
- Charité-Universitätsmedizin, 10117, Berlin, Germany.
| | - Sebastiaan van Heesch
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- Present Address: The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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11
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Takeuchi F, Liang YQ, Isono M, Tajima M, Cui ZH, Iizuka Y, Gotoda T, Nabika T, Kato N. Integrative genomic analysis of blood pressure and related phenotypes in rats. Dis Model Mech 2021; 14:dmm048090. [PMID: 34010951 PMCID: PMC8188887 DOI: 10.1242/dmm.048090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
Despite remarkable progress made in human genome-wide association studies, there remains a substantial gap between statistical evidence for genetic associations and functional comprehension of the underlying mechanisms governing these associations. As a means of bridging this gap, we performed genomic analysis of blood pressure (BP) and related phenotypes in spontaneously hypertensive rats (SHR) and their substrain, stroke-prone SHR (SHRSP), both of which are unique genetic models of severe hypertension and cardiovascular complications. By integrating whole-genome sequencing, transcriptome profiling, genome-wide linkage scans (maximum n=1415), fine congenic mapping (maximum n=8704), pharmacological intervention and comparative analysis with transcriptome-wide association study (TWAS) datasets, we searched causal genes and causal pathways for the tested traits. The overall results validated the polygenic architecture of elevated BP compared with a non-hypertensive control strain, Wistar Kyoto rats (WKY); e.g. inter-strain BP differences between SHRSP and WKY could be largely explained by an aggregate of BP changes in seven SHRSP-derived consomic strains. We identified 26 potential target genes, including rat homologs of human TWAS loci, for the tested traits. In this study, we re-discovered 18 genes that had previously been determined to contribute to hypertension or cardiovascular phenotypes. Notably, five of these genes belong to the kallikrein-kinin/renin-angiotensin systems (KKS/RAS), in which the most prominent differential expression between hypertensive and non-hypertensive alleles could be detected in rat Klk1 paralogs. In combination with a pharmacological intervention, we provide in vivo experimental evidence supporting the presence of key disease pathways, such as KKS/RAS, in a rat polygenic hypertension model.
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Affiliation(s)
- Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Yi-Qiang Liang
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Masato Isono
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Michiko Tajima
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Zong Hu Cui
- Department of Functional Pathology, Shimane University Faculty of Medicine, Izumo 693-0021, Japan
| | - Yoko Iizuka
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, University of Tokyo, Tokyo 113-0033, Japan
| | - Takanari Gotoda
- Department of Metabolism and Biochemistry, Kyorin University Faculty of Medicine, Tokyo 181-8611, Japan
| | - Toru Nabika
- Department of Functional Pathology, Shimane University Faculty of Medicine, Izumo 693-0021, Japan
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
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12
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Abstract
Complex multicellular life in mammals relies on functional cooperation of different organs for the survival of the whole organism. The kidneys play a critical part in this process through the maintenance of fluid volume and composition homeostasis, which enables other organs to fulfil their tasks. The renal endothelium exhibits phenotypic and molecular traits that distinguish it from endothelia of other organs. Moreover, the adult kidney vasculature comprises diverse populations of mostly quiescent, but not metabolically inactive, endothelial cells (ECs) that reside within the kidney glomeruli, cortex and medulla. Each of these populations supports specific functions, for example, in the filtration of blood plasma, the reabsorption and secretion of water and solutes, and the concentration of urine. Transcriptional profiling of these diverse EC populations suggests they have adapted to local microenvironmental conditions (hypoxia, shear stress, hyperosmolarity), enabling them to support kidney functions. Exposure of ECs to microenvironment-derived angiogenic factors affects their metabolism, and sustains kidney development and homeostasis, whereas EC-derived angiocrine factors preserve distinct microenvironment niches. In the context of kidney disease, renal ECs show alteration in their metabolism and phenotype in response to pathological changes in the local microenvironment, further promoting kidney dysfunction. Understanding the diversity and specialization of kidney ECs could provide new avenues for the treatment of kidney diseases and kidney regeneration.
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13
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Szpirer C. Rat models of human diseases and related phenotypes: a systematic inventory of the causative genes. J Biomed Sci 2020; 27:84. [PMID: 32741357 PMCID: PMC7395987 DOI: 10.1186/s12929-020-00673-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022] Open
Abstract
The laboratory rat has been used for a long time as the model of choice in several biomedical disciplines. Numerous inbred strains have been isolated, displaying a wide range of phenotypes and providing many models of human traits and diseases. Rat genome mapping and genomics was considerably developed in the last decades. The availability of these resources has stimulated numerous studies aimed at discovering causal disease genes by positional identification. Numerous rat genes have now been identified that underlie monogenic or complex diseases and remarkably, these results have been translated to the human in a significant proportion of cases, leading to the identification of novel human disease susceptibility genes, helping in studying the mechanisms underlying the pathological abnormalities and also suggesting new therapeutic approaches. In addition, reverse genetic tools have been developed. Several genome-editing methods were introduced to generate targeted mutations in genes the function of which could be clarified in this manner [generally these are knockout mutations]. Furthermore, even when the human gene causing a disease had been identified without resorting to a rat model, mutated rat strains (in particular KO strains) were created to analyze the gene function and the disease pathogenesis. Today, over 350 rat genes have been identified as underlying diseases or playing a key role in critical biological processes that are altered in diseases, thereby providing a rich resource of disease models. This article is an update of the progress made in this research and provides the reader with an inventory of these disease genes, a significant number of which have similar effects in rat and humans.
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Affiliation(s)
- Claude Szpirer
- Université Libre de Bruxelles, B-6041, Gosselies, Belgium.
- , Waterloo, Belgium.
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14
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Saroj C, Juthika M, Tao Y, Xi C, Ji-Youn Y, Cameron MG, Camilla WF, Lauren KG, Jennifer HW, Matam VK, Bina J. Metabolites and Hypertension: Insights into Hypertension as a Metabolic Disorder: 2019 Harriet Dustan Award. Hypertension 2020; 75:1386-1396. [PMID: 32336227 PMCID: PMC7225070 DOI: 10.1161/hypertensionaha.120.13896] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For over 100 years, essential hypertension has been researched from different perspectives ranging from genetics, physiology, and immunology to more recent ones encompassing microbiology (microbiota) as a previously underappreciated field of study contributing to the cause of hypertension. Each field of study in isolation has uniquely contributed to a variety of underlying mechanisms of blood pressure regulation. Even so, clinical management of essential hypertension has remained somewhat static. We, therefore, asked if there are any converging lines of evidence from these individual fields that could be amenable for a better clinical prognosis. Accordingly, here we present converging evidence which support the view that metabolic dysfunction underlies essential hypertension.
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Affiliation(s)
- Chakraborty Saroj
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Mandal Juthika
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Yang Tao
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Cheng Xi
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Yeo Ji-Youn
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - McCarthy G. Cameron
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Wenceslau F. Camilla
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Koch G. Lauren
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Hill W. Jennifer
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Vijay-Kumar Matam
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Joe Bina
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
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15
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Cowley AW, Dwinell MR. Chromosomal Substitution Strategies to Localize Genomic Regions Related to Complex Traits. Compr Physiol 2020; 10:365-388. [PMID: 32163204 DOI: 10.1002/cphy.c180029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Chromosomal substitution strategies provide a powerful tool to anonymously reveal the relationship between DNA sequence variants and a normal or disease phenotype of interest. Even in this age of CRISPR-Cas9 genome engineering, the knockdown or overexpression of a gene provides relevant information to our understanding of complex disease only when a close association of an allelic variant with the phenotype has first been established. Limitations of genetic linkage approaches led to the development of more efficient breeding strategies to substitute chromosomal segments from one animal strain into the genetic background of a different strain, enabling a direct comparison of the phenotypes of the strains with variant(s) that differ only at a defined locus. This substitution can be a whole chromosome (consomic), a part of a chromosome (congenic), or as small as only a single or several alleles (subcongenics). In contrast to complete knockout of a specific candidate gene of interest, which simply studies the effects of complete elimination of the gene, the substitution of naturally occurring variants can provide special insights into the functional actions of wild-type alleles. Strategies for production of these inbred strains are reviewed, and a number of examples are used to illustrate the utility of these model systems. Consomic/congenic strains provide a number of experimental advantages in the study of functions of genes and their variants, which are emphasized in this article, such as replication of experimental studies; determination of temporal relationships throughout a life; rigorously controlled experiments in which relations between genotype and phenotype can be tested with the confounding effects of heterogeneous genetic backgrounds, both targeted and multilayered; and "omic" studies performed at many levels of functionality, from molecules to organelles, cells to organs, and organs to organismal behavior across the life span. The application of chromosomal substitution strategies and development of consomic/congenic rat and mouse strains have greatly expanded our knowledge of genomic variants and their phenotypic relationship to physiological functions and to complex diseases such as hypertension and cancer. © 2020 American Physiological Society. Compr Physiol 10:365-388, 2020.
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Affiliation(s)
- Allen W Cowley
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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16
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Chen H, Moreno-Moral A, Pesce F, Devapragash N, Mancini M, Heng EL, Rotival M, Srivastava PK, Harmston N, Shkura K, Rackham OJL, Yu WP, Sun XM, Tee NGZ, Tan ELS, Barton PJR, Felkin LE, Lara-Pezzi E, Angelini G, Beltrami C, Pravenec M, Schafer S, Bottolo L, Hubner N, Emanueli C, Cook SA, Petretto E. WWP2 regulates pathological cardiac fibrosis by modulating SMAD2 signaling. Nat Commun 2019; 10:3616. [PMID: 31399586 PMCID: PMC6689010 DOI: 10.1038/s41467-019-11551-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 07/19/2019] [Indexed: 01/03/2023] Open
Abstract
Cardiac fibrosis is a final common pathology in inherited and acquired heart diseases that causes cardiac electrical and pump failure. Here, we use systems genetics to identify a pro-fibrotic gene network in the diseased heart and show that this network is regulated by the E3 ubiquitin ligase WWP2, specifically by the WWP2-N terminal isoform. Importantly, the WWP2-regulated pro-fibrotic gene network is conserved across different cardiac diseases characterized by fibrosis: human and murine dilated cardiomyopathy and repaired tetralogy of Fallot. Transgenic mice lacking the N-terminal region of the WWP2 protein show improved cardiac function and reduced myocardial fibrosis in response to pressure overload or myocardial infarction. In primary cardiac fibroblasts, WWP2 positively regulates the expression of pro-fibrotic markers and extracellular matrix genes. TGFβ1 stimulation promotes nuclear translocation of the WWP2 isoforms containing the N-terminal region and their interaction with SMAD2. WWP2 mediates the TGFβ1-induced nucleocytoplasmic shuttling and transcriptional activity of SMAD2.
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Affiliation(s)
- Huimei Chen
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Aida Moreno-Moral
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Francesco Pesce
- Department of Emergency and Organ Transplantation (DETO), University of Bari, 70124, Bari, Italy
| | - Nithya Devapragash
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Massimiliano Mancini
- SOC di Anatomia Patologica, Ospedale San Giovanni di Dio, 50123, Florence, Italy
| | - Ee Ling Heng
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Maxime Rotival
- Unit of Human Evolutionary Genetics, Institute Pasteur, 75015, Paris, France
| | - Prashant K Srivastava
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Nathan Harmston
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London, W12 0NN, UK
| | - Owen J L Rackham
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Wei-Ping Yu
- Animal Gene Editing Laboratory, BRC, A*STAR20 Biopolis Way, Singapore, 138668, Republic of Singapore
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore, 138673, Republic of Singapore
| | - Xi-Ming Sun
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
| | | | - Elisabeth Li Sa Tan
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Leanne E Felkin
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares - CNIC, 28029, Madrid, Spain
| | - Gianni Angelini
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Bristol Heart Institute, Bristol Medical School, University of Bristol, Bristol, BS2 89HW, UK
| | - Cristina Beltrami
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, 142 00, Praha 4, Czech Republic
| | - Sebastian Schafer
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London, SW7 2AZ, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield NHS Trust, London, SW3 6NP, UK
| | - Stuart A Cook
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK
- National Heart Centre Singapore, Singapore, 169609, Republic of Singapore
| | - Enrico Petretto
- Programme in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, 169857, Republic of Singapore.
- MRC London Institute of Medical Sciences (LMC), Imperial College, London, W12 0NN, UK.
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17
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Momeni-Moghaddam MA, Asadikaram G, Akbari H, Abolhassani M, Masoumi M, Nadimy Z, Khaksari M. CD36 gene polymorphism rs1761667 (G > A) is associated with hypertension and coronary artery disease in an Iranian population. BMC Cardiovasc Disord 2019; 19:140. [PMID: 31185924 PMCID: PMC6560776 DOI: 10.1186/s12872-019-1111-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 05/20/2019] [Indexed: 12/01/2022] Open
Abstract
Background CD36 is associated with regulation of lipid metabolism, atherosclerosis, and blood pressure. Moreover, its variation may be involved in the development of hypertension and/or coronary artery disease (CAD). The present study was conducted to investigate the possible association of CD36 rs1761667 (G > A) polymorphism with hypertension and/or CAD in the southeastern of Iran. Methods The present observational study was composed of 238 subjects who were admitted for coronary angiography, and divided into four groups: 1) hypertensive without CAD (H-Tens, n = 52); 2) hypertensive with CAD (CAD + H-Tens, n = 57); 3) CAD without hypertension (CAD, n = 65); and 4) non-hypertensive without CAD as the control group (Ctrl, n = 64). The CD36 rs1761667 polymorphism was genotyped with PCR-RFLP method. Association between CD36 rs1761667 genotypes and the risk of CAD and hypertension was assessed using multinomial regression by adjusting for age, sex, creatinine, fasting blood sugar (FBS), systolic blood pressure (SBP) and diastolic blood pressure (DBP). Results In the present study, minor allele (A) frequency was 0.36. The genotype, but not allele frequency of the CD36 rs1761667 was significantly different between the four study groups (p = 0.003). Furthermore, using a recessive inheritance model CD36 rs1761667 polymorphism was significantly associated with an increased risk of CAD with hypertension (OR = 5.677; 95% CI = 1.053–30.601; p = 0.043). However, using the dominant model of CD36 rs1761667 had a protective effect on H-Tens and CAD patients. Conclusion The present findings revealed an association between CD36 rs1761667 polymorphism and susceptibility to hypertension and/or CAD in a southeastern Iranian population.
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Affiliation(s)
- Mohammad Amin Momeni-Moghaddam
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran.,Department of Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Gholamreza Asadikaram
- Department of Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran. .,Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman, Iran.
| | - Hamed Akbari
- Department of Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran.,Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman, Iran
| | - Moslem Abolhassani
- Department of Biochemistry, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Masoumi
- Cardiovascular Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Zahra Nadimy
- Cardiovascular Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Khaksari
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
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18
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Cluster of differentiation 36 gene polymorphism (rs1761667) is associated with dietary MUFA intake and hypertension in a Japanese population. Br J Nutr 2019; 121:1215-1222. [PMID: 30924431 DOI: 10.1017/s0007114519000679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cluster of differentiation 36 (CD36) is a membrane receptor expressed on a wide variety of human cells. CD36 polymorphisms are reportedly associated with oral fat perception, dietary intake and metabolic disorders. The present study examined associations of two CD36 polymorphisms (rs1761667 and rs1527483) and dietary fat intake, and metabolic phenotypes in a Japanese population. This cross-sectional study was conducted based on clinical information collected from health check-ups in Japan (n 495). Dietary nutrient intake was estimated from a validated short FFQ and adjusted for total energy intake using the residual method. Mean blood pressure was calculated from systolic blood pressure (SBP) and diastolic blood pressure (DBP). Hypertension was defined as SBP ≥ 130 mmHg and/or DBP ≥ 85 mmHg, or use of antihypertensive drugs. Genotyping was performed using PCR with confronting two-pair primers method. Mean age was 63·4 (sd 9·9) years. Individuals with the AA genotype showed higher total fat and MUFA intake (standardised β = 0·110 and 0·087, P = 0·01 and 0·05, respectively) compared with the GG and GA genotypes. For metabolic phenotypes, the AA genotype of rs1761667 had a lower blood pressure compared with the GG genotype (standardised β = -0·123, P = 0·02). Our results suggested that the AA genotype of rs1761667 in the CD36 gene was associated with higher intake of total fat and MUFA and lower risk of hypertension in a Japanese population.
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19
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Fathi Dizaji B. The investigations of genetic determinants of the metabolic syndrome. Diabetes Metab Syndr 2018; 12:783-789. [PMID: 29673926 DOI: 10.1016/j.dsx.2018.04.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/09/2018] [Indexed: 11/17/2022]
Abstract
Metabolic syndrome is the aggregation of cardiovascular risk factors that increases the risk of type 2 diabetes and cardiovascular diseases. Family and twin studies, heritability spectrum for its components and different prevalence among ethnicities, have provided genetic susceptibility to the metabolic syndrome. The investigations of genetic base for the disorder have recognized numerous chromosomes, various DNA polymorphisms in candidate genes and many gene variants, that are associated with metabolic syndrome as an entity or its traits, which mostly are related to lipid metabolism. In addition, recent finding of the role of rare variants, epigenetic mechanisms, non-coding RNAs and evaluating the function of genes in molecular networks have improved our knowledge. However, a common genetic basis explaining the co-occurrence of its components has not been identified and more researches are essential.
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Affiliation(s)
- Behdokht Fathi Dizaji
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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20
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Changes in the activity of some metabolic enzymes in the heart of SHR rat incurred by transgenic expression of CD36. J Physiol Biochem 2018; 74:479-489. [PMID: 29916179 DOI: 10.1007/s13105-018-0641-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 06/12/2018] [Indexed: 01/12/2023]
Abstract
Hypertension, dyslipidemia, and insulin resistance in the spontaneously hypertensive rat (SHR) can be alleviated by rescuing CD36 fatty acid translocase. The present study investigated whether transgenic rescue of CD36 in SHR could affect mitochondrial function and activity of selected metabolic enzymes in the heart. These analyses were conducted on ventricular preparations derived from SHR and from transgenic strain SHR-Cd36 that expresses a functional wild-type CD36. Our respirometric measurements revealed that mitochondria isolated from the left ventricles exhibited two times higher respiratory activity than those isolated from the right ventricles. Whereas, we did not observe any significant changes in functioning of the mitochondrial respiratory system between both rat strains, enzyme activities of total hexokinase, and both mitochondrial and total malate dehydrogenase were markedly decreased in the left ventricles of transgenic rats, compared to SHR. We also detected downregulated expression of the succinate dehydrogenase subunit SdhB (complex II) and 70 kDa peroxisomal membrane protein in the left ventricles of SHR-Cd36. These data indicate that CD36 may affect in a unique fashion metabolic substrate flexibility of the left and right ventricles.
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21
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Teixeira SK, Pereira AC, Krieger JE. Genetics of Resistant Hypertension: the Missing Heritability and Opportunities. Curr Hypertens Rep 2018; 20:48. [PMID: 29779058 DOI: 10.1007/s11906-018-0852-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE OF THE REVIEW Blood pressure regulation in humans has long been known to be a genetically determined trait. The identification of causal genetic modulators for this trait has been unfulfilling at the least. Despite the recent advances of genome-wide genetic studies, loci associated with hypertension or blood pressure still explain a very low percentage of the overall variation of blood pressure in the general population. This has precluded the translation of discoveries in the genetics of human hypertension to clinical use. Here, we propose the combined use of resistant hypertension as a trait for mapping genetic determinants in humans and the integration of new large-scale technologies to approach in model systems the multidimensional nature of the problem. RECENT FINDINGS New large-scale efforts in the genetic and genomic arenas are paving the way for an increased and granular understanding of genetic determinants of hypertension. New technologies for whole genome sequence and large-scale forward genetic screens can help prioritize gene and gene-pathways for downstream characterization and large-scale population studies, and guided pharmacological design can be used to drive discoveries to the translational application through better risk stratification and new therapeutic approaches. Although significant challenges remain in the mapping and identification of genetic determinants of hypertension, new large-scale technological approaches have been proposed to surpass some of the shortcomings that have limited progress in the area for the last three decades. The incorporation of these technologies to hypertension research may significantly help in the understanding of inter-individual blood pressure variation and the deployment of new phenotyping and treatment approaches for the condition.
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Affiliation(s)
- Samantha K Teixeira
- Laboratorio de Genetica e Cardiologia Molecular, Faculdade Medicina da Universidade de São Paulo, Instituto do Coracao (InCor) HC.FMUSP, Av Dr Eneas C Aguiar 44, São Paulo, SP, 05403-000, Brazil
| | - Alexandre C Pereira
- Laboratorio de Genetica e Cardiologia Molecular, Faculdade Medicina da Universidade de São Paulo, Instituto do Coracao (InCor) HC.FMUSP, Av Dr Eneas C Aguiar 44, São Paulo, SP, 05403-000, Brazil
| | - Jose E Krieger
- Laboratorio de Genetica e Cardiologia Molecular, Faculdade Medicina da Universidade de São Paulo, Instituto do Coracao (InCor) HC.FMUSP, Av Dr Eneas C Aguiar 44, São Paulo, SP, 05403-000, Brazil.
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22
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Russo A, Di Gaetano C, Cugliari G, Matullo G. Advances in the Genetics of Hypertension: The Effect of Rare Variants. Int J Mol Sci 2018; 19:E688. [PMID: 29495593 PMCID: PMC5877549 DOI: 10.3390/ijms19030688] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/19/2018] [Accepted: 02/26/2018] [Indexed: 12/22/2022] Open
Abstract
Worldwide, hypertension still represents a serious health burden with nine million people dying as a consequence of hypertension-related complications. Essential hypertension is a complex trait supported by multifactorial genetic inheritance together with environmental factors. The heritability of blood pressure (BP) is estimated to be 30-50%. A great effort was made to find genetic variants affecting BP levels through Genome-Wide Association Studies (GWAS). This approach relies on the "common disease-common variant" hypothesis and led to the identification of multiple genetic variants which explain, in aggregate, only 2-3% of the genetic variance of hypertension. Part of the missing genetic information could be caused by variants too rare to be detected by GWAS. The use of exome chips and Next-Generation Sequencing facilitated the discovery of causative variants. Here, we report the advances in the detection of novel rare variants, genes, and/or pathways through the most promising approaches, and the recent statistical tests that have emerged to handle rare variants. We also discuss the need to further support rare novel variants with replication studies within larger consortia and with deeper functional studies to better understand how new genes might improve patient care and the stratification of the response to antihypertensive treatments.
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Affiliation(s)
- Alessia Russo
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy.
- Italian Institute for Genomic Medicine (IIGM, Formerly HuGeF), 10126 Turin, Italy.
| | - Cornelia Di Gaetano
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy.
- Italian Institute for Genomic Medicine (IIGM, Formerly HuGeF), 10126 Turin, Italy.
| | - Giovanni Cugliari
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy.
- Italian Institute for Genomic Medicine (IIGM, Formerly HuGeF), 10126 Turin, Italy.
| | - Giuseppe Matullo
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy.
- Italian Institute for Genomic Medicine (IIGM, Formerly HuGeF), 10126 Turin, Italy.
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23
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Pravenec M, Saba LM, Zídek V, Landa V, Mlejnek P, Šilhavý J, Šimáková M, Strnad H, Trnovská J, Škop V, Hüttl M, Marková I, Oliyarnyk O, Malínská H, Kazdová L, Smith H, Tabakoff B. Systems genetic analysis of brown adipose tissue function. Physiol Genomics 2017; 50:52-66. [PMID: 29127223 DOI: 10.1152/physiolgenomics.00091.2017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Brown adipose tissue (BAT) has been suggested to play an important role in lipid and glucose metabolism in rodents and possibly also in humans. In the current study, we used genetic and correlation analyses in the BXH/HXB recombinant inbred (RI) strains, derived from Brown Norway (BN) and spontaneously hypertensive rats (SHR), to identify genetic determinants of BAT function. Linkage analyses revealed a quantitative trait locus (QTL) associated with interscapular BAT mass on chromosome 4 and two closely linked QTLs associated with glucose oxidation and glucose incorporation into BAT lipids on chromosome 2. Using weighted gene coexpression network analysis (WGCNA) we identified 1,147 gene coexpression modules in the BAT from BXH/HXB rats and mapped their module eigengene QTLs. Through an unsupervised analysis, we identified modules related to BAT relative mass and function. The Coral4.1 coexpression module is associated with BAT relative mass (includes Cd36 highly connected gene), and the Darkseagreen coexpression module is associated with glucose incorporation into BAT lipids (includes Hiat1, Fmo5, and Sort1 highly connected transcripts). Because multiple statistical criteria were used to identify candidate modules, significance thresholds for individual tests were not adjusted for multiple comparisons across modules. In summary, a systems genetic analysis using genomic and quantitative transcriptomic and physiological information has produced confirmation of several known genetic factors and significant insight into novel genetic components functioning in BAT and possibly contributing to traits characteristic of the metabolic syndrome.
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Affiliation(s)
- Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences , Prague , Czech Republic
| | - Laura M Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus , Aurora, Colorado
| | - Václav Zídek
- Institute of Physiology of the Czech Academy of Sciences , Prague , Czech Republic
| | - Vladimír Landa
- Institute of Physiology of the Czech Academy of Sciences , Prague , Czech Republic
| | - Petr Mlejnek
- Institute of Physiology of the Czech Academy of Sciences , Prague , Czech Republic
| | - Jan Šilhavý
- Institute of Physiology of the Czech Academy of Sciences , Prague , Czech Republic
| | - Miroslava Šimáková
- Institute of Physiology of the Czech Academy of Sciences , Prague , Czech Republic
| | - Hynek Strnad
- Institute of Molecular Genetics of the Czech Academy of Sciences , Prague , Czech Republic
| | - Jaroslava Trnovská
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Vojtěch Škop
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Martina Hüttl
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Irena Marková
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Olena Oliyarnyk
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Hana Malínská
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Ludmila Kazdová
- Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Harry Smith
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus , Aurora, Colorado.,Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus , Aurora, Colorado
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus , Aurora, Colorado
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24
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Padmanabhan S, Joe B. Towards Precision Medicine for Hypertension: A Review of Genomic, Epigenomic, and Microbiomic Effects on Blood Pressure in Experimental Rat Models and Humans. Physiol Rev 2017; 97:1469-1528. [PMID: 28931564 PMCID: PMC6347103 DOI: 10.1152/physrev.00035.2016] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 04/28/2017] [Accepted: 04/29/2017] [Indexed: 12/11/2022] Open
Abstract
Compelling evidence for the inherited nature of essential hypertension has led to extensive research in rats and humans. Rats have served as the primary model for research on the genetics of hypertension resulting in identification of genomic regions that are causally associated with hypertension. In more recent times, genome-wide studies in humans have also begun to improve our understanding of the inheritance of polygenic forms of hypertension. Based on the chronological progression of research into the genetics of hypertension as the "structural backbone," this review catalogs and discusses the rat and human genetic elements mapped and implicated in blood pressure regulation. Furthermore, the knowledge gained from these genetic studies that provide evidence to suggest that much of the genetic influence on hypertension residing within noncoding elements of our DNA and operating through pervasive epistasis or gene-gene interactions is highlighted. Lastly, perspectives on current thinking that the more complex "triad" of the genome, epigenome, and the microbiome operating to influence the inheritance of hypertension, is documented. Overall, the collective knowledge gained from rats and humans is disappointing in the sense that major hypertension-causing genes as targets for clinical management of essential hypertension may not be a clinical reality. On the other hand, the realization that the polygenic nature of hypertension prevents any single locus from being a relevant clinical target for all humans directs future studies on the genetics of hypertension towards an individualized genomic approach.
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Affiliation(s)
- Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; and Center for Hypertension and Personalized Medicine; Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Bina Joe
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; and Center for Hypertension and Personalized Medicine; Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
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25
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Doris PA. Genetics of hypertension: an assessment of progress in the spontaneously hypertensive rat. Physiol Genomics 2017; 49:601-617. [PMID: 28916635 DOI: 10.1152/physiolgenomics.00065.2017] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The application of gene mapping methods to uncover the genetic basis of hypertension in the inbred spontaneously hypertensive rat (SHR) began over 25 yr ago. This animal provides a useful model of genetic high blood pressure, and some of its features are described. In particular, it appears to be a polygenic model of disease, and polygenes participate in human hypertension genetic risk. The SHR hypertension alleles were fixed rapidly by selective breeding in just a few generations and so are presumably common genetic variants present in the outbred Wistar strain from which SHR was created. This review provides a background to the origins and genesis of this rat line. It considers its usefulness as a model organism for a common cardiovascular disease. The progress and obstacles facing mapping are considered in depth, as are the emergence and application of other genome-wide genetic discovery approaches that have been applied to investigate this model. Candidate genes, their identification, and the evidence to support their potential role in blood pressure elevation are considered. The review assesses the progress that has arisen from this work has been limited. Consideration is given to some of the factors that have impeded progress, and prospects for advancing understanding of the genetic basis of hypertension in this model are discussed.
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Affiliation(s)
- Peter A Doris
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center, Houston, Texas
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26
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Seidel E, Scholl UI. Genetic mechanisms of human hypertension and their implications for blood pressure physiology. Physiol Genomics 2017; 49:630-652. [PMID: 28887369 DOI: 10.1152/physiolgenomics.00032.2017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Hypertension, or elevated blood pressure, constitutes a major public health burden that affects more than 1 billion people worldwide and contributes to ~9 million deaths annually. Hereditary factors are thought to contribute to up to 50% of interindividual blood pressure variability. Blood pressure in the general population approximately shows a normal distribution and is thought to be a polygenic trait. In rare cases, early-onset hypertension or hypotension are inherited as Mendelian traits. The identification of the underlying Mendelian genes and variants has contributed to our understanding of the physiology of blood pressure regulation, emphasizing renal salt handling and the renin angiotensin aldosterone system as players in the determination of blood pressure. Genome-wide association studies (GWAS) have revealed more than 100 variants that are associated with blood pressure, typically with small effect sizes, which cumulatively explain ~3.5% of blood pressure trait variability. Several GWAS associations point to a role of the vasculature in the pathogenesis of hypertension. Despite these advances, the majority of the genetic contributors to blood pressure regulation are currently unknown; whether large-scale exome or genome sequencing studies will unravel these factors remains to be determined.
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Affiliation(s)
- Eric Seidel
- Department of Nephrology, Medical School, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ute I Scholl
- Department of Nephrology, Medical School, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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27
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CD36 Gene Polymorphisms Are Associated with Intracerebral Hemorrhage Susceptibility in a Han Chinese Population. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5352071. [PMID: 28804718 PMCID: PMC5540265 DOI: 10.1155/2017/5352071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/12/2017] [Indexed: 12/20/2022]
Abstract
The CD36 gene encodes a membrane glycoprotein (type B scavenger receptor, SR-B2) that plays a crucial role in lipid sensing, innate immunity, atherogenesis, and glycolipid metabolism. In this study, we aimed to investigate the association between CD36 gene polymorphisms and intracerebral hemorrhage (ICH) in a Han Chinese population. We performed genotype and allele analyses for eleven single nucleotide polymorphisms (SNPs) of CD36 in a case-controlled study involving 292 ICH patients and 298 control participants. Eleven SNPs were genotyped by the Improved Multiple Ligase Detection Reaction (iMLDR) method. The results indicated that the SNP rs1194182 values were significantly different between ICH group and control group in a dominant model after adjusting for confounding factors. The subgroup analysis conducted for rs1194182 showed that the allele G frequencies were significantly different between ICH patients and controls in hypertension group via a dominant model. We then analyzed the rs1194182 genotype distributions among different groups of the serum lipid groups, including BMI, TC, TG, HDL, and LDL. However, no significant differences were found in the analysis of other subgroups. Taken together, these findings indicate that rs1194182 polymorphism in the CD36 gene was associated with ICH, and genotype GG could be an independent predictor.
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28
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Coan PM, Hummel O, Garcia Diaz A, Barrier M, Alfazema N, Norsworthy PJ, Pravenec M, Petretto E, Hübner N, Aitman TJ. Genetic, physiological and comparative genomic studies of hypertension and insulin resistance in the spontaneously hypertensive rat. Dis Model Mech 2017; 10:297-306. [PMID: 28130354 PMCID: PMC5374317 DOI: 10.1242/dmm.026716] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 01/23/2017] [Indexed: 12/18/2022] Open
Abstract
We previously mapped hypertension-related insulin resistance quantitative trait loci (QTLs) to rat chromosomes 4, 12 and 16 using adipocytes from F2 crosses between spontaneously hypertensive (SHR) and Wistar Kyoto (WKY) rats, and subsequently identified Cd36 as the gene underlying the chromosome 4 locus. The identity of the chromosome 12 and 16 genes remains unknown. To identify whole-body phenotypes associated with the chromosome 12 and 16 linkage regions, we generated and characterised new congenic strains, with WKY donor segments introgressed onto an SHR genetic background, for the chromosome 12 and 16 linkage regions. We found a >50% increase in insulin sensitivity in both the chromosome 12 and 16 strains. Blood pressure and left ventricular mass were reduced in the two congenic strains consistent with the congenic segments harbouring SHR genes for insulin resistance, hypertension and cardiac hypertrophy. Integrated genomic analysis, using physiological and whole-genome sequence data across 42 rat strains, identified variants within the congenic regions in Upk3bl, RGD1565131 and AABR06087018.1 that were associated with blood pressure, cardiac mass and insulin sensitivity. Quantitative trait transcript analysis across 29 recombinant inbred strains showed correlation between expression of Hspb1, Zkscan5 and Pdgfrl with adipocyte volume, systolic blood pressure and cardiac mass, respectively. Comparative genome analysis showed a marked enrichment of orthologues for human GWAS-associated genes for insulin resistance within the syntenic regions of both the chromosome 12 and 16 congenic intervals. Our study defines whole-body phenotypes associated with the SHR chromosome 12 and 16 insulin-resistance QTLs, identifies candidate genes for these SHR QTLs and finds human orthologues of rat genes in these regions that associate with related human traits. Further study of these genes in the congenic strains will lead to robust identification of the underlying genes and cellular mechanisms. Summary: Comparative genome analyses identify candidate genes for hypertension and insulin resistance on rat chromosomes 12 and 16, and marked enrichment of insulin resistance genes in the syntenic regions of the human genome.
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Affiliation(s)
- Philip M Coan
- Centre for Genomic and Experimental Medicine & Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Oliver Hummel
- Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Ana Garcia Diaz
- Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Marjorie Barrier
- Centre for Genomic and Experimental Medicine & Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Neza Alfazema
- Centre for Genomic and Experimental Medicine & Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Penny J Norsworthy
- MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | - Michal Pravenec
- Department of Model Diseases, Institute of Physiology, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Enrico Petretto
- MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK.,Duke-NUS Medical School, Singapore 169857, Republic of Singapore
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site, 13316 Berlin, Germany.,Charité-Universitätsmedizin, 10117 Berlin, Germany
| | - Timothy J Aitman
- Centre for Genomic and Experimental Medicine & Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH4 2XU, UK.,Department of Medicine, Imperial College London, London SW7 2AZ, UK
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29
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Maatz H, van Heesch S, Kreuchwig F, Faber A, Adami E, Hubner N, Heinig M. Epigenetics and Control of RNAs. Methods Mol Biol 2017; 1488:217-237. [PMID: 27933526 DOI: 10.1007/978-1-4939-6427-7_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Histone modifications are epigenetic marks that fundamentally impact the regulation of gene expression. Integrating histone modification information in the analysis of gene expression traits (eQTL mapping) has been shown to significantly enhance the prediction of eQTLs. In this chapter, we describe (1) how to perform quantitative trait locus (QTL) analysis using histone modification levels as traits and (2) how to integrate these data with information on RNA expression for the elucidation of the epigenetic control of transcript levels. We will provide a comprehensive introduction into the topic, describe in detail how ChIP-seq data are analyzed and elaborate on how to integrate ChIP-seq and RNA-seq data from a segregating disease animal model for the identification of the epigenetic control of RNA expression.
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Affiliation(s)
- Henrike Maatz
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125, Berlin, Germany
| | | | | | - Allison Faber
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125, Berlin, Germany
| | - Eleonora Adami
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125, Berlin, Germany
| | - Norbert Hubner
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site, 13347, Berlin, Germany.
- Charité-Universitätsmedizin, 10117, Berlin, Germany.
| | - Matthias Heinig
- Helmholtz Zentrum München, Institute of Computational Biology (ICB), Neuherberg, 85764, Germany.
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Moreno-Moral A, Petretto E. From integrative genomics to systems genetics in the rat to link genotypes to phenotypes. Dis Model Mech 2016; 9:1097-1110. [PMID: 27736746 PMCID: PMC5087832 DOI: 10.1242/dmm.026104] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Complementary to traditional gene mapping approaches used to identify the hereditary components of complex diseases, integrative genomics and systems genetics have emerged as powerful strategies to decipher the key genetic drivers of molecular pathways that underlie disease. Broadly speaking, integrative genomics aims to link cellular-level traits (such as mRNA expression) to the genome to identify their genetic determinants. With the characterization of several cellular-level traits within the same system, the integrative genomics approach evolved into a more comprehensive study design, called systems genetics, which aims to unravel the complex biological networks and pathways involved in disease, and in turn map their genetic control points. The first fully integrated systems genetics study was carried out in rats, and the results, which revealed conserved trans-acting genetic regulation of a pro-inflammatory network relevant to type 1 diabetes, were translated to humans. Many studies using different organisms subsequently stemmed from this example. The aim of this Review is to describe the most recent advances in the fields of integrative genomics and systems genetics applied in the rat, with a focus on studies of complex diseases ranging from inflammatory to cardiometabolic disorders. We aim to provide the genetics community with a comprehensive insight into how the systems genetics approach came to life, starting from the first integrative genomics strategies [such as expression quantitative trait loci (eQTLs) mapping] and concluding with the most sophisticated gene network-based analyses in multiple systems and disease states. Although not limited to studies that have been directly translated to humans, we will focus particularly on the successful investigations in the rat that have led to primary discoveries of genes and pathways relevant to human disease.
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Affiliation(s)
- Aida Moreno-Moral
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore (NUS) Medical School, Singapore
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31
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Yokoi H, Yanagita M. Targeting the fatty acid transport protein CD36, a class B scavenger receptor, in the treatment of renal disease. Kidney Int 2016; 89:740-2. [PMID: 26994570 DOI: 10.1016/j.kint.2016.01.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 01/10/2016] [Accepted: 01/13/2016] [Indexed: 10/22/2022]
Abstract
Augmentation of the CD36 pathway, which involves the uptake of several endogenous ligands including free fatty acids and oxidized low-density lipoprotein, contributes to the damage of proximal tubules and podocytes, whereas ablation of CD36 attenuates renal injury. Souza et al. demonstrate that 5A peptide can inhibit CD36 signaling, attenuate chronic kidney disease progression, and ameliorate inflammation and tubulointerstitial fibrosis by reducing the expression of inflammatory cytokines and chemokines, suggesting the therapeutic potential of 5A peptide against CD36-mediated renal injury.
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Affiliation(s)
- Hideki Yokoi
- Department of Nephrology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Motoko Yanagita
- Department of Nephrology, Kyoto University Graduate School of Medicine, Kyoto, Japan.
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32
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Jayewardene AF, Mavros Y, Gwinn T, Hancock DP, Rooney KB. Associations between CD36 gene polymorphisms and metabolic response to a short-term endurance-training program in a young-adult population. Appl Physiol Nutr Metab 2016; 41:157-67. [PMID: 26830498 DOI: 10.1139/apnm-2015-0430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent studies have shown that CD36 gene variants are associated with an increased prevalence of chronic disease. Although a genetic component to trainability has been proven, no data are available specifically on the influence of CD36 on training response. Two single nucleotide polymorphisms (SNPs) (rs1527479 and rs1984112) were assessed for associations with whole-body substrate oxidation, response to a 75-g dextrose oral glucose tolerance test, fasting plasma lipids, and cardiovascular disease risk factors in a young healthy cohort, both using cross-sectional analysis and following a 4-week endurance-exercise training program. Genotyping was performed using real-time polymerase chain reaction. Cross-sectional data were collected in 34 individuals (age, 22.7 ± 3.5 years), with 17 completing the training program. At baseline, TT SNP carriers at rs1527479 and wild-type GG carriers at rs1984112 were associated with significantly greater whole-body rate of fat oxidation (Fatox) during submaximal exercise (P < 0.05), whilst AA carriers at the same position were associated with elevated triglyceride (TG) levels. A significant genotype × time interaction in Fatox at SNP rs1984112 was identified at rest. Significant genotype × time interactions were present at rs1527479, with TT carriers exhibiting a favourable response to training when compared with C-allele carriers for fasting TG, diastolic blood pressure (DBP), and mean arterial pressure (MAP). In conclusion, cross-sectional assessment identified associations with Fatox and TG. Training response at both SNPs identified "at-risk" genotypes responding favourably to the training stimulus in Fatox, TG, DBP, and MAP. Although these data show potential pleiotropic influence of CD36 SNPs, assessment in a larger cohort is warranted.
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Affiliation(s)
- Avindra F Jayewardene
- a Exercise Health and Performance Faculty Research Group, Faculty of Health Sciences, University of Sydney, Lidcombe, NSW, Australia
| | - Yorgi Mavros
- a Exercise Health and Performance Faculty Research Group, Faculty of Health Sciences, University of Sydney, Lidcombe, NSW, Australia
| | - Tom Gwinn
- a Exercise Health and Performance Faculty Research Group, Faculty of Health Sciences, University of Sydney, Lidcombe, NSW, Australia
| | - Dale P Hancock
- b School of Molecular Biosciences, Faculty of Science, University of Sydney, Camperdown, NSW, Australia
| | - Kieron B Rooney
- a Exercise Health and Performance Faculty Research Group, Faculty of Health Sciences, University of Sydney, Lidcombe, NSW, Australia
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Garcia Diaz AI, Moyon B, Coan PM, Alfazema N, Venda L, Woollard K, Aitman T. New Wistar Kyoto and spontaneously hypertensive rat transgenic models with ubiquitous expression of green fluorescent protein. Dis Model Mech 2016; 9:463-71. [PMID: 26769799 PMCID: PMC4852507 DOI: 10.1242/dmm.024208] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/13/2016] [Indexed: 11/20/2022] Open
Abstract
The Wistar Kyoto (WKY) rat and the spontaneously hypertensive (SHR) rat inbred strains are well-established models for human crescentic glomerulonephritis (CRGN) and metabolic syndrome, respectively. Novel transgenic (Tg) strains add research opportunities and increase scientific value to well-established rat models. We have created two novel Tg strains using Sleeping Beauty transposon germline transgenesis, ubiquitously expressing green fluorescent protein (GFP) under the rat elongation factor 1 alpha (EF1a) promoter on the WKY and SHR genetic backgrounds. The Sleeping Beauty system functioned with high transgenesis efficiency; 75% of new rats born after embryo microinjections were transgene positive. By ligation-mediated PCR, we located the genome integration sites, confirming no exonic disruption and defining a single or low copy number of the transgenes in the new WKY-GFP and SHR-GFP Tg lines. We report GFP-bright expression in embryos, tissues and organs in both lines and show preliminaryin vitroandin vivoimaging data that demonstrate the utility of the new GFP-expressing lines for adoptive transfer, transplantation and fate mapping studies of CRGN, metabolic syndrome and other traits for which these strains have been extensively studied over the past four decades.
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Affiliation(s)
- Ana Isabel Garcia Diaz
- Division of Immunology and Inflammation, Imperial College London, London W2 1PG, UK MRC Clinical Sciences Centre and Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Ben Moyon
- Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | - Philip M Coan
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Neza Alfazema
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Lara Venda
- MRC Clinical Sciences Centre and Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Kevin Woollard
- Division of Immunology and Inflammation, Imperial College London, London W2 1PG, UK
| | - Tim Aitman
- MRC Clinical Sciences Centre and Department of Medicine, Imperial College London, London W12 0NN, UK Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
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Translational regulation shapes the molecular landscape of complex disease phenotypes. Nat Commun 2015; 6:7200. [PMID: 26007203 PMCID: PMC4455061 DOI: 10.1038/ncomms8200] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/17/2015] [Indexed: 01/05/2023] Open
Abstract
The extent of translational control of gene expression in mammalian tissues remains largely unknown. Here we perform genome-wide RNA sequencing and ribosome profiling in heart and liver tissues to investigate strain-specific translational regulation in the spontaneously hypertensive rat (SHR/Ola). For the most part, transcriptional variation is equally apparent at the translational level and there is limited evidence of translational buffering. Remarkably, we observe hundreds of strain-specific differences in translation, almost doubling the number of differentially expressed genes. The integration of genetic, transcriptional and translational data sets reveals distinct signatures in 3'UTR variation, RNA-binding protein motifs and miRNA expression associated with translational regulation of gene expression. We show that a large number of genes associated with heart and liver traits in human genome-wide association studies are primarily translationally regulated. Capturing interindividual differences in the translated genome will lead to new insights into the genes and regulatory pathways underlying disease phenotypes.
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Olejníková L, Polidarová L, Paušlyová L, Sládek M, Sumová A. Diverse development and higher sensitivity of the circadian clocks to changes in maternal-feeding regime in a rat model of cardio-metabolic disease. Chronobiol Int 2015; 32:531-47. [DOI: 10.3109/07420528.2015.1014095] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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36
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37
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Li Q, Cai H. ANO1 taking center stage: blood pressure regulation in SHRs. J Mol Cell Cardiol 2015; 82:216-7. [PMID: 25817885 DOI: 10.1016/j.yjmcc.2015.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 03/18/2015] [Indexed: 11/26/2022]
Affiliation(s)
- Qiang Li
- Divisions of Molecular Medicine and Cardiology, Departments of Anesthesiology and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California Los Angeles, 650 Charles E. Young Drive, Los Angeles, CA 90095, USA
| | - Hua Cai
- Divisions of Molecular Medicine and Cardiology, Departments of Anesthesiology and Medicine, Cardiovascular Research Laboratories, David Geffen School of Medicine at University of California Los Angeles, 650 Charles E. Young Drive, Los Angeles, CA 90095, USA.
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38
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Mell B, Jala VR, Mathew AV, Byun J, Waghulde H, Zhang Y, Haribabu B, Vijay-Kumar M, Pennathur S, Joe B. Evidence for a link between gut microbiota and hypertension in the Dahl rat. Physiol Genomics 2015; 47:187-97. [PMID: 25829393 DOI: 10.1152/physiolgenomics.00136.2014] [Citation(s) in RCA: 282] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/26/2015] [Indexed: 12/20/2022] Open
Abstract
The gut microbiota plays a critical role in maintaining physiological homeostasis. This study was designed to evaluate whether gut microbial composition affects hypertension. 16S rRNA genes obtained from cecal samples of Dahl salt-sensitive (S) and Dahl salt-resistant (R) rats were sequenced. Bacteria of the phylum Bacteroidetes were higher in the S rats compared with the R rats. Furthermore, the family S24-7 of the phylum Bacteroidetes and the family Veillonellaceae of the phylum Firmicutes were higher in the S rats compared with the R rats. Analyses of the various phylogenetic groups of cecal microbiota revealed significant differences between S and R rats. Both strains were maintained on a high-salt diet, administered antibiotics for ablation of microbiota, transplanted with S or R rat cecal contents, and monitored for blood pressure (BP). Systolic BP of the R rats remained unaltered irrespective of S or R rat cecal transplantation. Surprisingly, compared with the S rats given S rat cecal content, systolic BP of the S rats given a single bolus of cecal content from R rats was consistently and significantly elevated during the rest of their life, and they had a shorter lifespan. A lower level of fecal bacteria of the family Veillonellaceae and increased plasma acetate and heptanoate were features associated with the increased BP observed in the S rats given R rat microbiota compared with the S rats given S rat microbiota. These data demonstrate a link between microbial content and BP regulation and, because the S and R rats differ in their genomic composition, provide the necessary basis to further examine the relationship between the host genome and microbiome in the context of BP regulation in the Dahl rats.
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Affiliation(s)
- Blair Mell
- Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Venkatakrishna R Jala
- James Graham Brown Cancer Center, Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky
| | - Anna V Mathew
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, Michigan; and
| | - Jaeman Byun
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, Michigan; and
| | - Harshal Waghulde
- Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Youjie Zhang
- Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Bodduluri Haribabu
- James Graham Brown Cancer Center, Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky
| | - Matam Vijay-Kumar
- Department of Nutritional Sciences and Medicine, The Pennsylvania State University, University Park, Pennsylvania
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Medical School, Ann Arbor, Michigan; and
| | - Bina Joe
- Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio;
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Morris BJ. Renin, genes, microRNAs, and renal mechanisms involved in hypertension. Hypertension 2015; 65:956-62. [PMID: 25601934 DOI: 10.1161/hypertensionaha.114.04366] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 12/23/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Brian J Morris
- From the Basic & Clinical Genomics Laboratory, School of Medical Sciences and Bosch Institute, The University of Sydney, Sydney, New South Wales, Australia.
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40
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Scott-Boyer MP, Praktiknjo SD, Llamas B, Picard S, Deschepper CF. Dual Linkage of a Locus to Left Ventricular Mass and a Cardiac Gene Co-Expression Network Driven by a Chromosome Domain. Front Cardiovasc Med 2014; 1:11. [PMID: 26664861 PMCID: PMC4668859 DOI: 10.3389/fcvm.2014.00011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/27/2014] [Indexed: 12/22/2022] Open
Abstract
We have previously reported Lvm1 as a quantitative trait locus (QTL) on chromosome 13 that links to cardiac left ventricular mass (LVM) in a panel of AxB/BxA mouse recombinant inbred strains (RIS). When performing a gene expression QTL (eQTL) analysis, we detected 33 cis-eQTLs that correlated with LVM. Among the latter, a group of eight cis-eQTLs clustered in a genomic region smaller than 6 Mb and surrounding the Lvm1 peak on chr13. Co-variant analysis indicated that all eight genes correlated with the phenotype in a causal rather than a reactive fashion, a finding that (despite its functional interest) did not provide grounds to prioritize any of these candidate genes. As a complementary approach, we performed weighted gene co-expression network analysis, which allowed us to detect 49 modules of highly connected genes. The module that correlated best with LVM: (1) showed linkage to a module QTL whose boundaries matched closely those of the phenotypic Lvm1 QTL on chr13; (2) harbored a disproportionately high proportion of genes originating from a small genomic region on chromosome 13 (including the 8 previously detected cis-eQTL genes); (3) contained genes that, beyond their individual level of expression, correlated with LVM as a function of their inter-connectivity; and (4) showed increased abundance of polymorphic insertion–deletion elements in the same region. Taken together, these data suggest that a domain on chromosome 13 constitutes the biologic principle responsible for the organization and linkage of the gene co-expression module, and indicate a mechanism whereby genetic variants within chromosome domains may associate to phenotypic changes via coordinate changes in the expression of several genes. One other possible implication of these findings is that candidate genes to consider as contributors to a particular phenotype should extend further than those that are closest to the QTL peak.
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Affiliation(s)
- Marie-Pier Scott-Boyer
- Cardiovascular Biology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Université de Montréal , Montréal, QC , Canada
| | - Samantha D Praktiknjo
- Cardiovascular Biology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Université de Montréal , Montréal, QC , Canada
| | - Bastien Llamas
- Cardiovascular Biology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Université de Montréal , Montréal, QC , Canada
| | - Sylvie Picard
- Cardiovascular Biology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Université de Montréal , Montréal, QC , Canada
| | - Christian F Deschepper
- Cardiovascular Biology Research Unit, Institut de recherches cliniques de Montréal (IRCM), Université de Montréal , Montréal, QC , Canada
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41
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Johnson MD, Mueller M, Adamowicz-Brice M, Collins MJ, Gellert P, Maratou K, Srivastava PK, Rotival M, Butt S, Game L, Atanur SS, Silver N, Norsworthy PJ, Langley SR, Petretto E, Pravenec M, Aitman TJ. Genetic analysis of the cardiac methylome at single nucleotide resolution in a model of human cardiovascular disease. PLoS Genet 2014; 10:e1004813. [PMID: 25474312 PMCID: PMC4256262 DOI: 10.1371/journal.pgen.1004813] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 10/09/2014] [Indexed: 12/03/2022] Open
Abstract
Epigenetic marks such as cytosine methylation are important determinants of cellular and whole-body phenotypes. However, the extent of, and reasons for inter-individual differences in cytosine methylation, and their association with phenotypic variation are poorly characterised. Here we present the first genome-wide study of cytosine methylation at single-nucleotide resolution in an animal model of human disease. We used whole-genome bisulfite sequencing in the spontaneously hypertensive rat (SHR), a model of cardiovascular disease, and the Brown Norway (BN) control strain, to define the genetic architecture of cytosine methylation in the mammalian heart and to test for association between methylation and pathophysiological phenotypes. Analysis of 10.6 million CpG dinucleotides identified 77,088 CpGs that were differentially methylated between the strains. In F1 hybrids we found 38,152 CpGs showing allele-specific methylation and 145 regions with parent-of-origin effects on methylation. Cis-linkage explained almost 60% of inter-strain variation in methylation at a subset of loci tested for linkage in a panel of recombinant inbred (RI) strains. Methylation analysis in isolated cardiomyocytes showed that in the majority of cases methylation differences in cardiomyocytes and non-cardiomyocytes were strain-dependent, confirming a strong genetic component for cytosine methylation. We observed preferential nucleotide usage associated with increased and decreased methylation that is remarkably conserved across species, suggesting a common mechanism for germline control of inter-individual variation in CpG methylation. In the RI strain panel, we found significant correlation of CpG methylation and levels of serum chromogranin B (CgB), a proposed biomarker of heart failure, which is evidence for a link between germline DNA sequence variation, CpG methylation differences and pathophysiological phenotypes in the SHR strain. Together, these results will stimulate further investigation of the molecular basis of locally regulated variation in CpG methylation and provide a starting point for understanding the relationship between the genetic control of CpG methylation and disease phenotypes. Epigenetic marks provide information that is not encoded in the primary DNA sequence itself but in modifications of genomic DNA and of the associated proteins. Methylation of genomic DNA at cytosine residues is an important epigenetic modification that is associated with developmental processes, carcinogenesis and other diseases. Genome-wide extent of, and reasons for inter-individual differences in cytosine methylation, and their association with phenotypic variation are poorly characterised. To address these questions we have determined and compared the genome-wide methylation patterns in heart tissue of two inbred rat strains, the spontaneously hypertensive rat, an animal model of human disease and a control rat strain. Comparison of methylation differences between genetically identical animals from the same strain and differences between animals from different strains allowed us to quantify association of epigenetic and genetic differences. We show that differences in an individual's germline DNA sequence are important determinants of the variability in methylation between individuals. Comparison with previous reports implicates common mechanisms for regulation of cytosine methylation that are highly conserved across species. Finally, we find correlation between a proposed blood biomarker for heart failure and variation in DNA methylation, suggesting a link between germline DNA sequence variation, methylation and a disease-related phenotype.
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Affiliation(s)
- Michelle D. Johnson
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Michael Mueller
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Martyna Adamowicz-Brice
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Melissa J. Collins
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Pascal Gellert
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- Institute of Clinical Sciences, Imperial College, London, United Kingdom
| | - Klio Maratou
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- Institute of Clinical Sciences, Imperial College, London, United Kingdom
| | - Prashant K. Srivastava
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
| | - Maxime Rotival
- Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
| | - Shahena Butt
- Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
| | - Laurence Game
- Genomics Core Laboratory, MRC Clinical Sciences Centre, London, United Kingdom
| | - Santosh S. Atanur
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Nicholas Silver
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Penny J. Norsworthy
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
| | - Sarah R. Langley
- Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
| | - Enrico Petretto
- Integrative Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
| | - Michal Pravenec
- Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Prague, Czech Republic
| | - Timothy J. Aitman
- Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, London, United Kingdom
- Institute of Clinical Sciences, Imperial College, London, United Kingdom
- * E-mail:
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42
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Rintisch C, Heinig M, Bauerfeind A, Schafer S, Mieth C, Patone G, Hummel O, Chen W, Cook S, Cuppen E, Colomé-Tatché M, Johannes F, Jansen RC, Neil H, Werner M, Pravenec M, Vingron M, Hubner N. Natural variation of histone modification and its impact on gene expression in the rat genome. Genome Res 2014; 24:942-53. [PMID: 24793478 PMCID: PMC4032858 DOI: 10.1101/gr.169029.113] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Histone modifications are epigenetic marks that play fundamental roles in many biological processes including the control of chromatin-mediated regulation of gene expression. Little is known about interindividual variability of histone modification levels across the genome and to what extent they are influenced by genetic variation. We annotated the rat genome with histone modification maps, identified differences in histone trimethyl-lysine levels among strains, and described their underlying genetic basis at the genome-wide scale using ChIP-seq in heart and liver tissues in a panel of rat recombinant inbred and their progenitor strains. We identified extensive variation of histone methylation levels among individuals and mapped hundreds of underlying cis- and trans-acting loci throughout the genome that regulate histone methylation levels in an allele-specific manner. Interestingly, most histone methylation level variation was trans-linked and the most prominent QTL identified influenced H3K4me3 levels at 899 putative promoters throughout the genome in the heart. Cis- acting variation was enriched in binding sites of distinct transcription factors in heart and liver. The integrated analysis of DNA variation together with histone methylation and gene expression levels showed that histoneQTLs are an important predictor of gene expression and that a joint analysis significantly enhanced the prediction of gene expression traits (eQTLs). Our data suggest that genetic variation has a widespread impact on histone trimethylation marks that may help to uncover novel genotype-phenotype relationships.
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Affiliation(s)
- Carola Rintisch
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Matthias Heinig
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany; Department of Computational Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Anja Bauerfeind
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Sebastian Schafer
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Christin Mieth
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Giannino Patone
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Oliver Hummel
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Wei Chen
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany
| | - Stuart Cook
- National Heart and Lung Institute, Cardiovascular Genetics and Genomics, London, SW3 6NP, United Kingdom; Duke-NUS Graduate Medical School, 169857 Singapore; National Heart Center Singapore, 169609 Singapore
| | - Edwin Cuppen
- Center for Molecular Medicine, University Medical Center Utrecht, Hubrecht Institute KNAW, 3584 CT Utrecht, The Netherlands
| | - Maria Colomé-Tatché
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, NL-9713 AV Groningen, The Netherlands
| | - Frank Johannes
- Groningen Bioinformatics Centre (GBIC), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), 9747AG Groningen, The Netherlands
| | - Ritsert C Jansen
- Groningen Bioinformatics Centre (GBIC), Groningen Biomolecular Sciences and Biotechnology Institute (GBB), 9747AG Groningen, The Netherlands
| | - Helen Neil
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), iBiTec-S, Université Paris-Sud, CNRS FRE3377, F-91191 Gif-sur-Yvette cedex, France
| | - Michel Werner
- Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), iBiTec-S, Université Paris-Sud, CNRS FRE3377, F-91191 Gif-sur-Yvette cedex, France
| | - Michal Pravenec
- Institut of Physiology, Academy of Sciences of the Czech Republic, Videnska 1083, CZ-14220 Prague 4, Czech Republic
| | - Martin Vingron
- Department of Computational Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Norbert Hubner
- Max-Delbrück-Center for Molecular Medicine (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner site Berlin, 13125 Berlin, Germany
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43
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PRAVENEC M, KŘEN V, LANDA V, MLEJNEK P, MUSILOVÁ A, ŠILHAVÝ J, ŠIMÁKOVÁ M, ZÍDEK V. Recent Progress in the Genetics of Spontaneously Hypertensive Rats. Physiol Res 2014; 63:S1-8. [DOI: 10.33549/physiolres.932622] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The spontaneously hypertensive rat (SHR) is the most widely used animal model of essential hypertension and accompanying metabolic disturbances. Recent advances in sequencing of genomes of BN-Lx and SHR progenitors of the BXH/HXB recombinant inbred (RI) strains as well as accumulation of multiple data sets of intermediary phenotypes in the RI strains, including mRNA and microRNA abundance, quantitative metabolomics, proteomics, methylomics or histone modifications, will make it possible to systematically search for genetic variants involved in regulation of gene expression and in the etiology of complex pathophysiological traits. New advances in manipulation of the rat genome, including efficient transgenesis and gene targeting, will enable in vivo functional analyses of selected candidate genes to identify QTL at the molecular level or to provide insight into mechanisms whereby targeted genes affect pathophysiological traits in the SHR.
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Affiliation(s)
- M. PRAVENEC
- Institute of Physiology Academy of Sciences of the Czech Republic, Prague, Czech Republic
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44
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Xiao X, Moreno-Moral A, Rotival M, Bottolo L, Petretto E. Multi-tissue analysis of co-expression networks by higher-order generalized singular value decomposition identifies functionally coherent transcriptional modules. PLoS Genet 2014; 10:e1004006. [PMID: 24391511 PMCID: PMC3879165 DOI: 10.1371/journal.pgen.1004006] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 10/22/2013] [Indexed: 12/27/2022] Open
Abstract
Recent high-throughput efforts such as ENCODE have generated a large body of genome-scale transcriptional data in multiple conditions (e.g., cell-types and disease states). Leveraging these data is especially important for network-based approaches to human disease, for instance to identify coherent transcriptional modules (subnetworks) that can inform functional disease mechanisms and pathological pathways. Yet, genome-scale network analysis across conditions is significantly hampered by the paucity of robust and computationally-efficient methods. Building on the Higher-Order Generalized Singular Value Decomposition, we introduce a new algorithmic approach for efficient, parameter-free and reproducible identification of network-modules simultaneously across multiple conditions. Our method can accommodate weighted (and unweighted) networks of any size and can similarly use co-expression or raw gene expression input data, without hinging upon the definition and stability of the correlation used to assess gene co-expression. In simulation studies, we demonstrated distinctive advantages of our method over existing methods, which was able to recover accurately both common and condition-specific network-modules without entailing ad-hoc input parameters as required by other approaches. We applied our method to genome-scale and multi-tissue transcriptomic datasets from rats (microarray-based) and humans (mRNA-sequencing-based) and identified several common and tissue-specific subnetworks with functional significance, which were not detected by other methods. In humans we recapitulated the crosstalk between cell-cycle progression and cell-extracellular matrix interactions processes in ventricular zones during neocortex expansion and further, we uncovered pathways related to development of later cognitive functions in the cortical plate of the developing brain which were previously unappreciated. Analyses of seven rat tissues identified a multi-tissue subnetwork of co-expressed heat shock protein (Hsp) and cardiomyopathy genes (Bag3, Cryab, Kras, Emd, Plec), which was significantly replicated using separate failing heart and liver gene expression datasets in humans, thus revealing a conserved functional role for Hsp genes in cardiovascular disease.
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Affiliation(s)
- Xiaolin Xiao
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Aida Moreno-Moral
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Maxime Rotival
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Leonardo Bottolo
- Department of Mathematics, Imperial College, London, United Kingdom
| | - Enrico Petretto
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College, London, United Kingdom
- * E-mail:
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45
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Moreno-Moral A, Mancini M, D'Amati G, Camici P, Petretto E. Transcriptional network analysis for the regulation of left ventricular hypertrophy and microvascular remodeling. J Cardiovasc Transl Res 2013; 6:931-44. [PMID: 23929067 DOI: 10.1007/s12265-013-9504-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/21/2013] [Indexed: 12/31/2022]
Abstract
Hypertension and cardiomyopathies share maladaptive changes of cardiac morphology, eventually leading to heart failure. These include left ventricular hypertrophy (LVH), myocardial fibrosis, and structural remodeling of coronary microcirculation, which is the morphologic hallmark of coronary microvascular dysfunction. To pinpoint the complex molecular mechanisms and pathways underlying LVH-associated cardiac remodeling independent of blood pressure effects, we employed gene network approaches to the rat heart. We used the Spontaneously Hypertensive Rat model showing many features of human hypertensive cardiomyopathy, for which we collected histological and histomorphometric data of the heart and coronary vasculature, and genome-wide cardiac gene expression. Here, we provide a large catalogue of gene co-expression networks in the heart that are significantly associated with quantitative variation in LVH, microvascular remodeling, and fibrosis-related traits. Many of these networks were significantly conserved to human idiopathic and/or ischemic cardiomyopathy patients, suggesting a potential role for these co-expressed genes in human heart disease.
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Affiliation(s)
- Aida Moreno-Moral
- Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, Imperial Centre for Translational and Experimental Medicine (ICTEM) Building, Du Cane Road, London, W12 0NN, UK
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46
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Kato M, Atsumi T, Oku K, Amengual O, Nakagawa H, Fujieda Y, Otomo K, Horita T, Yasuda S, Koike T. The involvement of CD36 in monocyte activation by antiphospholipid antibodies. Lupus 2013; 22:761-71. [DOI: 10.1177/0961203313490242] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background CD36, known as a scavenger receptor, is a transmembrane glycoprotein expressed on monocytes, platelets and endothelial cells, recognizes multiple ligands, including phosphatidylserine, and regulates atherogenesis and thrombosis. The objective of this study is to investigate the possible involvement of CD36 in the pathophysiology of thrombosis in patients with antiphospholipid syndrome (APS). Methods First, rs3765187, a missense mutation linked to CD36 deficiency, was investigated by TaqMan polymerase chain reaction (PCR) genotyping method in 819 Japanese, including 132 patients with APS, 265 with systemic lupus erythematosus (SLE) in the absence of APS, and 422 healthy subjects. Then, the involvement of CD36 in antiphospholipid antibody (aPL)-induced tissue factor (TF) expression was examined using CD36-null mice or anti-CD36. Purified IgG from patients with APS and a monoclonal phosphatidylserine-dependent antiprothrombin antibody were used in these experiments. TF expression was tested by real-time PCR and flow cytometry. Results Minor allele carrier of rs3765187 was less frequent in patients with APS (3.8% p = 0.032), but not in patients with SLE in the absence of APS (7.9% p = 0.32), compared with healthy subjects (10.2%). The aPL-induced TF expression was significantly suppressed on peritoneal macrophages from CD36-null mice compared to wild type and significantly inhibited by anti-CD36 on human monocytes. Conclusions The gene mutation linked to CD36 deficiency was less frequent in patients with APS. The deficient or suppressed CD36 function significantly reduced aPL-induced TF expression in vitro. Taken together, in a susceptible background CD36 scavenger receptor function may be involved in the thrombotic pathophysiology in patients with APS.
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Affiliation(s)
- M Kato
- Department of Medicine II, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - T Atsumi
- Department of Medicine II, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - K Oku
- Department of Medicine II, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - O Amengual
- Department of Medicine II, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - H Nakagawa
- Department of Medicine II, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Y Fujieda
- Department of Medicine II, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - K Otomo
- Department of Medicine II, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - T Horita
- Department of Medicine II, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - S Yasuda
- Department of Medicine II, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - T Koike
- Department of Medicine II, Hokkaido University Graduate School of Medicine, Sapporo, Japan
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47
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Association study of CD36 single nucleotide polymorphisms with essential hypertension in the Northeastern Han Chinese. Gene 2013; 527:410-5. [PMID: 23792019 DOI: 10.1016/j.gene.2013.05.077] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 05/22/2013] [Accepted: 05/28/2013] [Indexed: 11/21/2022]
Abstract
We found that cluster determinant 36 (CD36) gene is up-regulated in essential hypertension (EH) patients in our former research, but the association between CD36 gene variations and EH has not yet been clearly demonstrated. The relationship between CD36 gene single nucleotide polymorphisms (SNPs) and EH in the northeastern Han Chinese was examined in the present study through direct sequencing and genotype-detection. A total of 589 unrelated northeastern Han Chinese including 276 with EH and 313 controls were studied. SNPs in exon 7, exon 13 and intron 4 were detected using PCR-sequencing. The genotypes were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) or polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). +216T/C, +273A/G, +132C/T, +217T/C, +212T/G and +233T/C polymorphisms were identified. Distributions of genotypes AA, GA and GG of +273A/G polymorphism were significantly different between EH group and the control group (χ2: 9.056, p=0.011) and G allelic frequency was higher in EH (p=0.006, OR=1.629, 95% CI [1.224-2.168]). Logistic regression analysis showed that +273A/G polymorphism was closely associated with blood pressure (BP) after adjusting for ages. When subclassified by sex, the genotype distribution of +273A/G (p=0.011) and allelic frequency of G allele (p=0.006) were significantly different between EH participants and controls in males, but not in females. Subgroup analysis performed by body mass index (BMI) suggested that the genotype distribution of +273A/G and allelic frequency were significantly different in non-obese group and non-obese men, but the associations were not significant (non-obese group: p=0.016, OR=1.664, 95% CI [1.459-2.409]; non-obese men: p=0.073, OR=1.898, 95% CI [1.033-3.487]). +273A/G polymorphism in CD36 gene was associated with EH, and +273G could be an independent predictor.
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Dall’Asta M, Derlindati E, Curella V, Mena P, Calani L, Ray S, Zavaroni I, Brighenti F, Del Rio D. Effects of naringenin and its phase II metabolites onin vitrohuman macrophage gene expression. Int J Food Sci Nutr 2013; 64:843-9. [DOI: 10.3109/09637486.2013.804039] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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49
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Mancini M, Petretto E, Kleinert C, Scavone A, De T, Cook S, Silhavy J, Zidek V, Pravenec M, d'Amati G, Camici PG. Mapping genetic determinants of coronary microvascular remodeling in the spontaneously hypertensive rat. Basic Res Cardiol 2013; 108:316. [PMID: 23197152 DOI: 10.1007/s00395-012-0316-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 11/13/2012] [Accepted: 11/19/2012] [Indexed: 02/01/2023]
Abstract
The mechanisms underlying coronary microvascular remodeling and dysfunction, which are critical determinants of abnormal myocardial blood flow regulation in human hypertension, are poorly understood. The spontaneously hypertensive rat (SHR) exhibits many features of human hypertensive cardiomyopathy. We demonstrate that remodeling of intramural coronary arterioles is apparent in the SHR already at 4 weeks of age, i.e. before the onset of systemic hypertension. To uncover possible genetic determinants of coronary microvascular remodeling, we carried out detailed histological and histomorphometric analysis of the heart and coronary vasculature in 30 weeks old SHR, age-matched Brown Norway (BN-Lx) parentals and BXH/HXB recombinant inbred (RI) strains. Using previously mapped expression quantitative trait loci (eQTLs), we carried out a genome-wide association analysis between genetic determinants of cardiac gene expression and histomorphometric traits. This identified 36 robustly mapped eQTLs in the heart which were associated with medial area of intramural coronary arterioles [false discovery rate (FDR) ~5%]. Transcripts, which were both under cis-acting genetic regulation and significantly correlated with medial area (FDR <5%), but not with blood pressure indices, were prioritized and four candidate genes were identified (Rtel1, Pla2g5, Dnaja4 and Rcn2) according to their expression levels and biological functions. Our results demonstrate that genetic factors play a role in the development of coronary microvascular remodeling and suggest blood pressure independent candidate genes for further functional experiments.
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Affiliation(s)
- Massimiliano Mancini
- Department of Radiology, Oncology and Pathology, Sapienza University of Rome, Rome, Italy
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50
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Langley SR, Bottolo L, Kunes J, Zicha J, Zidek V, Hubner N, Cook SA, Pravenec M, Aitman TJ, Petretto E. Systems-level approaches reveal conservation of trans-regulated genes in the rat and genetic determinants of blood pressure in humans. Cardiovasc Res 2012; 97:653-65. [PMID: 23118132 DOI: 10.1093/cvr/cvs329] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
AIMS Human genome-wide association studies (GWAS) of hypertension identified only few susceptibility loci with large effect that were replicated across populations. The vast majority of genes detected by GWAS has small effect and the regulatory mechanisms through which these genetic variants cause disease remain mostly unclear. Here, we used comparative genomics between human and an established rat model of hypertension to explore the transcriptional mechanisms mediating the effect of genes identified in 15 hypertension GWAS. METHODS AND RESULTS Time series analysis of radiotelemetric blood pressure (BP) was performed to assess 11 parameters of BP variation in recombinant inbred strains derived from the spontaneously hypertensive rat. BP data were integrated with ∼27 000 expression quantative trait loci (eQTLs) mapped across seven tissues, detecting >8000 significant associations between eQTL genes and BP variation in the rat. We then compiled a large catalogue of human genes from GWAS of hypertension and identified a subset of 2292 rat-human orthologous genes. Expression levels for 795 (34%) of these genes correlated with BP variation across rat tissues: 51 genes were cis-regulated, whereas 459 were trans-regulated and enriched for 'calcium signalling pathway' (P = 9.6 × 10(-6)) and 'ion channel' genes (P = 3.5 × 10(-7)), which are important determinants of hypertension. We identified 158 clusters of trans-eQTLs, annotated the underlying 'master regulator' genes and found significant over-representation in the human hypertension gene set (enrichment P = 5 × 10(-4)). CONCLUSION We showed extensive conservation of trans-regulated genes and their master regulators between rat and human hypertension. These findings reveal that small-effect genes associated with hypertension by human GWAS are likely to exert their action through coordinate regulation of pathogenic pathways.
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Affiliation(s)
- Sarah R Langley
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
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