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Allayee H, Farber CR, Seldin MM, Williams EG, James DE, Lusis AJ. Systems genetics approaches for understanding complex traits with relevance for human disease. eLife 2023; 12:e91004. [PMID: 37962168 PMCID: PMC10645424 DOI: 10.7554/elife.91004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
Quantitative traits are often complex because of the contribution of many loci, with further complexity added by environmental factors. In medical research, systems genetics is a powerful approach for the study of complex traits, as it integrates intermediate phenotypes, such as RNA, protein, and metabolite levels, to understand molecular and physiological phenotypes linking discrete DNA sequence variation to complex clinical and physiological traits. The primary purpose of this review is to describe some of the resources and tools of systems genetics in humans and rodent models, so that researchers in many areas of biology and medicine can make use of the data.
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Affiliation(s)
- Hooman Allayee
- Departments of Population & Public Health Sciences, University of Southern CaliforniaLos AngelesUnited States
- Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Charles R Farber
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Departments of Biochemistry & Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Public Health Sciences, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Marcus M Seldin
- Department of Biological Chemistry, University of California, IrvineIrvineUnited States
| | - Evan Graehl Williams
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgLuxembourgLuxembourg
| | - David E James
- School of Life and Environmental Sciences, University of SydneyCamperdownAustralia
- Faculty of Medicine and Health, University of SydneyCamperdownAustralia
- Charles Perkins Centre, University of SydneyCamperdownAustralia
| | - Aldons J Lusis
- Departments of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Medicine, University of California, Los AngelesLos AngelesUnited States
- Microbiology, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLALos AngelesUnited States
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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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3
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Cheng Y, Sun D, Zhu B, Zhou W, Lv C, Kou F, Wei H. Integrative Metabolic and Proteomic Profiling of the Brainstem in Spontaneously Hypertensive Rats. J Proteome Res 2020; 19:4114-4124. [DOI: 10.1021/acs.jproteome.0c00585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yu Cheng
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongmei Sun
- School of Acupuncture-Moxibustion and Tuina, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Bangjie Zhu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenbin Zhou
- Shanghai Zhulian Intelligent Technology Ltd. Co., Shanghai 201323, China
| | - Chunming Lv
- Shanghai Zhulian Intelligent Technology Ltd. Co., Shanghai 201323, China
| | - Fang Kou
- Institute of Interdisciplinary Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hai Wei
- Institute of Interdisciplinary Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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Adriaens ME, Lodder EM, Moreno‐Moral A, Šilhavý J, Heinig M, Glinge C, Belterman C, Wolswinkel R, Petretto E, Pravenec M, Remme CA, Bezzina CR. Systems Genetics Approaches in Rat Identify Novel Genes and Gene Networks Associated With Cardiac Conduction. J Am Heart Assoc 2019; 7:e009243. [PMID: 30608189 PMCID: PMC6404199 DOI: 10.1161/jaha.118.009243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Background Electrocardiographic (ECG) parameters are regarded as intermediate phenotypes of cardiac arrhythmias. Insight into the genetic underpinnings of these parameters is expected to contribute to the understanding of cardiac arrhythmia mechanisms. Here we used HXB/BXH recombinant inbred rat strains to uncover genetic loci and candidate genes modulating ECG parameters. Methods and Results RR interval, PR interval, QRS duration, and QTc interval were measured from ECGs obtained in 6 male rats from each of the 29 available HXB/BXH recombinant inbred strains. Genes at loci displaying significant quantitative trait loci (QTL) effects were prioritized by assessing the presence of protein‐altering variants, and by assessment of cis expression QTL (eQTL) effects and correlation of transcript abundance to the respective trait in the heart. Cardiac RNA‐seq data were additionally used to generate gene co‐expression networks. QTL analysis of ECG parameters identified 2 QTL for PR interval, respectively, on chromosomes 10 and 17. At the chromosome 10 QTL, cis‐eQTL effects were identified for Acbd4, Cd300lg, Fam171a2, and Arhgap27; the transcript abundance in the heart of these 4 genes was correlated with PR interval. At the chromosome 17 QTL, a cis‐eQTL was uncovered for Nhlrc1 candidate gene; the transcript abundance of this gene was also correlated with PR interval. Co‐expression analysis furthermore identified 50 gene networks, 6 of which were correlated with PR interval or QRS duration, both parameters of cardiac conduction. Conclusions These newly identified genetic loci and gene networks associated with the ECG parameters of cardiac conduction provide a starting point for future studies with the potential of identifying novel mechanisms underlying cardiac electrical function.
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Affiliation(s)
- Michiel E. Adriaens
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
- Maastricht Centre for Systems BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Elisabeth M. Lodder
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
| | | | - Jan Šilhavý
- Institute of PhysiologyAcademy of Sciences of the Czech RepublicPragueCzech Republic
| | - Matthias Heinig
- Institute of Computational BiologyHelmholtz Zentrum MünchenMünchenGermany
| | - Charlotte Glinge
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
| | - Charly Belterman
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
| | - Rianne Wolswinkel
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
| | - Enrico Petretto
- The MRC London Institute of Medical SciencesImperial College LondonLondonUnited Kingdom
- Duke‐NUS Medical SchoolSingapore
| | - Michal Pravenec
- Institute of PhysiologyAcademy of Sciences of the Czech RepublicPragueCzech Republic
| | - Carol Ann Remme
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
| | - Connie R. Bezzina
- Department of Experimental CardiologyHeart CentreAcademic Medical Center AmsterdamAmsterdamThe Netherlands
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Alfazema N, Barrier M, de Procé SM, Menzies RI, Carter R, Stewart K, Diaz AG, Moyon B, Webster Z, Bellamy COC, Arends MJ, Stimson RH, Morton NM, Aitman TJ, Coan PM. Camk2n1 Is a Negative Regulator of Blood Pressure, Left Ventricular Mass, Insulin Sensitivity, and Promotes Adiposity. Hypertension 2019; 74:687-696. [PMID: 31327268 PMCID: PMC6686962 DOI: 10.1161/hypertensionaha.118.12409] [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] [Indexed: 12/13/2022]
Abstract
Supplemental Digital Content is available in the text. Metabolic syndrome is a cause of coronary artery disease and type 2 diabetes mellitus. Camk2n1 resides in genomic loci for blood pressure, left ventricle mass, and type 2 diabetes mellitus, and in the spontaneously hypertensive rat model of metabolic syndrome, Camk2n1 expression is cis-regulated in left ventricle and fat and positively correlates with adiposity. Therefore, we knocked out Camk2n1 in spontaneously hypertensive rat to investigate its role in metabolic syndrome. Compared with spontaneously hypertensive rat, Camk2n1−/− rats had reduced cardiorenal CaMKII (Ca2+/calmodulin-dependent kinase II) activity, lower blood pressure, enhanced nitric oxide bioavailability, and reduced left ventricle mass associated with altered hypertrophic networks. Camk2n1 deficiency reduced insulin resistance, visceral fat, and adipogenic capacity through the altered cell cycle and complement pathways, independent of CaMKII. In human visceral fat, CAMK2N1 expression correlated with adiposity and genomic variants that increase CAMK2N1 expression associated with increased risk of coronary artery disease and type 2 diabetes mellitus. Camk2n1 regulates multiple networks that control metabolic syndrome traits and merits further investigation as a therapeutic target in humans.
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Affiliation(s)
- Neza Alfazema
- From the MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom (N.A., M.B., S.M.d.P., T.J.A., P.M.C.)
| | - Marjorie Barrier
- From the MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom (N.A., M.B., S.M.d.P., T.J.A., P.M.C.)
| | - Sophie Marion de Procé
- From the MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom (N.A., M.B., S.M.d.P., T.J.A., P.M.C.)
| | - Robert I Menzies
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, United Kingdom (R.I.M., R.C., K.S., R.H.S., N.M.M.)
| | - Roderick Carter
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, United Kingdom (R.I.M., R.C., K.S., R.H.S., N.M.M.)
| | - Kevin Stewart
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, United Kingdom (R.I.M., R.C., K.S., R.H.S., N.M.M.)
| | - Ana Garcia Diaz
- MRC London Institute of Medical Sciences, Imperial College London, United Kingdom (A.G.D., B.M., Z.W.)
| | - Ben Moyon
- MRC London Institute of Medical Sciences, Imperial College London, United Kingdom (A.G.D., B.M., Z.W.)
| | - Zoe Webster
- MRC London Institute of Medical Sciences, Imperial College London, United Kingdom (A.G.D., B.M., Z.W.)
| | - Christopher O C Bellamy
- Division of Pathology, Centre for Comparative Pathology, Edinburgh CRUK Cancer Centre, United Kingdom (C.O.C.B., M.J.A.)
| | - Mark J Arends
- Division of Pathology, Centre for Comparative Pathology, Edinburgh CRUK Cancer Centre, United Kingdom (C.O.C.B., M.J.A.)
| | - Roland H Stimson
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, United Kingdom (R.I.M., R.C., K.S., R.H.S., N.M.M.)
| | - Nicholas M Morton
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, United Kingdom (R.I.M., R.C., K.S., R.H.S., N.M.M.)
| | - Timothy J Aitman
- From the MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom (N.A., M.B., S.M.d.P., T.J.A., P.M.C.)
| | - Philip M Coan
- From the MRC Institute of Genetics and Molecular Medicine, Edinburgh, United Kingdom (N.A., M.B., S.M.d.P., T.J.A., P.M.C.)
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Abstract
One of the most fruitful resources for systems genetic studies of nonhuman mammals is a panel of inbred strains that exhibits significant genetic diversity between strains but genetic stability (isogenicity) within strains. These characteristics allow for fine mapping of complex phenotypes (QTLs) and provide statistical power to identify loci which contribute nominally to the phenotype. This type of resource also allows the planning and performance of investigations using the same genetic backgrounds over several generations of the test animals. Often, rats are preferred over mice for physiologic and behavioral studies because of their larger size and more distinguishable anatomy (particularly for their central nervous system). The Hybrid Rat Diversity Panel (HRDP) is a panel of inbred rat strains, which combines two recombinant inbred panels (the HXB/BXH, 30 strains; the LEXF/FXLE, 34 strains and 35 more strains of inbred rats which were selected for genetic diversity, based on their fully sequenced genomes and/or thorough genotyping). The genetic diversity and statistical power of this panel for mapping studies rivals or surpasses currently available panels in mouse. The genetic stability of this panel makes it particularly suitable for collection of high-throughput omics data as relevant technology becomes available for engaging in truly integrative systems biology. The PhenoGen website ( http://phenogen.org ) is the repository for the initial transcriptome data, making the raw data, the processed data, and the analysis results, e.g., organ-specific protein coding and noncoding transcripts, isoform analysis, expression quantitative trait loci, and co-expression networks, available to the research public. The data sets and tools being developed will complement current efforts to analyze the human transcriptome and its genetic controls (the Genotype-Tissue Expression Project (GTEx)) and allow for dissection of genetic networks that predispose to particular phenotypes and gene-by-environment interactions that are difficult or even impossible to study in humans. The HRDP is an essential population for exploring truly integrative systems genetics.
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Zhang HN, Xu QQ, Thakur A, Alfred MO, Chakraborty M, Ghosh A, Yu XB. Endothelial dysfunction in diabetes and hypertension: Role of microRNAs and long non-coding RNAs. Life Sci 2018; 213:258-268. [PMID: 30342074 DOI: 10.1016/j.lfs.2018.10.028] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 10/13/2018] [Accepted: 10/15/2018] [Indexed: 12/11/2022]
Abstract
The vascular endothelium acts as a barrier between the blood flow and the inner lining of the vessel wall, and it functions as a filtering machinery to filter out any unwanted transfer of materials from both sides (i.e. the blood and the surrounding tissues). It is evident that diseases such as diabetes, obesity, and hypertension disturb the normal endothelial functions in humans and lead to endothelial dysfunction, which may further precede to the development of atherosclerosis. Long non-coding RNAs and micro RNAs both are types of non-coding RNAs which, in the recent years, have increasingly been studied in the pathophysiology of many diseases including diabetes, obesity, cardiovascular diseases, neurological diseases, and others. Recent findings have pointed out important aspects on their relevance to endothelial function as well as dysfunction of the system which may arise from presence of diseases such as diabetes and hypertension. Diabetes or hypertension-mediated endothelial dysfunction show characteristics such as reduced nitric oxide synthesis through suppression of endothelial nitric oxide synthase activity in endothelial cells, reduced sensitivity of nitric oxide in smooth muscle cells, and inflammation - all of which have been either shown to be directly caused by gene regulatory mechanisms of non-coding RNAs or shown to be having a correlation with them. In this review, we aim to discuss such findings on the role of these non-coding RNAs in diabetes or hypertension-associated endothelial dysfunction and the related mechanisms that may pave the way for alleviating endothelial dysfunction and its related complications such as atherosclerosis.
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Affiliation(s)
- Hai-Na Zhang
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qiao-Qiao Xu
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Abhimanyu Thakur
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology Mesra, Ranchi, India
| | - Martin Omondi Alfred
- Institute of Primate Research, Nairobi, Kenya; School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Manas Chakraborty
- Department of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Arunima Ghosh
- Department of Medical Coding Analysis - Emblem Health, Cognizant Technology Solutions India Pvt Ltd., Bangalore, India
| | - Xu-Ben Yu
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
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Genomic approaches for the elucidation of genes and gene networks underlying cardiovascular traits. Biophys Rev 2018; 10:1053-1060. [PMID: 29934864 PMCID: PMC6082306 DOI: 10.1007/s12551-018-0435-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/13/2018] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies have shed light on the association between natural genetic variation and cardiovascular traits. However, linking a cardiovascular trait associated locus to a candidate gene or set of candidate genes for prioritization for follow-up mechanistic studies is all but straightforward. Genomic technologies based on next-generation sequencing technology nowadays offer multiple opportunities to dissect gene regulatory networks underlying genetic cardiovascular trait associations, thereby aiding in the identification of candidate genes at unprecedented scale. RNA sequencing in particular becomes a powerful tool when combined with genotyping to identify loci that modulate transcript abundance, known as expression quantitative trait loci (eQTL), or loci modulating transcript splicing known as splicing quantitative trait loci (sQTL). Additionally, the allele-specific resolution of RNA-sequencing technology enables estimation of allelic imbalance, a state where the two alleles of a gene are expressed at a ratio differing from the expected 1:1 ratio. When multiple high-throughput approaches are combined with deep phenotyping in a single study, a comprehensive elucidation of the relationship between genotype and phenotype comes into view, an approach known as systems genetics. In this review, we cover key applications of systems genetics in the broad cardiovascular field.
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Saba L, Hoffman P, Tabakoff B. Using Baseline Transcriptional Connectomes in Rat to Identify Genetic Pathways Associated with Predisposition to Complex Traits. Methods Mol Biol 2018; 1488:299-317. [PMID: 27933531 DOI: 10.1007/978-1-4939-6427-7_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although rat is a critical model organism in preclinical medications development, its use in systems genetics studies remains sparse. The PhenoGen database and website contain detailed information on the qualitative and quantitative aspects of the rat brain, liver, heart, and brown adipose transcriptome. This database has been generated using the HXB/BXH recombinant inbred panel and is being expanded to a hybrid rat diversity panel that includes many common inbred strains as well. By using such a panel, the PhenoGen project has created a renewable and cumulative resource for the rat genomics community. The database has been used to reconstruct the brain transcriptome identifying both annotated and unannotated transcribed elements that range in size from 20 nucleotides to over 30,000 nucleotides and elements that have a wide variety of roles in the cell including generation of proteins and regulation of the transcription and translation processes. In all 4 tissues, baseline transcriptional connectomes have been generated to model the relationships among transcripts. These connectomes can be used to identify genetic pathways associated with complex traits and to gain insight into biological function of individual transcripts. The PhenoGen website contains tools that allow the user to explore qualitative features of individual genes and to see how the gene relates to other genes within a tissue. The PhenoGen database and website continue to grow and to make use of the latest statistical methods for systems genetics creating a national resource for the rat genomics community.
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Affiliation(s)
- Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd., Aurora, CO, 80045, USA.
| | - Paula Hoffman
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd., Aurora, CO, 80045, USA
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Coan PM, Barrier M, Alfazema N, Carter RN, Marion de Procé S, Dopico XC, Garcia Diaz A, Thomson A, Jackson-Jones LH, Moyon B, Webster Z, Ross D, Moss J, Arends MJ, Morton NM, Aitman TJ. Complement Factor B Is a Determinant of Both Metabolic and Cardiovascular Features of Metabolic Syndrome. Hypertension 2017; 70:HYPERTENSIONAHA.117.09242. [PMID: 28739975 PMCID: PMC5548512 DOI: 10.1161/hypertensionaha.117.09242] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 02/22/2017] [Accepted: 06/02/2017] [Indexed: 12/28/2022]
Abstract
CFB (complement factor B) is elevated in adipose tissue and serum from patients with type 2 diabetes mellitus and cardiovascular disease, but the causal relationship to disease pathogenesis is unclear. Cfb is also elevated in adipose tissue and serum of the spontaneously hypertensive rat, a well-characterized model of metabolic syndrome. To establish the role of CFB in metabolic syndrome, we knocked out the Cfb gene in the spontaneously hypertensive rat. Cfb-/- rats showed improved glucose tolerance and insulin sensitivity, redistribution of visceral to subcutaneous fat, increased adipocyte mitochondrial respiration, and marked changes in gene expression. Cfb-/- rats also had lower blood pressure, increased ejection fraction and fractional shortening, and reduced left ventricular mass. These changes in metabolism and gene expression, in adipose tissue and left ventricle, suggest new adipose tissue-intrinsic and blood pressure-independent mechanisms for insulin resistance and cardiac hypertrophy in the spontaneously hypertensive rat. In silico analysis of the human CFB locus revealed 2 cis-regulated expression quantitative trait loci for CFB expression significantly associated with visceral fat, circulating triglycerides and hypertension in genome-wide association studies. Together, these data demonstrate a key role for CFB in the development of spontaneously hypertensive rat metabolic syndrome phenotypes and of related traits in humans and indicate the potential for CFB as a novel target for treatment of cardiometabolic disease.
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Affiliation(s)
- Philip M Coan
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.).
| | - Marjorie Barrier
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Neza Alfazema
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Roderick N Carter
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Sophie Marion de Procé
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Xaquin C Dopico
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Ana Garcia Diaz
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Adrian Thomson
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Lucy H Jackson-Jones
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Ben Moyon
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Zoe Webster
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - David Ross
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Julie Moss
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Mark J Arends
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Nicholas M Morton
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
| | - Timothy J Aitman
- From the Centre for Genomic and Experimental Medicine, MRC Institute for Genetics and Molecular Medicine, Edinburgh, United Kingdom (P.M.C., M.B., N.A., S.M.P., X.C.D., D.R., J.M., T.J.A.); British Heart Foundation Centre for Cardiovascular Science, Queen's Medical Research Institute (P.M.C., M.B., N.A., R.N.C., A.T., L.H.J.-J., N.M.M., T.J.A.) and Royal (Dick) School of Veterinary Studies (X.C.D.), University of Edinburgh, United Kingdom; Department of Medicine (A.G.D., T.J.A) and Embryonic Stem Cell and Transgenics Facility, MRC Clinical Sciences Centre (B.M., Z.W.), Imperial College London, United Kingdom; and Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, United Kingdom (M.J.A.)
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11
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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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12
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Moreno-Moral A, Pesce F, Behmoaras J, Petretto E. Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease. Methods Mol Biol 2017; 1488:337-362. [PMID: 27933533 DOI: 10.1007/978-1-4939-6427-7_16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease. In addition, systems genetics has proven useful in the discovery of master trans-acting genetic regulators of functional networks and pathways, which in many cases revealed unexpected gene targets for disease. Here we detail the central components of a fully integrated systems genetics approach to complex disease, starting from assessment of genetic and gene expression variation, linking DNA sequence variation to mRNA (expression QTL mapping), gene regulatory network analysis and mapping the genetic control of regulatory networks. By summarizing a few illustrative (and successful) examples, we highlight how different data-modeling strategies can be effectively integrated in a systems genetics study.
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Affiliation(s)
- Aida Moreno-Moral
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Francesco Pesce
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, Hammersmith Campus, Imperial Centre for Translational and Experimental Medicine, London, UK
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Enrico Petretto
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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13
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Endothelial dysfunction and cardiometabolic diseases: Role of long non-coding RNAs. Life Sci 2016; 167:6-11. [DOI: 10.1016/j.lfs.2016.11.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/02/2016] [Accepted: 11/07/2016] [Indexed: 12/19/2022]
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14
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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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15
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Nie Y, Kumarasamy S, Waghulde H, Cheng X, Mell B, Czernik PJ, Lecka-Czernik B, Joe B. High-resolution mapping of a novel rat blood pressure locus on chromosome 9 to a region containing the Spp2 gene and colocalization of a QTL for bone mass. Physiol Genomics 2016; 48:409-19. [PMID: 27113531 DOI: 10.1152/physiolgenomics.00004.2016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 04/20/2016] [Indexed: 01/11/2023] Open
Abstract
Through linkage analysis of the Dahl salt-sensitive (S) rat and the spontaneously hypertensive rat (SHR), a blood pressure (BP) quantitative trait locus (QTL) was previously located on rat chromosome 9. Subsequent substitution mapping studies of this QTL revealed multiple BP QTLs within the originally identified logarithm of odds plot by linkage analysis. The focus of this study was on a 14.39 Mb region, the distal portion of which remained unmapped in our previous studies. High-resolution substitution mapping for a BP QTL in the setting of a high-salt diet indicated that an SHR-derived congenic segment of 787.9 kb containing the gene secreted phosphoprotein-2 (Spp2) lowered BP and urinary protein excretion. A nonsynonymous G/T polymorphism in the Spp2 gene was detected between the S and S.SHR congenic rats. A survey of 45 strains showed that the T allele was rare, being detected only in some substrains of SHR and WKY. Protein modeling prediction through SWISSPROT indicated that the predicted protein product of this variant was significantly altered. Importantly, in addition to improved cardiovascular and renal function, high salt-fed congenic animals carrying the SHR T variant of Spp2 had significantly lower bone mass and altered bone microarchitecture. Total bone volume and volume of trabecular bone, cortical thickness, and degree of mineralization of cortical bone were all significantly reduced in congenic rats. Our study points to opposing effects of a congenic segment containing the prioritized candidate gene Spp2 on BP and bone mass.
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Affiliation(s)
- Ying Nie
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Sivarajan Kumarasamy
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Harshal Waghulde
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Xi Cheng
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Blair Mell
- Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Piotr J Czernik
- Center for Diabetes and Endocrine Research, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio; and Department of Orthopedics, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Beata Lecka-Czernik
- Center for Diabetes and Endocrine Research, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio; and Department of Orthopedics, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio
| | - Bina Joe
- Program in Physiological Genomics, 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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16
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Bischoff R, Permentier H, Guryev V, Horvatovich P. Genomic variability and protein species — Improving sequence coverage for proteogenomics. J Proteomics 2016; 134:25-36. [DOI: 10.1016/j.jprot.2015.09.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 09/06/2015] [Accepted: 09/14/2015] [Indexed: 12/30/2022]
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Abstract
The genetic basis of type 2 diabetes remains incompletely defined despite the use of multiple genetic strategies. Multiparental populations such as heterogeneous stocks (HS) facilitate gene discovery by allowing fine mapping to only a few megabases, significantly decreasing the number of potential candidate genes compared to traditional mapping strategies. In the present work, we employed expression and sequence analysis in HS rats (Rattus norvegicus) to identify Tpcn2 as a likely causal gene underlying a 3.1-Mb locus for glucose and insulin levels. Global gene expression analysis on liver identified Tpcn2 as the only gene in the region that is differentially expressed between HS rats with glucose intolerance and those with normal glucose regulation. Tpcn2 also maps as a cis-regulating expression QTL and is negatively correlated with fasting glucose levels. We used founder sequence to identify variants within this region and assessed association between 18 variants and diabetic traits by conducting a mixed-model analysis, accounting for the complex family structure of the HS. We found that two variants were significantly associated with fasting glucose levels, including a nonsynonymous coding variant within Tpcn2. Studies in Tpcn2 knockout mice demonstrated a significant decrease in fasting glucose levels and insulin response to a glucose challenge relative to those in wild-type mice. Finally, we identified variants within Tpcn2 that are associated with fasting insulin in humans. These studies indicate that Tpcn2 is a likely causal gene that may play a role in human diabetes and demonstrate the utility of multiparental populations for positionally cloning genes within complex loci.
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18
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Murakami K. Non-coding RNAs and hypertension-unveiling unexpected mechanisms of hypertension by the dark matter of the genome. Curr Hypertens Rev 2015; 11:80-90. [PMID: 25828869 PMCID: PMC5384352 DOI: 10.2174/1573402111666150401105317] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/05/2015] [Accepted: 03/30/2015] [Indexed: 12/23/2022]
Abstract
Hypertension is a major risk factor of cardiovascular diseases and a most important health problem in developed countries. Investigations on pathophysiology of hypertension have been based on gene products from coding region that occupies only about 1% of total genome region. On the other hand, non-coding region that occupies almost 99% of human genome has been regarded as "junk" for a long time and went unnoticed until these days. But recently, it turned out that noncoding region is extensively transcribed to non-coding RNAs and has various functions. This review highlights recent updates on the significance of non-coding RNAs such as micro RNAs and long non-coding RNAs (lncRNAs) on the pathogenesis of hypertension, also providing an introduction to basic biology of noncoding RNAs. For example, microRNAs are associated with hypertension via neuro-fumoral factor, sympathetic nerve activity, ion transporters in kidneys, endothelial function, vascular smooth muscle phenotype transformation, or communication between cells. Although reports of lncRNAs on pathogenesis of hypertension are scarce at the moment, new lncRNAs in relation to hypertension are being discovered at a rapid pace owing to novel techniques such as microarray or next-generation sequencing. In the clinical settings, clinical use of non-coding RNAs in identifying cardiovascular risks or developing novel tools for treating hypertension such as molecular decoy or mimicks is promising, although improvement in chemical modification or drug delivery system is necessary.
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Affiliation(s)
- Kazuo Murakami
- Department of Health Care and Preventive Medicine, Matsuyama Red Cross Hospital, 1 Bunkyo-cho, Matsuyama, Ehime, 790-8524, Japan.
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19
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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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Gopalakrishnan K, Kumarasamy S, Mell B, Joe B. Genome-wide identification of long noncoding RNAs in rat models of cardiovascular and renal disease. Hypertension 2014; 65:200-10. [PMID: 25385761 DOI: 10.1161/hypertensionaha.114.04498] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Long noncoding RNAs (lncRNAs) are an emerging class of genomic regulatory molecules reported in various species. In the rat, which is one of the major mammalian model organisms, discovery of lncRNAs on a genome-wide scale is lagging. Renal lncRNA sequencing and lncRNA transcriptome analysis were conducted in 3 rat strains that are widely used in cardiovascular and renal research: the Dahl salt-sensitive rat, the spontaneously hypertensive rat, and the Dahl salt-resistant rat. Through the RNA sequencing approach, 3273 transcripts were identified as rat lncRNAs. A majority of lncRNAs were without predicted target genes. Differential expression of 273 and 749 lncRNAs was detected between Dahl salt-sensitive versus Dahl salt-resistant and Dahl salt-sensitive versus spontaneously hypertensive rat comparisons, respectively. To couple the observed differential expression of lncRNAs with the status of mRNAs, an mRNA transcriptome analysis was conducted. Several cis mRNA genes were coregulated with lncRNAs. Of these, the protein expression status of 4 target genes, Asb3, Chac2, Pex11b, and Sp5, were differentially expressed between the relevant strain comparisons, thereby suggesting that the differentially expressed lncRNAs associated with these genes are candidate genetic determinants of blood pressure. This study serves as a first-generation catalog of rat lncRNAs and illustrates the prioritization of lncRNAs as candidates for complex polygenic traits.
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Affiliation(s)
- Kathirvel Gopalakrishnan
- From the Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, OH
| | - Sivarajan Kumarasamy
- From the Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, OH
| | - Blair Mell
- From the Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, OH
| | - Bina Joe
- From the Program in Physiological Genomics, Center for Hypertension and Personalized Medicine, Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, OH.
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21
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Kodavanti UP, Thomas RF, Ledbetter AD, Schladweiler MC, Bass V, Krantz QT, King C, Nyska A, Richards JE, Andrews D, Gilmour MI. Diesel exhaust induced pulmonary and cardiovascular impairment: the role of hypertension intervention. Toxicol Appl Pharmacol 2013; 268:232-40. [PMID: 23415681 DOI: 10.1016/j.taap.2013.02.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 01/28/2013] [Accepted: 02/04/2013] [Indexed: 11/17/2022]
Abstract
Exposure to diesel exhaust (DE) and associated gases is linked to cardiovascular impairments; however, the susceptibility of hypertensive individuals is poorly understood. The objectives of this study were (1) to determine cardiopulmonary effects of gas-phase versus whole-DE and (2) to examine the contribution of systemic hypertension in pulmonary and cardiovascular effects. Male Wistar Kyoto (WKY) rats were treated with hydralazine to reduce blood pressure (BP) or l-NAME to increase BP. Spontaneously hypertensive (SH) rats were treated with hydralazine to reduce BP. Control and drug-pretreated rats were exposed to air, particle-filtered exhaust (gas), or whole DE (1500μg/m(3)), 4h/day for 2days or 5days/week for 4weeks. Acute and 4-week gas and DE exposures increased neutrophils and γ-glutamyl transferase (γ-GT) activity in lavage fluid of WKY and SH rats. DE (4weeks) caused pulmonary albumin leakage and inflammation in SH rats. Two-day DE increased serum fatty acid binding protein-3 (FABP-3) in WKY. Marked increases occurred in aortic mRNA after 4-week DE in SH (eNOS, TF, tPA, TNF-α, MMP-2, RAGE, and HMGB-1). Hydralazine decreased BP in SH while l-NAME tended to increase BP in WKY; however, neither changed inflammation nor BALF γ-GT. DE-induced and baseline BALF albumin leakage was reduced by hydralazine in SH rats and increased by l-NAME in WKY rats. Hydralazine pretreatment reversed DE-induced TF, tPA, TNF-α, and MMP-2 expression but not eNOS, RAGE, and HMGB-1. ET-1 was decreased by HYD. In conclusion, antihypertensive drug treatment reduces gas and DE-induced pulmonary protein leakage and expression of vascular atherogenic markers.
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Affiliation(s)
- Urmila P Kodavanti
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory (NHEERL), Office of Research and Development (ORD), U.S. Environmental Protection Agency (EPA), Research Triangle Park, NC 27711, USA.
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22
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Abstract
Integrative genomics studies have greatly advanced our understanding of cardiovascular pathophysiology over the last decade. Here, we highlight the strengths and challenges of this cutting-edge approach and provide examples where novel insights have arisen through the integration of multi-level genomic information and cardiac physiology. Going forward, the integration of comprehensive next-generation sequencing data sets with quantitative phenotypes at the molecular, cellular, and whole-heart level using advanced modelling approaches provides an unprecedented opportunity for cardiovascular science.
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Affiliation(s)
- James S Ware
- MRC Clinical Sciences Centre, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Du Cane Road, London, W12 0NN, UK
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23
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Nabika T, Ohara H, Kato N, Isomura M. The stroke-prone spontaneously hypertensive rat: still a useful model for post-GWAS genetic studies? Hypertens Res 2012; 35:477-84. [PMID: 22399095 DOI: 10.1038/hr.2012.30] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The stroke-prone spontaneously hypertensive rat (SHRSP) is a unique genetic model of severe hypertension and cerebral stroke. SHRSP, as well as the spontaneously hypertensive rat, the parental strain of SHRSP, has made a tremendous contribution to cardiovascular research. However, the genetic mechanisms underlying hypertension and stroke in these rats have not yet been clarified. Recent studies using whole-genome sequencing and comprehensive gene expression analyses combined with classical quantitative trait loci analyses provided several candidate genes, such as Ephx2, Gstm1 and Slc34a1, which still need further evidence to define their pathological roles. Currently, genome-wide association studies can directly identify candidate genes for hypertension in the human genome. Thus, genetic studies in SHRSP and other rat models must be focused on the pathogenetic roles of 'networks of interacting genes' in hypertension, instead of searching for individual candidate genes.
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Affiliation(s)
- Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan.
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