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Munro D, Wang T, Chitre AS, Polesskaya O, Ehsan N, Gao J, Gusev A, Woods LS, Saba L, Chen H, Palmer A, Mohammadi P. The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats. Nucleic Acids Res 2022; 50:10882-10895. [PMID: 36263809 PMCID: PMC9638908 DOI: 10.1093/nar/gkac912] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/17/2022] [Accepted: 10/05/2022] [Indexed: 11/14/2022] Open
Abstract
Heterogeneous Stock (HS) rats are a genetically diverse outbred rat population that is widely used for studying genetics of behavioral and physiological traits. Mapping Quantitative Trait Loci (QTL) associated with transcriptional changes would help to identify mechanisms underlying these traits. We generated genotype and transcriptome data for five brain regions from 88 HS rats. We identified 21 392 cis-QTLs associated with expression and splicing changes across all five brain regions and validated their effects using allele specific expression data. We identified 80 cases where eQTLs were colocalized with genome-wide association study (GWAS) results from nine physiological traits. Comparing our dataset to human data from the Genotype-Tissue Expression (GTEx) project, we found that the HS rat data yields twice as many significant eQTLs as a similarly sized human dataset. We also identified a modest but highly significant correlation between genetic regulatory variation among orthologous genes. Surprisingly, we found less genetic variation in gene regulation in HS rats relative to humans, though we still found eQTLs for the orthologs of many human genes for which eQTLs had not been found. These data are available from the RatGTEx data portal (RatGTEx.org) and will enable new discoveries of the genetic influences of complex traits.
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Affiliation(s)
- Daniel Munro
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA,Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Nava Ehsan
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Jianjun Gao
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Leah C Solberg Woods
- Section of Molecular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Laura M Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Abraham A Palmer
- Correspondence may also be addressed to Abraham A. Palmer. Tel: +1 858 534 2093;
| | - Pejman Mohammadi
- To whom correspondence should be addressed. Tel: +1 858 784 8746;
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Van Dyke K, Lutz S, Mekonnen G, Myers CL, Albert FW. Trans-acting genetic variation affects the expression of adjacent genes. Genetics 2021; 217:6126816. [PMID: 33789351 DOI: 10.1093/genetics/iyaa051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/16/2020] [Indexed: 11/13/2022] Open
Abstract
Gene expression differences among individuals are shaped by trans-acting expression quantitative trait loci (eQTLs). Most trans-eQTLs map to hotspot locations that influence many genes. The molecular mechanisms perturbed by hotspots are often assumed to involve "vertical" cascades of effects in pathways that can ultimately affect the expression of thousands of genes. Here, we report that trans-eQTLs can affect the expression of adjacent genes via "horizontal" mechanisms that extend along a chromosome. Genes affected by trans-eQTL hotspots in the yeast Saccharomyces cerevisiae were more likely to be located next to each other than expected by chance. These paired hotspot effects tended to occur at adjacent genes that also show coexpression in response to genetic and environmental perturbations, suggesting shared mechanisms. Physical proximity and shared chromatin state, in addition to regulation of adjacent genes by similar transcription factors, were independently associated with paired hotspot effects among adjacent genes. Paired effects of trans-eQTLs can occur at neighboring genes even when these genes do not share a common function. This phenomenon could result in unexpected connections between regulatory genetic variation and phenotypes.
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Affiliation(s)
- Krisna Van Dyke
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sheila Lutz
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gemechu Mekonnen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
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3
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Swanzey E, O'Connor C, Reinholdt LG. Mouse Genetic Reference Populations: Cellular Platforms for Integrative Systems Genetics. Trends Genet 2021; 37:251-265. [PMID: 33010949 PMCID: PMC7889615 DOI: 10.1016/j.tig.2020.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023]
Abstract
Interrogation of disease-relevant cellular and molecular traits exhibited by genetically diverse cell populations enables in vitro systems genetics approaches for uncovering the basic properties of cellular function and identity. Primary cells, stem cells, and organoids derived from genetically diverse mouse strains, such as Collaborative Cross and Diversity Outbred populations, offer the opportunity for parallel in vitro/in vivo screening. These panels provide genetic resolution for variant discovery and functional characterization, as well as disease modeling and in vivo validation capabilities. Here we review mouse cellular systems genetics approaches for characterizing the influence of genetic variation on signaling networks and phenotypic diversity, and we discuss approaches for data integration and cross-species validation.
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Affiliation(s)
| | - Callan O'Connor
- The Jackson Laboratory, Bar Harbor, ME, USA; Tufts Graduate School of Biomedical Sciences, Boston, MA, USA
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4
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Školníková E, Šedová L, Chylíková B, Kábelová A, Liška F, Šeda O. Maternal High-Sucrose Diet Affects Phenotype Outcome in Adult Male Offspring: Role of Zbtb16. Front Genet 2020; 11:529421. [PMID: 33061941 PMCID: PMC7518089 DOI: 10.3389/fgene.2020.529421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 08/19/2020] [Indexed: 11/13/2022] Open
Abstract
Overnutrition in pregnancy and lactation affects fetal and early postnatal development, which can result in metabolic disorders in adulthood. We tested a hypothesis that variation of the Zbtb16 gene, a significant energy metabolism regulator, modulates the effect of maternal high-sucrose diet (HSD) on metabolic and transcriptomic profiles of the offspring. We used the spontaneously hypertensive rat (SHR) strain and a minimal congenic rat strain SHR-Zbtb16, carrying the Zbtb16 gene allele originating from the PD/Cub rat, a metabolic syndrome model. Sixteen-week-old SHR and SHR-Zbtb16 rat dams were fed either standard diet (control groups) or a high-sucrose diet (HSD, 70% calories as sucrose) during pregnancy and 4 weeks of lactation. In dams of both strains, we observed an HSD-induced increase of cholesterol and triacylglycerol concentrations in VLDL particles and a decrease of cholesterol and triacylglycerols content in medium to very small LDL particles. In male offspring, exposure to maternal HSD substantially increased brown fat weight in both strains, decreased triglycerides in LDL particles, and impaired glucose tolerance exclusively in SHR. The transcriptome assessment revealed networks of transcripts reflecting the shifts induced by maternal HSD with major nodes including mir-126, Hsd11b1 in the brown adipose tissue, Pcsk9, Nr0b2 in the liver and Hsd11b1, Slc2a4 in white adipose tissue. In summary, maternal HSD feeding during pregnancy and lactation affected brown fat deposition and lipid metabolism in adult male offspring and induced major transcriptome shifts in liver, white, and brown adipose tissues. The Zbtb16 variation present in the SHR-Zbtb16 led to several strain-specific effects of the maternal HSD, particularly the transcriptomic profile shifts of the adult male offspring.
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Affiliation(s)
- Elena Školníková
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czechia
| | - Lucie Šedová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czechia
| | - Blanka Chylíková
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czechia
| | - Adéla Kábelová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czechia
| | - František Liška
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czechia
| | - Ondřej Šeda
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czechia
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5
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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: 28] [Impact Index Per Article: 5.6] [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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Affiliation(s)
- Amela Jusic
- From the Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, Bosnia and Herzegovina (A.J.)
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health (Y.D.)
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7
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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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8
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Generation of Immunodeficient Rats With Rag1 and Il2rg Gene Deletions and Human Tissue Grafting Models. Transplantation 2018; 102:1271-1278. [DOI: 10.1097/tp.0000000000002251] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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9
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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: 32] [Impact Index Per Article: 5.3] [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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10
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Rossier BC, Bochud M, Devuyst O. The Hypertension Pandemic: An Evolutionary Perspective. Physiology (Bethesda) 2017; 32:112-125. [PMID: 28202622 DOI: 10.1152/physiol.00026.2016] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hypertension affects over 1.2 billion individuals worldwide and has become the most critical and expensive public health problem. Hypertension is a multifactorial disease involving environmental and genetic factors together with risk-conferring behaviors. The cause of the disease is identified in ∼10% of the cases (secondary hypertension), but in 90% of the cases no etiology is found (primary or essential hypertension). For this reason, a better understanding of the mechanisms controlling blood pressure in normal and hypertensive patients is the aim of very active experimental and clinical research. In this article, we review the importance of the renin-angiotensin-aldosterone system (RAAS) for the control of blood pressure, focusing on the evolution of the system and its critical importance for adaptation of vertebrates to a terrestrial and dry environment. The evolution of blood pressure control during the evolution of primates, hominins, and humans is discussed, together with the role of common genetic factors and the possible causes of the current hypertension pandemic in the light of evolutionary medicine.
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Affiliation(s)
- Bernard C Rossier
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland;
| | - Murielle Bochud
- Institute of Social and Preventive Medicine, Lausanne University Hospital, Lausanne, Switzerland; and
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland
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11
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ŠEDA O, LIŠKA F, PRAVENEC M, VERNEROVÁ Z, KAZDOVÁ L, KŘENOVÁ D, ZÍDEK V, ŠEDOVÁ L, KRUPKOVÁ M, KŘEN V. Connexin 50 Mutation Lowers Blood Pressure in Spontaneously Hypertensive Rat. Physiol Res 2017; 66:15-28. [DOI: 10.33549/physiolres.933432] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We assessed the effect of the previously uncovered gap junction protein alpha 8 (Gja8) mutation present in spontaneously hypertensive rat – dominant cataract (SHR-Dca) strain on blood pressure, metabolic profile, and heart and renal transcriptomes. Adult, standard chow-fed male rats of SHR and SHR-Dca strains were used. We found a significant, consistent 10-15 mmHg decrease in both systolic and diastolic blood pressures in SHR-Dca compared with SHR (P<0.01 and P<0.05, respectively; repeated measures analysis of variance (ANOVA)). With immunohistochemistry, we were able to localize Gja8 in heart, kidney, aorta, liver, and lungs, mostly in endothelium; with no differences in expression between strains. SHR-Dca rats showed decreased body weight, high-density lipoprotein cholesterol concentrations and basal insulin sensitivity in muscle. There were 21 transcripts common to the sets of 303 transcripts in kidney and 487 in heart showing >1.2-fold difference in expression between SHR and SHR-Dca. Tumor necrosis factor was the most significant upstream regulator and glial cell-derived neurotrophic factor family ligand-receptor interactions was the common enriched and downregulated canonical pathway both in heart and kidney of SHR-Dca. The connexin 50 mutation L7Q lowers blood pressure in the SHR-Dca strain, decreases high-density lipoprotein cholesterol, and leads to substantial transcriptome changes in heart and kidney.
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Affiliation(s)
- O. ŠEDA
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
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12
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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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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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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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Šedová L, Pravenec M, Křenová D, Kazdová L, Zídek V, Krupková M, Liška F, Křen V, Šeda O. Isolation of a Genomic Region Affecting Most Components of Metabolic Syndrome in a Chromosome-16 Congenic Rat Model. PLoS One 2016; 11:e0152708. [PMID: 27031336 PMCID: PMC4816345 DOI: 10.1371/journal.pone.0152708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/17/2016] [Indexed: 11/17/2022] Open
Abstract
Metabolic syndrome is a highly prevalent human disease with substantial genomic and environmental components. Previous studies indicate the presence of significant genetic determinants of several features of metabolic syndrome on rat chromosome 16 (RNO16) and the syntenic regions of human genome. We derived the SHR.BN16 congenic strain by introgression of a limited RNO16 region from the Brown Norway congenic strain (BN-Lx) into the genomic background of the spontaneously hypertensive rat (SHR) strain. We compared the morphometric, metabolic, and hemodynamic profiles of adult male SHR and SHR.BN16 rats. We also compared in silico the DNA sequences for the differential segment in the BN-Lx and SHR parental strains. SHR.BN16 congenic rats had significantly lower weight, decreased concentrations of total triglycerides and cholesterol, and improved glucose tolerance compared with SHR rats. The concentrations of insulin, free fatty acids, and adiponectin were comparable between the two strains. SHR.BN16 rats had significantly lower systolic (18-28 mmHg difference) and diastolic (10-15 mmHg difference) blood pressure throughout the experiment (repeated-measures ANOVA, P < 0.001). The differential segment spans approximately 22 Mb of the telomeric part of the short arm of RNO16. The in silico analyses revealed over 1200 DNA variants between the BN-Lx and SHR genomes in the SHR.BN16 differential segment, 44 of which lead to missense mutations, and only eight of which (in Asb14, Il17rd, Itih1, Syt15, Ercc6, RGD1564958, Tmem161a, and Gatad2a genes) are predicted to be damaging to the protein product. Furthermore, a number of genes within the RNO16 differential segment associated with metabolic syndrome components in human studies showed polymorphisms between SHR and BN-Lx (including Lpl, Nrg3, Pbx4, Cilp2, and Stab1). Our novel congenic rat model demonstrates that a limited genomic region on RNO16 in the SHR significantly affects many of the features of metabolic syndrome.
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Affiliation(s)
- Lucie Šedová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic.,Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Pravenec
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic.,Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Drahomíra Křenová
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic
| | - Ludmila Kazdová
- Department of Metabolism and Diabetes, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Václav Zídek
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michaela Krupková
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic
| | - František Liška
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic
| | - Vladimír Křen
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic.,Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondřej Šeda
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic.,Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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17
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Albert FW, Kruglyak L. The role of regulatory variation in complex traits and disease. Nat Rev Genet 2015; 16:197-212. [DOI: 10.1038/nrg3891] [Citation(s) in RCA: 684] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Hodúlová M, Šedová L, Křenová D, Liška F, Krupková M, Kazdová L, Tremblay J, Hamet P, Křen V, Šeda O. Genomic determinants of triglyceride and cholesterol distribution into lipoprotein fractions in the rat. PLoS One 2014; 9:e109983. [PMID: 25296178 PMCID: PMC4190321 DOI: 10.1371/journal.pone.0109983] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 09/05/2014] [Indexed: 11/18/2022] Open
Abstract
The plasma profile of major lipoprotein classes and its subdivision into particular fractions plays a crucial role in the pathogenesis of atherosclerosis and is a major predictor of coronary artery disease. Our aim was to identify genomic determinants of triglyceride and cholesterol distribution into lipoprotein fractions and lipoprotein particle sizes in the recombinant inbred rat set PXO, in which alleles of two rat models of the metabolic syndrome (SHR and PD inbred strains) segregate together with those from Brown Norway rat strain. Adult male rats of 15 PXO strains (n = 8–13/strain) and two progenitor strains SHR-Lx (n = 13) and BXH2/Cub (n = 18) were subjected to one-week of high-sucrose diet feeding. We performed association analyses of triglyceride (TG) and cholesterol (C) concentrations in 20 lipoprotein fractions and the size of major classes of lipoprotein particles utilizing 704 polymorphic microsatellite markers, the genome-wide significance was validated by 2,000 permutations per trait. Subsequent in silico focusing of the identified quantitative trait loci was completed using a map of over 20,000 single nucleotide polymorphisms. In most of the phenotypes we identified substantial gradient among the strains (e.g. VLDL-TG from 5.6 to 66.7 mg/dl). We have identified 14 loci (encompassing 1 to 65 genes) on rat chromosomes 3, 4, 7, 8, 11 and 12 showing suggestive or significant association to one or more of the studied traits. PXO strains carrying the SHR allele displayed significantly higher values of the linked traits except for LDL-TG and adiposity index. Cholesterol concentrations in large, medium and very small LDL particles were significantly associated to a haplotype block spanning part of a single gene, low density lipoprotein receptor-related protein 1B (Lrp1b). Using genome-wide association we have identified new genetic determinants of triglyceride and cholesterol distribution into lipoprotein fractions in the recombinant inbred panel of rat model strains.
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Affiliation(s)
- Miloslava Hodúlová
- Institute of Biology and Medical Genetics, the First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Lucie Šedová
- Institute of Biology and Medical Genetics, the First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic
| | - Drahomíra Křenová
- Institute of Biology and Medical Genetics, the First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic
| | - František Liška
- Institute of Biology and Medical Genetics, the First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic
| | - Michaela Krupková
- Institute of Biology and Medical Genetics, the First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic
| | - Ludmila Kazdová
- Department of Metabolism and Diabetes, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Johanne Tremblay
- Centre de recherche, Centre hospitalier de l’Université de Montréal (CRCHUM) – Technôpole Angus, Montreal, Quebec, Canada
| | - Pavel Hamet
- Centre de recherche, Centre hospitalier de l’Université de Montréal (CRCHUM) – Technôpole Angus, Montreal, Quebec, Canada
| | - Vladimír Křen
- Institute of Biology and Medical Genetics, the First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic
| | - Ondřej Šeda
- Institute of Biology and Medical Genetics, the First Faculty of Medicine, Charles University and the General Teaching Hospital, Prague, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- * E-mail:
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19
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Abstract
Interindividual differences in many behaviors are partly due to genetic differences, but the identification of the genes and variants that influence behavior remains challenging. Here, we studied an F2 intercross of two outbred lines of rats selected for tame and aggressive behavior toward humans for >64 generations. By using a mapping approach that is able to identify genetic loci segregating within the lines, we identified four times more loci influencing tameness and aggression than by an approach that assumes fixation of causative alleles, suggesting that many causative loci were not driven to fixation by the selection. We used RNA sequencing in 150 F2 animals to identify hundreds of loci that influence brain gene expression. Several of these loci colocalize with tameness loci and may reflect the same genetic variants. Through analyses of correlations between allele effects on behavior and gene expression, differential expression between the tame and aggressive rat selection lines, and correlations between gene expression and tameness in F2 animals, we identify the genes Gltscr2, Lgi4, Zfp40, and Slc17a7 as candidate contributors to the strikingly different behavior of the tame and aggressive animals.
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20
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Kang H, Kerloc'h A, Rotival M, Xu X, Zhang Q, D'Souza Z, Kim M, Scholz JC, Ko JH, Srivastava PK, Genzen JR, Cui W, Aitman TJ, Game L, Melvin JE, Hanidu A, Dimock J, Zheng J, Souza D, Behera AK, Nabozny G, Cook HT, Bassett JHD, Williams GR, Li J, Vignery A, Petretto E, Behmoaras J. Kcnn4 is a regulator of macrophage multinucleation in bone homeostasis and inflammatory disease. Cell Rep 2014; 8:1210-24. [PMID: 25131209 PMCID: PMC4471813 DOI: 10.1016/j.celrep.2014.07.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 05/19/2014] [Accepted: 07/20/2014] [Indexed: 12/29/2022] Open
Abstract
Macrophages can fuse to form osteoclasts in bone or multinucleate giant cells (MGCs) as part of the immune response. We use a systems genetics approach in rat macrophages to unravel their genetic determinants of multinucleation and investigate their role in both bone homeostasis and inflammatory disease. We identify a trans-regulated gene network associated with macrophage multinucleation and Kcnn4 as being the most significantly trans-regulated gene in the network and induced at the onset of fusion. Kcnn4 is required for osteoclast and MGC formation in rodents and humans. Genetic deletion of Kcnn4 reduces macrophage multinucleation through modulation of Ca2+ signaling, increases bone mass, and improves clinical outcome in arthritis. Pharmacological blockade of Kcnn4 reduces experimental glomerulonephritis. Our data implicate Kcnn4 in macrophage multinucleation, identifying it as a potential therapeutic target for inhibition of bone resorption and chronic inflammation. We identified a gene network that regulates macrophage multinucleation and includes Kcnn4 Kcnn4 can be targeted in two inflammatory conditions with macrophage multinucleation Kcnn4 regulates bone mass under physiological conditions Kcnn4 is a drug target for which inhibitors reached phase III of clinical trials
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Affiliation(s)
- Heeseog Kang
- Departments of Orthopaedics and Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Audrey Kerloc'h
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, London W12 0NN, UK
| | - Maxime Rotival
- Integrative Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | - Xiaoqing Xu
- Departments of Orthopaedics and Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Qing Zhang
- Departments of Orthopaedics and Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Zelpha D'Souza
- Physiological Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | - Michael Kim
- Departments of Orthopaedics and Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Jodi Carlson Scholz
- Section of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jeong-Hun Ko
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, London W12 0NN, UK
| | - Prashant K Srivastava
- Integrative Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | - Jonathan R Genzen
- Department of Pathology, University of Utah and ARUP Laboratories, Salt Lake City, UT 84108, USA
| | - Weiguo Cui
- Blood Center of Wisconsin, Milwaukee, WI 53213, USA
| | - Timothy J Aitman
- Physiological Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK
| | - Laurence Game
- Genomics Laboratory, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, London, UK
| | - James E Melvin
- National Institute of Dental and Craniofacial Research (NIDCR), National Institute of Health, Bethesda, MD 20892, USA
| | - Adedayo Hanidu
- Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA
| | - Janice Dimock
- Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA
| | - Jie Zheng
- Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA
| | - Donald Souza
- Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA
| | - Aruna K Behera
- Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA
| | - Gerald Nabozny
- Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA
| | - H Terence Cook
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, London W12 0NN, UK
| | - J H Duncan Bassett
- Molecular Endocrinology Group, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Graham R Williams
- Molecular Endocrinology Group, Department of Medicine, Imperial College London, London W12 0NN, UK
| | - Jun Li
- Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 06877, USA
| | - Agnès Vignery
- Departments of Orthopaedics and Cell Biology, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Enrico Petretto
- Integrative Genomics and Medicine, MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, UK.
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, London W12 0NN, UK.
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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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22
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Abstract
Systems genetics is an approach to understand the flow of biological information that underlies complex traits. It uses a range of experimental and statistical methods to quantitate and integrate intermediate phenotypes, such as transcript, protein or metabolite levels, in populations that vary for traits of interest. Systems genetics studies have provided the first global view of the molecular architecture of complex traits and are useful for the identification of genes, pathways and networks that underlie common human diseases. Given the urgent need to understand how the thousands of loci that have been identified in genome-wide association studies contribute to disease susceptibility, systems genetics is likely to become an increasingly important approach to understanding both biology and disease.
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Affiliation(s)
- Mete Civelek
- 1] Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles. [2] Department of Human Genetics, University of California, Los Angeles. [3] Department of Medicine, A2-237 Center for Health Sciences, University of California, Los Angeles, California 90095-1679, USA
| | - Aldons J Lusis
- 1] Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles. [2] Department of Human Genetics, University of California, Los Angeles. [3] Department of Medicine, A2-237 Center for Health Sciences, University of California, Los Angeles, California 90095-1679, USA
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