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Li H, Ma Y, Li T, Zeng Z, Luo L, Liu X, Li Y, Chen Y. CAPN5 attenuates cigarette smoke extract-induced apoptosis and inflammation in BEAS-2B cells. Tob Induc Dis 2024; 22:TID-22-65. [PMID: 38650847 PMCID: PMC11033979 DOI: 10.18332/tid/186183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 11/05/2023] [Accepted: 03/17/2024] [Indexed: 04/25/2024] Open
Abstract
INTRODUCTION Apoptosis and chronic inflammation are the main phenotypes in chronic obstructive pulmonary disease (COPD) pathogenesis. Cigarette smoke exposure is the leading risk factor for COPD, which causes aberrant airway epithelial structure and function. As a non-classical calpain, the molecular function of calpain5 (CAPN5) in COPD remains unclear. This study investigated the role of CAPN5 in mediating cigarette smoke extract (CSE)-induced apoptosis and inflammation. METHODS Immunohistochemistry (IHC) and Western blotting (WB) were performed to detect the location and expression of CAPN5. In vitro, BEAS-2B cells were transfected with CAPN5 siRNA or CAPN5 plasmid, followed by phosphate-buffered saline (PBS) or cigarette smoke extract (CSE) treatment. The protein expression levels of CAPN5, NF-κB p65, p-p65, IκBα, p-IκBα and apoptosis proteins (BCL-2, BAX) were measured by WB. Flow cytometry (FCM) was performed to analyze the cell apoptosis index. RESULTS CAPN5 was mainly expressed in the airway epithelium and significantly decreased in the COPD-smoker and emphysema-mouse groups. Silencing CAPN5 significantly decreased the protein expression of BCL-2, IκBα, and increased p-p65 and BAX protein expression. Additionally, an increased apoptosis index was detected after silencing CAPN5. Moreover, overexpression of CAPN5 partly inhibited IκBα degradation and p65 activation, and reduced CSE-induced inflammation and apoptosis. CONCLUSIONS These combined results indicate that CAPN5 could protect against CSE-induced apoptosis and inflammation, which may provide a potential therapeutic target for smoking-related COPD.
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Affiliation(s)
- Herui Li
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Diseases, Central South University, Changsha, China
- Clinical Medical Research Center for Respiratory and Critical Care Medicine in Hunan Province, Changsha, China
- Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, China
| | - Yiming Ma
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Diseases, Central South University, Changsha, China
- Clinical Medical Research Center for Respiratory and Critical Care Medicine in Hunan Province, Changsha, China
- Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, China
| | - Tiao Li
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Diseases, Central South University, Changsha, China
- Clinical Medical Research Center for Respiratory and Critical Care Medicine in Hunan Province, Changsha, China
- Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, China
| | - Zihang Zeng
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Diseases, Central South University, Changsha, China
- Clinical Medical Research Center for Respiratory and Critical Care Medicine in Hunan Province, Changsha, China
- Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, China
| | - Lijuan Luo
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Diseases, Central South University, Changsha, China
- Clinical Medical Research Center for Respiratory and Critical Care Medicine in Hunan Province, Changsha, China
- Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, China
| | - Xiangming Liu
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Diseases, Central South University, Changsha, China
- Clinical Medical Research Center for Respiratory and Critical Care Medicine in Hunan Province, Changsha, China
- Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, China
| | - Yi Li
- Department of Infectious Disease, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yan Chen
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Diseases, Central South University, Changsha, China
- Clinical Medical Research Center for Respiratory and Critical Care Medicine in Hunan Province, Changsha, China
- Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, China
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2
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Wang Y, Selvaraj MS, Li X, Li Z, Holdcraft JA, Arnett DK, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Cade BE, Carlson JC, Carson AP, Chen YDI, Curran JE, de Vries PS, Dutcher SK, Ellinor PT, Floyd JS, Fornage M, Freedman BI, Gabriel S, Germer S, Gibbs RA, Guo X, He J, Heard-Costa N, Hildalgo B, Hou L, Irvin MR, Joehanes R, Kaplan RC, Kardia SLR, Kelly TN, Kim R, Kooperberg C, Kral BG, Levy D, Li C, Liu C, Lloyd-Jone D, Loos RJF, Mahaney MC, Martin LW, Mathias RA, Minster RL, Mitchell BD, Montasser ME, Morrison AC, Murabito JM, Naseri T, O’Connell JR, Palmer ND, Preuss MH, Psaty BM, Raffield LM, Rao DC, Redline S, Reiner AP, Rich SS, Ruepena MS, Sheu WHH, Smith JA, Smith A, Tiwari HK, Tsai MY, Viaud-Martinez KA, Wang Z, Yanek LR, Zhao W, Rotter JI, Lin X, Natarajan P, Peloso GM. Rare variants in long non-coding RNAs are associated with blood lipid levels in the TOPMed Whole Genome Sequencing Study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.28.23291966. [PMID: 37425772 PMCID: PMC10327287 DOI: 10.1101/2023.06.28.23291966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Long non-coding RNAs (lncRNAs) are known to perform important regulatory functions. Large-scale whole genome sequencing (WGS) studies and new statistical methods for variant set tests now provide an opportunity to assess the associations between rare variants in lncRNA genes and complex traits across the genome. In this study, we used high-coverage WGS from 66,329 participants of diverse ancestries with blood lipid levels (LDL-C, HDL-C, TC, and TG) in the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) program to investigate the role of lncRNAs in lipid variability. We aggregated rare variants for 165,375 lncRNA genes based on their genomic locations and conducted rare variant aggregate association tests using the STAAR (variant-Set Test for Association using Annotation infoRmation) framework. We performed STAAR conditional analysis adjusting for common variants in known lipid GWAS loci and rare coding variants in nearby protein coding genes. Our analyses revealed 83 rare lncRNA variant sets significantly associated with blood lipid levels, all of which were located in known lipid GWAS loci (in a ±500 kb window of a Global Lipids Genetics Consortium index variant). Notably, 61 out of 83 signals (73%) were conditionally independent of common regulatory variations and rare protein coding variations at the same loci. We replicated 34 out of 61 (56%) conditionally independent associations using the independent UK Biobank WGS data. Our results expand the genetic architecture of blood lipids to rare variants in lncRNA, implicating new therapeutic opportunities.
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Affiliation(s)
- Yuxuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Margaret Sunitha Selvaraj
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology & Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jacob A. Holdcraft
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Donna K. Arnett
- Provost Office, University of South Carolina, Columbia, SC, USA
- Department of Epidemiology and Biostatistics, University of South Carolina Arnold School of Public Health, Columbia, SC, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Brian E. Cade
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Jenna C. Carlson
- Department of Human Genetics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Susan K. Dutcher
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick T. Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - James S. Floyd
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Myriam Fornage
- Center for Human Genetics, University of Texas Health at Houston, Houston, TX, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | | | | | - Richard A. Gibbs
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Nancy Heard-Costa
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Bertha Hildalgo
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Marguerite R. Irvin
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Roby Joehanes
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sharon LR. Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Tanika N. Kelly
- Department of Medicine, Division of Nephrology, University of Illinois Chicago, Chicago, IL, USA
| | - Ryan Kim
- Psomagen, Inc. (formerly Macrogen USA), Rockville, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brian G. Kral
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Changwei Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Don Lloyd-Jone
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Ruth JF. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- NNF Center for Basic Metabolic Research, University of Copenhagen, Cophenhagen, Denmark
| | - Michael C. Mahaney
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Lisa W. Martin
- George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Rasika A. Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryan L. Minster
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Braxton D. Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - May E. Montasser
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joanne M. Murabito
- Framingham Heart Study, Framingham, MA, USA
- Department of Medicine, Boston Medical Center, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | | | - Jeffrey R. O’Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Michael H. Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dabeeru C. Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | | | | | - Jennifer A. Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Albert Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Hemant K. Tiwari
- Department of Biostatistics, University of Alabama, Birmingham, AL, USA
| | - Michael Y. Tsai
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | | | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisa R. Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wei Zhao
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xihong Lin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
| | - Pradeep Natarajan
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
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3
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Juibari AD, Rezadoost MH, Soleimani M. The key role of Calpain in COVID-19 as a therapeutic strategy. Inflammopharmacology 2022; 30:1479-1491. [PMID: 35635676 PMCID: PMC9149670 DOI: 10.1007/s10787-022-01002-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/24/2022] [Indexed: 12/02/2022]
Abstract
COVID-19 is one of the viral diseases that has caused many deaths and financial losses to humans. Using the available information, this virus appears to activate the host cell-death mechanism through Calpain activation. Calpain inhibition can stop its downstream cascade reactions that cause cell death. Given the main roles of Calpain in the entry and pathogenicity of the SARS-CoV-2, its inhibition can be effective in controlling the COVID-19. This review describes how the virus activates Calpain by altering calcium flow. When Calpain was activated, the virus can enter the target cell. Subsequently, many complications of the disease, such as inflammation, cytokine storm and pulmonary fibrosis, are caused by virus-activated Calpain function. Calpain inhibitors appear to be a potential drug to control the disease and prevent death from COVID-19.
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Affiliation(s)
- Aref Doozandeh Juibari
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Masoud Soleimani
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modarres University, Tehran, Iran
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4
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Declercq M, de Zeeuw P, Conchinha NV, Geldhof V, Ramalho AS, García-Caballero M, Brepoels K, Ensinck M, Carlon MS, Bird MJ, Vinckier S, Proesmans M, Vermeulen F, Dupont L, Ghesquière B, Dewerchin M, Carmeliet P, Cassiman D, Treps L, Eelen G, Witters P. Transcriptomic analysis of CFTR-impaired endothelial cells reveals a pro-inflammatory phenotype. Eur Respir J 2021; 57:13993003.00261-2020. [PMID: 33184117 DOI: 10.1183/13993003.00261-2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 10/04/2020] [Indexed: 12/15/2022]
Abstract
Cystic fibrosis (CF) is a life-threatening disorder characterised by decreased pulmonary mucociliary and pathogen clearance, and an exaggerated inflammatory response leading to progressive lung damage. CF is caused by bi-allelic pathogenic variants of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encodes a chloride channel. CFTR is expressed in endothelial cells (ECs) and EC dysfunction has been reported in CF patients, but a role for this ion channel in ECs regarding CF disease progression is poorly described.We used an unbiased RNA sequencing approach in complementary models of CFTR silencing and blockade (by the CFTR inhibitor CFTRinh-172) in human ECs to characterise the changes upon CFTR impairment. Key findings were further validated in vitro and in vivo in CFTR-knockout mice and ex vivo in CF patient-derived ECs.Both models of CFTR impairment revealed that EC proliferation, migration and autophagy were downregulated. Remarkably though, defective CFTR function led to EC activation and a persisting pro-inflammatory state of the endothelium with increased leukocyte adhesion. Further validation in CFTR-knockout mice revealed enhanced leukocyte extravasation in lung and liver parenchyma associated with increased levels of EC activation markers. In addition, CF patient-derived ECs displayed increased EC activation markers and leukocyte adhesion, which was partially rescued by the CFTR modulators VX-770 and VX-809.Our integrated analysis thus suggests that ECs are no innocent bystanders in CF pathology, but rather may contribute to the exaggerated inflammatory phenotype, raising the question of whether normalisation of vascular inflammation might be a novel therapeutic strategy to ameliorate the disease severity of CF.
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Affiliation(s)
- Mathias Declercq
- Dept of Development and Regeneration, CF Centre, Woman and Child, KU Leuven, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Centre for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Dept of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Pauline de Zeeuw
- Laboratory of Angiogenesis and Vascular Metabolism, Centre for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Dept of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Nadine V Conchinha
- Laboratory of Angiogenesis and Vascular Metabolism, Centre for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Dept of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Vincent Geldhof
- Laboratory of Angiogenesis and Vascular Metabolism, Centre for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Dept of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Anabela S Ramalho
- Stem Cell and Developmental Biology, CF Centre, Woman and Child, KU Leuven, Leuven, Belgium
| | - Melissa García-Caballero
- Laboratory of Angiogenesis and Vascular Metabolism, Centre for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Dept of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Katleen Brepoels
- Laboratory of Angiogenesis and Vascular Metabolism, Centre for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Dept of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Marjolein Ensinck
- Laboratory for Molecular Virology and Drug Discovery, Dept of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Marianne S Carlon
- Laboratory for Molecular Virology and Drug Discovery, Dept of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Matthew J Bird
- Laboratory of Hepatology, Dept of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium.,Metabolomics Expertise Centre, Centre for Cancer Biology, VIB, Leuven, Belgium
| | - Stefan Vinckier
- Laboratory of Angiogenesis and Vascular Metabolism, Centre for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Dept of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | | | - François Vermeulen
- Dept of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Lieven Dupont
- Dept of Pneumology, University Hospitals Leuven, Leuven, Belgium
| | - Bart Ghesquière
- Metabolomics Expertise Centre, Centre for Cancer Biology, VIB, Leuven, Belgium.,Metabolomics Expertise Centre, Dept of Oncology, KU Leuven, Leuven, Belgium
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Centre for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Dept of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Centre for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Dept of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
| | - David Cassiman
- Laboratory of Hepatology, Dept of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium.,Centre of Metabolic Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Lucas Treps
- Laboratory of Angiogenesis and Vascular Metabolism, Centre for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Dept of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.,Equal co-authorship
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Centre for Cancer Biology, VIB, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Dept of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.,Equal co-authorship
| | - Peter Witters
- Dept of Development and Regeneration, CF Centre, Woman and Child, KU Leuven, Leuven, Belgium.,Dept of Paediatrics, University Hospitals Leuven, Leuven, Belgium.,Centre of Metabolic Diseases, University Hospitals Leuven, Leuven, Belgium.,Equal co-authorship
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5
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Medeiros de Oliveira Silva R, Bonvino Stafuzza N, de Oliveira Fragomeni B, Miguel Ferreira de Camargo G, Matos Ceacero T, Noely dos Santos Gonçalves Cyrillo J, Baldi F, Augusti Boligon A, Zerlotti Mercadante ME, Lino Lourenco D, Misztal I, Galvão de Albuquerque L. Genome-Wide Association Study for Carcass Traits in an Experimental Nelore Cattle Population. PLoS One 2017; 12:e0169860. [PMID: 28118362 PMCID: PMC5261778 DOI: 10.1371/journal.pone.0169860] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 12/22/2016] [Indexed: 12/22/2022] Open
Abstract
The purpose of this study was to identify genomic regions associated with carcass traits in an experimental Nelore cattle population. The studied data set contained 2,306 ultrasound records for longissimus muscle area (LMA), 1,832 for backfat thickness (BF), and 1,830 for rump fat thickness (RF). A high-density SNP panel (BovineHD BeadChip assay 700k, Illumina Inc., San Diego, CA) was used for genotyping. After genomic data quality control, 437,197 SNPs from 761 animals were available, of which 721 had phenotypes for LMA, 669 for BF, and 718 for RF. The SNP solutions were estimated using a single-step genomic BLUP approach (ssGWAS), which calculated the variance for windows of 50 consecutive SNPs and the regions that accounted for more than 0.5% of the additive genetic variance were used to search for candidate genes. The results indicated that 12, 18, and 15 different windows were associated to LMA, BF, and RF, respectively. Confirming the polygenic nature of the studied traits, 43, 65, and 53 genes were found in those associated windows, respectively for LMA, BF, and RF. Among the candidate genes, some of them, which already had their functions associated with the expression of energy metabolism, were found associated with fat deposition in this study. In addition, ALKBH3 and HSD17B12 genes, which are related in fibroblast death and metabolism of steroids, were found associated with LMA. The results presented here should help to better understand the genetic and physiologic mechanism regulating the muscle tissue deposition and subcutaneous fat cover expression of Zebu animals. The identification of candidate genes should contribute for Zebu breeding programs in order to consider carcass traits as selection criteria in their genetic evaluation.
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Affiliation(s)
- Rafael Medeiros de Oliveira Silva
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
| | - Nedenia Bonvino Stafuzza
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
| | | | - Gregório Miguel Ferreira de Camargo
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
| | - Thaís Matos Ceacero
- APTA Center of Beef Cattle, Animal Science Institute, Sertaozinho, SP, Brazil
| | | | - Fernando Baldi
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
| | | | | | - Daniela Lino Lourenco
- University of Georgia, Department of Animal and Dairy Science, Athens, GA, United States of America
| | - Ignacy Misztal
- University of Georgia, Department of Animal and Dairy Science, Athens, GA, United States of America
| | - Lucia Galvão de Albuquerque
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
- * E-mail:
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6
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Bassuk AG, Yeh S, Wu S, Martin DF, Tsang SH, Gakhar L, Mahajan VB. Structural modeling of a novel CAPN5 mutation that causes uveitis and neovascular retinal detachment. PLoS One 2015; 10:e0122352. [PMID: 25856303 PMCID: PMC4391918 DOI: 10.1371/journal.pone.0122352] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/14/2015] [Indexed: 01/03/2023] Open
Abstract
CAPN5 mutations have been linked to autosomal dominant neovascular inflammatory vitreoretinopathy (ADNIV), a blinding autoimmune eye disease. Here, we link a new CAPN5 mutation to ADNIV and model the three-dimensional structure of the resulting mutant protein. In our study, a kindred with inflammatory vitreoretinopathy was evaluated by clinical eye examinations, DNA sequencing, and protein structural modeling to investigate the disease-causing mutation. Two daughters of an affected mother demonstrated symptoms of stage III ADNIV, with posterior uveitis, cystoid macular edema, intraocular fibrosis, retinal neovascularization, retinal degeneration, and cataract. The women also harbored a novel guanine to thymine (c.750G>T, p.Lys250Asn) missense mutation in exon 6 of CAPN5, a gene that encodes a calcium-activated cysteine protease, calpain-5. Modeling based on the structures of all known calpains revealed the mutation falls within a calcium-sensitive flexible gating loop that controls access to the catalytic groove. Three-dimensional modeling placed the new mutation in a region adjacent to two previously identified disease-causing mutations, all three of which likely disrupt hydrogen bonding within the gating loop, yielding a CAPN5 with altered enzymatic activity. This is the third case of a CAPN5 mutation leading to inherited uveitis and neovascular vitreoretinopathy, suggesting patients with ADNIV features should be tested for CAPN5 mutations. Structural modeling of novel variants can be used to support mechanistic consequences of the disease-causing variants.
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Affiliation(s)
- Alexander G. Bassuk
- Department of Pediatrics, University of Iowa, Iowa City, IA, United States of America
- Omics Lab, University of Iowa, Iowa City, IA, United States of America
| | - Steven Yeh
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, GA, United States of America
| | - Shu Wu
- Omics Lab, University of Iowa, Iowa City, IA, United States of America
| | - Daniel F. Martin
- Cole Eye Institute, Cleveland Clinic, Cleveland, OH, United States of America
| | - Stephen H. Tsang
- Bernard & Shirlee Brown Glaucoma Laboratory and Barbara & Donald Jonas Laboratory of Regenerative Medicine, Departments of Ophthalmology and Pathology and Cell Biology, Columbia University, New York, NY, United States of America
| | - Lokesh Gakhar
- Department of Biochemistry, University of Iowa, Iowa City, IA, United States of America
- Protein Crystallography Facility, University of Iowa, Iowa City, IA, United States of America
| | - Vinit B. Mahajan
- Omics Lab, University of Iowa, Iowa City, IA, United States of America
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, United States of America
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7
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Singh R, Brewer MK, Mashburn CB, Lou D, Bondada V, Graham B, Geddes JW. Calpain 5 is highly expressed in the central nervous system (CNS), carries dual nuclear localization signals, and is associated with nuclear promyelocytic leukemia protein bodies. J Biol Chem 2014; 289:19383-94. [PMID: 24838245 PMCID: PMC4094050 DOI: 10.1074/jbc.m114.575159] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 05/14/2014] [Indexed: 12/20/2022] Open
Abstract
Calpain 5 (CAPN5) is a non-classical member of the calpain family. It lacks the EF hand motif characteristic of classical calpains but retains catalytic and Ca(2+) binding domains, and it contains a unique C-terminal domain. TRA-3, an ortholog of CAPN5, has been shown to be involved in necrotic cell death in Caenorhabditis elegans. CAPN5 is expressed throughout the CNS, but its expression relative to other calpains and subcellular distribution has not been investigated previously. Based on relative mRNA levels, Capn5 is the second most highly expressed calpain in the rat CNS, with Capn2 mRNA being the most abundant. Unlike classical calpains, CAPN5 is a non-cytosolic protein localized to the nucleus and extra-nuclear locations. CAPN5 possesses two nuclear localization signals (NLS): an N-terminal monopartite NLS and a unique bipartite NLS closer to the C terminus. The C-terminal NLS contains a SUMO-interacting motif that contributes to nuclear localization, and mutation or deletion of both NLS renders CAPN5 exclusively cytosolic. Dual NLS motifs are common among transcription factors. Interestingly, CAPN5 is found in punctate domains associated with promyelocytic leukemia (PML) protein within the nucleus. PML nuclear bodies are implicated in transcriptional regulation, cell differentiation, cellular response to stress, viral defense, apoptosis, and cell senescence as well as protein sequestration, modification, and degradation. The roles of nuclear CAPN5 remain to be determined.
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Affiliation(s)
- Ranjana Singh
- From the Spinal Cord and Brain Injury Research Center and the Department of Anatomy and Neurobiology, University of Kentucky, Lexington, Kentucky 40536
| | | | | | - Dingyuan Lou
- From the Spinal Cord and Brain Injury Research Center and
| | - Vimala Bondada
- From the Spinal Cord and Brain Injury Research Center and
| | | | - James W Geddes
- From the Spinal Cord and Brain Injury Research Center and the Department of Anatomy and Neurobiology, University of Kentucky, Lexington, Kentucky 40536
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Calpain-5 mutations cause autoimmune uveitis, retinal neovascularization, and photoreceptor degeneration. PLoS Genet 2012; 8:e1003001. [PMID: 23055945 PMCID: PMC3464205 DOI: 10.1371/journal.pgen.1003001] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 08/14/2012] [Indexed: 12/30/2022] Open
Abstract
Autosomal dominant neovascular inflammatory vitreoretinopathy (ADNIV) is an autoimmune condition of the eye that sequentially mimics uveitis, retinitis pigmentosa, and proliferative diabetic retinopathy as it progresses to complete blindness. We identified two different missense mutations in the CAPN5 gene in three ADNIV kindreds. CAPN5 encodes calpain-5, a calcium-activated cysteine protease that is expressed in retinal photoreceptor cells. Both mutations cause mislocalization from the cell membrane to the cytosol, and structural modeling reveals that both mutations lie within a calcium-sensitive domain near the active site. CAPN5 is only the second member of the large calpain gene family to cause a human Mendelian disorder, and this is the first report of a specific molecular cause for autoimmune eye disease. Further investigation of these mutations is likely to provide insight into the pathophysiologic mechanisms of common diseases ranging from autoimmune disorders to diabetic retinopathy.
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Abstract
Several candidate gene studies on the metabolic syndrome (MetS) have been conducted. However, for most single nucleotide polymorphisms (SNPs) no systematic review on their association with MetS exists. A systematic electronic literature search was conducted until the 2nd of June 2010, using HuGE Navigator. English language articles were selected. Only genes of which at least one SNP-MetS association was studied in an accumulative total population ≥ 4000 subjects were included. Meta-analyses were conducted on SNPs with three or more studies available in a generally healthy population. In total 88 studies on 25 genes were reviewed. Additionally, for nine SNPs in seven genes (GNB3, PPARG, TCF7L2, APOA5, APOC3, APOE, CETP) a meta-analysis was conducted. The minor allele of rs9939609 (FTO), rs7903146 (TCF7L2), C56G (APOA5), T1131C (APOA5), C482T (APOC3), C455T (APOC3) and 174G>C (IL6) were more prevalent in subjects with MetS, whereas the minor allele of Taq-1B (CETP) was less prevalent in subjects with the MetS. After having systematically reviewed the most studied SNP-MetS associations, we found evidence for an association with the MetS for eight SNPs, mostly located in genes involved in lipid metabolism.
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Affiliation(s)
- C M Povel
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands.
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10
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Abstract
Calpain has long been an enigmatic enzyme, although it is involved in a variety of biological phenomena. Recent progress in calpain genetics has highlighted numerous physiological contexts in which the functions of calpain are of great significance. This review focuses on recent findings in the field of calpain genetics and the importance of calpain function. Calpain is an intracellular Ca(2+)-dependent cysteine protease (EC 3.4.22.17; Clan CA, family C02) found in almost all eukaryotes. It is also present in a few bacteria, but not in archaebacteria. Calpain has limited proteolytic activity; rather, it transforms or modulates the structure and/or activity of its substrates. It is, therefore, referred to as a 'modulator protease'. Within the human genome, 15 genes (CAPN1-3, CAPN5-16) encode a calpain-like protease (CysPc) domain along with several different functional domains. Thus, calpains can be regarded as a distinct family of versatile enzymes that fulfil numerous tasks in vivo. Genetic studies show that a variety of defects in many different organisms, including lethality, muscular dystrophies and gastropathy, actually stem from calpain deficiencies. The cause-effect relationships identified by these studies form the basis for ongoing and future studies regarding the physiological role of calpains.
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Affiliation(s)
- Hiroyuki Sorimachi
- Calpain Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo156-8506, Japan.
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Abstract
The calpains are a conserved family of cysteine proteinases that catalyse the controlled proteolysis of many specific substrates. Calpain activity is implicated in several fundamental physiological processes, including cytoskeletal remodelling, cellular signalling, apoptosis and cell survival. Calpain expression is altered during tumorigenesis, and the proteolysis of numerous substrates, such as inhibitors of nuclear factor-κB (IκB), focal adhesion proteins (including, focal adhesion kinase and talin) and proto-oncogenes (for example, MYC), has been implicated in tumour pathogenesis. Recent evidence indicates that the increased expression of certain family members might influence the response to cancer therapies, providing justification for the development of novel calpain inhibitors.
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Affiliation(s)
- Sarah J Storr
- University of Nottingham, School of Molecular Medical Sciences, Nottingham NG5 1PB, UK
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Sorimachi H, Hata S, Ono Y. Calpain chronicle--an enzyme family under multidisciplinary characterization. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2011; 87:287-327. [PMID: 21670566 PMCID: PMC3153876 DOI: 10.2183/pjab.87.287] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Accepted: 03/04/2011] [Indexed: 05/29/2023]
Abstract
Calpain is an intracellular Ca2+-dependent cysteine protease (EC 3.4.22.17; Clan CA, family C02) discovered in 1964. It was also called CANP (Ca2+-activated neutral protease) as well as CASF, CDP, KAF, etc. until 1990. Calpains are found in almost all eukaryotes and a few bacteria, but not in archaebacteria. Calpains have a limited proteolytic activity, and function to transform or modulate their substrates' structures and activities; they are therefore called, "modulator proteases." In the human genome, 15 genes--CAPN1, CAPN2, etc.--encode a calpain-like protease domain. Their products are calpain homologs with divergent structures and various combinations of functional domains, including Ca2+-binding and microtubule-interaction domains. Genetic studies have linked calpain deficiencies to a variety of defects in many different organisms, including lethality, muscular dystrophies, gastropathy, and diabetes. This review of the study of calpains focuses especially on recent findings about their structure-function relationships. These discoveries have been greatly aided by the development of 3D structural studies and genetic models.
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Affiliation(s)
- Hiroyuki Sorimachi
- Calpain Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
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Sáez ME, Grilo A, Morón FJ, Manzano L, Martínez-Larrad MT, González-Pérez A, Serrano-Hernando J, Ruiz A, Ramírez-Lorca R, Serrano-Ríos M. Interaction between Calpain 5, Peroxisome proliferator-activated receptor-gamma and Peroxisome proliferator-activated receptor-delta genes: a polygenic approach to obesity. Cardiovasc Diabetol 2008; 7:23. [PMID: 18657264 PMCID: PMC2527300 DOI: 10.1186/1475-2840-7-23] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Accepted: 07/25/2008] [Indexed: 11/10/2022] Open
Abstract
Context Obesity is a multifactorial disorder, that is, a disease determined by the combined effect of genes and environment. In this context, polygenic approaches are needed. Objective To investigate the possibility of the existence of a crosstalk between the CALPAIN 10 homologue CALPAIN 5 and nuclear receptors of the peroxisome proliferator-activated receptors family. Design Cross-sectional, genetic association study and gene-gene interaction analysis. Subjects The study sample comprise 1953 individuals, 725 obese (defined as body mass index ≥ 30) and 1228 non obese subjects. Results In the monogenic analysis, only the peroxisome proliferator-activated receptor delta (PPARD) gene was associated with obesity (OR = 1.43 [1.04–1.97], p = 0.027). In addition, we have found a significant interaction between CAPN5 and PPARD genes (p = 0.038) that reduces the risk for obesity in a 55%. Conclusion Our results suggest that CAPN5 and PPARD gene products may also interact in vivo.
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Affiliation(s)
- María E Sáez
- Departamento de Genómica Estructural, Neocodex, C/.,Charles Darwin 6, Acc. A, 41092, Sevilla, Spain.
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