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Wei W, Pan J, Wang J, Mao S, Qian Y, Lin X, Ling Q, Ye W, Zhou Y, Zhao Y, Huang J, Huang X, Ma Z, Wang H, Li C, Sun J, Jin J. circSLC25A13 acts as a ceRNA to regulate AML progression via miR-616-3p/ADCY2 axis. Mol Carcinog 2023; 62:1546-1562. [PMID: 37493101 DOI: 10.1002/mc.23598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/24/2023] [Accepted: 06/08/2023] [Indexed: 07/27/2023]
Abstract
Circular RNAs (circRNAs), a type of endogenous noncoding RNA (ncRNA), exert vital roles in leukemia progression and are promising prognostic factors. Here, we report a novel circRNA, circSLC25A13 (hsa_circ_0081188), which was increased in acute myeloid leukemia (AML) patients with poor overall survival (OS) comparing to patients with good prognosis. Knockdown of circSLC25A13 in AML cells inhibited proliferation and increased cell apoptosis in vitro and in vivo. Enhanced circSLC25A13 expression promoted the survival of AML cells. Mechanistically, circSLC25A13 played as a microRNA sponge of miR-616-3p, which inhibited the expression of adenylate cyclase 2 (ADCY2). Downregulation of miR-616-3p and overexpression of ADCY2 partially rescued circSLC25A13 deficient induced cell growth arrest. In summary, through competitive absorption of miR-616-3p and thereby upregulating ADCY2 expression, circSLC25A13 promoted AML progression. Moreover, circSLC25A13 may represent a potential novel biomarker for the prognosis of AML and offer a potential therapeutic target for AML treatment.
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Affiliation(s)
- Wenwen Wei
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Jiajia Pan
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Jinghan Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Shihui Mao
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Yu Qian
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Xiangjie Lin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Qing Ling
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Wenle Ye
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Yutong Zhou
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Yanchun Zhao
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Jiansong Huang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Xin Huang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Zhixin Ma
- Department of Laboratorial Medicine, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Huanping Wang
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Chenying Li
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Jie Sun
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Key Laboratory of Hematologic Malignancy, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang Provincial Clinical Research Center for Hematological Disorders, Hangzhou, Zhejiang, People's Republic of China
- Zhejiang University Cancer Center, Hangzhou, Zhejiang, People's Republic of China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, People's Republic of China
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Carlin DE, Larsen SJ, Sirupurapu V, Cho MH, Silverman EK, Baumbach J, Ideker T. Hierarchical association of COPD to principal genetic components of biological systems. PLoS One 2023; 18:e0286064. [PMID: 37228113 DOI: 10.1371/journal.pone.0286064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 05/08/2023] [Indexed: 05/27/2023] Open
Abstract
Many disease-causing genetic variants converge on common biological functions and pathways. Precisely how to incorporate pathway knowledge in genetic association studies is not yet clear, however. Previous approaches employ a two-step approach, in which a regular association test is first performed to identify variants associated with the disease phenotype, followed by a test for functional enrichment within the genes implicated by those variants. Here we introduce a concise one-step approach, Hierarchical Genetic Analysis (Higana), which directly computes phenotype associations against each function in the large hierarchy of biological functions documented by the Gene Ontology. Using this approach, we identify risk genes and functions for Chronic Obstructive Pulmonary Disease (COPD), highlighting microtubule transport, muscle adaptation, and nicotine receptor signaling pathways. Microtubule transport has not been previously linked to COPD, as it integrates genetic variants spread over numerous genes. All associations validate strongly in a second COPD cohort.
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Affiliation(s)
- Daniel E Carlin
- Department of Medicine, Division of Genetics, University of California San Diego, La Jolla, CA, United States of America
| | | | - Vikram Sirupurapu
- Department of Medicine, Division of Genetics, University of California San Diego, La Jolla, CA, United States of America
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
| | - Jan Baumbach
- Department of Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Trey Ideker
- Department of Medicine, Division of Genetics, University of California San Diego, La Jolla, CA, United States of America
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3
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Faherty L, Kenny S, Cloonan SM. Iron and mitochondria in the susceptibility, pathogenesis and progression of COPD. Clin Sci (Lond) 2023; 137:219-237. [PMID: 36729089 DOI: 10.1042/cs20210504] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 02/03/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a debilitating lung disease characterised by airflow limitation, chronic bronchitis, emphysema and airway remodelling. Cigarette smoke is considered the primary risk factor for the development of COPD; however, genetic factors, host responses and infection also play an important role. Accumulating evidence highlights a role for iron dyshomeostasis and cellular iron accumulation in the lung as a key contributing factor in the development and pathogenesis of COPD. Recent studies have also shown that mitochondria, the central players in cellular iron utilisation, are dysfunctional in respiratory cells in individuals with COPD, with alterations in mitochondrial bioenergetics and dynamics driving disease progression. Understanding the molecular mechanisms underlying the dysfunction of mitochondria and cellular iron metabolism in the lung may unveil potential novel investigational avenues and therapeutic targets to aid in the treatment of COPD.
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Affiliation(s)
- Lynne Faherty
- School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
| | - Sarah Kenny
- School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
| | - Suzanne M Cloonan
- School of Medicine, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, New York, NY, U.S.A
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4
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Aloufi N, Alluli A, Eidelman DH, Baglole CJ. Aberrant Post-Transcriptional Regulation of Protein Expression in the Development of Chronic Obstructive Pulmonary Disease. Int J Mol Sci 2021; 22:ijms222111963. [PMID: 34769392 PMCID: PMC8584689 DOI: 10.3390/ijms222111963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is an incurable and prevalent respiratory disorder that is characterized by chronic inflammation and emphysema. COPD is primarily caused by cigarette smoke (CS). CS alters numerous cellular processes, including the post-transcriptional regulation of mRNAs. The identification of RNA-binding proteins (RBPs), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) as main factors engaged in the regulation of RNA biology opens the door to understanding their role in coordinating physiological cellular processes. Dysregulation of post-transcriptional regulation by foreign particles in CS may lead to the development of diseases such as COPD. Here we review current knowledge about post-transcriptional events that may be involved in the pathogenesis of COPD.
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Affiliation(s)
- Noof Aloufi
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; (N.A.); (A.A.)
- Department of Medical Laboratory Technology, Applied Medical Science, Taibah University, Universities Road, Medina P.O. Box 344, Saudi Arabia
| | - Aeshah Alluli
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; (N.A.); (A.A.)
| | - David H. Eidelman
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada;
| | - Carolyn J. Baglole
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; (N.A.); (A.A.)
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada;
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
- Correspondence:
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5
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Ostrom KF, LaVigne JE, Brust TF, Seifert R, Dessauer CW, Watts VJ, Ostrom RS. Physiological Roles of Mammalian Transmembrane Adenylyl Cyclase Isoforms. Physiol Rev 2021; 102:815-857. [PMID: 34698552 DOI: 10.1152/physrev.00013.2021] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Adenylyl cyclases (ACs) catalyze the conversion of ATP to the ubiquitous second messenger cAMP. Mammals possess nine isoforms of transmembrane ACs, dubbed AC1-9, that serve as major effector enzymes of G protein-coupled receptors. The transmembrane ACs display varying expression patterns across tissues, giving potential for them having a wide array of physiologic roles. Cells express multiple AC isoforms, implying that ACs have redundant functions. Furthermore, all transmembrane ACs are activated by Gαs so it was long assumed that all ACs are activated by Gαs-coupled GPCRs. AC isoforms partition to different microdomains of the plasma membrane and form prearranged signaling complexes with specific GPCRs that contribute to cAMP signaling compartments. This compartmentation allows for a diversity of cellular and physiological responses by enabling unique signaling events to be triggered by different pools of cAMP. Isoform specific pharmacological activators or inhibitors are lacking for most ACs, making knockdown and overexpression the primary tools for examining the physiological roles of a given isoform. Much progress has been made in understanding the physiological effects mediated through individual transmembrane ACs. GPCR-AC-cAMP signaling pathways play significant roles in regulating functions of every cell and tissue, so understanding each AC isoform's role holds potential for uncovering new approaches for treating a vast array of pathophysiological conditions.
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Affiliation(s)
- Katrina F Ostrom
- W. M. Keck Science Department, Claremont McKenna College, Claremont, CA, United States
| | - Justin E LaVigne
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States
| | - Tarsis F Brust
- Department of Pharmaceutical Sciences, Palm Beach Atlantic University, West Palm Beach, FL, United States
| | - Roland Seifert
- Institute of Pharmacology, Hannover Medical School, Hannover, Germany
| | - Carmen W Dessauer
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Sciences Center at Houston, Houston, Texas, United States
| | - Val J Watts
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States.,Purdue Institute for Drug Discovery, Purdue University, West Lafayette, IN, United States.,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, United States
| | - Rennolds S Ostrom
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, United States
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Ye Z, Mo C, Liu S, Hatch KS, Gao S, Ma Y, Hong LE, Thompson PM, Jahanshad N, Acheson A, Garavan H, Shen L, Nichols TE, Kochunov P, Chen S, Ma T. White Matter Integrity and Nicotine Dependence: Evaluating Vertical and Horizontal Pleiotropy. Front Neurosci 2021; 15:738037. [PMID: 34720862 PMCID: PMC8551454 DOI: 10.3389/fnins.2021.738037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/01/2021] [Indexed: 01/26/2023] Open
Abstract
Tobacco smoking is an addictive behavior that supports nicotine dependence and is an independent risk factor for cancer and other illnesses. Its neurogenetic mechanisms are not fully understood but may act through alterations in the cerebral white matter (WM). We hypothesized that the vertical pleiotropic pathways, where genetic variants influence a trait that in turn influences another trait, link genetic factors, integrity of cerebral WM, and nicotine addiction. We tested this hypothesis using individual genetic factors, WM integrity measured by fractional anisotropy (FA), and nicotine dependence-related smoking phenotypes, including smoking status (SS) and cigarettes per day (CPDs), in a large epidemiological sample collected by the UK Biobank. We performed a genome-wide association study (GWAS) to identify previously reported loci associated with smoking behavior. Smoking was found to be associated with reduced WM integrity in multiple brain regions. We then evaluated two competing vertical pathways: Genes → WM integrity → Smoking versus Genes → Smoking → WM integrity and a horizontal pleiotropy pathway where genetic factors independently affect both smoking and WM integrity. The causal pathway analysis identified 272 pleiotropic single-nucleotide polymorphisms (SNPs) whose effects on SS were mediated by FA, as well as 22 pleiotropic SNPs whose effects on FA were mediated by CPD. These SNPs were mainly located in important susceptibility genes for smoking-induced diseases NCAM1 and IREB2. Our findings revealed the role of cerebral WM in the maintenance of the complex addiction and provided potential genetic targets for future research in examining how changes in WM integrity contribute to the nicotine effects on the brain.
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Affiliation(s)
- Zhenyao Ye
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Chen Mo
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Song Liu
- School of Computer Science and Technology, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Kathryn S Hatch
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Si Gao
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Yizhou Ma
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - L Elliot Hong
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, United States
| | - Neda Jahanshad
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, United States
| | - Ashley Acheson
- Department of Psychiatry and Behavioral Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Hugh Garavan
- Department of Psychiatry, The University of Vermont, Burlington, VT, United States
| | - Li Shen
- Department of Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Thomas E Nichols
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Peter Kochunov
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Shuo Chen
- Maryland Psychiatric Research Center, Department of Psychiatry, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
- Division of Biostatistics and Bioinformatics, Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Tianzhou Ma
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, College Park, MD, United States
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Mizumura K, Gon Y. Iron-Regulated Reactive Oxygen Species Production and Programmed Cell Death in Chronic Obstructive Pulmonary Disease. Antioxidants (Basel) 2021; 10:antiox10101569. [PMID: 34679704 PMCID: PMC8533398 DOI: 10.3390/antiox10101569] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 01/01/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by persistent respiratory symptoms and airflow limitation. However, the pathogenesis of COPD remains unclear. Currently, it is known to involve the loss of alveolar surface area (emphysema) and airway inflammation (bronchitis), primarily due to exposure to cigarette smoke (CS). CS causes epithelial cell death, resulting in pulmonary emphysema. Moreover, CS induces iron accumulation in the mitochondria and cytosol, resulting in programmed cell death. Although apoptosis has long been investigated as the sole form of programmed cell death in COPD, accumulating evidence indicates that a regulated form of necrosis, called necroptosis, and a unique iron-dependent form of non-apoptotic cell death, called ferroptosis, is implicated in the pathogenesis of COPD. Iron metabolism plays a key role in producing reactive oxygen species (ROS), including mitochondrial ROS and lipid peroxidation end-products, and activating both necroptosis and ferroptosis. This review outlines recent studies exploring CS-mediated iron metabolism and ROS production, along with the regulation of programmed cell death in COPD. Elucidating the mechanisms of these pathways may provide novel therapeutic targets for COPD.
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Genetic Susceptibility to Pneumonia: A GWAS Meta-Analysis Between the UK Biobank and FinnGen. Twin Res Hum Genet 2021; 24:145-154. [PMID: 34340725 DOI: 10.1017/thg.2021.27] [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] [Indexed: 12/31/2022]
Abstract
Pneumonia is a respiratory condition with complex etiology. Host genetic variation is thought to contribute to individual differences in susceptibility and symptom manifestation. Here, we analyze pneumonia data from the UK Biobank (14,780 cases and 439,096 controls) and FinnGen (9980 cases and 86,519 controls) and perform a genomewide association study meta-analysis. We use gene-based tests, colocalization, genetic correlation, latent causal variable (LCV) and polygenic prediction in an independent Australian sample (N = 5595) to draw insights into the etiology of pneumonia risk. We identify two independent loci on chromosome 15 (lead single-nucleotide polymorphisms rs2009746 and rs76474922) to be associated with pneumonia (p < 5e-8). Gene-based tests revealed 18 genes in chromosomes 15, 16 and 9, including IL127, PBX3, ApoB receptor (APOBR) and smoking related genes CHRNA3/5, statistically associated with pneumonia. We observed genetic correlations between pneumonia and cardiorespiratory, psychiatric and inflammatory related traits. LCV analysis suggests a strong genetic causal relationship with cardiovascular health phenotypes. Polygenic risk scores for pneumonia significantly predicted self-reported pneumonia in an independent sample, albeit with a small effect size (OR = 1.11 95% CI [1.04, 1.19], p < .05). Sensitivity analyses suggested the associations in chromosome 15 are mediated by smoking history, but the associations in chromosomes 16 and 9, and polygenic prediction were robust to adjustment for smoking. Altogether, our results highlight common genetic variants, genes and potential pathways that contribute to individual differences in susceptibility to pneumonia, and advance our understanding of the genetic factors underlying heterogeneity in respiratory medical outcomes.
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Nutritional immunity: the impact of metals on lung immune cells and the airway microbiome during chronic respiratory disease. Respir Res 2021; 22:133. [PMID: 33926483 PMCID: PMC8082489 DOI: 10.1186/s12931-021-01722-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
Nutritional immunity is the sequestration of bioavailable trace metals such as iron, zinc and copper by the host to limit pathogenicity by invading microorganisms. As one of the most conserved activities of the innate immune system, limiting the availability of free trace metals by cells of the immune system serves not only to conceal these vital nutrients from invading bacteria but also operates to tightly regulate host immune cell responses and function. In the setting of chronic lung disease, the regulation of trace metals by the host is often disrupted, leading to the altered availability of these nutrients to commensal and invading opportunistic pathogenic microbes. Similarly, alterations in the uptake, secretion, turnover and redox activity of these vitally important metals has significant repercussions for immune cell function including the response to and resolution of infection. This review will discuss the intricate role of nutritional immunity in host immune cells of the lung and how changes in this fundamental process as a result of chronic lung disease may alter the airway microbiome, disease progression and the response to infection.
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Cao YH, Xu SS, Shen M, Chen ZH, Gao L, Lv FH, Xie XL, Wang XH, Yang H, Liu CB, Zhou P, Wan PC, Zhang YS, Yang JQ, Pi WH, Hehua EE, Berry DP, Barbato M, Esmailizadeh A, Nosrati M, Salehian-Dehkordi H, Dehghani-Qanatqestani M, Dotsev AV, Deniskova TE, Zinovieva NA, Brem G, Štěpánek O, Ciani E, Weimann C, Erhardt G, Mwacharo JM, Ahbara A, Han JL, Hanotte O, Miller JM, Sim Z, Coltman D, Kantanen J, Bruford MW, Lenstra JA, Kijas J, Li MH. Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep. Mol Biol Evol 2021; 38:838-855. [PMID: 32941615 PMCID: PMC7947771 DOI: 10.1093/molbev/msaa236] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.
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Affiliation(s)
- Yin-Hong Cao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Min Shen
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Ze-Hui Chen
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Lei Gao
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xin-Hua Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Hua Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Chang-Bin Liu
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Peng-Cheng Wan
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Yun-Sheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Jing-Quan Yang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - Wen-Hui Pi
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Academy of Agricultural and Reclamation Sciences, State Key Laboratory of Sheep Genetic Improvement and Healthy Breeding, Shihezi, China
| | - EEr Hehua
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Hui Autonomous Region, Yinchuan, Ningxia, China
| | - Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland
| | - Mario Barbato
- Department of Animal Sciences, Food and Nutrition, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Maryam Nosrati
- Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | | | - Arsen V Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Tatiana E Deniskova
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Natalia A Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Moscow Region, Podolsk, Russian Federation
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Ondřej Štěpánek
- Department of Virology, State Veterinary Institute Jihlava, Jihlava, Czech Republic
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo 24, Moro, Bari, Italy
| | - Christina Weimann
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Georg Erhardt
- Department of Animal Breeding and Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Joram M Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Olivier Hanotte
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Addis Abeba, Ethiopia
- Center for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Joshua M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Zijian Sim
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
- Fish and Wildlife Enforcement Branch Forensic Unit, Government of Alberta, Edmonton, AB, Canada
| | - David Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Juha Kantanen
- Production Systems, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, United Kingdom
- Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - James Kijas
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Brisbane, QLD, Australia
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
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11
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Zeng Q, Chen Q, Zou D, Guo R, Xiao D, Jiang S, Chen R, Wang Y, Ma G. Different Associations Between the IREB2 Variants and Chronic Obstructive Pulmonary Disease Susceptibility. Front Genet 2020; 11:598053. [PMID: 33304392 PMCID: PMC7701307 DOI: 10.3389/fgene.2020.598053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/20/2020] [Indexed: 01/14/2023] Open
Abstract
Background: Iron responsive element binding protein 2 (IREB2) variants may be involved in the pathogenesis of chronic obstructive pulmonary disease (COPD). Recently, many studies have been performed on IREB2 susceptibility variants, including rs2568494, rs2656069, rs10851906, rs12593229, and rs13180, associated with COPD. However, inconsistent findings have been reported. The aim of our research was to determine the association of IREB2 SNPs with COPD. Methods: A comprehensive meta-analysis was performed to accurately estimate the association between IREB2 variants and COPD among four different genetic models. Results: This meta-analysis included a total of 4,096 patients and 5,870 controls. Here, we investigated the 5 IREB2 variants to identify COPD risk. Our results indicate that rs2568494 was associated with an increased risk of COPD for the dominant model (AA+GA vs. GG: OR = 1.150, 95% CI: 1.5–1.304, P = 0.029); rs2656069 was associated with a decreased risk of COPD for the recessive model (GG vs. AA+AG: OR = 0.589, 95% CI: 0.440–0.789; P = 0.000), additive model (GG vs. AA: OR =0.641, 95% CI: 0.441–0.931; P = 0.020), and allele model (G vs. A: OR = 0.812, 95% CI: 0.668–0.988; P = 0.037); and rs10851906 was associated with a decreased risk of COPD for the recessive model (GG vs. AA+AG: OR = 0.732, 95% CI: 0.560–0.958; P = 0.023) and additive model (GG vs. AA: OR = 0.777, 95% CI: 0.637–0.947; P = 0.012). Conclusion: Our findings suggest that the IREB2 rs2568494 minor alleles A may be a genetic factor in susceptibility to COPD. In addition, the minor alleles G of rs2656069 and rs10851906 appear to have a protective effect.
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Affiliation(s)
- Qiaoli Zeng
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Qikang Chen
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Dehua Zou
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Runmin Guo
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China.,Department of Medicine, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Dawei Xiao
- Department of Medicine, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Shaohu Jiang
- Department of Pediatrics, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Riling Chen
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China.,Department of Pediatrics, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Yajun Wang
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China.,Department of Medicine, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
| | - Guoda Ma
- Maternal and Child Research Institute, Shunde Women and Children's Hospital, Guangdong Medical University, Foshan, China
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12
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Perez E, Baker JR, Di Giandomenico S, Kermani P, Parker J, Kim K, Yang J, Barnes PJ, Vaulont S, Scandura JM, Donnelly LE, Stout-Delgado H, Cloonan SM. Hepcidin Is Essential for Alveolar Macrophage Function and Is Disrupted by Smoke in a Murine Chronic Obstructive Pulmonary Disease Model. THE JOURNAL OF IMMUNOLOGY 2020; 205:2489-2498. [PMID: 32958690 DOI: 10.4049/jimmunol.1901284] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 08/31/2020] [Indexed: 12/21/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a debilitating lung disease associated with cigarette smoking. Alterations in local lung and systemic iron regulation are associated with disease progression and pathogenesis. Hepcidin, an iron regulatory peptide hormone, is altered in subjects with COPD; however, the molecular role of hepcidin in COPD pathogenesis remains to be determined. In this study, using a murine model of smoke-induced COPD, we demonstrate that lung and circulating hepcidin levels are inhibited by cigarette smoke. We show that cigarette smoke exposure increases erythropoietin and bone marrow-derived erythroferrone and leads to expanded but inefficient erythropoiesis in murine bone marrow and an increase in ferroportin on alveolar macrophages (AMs). AMs from smokers and subjects with COPD display increased expression of ferroportin as well as hepcidin. Notably, murine AMs exposed to smoke fail to increase hepcidin in response to Gram-negative or Gram-positive infection. Loss of hepcidin in vivo results in blunted functional responses of AMs and exaggerated responses to Streptococcus pneumoniae infection.
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Affiliation(s)
- Elizabeth Perez
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065
| | - Jonathan R Baker
- Airway Disease Section, National Heart and Lung Institute, Imperial College London and Royal Brompton Hospital, London SW3 6NP, United Kingdom
| | - Silvana Di Giandomenico
- Division of Hematology and Oncology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065
| | - Pouneh Kermani
- Division of Hematology and Oncology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065
| | - Jacqueline Parker
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065.,New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY 10065
| | - Kihwan Kim
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065
| | - Jianjun Yang
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065
| | - Peter J Barnes
- Airway Disease Section, National Heart and Lung Institute, Imperial College London and Royal Brompton Hospital, London SW3 6NP, United Kingdom
| | - Sophie Vaulont
- Université de Paris, INSERM U1016, Institut Cochin, CNRS UMR8104, 75014 Paris, France.,Laboratory of Excellence GR-Ex, 75015 Paris, France; and
| | - Joseph M Scandura
- Division of Hematology and Oncology, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065.,New York-Presbyterian Hospital, Weill Cornell Medicine, New York, NY 10065
| | - Louise E Donnelly
- Airway Disease Section, National Heart and Lung Institute, Imperial College London and Royal Brompton Hospital, London SW3 6NP, United Kingdom
| | - Heather Stout-Delgado
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065
| | - Suzanne M Cloonan
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, NY 10065; .,School of Medicine, Trinity College Dublin and Tallaght University Hospital, Dublin D24 NR04, Ireland
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13
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Abbas SZ, Qadir MI, Muhammad SA. Systems-level differential gene expression analysis reveals new genetic variants of oral cancer. Sci Rep 2020; 10:14667. [PMID: 32887903 PMCID: PMC7473858 DOI: 10.1038/s41598-020-71346-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 07/20/2020] [Indexed: 01/28/2023] Open
Abstract
Oral cancer (OC) ranked as eleventh malignancy worldwide, with the increasing incidence among young patients. Limited understanding of complications in cancer progression, its development system, and their interactions are major restrictions towards the progress of optimal and effective treatment strategies. The system-level approach has been designed to explore genetic complexity of the disease and to identify novel oral cancer related genes to detect genomic alterations at molecular level, through cDNA differential analysis. We analyzed 21 oral cancer-related cDNA datasets and listed 30 differentially expressed genes (DEGs). Among 30, we found 6 significant DEGs including CYP1A1, CYP1B1, ADCY2, C7, SERPINB5, and ANAPC13 and studied their functional role in OC. Our genomic and interactive analysis showed significant enrichment of xenobiotics metabolism, p53 signaling pathway and microRNA pathways, towards OC progression and development. We used human proteomic data for post-translational modifications to interpret disease mutations and inter-individual genetic variations. The mutational analysis revealed the sequence predicted disordered region of 14%, 12.5%, 10.5% for ADCY2, CYP1B1, and C7 respectively. The MiRNA target prediction showed functional molecular annotation including specific miRNA-targets hsa-miR-4282, hsa-miR-2052, hsa-miR-216a-3p, for CYP1B1, C7, and ADCY2 respectively associated with oral cancer. We constructed the system level network and found important gene signatures. The drug-gene interaction of OC source genes with seven FDA approved OC drugs help to design or identify new drug target or establishing novel biomedical linkages regarding disease pathophysiology. This investigation demonstrates the importance of system genetics for identifying 6 OC genes (CYP1A1, CYP1B1, ADCY2, C7, SERPINB5, and ANAPC13) as potential drugs targets. Our integrative network-based system-level approach would help to find the genetic variants of OC that can accelerate drug discovery outcomes to develop a better understanding regarding treatment strategies for many cancer types.
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Affiliation(s)
- Syeda Zahra Abbas
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Imran Qadir
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Syed Aun Muhammad
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan.
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14
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He LX, Tang ZH, Huang QS, Li WH. DNA Methylation: A Potential Biomarker of Chronic Obstructive Pulmonary Disease. Front Cell Dev Biol 2020; 8:585. [PMID: 32733890 PMCID: PMC7358425 DOI: 10.3389/fcell.2020.00585] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a serious public health concern worldwide. By 2040, 4.41 million people are estimated to expire annually due to COPD. However, till date, it has remained difficult to alter the activity or progress of the disease through treatment. In order to address this issue, the best way would be to find biomarkers and new therapeutic targets for COPD. DNA methylation (DNAm) may be a potential biomarker for disease prevention, diagnosis, and prognosis, and its reversibility further makes it a potential drug design target in COPD. In this review, we aimed to explore the role of DNAm as biomarkers and disease mediators in different tissue samples from patients with COPD.
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Affiliation(s)
- Lin-Xi He
- School of Basic Medicine Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhao-Hui Tang
- School of Basic Medicine Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qing-Song Huang
- Department of Respiratory, Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wei-Hong Li
- School of Basic Medicine Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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15
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Ma X, Wu Y, Zhang L, Yuan W, Yan L, Fan S, Lian Y, Zhu X, Gao J, Zhao J, Zhang P, Tang H, Jia W. Comparison and development of machine learning tools for the prediction of chronic obstructive pulmonary disease in the Chinese population. J Transl Med 2020; 18:146. [PMID: 32234053 PMCID: PMC7110698 DOI: 10.1186/s12967-020-02312-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 03/17/2020] [Indexed: 02/08/2023] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a major public health problem and cause of mortality worldwide. However, COPD in the early stage is usually not recognized and diagnosed. It is necessary to establish a risk model to predict COPD development. Methods A total of 441 COPD patients and 192 control subjects were recruited, and 101 single-nucleotide polymorphisms (SNPs) were determined using the MassArray assay. With 5 clinical features as well as SNPs, 6 predictive models were established and evaluated in the training set and test set by the confusion matrix AU-ROC, AU-PRC, sensitivity (recall), specificity, accuracy, F1 score, MCC, PPV (precision) and NPV. The selected features were ranked. Results Nine SNPs were significantly associated with COPD. Among them, 6 SNPs (rs1007052, OR = 1.671, P = 0.010; rs2910164, OR = 1.416, P < 0.037; rs473892, OR = 1.473, P < 0.044; rs161976, OR = 1.594, P < 0.044; rs159497, OR = 1.445, P < 0.045; and rs9296092, OR = 1.832, P < 0.045) were risk factors for COPD, while 3 SNPs (rs8192288, OR = 0.593, P < 0.015; rs20541, OR = 0.669, P < 0.018; and rs12922394, OR = 0.651, P < 0.022) were protective factors for COPD development. In the training set, KNN, LR, SVM, DT and XGboost obtained AU-ROC values above 0.82 and AU-PRC values above 0.92. Among these models, XGboost obtained the highest AU-ROC (0.94), AU-PRC (0.97), accuracy (0.91), precision (0.95), F1 score (0.94), MCC (0.77) and specificity (0.85), while MLP obtained the highest sensitivity (recall) (0.99) and NPV (0.87). In the validation set, KNN, LR and XGboost obtained AU-ROC and AU-PRC values above 0.80 and 0.85, respectively. KNN had the highest precision (0.82), both KNN and LR obtained the same highest accuracy (0.81), and KNN and LR had the same highest F1 score (0.86). Both DT and MLP obtained sensitivity (recall) and NPV values above 0.94 and 0.84, respectively. In the feature importance analyses, we identified that AQCI, age, and BMI had the greatest impact on the predictive abilities of the models, while SNPs, sex and smoking were less important. Conclusions The KNN, LR and XGboost models showed excellent overall predictive power, and the use of machine learning tools combining both clinical and SNP features was suitable for predicting the risk of COPD development.
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Affiliation(s)
- Xia Ma
- Department of Pulmonary and Critical Care Medicine, General Hospital of Datong Coal Mine Group Co., Ltd., Datong, 037000, China.,Department of Pulmonary and Critical Care Medicine, The First Hospital of Shanxi Medical University, Taiyuan, 030001, China
| | - Yanping Wu
- Department of Respiratory, General Hospital of Tisco (Sixth Hospital of Shanxi Medical University), 2 Yingxin Street, Jiancaoping District, Taiyuan, 030008, Shanxi Province, China
| | - Ling Zhang
- Department of Respiratory, Linfen People's Hospital, Linfen, 041000, China
| | - Weilan Yuan
- Shanghai Biotecan Pharmaceuticals Co., Ltd., 180 Zhangheng Road, Shanghai, 201204, China.,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, China
| | - Li Yan
- Department of Respiratory Medicine, Hebei General Hospital, Shijiazhuang, 050000, China
| | - Sha Fan
- Department of Respiratory Medicine, Heji Hospital Affiliated with Changzhi Medical College, Changzhi, 046011, China
| | - Yunzhi Lian
- Department of Clinical Laboratory, JinCheng People's Hospital, Jincheng, 048000, China
| | - Xia Zhu
- Department of Respiratory, General Hospital of Tisco (Sixth Hospital of Shanxi Medical University), 2 Yingxin Street, Jiancaoping District, Taiyuan, 030008, Shanxi Province, China
| | - Junhui Gao
- Shanghai Biotecan Pharmaceuticals Co., Ltd., 180 Zhangheng Road, Shanghai, 201204, China.,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, China
| | - Jiangman Zhao
- Shanghai Biotecan Pharmaceuticals Co., Ltd., 180 Zhangheng Road, Shanghai, 201204, China.,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, China
| | - Ping Zhang
- Department of Clinical Laboratory, Linfen People's Hospital, West of Rainbow Bridge, West Binhe Road, Yaodu District, Linfen, 041000, Shanxi Province, China.
| | - Hui Tang
- Shanghai Biotecan Pharmaceuticals Co., Ltd., 180 Zhangheng Road, Shanghai, 201204, China. .,Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, 201204, China.
| | - Weihua Jia
- Department of Respiratory, General Hospital of Tisco (Sixth Hospital of Shanxi Medical University), 2 Yingxin Street, Jiancaoping District, Taiyuan, 030008, Shanxi Province, China.
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16
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Ranjan A, Singh A, Walia GK, Sachdeva MP, Gupta V. Genetic underpinnings of lung function and COPD. J Genet 2019; 98:76. [PMID: 31544798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Spirometry based measurement of lung function is a global initiative for chronic obstructive lung disease (GOLD) standard to diagnose chronic obstructive pulmonary disease (COPD), one of the leading causes of mortality worldwide. The environmental and behavioural risk factors for COPD includes tobacco smoking, air pollutants and biomass fuel exposure, which can induce one or more abnormal lung function patterns. While smoking remains the primary risk factor, only 15-20% smokers develop COPD, indicating that the genetic factors are also likely to play a role. According to the study of Global Burden of Disease 2015, ∼174 million people across the world have COPD. From a comprehensive literature search conducted using the 'PubMed' and 'GWAS Catalogue' databases, and reviewing the literature available, only a limited number of studies were identified which had attempted to investigate the genetics of COPD and lung volumes, implying a huge research gap. With the advent of genomewide association studies several genetic variants linked to lung function and COPD, like HHIP, HTR4, ADAM19 and GSTCD etc., have been found and validated in different population groups, suggesting their potential role in determining lung volume and risk for COPD. This article aims at reviewing the present knowledge of the genetics of lung function and COPD.
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Affiliation(s)
- Astha Ranjan
- Department of Anthropology, University of Delhi, Delhi 110 007, India.
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17
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Xie J. Do obstructive sleep apnea and chronic obstructive pulmonary disease overlap coincidently or intrinsically? Heart Lung 2019; 48:466. [DOI: 10.1016/j.hrtlng.2019.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Ranjan A, Singh A, Walia GK, Sachdeva MP, Gupta V. Genetic underpinnings of lung function and COPD. J Genet 2019. [DOI: 10.1007/s12041-019-1119-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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19
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Huang X, Mu X, Deng L, Fu A, Pu E, Tang T, Kong X. The etiologic origins for chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis 2019; 14:1139-1158. [PMID: 31213794 PMCID: PMC6549659 DOI: 10.2147/copd.s203215] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/18/2019] [Indexed: 12/27/2022] Open
Abstract
COPD, characterized by long-term poorly irreversible airway limitation and persistent respiratory symptoms, has resulted in enormous challenges to human health worldwide, with increasing rates of prevalence, death, and disability. Although its origin was thought to be in the interactions of genetic with environmental factors, the effects of environmental factors on the disease during different life stages remain little known. Without clear mechanisms and radical cure for it, early screening and prevention of COPD seem to be important. In this review, we will discuss the etiologic origins for poor lung function and COPD caused by specific adverse effects during corresponding life stages, as well as try to find new insights and potential prevention strategies for this disease.
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Affiliation(s)
- Xinwei Huang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming City, Yunnan Province, People's Republic of China.,Medical School, Kunming University of Science and Technology, Kunming City, Yunnan Province, People's Republic of China
| | - Xi Mu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming City, Yunnan Province, People's Republic of China
| | - Li Deng
- The Pathology Department, First People's Hospital of Yunnan Province, Kunming City, Yunnan Province, People's Republic of China
| | - Aili Fu
- Department of Oncology, Yunfeng Hospital, Xuanwei City, Yunnan Province, People's Republic of China
| | - Endong Pu
- Department of Thoracic Surgery, Yunfeng Hospital, Xuanwei City, Yunnan Province, People's Republic of China
| | - Tao Tang
- Medical School, Kunming University of Science and Technology, Kunming City, Yunnan Province, People's Republic of China
| | - Xiangyang Kong
- Medical School, Kunming University of Science and Technology, Kunming City, Yunnan Province, People's Republic of China
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20
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Corrêa T, Feltes BC, Riegel M. Integrated analysis of the critical region 5p15.3-p15.2 associated with cri-du-chat syndrome. Genet Mol Biol 2019; 42:186-196. [PMID: 30985858 PMCID: PMC6687350 DOI: 10.1590/1678-4685-gmb-2018-0173] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 07/29/2018] [Indexed: 11/21/2022] Open
Abstract
Cri-du-chat syndrome (CdCs) is one of the most common contiguous gene syndromes,
with an incidence of 1:15,000 to 1:50,000 live births. To better understand the
etiology of CdCs at the molecular level, we investigated theprotein–protein
interaction (PPI) network within the critical chromosomal region 5p15.3–p15.2
associated with CdCs using systemsbiology. Data were extracted from cytogenomic
findings from patients with CdCs. Based on clinical findings, molecular
characterization of chromosomal rearrangements, and systems biology data, we
explored possible genotype–phenotype correlations involving biological processes
connected with CdCs candidate genes. We identified biological processes
involving genes previously found to be associated with CdCs, such as
TERT, SLC6A3, and
CTDNND2, as well as novel candidate proteins with potential
contributions to CdCs phenotypes, including CCT5, TPPP, MED10, ADCY2, MTRR,
CEP72, NDUFS6, and MRPL36. Although further functional analyses of these
proteins are required, we identified candidate proteins for the development of
new multi-target genetic editing tools to study CdCs. Further research may
confirm those that are directly involved in the development of CdCs phenotypes
and improve our understanding of CdCs-associated molecular mechanisms.
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Affiliation(s)
- Thiago Corrêa
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Bruno César Feltes
- Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Mariluce Riegel
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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21
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Haider SH, Oskuei A, Crowley G, Kwon S, Lam R, Riggs J, Mikhail M, Talusan A, Veerappan A, Kim JS, Caraher EJ, Nolan A. Receptor for advanced glycation end-products and environmental exposure related obstructive airways disease: a systematic review. Eur Respir Rev 2019; 28:28/151/180096. [PMID: 30918021 PMCID: PMC7006869 DOI: 10.1183/16000617.0096-2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/09/2019] [Indexed: 12/11/2022] Open
Abstract
Background Our group has identified the receptor for advanced glycation end-products (RAGE) as a predictor of World Trade Center particulate matter associated lung injury. The aim of this systematic review is to assess the relationship between RAGE and obstructive airways disease secondary to environmental exposure. Methods A comprehensive search using PubMed and Embase was performed on January 5, 2018 utilising keywords focusing on environmental exposure, obstructive airways disease and RAGE and was registered with PROSPERO (CRD42018093834). We included original human research studies in English, focusing on pulmonary end-points associated with RAGE and environmental exposure. Results A total of 213 studies were identified by the initial search. After removing the duplicates and applying inclusion and exclusion criteria, we screened the titles and abstracts of 61 studies. Finally, 19 full-text articles were included. The exposures discussed in these articles include particulate matter (n=2) and cigarette smoke (n=17). Conclusion RAGE is a mediator of inflammation associated end-organ dysfunction such as obstructive airways disease. Soluble RAGE, a decoy receptor, may have a protective effect in some pulmonary processes. Overall, RAGE is biologically relevant in environmental exposure associated lung disease. Future investigations should focus on further understanding the role and therapeutic potential of RAGE in particulate matter exposure associated lung disease. RAGE is biologically relevant in environmental exposure associated lung disease. Future investigations should focus on further understanding the role and therapeutic potential of RAGE in particulate matter exposure associated lung diseasehttp://ow.ly/gfZz30o7otU
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Affiliation(s)
- Syed H Haider
- Dept of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA.,Bureau of Health Services and Office of Medical Affairs, Fire Department of New York, New York, NY, USA
| | - Assad Oskuei
- Dept of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - George Crowley
- Dept of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Sophia Kwon
- Dept of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Rachel Lam
- Dept of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Jessica Riggs
- Dept of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Mena Mikhail
- Dept of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Angela Talusan
- Dept of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Arul Veerappan
- Dept of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - James S Kim
- Dept of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Erin J Caraher
- Dept of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA
| | - Anna Nolan
- Dept of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, New York University School of Medicine, New York, NY, USA .,Bureau of Health Services and Office of Medical Affairs, Fire Department of New York, New York, NY, USA.,Dept of Environmental Medicine, New York University School of Medicine, New York, NY, USA
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22
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Wadhwa R, Aggarwal T, Malyla V, Kumar N, Gupta G, Chellappan DK, Dureja H, Mehta M, Satija S, Gulati M, Maurya PK, Collet T, Hansbro PM, Dua K. Identification of biomarkers and genetic approaches toward chronic obstructive pulmonary disease. J Cell Physiol 2019; 234:16703-16723. [DOI: 10.1002/jcp.28482] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/10/2019] [Accepted: 02/14/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Ridhima Wadhwa
- Faculty of Life Sciences and Biotechnology South Asian University New Delhi India
| | - Taru Aggarwal
- Amity Institute of Biotechnology Amity University Noida Uttar Pradesh India
| | - Vamshikrishna Malyla
- Discipline of Pharmacy, Graduate School of Health University of Technology Sydney New South Wales Australia
- Centre for Inflammation Centenary Institute Sydney New South Wales Australia
| | - Nitesh Kumar
- Amity Institute for Advanced Research & Studies (M&D) Amity University Noida Uttar Pradesh India
| | - Gaurav Gupta
- School of Pharmaceutical Sciences Jaipur National University, Jagatpura Jaipur Rajasthan India
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy International Medical University Bukit Jalil Kuala Lumpur Malaysia
| | - Harish Dureja
- Department of Pharmaceutical Sciences Maharishi Dayanand University Rohtak Haryana India
| | - Meenu Mehta
- School of Pharmaceutical Sciences Lovely Professional University Phagwara Punjab India
| | - Saurabh Satija
- School of Pharmaceutical Sciences Lovely Professional University Phagwara Punjab India
| | - Monica Gulati
- School of Pharmaceutical Sciences Lovely Professional University Phagwara Punjab India
| | - Pawan Kumar Maurya
- Department of Biochemistry Central University of Haryana Mahendergarh Haryana India
| | - Trudi Collet
- Innovative Medicines Group, Institute of Health & Biomedical Innovation Queensland University of Technology Brisbane Queensland Australia
| | - Philip Michael Hansbro
- Priority Research Centre for Healthy Lungs University of Newcastle & Hunter Medical Research Institute Newcastle New South Wales Australia
- Centre for Inflammation Centenary Institute Sydney New South Wales Australia
- School of Life Sciences University of Technology Sydney Sydney New South Wales Australia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health University of Technology Sydney New South Wales Australia
- Priority Research Centre for Healthy Lungs University of Newcastle & Hunter Medical Research Institute Newcastle New South Wales Australia
- Centre for Inflammation Centenary Institute Sydney New South Wales Australia
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23
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Zhang WZ, Butler JJ, Cloonan SM. Smoking-induced iron dysregulation in the lung. Free Radic Biol Med 2019; 133:238-247. [PMID: 30075191 PMCID: PMC6355389 DOI: 10.1016/j.freeradbiomed.2018.07.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022]
Abstract
Iron is one of the most abundant transition elements and is indispensable for almost all organisms. While the ability of iron to participate in redox chemistry is an essential requirement for participation in a range of vital enzymatic reactions, this same feature of iron also makes it dangerous in the generation of hydroxyl radicals and superoxide anions. Given the high local oxygen tensions in the lung, the regulation of iron acquisition, utilization, and storage therefore becomes vitally important, perhaps more so than in any other biological system. Iron plays a critical role in the biology of essentially every cell type in the lung, and in particular, changes in iron levels have important ramifications on immune function and the local lung microenvironment. There is substantial evidence that cigarette smoke causes iron dysregulation, with the implication that iron may be the link between smoking and smoking-related lung diseases. A better understanding of the connection between cigarette smoke, iron, and respiratory diseases will help to elucidate pathogenic mechanisms and aid in the identification of novel therapeutic targets.
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Affiliation(s)
- William Z Zhang
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA; Department of Medicine, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY 10021, USA
| | - James J Butler
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
| | - Suzanne M Cloonan
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA.
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24
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Trade-offs in aging lung diseases: a review on shared but opposite genetic risk variants in idiopathic pulmonary fibrosis, lung cancer and chronic obstructive pulmonary disease. Curr Opin Pulm Med 2019. [PMID: 29517586 PMCID: PMC5895171 DOI: 10.1097/mcp.0000000000000476] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW The process of aging involves biological changes that increases susceptibility for disease. In the aging lung disease IPF, GWAS studies identified genes associated with risk for disease. Recently, several of these genes were also found to be involved in risk for COPD or lung cancer. This review describes GWAS-derived risk genes for IPF that overlap with risk genes for lung cancer or COPD. RECENT FINDINGS Risk genes that overlap between aging lung diseases, include FAM13A, DSP and TERT. Most interestingly, disease predisposing alleles for IPF are opposite to those for COPD or lung cancer. Studies show that the alleles are associated with differential gene expression and with physiological traits in the general population. The opposite allelic effect sizes suggest the presence of trade-offs in the aging lung. For TERT, the trade-off involves cellular senescence versus proliferation and repair. For FAM13A and DSP, trade-offs may involve protection from noxious gases or tissue integrity. SUMMARY The overlap in risk genes in aging lung diseases provides evidence that processes associated with FAM13A, DSP and TERT are important for healthy aging. The opposite effect size of the disease risk alleles may represent trade-offs, for which a model involving an apicobasal gene expression gradient is presented.
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25
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Qiao D, Ameli A, Prokopenko D, Chen H, Kho AT, Parker MM, Morrow J, Hobbs BD, Liu Y, Beaty TH, Crapo JD, Barnes KC, Nickerson DA, Bamshad M, Hersh CP, Lomas DA, Agusti A, Make BJ, Calverley PMA, Donner CF, Wouters EF, Vestbo J, Paré PD, Levy RD, Rennard SI, Tal-Singer R, Spitz MR, Sharma A, Ruczinski I, Lange C, Silverman EK, Cho MH. Whole exome sequencing analysis in severe chronic obstructive pulmonary disease. Hum Mol Genet 2018; 27:3801-3812. [PMID: 30060175 PMCID: PMC6196654 DOI: 10.1093/hmg/ddy269] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/09/2018] [Accepted: 07/17/2018] [Indexed: 12/13/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), one of the leading causes of death worldwide, is substantially influenced by genetic factors. Alpha-1 antitrypsin deficiency demonstrates that rare coding variants of large effect can influence COPD susceptibility. To identify additional rare coding variants in patients with severe COPD, we conducted whole exome sequencing analysis in 2543 subjects from two family-based studies (Boston Early-Onset COPD Study and International COPD Genetics Network) and one case-control study (COPDGene). Applying a gene-based segregation test in the family-based data, we identified significant segregation of rare loss of function variants in TBC1D10A and RFPL1 (P-value < 2x10-6), but were unable to find similar variants in the case-control study. In single-variant, gene-based and pathway association analyses, we were unable to find significant findings that replicated or were significant in meta-analysis. However, we found that the top results in the two datasets were in proximity to each other in the protein-protein interaction network (P-value = 0.014), suggesting enrichment of these results for similar biological processes. A network of these association results and their neighbors was significantly enriched in the transforming growth factor beta-receptor binding and cilia-related pathways. Finally, in a more detailed examination of candidate genes, we identified individuals with putative high-risk variants, including patients harboring homozygous mutations in genes associated with cutis laxa and Niemann-Pick Disease Type C. Our results likely reflect heterogeneity of genetic risk for COPD along with limitations of statistical power and functional annotation, and highlight the potential of network analysis to gain insight into genetic association studies.
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Affiliation(s)
- Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Asher Ameli
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Han Chen
- 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, Texas, United States of America
- Center for Precision Health, School of Public Health and School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Alvin T Kho
- Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yanhong Liu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - James D Crapo
- National Jewish Health, Denver, Colorado, United States of America
| | - Kathleen C Barnes
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Michael Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children’s Hospital, Seattle, Washington , United States of America
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Alvar Agusti
- Respiratory Institute, Hospital Clinic, IDIBAPS, University of Barcelona, CIBERES, Barcelona, Spain
| | - Barry J Make
- National Jewish Health, Denver, Colorado, United States of America
| | | | - Claudio F Donner
- Mondo Medico di I.F.I.M. srl, Multidisciplinary and Rehabilitation Outpatient Clinic, Borgomanero, Novara, Italy
| | - Emiel F Wouters
- Department of Respiratory Medicine, Maastricht University Medical Center, AZ Maastricht, The Netherlands
| | - Jørgen Vestbo
- University of Manchester, Manchester, United Kingdom
| | - Peter D Paré
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T, Canada
| | - Robert D Levy
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T, Canada
| | - Stephen I Rennard
- University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- AstraZeneca, Cambridge CB2 0RE, United Kingdom
| | - Ruth Tal-Singer
- GSK Research and Development, KingOf Prussia, Pennsylvania, United States of America
| | - Margaret R Spitz
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Amitabh Sharma
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Christoph Lange
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Channing Division of Network Medicine, Longwood Avenue, Boston, MA, USA
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26
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Zhang Y, Qiu J, Zhang P, Zhang J, Jiang M, Ma Z. Genetic variants in FAM13A and IREB2 are associated with the susceptibility to COPD in a Chinese rural population: a case-control study. Int J Chron Obstruct Pulmon Dis 2018; 13:1735-1745. [PMID: 29872291 PMCID: PMC5973397 DOI: 10.2147/copd.s162241] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Genome-wide association studies identified several genomic regions associated with the risk of chronic obstructive pulmonary disease (COPD), including the 4q22 and 15q25 regions. These regions contain the FAM13A and IREB2 genes, which have been associated with COPD but data are lacking for Chinese patients. The objective of the study was to identify new genetic variants in the FAM13A and IREB2 associated with COPD in Northwestern China. Methods This was a case-control study performed in the Ningxia Hui Autonomous Region between January 2014 and December 2016. Patients were grouped as COPD and controls based on FEV1/FVC<70%. Seven tag single-nucleotide polymorphisms (SNPs) in the FAM13A and IREB2 genes were genotyped using the Agena MassARRAY platform. Logistic regression was used to determine the association between SNPs and COPD risk. Results rs17014601 in FAM13A was significantly associated with COPD in the additive (odds ratio [OR]=1.36, 95% confidence interval [CI]: 1.11-1.67, P=0.003), heterozygote (OR=1.76, 95% CI: 1.33-2.32, P=0.0001), and dominant (OR=1.67, 95% CI: 1.28-2.18, P=0.0001) models. Stratified analyses indicated that the risk was higher in never smokers. rs16969858 in IREB2 was significantly associated with COPD but in the univariate analysis only, and the multivariate analysis did not show any association. Conclusion The results suggest that the new variant rs17014601 in the FAM13A gene was significantly associated with COPD risk in a Chinese rural population. Additional studies are required to confirm the role of this variant in COPD development and progression.
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Affiliation(s)
- Yanan Zhang
- Department of Respiratory and Critical Care Medicine, General Hospital of Ningxia Medical University, Ningxia Medical University, Yinchuan, People's Republic of China
| | - Jie Qiu
- Department of Respiratory and Critical Care Medicine, General Hospital of Ningxia Medical University, Ningxia Medical University, Yinchuan, People's Republic of China
| | - Peng Zhang
- Department of Respiratory and Critical Care Medicine, General Hospital of Ningxia Medical University, Ningxia Medical University, Yinchuan, People's Republic of China
| | - Jin Zhang
- Department of Respiratory and Critical Care Medicine, General Hospital of Ningxia Medical University, Ningxia Medical University, Yinchuan, People's Republic of China
| | - Min Jiang
- National Engineering Research Center for Beijing Biochip Technology, Sub-center in Ningxia, General Hospital of Ningxia Medical University, Yinchuan, People's Republic of China
| | - Zhanbing Ma
- Department of Medical Genetic and Cell Biology, Ningxia Medical University, Yinchuan, People's Republic of China
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27
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Nedeljkovic I, Carnero-Montoro E, Lahousse L, van der Plaat DA, de Jong K, Vonk JM, van Diemen CC, Faiz A, van den Berge M, Obeidat M, Bossé Y, Nickle DC, Consortium B, Uitterlinden AG, van Meurs JJB, Stricker BCH, Brusselle GG, Postma DS, Boezen HM, van Duijn CM, Amin N. Understanding the role of the chromosome 15q25.1 in COPD through epigenetics and transcriptomics. Eur J Hum Genet 2018; 26:709-722. [PMID: 29422661 PMCID: PMC5945654 DOI: 10.1038/s41431-017-0089-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 11/06/2017] [Accepted: 12/19/2017] [Indexed: 12/25/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a major health burden in adults and cigarette smoking is considered the most important environmental risk factor of COPD. Chromosome 15q25.1 locus is associated with both COPD and smoking. Our study aims at understanding the mechanism underlying the association of chromosome 15q25.1 with COPD through epigenetic and transcriptional variation in a population-based setting. To assess if COPD-associated variants in 15q25.1 are methylation quantitative trait loci, epigenome-wide association analysis of four genetic variants, previously associated with COPD (P < 5 × 10-8) in the 15q25.1 locus (rs12914385:C>T-CHRNA3, rs8034191:T>C-HYKK, rs13180:C>T-IREB2 and rs8042238:C>T-IREB2), was performed in the Rotterdam study (n = 1489). All four variants were significantly associated (P < 1.4 × 10-6) with blood DNA methylation of IREB2, CHRNA3 and PSMA4, of which two, including IREB2 and PSMA4, were also differentially methylated in COPD cases and controls (P < 0.04). Further additive and multiplicative effects of smoking were evaluated and no significant effect was observed. To evaluate if these four genetic variants are expression quantitative trait loci, transcriptome-wide association analysis was performed in 1087 lung samples. All four variants were also significantly associated with differential expression of the IREB2 3'UTR in lung tissues (P < 5.4 × 10-95). We conclude that regulatory mechanisms affecting the expression of IREB2 gene, such as DNA methylation, may explain the association between genetic variants in chromosome 15q25.1 and COPD, largely independent of smoking.
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Affiliation(s)
- Ivana Nedeljkovic
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Elena Carnero-Montoro
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
- Pfizer University of Granada, GENYO Centre for Genomics and Oncological Research, Andalusian Region Government, Granada, Spain
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Bioanalysis Pharmaceutical Care Unit, Ghent University Hospital, Ghent, Belgium
| | - Diana A van der Plaat
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Kim de Jong
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Judith M Vonk
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Cleo C van Diemen
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Alen Faiz
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Department of Pulmonology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Ma'en Obeidat
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Institut universitaire de cardiologie et de pneumologie de Québec, Quebec, QC, Canada
| | - David C Nickle
- Genetics and Pharmacogenomics (GpGx), Merck Research Laboratories, Seattle, WA, USA
| | | | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Joyce J B van Meurs
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Bruno C H Stricker
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Guy G Brusselle
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
- Department of Bioanalysis Pharmaceutical Care Unit, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Dirkje S Postma
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
- Department of Pulmonology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - H Marike Boezen
- Department of Epidemiology University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | | | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands.
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Korytina GF, Akhmadishina LZ, Viktorova EV, Kochetova OV, Viktorova TV. IREB2, CHRNA5, CHRNA3, FAM13A & hedgehog interacting protein genes polymorphisms & risk of chronic obstructive pulmonary disease in Tatar population from Russia. Indian J Med Res 2018; 144:865-876. [PMID: 28474623 PMCID: PMC5433279 DOI: 10.4103/ijmr.ijmr_1233_14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background & objectives: Chronic obstructive pulmonary disease (COPD) is a complex chronic inflammatory disease of the respiratory system affecting primarily distal respiratory pathways and lung parenchyma. This study was aimed at investigating the association of COPD with IREB2, CHRNA5, CHRNA3, FAM13A and hedgehog interacting protein (HHIP) genes in a Tatar population from Russia. Methods: Six single nucleotide polymorphisms (SNPs) (rs13180, rs16969968, rs1051730, rs6495309, rs7671167, rs13118928) were genotyped by the real-time polymerase chain reaction in this study (511 COPD patients and 508 controls). Logistic regression was used to detect the association of SNPs and haplotypes of linked loci in different models. Linear regression analyses were performed to estimate the relationship between SNPs and lung function parameters and pack-years. Results: The rs13180 (IREB2), rs16969968 (CHRNA5) and rs1051730 (CHRNA3) were significantly associated with COPD in additive model [Padj=0.00001, odds ratio (OR)=0.64; Padj=0.0001, OR=1.41 and Padj=0.0001, OR=1.47]. The C-G haplotype by rs13180 and rs1051730 was a protective factor for COPD in our population (Padj=0.0005, OR=0.61). These results were confirmed only in smokers. The rs16969968 and rs1051730 were associated with decrease of forced expiratory volume in 1 sec % predicted (Padj=0.005 and Padj=0.0019). Interpretation & conclusions: Our study showed the association of rs13180, rs16969968 and rs1051730 with COPD and lung function in Tatar population from Russia. Further studies need to be done in other ethnic populations.
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Affiliation(s)
- Gulnaz Faritovna Korytina
- Department of Genomics, Institute of Biochemistry & Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Russian Federation
| | - Leysan Zinurovna Akhmadishina
- Department of Genomics, Institute of Biochemistry & Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Russian Federation
| | | | - Olga Vladimirovna Kochetova
- Department of Genomics, Institute of Biochemistry & Genetics, Ufa Scientific Centre, Russian Academy of Sciences, Ufa, Russian Federation
| | - Tatyana Victorovna Viktorova
- Department of Genomics, Institute of Biochemistry & Genetics, Ufa Scientific Centre, Russian Academy of Sciences; Department of Biology, Bashkortostan State Medical University, Ufa, Russian Federation
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29
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Morrow JD, Cho MH, Platig J, Zhou X, DeMeo DL, Qiu W, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Silverman EK, Hersh CP. Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. Hum Genomics 2018; 12:1. [PMID: 29335020 PMCID: PMC5769240 DOI: 10.1186/s40246-018-0132-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/02/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic obstructive pulmonary disease (COPD). However, many genetic variants show suggestive evidence for association but do not meet the strict threshold for genome-wide significance. Integrative analysis of multiple omics datasets has the potential to identify novel genes involved in disease pathogenesis by leveraging these variants in a functional, regulatory context. RESULTS We performed expression quantitative trait locus (eQTL) analysis using genome-wide SNP genotyping and gene expression profiling of lung tissue samples from 86 COPD cases and 31 controls, testing for SNPs associated with gene expression levels. These results were integrated with a prior COPD GWAS using an ensemble statistical and network methods approach to identify relevant genes and observe them in the context of overall genetic control of gene expression to highlight co-regulated genes and disease pathways. We identified 250,312 unique SNPs and 4997 genes in the cis(local)-eQTL analysis (5% false discovery rate). The top gene from the integrative analysis was MAPT, a gene recently identified in an independent GWAS of lung function. The genes HNRNPAB and PCBP2 with RNA binding activity and the gene ACVR1B were identified in network communities with validated disease relevance. CONCLUSIONS The integration of lung tissue gene expression with genome-wide SNP genotyping and subsequent intersection with prior GWAS and omics studies highlighted candidate genes within COPD loci and in communities harboring known COPD genes. This integration also identified novel disease genes in sub-threshold regions that would otherwise have been missed through GWAS.
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Affiliation(s)
- Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - John Platig
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Bartholome Celli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Nathaniel Marchetti
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Gerard J Criner
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - George R Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
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30
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Cloonan SM, Mumby S, Adcock IM, Choi AMK, Chung KF, Quinlan GJ. The "Iron"-y of Iron Overload and Iron Deficiency in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2017; 196:1103-1112. [PMID: 28410559 DOI: 10.1164/rccm.201702-0311pp] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Suzanne M Cloonan
- 1 Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, New York
| | | | | | - Augustine M K Choi
- 1 Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, New York.,3 New York-Presbyterian Hospital, New York, New York
| | | | - Gregory J Quinlan
- 4 Vascular Biology, National Heart and Lung Institute, Imperial College London, London, United Kingdom; and
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31
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Kim WJ, Yim JJ, Kim DK, Lee MG, Fuhlbrigge AL, Sliwinski P, Hawrylkiewicz I, Wan ES, Cho MH, Silverman EK. Severe COPD cases from Korea, Poland, and USA have substantial differences in respiratory symptoms and other respiratory illnesses. Int J Chron Obstruct Pulmon Dis 2017; 12:3415-3423. [PMID: 29238186 PMCID: PMC5716321 DOI: 10.2147/copd.s145908] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Purpose Chronic obstructive pulmonary disease (COPD), characterized by irreversible airflow obstruction, is a major cause of morbidity and mortality worldwide. However, geographic differences in the clinical characteristics of severe COPD patients have not been widely studied. Methods We recruited a total of 828 severe COPD cases from three continents. Subjects in Poland were enrolled by the Institute of Tuberculosis and Lung Diseases in Warsaw; subjects in Korea participated at several university hospitals in Korea; and subjects in USA were enrolled at two clinics affiliated with academic medical centers. All subjects were over the age of 30 with at least 10 pack-years of cigarette smoking history. Cases manifested severe to very severe airflow obstruction with post-bronchodilator forced expiratory volume in 1 second (FEV1) <50% predicted and FEV1/forced vital capacity <0.7. All subjects completed a detailed questionnaire and underwent standardized pre-bronchodilator and post-bronchodilator spirometry. Subjects with known tuberculosis (TB)-associated lung parenchymal destruction were excluded. Univariate and multivariate assessments of the impact of the country of origin on respiratory symptoms and respiratory illness were performed. Results In both univariate and multivariate analyses, a history of TB (38.7%) and physician-diagnosed asthma (43.9%) were significantly more common in subjects with severe COPD from Korea than USA or Poland, while attacks of bronchitis (64.2%) were more common in subjects with severe COPD from Poland. COPD subjects from Poland had more severe dyspnea (modified Medical Research Council 3.3±1.0) and more frequently reported symptoms of chronic bronchitis (52.2%). A history of TB was also more common in Poland (10.8%) than in USA (0.3%) severe COPD patients. Conclusion Respiratory symptoms and other respiratory illnesses associated with severe COPD differed widely among three continents.
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Affiliation(s)
- Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University Hospital, Chuncheon
| | - Jae-Joon Yim
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Seoul National University College of Medicine, Seoul
| | - Deog Kyeom Kim
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul National University College of Medicine, Seoul
| | - Myung Goo Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Hallym University Chuncheon Sacred Heart Hospital, Chuncheon, Korea
| | - Anne L Fuhlbrigge
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Pawel Sliwinski
- 2nd Department of Respiratory Medicine, Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - Iwona Hawrylkiewicz
- 2nd Department of Respiratory Medicine, Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - Emily S Wan
- Channing Division of Network Medicine.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
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32
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Koopmans T, Gosens R. Revisiting asthma therapeutics: focus on WNT signal transduction. Drug Discov Today 2017; 23:49-62. [PMID: 28890197 DOI: 10.1016/j.drudis.2017.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 07/20/2017] [Accepted: 09/01/2017] [Indexed: 12/16/2022]
Abstract
Asthma is a complex disease of the airways that develops as a consequence of both genetic and environmental factors. This interaction has highlighted genes important in early life, particularly those that control lung development, such as the Wingless/Integrase-1 (WNT) signalling pathway. Although aberrant WNT signalling is involved with an array of human conditions, it has received little attention within the context of asthma. Yet it is highly relevant, driving events involved with inflammation, airway remodelling, and airway hyper-responsiveness (AHR). In this review, we revisit asthma therapeutics by examining whether WNT signalling is a valid therapeutic target for asthma.
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Affiliation(s)
- Tim Koopmans
- Department of Molecular Pharmacology, University of Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, The Netherlands
| | - Reinoud Gosens
- Department of Molecular Pharmacology, University of Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, The Netherlands.
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33
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Genetic Variants in the Hedgehog Interacting Protein Gene Are Associated with the FEV1/FVC Ratio in Southern Han Chinese Subjects with Chronic Obstructive Pulmonary Disease. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2756726. [PMID: 28929109 PMCID: PMC5591965 DOI: 10.1155/2017/2756726] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/11/2017] [Accepted: 07/18/2017] [Indexed: 01/10/2023]
Abstract
BACKGROUND Convincing evidences have demonstrated the associations between HHIP and FAM13a polymorphisms and COPD in non-Asian populations. Here genetic variants in HHIP and FAM13a were investigated in Southern Han Chinese COPD. METHODS A case-control study was conducted, including 989 cases and 999 controls. The associations between SNPs genotypes and COPD were performed by a logistic regression model; for SNPs and COPD-related phenotypes such as lung function, COPD severity, pack-year of smoking, and smoking status, a linear regression model was employed. Effects of risk alleles, genotypes, and haplotypes of the 3 significant SNPs in the HHIP gene on FEV1/FVC were also assessed in a linear regression model in COPD. RESULTS The mean FEV1/FVC% value was 46.8 in combined COPD population. None of the 8 selected SNPs apparently related to COPD susceptibility. However, three SNPs (rs12509311, rs13118928, and rs182859) in HHIP were associated significantly with the FEV1/FVC% (Pmax = 4.1 × 10-4) in COPD adjusting for gender, age, and smoking pack-years. Moreover, statistical significance between risk alleles and the FEV1/FVC% (P = 2.3 × 10-4), risk genotypes, and the FEV1/FVC% (P = 3.5 × 10-4) was also observed in COPD. CONCLUSIONS Genetic variants in HHIP were related with FEV1/FVC in COPD. Significant relationships between risk alleles and risk genotypes and FEV1/FVC in COPD were also identified.
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Ruan X, Chen T, Wang X, Li Y. Suxiao Jiuxin Pill protects cardiomyocytes against mitochondrial injury and alters gene expression during ischemic injury. Exp Ther Med 2017; 14:3523-3532. [PMID: 29042943 PMCID: PMC5639384 DOI: 10.3892/etm.2017.4964] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 06/16/2017] [Indexed: 12/11/2022] Open
Abstract
Suxiao Jiuxin Pill (SX), a traditional Chinese medicine compound consisting primarily of tetramethylpyrazine and borneol, has been reported to protect against ischemic heart disease. However, the effects of SX on mitochondrial injury and gene expression in various signaling pathways are unclear. The aim of the present study was to investigate the effects of SX on mitochondrial injury and to screen the expression of genes potentially altered by SX using a cell culture model of ischemic injury. Simulated ischemia was established by culturing HL-1 cardiomyocytes in Dulbecco's modified Eagle medium without glucose or serum in a hypoxic chamber containing 95% N2 and 5% CO2 for 24 h. HL-1 cardiomyocytes were divided into 3 groups: Control, ischemic injury and ischemic injury + SX (100 µg/ml; n=3 wells/group). Mitochondrial membrane potential was detected by staining with JC-1 dye. The mRNA expression levels of adenylyl cyclase (Adcy) 1–9, adrenoceptor β1, Akt1, ATPase Na+/K+ transporting subunit β2, calcium voltage-gated channel auxiliary subunit α2δ (Cacna2d)2, Cacna2d3, calcium channel voltage-dependent γ subunit 8, cytochrome C oxidase subunit 6A2 (Cox6a2), fibroblast growth factor receptor (Fgfr) 4, Fgf8, Fgf12, Gnas complex locus, glycogen synthase kinase 3β (Gsk3b), mitogen-activated protein kinase (Mapk)11-14, Mapk kinase kinase kinase 1 (Map4k1), Mas1, nitric oxide synthase 3 (Nos3), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (Pik3ca), phospholipase A2 group 4A, rap guanine nucleotide exchange factor 4 and ryanodine receptor 2 were detected using reverse transcription-quantitative polymerase chain reaction. The protein expression levels of phosphoinositide 3-kinase (PI3K), MAS-1 and phosphorylated-endothelial NOS were also examined by immunofluorescence staining. The decrease in mitochondrial membrane potential in the cell culture model of ischemic injury (P<0.001) was significantly attenuated by SX treatment (P<0.001). Furthermore, increases in the mRNA expression levels of Adcy2 (P<0.05), 3 (P<0.01) and 8 (P<0.05) in the ischemic injury model were significantly attenuated by SX treatment (P<0.01), and SX treatment significantly decreased the mRNA expression levels of Adcy1 (P<0.01) and 6 (P<0.05) in ischemic cells. Decreases in the mRNA expression levels of Cox6a2 (P<0.001), Gsk3b (P<0.01) and Pik3ca (P<0.001) in the ischemic injury model were also significantly attenuated by SX treatment (P<0.05, P<0.01 and P<0.001, respectively). In addition, the decrease in the protein expression of PI3K (P<0.001) was significantly attenuated by SX treatment (P<0.001). The present findings indicate that SX may protect cardiomyocytes against mitochondrial injury and attenuate alterations in the gene expression of Adcy2, 3 and 8, Cox6a2, Gsk3b and Pik3ca during ischemic injury.
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Affiliation(s)
- Xiaofen Ruan
- Cardiovascular Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, P.R. China
| | - Tiejun Chen
- Cardiovascular Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, P.R. China
| | - Xiaolong Wang
- Cardiovascular Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, P.R. China
| | - Yiping Li
- Cardiovascular Department, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, P.R. China
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Rajput C. Chronic Obstructive Pulmonary Disease Meta Genome-Wide Association Studies. New Insights into the Genetics of Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2017; 57:1-2. [DOI: 10.1165/rcmb.2017-0070ed] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Charu Rajput
- Department of PediatricsUniversity of Michigan Medical SchoolAnn Arbor, Michigan
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36
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Dessauer CW, Watts VJ, Ostrom RS, Conti M, Dove S, Seifert R. International Union of Basic and Clinical Pharmacology. CI. Structures and Small Molecule Modulators of Mammalian Adenylyl Cyclases. Pharmacol Rev 2017; 69:93-139. [PMID: 28255005 PMCID: PMC5394921 DOI: 10.1124/pr.116.013078] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Adenylyl cyclases (ACs) generate the second messenger cAMP from ATP. Mammalian cells express nine transmembrane AC (mAC) isoforms (AC1-9) and a soluble AC (sAC, also referred to as AC10). This review will largely focus on mACs. mACs are activated by the G-protein Gαs and regulated by multiple mechanisms. mACs are differentially expressed in tissues and regulate numerous and diverse cell functions. mACs localize in distinct membrane compartments and form signaling complexes. sAC is activated by bicarbonate with physiologic roles first described in testis. Crystal structures of the catalytic core of a hybrid mAC and sAC are available. These structures provide detailed insights into the catalytic mechanism and constitute the basis for the development of isoform-selective activators and inhibitors. Although potent competitive and noncompetitive mAC inhibitors are available, it is challenging to obtain compounds with high isoform selectivity due to the conservation of the catalytic core. Accordingly, caution must be exerted with the interpretation of intact-cell studies. The development of isoform-selective activators, the plant diterpene forskolin being the starting compound, has been equally challenging. There is no known endogenous ligand for the forskolin binding site. Recently, development of selective sAC inhibitors was reported. An emerging field is the association of AC gene polymorphisms with human diseases. For example, mutations in the AC5 gene (ADCY5) cause hyperkinetic extrapyramidal motor disorders. Overall, in contrast to the guanylyl cyclase field, our understanding of the (patho)physiology of AC isoforms and the development of clinically useful drugs targeting ACs is still in its infancy.
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Affiliation(s)
- Carmen W Dessauer
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Sciences Center at Houston, Houston, Texas (C.W.D.); Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana (V.J.W.); Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California (R.S.O.); Center for Reproductive Sciences, University of California San Francisco, San Francisco, California (M.C.); Institute of Pharmacy, University of Regensburg, Regensburg, Germany (S.D.); and Institute of Pharmacology, Hannover Medical School, Hannover, Germany (R.S.)
| | - Val J Watts
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Sciences Center at Houston, Houston, Texas (C.W.D.); Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana (V.J.W.); Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California (R.S.O.); Center for Reproductive Sciences, University of California San Francisco, San Francisco, California (M.C.); Institute of Pharmacy, University of Regensburg, Regensburg, Germany (S.D.); and Institute of Pharmacology, Hannover Medical School, Hannover, Germany (R.S.)
| | - Rennolds S Ostrom
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Sciences Center at Houston, Houston, Texas (C.W.D.); Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana (V.J.W.); Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California (R.S.O.); Center for Reproductive Sciences, University of California San Francisco, San Francisco, California (M.C.); Institute of Pharmacy, University of Regensburg, Regensburg, Germany (S.D.); and Institute of Pharmacology, Hannover Medical School, Hannover, Germany (R.S.)
| | - Marco Conti
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Sciences Center at Houston, Houston, Texas (C.W.D.); Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana (V.J.W.); Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California (R.S.O.); Center for Reproductive Sciences, University of California San Francisco, San Francisco, California (M.C.); Institute of Pharmacy, University of Regensburg, Regensburg, Germany (S.D.); and Institute of Pharmacology, Hannover Medical School, Hannover, Germany (R.S.)
| | - Stefan Dove
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Sciences Center at Houston, Houston, Texas (C.W.D.); Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana (V.J.W.); Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California (R.S.O.); Center for Reproductive Sciences, University of California San Francisco, San Francisco, California (M.C.); Institute of Pharmacy, University of Regensburg, Regensburg, Germany (S.D.); and Institute of Pharmacology, Hannover Medical School, Hannover, Germany (R.S.)
| | - Roland Seifert
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Sciences Center at Houston, Houston, Texas (C.W.D.); Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana (V.J.W.); Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California (R.S.O.); Center for Reproductive Sciences, University of California San Francisco, San Francisco, California (M.C.); Institute of Pharmacy, University of Regensburg, Regensburg, Germany (S.D.); and Institute of Pharmacology, Hannover Medical School, Hannover, Germany (R.S.)
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37
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Morrow JD, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Glass K, Choi AMK, Quackenbush J, Silverman EK, DeMeo DL. DNA methylation profiling in human lung tissue identifies genes associated with COPD. Epigenetics 2016; 11:730-739. [PMID: 27564456 PMCID: PMC5094634 DOI: 10.1080/15592294.2016.1226451] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/05/2016] [Accepted: 08/10/2016] [Indexed: 10/21/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a smoking-related disease characterized by genetic and phenotypic heterogeneity. Although association studies have identified multiple genomic regions with replicated associations to COPD, genetic variation only partially explains the susceptibility to lung disease, and suggests the relevance of epigenetic investigations. We performed genome-wide DNA methylation profiling in homogenized lung tissue samples from 46 control subjects with normal lung function and 114 subjects with COPD, all former smokers. The differentially methylated loci were integrated with previous genome-wide association study results. The top 535 differentially methylated sites, filtered for a minimum mean methylation difference of 5% between cases and controls, were enriched for CpG shelves and shores. Pathway analysis revealed enrichment for transcription factors. The top differentially methylated sites from the intersection with previous GWAS were in CHRM1, GLT1D1, and C10orf11; sorted by GWAS P-value, the top sites included FRMD4A, THSD4, and C10orf11. Epigenetic association studies complement genetic association studies to identify genes potentially involved in COPD pathogenesis. Enrichment for genes implicated in asthma and lung function and for transcription factors suggests the potential pathogenic relevance of genes identified through differential methylation and the intersection with a broader range of GWAS associations.
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Affiliation(s)
- Jarrett D. Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Craig P. Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Bartolome Celli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nathaniel Marchetti
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, USA
| | - Gerard Criner
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - George Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Augustine M. K. Choi
- Department of Medicine, New York Presbyterian/Weill Cornell Medical Center, New York, NY, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
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Condreay L, Huang L, Harris E, Brooks J, Riley JH, Church A, Ghosh S. Genetic effects on treatment response of umeclidinium/vilanterol in chronic obstructive pulmonary disease. Respir Med 2016; 114:123-6. [PMID: 27109822 DOI: 10.1016/j.rmed.2016.03.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/10/2016] [Accepted: 03/21/2016] [Indexed: 01/19/2023]
Abstract
BACKGROUND Treatment with long-acting β2-agonists (LABAs) and long-acting muscarinic antagonists (LAMAs) for chronic obstructive pulmonary disease (COPD) is standard, but response varies. We investigated genetic association with treatment response to umeclidinium (UMEC, a LAMA), vilanterol (VI, a LABA), and combination therapy. METHODS Data from 17 clinical trials (N = 6075) in patients with COPD receiving once-daily UMEC/VI (125/25mcg or 62.5/25mcg), UMEC (125 or 62.5mcg), VI (25mcg) or placebo were used. Genetic association with change from baseline in trough forced expiratory volume in 1 s (FEV1) ∼24 h post-dosing was assessed for: (i) 3 β2-adrenoceptor (ADRB2) gene variants; (ii) 298 single-nucleotide polymorphisms (SNPs) with prior evidence of associations; (iii) human leukocyte antigen (HLA) alleles and (iv) genome-wide association study (GWAS) SNPs. Other endpoints were (i) reversibility at screening; and at baseline: (ii) FEV1; (iii) forced vital capacity (FVC), and (iv) FEV1/FVC ratio. Using linear regression, the inverse normal transformed residuals were pooled together, first across treatment group, then across studies for each monotherapy, then combination therapy and finally for every treated patient. RESULTS Of 6075 patients, 1849 received UMEC/VI, 1390 received UMEC, 1795 received VI, and 1041 received placebo. None of the ADRB2 variants, HLA alleles or GWAS variants tested were associated with treatment response or baseline endpoints. Four SNPs in FAM13A (rs7671167, rs2869967, rs1964516, rs1903003) were significantly associated with baseline FEV1/FVC ratio (p < 3 × 10(-5)) after adjusting for multiple testing. CONCLUSIONS No genetic association was found with treatment response to UMEC or VI when administered as monotherapies or in combination.
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Affiliation(s)
| | | | | | - Jean Brooks
- GlaxoSmithKline, Stockley Park West, Middlesex, UK
| | - John H Riley
- GlaxoSmithKline, Stockley Park West, Middlesex, UK
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Cloonan SM, Glass K, Laucho-Contreras ME, Bhashyam AR, Cervo M, Pabón MA, Konrad C, Polverino F, Siempos II, Perez E, Mizumura K, Ghosh MC, Parameswaran H, Williams NC, Rooney KT, Chen ZH, Goldklang MP, Yuan GC, Moore SC, Demeo DL, Rouault TA, D’Armiento JM, Schon EA, Manfredi G, Quackenbush J, Mahmood A, Silverman EK, Owen CA, Choi AM. Mitochondrial iron chelation ameliorates cigarette smoke-induced bronchitis and emphysema in mice. Nat Med 2016; 22:163-74. [PMID: 26752519 PMCID: PMC4742374 DOI: 10.1038/nm.4021] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/01/2015] [Indexed: 12/20/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is linked to both cigarette smoking and genetic determinants. We have previously identified iron-responsive element-binding protein 2 (IRP2) as an important COPD susceptibility gene and have shown that IRP2 protein is increased in the lungs of individuals with COPD. Here we demonstrate that mice deficient in Irp2 were protected from cigarette smoke (CS)-induced experimental COPD. By integrating RNA immunoprecipitation followed by sequencing (RIP-seq), RNA sequencing (RNA-seq), and gene expression and functional enrichment clustering analysis, we identified Irp2 as a regulator of mitochondrial function in the lungs of mice. Irp2 increased mitochondrial iron loading and levels of cytochrome c oxidase (COX), which led to mitochondrial dysfunction and subsequent experimental COPD. Frataxin-deficient mice, which had higher mitochondrial iron loading, showed impaired airway mucociliary clearance (MCC) and higher pulmonary inflammation at baseline, whereas mice deficient in the synthesis of cytochrome c oxidase, which have reduced COX, were protected from CS-induced pulmonary inflammation and impairment of MCC. Mice treated with a mitochondrial iron chelator or mice fed a low-iron diet were protected from CS-induced COPD. Mitochondrial iron chelation also alleviated CS-induced impairment of MCC, CS-induced pulmonary inflammation and CS-associated lung injury in mice with established COPD, suggesting a critical functional role and potential therapeutic intervention for the mitochondrial-iron axis in COPD.
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MESH Headings
- Aged
- Aged, 80 and over
- Airway Remodeling
- Animals
- Bronchitis/etiology
- Bronchitis/genetics
- Disease Models, Animal
- Electron Transport Complex IV/metabolism
- Electrophoretic Mobility Shift Assay
- Enzyme-Linked Immunosorbent Assay
- Flow Cytometry
- Gene Expression Profiling
- Humans
- Immunoblotting
- Immunohistochemistry
- Immunoprecipitation
- Iron/metabolism
- Iron Chelating Agents/pharmacology
- Iron Regulatory Protein 2/genetics
- Iron Regulatory Protein 2/metabolism
- Iron, Dietary
- Iron-Binding Proteins/genetics
- Lung/drug effects
- Lung/metabolism
- Lung Injury/etiology
- Lung Injury/genetics
- Membrane Potential, Mitochondrial
- Mice
- Mice, Knockout
- Microscopy, Confocal
- Microscopy, Electron, Transmission
- Microscopy, Fluorescence
- Mitochondria/drug effects
- Mitochondria/metabolism
- Mucociliary Clearance/genetics
- Pneumonia/etiology
- Pneumonia/genetics
- Pulmonary Disease, Chronic Obstructive/etiology
- Pulmonary Disease, Chronic Obstructive/genetics
- Pulmonary Disease, Chronic Obstructive/metabolism
- Pulmonary Emphysema/etiology
- Pulmonary Emphysema/genetics
- Real-Time Polymerase Chain Reaction
- Smoke/adverse effects
- Smoking/adverse effects
- Nicotiana
- Frataxin
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Affiliation(s)
- Suzanne M. Cloonan
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria E. Laucho-Contreras
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Abhiram R. Bhashyam
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Morgan Cervo
- Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria A. Pabón
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
| | - Csaba Konrad
- Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY, USA
| | - Francesca Polverino
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Lovelace Respiratory Research institute, Albuquerque, NM, USA
- Pulmonary Department, University of Parma, Parma, Italy
| | - Ilias I. Siempos
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
- First Department of Critical Care Medicine and Pulmonary Services, Evangelismos Hospital, University of Athens, Medical School, Athens, Greece
| | - Elizabeth Perez
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
| | - Kenji Mizumura
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Manik C. Ghosh
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, USA
| | | | - Niamh C. Williams
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
| | - Kristen T. Rooney
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
| | - Zhi-Hua Chen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Respiratory and Critical Care Medicine, Second Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Monica P. Goldklang
- Department of Anesthesiology, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stephen C. Moore
- Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Dawn L. Demeo
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Tracey A. Rouault
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, USA
| | - Jeanine M. D’Armiento
- Department of Anesthesiology, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
- Department of Physiology & Cellular Biophysics, Columbia University, New York, NY, USA
| | - Eric A. Schon
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
| | - Giovanni Manfredi
- Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Ashfaq Mahmood
- Department of Radiology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin K. Silverman
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Caroline A. Owen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Lovelace Respiratory Research institute, Albuquerque, NM, USA
| | - Augustine M.K. Choi
- Joan and Sanford I. Weill Department of Medicine, New York-Presbyterian Hospital, Weill Cornell Medical College, New York, NY, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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Du Y, Xue Y, Xiao W. Association of IREB2 Gene rs2568494 Polymorphism with Risk of Chronic Obstructive Pulmonary Disease: A Meta-Analysis. Med Sci Monit 2016; 22:177-82. [PMID: 26775557 PMCID: PMC4723059 DOI: 10.12659/msm.894524] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Background It is reported that the iron-responsive element-binding protein 2 (IREB2) gene rs2568494 polymorphism might be associated with COPD risk. The purpose of this meta-analysis was to collect all eligible studies to review the association between IREB2 gene rs2568494 polymorphism and susceptibility to COPD. Material/Methods We carried out a comprehensive document search of electronic databases of PubMed, MEDLIN, Web of Science, and included 4 eligible studies that examined the association between IREB2 rs2568494 polymorphism and COPD susceptibility. We performed a meta-analysis of these studies based on IREB2 rs2568494 genotypes. Results After meta-analysis with fixed or random effects, no significant associations were found under the heterozygote model (GG/GA; OR=0.908, 95%CI: 0.790–1.043; P=0.172), homozygote model (GG/AA; OR=0.880, 95%CI: 0.497–1.557; P=0.661), dominant model (GG/AA+GA; OR=0.941, 95%CI: 0.748–1.182; P=0.599), or allelic model (G/A; OR=0.953, 95%CI: 0.770–1.179; P=0.655). However, we found a significant correlation under the recessive model (AA/GA+GG; OR=1.384, 95%CI: 1.092–1.755; P=0.007). Conclusions The current results revealed that there was significant association between IREB2 gene rs2568494 polymorphism with susceptibility to COPD; the presence of allelic A might a genetic factor conferring susceptibility to COPD.
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Affiliation(s)
- Yiming Du
- Department of Health Care, Qianfoshan Hospital, Shandong University, Jinan, Shandong, China (mainland)
| | - Yuwen Xue
- Department of Pulmonary Medicine, Qilu Hospital of Shandong University, Jinan, Shandong, China (mainland)
| | - Wei Xiao
- Department of Pulmonary Medicine, Qilu Hospital of Shandong University, Jinan, Shandong, China (mainland)
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41
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Lutz SM, Cho MH, Young K, Hersh CP, Castaldi PJ, McDonald ML, Regan E, Mattheisen M, DeMeo DL, Parker M, Foreman M, Make BJ, Jensen RL, Casaburi R, Lomas DA, Bhatt SP, Bakke P, Gulsvik A, Crapo JD, Beaty TH, Laird NM, Lange C, Hokanson JE, Silverman EK. A genome-wide association study identifies risk loci for spirometric measures among smokers of European and African ancestry. BMC Genet 2015; 16:138. [PMID: 26634245 PMCID: PMC4668640 DOI: 10.1186/s12863-015-0299-4] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 11/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pulmonary function decline is a major contributor to morbidity and mortality among smokers. Post bronchodilator FEV1 and FEV1/FVC ratio are considered the standard assessment of airflow obstruction. We performed a genome-wide association study (GWAS) in 9919 current and former smokers in the COPDGene study (6659 non-Hispanic Whites [NHW] and 3260 African Americans [AA]) to identify associations with spirometric measures (post-bronchodilator FEV1 and FEV1/FVC). We also conducted meta-analysis of FEV1 and FEV1/FVC GWAS in the COPDGene, ECLIPSE, and GenKOLS cohorts (total n = 13,532). RESULTS Among NHW in the COPDGene cohort, both measures of pulmonary function were significantly associated with SNPs at the 15q25 locus [containing CHRNA3/5, AGPHD1, IREB2, CHRNB4] (lowest p-value = 2.17 × 10(-11)), and FEV1/FVC was associated with a genomic region on chromosome 4 [upstream of HHIP] (lowest p-value = 5.94 × 10(-10)); both regions have been previously associated with COPD. For the meta-analysis, in addition to confirming associations to the regions near CHRNA3/5 and HHIP, genome-wide significant associations were identified for FEV1 on chromosome 1 [TGFB2] (p-value = 8.99 × 10(-9)), 9 [DBH] (p-value = 9.69 × 10(-9)) and 19 [CYP2A6/7] (p-value = 3.49 × 10(-8)) and for FEV1/FVC on chromosome 1 [TGFB2] (p-value = 8.99 × 10(-9)), 4 [FAM13A] (p-value = 3.88 × 10(-12)), 11 [MMP3/12] (p-value = 3.29 × 10(-10)) and 14 [RIN3] (p-value = 5.64 × 10(-9)). CONCLUSIONS In a large genome-wide association study of lung function in smokers, we found genome-wide significant associations at several previously described loci with lung function or COPD. We additionally identified a novel genome-wide significant locus with FEV1 on chromosome 9 [DBH] in a meta-analysis of three study populations.
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Affiliation(s)
- Sharon M Lutz
- Department of Biostatistics, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, B119 Bldg. 500, W3128, Aurora, CO, 80045, USA.
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Kendra Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Merry-Lynn McDonald
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Elizabeth Regan
- Department of Medicine, National Jewish Health, Denver, CO, USA.
| | - Manuel Mattheisen
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Margaret Parker
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | | | - Barry J Make
- Department of Medicine, National Jewish Health, Denver, CO, USA.
| | - Robert L Jensen
- Division of Pulmonary, Allergy & Critical Care Medicine, LDS Hospital, Salt Lake City, UT, USA.
| | - Richard Casaburi
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA.
| | - David A Lomas
- Wolfson Institute for Biomedical Research, University College London, London, UK.
| | - Surya P Bhatt
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - James D Crapo
- Department of Medicine, National Jewish Health, Denver, CO, USA.
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Nan M Laird
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
| | - Christoph Lange
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Abstract
Respiratory disease accounts for a large proportion of emergency admissions to hospital and diseaseassociated mortality. Genetic association studies demonstrate a link between iron metabolism and pulmonary disease phenotypes. IREB2 is a gene that produces iron regulatory protein 2 (IRP2), which has a key role in iron homeostasis. This review addresses pathways involved in iron metabolism, particularly focusing on the role of IREB2. In addition to this, environmental factors also influence phenotypic variation in respiratory disease, for example inhaled iron from cigarette smoke is deposited in the lung and causes tissue damage by altering iron homeostasis. The effects of cigarette smoke are detailed in this article, particularly in relation to lung conditions that favour the upper lobes, such as emphysema and lung cancer. Clinical applications of iron homeostasis are also discussed in this review, especially looking at the pathophysiology of chronic obstructive pulmonary disease, lung cancer, pulmonary infections and acute respiratory distress syndrome. Promising new treatments involving iron are also covered.
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43
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Abstract
COPD is a common complex disease characterized by progressive airflow limitation. Several genome-wide association studies (GWASs) have discovered genes that are associated with COPD. Recently, candidate genes for COPD identified by GWASs include CHRNA3/5 (cholinergic nicotine receptor alpha 3/5), IREB2 (iron regulatory binding protein 2), HHIP (hedgehog-interacting protein), FAM13A (family with sequence similarity 13, member A), and AGER (advanced glycosylation end product–specific receptor). Their association with COPD susceptibility has been replicated in multiple populations. Since these candidate genes have not been considered in COPD, their pathological roles are still largely unknown. Herein, we review some evidences that they can be effective drug targets or serve as biomarkers for diagnosis or subtyping. However, more study is required to understand the functional roles of these candidate genes. Future research is needed to characterize the effect of genetic variants, validate gene function in humans and model systems, and elucidate the genes’ transcriptional and posttranscriptional regulatory mechanisms.
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Affiliation(s)
- Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Chuncheon, South Korea
| | - Sang Do Lee
- Department of Pulmonary and Critical Care Medicine, Clinical Research Center for Chronic Obstructive Airway Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
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Obeidat M, Hao K, Bossé Y, Nickle DC, Nie Y, Postma DS, Laviolette M, Sandford AJ, Daley DD, Hogg JC, Elliott WM, Fishbane N, Timens W, Hysi PG, Kaprio J, Wilson JF, Hui J, Rawal R, Schulz H, Stubbe B, Hayward C, Polasek O, Järvelin MR, Zhao JH, Jarvis D, Kähönen M, Franceschini N, North KE, Loth DW, Brusselle GG, Smith AV, Gudnason V, Bartz TM, Wilk JB, O'Connor GT, Cassano PA, Tang W, Wain LV, Soler Artigas M, Gharib SA, Strachan DP, Sin DD, Tobin MD, London SJ, Hall IP, Paré PD. Molecular mechanisms underlying variations in lung function: a systems genetics analysis. THE LANCET. RESPIRATORY MEDICINE 2015; 3:782-95. [PMID: 26404118 PMCID: PMC5021067 DOI: 10.1016/s2213-2600(15)00380-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/06/2015] [Accepted: 08/12/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Lung function measures reflect the physiological state of the lung, and are essential to the diagnosis of chronic obstructive pulmonary disease (COPD). The SpiroMeta-CHARGE consortium undertook the largest genome-wide association study (GWAS) so far (n=48,201) for forced expiratory volume in 1 s (FEV1) and the ratio of FEV1 to forced vital capacity (FEV1/FVC) in the general population. The lung expression quantitative trait loci (eQTLs) study mapped the genetic architecture of gene expression in lung tissue from 1111 individuals. We used a systems genetics approach to identify single nucleotide polymorphisms (SNPs) associated with lung function that act as eQTLs and change the level of expression of their target genes in lung tissue; termed eSNPs. METHODS The SpiroMeta-CHARGE GWAS results were integrated with lung eQTLs to map eSNPs and the genes and pathways underlying the associations in lung tissue. For comparison, a similar analysis was done in peripheral blood. The lung mRNA expression levels of the eSNP-regulated genes were tested for associations with lung function measures in 727 individuals. Additional analyses identified the pleiotropic effects of eSNPs from the published GWAS catalogue, and mapped enrichment in regulatory regions from the ENCODE project. Finally, the Connectivity Map database was used to identify potential therapeutics in silico that could reverse the COPD lung tissue gene signature. FINDINGS SNPs associated with lung function measures were more likely to be eQTLs and vice versa. The integration mapped the specific genes underlying the GWAS signals in lung tissue. The eSNP-regulated genes were enriched for developmental and inflammatory pathways; by comparison, SNPs associated with lung function that were eQTLs in blood, but not in lung, were only involved in inflammatory pathways. Lung function eSNPs were enriched for regulatory elements and were over-represented among genes showing differential expression during fetal lung development. An mRNA gene expression signature for COPD was identified in lung tissue and compared with the Connectivity Map. This in-silico drug repurposing approach suggested several compounds that reverse the COPD gene expression signature, including a nicotine receptor antagonist. These findings represent novel therapeutic pathways for COPD. INTERPRETATION The system genetics approach identified lung tissue genes driving the variation in lung function and susceptibility to COPD. The identification of these genes and the pathways in which they are enriched is essential to understand the pathophysiology of airway obstruction and to identify novel therapeutic targets and biomarkers for COPD, including drugs that reverse the COPD gene signature in silico. FUNDING The research reported in this article was not specifically funded by any agency. See Acknowledgments for a full list of funders of the lung eQTL study and the Spiro-Meta CHARGE GWAS.
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Affiliation(s)
- Ma'en Obeidat
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Ke Hao
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec, QC, Canada; Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, QC, Canada
| | - David C Nickle
- Merck Research Laboratories, Genetics and Pharmacogenomics, Boston, MA, USA
| | - Yunlong Nie
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Dirkje S Postma
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute, University of Groningen, Groningen, Netherlands
| | - Michel Laviolette
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, QC, Canada
| | - Andrew J Sandford
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Denise D Daley
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - James C Hogg
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - W Mark Elliott
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Nick Fishbane
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, Groningen, Netherlands
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College, London, UK
| | - Jaakko Kaprio
- Department of Public Health, and Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland; National Institute for Health and Welfare, Helsinki, Finland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jennie Hui
- Busselton Population Medical Research Institute, Busselton, WA, Australia; PathWest Laboratory Medicine of Western Australia, Nedlands, WA, Australia; School of Population Health and School of Pahology and Laboratory Medicine, University of Western Australia, Nedlands, WA, Australia
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Genetic Epidemiology, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research, Munich, Germany
| | - Beate Stubbe
- University Hospital, Department of Internal Medicine B, Greifswald, Germany
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Ozren Polasek
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK; Faculty of Medicine, University of Split, Croatia
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK; Center for Life Course Epidemiology, Faculty of Medicine, Biocenter Oulu, and Unit of Primary Care, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge UK
| | - Deborah Jarvis
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK; Respiratory Epidemiology and Public Health Group, National Heart and Lung Institute, Imperial College, London, UK
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Nora Franceschini
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Kari E North
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA; University of North Carolina Center for Genome Sciences, Chapel Hill, NC, USA
| | - Daan W Loth
- Departments of Epidemiology and Respiratory Medicine, Erasmus MC, Rotterdam, Netherlands
| | - Guy G Brusselle
- Departments of Epidemiology and Respiratory Medicine, Erasmus MC, Rotterdam, Netherlands; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Albert Vernon Smith
- Icelandic Heart Association, Kopavogur, Iceland; Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland; Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, USA
| | - Jemma B Wilk
- Human Genetics & Computational Biomedicine, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - George T O'Connor
- Pulmonary Center, Boston University School of Medicine, Boston, MA, USA; NHLBI Framingham Heart Study, Framingham, MA, USA
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA; Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medical College, NY, USA
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA; Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Louise V Wain
- University of Leicester, Genetic Epidemiology Group, Department of Health Sciences, Leicester, UK; National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - María Soler Artigas
- University of Leicester, Genetic Epidemiology Group, Department of Health Sciences, Leicester, UK; National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, University of Washington, Seattle, WA, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Don D Sin
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Martin D Tobin
- University of Leicester, Genetic Epidemiology Group, Department of Health Sciences, Leicester, UK; National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Ian P Hall
- University of Nottingham Division of Respiratory Medicine, University Hospital of Nottingham, Nottingham, UK
| | - Peter D Paré
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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Ziółkowska-Suchanek I, Mosor M, Gabryel P, Grabicki M, Żurawek M, Fichna M, Strauss E, Batura-Gabryel H, Dyszkiewicz W, Nowak J. Susceptibility loci in lung cancer and COPD: association of IREB2 and FAM13A with pulmonary diseases. Sci Rep 2015; 5:13502. [PMID: 26310313 PMCID: PMC4550915 DOI: 10.1038/srep13502] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/29/2015] [Indexed: 12/23/2022] Open
Abstract
Genome-wide association studies have identified loci at 15q25 (IREB2) and 4q22 (FAM13A), associated with lung cancer (LC) and chronic obstructive pulmonary disease (COPD). The aim of our research was to determine the association of IREB2 and FAM13A SNPs with LC and severe/very severe COPD patients. We examined IREB2 variants (rs2568494, rs2656069, rs10851906, rs13180) and FAM13A (rs1903003, rs7671167, rs2869967) among 1.141 participants (468 LC, 149 COPD, 524 smoking controls). The frequency of the minor IREB2 rs2568494 AA genotype, was higher in LC vs controls (P = 0.0081, OR = 1.682). The FAM13A rs2869967 was associated with COPD (minor CC genotype: P = 0.0007, OR = 2.414). The rs1903003, rs7671167 FAM13A variants confer a protective effect on COPD (both P < 0.002, OR < 0.405). Haplotype-based tests identified an association of the IREB2 AAAT haplotype with LC (P = 0.0021, OR = 1.513) and FAM13A TTC with COPD (P = 0.0013, OR = 1.822). Cumulative genetic risk score analyses (CGRS), derived by adding risk alleles, revealed that the risk for COPD increased with the growing number of the FAM13A risk alleles. OR (95% CI) for carriers of ≥5 risk alleles reached 2.998 (1.8 to 4.97) compared to the controls. This study confirms that the IREB2 variants contribute to an increased risk of LC, whereas FAM13A predisposes to increased susceptibility to COPD.
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Affiliation(s)
| | - Maria Mosor
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, Poznań, Poland
| | - Piotr Gabryel
- Department of Thoracic Surgery, University of Medical Sciences, 62 Szamarzewskiego Street, 60-569 Poznań, Poland
| | - Marcin Grabicki
- Department of Pulmonology, Allergology and Respiratory Oncology, Poznań University of Medical Sciences, 84 Szamarzewskiego Street, 60-569 Poland
| | - Magdalena Żurawek
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, Poznań, Poland
| | - Marta Fichna
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, Poznań, Poland.,Department of Endocrinology, Metabolism and Internal Diseases, Poznań University of Medical Sciences, 49 Przybyszewskiego Street, Poland
| | - Ewa Strauss
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, Poznań, Poland.,Laboratory for Basic Research and Translational Medicine in Vascular Diseases, Clinic of Internal and Vascular Surgery, Poznan University of Medical Sciences, Dluga ½ Street, 61-848 Poland
| | - Halina Batura-Gabryel
- Department of Pulmonology, Allergology and Respiratory Oncology, Poznań University of Medical Sciences, 84 Szamarzewskiego Street, 60-569 Poland
| | - Wojciech Dyszkiewicz
- Department of Thoracic Surgery, University of Medical Sciences, 62 Szamarzewskiego Street, 60-569 Poznań, Poland
| | - Jerzy Nowak
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, Poznań, Poland
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Ding Y, Yang D, Zhou L, Xu J, Chen Y, He P, Yao J, Chen J, Niu H, Sun P, Jin T. Variants in multiple genes polymorphism association analysis of COPD in the Chinese Li population. Int J Chron Obstruct Pulmon Dis 2015; 10:1455-63. [PMID: 26251585 PMCID: PMC4524388 DOI: 10.2147/copd.s86721] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Background It is known that the contribution of risk alleles to chronic obstructive pulmonary disease (COPD) may vary between populations. Further, previous studies involving various ethnic groups have revealed associations between COPD and genetic polymorphisms in families with sequence similarity 13, member A (FAM13A), micro-RNA 2054 (MIR2054), SET domain containing protein 7 (SETD7), ring finger protein 150 (RNF150), hedgehog interacting protein (HHIP), and vascular endothelial growth factor A (VEGFA). Our objective was to explore the association between these gene polymorphism and COPD in members of Chinese Li minority population. Materials and methods The Chinese Li population case–control study was conducted to assess genetic associations with COPD risk. Seven single nucleotide polymorphisms (SNPs) located on chromosome 4, including FAM13A, MIR2054, SETD7, RNF150, and HHIP, and nine SNPs in the VEGFA gene were genotyped among 234 cases and 240 controls using Sequenom Mass-ARRAY® platform. Linkage disequilibrium (LD) analysis was performed using Haploview software and the associations of the SNP frequencies with COPD were analyzed using chi-square (χ2) tests, genetic models analysis, and haplotype analysis. Results By χ2 we found the minor allele “G” of rs17050782 was with increased COPD risk in allele model. In genetic models, we found the minor allele of rs7671167 (P=0.028 by dominant model) and rs17050782 (P=0.008 by recessive model) was associated with the increased risk of COPD disease. Likewise, an increased risk of developing COPD was associated with the “GGCGC” haplotype of VEGFA (odds ratio =1.48, 95% confidence interval =1.02–2.12, P=0.037). Conclusion Our results were the first time to reveal that SNPs from FAM13A (rs7671167), SETD7 (rs17050782), and a haplotype of VEGFA (“GGCGC”) are potential susceptibility loci associated with increased COPD risk in Chinese Li minority population.
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Affiliation(s)
- Yipeng Ding
- Department of Emergency, People's Hospital of Hainan Province, Haikou, Hainan, People's Republic of China
| | - Danlei Yang
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Medical College, Wuhan, Hainan, People's Republic of China ; Department of Science and Technology, Huazhong University, Wuhan, Hainan, People's Republic of China
| | - Long Zhou
- School of Life Sciences, Northwest University, Xi'an, Hainan, People's Republic of China
| | - Junxu Xu
- Department of Respiration Emergency, The Third People's Hospital of Haikou, Haikou, Hainan, People's Republic of China
| | - Yu Chen
- Department of Respiration Emergency, The Third People's Hospital of Haikou, Haikou, Hainan, People's Republic of China
| | - Ping He
- Department of Emergency, People's Hospital of Hainan Province, Haikou, Hainan, People's Republic of China
| | - Jinjian Yao
- Department of Emergency, People's Hospital of Hainan Province, Haikou, Hainan, People's Republic of China
| | - Jiannan Chen
- Department of Emergency, People's Hospital of Hainan Province, Haikou, Hainan, People's Republic of China
| | - Huan Niu
- Department of Emergency, People's Hospital of Hainan Province, Haikou, Hainan, People's Republic of China
| | - Pei Sun
- Department of Emergency, People's Hospital of Hainan Province, Haikou, Hainan, People's Republic of China
| | - Tianbo Jin
- School of Life Sciences, Northwest University, Xi'an, Hainan, People's Republic of China
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Zhou JJ, Cho MH, Lange C, Lutz S, Silverman EK, Laird NM. Integrating Multiple Correlated Phenotypes for Genetic Association Analysis by Maximizing Heritability. Hum Hered 2015; 79:93-104. [PMID: 26111731 DOI: 10.1159/000381641] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 03/13/2015] [Indexed: 11/19/2022] Open
Abstract
Many correlated disease variables are analyzed jointly in genetic studies in the hope of increasing power to detect causal genetic variants. One approach involves assessing the relationship between each phenotype and each SNP individually and using a Bonferroni correction for the effective number of tests conducted. Alternatively, one can apply a multivariate regression or a dimension reduction technique, such as principal component analysis, and test for the association with the principal components of the phenotypes rather than the individual phenotypes. Inspired by the previous approaches of combining phenotypes to maximize heritability at individual SNPs, in this paper, we propose to construct a maximally heritable (MaxH) phenotype by taking advantage of the estimated total heritability and co-heritability. The heritability and co-heritability only need to be estimated once; therefore, our method is applicable to genome-wide scans. The MaxH phenotype is a linear combination of the individual phenotypes with increased heritability and power over the phenotypes being combined. Simulations show that the heritability and power achieved agree well with the theory for large samples and two phenotypes. We compare our approach with commonly used methods and assess both the heritability and the power of the MaxH phenotype. Moreover, we provide suggestions for how to choose the phenotypes for combination. An application of our approach to a GWAS on chronic obstructive pulmonary disease shows its practical relevance.
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Affiliation(s)
- Jin J Zhou
- Division of Epidemiology and Biostatistics, College of Public Health, University of Arizona, Tucson, Ariz., USA
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Zhao Z, Peng F, Zhou Y, Hu G, He H, He F, Zou W, Zhao Z, Li B, Ran P. Exon sequencing identifies a novelCHRNA3-CHRNA5-CHRNB4variant that increases the risk for chronic obstructive pulmonary disease. Respirology 2015; 20:790-8. [PMID: 25891420 DOI: 10.1111/resp.12539] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 01/28/2015] [Accepted: 02/16/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Zhuxiang Zhao
- State Key Laboratory of Respiratory Diseases, First Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
- First Affiliated Municipal Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Fang Peng
- State Key Laboratory of Respiratory Diseases, First Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Yumin Zhou
- State Key Laboratory of Respiratory Diseases, First Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Guoping Hu
- Third Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Hua He
- First Affiliated Municipal Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Fang He
- State Key Laboratory of Respiratory Diseases, First Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Weifeng Zou
- State Key Laboratory of Respiratory Diseases, First Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Ziwen Zhao
- First Affiliated Municipal Hospital; Guangzhou Medical University; Guangzhou Guangdong China
| | - Bing Li
- Research Center of Experiment Medicine; Guangzhou Medical University; Guangzhou Guangdong China
| | - Pixin Ran
- State Key Laboratory of Respiratory Diseases, First Affiliated Hospital; Guangzhou Medical University; Guangzhou Guangdong China
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Xie J, Wu H, Xu Y, Wu X, Liu X, Shang J, Zhao J, Zhao J, Wang J, Dela Cruz CS, Xiong W, Xu Y. Gene susceptibility identification in a longitudinal study confirms new loci in the development of chronic obstructive pulmonary disease and influences lung function decline. Respir Res 2015; 16:49. [PMID: 25928290 PMCID: PMC4427922 DOI: 10.1186/s12931-015-0209-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/27/2015] [Indexed: 12/22/2022] Open
Abstract
Background To identify COPD associated gene susceptibility and lung function in a longitudinal cohort including COPD and subjects who were at risk for developing COPD, and to replicate this in two cross-sectional and longitudinal populations in Chinese Han population. Methods Three cohorts were recruited in this study, including an 18-year follow-up population (306 COPD and 743 control subjects) in one village in 1992 and it changed to 409 COPD and 611 controls in 2010, a 2 year follow-up study in another village (374 COPD and 377 controls) and another 2 year follow-up one in a city (541 COPD and 560 controls) in 2010. Sixteen candidate single nucleotide polymorphisms (SNPs) were selected for genotyping. Among them, 5SNPs in or near HHIP, 1SNP in IREB2 and 1SNP in FAM13A were previously reported to be associated with COPD susceptibility or lung function decline. And another 9SNPs were selected from HapMap website as HHIP tags. In 2010, totaling 1,324 COPD patients and 1,548 healthy controls were finally included in our genetic susceptibility analyses. Results We identified two new regions showing an association with COPD susceptibility in the Human Hedgehog interacting protein (HHIP) rs11100865 and rs7654947, and we confirmed that the family with sequence similarity 13 member A gene (FAM13A) rs7671167 was associated with the development of COPD in Chinese Han population. And the HHIP rs7654947 and FAM13A rs7671167 were associated with lung function decline, and this result was replicated in other two populations. Conclusions These results suggest an important role of the HHIP and FAM13A regions as genetic risk factors for COPD development and lung function decline in Chinese Han population. Future research on these genes should focus on the molecular mechanisms of these genes on developing COPD and creating therapies to alleviate reduced lung function. Electronic supplementary material The online version of this article (doi:10.1186/s12931-015-0209-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jungang Xie
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Hongxu Wu
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yuzhu Xu
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiaojie Wu
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xue Liu
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Jin Shang
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Jianping Zhao
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Junling Zhao
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Jianmiao Wang
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. .,Section of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, USA.
| | - Charles S Dela Cruz
- Section of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, USA.
| | - Weining Xiong
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yongjian Xu
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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50
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Ding Y, Yang D, Xun X, Wang Z, Sun P, Xu D, He P, Niu H, Jin T. Association of genetic polymorphisms with chronic obstructive pulmonary disease in the Hainan population: a case-control study. Int J Chron Obstruct Pulmon Dis 2014; 10:7-13. [PMID: 25565795 PMCID: PMC4279605 DOI: 10.2147/copd.s73042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Purpose Chronic obstructive pulmonary disease (COPD) is predicted to become the third most common cause of death and the fifth most common cause of disability in the world by 2020. Recently, variants in the hypoxia-inducible factor 1α (HIF1A), cholinergic receptor, neuronal nicotinic, alpha polypeptide-5, and iron-responsive element-binding protein 2 gene (IREB2) genes were found to be associated with COPD. This study aims to identify whether the variations in these genes are related to COPD in the Hainan population of the People’s Republic of China. Patients and methods We genotyped 12 single nucleotide polymorphisms in a case-control study with 200 COPD cases and 401 controls from Hainan, People’s Republic of China. Odds ratios and 95% confidence intervals were estimated using the chi-squared (χ2) test, genetic model analysis, haplotype analysis, and stratification analysis. Results In the genetic model analysis, we found that the genotype T/T of rs13180 of IREB2 decreased the COPD risk by 0.52-fold (P=0.025). But in the further stratification analysis, we failed to find the association between the selected single nucleotide polymorphisms with COPD risk in Han population. In addition, the haplotype analysis of HIF1A gene also was not found to be the possible haplotype associated with COPD risk. Conclusion Our results support that IREB2 rs13180 is associated with COPD in Hainan population. And this is the first time the HIF1A polymorphisms in COPD in a Chinese population has been reported, although we failed to find any significant result.
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Affiliation(s)
- Yipeng Ding
- Department of Emergency, People's Hospital of Hainan Province, Haikou, Hainan, People's Republic of China
| | - Danlei Yang
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Xiaojie Xun
- School of Life Sciences, Northwest University, Xi'an, People's Republic of China
| | - Zhifeng Wang
- Department of Respiration, People's Hospital of Qionghai, Qionghai, Hainan, People's Republic of China
| | - Pei Sun
- Department of Emergency, People's Hospital of Hainan Province, Haikou, Hainan, People's Republic of China
| | - Dongchuan Xu
- Department of Emergency, People's Hospital of Hainan Province, Haikou, Hainan, People's Republic of China
| | - Ping He
- Department of Emergency, People's Hospital of Hainan Province, Haikou, Hainan, People's Republic of China
| | - Huan Niu
- Department of Emergency, People's Hospital of Hainan Province, Haikou, Hainan, People's Republic of China
| | - Tianbo Jin
- School of Life Sciences, Northwest University, Xi'an, People's Republic of China ; National Engineering Research Center for Miniaturized Detection Systems, Xi'an, People's Republic of China
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