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Sonawane AR, Aikawa E, Aikawa M. Connections for Matters of the Heart: Network Medicine in Cardiovascular Diseases. Front Cardiovasc Med 2022; 9:873582. [PMID: 35665246 PMCID: PMC9160390 DOI: 10.3389/fcvm.2022.873582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/19/2022] [Indexed: 01/18/2023] Open
Abstract
Cardiovascular diseases (CVD) are diverse disorders affecting the heart and vasculature in millions of people worldwide. Like other fields, CVD research has benefitted from the deluge of multiomics biomedical data. Current CVD research focuses on disease etiologies and mechanisms, identifying disease biomarkers, developing appropriate therapies and drugs, and stratifying patients into correct disease endotypes. Systems biology offers an alternative to traditional reductionist approaches and provides impetus for a comprehensive outlook toward diseases. As a focus area, network medicine specifically aids the translational aspect of in silico research. This review discusses the approach of network medicine and its application to CVD research.
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Affiliation(s)
- Abhijeet Rajendra Sonawane
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Elena Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
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2
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Yang Z, Ma H, Liu W. In silico identification of common and specific signatures in coronary heart diseases. Exp Ther Med 2020; 20:3595-3614. [PMID: 32905032 PMCID: PMC7464937 DOI: 10.3892/etm.2020.9121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/15/2020] [Indexed: 12/03/2022] Open
Abstract
Coronary heart disease (CHD) is on the increase in developing countries, where lifestyle choices such as smoking, bad diet, and no exercise contribute and increase the incidence of high blood pressure and high cholesterol levels to cause CHD. Through utilization of a biomarker-based approach for developing interventions, the aim of the study was to identify differentially expressed genes (DEGs) and their association and impact on various bio-targets. The microarray datasets of both healthy and CHD patients were analyzed to identify the DEGs and their interactions using Gene Ontology, PANTHER, Reactome, and STRING (for the possible associated genes with multiple targets). Our data mining approach suggests that the DEGs were associated with molecular functions, including protein binding (75%) and catalytic activity (56%); biological processes such as cellular process (83%), biological regulation (57%), and metabolic process (44%); and cellular components such as cell (65%) and organelle (58%); as well as other associations including apoptosis, inflammatory, cell development and metabolic pathways. The molecular functions were further analyzed, and protein binding in particular was analyzed using network analysis to determine whether there was a clear association with CHD and disease. The ingenuity pathway analysis revealed pathways related to cell cholesterol biosynthesis, the immune system including cytokinin signaling, in which, the understanding of DEGs is crucial to predict the advancement of preventive strategies. Results of the present study showed that, there is a need to validate the top DEGs to rule out their molecular mechanism in heart failure caused by CHD.
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Affiliation(s)
- Zhijia Yang
- The Third Department of Cardiovascular Medicine, Handan Central Hospital, Handan, Hebei 056002, P.R. China
| | - Haifang Ma
- The First Department of Cardiovascular Medicine, Affiliated Hospital of Hebei University of Technology, Handan, Hebei 056002, P.R. China
| | - Wei Liu
- The First Department of Cardiovascular Medicine, Handan Central Hospital, Handan, Hebei 056001, P.R. China
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3
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Infante T, Del Viscovo L, De Rimini ML, Padula S, Caso P, Napoli C. Network Medicine: A Clinical Approach for Precision Medicine and Personalized Therapy in Coronary Heart Disease. J Atheroscler Thromb 2020; 27:279-302. [PMID: 31723086 PMCID: PMC7192819 DOI: 10.5551/jat.52407] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022] Open
Abstract
Early identification of coronary atherosclerotic pathogenic mechanisms is useful for predicting the risk of coronary heart disease (CHD) and future cardiac events. Epigenome changes may clarify a significant fraction of this "missing hereditability", thus offering novel potential biomarkers for prevention and care of CHD. The rapidly growing disciplines of systems biology and network science are now poised to meet the fields of precision medicine and personalized therapy. Network medicine integrates standard clinical recording and non-invasive, advanced cardiac imaging tools with epigenetics into deep learning for in-depth CHD molecular phenotyping. This approach could potentially explore developing novel drugs from natural compounds (i.e. polyphenols, folic acid) and repurposing current drugs, such as statins and metformin. Several clinical trials have exploited epigenetic tags and epigenetic sensitive drugs both in primary and secondary prevention. Due to their stability in plasma and easiness of detection, many ongoing clinical trials are focused on the evaluation of circulating miRNAs (e.g. miR-8059 and miR-320a) in blood, in association with imaging parameters such as coronary calcifications and stenosis degree detected by coronary computed tomography angiography (CCTA), or functional parameters provided by FFR/CT and PET/CT. Although epigenetic modifications have also been prioritized through network based approaches, the whole set of molecular interactions (interactome) in CHD is still under investigation for primary prevention strategies.
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Affiliation(s)
- Teresa Infante
- Department of Advanced Clinical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Luca Del Viscovo
- Department of Precision Medicine, Section of Diagnostic Imaging, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | | | - Sergio Padula
- Department of Cardiology, A.O.R.N. Dei Colli, Monaldi Hospital, Naples, Italy
| | - Pio Caso
- Department of Cardiology, A.O.R.N. Dei Colli, Monaldi Hospital, Naples, Italy
| | - Claudio Napoli
- Clinical Department of Internal Medicine and Specialistics, Department of Advanced Clinical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, Naples, Italy
- IRCCS SDN, Naples, Italy
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4
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Lipid-associated genetic polymorphisms are associated with FBP and LDL-c levels among myocardial infarction patients in Chinese population. Gene 2018; 676:22-28. [DOI: 10.1016/j.gene.2018.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 06/29/2018] [Accepted: 07/05/2018] [Indexed: 12/18/2022]
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5
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Palluzzi F, Ferrari R, Graziano F, Novelli V, Rossi G, Galimberti D, Rainero I, Benussi L, Nacmias B, Bruni AC, Cusi D, Salvi E, Borroni B, Grassi M. A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia. PLoS One 2017; 12:e0185797. [PMID: 29020091 PMCID: PMC5636111 DOI: 10.1371/journal.pone.0185797] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 09/19/2017] [Indexed: 01/04/2023] Open
Abstract
Frontotemporal Dementia (FTD) is the form of neurodegenerative dementia with the highest prevalence after Alzheimer’s disease, equally distributed in men and women. It includes several variants, generally characterized by behavioural instability and language impairments. Although few mendelian genes (MAPT, GRN, and C9orf72) have been associated to the FTD phenotype, in most cases there is only evidence of multiple risk loci with relatively small effect size. To date, there are no comprehensive studies describing FTD at molecular level, highlighting possible genetic interactions and signalling pathways at the origin FTD-associated neurodegeneration. In this study, we designed a broad FTD genetic interaction map of the Italian population, through a novel network-based approach modelled on the concepts of disease-relevance and interaction perturbation, combining Steiner tree search and Structural Equation Model (SEM) analysis. Our results show a strong connection between Calcium/cAMP metabolism, oxidative stress-induced Serine/Threonine kinases activation, and postsynaptic membrane potentiation, suggesting a possible combination of neuronal damage and loss of neuroprotection, leading to cell death. In our model, Calcium/cAMP homeostasis and energetic metabolism impairments are primary causes of loss of neuroprotection and neural cell damage, respectively. Secondly, the altered postsynaptic membrane potentiation, due to the activation of stress-induced Serine/Threonine kinases, leads to neurodegeneration. Our study investigates the molecular underpinnings of these processes, evidencing key genes and gene interactions that may account for a significant fraction of unexplained FTD aetiology. We emphasized the key molecular actors in these processes, proposing them as novel FTD biomarkers that could be crucial for further epidemiological and molecular studies.
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Affiliation(s)
- Fernando Palluzzi
- Department of Brain and Behavioural Sciences, Medical and Genomic Statistics Unit, University of Pavia, Pavia, Italy
- * E-mail:
| | - Raffaele Ferrari
- Department of Molecular Neuroscience, Institute of Neurology, University College London (UCL), London, United Kingdom
| | - Francesca Graziano
- Department of Brain and Behavioural Sciences, Medical and Genomic Statistics Unit, University of Pavia, Pavia, Italy
| | - Valeria Novelli
- Department of Genetics, Fondazione Policlinico A. Gemelli, Roma, Italy
| | - Giacomina Rossi
- Division of Neurology V and Neuropathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Daniela Galimberti
- Department of Neurological Sciences, Dino Ferrari Institute, University of Milan, Milano, Italy
| | - Innocenzo Rainero
- Department of Neuroscience, Neurology I, University of Torino and Città della Salute e della Scienza di Torino, Torino, Italy
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Firenze, Italy
| | - Amalia C. Bruni
- Neurogenetic Regional Centre ASPCZ Lamezia Terme, Lamezia Terme (CZ), Italy
| | - Daniele Cusi
- Department of Health Sciences, University of Milan at San Paolo Hospital, Milano, Italy
- Institute of Biomedical Technologies, Italian National Research Council, Milano, Italy
| | - Erika Salvi
- Institute of Biomedical Technologies, Italian National Research Council, Milano, Italy
| | - Barbara Borroni
- Department of Medical Sciences, Neurology Clinic, University of Brescia, Brescia, Italy
| | - Mario Grassi
- Department of Brain and Behavioural Sciences, Medical and Genomic Statistics Unit, University of Pavia, Pavia, Italy
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Chandra M, Escalante-Alcalde D, Bhuiyan MS, Orr AW, Kevil C, Morris AJ, Nam H, Dominic P, McCarthy KJ, Miriyala S, Panchatcharam M. Cardiac-specific inactivation of LPP3 in mice leads to myocardial dysfunction and heart failure. Redox Biol 2017; 14:261-271. [PMID: 28982073 PMCID: PMC5635346 DOI: 10.1016/j.redox.2017.09.015] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 11/28/2022] Open
Abstract
Lipid Phosphate phosphatase 3 (LPP3), encoded by the Plpp3 gene, is an enzyme that dephosphorylates the bioactive lipid mediator lysophosphatidic acid (LPA). To study the role of LPP3 in the myocardium, we generated a cardiac specific Plpp3 deficient mouse strain. Although these mice were viable at birth in contrast to global Plpp3 knockout mice, they showed increased mortality ~ 8 months. LPP3 deficient mice had enlarged hearts with reduced left ventricular performance as seen by echocardiography. Cardiac specific Plpp3 deficient mice had longer ventricular effective refractory periods compared to their Plpp3 littermates. We observed that lack of Lpp3 enhanced cardiomyocyte hypertrophy based on analysis of cell surface area. We found that lack of Lpp3 signaling was mediated through the activation of Rho and phospho-ERK pathways. There are increased levels of fetal genes Natriuretic Peptide A and B (Nppa and Nppb) expression indicating myocardial dysfunction. These mice also demonstrate mitochondrial dysfunction as evidenced by a significant decrease (P < 0.001) in the basal oxygen consumption rate, mitochondrial ATP production, and spare respiratory capacity as measured through mitochondrial bioenergetics. Histology and transmission electron microscopy of these hearts showed disrupted sarcomere organization and intercalated disc, with a prominent disruption of the cristae and vacuole formation in the mitochondria. Our findings suggest that LPA/LPP3-signaling nexus plays an important role in normal function of cardiomyocytes. PLPP3 plays a prominent role in the heart compared to other isoforms of PLPP. Lack of PLPP3 results in deteriorating cardiac function. PLPP3 regulates LPA signaling in cardiomyocytes. Presence of PLPP3 is required for optimal mitochondrial function. Increased free radical production is mitigated with activated PLPP3.
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Affiliation(s)
- Mini Chandra
- Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Diana Escalante-Alcalde
- División de Neurociencias, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México DF, Mexico
| | - Md Shenuarin Bhuiyan
- Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Anthony Wayne Orr
- Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Christopher Kevil
- Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Andrew J Morris
- Division of Cardiovascular Medicine, University of Kentucky, Lexington, USA
| | - Hyung Nam
- Department of Pharmacology and Toxicology, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Paari Dominic
- Division of Cardiology, Department of Medicine, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Kevin J McCarthy
- Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport, USA; Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, USA
| | - Sumitra Miriyala
- Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport, USA.
| | - Manikandan Panchatcharam
- Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport, USA.
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Parmar PG, Taal HR, Timpson NJ, Thiering E, Lehtimäki T, Marinelli M, Lind PA, Howe LD, Verwoert G, Aalto V, Uitterlinden AG, Briollais L, Evans DM, Wright MJ, Newnham JP, Whitfield JB, Lyytikäinen LP, Rivadeneira F, Boomsma DI, Viikari J, Gillman MW, St Pourcain B, Hottenga JJ, Montgomery GW, Hofman A, Kähönen M, Martin NG, Tobin MD, Raitakari O, Vioque J, Jaddoe VW, Jarvelin MR, Beilin LJ, Heinrich J, van Duijn CM, Pennell CE, Lawlor DA, Palmer LJ. International Genome-Wide Association Study Consortium Identifies Novel Loci Associated With Blood Pressure in Children and Adolescents. CIRCULATION. CARDIOVASCULAR GENETICS 2016; 9:266-278. [PMID: 26969751 PMCID: PMC5279885 DOI: 10.1161/circgenetics.115.001190] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 02/25/2016] [Indexed: 01/11/2023]
Abstract
BACKGROUND Our aim was to identify genetic variants associated with blood pressure (BP) in childhood and adolescence. METHODS AND RESULTS Genome-wide association study data from participating European ancestry cohorts of the Early Genetics and Lifecourse Epidemiology (EAGLE) Consortium was meta-analyzed across 3 epochs; prepuberty (4-7 years), puberty (8-12 years), and postpuberty (13-20 years). Two novel loci were identified as having genome-wide associations with systolic BP across specific age epochs: rs1563894 (ITGA11, located in active H3K27Ac mark and transcription factor chromatin immunoprecipitation and 5'-C-phosphate-G-3' methylation site) during prepuberty (P=2.86×10(-8)) and rs872256 during puberty (P=8.67×10(-9)). Several single-nucleotide polymorphism clusters were also associated with childhood BP at P<5×10(-3). Using a P value threshold of <5×10(-3), we found some overlap in variants across the different age epochs within our study and between several single-nucleotide polymorphisms in any of the 3 epochs and adult BP-related single-nucleotide polymorphisms. CONCLUSIONS Our results suggest that genetic determinants of BP act from childhood, develop over the lifecourse, and show some evidence of age-specific effects.
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8
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Chatterjee I, Baruah J, Lurie EE, Wary KK. Endothelial lipid phosphate phosphatase-3 deficiency that disrupts the endothelial barrier function is a modifier of cardiovascular development. Cardiovasc Res 2016; 111:105-18. [PMID: 27125875 PMCID: PMC4909162 DOI: 10.1093/cvr/cvw090] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/21/2016] [Indexed: 01/08/2023] Open
Abstract
Aims Lipid phosphate phosphatase-3 (LPP3) is expressed at high levels in endothelial cells (ECs). Although LPP3 is known to hydrolyse the phosphate group from lysolipids such as spingosine-1-phosphate and its structural homologues, the function of Lpp3 in ECs is not completely understood. In this study, we investigated how tyrosine-protein kinase receptor (TEK or Tie2) promoter–dependent deletion of Lpp3 alters EC activities. Methods and results Lpp3fl/fl mice were crossed with the tg.Tie2Cre transgenic line. Vasculogenesis occurred normally in embryos with Tie2Cre-mediated deletion of Lpp3 (called Lpp3ECKO), but embryonic lethality occurred in two waves, the first wave between E8.5 and E10.5, while the second between E11.5 and E13.5. Lethality in Lpp3ECKO embryos after E11.5 was accompanied by vascular leakage and haemorrhage, which likely resulted in insufficient cardiovascular development. Analyses of haematoxylin- and eosin-stained heart sections from E11.5 Lpp3ECKO embryos showed insufficient heart growth associated with decreased trabeculation, reduced growth of the compact wall, and absence of cardiac cushions. Staining followed by microscopic analyses of Lpp3ECKO embryos revealed the presence of apoptotic ECs. Furthermore, Lpp3-deficient ECs showed decreased gene expression and protein levels of Cyclin-D1, VE-cadherin, Fibronectin, Klf2, and Klf4. To determine the underlying mechanisms of vascular leakage and barrier disruption, we performed knockdown and rescue experiments in cultured ECs. LPP3 knockdown decreased transendothelial electrical resistance and increased permeability. Re-expression of β-catenin cDNA in LPP3-knockdown ECs partially restored the effect of the LPP3 loss, whereas re-expression of p120ctn cDNA did not. Conclusion These findings demonstrate the essential roles of LPP3 in the maturation of EC barrier integrity and normal cardiovascular development.
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Affiliation(s)
- Ishita Chatterjee
- Department of Pharmacology, University of Illinois, 835 S. Wolcott Avenue, Room E403, Chicago, IL 60612, USA
| | - Jugajyoti Baruah
- Department of Pharmacology, University of Illinois, 835 S. Wolcott Avenue, Room E403, Chicago, IL 60612, USA
| | - Erin E Lurie
- Department of Pharmacology, University of Illinois, 835 S. Wolcott Avenue, Room E403, Chicago, IL 60612, USA
| | - Kishore K Wary
- Department of Pharmacology, University of Illinois, 835 S. Wolcott Avenue, Room E403, Chicago, IL 60612, USA
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Weng L, Taylor KD, Chen YDI, Sopko G, Kelsey SF, Bairey Merz CN, Pepine CJ, Miller VM, Rotter JI, Gulati M, Goodarzi MO, Cooper-DeHoff RM. Genetic loci associated with nonobstructive coronary artery disease in Caucasian women. Physiol Genomics 2015; 48:12-20. [PMID: 26534935 DOI: 10.1152/physiolgenomics.00067.2015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/29/2015] [Indexed: 01/11/2023] Open
Abstract
Nonobstructive coronary artery disease (CAD) in women is associated with adverse cardiovascular (CV) outcomes; however, information regarding genetic variants that predispose women to nonobstructive CAD is lacking. Women from the Women's Ischemia Syndrome Evaluation (WISE) Study and the St. James Women Take Heart (WTH) Study were genotyped with the Cardio-MetaboChip. WISE enrolled women with symptoms and signs of ischemia referred for coronary angiography; WTH enrolled asymptomatic, community-based women without heart disease. Analyses were conducted with a case (WISE)--control (WTH) design and multivariate logistic regression models to investigate genetic variation associated with likelihood of nonobstructive CAD. One genetic marker, single nucleotide polymorphism (SNP) rs2301753 on chromosome 6 in RNF39, achieved chip-wide significance for nonobstructive CAD (P < 9.5 × 10(-7)). After adjusting for baseline characteristics, we found no variants achieved chip-wide significance. However, SNP rs2301753 on chromosome 6 in RNF39 was associated with reduced likelihood of nonobstructive CAD [odds ratio (OR) 0.42 and 95% confidence interval (CI) of 0.29 to 0.68], at a nominal level of P = 5.6 × 10(-6), while SNP rs12818945 in the ATP2B1 locus on chromosome 12 was associated with increased odds for nonobstructive CAD (OR 2.38 and 95% CI of 1.63 to 3.45) and nominal P = 5.8 × 10(-6). The functions of RNF39 and ATP2B1 raise the possibility that genes involved in cardio-dysfunction may contribute to nonobstructive CAD in Caucasian women and may provide insights into novel approaches for therapy and prevention. If replicated, incorporation of these genetic variants into diagnostic evaluation may identify women at high risk for nonobstructive CAD.
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Affiliation(s)
- Liming Weng
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, Florida
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics and Los Angeles BioMedical Research Institute, Harbor-UCLA Medical Center, Torrance, California
| | - Yii-Der Ida Chen
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics and Los Angeles BioMedical Research Institute, Harbor-UCLA Medical Center, Torrance, California
| | - George Sopko
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Sheryl F Kelsey
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - C Noel Bairey Merz
- Barbra Streisand Women's Heart Center, Cedars-Sinai Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Carl J Pepine
- Division of Cardiology, College of Medicine, University of Florida, Gainesville, Florida
| | - Virginia M Miller
- Departments of Surgery and Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics and Los Angeles BioMedical Research Institute, Harbor-UCLA Medical Center, Torrance, California
| | - Martha Gulati
- Department of Medicine (Cardiology), The Ohio State University, Columbus, Ohio; and
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, California
| | - Rhonda M Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, College of Pharmacy, Gainesville, Florida; Division of Cardiology, College of Medicine, University of Florida, Gainesville, Florida;
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10
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Ye H, Zhou A, Hong Q, Chen X, Xin Y, Tang L, Dai D, Ji H, Xu M, Wang DW, Duan S. Association of seven thrombotic pathway gene CpG-SNPs with coronary heart disease. Biomed Pharmacother 2015; 72:98-102. [PMID: 26054681 DOI: 10.1016/j.biopha.2015.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 04/03/2015] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Coronary heart disease (CHD) has been considered a thromboembolic arterial diseases. The aim of this case-control study was to explore whether the CpG-SNPs of the thrombotic pathway genes contributed to the risk of CHD. METHODS AND MATERIALS A total of 784 CHD patients and 738 healthy controls were recruited in the current association study, which evaluated 7 CpG-SNPs of the thrombotic pathway genes. The CpG-SNPs included THBS4 rs17878919, CYP2C19 rs12773342, P2RY12 rs1491974, ITGA2 rs26680, FGB rs2227389, F7 rs510317 and F5 rs2269648. SNP genotyping was performed with a Sequenom Mass Spectrometry Genetic Analyzer. RESULTS Our results demonstrated that CYP2C19 rs12773342 polymorphism was significantly associated with CHD in the recessive model (χ(2)=5.41, df=1, P=0.020, OR=1.455, 95% CI=1.060-1.996). A breakdown analysis by age showed that the association of CYP2C19 rs12773342 with CHD was mainly found in individuals aged 55-65 (genotype: χ(2)=7.93, df=2, P=0.019; allele: χ(2)=4.45, df=1, P=0.035). In addition, we also observed a significant association between F7 rs510317 polymorphism and CHD in males (genotype: χ(2)=7.24, df=2, P=0.027). There was no significant association with CHD for the remaining CpG-SNPs. CONCLUSION Our results supported that the CYP2C19 rs12773342 and F7 rs510317 polymorphisms were associated with CHD in the Han Chinese population.
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Affiliation(s)
- Huadan Ye
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Annan Zhou
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Qingxiao Hong
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Xiaoying Chen
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yanfei Xin
- Center of Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Linlin Tang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Dongjun Dai
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Huihui Ji
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Mingqing Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
| | - Dao Wen Wang
- Institute of Hypertension and Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.
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Ge YZ, Xu Z, Xu LW, Yu P, Zhao Y, Xin H, Wu R, Tan SJ, Song Q, Wu JP, Li WC, Zhu JG, Jia RP. Pathway analysis of genome-wide association study on serum prostate-specific antigen levels. Gene 2014; 551:86-91. [PMID: 25168891 DOI: 10.1016/j.gene.2014.08.044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 08/19/2014] [Accepted: 08/23/2014] [Indexed: 12/24/2022]
Abstract
The wide application of prostate-specific antigen (PSA) has contributed to the early diagnosis and improved management of prostate cancer (PCa). Accumulating evidence has suggested the involvement of genetic components in regulating serum PSA levels, and several single nucleotide polymorphisms (SNPs) have been identified by genome-wide association studies (GWASs). However, the GWASs' results have the limited power to identify the causal variants and pathways. After the quality control filters, a total of 330,540 genotyped SNPs from one GWAS with 657 PCa-free Caucasian males were included for the identify candidate causal SNPs and pathways (ICSNPathway) analysis. In addition, the genotype-phenotype association analysis has been conducted with the data from HapMap database. Overall, a total of four SNPs in three genes and six pathways were identified by ICSNPathway analysis, which in total provided three hypothetical mechanisms. First, CYP26B1 rs2241057 polymorphism (nonsynonymous coding) which leads to a Leu-to-Ser amino acid shift at position 264, was implicated in the pathways including meiosis, proximal/distal pattern formation, and M phase of meiotic cell cycle. Second, CLIC5 rs3734207 and rs11752816 polymorphisms (regulatory region) to the 2 iron, 2 sulfur cluster binding pathway through regulating expression levels of CLIC5 mRNA. Third, rs4819522 polymorphism (nonsynonymous coding) leads to a Thr-to-Met transition at position 350 of TBX1 and involves in the pathways about gland and endocrine system development. In summary, our results demonstrated four candidate SNPs in three genes (CYP26B1 rs2241057, CISD1 rs2251039, rs2590370, and TBX1 rs4819522 polymorphisms), which were involved in six potential pathways to influence serum PSA levels.
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Affiliation(s)
- Yu-Zheng Ge
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China
| | - Zheng Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China
| | - Lu-Wei Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China
| | - Peng Yu
- Department of Urology, The First Hospital of Nanchang, Nanchang University, 128 Xiangshan North Road, Nanchang 330008, China
| | - Yan Zhao
- Department of Urology, Xuzhou Third People's Hospital, Jiangsu University, 131 Huancheng Road, Xuzhou 221005, China
| | - Hui Xin
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China
| | - Ran Wu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China
| | - Si-Jia Tan
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China
| | - Qun Song
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China
| | - Jian-Ping Wu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China
| | - Wen-Cheng Li
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China
| | - Jia-Geng Zhu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China
| | - Rui-Peng Jia
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, 68 Changle Road, Nanjing 210006, China.
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12
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Lian J, Fang P, Dai D, Ba Y, Yang X, Huang X, Li J, Chen X, Guo J, Guan F, Peng P, Zhao R, Zhang S, Gao F, Tang L, Zhang C, Ji H, Hong Q, Ye H, Xu L, Zhong Q, Liu P, Zhou J, Duan S. Association between LGALS2 3279C>T and coronary artery disease: A case-control study and a meta-analysis. Biomed Rep 2014; 2:879-885. [PMID: 25279163 DOI: 10.3892/br.2014.325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 06/16/2014] [Indexed: 11/05/2022] Open
Abstract
Coronary artery disease (CAD) has become the main cause of mortality worldwide. Lectin galactoside-binding soluble-2 (LGALS2) is involved in the cytokine lymphotoxin-α (LTA) cascade that may influence the progress of CAD. The aim of the present study was to assess the association between the LGALS2 3279C>T (rs7291467) polymorphism and CAD. A total of 562 cases and 572 controls were recruited to examine the association. A systematic meta-analysis was performed to evaluate the contribution of LGALS2 3279C>T polymorphism to the risk of CAD among 12,093 cases and 11,020 controls. There was no significant association found in the present case-control study. However, the meta-analysis showed that LGALS2 3279C>T played a protective role in CAD [P=0.008, odds ratio (OR), 0.90; 95% confidence interval (95% CI), 0.82-0.97] and particularly in the Asian population (P=0.006; OR, 0.82; 95% CI, 0.71-0.94). The present case-control study did not find a significant association between LGALS2 3279C>T and CAD in the Eastern Han Chinese population. However, the meta-analysis indicated that LGALS2 3279C>T played a protective role in CAD, suggesting an ethnic difference in the association of the locus with CAD.
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Affiliation(s)
- Jiangfang Lian
- Ningbo Medical Center, Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, P.R. China
| | - Peiliang Fang
- Ningbo Medical Center, Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, P.R. China ; Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Dongjun Dai
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Yanna Ba
- Ningbo Medical Center, Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, P.R. China ; Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Xi Yang
- Ningbo Medical Center, Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, P.R. China
| | - Xiaoyan Huang
- Ningbo Medical Center, Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, P.R. China
| | - Junxin Li
- Ningbo Medical Center, Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, P.R. China ; Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Xiaoliang Chen
- Ningbo Medical Center, Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, P.R. China ; Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Jian Guo
- Ningbo Medical Center, Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, P.R. China ; Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Feng Guan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Ping Peng
- Ningbo Medical Center, Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, P.R. China ; Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Ruochi Zhao
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Shangshi Zhang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Fang Gao
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Linlin Tang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Cheng Zhang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Huihui Ji
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Qingxiao Hong
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Huadan Ye
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Limin Xu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Qilong Zhong
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Panpan Liu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
| | - Jianqing Zhou
- Ningbo Medical Center, Lihuili Hospital, Ningbo University, Ningbo, Zhejiang 315041, P.R. China
| | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315000, P.R. China
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13
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Mäkinen VP, Civelek M, Meng Q, Zhang B, Zhu J, Levian C, Huan T, Segrè AV, Ghosh S, Vivar J, Nikpay M, Stewart AFR, Nelson CP, Willenborg C, Erdmann J, Blakenberg S, O'Donnell CJ, März W, Laaksonen R, Epstein SE, Kathiresan S, Shah SH, Hazen SL, Reilly MP, Lusis AJ, Samani NJ, Schunkert H, Quertermous T, McPherson R, Yang X, Assimes TL. Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease. PLoS Genet 2014; 10:e1004502. [PMID: 25033284 PMCID: PMC4102418 DOI: 10.1371/journal.pgen.1004502] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 05/27/2014] [Indexed: 12/13/2022] Open
Abstract
The majority of the heritability of coronary artery disease (CAD) remains unexplained, despite recent successes of genome-wide association studies (GWAS) in identifying novel susceptibility loci. Integrating functional genomic data from a variety of sources with a large-scale meta-analysis of CAD GWAS may facilitate the identification of novel biological processes and genes involved in CAD, as well as clarify the causal relationships of established processes. Towards this end, we integrated 14 GWAS from the CARDIoGRAM Consortium and two additional GWAS from the Ottawa Heart Institute (25,491 cases and 66,819 controls) with 1) genetics of gene expression studies of CAD-relevant tissues in humans, 2) metabolic and signaling pathways from public databases, and 3) data-driven, tissue-specific gene networks from a multitude of human and mouse experiments. We not only detected CAD-associated gene networks of lipid metabolism, coagulation, immunity, and additional networks with no clear functional annotation, but also revealed key driver genes for each CAD network based on the topology of the gene regulatory networks. In particular, we found a gene network involved in antigen processing to be strongly associated with CAD. The key driver genes of this network included glyoxalase I (GLO1) and peptidylprolyl isomerase I (PPIL1), which we verified as regulatory by siRNA experiments in human aortic endothelial cells. Our results suggest genetic influences on a diverse set of both known and novel biological processes that contribute to CAD risk. The key driver genes for these networks highlight potential novel targets for further mechanistic studies and therapeutic interventions. Sudden death due to heart attack ranks among the top causes of death in the world, and family studies have shown that genetics has a substantial effect on heart disease risk. Recent studies suggest that multiple genetic factors each with modest effects are necessary for the development of CAD, but the genes and molecular processes involved remain poorly understood. We conducted an integrative genomics study where we used the information of gene-gene interactions to capture groups of genes that are most likely to increase heart disease risk. We not only confirmed the importance of several known CAD risk processes such as the metabolism and transport of cholesterol, immune response, and blood coagulation, but also revealed many novel processes such as neuroprotection, cell cycle, and proteolysis that were not previously implicated in CAD. In particular, we highlight several genes such as GLO1 with key regulatory roles within these processes not detected by the first wave of genetic analyses. These results highlight the value of integrating population genetic data with diverse resources that functionally annotate the human genome. Such integration facilitates the identification of novel molecular processes involved in the pathogenesis of CAD as well as potential novel targets for the development of efficacious therapeutic interventions.
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Affiliation(s)
- Ville-Petteri Mäkinen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, United States of America
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Mete Civelek
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Qingying Meng
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Candace Levian
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Tianxiao Huan
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Ayellet V. Segrè
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Sujoy Ghosh
- Department of Cardiovascular and Metabolic Research, Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, North Carolina, United States of America
- Program in Cardiovascular and Metabolic Disorders and Centre for Computational Biology, Duke-NUS Graduate Medical School, Singapore
| | - Juan Vivar
- Department of Cardiovascular and Metabolic Research, Biomedical Biotechnology Research Institute, North Carolina Central University, Durham, North Carolina, United States of America
| | - Majid Nikpay
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Alexandre F. R. Stewart
- John and Jennifer Ruddy Canadian Cardiovascular Research Center, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Christopher P. Nelson
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
- National Institute for Health Research (NIHR) Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Christina Willenborg
- Institut für Integrative und Experimentelle Genomik, University of Lübeck, Lübeck, Germany
| | - Jeanette Erdmann
- Institut für Integrative und Experimentelle Genomik, University of Lübeck, Lübeck, Germany
- DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg, Kiel, Lübeck, Germany
| | - Stefan Blakenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Hamburg, Germany
| | - Christopher J. O'Donnell
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
- Cardiology Division, Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Winfried März
- Mannheim Institute of Public Health, Social and Preventive Medicine, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
- Synlab Academy, Mannheim, Germany
| | - Reijo Laaksonen
- Science Center, Tampere University Hospital, Tampere, Finland
| | - Stephen E. Epstein
- Cardiovascular Research Institute, Washington Hospital Center, Washington, D.C., United States of America
| | - Sekar Kathiresan
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
- Cardiology Division, Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Svati H. Shah
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | | | - Muredach P. Reilly
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Aldons J. Lusis
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, United Kingdom
- National Institute for Health Research (NIHR) Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Heribert Schunkert
- DZHK (German Research Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Thomas Quertermous
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ruth McPherson
- Atherogenomics Laboratory, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail: (XY); (TLA)
| | - Themistocles L. Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (XY); (TLA)
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14
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Stevens A, Meyer S, Hanson D, Clayton P, Donn RP. Network analysis identifies protein clusters of functional importance in juvenile idiopathic arthritis. Arthritis Res Ther 2014; 16:R109. [PMID: 24886659 PMCID: PMC4062926 DOI: 10.1186/ar4559] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 04/29/2014] [Indexed: 02/06/2023] Open
Abstract
Introduction Our objective was to utilise network analysis to identify protein clusters of greatest potential functional relevance in the pathogenesis of oligoarticular and rheumatoid factor negative (RF-ve) polyarticular juvenile idiopathic arthritis (JIA). Methods JIA genetic association data were used to build an interactome network model in BioGRID 3.2.99. The top 10% of this protein:protein JIA Interactome was used to generate a minimal essential network (MEN). Reactome FI Cytoscape 2.83 Plugin and the Disease Association Protein-Protein Link Evaluator (Dapple) algorithm were used to assess the functionality of the biological pathways within the MEN and to statistically rank the proteins. JIA gene expression data were integrated with the MEN and clusters of functionally important proteins derived using MCODE. Results A JIA interactome of 2,479 proteins was built from 348 JIA associated genes. The MEN, representing the most functionally related components of the network, comprised of seven clusters, with distinct functional characteristics. Four gene expression datasets from peripheral blood mononuclear cells (PBMC), neutrophils and synovial fluid monocytes, were mapped onto the MEN and a list of genes enriched for functional significance identified. This analysis revealed the genes of greatest potential functional importance to be PTPN2 and STAT1 for oligoarticular JIA and KSR1 for RF-ve polyarticular JIA. Clusters of 23 and 14 related proteins were derived for oligoarticular and RF-ve polyarticular JIA respectively. Conclusions This first report of the application of network biology to JIA, integrating genetic association findings and gene expression data, has prioritised protein clusters for functional validation and identified new pathways for targeted pharmacological intervention.
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15
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Dong C, Tang L, Liu Z, Bu S, Liu Q, Wang Q, Mai Y, Wang DW, Duan S. Landscape of the relationship between type 2 diabetes and coronary heart disease through an integrated gene network analysis. Gene 2014; 539:30-6. [PMID: 24508273 DOI: 10.1016/j.gene.2014.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/23/2014] [Accepted: 02/02/2014] [Indexed: 11/30/2022]
Abstract
Type 2 diabetes (T2D) and coronary artery disease (CAD) are closely related chronic diseases with high prevalence and morbidity. However, a comprehensive comparison of the two diseases is lacking. Recent genome-wide association studies (GWAS) have identified a handful of single nucleotide polymorphisms (SNPs) that are significantly associated with the risk of T2D and CAD. These most significant findings may help interpret the pathogenesis of T2D and CAD. However, tremendous results from these GWAS are ignored. Here we revisited the raw datasets of these GWAS and performed an integrated gene network analysis to unveil the relationship between T2D and CAD by combining multiple datasets including protein-protein interaction (PPI) database, publication libraries, and pathway datasets. Our results showed that majority of genes were involved in the first module (1122 genes in T2D and 895 in CAD). Four pathways were found to be common in both T2D and CAD, including regulation of actin cytoskeleton, calcium signaling pathway, MAPK signaling pathway and focal adhesion (all P<0.00001). MAX which was involved in small cell lung cancer pathway was a hub gene unique to T2D (OR=1.2, P=0.006) but not in CAD. In contrast, three hub genes including PLEKHG5 (T2D: OR=1, P=1; CAD: OR=1.12, P=0.006), TIAM1 (T2D: OR=1, P=1; CAD: OR=1.48, P=0.004) and AKAP13 (T2D: OR=1, P=1; CAD: OR=1.38, P=0.001) were hub genes unique to CAD. Moreover, for some hub genes (such as SMAD3) that were susceptible to both T2D and CAD, their associated polymorphisms were unique to each of the two diseases. Our findings might provide a landscape of the relationship between T2D and CAD.
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Affiliation(s)
- Changzheng Dong
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.
| | - Linlin Tang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Zhifang Liu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Shizhong Bu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China; Diabetes Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Qiong Liu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China; Diabetes Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Qinwen Wang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China; Diabetes Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yifeng Mai
- The Affiliated Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Dao Wen Wang
- Institute of Hypertension and Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China; Diabetes Center, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.
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16
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Lian J, Ba Y, Dai D, Chen Z, Lou Y, Jiang Q, Zhao R, Sun L, Huang X, Yang X, Ye M, Wang Y, Mao H, Guan H, Xu L, Guo J, Fang P, Li J, Ye H, Chen X, Peng P, Zhou J, Duan S. A Replication Study and a Meta-Analysis of the Association between the CDKN2A rs1333049 Polymorphism and Coronary Heart Disease. J Atheroscler Thromb 2014; 21:1109-20. [DOI: 10.5551/jat.23507] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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17
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Zeltz C, Orgel J, Gullberg D. Molecular composition and function of integrin-based collagen glues-introducing COLINBRIs. Biochim Biophys Acta Gen Subj 2013; 1840:2533-48. [PMID: 24361615 DOI: 10.1016/j.bbagen.2013.12.022] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/13/2013] [Accepted: 12/14/2013] [Indexed: 01/06/2023]
Abstract
BACKGROUND Despite detailed knowledge about the structure and signaling properties of individual collagen receptors, much remains to be learned about how these receptors participate in linking cells to fibrillar collagen matrices in tissues. In addition to collagen-binding integrins, a group of proteins with affinity both for fibrillar collagens and integrins link these two protein families together. We have introduced the name COLINBRI (COLlagen INtegrin BRIdging) for this set of molecules. Whereas collagens are the major building blocks in tissues and defects in these structural proteins have severe consequences for tissue integrity, the mild phenotypes of the integrin type of collagen receptors have raised questions about their importance in tissue biology and pathology. SCOPE OF REVIEW We will discuss the two types of cell linkages to fibrillar collagen (direct- versus indirect COLINBRI-mediated) and discuss how the parallel existence of direct and indirect linkages to collagens may ensure tissue integrity. MAJOR CONCLUSIONS The observed mild phenotypes of mice deficient in collagen-binding integrins and the relatively restricted availability of integrin-binding sequences in mature fibrillar collagen matrices support the existence of indirect collagen-binding mechanisms in parallel with direct collagen binding in vivo. GENERAL SIGNIFICANCE A continued focus on understanding the molecular details of cell adhesion mechanisms to collagens will be important and will benefit our understanding of diseases like tissue- and tumor fibrosis where collagen dynamics are disturbed. This article is part of a Special Issue entitled Matrix-mediated cell behaviour and properties.
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Affiliation(s)
- Cédric Zeltz
- Department of Biomedicine and Centre for Cancer Biomarkers, Norwegian Centre of Excellence, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway
| | - Joseph Orgel
- Departments of Biology, Physics and Biomedical Engineering, Pritzker Institute of Biomedical Science and Engineering, Illinois Institute of Technology, 3440 S. Dearborn Ave, Chicago, IL 60616, USA
| | - Donald Gullberg
- Department of Biomedicine and Centre for Cancer Biomarkers, Norwegian Centre of Excellence, University of Bergen, Jonas Lies vei 91, N-5009 Bergen, Norway.
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