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Xu F, Ziebarth JD, Goeminne LJ, Gao J, Williams EG, Quarles LD, Makowski L, Cui Y, Williams RW, Auwerx J, Lu L. Gene network based analysis identifies a coexpression module involved in regulating plasma lipids with high-fat diet response. J Nutr Biochem 2023; 119:109398. [PMID: 37302664 PMCID: PMC10896179 DOI: 10.1016/j.jnutbio.2023.109398] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/08/2023] [Accepted: 05/30/2023] [Indexed: 06/13/2023]
Abstract
Plasma lipids are modulated by gene variants and many environmental factors, including diet-associated weight gain. However, understanding how these factors jointly interact to influence molecular networks that regulate plasma lipid levels is limited. Here, we took advantage of the BXD recombinant inbred family of mice to query weight gain as an environmental stressor on plasma lipids. Coexpression networks were examined in both nonobese and obese livers, and a network was identified that specifically responded to the obesogenic diet. This obesity-associated module was significantly associated with plasma lipid levels and enriched with genes known to have functions related to inflammation and lipid homeostasis. We identified key drivers of the module, including Cidec, Cidea, Pparg, Cd36, and Apoa4. The Pparg emerged as a potential master regulator of the module as it can directly target 19 of the top 30 hub genes. Importantly, activation of this module is causally linked to lipid metabolism in humans, as illustrated by correlation analysis and inverse-variance weighed Mendelian randomization. Our findings provide novel insights into gene-by-environment interactions for plasma lipid metabolism that may ultimately contribute to new biomarkers, better diagnostics, and improved approaches to prevent or treat dyslipidemia in patients.
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Affiliation(s)
- Fuyi Xu
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong, China; Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jesse D Ziebarth
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Ludger Je Goeminne
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, Lausanne, Switzerland
| | - Jun Gao
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Evan G Williams
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Leigh D Quarles
- Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Liza Makowski
- Department of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA; Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Yan Cui
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Robert W Williams
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA; Center for Cancer Research, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, Lausanne, Switzerland.
| | - Lu Lu
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee, USA.
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Sharma A, Rijavec M, Tomar S, Yamani A, Ganesan V, Krempski J, Schuler CF, Bunyavanich S, Korosec P, Hogan SP. Acute systemic myeloid inflammatory and stress response in severe food allergic reactions. Clin Exp Allergy 2023; 53:536-549. [PMID: 36756745 PMCID: PMC11157667 DOI: 10.1111/cea.14273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/28/2022] [Accepted: 11/20/2022] [Indexed: 02/10/2023]
Abstract
INTRODUCTION Food allergic reactions can be severe and potentially life-threatening and the underlying immunological processes that contribute to the severity of reactions are poorly understood. The aim of this study is to integrate bulk RNA-sequencing of human and mouse peripheral blood mononuclear cells during food allergic reactions and in vivo mouse models of food allergy to identify dysregulated immunological processes associated with severe food allergic reactions. METHODS Bulk transcriptomics of whole blood from human and mouse following food allergic reactions combined with integrative differential expressed gene bivariate and module eigengene network analyses to identify the whole blood transcriptome associated with food allergy severity. In vivo validation immune cell and gene expression in mice following IgE-mediated reaction. RESULTS Bulk transcriptomics of whole blood from mice with different severity of food allergy identified gene ontology (GO) biological processes associated with innate and inflammatory immune responses, dysregulation of MAPK and NFkB signalling and identified 429 genes that correlated with reaction severity. Utilizing two independent human cohorts, we identified 335 genes that correlated with severity of peanut-induced food allergic reactions. Mapping mouse food allergy severity transcriptome onto the human transcriptome revealed 11 genes significantly dysregulated and correlated with severity. Analyses of whole blood from mice undergoing an IgE-mediated reaction revealed a rapid change in blood leukocytes particularly inflammatory monocytes (Ly6Chi Ly6G- ) and neutrophils that was associated with changes in CLEC4E, CD218A and GPR27 surface expression. CONCLUSIONS Collectively, IgE-mediated food allergy severity is associated with a rapid innate inflammatory response associated with acute cellular stress processes and dysregulation of peripheral blood inflammatory myeloid cell frequencies.
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Affiliation(s)
- Ankit Sharma
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
| | - Matija Rijavec
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Sunil Tomar
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
| | - Amnah Yamani
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Varsha Ganesan
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
| | - James Krempski
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
| | - Charles F Schuler
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
- Division of Allergy and Immunology, Michigan medicine University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
| | - Supinda Bunyavanich
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY; Icahn Institute for Data Science and Genome Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Peter Korosec
- University Clinic of Respiratory and Allergic Diseases Golnik, 4204 Golnik, Slovenia
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Simon P. Hogan
- Mary H Weiser Food Allergy Center, Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
- Department of Pathology, Michigan Medicine, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, MI 48109-2200
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Yazar V, Yilmaz IC, Bulbul A, Klinman DM, Gursel I. Gene network landscape of mouse splenocytes reveals integrin complex as the A151 ODN-responsive hub molecule in the immune transcriptome. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:553-565. [PMID: 36895952 PMCID: PMC9989320 DOI: 10.1016/j.omtn.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Homeostatic restoration of an inflammatory response requires quenching of the immune system after pathogen threats vanish. A continued assault orchestrated by host defense results in tissue destruction or autoimmunity. A151 is the epitome of synthetic oligodeoxynucleotides (ODNs) that curb the immune response by a subset of white corpuscles through repetitive telomere-derived TTAGGG sequences. Currently, the genuine effect of A151 on the immune cell transcriptome remains unknown. Here, we leveraged an integrative approach where weighted gene co-expression network analysis (WGCNA), differential gene expression analysis, and gene set enrichment analysis (GSEA) of our in-house microarray datasets aided our understanding of how A151 ODN suppresses the immune response in mouse splenocytes. Our bioinformatics results, together with experimental validations, indicated that A151 ODN acts on components of integrin complexes, Itgam and Itga6, to interfere with immune cell adhesion and thereby suppresses the immune response in mice. Moreover, independent lines of evidence in this work converged on the observation that cell adhesion by integrin complexes serves as a focal point for cellular response to A151 ODN treatment in immune cells. Taken together, the outcome of this study sheds light on the molecular basis of immune suppression by a clinically useful DNA-based therapeutic agent.
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Affiliation(s)
- Volkan Yazar
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Thorlab, Molecular Biology and Genetics Department, Faculty of Science, Ihsan Dogramaci Bilkent University, 06800 Ankara, Turkey
| | - Ismail Cem Yilmaz
- Thorlab, Molecular Biology and Genetics Department, Faculty of Science, Ihsan Dogramaci Bilkent University, 06800 Ankara, Turkey
- Izmir Biomedicine and Genome Center, Dokuz Eylul University, Balcova, Izmir, Turkey
| | - Artun Bulbul
- Thorlab, Molecular Biology and Genetics Department, Faculty of Science, Ihsan Dogramaci Bilkent University, 06800 Ankara, Turkey
| | - Dennis M. Klinman
- Immune Modulation Section, Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ihsan Gursel
- Thorlab, Molecular Biology and Genetics Department, Faculty of Science, Ihsan Dogramaci Bilkent University, 06800 Ankara, Turkey
- Izmir Biomedicine and Genome Center, Dokuz Eylul University, Balcova, Izmir, Turkey
- Corresponding author: Ihsan Gursel, PhD, Izmir Biomedicine and Genome Center, Dokuz Eylul University, Balcova, Izmir, Turkey.
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He Y, Chen Y, Yao L, Wang J, Sha X, Wang Y. The Inflamm-Aging Model Identifies Key Risk Factors in Atherosclerosis. Front Genet 2022; 13:865827. [PMID: 35706446 PMCID: PMC9191626 DOI: 10.3389/fgene.2022.865827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Atherosclerosis, one of the main threats to human life and health, is driven by abnormal inflammation (i.e., chronic inflammation or oxidative stress) during accelerated aging. Many studies have shown that inflamm-aging exerts a significant impact on the occurrence of atherosclerosis, particularly by inducing an immune homeostasis imbalance. However, the potential mechanism by which inflamm-aging induces atherosclerosis needs to be studied more thoroughly, and there is currently a lack of powerful prediction models.Methods: First, an improved inflamm-aging prediction model was constructed by integrating aging, inflammation, and disease markers with the help of machine learning methods; then, inflamm-aging scores were calculated. In addition, the causal relationship between aging and disease was identified using Mendelian randomization. A series of risk factors were also identified by causal analysis, sensitivity analysis, and network analysis.Results: Our results revealed an accelerated inflamm-aging pattern in atherosclerosis and suggested a causal relationship between inflamm-aging and atherosclerosis. Mechanisms involving inflammation, nutritional balance, vascular homeostasis, and oxidative stress were found to be driving factors of atherosclerosis in the context of inflamm-aging.Conclusion: In summary, we developed a model integrating crucial risk factors in inflamm-aging and atherosclerosis. Our computation pipeline could be used to explore potential mechanisms of related diseases.
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Affiliation(s)
- Yudan He
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Yao Chen
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Lilin Yao
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Junyi Wang
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Xianzheng Sha
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Yin Wang
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
- *Correspondence: Yin Wang,
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5
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Pyroptosis-Related Gene Signature and Expression Patterns in the Deterioration of Atherosclerosis. DISEASE MARKERS 2022; 2022:1356618. [PMID: 35571620 PMCID: PMC9098329 DOI: 10.1155/2022/1356618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/12/2022] [Accepted: 04/16/2022] [Indexed: 11/17/2022]
Abstract
Background Pyroptosis has been shown to be involved in the overall process of atherosclerosis. This study was aimed at investigating pyroptosis-related gene expression patterns in atherosclerosis and their diagnostic significance. Methods and Results In GSE100927, fifty-four pyroptosis-related genes were identified. Between atherosclerotic plaques and normal samples, the expression patterns of pyroptosis-related genes were significantly different. In order to construct a pyroptosis-related risk score signature (PRSS), the least absolute shrinkage and selection operator (LASSO) was combined with multivariate logistic regression to screen twelve genes. The diagnostic efficiency of the PRSS performed well in GSE43292, as shown by the results of receiver-operating characteristics (ROCs). Consensus clustering identified two expression patterns of pyroptosis-related genes in different statuses of atherosclerotic plaque in GSE163154. The biological behavior of the different clusters was examined by the gene set variation analysis (GSVA). The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses revealed that the differentially expressed genes (DEGs) in the two clusters were enriched in the immune response. The Cytoscape software was used to construct protein-protein interaction (PPI) networks for hub gene screening. Following that, the Drug Gene Interaction Database (DGIdb) was utilized to find 47 possible medicines and chemical compounds that interact with hub genes in atherosclerotic plaques. Conclusion The results of this study showed that pyroptosis-related genes contribute to the progression of atherosclerosis and may serve as biomarkers in clinical diagnosis as well as novel therapeutic targets for the treatment of AS.
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Xia M, Wu Q, Chen P, Qian C. Regulatory T Cell-Related Gene Biomarkers in the Deterioration of Atherosclerosis. Front Cardiovasc Med 2021; 8:661709. [PMID: 34095251 PMCID: PMC8172618 DOI: 10.3389/fcvm.2021.661709] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/07/2021] [Indexed: 01/16/2023] Open
Abstract
Background: Regulatory T cells (Tregs) have shown to be protective against the development of atherosclerosis, a major pathological cause for cardiovascular events. Here, we aim to explore the roles of Tregs-related genes in atherosclerosis deterioration. Methods and Results: We downloaded the gene expression profile of 29 atherosclerotic samples from the Gene Expression Omnibus database with an accession number of GSE28829. The abundance of Tregs estimated by the CIBERSORT algorithm was negatively correlated with the atherosclerotic stage. Using the limma test and correlation analysis, a total of 159 differentially expressed Tregs-related genes (DETregRGs) between early and advanced atherosclerotic plaques were documented. Functional annotation analysis using the DAVID tool indicated that the DETregRGs were mainly enriched in inflammatory responses, immune-related mechanisms, and pathways such as complement and coagulation cascades, platelet activation, leukocyte trans-endothelial migration, vascular smooth muscle contraction, and so on. A protein-protein interaction network of the DETregRGs was then constructed, and five hub genes (PTPRC, C3AR1, CD53, TLR2, and CCR1) were derived from the network with node degrees ≥20. The expression patterns of these hub DETregRGs were further validated in several independent datasets. Finally, a single sample scoring method was used to build a gene signature for the five DETregRGs, which could distinguish patients with myocardial infarction from those with stable coronary disease. Conclusion: The results of this study will improve our understanding about the Tregs-associated molecular mechanisms in the progression of atherosclerosis and facilitate the discovery of novel biomarkers for acute cardiovascular events.
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Affiliation(s)
- Meng Xia
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qingmeng Wu
- Healthcare-Associated Infections Control Center, The Affiliated Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Pengfei Chen
- Department of Gastroenterology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Cheng Qian
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Cheng CW, Beech DJ, Wheatcroft SB. Advantages of CEMiTool for gene co-expression analysis of RNA-seq data. Comput Biol Med 2020; 125:103975. [DOI: 10.1016/j.compbiomed.2020.103975] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/11/2020] [Accepted: 08/13/2020] [Indexed: 12/29/2022]
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Chen S, Yang D, Liu Z, Li F, Liu B, Chen Y, Ye W, Zheng Y. Crucial Gene Identification in Carotid Atherosclerosis Based on Peripheral Blood Mononuclear Cell (PBMC) Data by Weighted (Gene) Correlation Network Analysis (WGCNA). Med Sci Monit 2020; 26:e921692. [PMID: 32160184 PMCID: PMC7085238 DOI: 10.12659/msm.921692] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background Many patients are not responsive or tolerant to medical therapies for carotid atherosclerosis. Thus, elucidating the molecular mechanism for the pathogenesis and progression of carotid atherosclerosis and identifying new potential molecular targets for medical therapies that can slow progression of carotid atherosclerosis and prevent ischemic events are quite important. Material/Methods We downloaded the expression profiling data of PBMC in Biobank of Karolinska Endarterectomy (BiKE, GSE21545) for GEO. The WGCNA and DEG screening were conducted. The co-expression pattern between patients with ischemic events (the events group) and patients without ischemic events (the no-events group) were compared. Then, we identified hub genes of each module. Finally, the DEG co-expression network was constructed and MCODE was used to identify crucial genes based on this co-expression network. Results In the study, 183 DEGs were screened and 8 and 6 modules were assessed in the events group and no-events group, respectively. Compared to the no-events group, genes associated with inflammation and immune response were clustered in the green-yellow module of the events group. The hub gene of the green-yellow module of the events group was KIR2DL5A. We obtained 1 DEG co-expression network, which has 16 nodes and 24 edges, and we detected 5 crucial genes: SIRT1, THRAP3, RBM43, PEX1, and KLHDC2. The upregulated genes (THRAP3 and RBM43) showed potential diagnostic and prognostic value for the occurrence of ischemic events. Conclusions We detected 8 modules for the events group and 6 modules for the no-events group. The hub genes for modules and crucial genes of the DEG co-expression network were also identified. These genes might serve as potential targets for medical therapies and biomarkers for diagnosis and prognosis. Further experimental and biological studies are needed to elucidate the role of these crucial genes in the progression of carotid atherosclerosis.
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Affiliation(s)
- Siliang Chen
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
| | - Dan Yang
- Department of Computational Biology and Bioinformatics, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
| | - Zhili Liu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
| | - Fangda Li
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
| | - Bao Liu
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
| | - Yuexin Chen
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
| | - Wei Ye
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
| | - Yuehong Zheng
- Department of Vascular Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (mainland)
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Walter NAR, Denmark DL, Kozell LB, Buck KJ. A Systems Approach Implicates a Brain Mitochondrial Oxidative Homeostasis Co-expression Network in Genetic Vulnerability to Alcohol Withdrawal. Front Genet 2017; 7:218. [PMID: 28096806 PMCID: PMC5206817 DOI: 10.3389/fgene.2016.00218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/08/2016] [Indexed: 12/31/2022] Open
Abstract
Genetic factors significantly affect vulnerability to alcohol dependence (alcoholism). We previously identified quantitative trait loci on distal mouse chromosome 1 with large effects on predisposition to alcohol physiological dependence and associated withdrawal following both chronic and acute alcohol exposure in mice (Alcdp1 and Alcw1, respectively). We fine-mapped these loci to a 1.1–1.7 Mb interval syntenic with human 1q23.2-23.3. Alcw1/Alcdp1 interval genes show remarkable genetic variation among mice derived from the C57BL/6J and DBA/2J strains, the two most widely studied genetic animal models for alcohol-related traits. Here, we report the creation of a novel recombinant Alcw1/Alcdp1 congenic model (R2) in which the Alcw1/Alcdp1 interval from a donor C57BL/6J strain is introgressed onto a uniform, inbred DBA/2J genetic background. As expected, R2 mice demonstrate significantly less severe alcohol withdrawal compared to wild-type littermates. Additionally, comparing R2 and background strain animals, as well as reciprocal congenic (R8) and appropriate background strain animals, we assessed Alcw1/Alcdp1 dependent brain gene expression using microarray and quantitative PCR analyses. To our knowledge this includes the first Weighted Gene Co-expression Network Analysis using reciprocal congenic models. Importantly, this allows detection of co-expression patterns limited to one or common to both genetic backgrounds with high or low predisposition to alcohol withdrawal severity. The gene expression patterns (modules) in common contain genes related to oxidative phosphorylation, building upon human and animal model studies that implicate involvement of oxidative phosphorylation in alcohol use disorders (AUDs). Finally, we demonstrate that administration of N-acetylcysteine, an FDA-approved antioxidant, significantly reduces symptoms of alcohol withdrawal (convulsions) in mice, thus validating a phenotypic role for this network. Taken together, these studies support the importance of mitochondrial oxidative homeostasis in alcohol withdrawal and identify this network as a valuable therapeutic target in human AUDs.
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Affiliation(s)
- Nicole A R Walter
- Research and Development, Portland Veterans Affairs Medical Center, PortlandOR, USA; Department of Behavioral Neuroscience, School of Medicine, Oregon Health and Science University, PortlandOR, USA
| | - DeAunne L Denmark
- Research and Development, Portland Veterans Affairs Medical Center, PortlandOR, USA; Department of Behavioral Neuroscience, School of Medicine, Oregon Health and Science University, PortlandOR, USA
| | - Laura B Kozell
- Research and Development, Portland Veterans Affairs Medical Center, PortlandOR, USA; Department of Behavioral Neuroscience, School of Medicine, Oregon Health and Science University, PortlandOR, USA
| | - Kari J Buck
- Research and Development, Portland Veterans Affairs Medical Center, PortlandOR, USA; Department of Behavioral Neuroscience, School of Medicine, Oregon Health and Science University, PortlandOR, USA
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10
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Sharma A, Deshpande V, Ghatge M, Vangala RK. In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:4430890. [PMID: 29220465 PMCID: PMC5737197 DOI: 10.1093/database/bax077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/03/2017] [Indexed: 11/29/2022]
Abstract
Coronary artery disease (CAD) is a leading cause of death worldwide. Prevention, diagnosis and clinical interventions are dependent on the conventional risk factors like hypertension, diabetes and obesity. However, these conventional risk factors do not completely identify high risk individuals. One major hurdle in the improvement of diagnosis and treatment for CAD is the lack of integration of knowledge from different areas of research like molecular, clinical and drug development. In order to provide comprehensive information from hitherto dispersed data, we developed an integrative knowledgebase called “In-Cardiome or Integrated Cardiome” for all the stake holders in healthcare such as scientists, clinicians and pharmaceutical companies. It is created by integrating 16 different data sources, 995 curated genes classified into 12 different functional categories associated with disease, 1204 completed clinical trials, 12 therapy or drug classifications with 62 approved drugs and drug target networks. This knowledgebase gives the most needed opportunity to understand the disease process and therapeutic impact along with gene expression data from both animal models and patients. The data is classified into three different search categories functional groups, risk factors and therapy/drug based classes. One more unique aspect of In-Cardiome is integration of clinical data of 10,217 subject data from our ongoing Indian Atherosclerosis Research Study (IARS) (6357 unaffected and 3860 CAD affected). IARS data showing demographics and associations of individual and combinations of risk factors in Indian population along with molecular information will enable better translational and drug development research.
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Affiliation(s)
- Ankit Sharma
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India.,Bioinformatics and Biostatistics Unit, Thrombosis Research Institute, Narayana Hrudayalaya, 258/A, Bommasandra Industrial Area, Anekal Taluk, Bangalore, Karnataka 560099, India
| | - Vrushali Deshpande
- Transcriptomics and Histopathology Unit, Thrombosis Research Institute, Narayana Hrudayalaya, 258/A, Bommasandra Industrial Area, Anekal Taluk, Bangalore, Karnataka 560099, India
| | - Madankumar Ghatge
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104, India.,Proteomics and Coagulation Unit, Thrombosis Research Institute, Narayana Hrudayalaya, 258/A, Bommasandra Industrial Area, Anekal Taluk, Bangalore, Karnataka 560099, India
| | - Rajani Kanth Vangala
- Bioinformatics and Biostatistics Unit, Thrombosis Research Institute, Narayana Hrudayalaya, 258/A, Bommasandra Industrial Area, Anekal Taluk, Bangalore, Karnataka 560099, India.,Proteomics and Coagulation Unit, Thrombosis Research Institute, Narayana Hrudayalaya, 258/A, Bommasandra Industrial Area, Anekal Taluk, Bangalore, Karnataka 560099, India
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