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Integration of Gene Expression Profile Data of Human Epicardial Adipose Tissue from Coronary Artery Disease to Verification of Hub Genes and Pathways. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8567306. [PMID: 31886261 PMCID: PMC6900948 DOI: 10.1155/2019/8567306] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/22/2019] [Indexed: 12/12/2022]
Abstract
Background This study aim to identify the core pathogenic genes and explore the potential molecular mechanisms of human coronary artery disease (CAD). Methodology Two gene profiles of epicardial adipose tissue from CAD patients including GSE 18612 and GSE 64554 were downloaded and integrated by R software packages. All the coexpression of deferentially expressed genes (DEGs) were picked out and analyzed by DAVID online bioinformatic tools. In addition, the DEGs were totally typed into protein-protein interaction (PPI) networks to get the interaction data among all coexpression genes. Pictures were drawn by cytoscape software with the PPI networks data. CytoHubba were used to predict the hub genes by degree analysis. Finally all the top 10 hub genes and prediction genes in Molecular complex detection were analyzed by Gene ontology and Kyoto encyclopedia of genes and genomes pathway analysis. qRT-PCR were used to identified all the 10 hub genes. Results The top 10 hub genes calculated by the degree method were AKT1, MYC, EGFR, ACTB, CDC42, IGF1, FGF2, CXCR4, MMP2 and LYN, which relevant with the focal adhesion pathway. Module analysis revealed that the focal adhesion was also acted an important role in CAD, which was consistence with cytoHubba. All the top 10 hub genes were verified by qRT-PCR which presented that AKT1, EGFR, CDC42, FGF2, and MMP2 were significantly decreased in epicardial adipose tissue of CAD samples (p < 0.05) and MYC, ACTB, IGF1, CXCR4, and LYN were significantly increased (p < 0.05). Conclusions These candidate genes could be used as potential diagnostic biomarkers and therapeutic targets of CAD.
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Schanstra JP, Luong TT, Makridakis M, Van Linthout S, Lygirou V, Latosinska A, Alesutan I, Boehme B, Schelski N, Von Lewinski D, Mullen W, Nicklin S, Delles C, Feuillet G, Denis C, Lang F, Pieske B, Bascands JL, Mischak H, Saulnier-Blache JS, Voelkl J, Vlahou A, Klein J. Systems biology identifies cytosolic PLA2 as a target in vascular calcification treatment. JCI Insight 2019; 4:125638. [PMID: 31092728 DOI: 10.1172/jci.insight.125638] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/17/2019] [Indexed: 01/15/2023] Open
Abstract
Although cardiovascular disease (CVD) is the leading cause of morbimortality worldwide, promising new drug candidates are lacking. We compared the arterial high-resolution proteome of patients with advanced versus early-stage CVD to predict, from a library of small bioactive molecules, drug candidates able to reverse this disease signature. Of the approximately 4000 identified proteins, 100 proteins were upregulated and 52 were downregulated in advanced-stage CVD. Arachidonyl trifluoromethyl ketone (AACOCF3), a cytosolic phospholipase A2 (cPLA2) inhibitor was predicted as the top drug able to reverse the advanced-stage CVD signature. Vascular cPLA2 expression was increased in patients with advanced-stage CVD. Treatment with AACOCF3 significantly reduced vascular calcification in a cholecalciferol-overload mouse model and inhibited osteoinductive signaling in vivo and in vitro in human aortic smooth muscle cells. In conclusion, using a systems biology approach, we have identified a potentially new compound that prevented typical vascular calcification in CVD in vivo. Apart from the clear effect of this approach in CVD, such strategy should also be able to generate novel drug candidates in other complex diseases.
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Affiliation(s)
- Joost P Schanstra
- Institute of Cardiovascular and Metabolic Disease, INSERM, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Trang Td Luong
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - Manousos Makridakis
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Sophie Van Linthout
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany.,Charité - Universitätsmedizin Berlin, Berlin Institute of Health Center for Regenerative Therapies (BCRT), Berlin, Germany.,German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
| | - Vasiliki Lygirou
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | | | - Ioana Alesutan
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Institute for Physiology and Pathophysiology, Johannes Kepler University Linz, Linz, Austria
| | - Beate Boehme
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | - Nadeshda Schelski
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany
| | | | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Stuart Nicklin
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Guylène Feuillet
- Institute of Cardiovascular and Metabolic Disease, INSERM, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Colette Denis
- Institute of Cardiovascular and Metabolic Disease, INSERM, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Florian Lang
- Department of Physiology I, University of Tubingen, Tubingen, Germany
| | - Burkert Pieske
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
| | - Jean-Loup Bascands
- INSERM, U1188, Université de La Réunion, Sainte-Clotilde, La Réunion, France
| | | | - Jean-Sebastien Saulnier-Blache
- Institute of Cardiovascular and Metabolic Disease, INSERM, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jakob Voelkl
- Department of Internal Medicine and Cardiology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany.,Institute for Physiology and Pathophysiology, Johannes Kepler University Linz, Linz, Austria
| | - Antonia Vlahou
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Julie Klein
- Institute of Cardiovascular and Metabolic Disease, INSERM, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
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Hicks DF, Goossens N, Blas-García A, Tsuchida T, Wooden B, Wallace MC, Nieto N, Lade A, Redhead B, Cederbaum AI, Dudley JT, Fuchs BC, Lee YA, Hoshida Y, Friedman SL. Transcriptome-based repurposing of apigenin as a potential anti-fibrotic agent targeting hepatic stellate cells. Sci Rep 2017; 7:42563. [PMID: 28256512 PMCID: PMC5335661 DOI: 10.1038/srep42563] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/10/2017] [Indexed: 02/07/2023] Open
Abstract
We have used a computational approach to identify anti-fibrotic therapies by querying a transcriptome. A transcriptome signature of activated hepatic stellate cells (HSCs), the primary collagen-secreting cell in liver, and queried against a transcriptomic database that quantifies changes in gene expression in response to 1,309 FDA-approved drugs and bioactives (CMap). The flavonoid apigenin was among 9 top-ranked compounds predicted to have anti-fibrotic activity; indeed, apigenin dose-dependently reduced collagen I in the human HSC line, TWNT-4. To identify proteins mediating apigenin's effect, we next overlapped a 122-gene signature unique to HSCs with a list of 160 genes encoding proteins that are known to interact with apigenin, which identified C1QTNF2, encoding for Complement C1q tumor necrosis factor-related protein 2, a secreted adipocytokine with metabolic effects in liver. To validate its disease relevance, C1QTNF2 expression is reduced during hepatic stellate cell activation in culture and in a mouse model of alcoholic liver injury in vivo, and its expression correlates with better clinical outcomes in patients with hepatitis C cirrhosis (n = 216), suggesting it may have a protective role in cirrhosis progression.These findings reinforce the value of computational approaches to drug discovery for hepatic fibrosis, and identify C1QTNF2 as a potential mediator of apigenin's anti-fibrotic activity.
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Affiliation(s)
- Daniel F. Hicks
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Nicolas Goossens
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Division of Gastroenterology and Hepatology, Geneva University Hospital, Geneva, Switzerland
| | - Ana Blas-García
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Pharmacology, University of Valencia-FISABIO, Valencia, Spain
| | - Takuma Tsuchida
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Research Division, Mitsubishi Tanabe Pharma Corporation, Saitama, Japan
| | - Benjamin Wooden
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Michael C. Wallace
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- University of Western Australia, West Leederville, WA, Australia
| | - Natalia Nieto
- Department of Pathology, University of Illinois at Chicago, Chicago, USA
| | - Abigale Lade
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Benjamin Redhead
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Arthur I Cederbaum
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Joel T. Dudley
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Bryan C. Fuchs
- Division of Surgical Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, USA
| | - Youngmin A. Lee
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Yujin Hoshida
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Scott L. Friedman
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
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