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Rychkov D, Neely J, Oskotsky T, Yu S, Perlmutter N, Nititham J, Carvidi A, Krueger M, Gross A, Criswell LA, Ashouri JF, Sirota M. Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis. Front Immunol 2021; 12:638066. [PMID: 34177888 PMCID: PMC8223752 DOI: 10.3389/fimmu.2021.638066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/17/2021] [Indexed: 01/20/2023] Open
Abstract
There is an urgent need to identify biomarkers for diagnosis and disease activity monitoring in rheumatoid arthritis (RA). We leveraged publicly available microarray gene expression data in the NCBI GEO database for whole blood (N=1,885) and synovial (N=284) tissues from RA patients and healthy controls. We developed a robust machine learning feature selection pipeline with validation on five independent datasets culminating in 13 genes: TNFAIP6, S100A8, TNFSF10, DRAM1, LY96, QPCT, KYNU, ENTPD1, CLIC1, ATP6V0E1, HSP90AB1, NCL and CIRBP which define the RA score and demonstrate its clinical utility: the score tracks the disease activity DAS28 (p = 7e-9), distinguishes osteoarthritis (OA) from RA (OR 0.57, p = 8e-10) and polyJIA from healthy controls (OR 1.15, p = 2e-4) and monitors treatment effect in RA (p = 2e-4). Finally, the immunoblotting analysis of six proteins on an independent cohort confirmed two proteins, TNFAIP6/TSG6 and HSP90AB1/HSP90.
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Affiliation(s)
- Dmitry Rychkov
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, United States
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States
| | - Jessica Neely
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States
| | - Tomiko Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, United States
| | - Steven Yu
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, United States
| | - Noah Perlmutter
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Joanne Nititham
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Alexander Carvidi
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Melissa Krueger
- Department of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Andrew Gross
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Lindsey A. Criswell
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
- Institute for Human Genetics (IHG), University of California San Francisco, San Francisco, CA, United States
- Department of Medicine, University of California San Francisco, San Francisco, CA, United States
- Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, United States
| | - Judith F. Ashouri
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, United States
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States
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2
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Serhan CN, Gupta SK, Perretti M, Godson C, Brennan E, Li Y, Soehnlein O, Shimizu T, Werz O, Chiurchiù V, Azzi A, Dubourdeau M, Gupta SS, Schopohl P, Hoch M, Gjorgevikj D, Khan FM, Brauer D, Tripathi A, Cesnulevicius K, Lescheid D, Schultz M, Särndahl E, Repsilber D, Kruse R, Sala A, Haeggström JZ, Levy BD, Filep JG, Wolkenhauer O. The Atlas of Inflammation Resolution (AIR). Mol Aspects Med 2020; 74:100894. [PMID: 32893032 PMCID: PMC7733955 DOI: 10.1016/j.mam.2020.100894] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Acute inflammation is a protective reaction by the immune system in response to invading pathogens or tissue damage. Ideally, the response should be localized, self-limited, and returning to homeostasis. If not resolved, acute inflammation can result in organ pathologies leading to chronic inflammatory phenotypes. Acute inflammation and inflammation resolution are complex coordinated processes, involving a number of cell types, interacting in space and time. The biomolecular complexity and the fact that several biomedical fields are involved, make a multi- and interdisciplinary approach necessary. The Atlas of Inflammation Resolution (AIR) is a web-based resource capturing an essential part of the state-of-the-art in acute inflammation and inflammation resolution research. The AIR provides an interface for users to search thousands of interactions, arranged in inter-connected multi-layers of process diagrams, covering a wide range of clinically relevant phenotypes. By mapping experimental data onto the AIR, it can be used to elucidate drug action as well as molecular mechanisms underlying different disease phenotypes. For the visualization and exploration of information, the AIR uses the Minerva platform, which is a well-established tool for the presentation of disease maps. The molecular details of the AIR are encoded using international standards. The AIR was created as a freely accessible resource, supporting research and education in the fields of acute inflammation and inflammation resolution. The AIR connects research communities, facilitates clinical decision making, and supports research scientists in the formulation and validation of hypotheses. The AIR is accessible through https://air.bio.informatik.uni-rostock.de.
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Affiliation(s)
- Charles N Serhan
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Shailendra K Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany
| | - Mauro Perretti
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Catherine Godson
- Diabetes Complications Research Centre, Conway Institute & School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Eoin Brennan
- Diabetes Complications Research Centre, Conway Institute & School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Yongsheng Li
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Oliver Soehnlein
- Department of Physiology and Pharmacology (FyFA), Karolinska Institutet, 17177, Stockholm, Sweden; German Center for Cardiovascular Research (DZHK), München, Germany; Institute for Cardiovascular Prevention (IPEK), Ludwig Maximilian University, 80336, München, Germany
| | - Takao Shimizu
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 113-0033 Tokyo, Japan; National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, Japan
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Valerio Chiurchiù
- Institute of Translational Pharmacology, National Research Council, 00133, Rome, Italy; Laboratory of Resolution of Neuroinflammation, IRCCS Santa Lucia Foundation, 00143, Rome, Italy
| | - Angelo Azzi
- School of Graduate Biomedical Pharmacology and Drug Development Program at Tufts University, Boston, MA 02111, USA
| | - Marc Dubourdeau
- Ambiotis, Canal Biotech 2 - 3 Rue des Satellites, 31400, Toulouse, France
| | - Suchi Smita Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany
| | - Patrick Schopohl
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany
| | - Matti Hoch
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany
| | - Dragana Gjorgevikj
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany
| | - Faiz M Khan
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany
| | - David Brauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany
| | - Anurag Tripathi
- CSIR - Indian Institute of Toxicology Research, 226001, Lucknow, India
| | | | - David Lescheid
- Department of Medical Affairs & Research, Heel GmbH, 76532, Baden-Baden, Germany
| | - Myron Schultz
- Department of Medical Affairs & Research, Heel GmbH, 76532, Baden-Baden, Germany
| | - Eva Särndahl
- iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, SE-701 82, Örebro, Sweden; School of Medical Sciences, Örebro University, SE-701 82, Örebro, Sweden
| | - Dirk Repsilber
- School of Medical Sciences, Örebro University, SE-701 82, Örebro, Sweden
| | - Robert Kruse
- iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, SE-701 82, Örebro, Sweden; Department of Clinical Research Laboratory, Faculty of Medicine and Health, Örebro University, SE-701 82, Örebro, Sweden
| | - Angelo Sala
- Department of Pharmaceutical Sciences, University of Milan, 20133 Milano, and IRIB, C.N.R, 90146, Palermo, Italy
| | - Jesper Z Haeggström
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77, Stockholm, Sweden
| | - Bruce D Levy
- Brigham and Women's Hospital, Department of Medicine, Pulmonary and Critical Care Medicine and Harvard Medical School, Boston, MA, 02115, USA
| | - János G Filep
- Department of Pathology and Cell Biology, University of Montreal, and Research Center, Maisonneuve-Rosemont Hospital, Montreal, QC, H1T 2M4, Canada
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany; Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa.
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3
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Singh V, Kalliolias GD, Ostaszewski M, Veyssiere M, Pilalis E, Gawron P, Mazein A, Bonnet E, Petit-Teixeira E, Niarakis A. RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. Database (Oxford) 2020; 2020:baaa017. [PMID: 32311035 PMCID: PMC7170216 DOI: 10.1093/database/baaa017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 01/21/2020] [Accepted: 02/13/2020] [Indexed: 02/07/2023]
Abstract
Rheumatoid arthritis (RA) is a progressive, inflammatory autoimmune disease of unknown aetiology. The complex mechanism of aetiopathogenesis, progress and chronicity of the disease involves genetic, epigenetic and environmental factors. To understand the molecular mechanisms underlying disease phenotypes, one has to place implicated factors in their functional context. However, integration and organization of such data in a systematic manner remains a challenging task. Molecular maps are widely used in biology to provide a useful and intuitive way of depicting a variety of biological processes and disease mechanisms. Recent large-scale collaborative efforts such as the Disease Maps Project demonstrate the utility of such maps as versatile tools to organize and formalize disease-specific knowledge in a comprehensive way, both human and machine-readable. We present a systematic effort to construct a fully annotated, expert validated, state-of-the-art knowledge base for RA in the form of a molecular map. The RA map illustrates molecular and signalling pathways implicated in the disease. Signal transduction is depicted from receptors to the nucleus using the Systems Biology Graphical Notation (SBGN) standard representation. High-quality manual curation, use of only human-specific studies and focus on small-scale experiments aim to limit false positives in the map. The state-of-the-art molecular map for RA, using information from 353 peer-reviewed scientific publications, comprises 506 species, 446 reactions and 8 phenotypes. The species in the map are classified to 303 proteins, 61 complexes, 106 genes, 106 RNA entities, 2 ions and 7 simple molecules. The RA map is available online at ramap.elixir-luxembourg.org as an open-access knowledge base allowing for easy navigation and search of molecular pathways implicated in the disease. Furthermore, the RA map can serve as a template for omics data visualization.
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Affiliation(s)
- Vidisha Singh
- Laboratoire Européen de Recherche pour la Polyarthrite Rhumatoïde - Genhotel, Univ Evry, Université Paris-Saclay, 2, rue Gaston Crémieux, 91057 EVRY-GENOPOLE cedex, Evry, France
| | - George D Kalliolias
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, 535 East 70th Street, New York, NY 10021, USA
- Weill Cornell Medical Center, Weill Department of Medicine, 525 East 68th Street, New York, NY 10065, USA
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Maëva Veyssiere
- Laboratoire Européen de Recherche pour la Polyarthrite Rhumatoïde - Genhotel, Univ Evry, Université Paris-Saclay, 2, rue Gaston Crémieux, 91057 EVRY-GENOPOLE cedex, Evry, France
| | - Eleftherios Pilalis
- eNIOS Applications P.C., R&D department, Alexandrou Pantou 25, 17671, Kallithea-Athens, Greece
| | - Piotr Gawron
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Alexander Mazein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 Avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Eric Bonnet
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, 2 rue Gaston Crémieux, CP5706 91057 EVRY-GENOPOLE cedex, Evry, France
| | - Elisabeth Petit-Teixeira
- Laboratoire Européen de Recherche pour la Polyarthrite Rhumatoïde - Genhotel, Univ Evry, Université Paris-Saclay, 2, rue Gaston Crémieux, 91057 EVRY-GENOPOLE cedex, Evry, France
| | - Anna Niarakis
- Laboratoire Européen de Recherche pour la Polyarthrite Rhumatoïde - Genhotel, Univ Evry, Université Paris-Saclay, 2, rue Gaston Crémieux, 91057 EVRY-GENOPOLE cedex, Evry, France
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4
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Zhou W, He X, Chen Z, Fan D, Wang Y, Feng H, Zhang G, Lu A, Xiao L. LncRNA HOTAIR-mediated Wnt/β-catenin network modeling to predict and validate therapeutic targets for cartilage damage. BMC Bioinformatics 2019; 20:412. [PMID: 31366320 PMCID: PMC6670131 DOI: 10.1186/s12859-019-2981-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 07/02/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Cartilage damage is a crucial feature involved in several pathological conditions characterized by joint disorders, such as osteoarthritis and rheumatoid arthritis. Accumulated evidences showed that Wnt/β-catenin pathway plays a role in the pathogenesis of cartilage damage. In addition, it is experimentally documented that lncRNA (long non-coding RNA) HOTAIR plays a key role in the regulation of Wnt/β-catenin pathway based on directly decreased WIF-1 expression. Further, it is reported that Wnt/β-catenin pathway is a potent pathway to regulate the expression of MMP-13, which is responsible for degradation of collagen type II in articular cartilage. It is increasingly recognized that systems modeling approach provides an opportunity to understand the complex relationships and direct quantitative analysis of dynamic network in various diseases. RESULTS A dynamic network of lncRNA HOTAIR-mediated Wnt/β-catenin pathway regulating MMP-13 is developed to investigate the dynamic mechanism of the network involved in the pathogenesis of cartilage damage. Based on the network modeling, the potential therapeutic intervention point Axin is predicted and confirmed by the experimental validation. CONCLUSIONS Our study provides a promising strategy for revealing potential dynamic mechanism and assessing potential targets which contribute to the prevention of the pathological conditions related to cartilage damage.
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Affiliation(s)
- Wei Zhou
- Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Guanghua Integrative Medicine Hospital / Shanghai University of T.C.M, Shanghai, 200052, China.,Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.,Department of Allergy, The Third Affiliated Hospital of Shenzhen University, Shenzhen, 518020, China.,Institute of Integrated Bioinformedicine & Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Xiaojuan He
- Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Guanghua Integrative Medicine Hospital / Shanghai University of T.C.M, Shanghai, 200052, China.,Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.,Institute of Integrated Bioinformedicine & Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Ziyi Chen
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, 999077, SAR, China
| | - Danping Fan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yonghua Wang
- College of Life Science, Northwest University, Xi'an, 710000, Shaanxi, China
| | - Hui Feng
- Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Guanghua Integrative Medicine Hospital / Shanghai University of T.C.M, Shanghai, 200052, China
| | - Ge Zhang
- Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Guanghua Integrative Medicine Hospital / Shanghai University of T.C.M, Shanghai, 200052, China. .,Institute of Integrated Bioinformedicine & Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
| | - Aiping Lu
- Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Guanghua Integrative Medicine Hospital / Shanghai University of T.C.M, Shanghai, 200052, China. .,Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China. .,Institute of Integrated Bioinformedicine & Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China.
| | - Lianbo Xiao
- Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Guanghua Integrative Medicine Hospital / Shanghai University of T.C.M, Shanghai, 200052, China.
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5
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Long NP, Park S, Anh NH, Min JE, Yoon SJ, Kim HM, Nghi TD, Lim DK, Park JH, Lim J, Kwon SW. Efficacy of Integrating a Novel 16-Gene Biomarker Panel and Intelligence Classifiers for Differential Diagnosis of Rheumatoid Arthritis and Osteoarthritis. J Clin Med 2019; 8:E50. [PMID: 30621359 PMCID: PMC6352223 DOI: 10.3390/jcm8010050] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 12/15/2022] Open
Abstract
Introducing novel biomarkers for accurately detecting and differentiating rheumatoid arthritis (RA) and osteoarthritis (OA) using clinical samples is essential. In the current study, we searched for a novel data-driven gene signature of synovial tissues to differentiate RA from OA patients. Fifty-three RA, 41 OA, and 25 normal microarray-based transcriptome samples were utilized. The area under the curve random forests (RF) variable importance measurement was applied to seek the most influential differential genes between RA and OA. Five algorithms including RF, k-nearest neighbors (kNN), support vector machines (SVM), naïve-Bayes, and a tree-based method were employed for the classification. We found a 16-gene signature that could effectively differentiate RA from OA, including TMOD1, POP7, SGCA, KLRD1, ALOX5, RAB22A, ANK3, PTPN3, GZMK, CLU, GZMB, FBXL7, TNFRSF4, IL32, MXRA7, and CD8A. The externally validated accuracy of the RF model was 0.96 (sensitivity = 1.00, specificity = 0.90). Likewise, the accuracy of kNN, SVM, naïve-Bayes, and decision tree was 0.96, 0.96, 0.96, and 0.91, respectively. Functional meta-analysis exhibited the differential pathological processes of RA and OA; suggested promising targets for further mechanistic and therapeutic studies. In conclusion, the proposed genetic signature combined with sophisticated classification methods may improve the diagnosis and management of RA patients.
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Affiliation(s)
- Nguyen Phuoc Long
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Seongoh Park
- Department of Statistics, Seoul National University, Seoul 08826, Korea.
| | - Nguyen Hoang Anh
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Jung Eun Min
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Sang Jun Yoon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Hyung Min Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Tran Diem Nghi
- School of Medicine, Vietnam National University, Ho Chi Minh 700000, Vietnam.
| | - Dong Kyu Lim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Jeong Hill Park
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
| | - Johan Lim
- Department of Statistics, Seoul National University, Seoul 08826, Korea.
| | - Sung Won Kwon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea.
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Harshan S, Dey P, Ragunathan S. Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium. PeerJ 2018; 6:e5743. [PMID: 30324023 PMCID: PMC6186409 DOI: 10.7717/peerj.5743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/12/2018] [Indexed: 12/15/2022] Open
Abstract
Background Osteoclast differentiation in the inflamed synovium of rheumatoid arthritis (RA) affected joints leads to the formation of bone lesions. Reconstruction and analysis of protein interaction networks underlying specific disease phenotypes are essential for designing therapeutic interventions. In this study, we have created a network that captures signal flow leading to osteoclast differentiation. Based on transcriptome analysis, we have indicated the potential mechanisms responsible for the phenotype in the RA affected synovium. Method We collected information on gene expression, pathways and protein interactions related to RA from literature and databases namely Gene Expression Omnibus, Kyoto Encyclopedia of Genes and Genomes pathway and STRING. Based on these information, we created a network for the differentiation of osteoclasts. We identified the differentially regulated network genes and reported the signaling that are responsible for the process in the RA affected synovium. Result Our network reveals the mechanisms underlying the activation of the neutrophil cytosolic factor complex in connection to osteoclastogenesis in RA. Additionally, the study reports the predominance of the canonical pathway of NF-κB activation in the diseased synovium. The network also confirms that the upregulation of T cell receptor signaling and downregulation of transforming growth factor beta signaling pathway favor osteoclastogenesis in RA. To the best of our knowledge, this is the first comprehensive protein–protein interaction network describing RA driven osteoclastogenesis in the synovium. Discussion This study provides information that can be used to build models of the signal flow involved in the process of osteoclast differentiation. The models can further be used to design therapies to ameliorate bone destruction in the RA affected joints.
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Affiliation(s)
- Shilpa Harshan
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - Poulami Dey
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Srivatsan Ragunathan
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
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7
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Yu F, Duan C, Zhang X, Yao D, Si G, Gao Y, Gao Z, Umer F, Guo X. RNA-seq analysis reveals different gene ontologies and pathways in rheumatoid arthritis and Kashin-Beck disease. Int J Rheum Dis 2018; 21:1686-1694. [PMID: 30256536 DOI: 10.1111/1756-185x.13358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 06/13/2018] [Accepted: 07/02/2018] [Indexed: 11/30/2022]
Abstract
AIMS To understand the pathogenesis of cartilage damage in Kashin-Beck disease (KBD) and rheumatoid arthritis (RA) which similar clinical symptoms. METHODS RNA sequencing (RAN-seq) analysis was used to reveal the different pathogeneses between KBD and RA. The messenger RNA expression profiles of articular cartilage isolated from KBD patients (n = 3) and RA patients (n = 3) were compared using RNA-seq analysis. Differentially expressed genes (DEGs) were determined using the Benjamini-Hochberg approach. The Database for Annotation, Visualization and Integrated Discovery (DAVID 6.7) was employed to assess functional categories and Gene Ontology (GO). The Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology Based Annotation System (KOBAS 2.0) was used to identify significantly enriched KEGG pathways. RESULTS In the individually sequenced dataset, we identified 1568 significant DEGs in KBD compared to RA (232 up-regulated genes and 1336 down-regulated genes). GO function analysis identified nine significant biological processes (BPs), eight molecular functions (MFs), and five cell components (CCs) in KBD, and also the top ten ranked significant BPs, MFs and CCs were found in RA. The KEGG pathway enrichment analysis identified biosynthesis of amino acids involved in KBD. The chemokine signaling pathway, nuclear factor-kappa B signaling pathway, B cell receptor signaling pathway, leukocyte transendothelial migration, and osteoclast differentiation were involved in RA. CONCLUSIONS RNA-seq revealed that proteoglycan-mediated metabolic disorders contributed to the onset of KBD, whereas immune dysregulation was apparently involved in the pathogenesis of RA.
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Affiliation(s)
- Fangfang Yu
- School of Public Health, Health Science Center of Xi'an Jiaotong University, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an, China
| | - Chen Duan
- School of Public Health, Health Science Center of Xi'an Jiaotong University, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an, China
| | - Xiaodong Zhang
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dandan Yao
- The City College of Xi'an Jiaotong University, Xi'an, China
| | - Gangquan Si
- State Key Laboratory of Electrical Insulation and Power Equipment, School of Electrical Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Ying Gao
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zongqiang Gao
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | | | - Xiong Guo
- School of Public Health, Health Science Center of Xi'an Jiaotong University, Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, Xi'an, China
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8
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Zhou S, Appleman VA, Rose CM, Jun HJ, Yang J, Zhou Y, Bronson RT, Gygi SP, Charest A. Chronic platelet-derived growth factor receptor signaling exerts control over initiation of protein translation in glioma. Life Sci Alliance 2018; 1:e201800029. [PMID: 30456354 PMCID: PMC6238596 DOI: 10.26508/lsa.201800029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/29/2018] [Accepted: 05/29/2018] [Indexed: 01/23/2023] Open
Abstract
Using phospho-proteomics in a new model of malignant glioma, we reveal that clinically relevant, chronic PDGFRα signaling differs considerably from acute receptor stimulation and unveils previously unrecognized control over key elements of the translation initiation machinery. Activation of the platelet-derived growth factor receptors (PDGFRs) gives rise to some of the most important signaling pathways that regulate mammalian cellular growth, survival, proliferation, and differentiation and their misregulation is common in a variety of diseases. Herein, we present a comprehensive and detailed map of PDGFR signaling pathways assembled from literature and integrate this map in a bioinformatics protocol designed to extract meaningful information from large-scale quantitative proteomics mass spectrometry data. We demonstrate the usefulness of this approach using a new genetically engineered mouse model of PDGFRα-driven glioma. We discovered that acute PDGFRα stimulation differs considerably from chronic receptor activation in the regulation of protein translation initiation. Transient stimulation activates several key components of the translation initiation machinery, whereas the clinically relevant chronic activity of PDGFRα is associated with a significant shutdown of translational members. Our work defines a step-by-step approach to extract biologically relevant insights from global unbiased phospho-protein datasets to uncover targets for therapeutic assessment.
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Affiliation(s)
- Shuang Zhou
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Vicky A Appleman
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | - Hyun Jung Jun
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Juechen Yang
- Department of Computer Science, North Dakota State University, Fargo, ND, USA
| | - Yue Zhou
- Department of Statistics, North Dakota State University, Fargo, ND, USA
| | - Roderick T Bronson
- Rodent Histopathology Core, Dana-Farber/Harvard Cancer Center, Boston, MA, USA
| | - Steve P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Al Charest
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
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9
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Khan FM, Sadeghi M, Gupta SK, Wolkenhauer O. A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression. Methods Mol Biol 2018; 1702:247-276. [PMID: 29119509 DOI: 10.1007/978-1-4939-7456-6_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Unraveling mechanisms underlying diseases has motivated the development of systems biology approaches. The key challenges for the development of mathematical models and computational tool are (1) the size of molecular networks, (2) the nonlinear nature of spatio-temporal interactions, and (3) feedback loops in the structure of interaction networks. We here propose an integrative workflow that combines structural analyses of networks, high-throughput data, and mechanistic modeling. As an illustration of the workflow, we use prostate cancer as a case study with the aim of identifying key functional components associated with primary to metastasis transitions. Analysis carried out by the workflow revealed that HOXD10, BCL2, and PGR are the most important factors affected in primary prostate samples, whereas, in the metastatic state, STAT3, JUN, and JUNB are playing a central role. The identified key elements of each network are validated using patient survival analysis. The workflow presented here allows experimentalists to use heterogeneous data sources for the identification of diagnostic and prognostic signatures.
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Affiliation(s)
- Faiz M Khan
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany
| | - Mehdi Sadeghi
- Research Institute for Fundamental Sciences (RIFS), University of Tabriz, Tabriz, Iran
| | - Shailendra K Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany.,Chhattisgarh Swami Vivekanand Technical University, Bhilai, Chhattisgarh, India
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051, Rostock, Germany. .,Chhattisgarh Swami Vivekanand Technical University, Bhilai, Chhattisgarh, India. .,Stellenbosch Institute of Advanced Study (STIAS), Wallenberg Research Centre, Stellenbosch University, Stellenbosch, South Africa.
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10
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Singh V, Ostaszewski M, Kalliolias GD, Chiocchia G, Olaso R, Petit-Teixeira E, Helikar T, Niarakis A. Computational Systems Biology Approach for the Study of Rheumatoid Arthritis: From a Molecular Map to a Dynamical Model. GENOMICS AND COMPUTATIONAL BIOLOGY 2017; 4:e100050. [PMID: 29951575 PMCID: PMC6016388 DOI: 10.18547/gcb.2018.vol4.iss1.e100050] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In this work we present a systematic effort to summarize current biological pathway knowledge concerning Rheumatoid Arthritis (RA). We are constructing a detailed molecular map based on exhaustive literature scanning, strict curation criteria, re-evaluation of previously published attempts and most importantly experts' advice. The RA map will be web-published in the coming months in the form of an interactive map, using the MINERVA platform, allowing for easy access, navigation and search of all molecular pathways implicated in RA, serving thus, as an on line knowledgebase for the disease. Moreover the map could be used as a template for Omics data visualization offering a first insight about the pathways affected in different experimental datasets. The second goal of the project is a dynamical study focused on synovial fibroblasts' behavior under different initial conditions specific to RA, as recent studies have shown that synovial fibroblasts play a crucial role in driving the persistent, destructive characteristics of the disease. Leaning on the RA knowledgebase and using the web platform Cell Collective, we are currently building a Boolean large scale dynamical model for the study of RA fibroblasts' activation.
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Affiliation(s)
- Vidisha Singh
- GenHotel EA3886, Univ Evry, Université Paris-Saclay, 91025, Evry, France
| | - Marek Ostaszewski
- Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, Esch-sur-Alzette, Luxembourg
| | - George D. Kalliolias
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, USA; Department of Medicine, Weill Cornell Medical College, New York City, USA
| | - Gilles Chiocchia
- Faculty of Health Sciences Simone Veil, INSERM U1173, University of Versailles Saint-Quentin-en-Yvelines, Montigny-le-Bretonneux, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), CEA, Evry, France
| | | | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Anna Niarakis
- GenHotel EA3886, Univ Evry, Université Paris-Saclay, 91025, Evry, France
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11
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Pathak RK, Baunthiyal M, Pandey N, Pandey D, Kumar A. Modeling of the jasmonate signaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in Brassica. Sci Rep 2017; 7:16790. [PMID: 29196636 PMCID: PMC5711873 DOI: 10.1038/s41598-017-16884-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/08/2017] [Indexed: 01/01/2023] Open
Abstract
The productivity of Oilseed Brassica, one of the economically important crops of India, is seriously affected by the disease, Alternaria blight. The disease is mainly caused by two major necrotrophic fungi, Alternaria brassicae and Alternaria brassicicola which are responsible for significant yield losses. Till date, no resistant source is available against Alternaria blight, hence plant breeding methods can not be used to develop disease resistant varieties. Jasmonate mediated signalling pathway, which is known to play crucial role during defense response against necrotrophs, could be strengthened in Brassica plants to combat the disease. Since scanty information is available in Brassica-Alternaria pathosystems at molecular level therefore, in the present study efforts have been made to model jasmonic acid pathway in Arabidopsis thaliana to simulate the dynamic behaviour of molecular species in the model. Besides, the developed model was also analyzed topologically for investigation of the hubs node. COI1 is identified as one of the promising candidate genes in response to Alternaria and other linked components of plant defense mechanisms against the pathogens. The findings from present study are therefore informative for understanding the molecular basis of pathophysiology and rational management of Alternaria blight for securing food and nutritional security.
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Affiliation(s)
- Rajesh Kumar Pathak
- Department of Biotechnology, Govind Ballabh Pant Institute of Engineering & Technology, Pauri Garhwal, 246194, Uttarakhand, India
| | - Mamta Baunthiyal
- Department of Biotechnology, Govind Ballabh Pant Institute of Engineering & Technology, Pauri Garhwal, 246194, Uttarakhand, India.
| | - Neetesh Pandey
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute (IASRI), Pusa, 110012, New Delhi, India
| | - Dinesh Pandey
- Department of Molecular Biology & Genetic Engineering, College of Basic Sciences & Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar, 263145, India
| | - Anil Kumar
- Department of Molecular Biology & Genetic Engineering, College of Basic Sciences & Humanities, G. B. Pant University of Agriculture & Technology, Pantnagar, 263145, India.
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12
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Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures. Nat Commun 2017; 8:198. [PMID: 28775339 PMCID: PMC5543083 DOI: 10.1038/s41467-017-00268-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 06/15/2017] [Indexed: 12/18/2022] Open
Abstract
Cancer is a disease of subverted regulatory pathways. In this paper, we reconstruct the regulatory network around E2F, a family of transcription factors whose deregulation has been associated to cancer progression, chemoresistance, invasiveness, and metastasis. We integrate gene expression profiles of cancer cell lines from two E2F1-driven highly aggressive bladder and breast tumors, and use network analysis methods to identify the tumor type-specific core of the network. By combining logic-based network modeling, in vitro experimentation, and gene expression profiles from patient cohorts displaying tumor aggressiveness, we identify and experimentally validate distinctive, tumor type-specific signatures of receptor proteins associated to epithelial-mesenchymal transition in bladder and breast cancer. Our integrative network-based methodology, exemplified in the case of E2F1-induced aggressive tumors, has the potential to support the design of cohort- as well as tumor type-specific treatments and ultimately, to fight metastasis and therapy resistance.Deregulation of E2F family transcription factors is associated with cancer progression and metastasis. Here, the authors construct a map of the regulatory network around the E2F family, and using gene expression profiles, identify tumour type-specific regulatory cores and receptor expression signatures associated with epithelial-mesenchymal transition in bladder and breast cancer.
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13
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Xu X, Chen H, Zhang Q, Xu J, Shi Q, Wang M. MiR-650 inhibits proliferation, migration and invasion of rheumatoid arthritis synovial fibroblasts by targeting AKT2. Biomed Pharmacother 2017; 88:535-541. [DOI: 10.1016/j.biopha.2017.01.063] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/03/2017] [Accepted: 01/10/2017] [Indexed: 01/09/2023] Open
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14
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Durso DF, Bacalini MG, do Valle ÍF, Pirazzini C, Bonafé M, Castellani G, Faria AMC, Franceschi C, Garagnani P, Nardini C. Aberrant methylation patterns in colorectal cancer: a meta-analysis. Oncotarget 2017; 8:12820-12830. [PMID: 28086223 PMCID: PMC5355058 DOI: 10.18632/oncotarget.14590] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 12/27/2016] [Indexed: 12/30/2022] Open
Abstract
Colorectal cancer is among the leading causes of cancer death worldwide. Despite numerous molecular characterizations of the phenomenon, the exact dynamics of its onset and progression remain elusive. Colorectal cancer onset has been characterized by changes in DNA methylation profiles, that, owing to the stability of their patterns, are promising candidates to shed light on the molecular events laying at the base of this phenomenon.To exploit this stability and reinforce it, we conducted a meta-analysis on publicly available DNA methylation datasets generated on: normal colorectal, adenoma (ADE) and adenocarcinoma (CRC) samples using the Illumina 450k array, in the systems medicine frame, searching for tumor gene episignatures, to produce a carefully selected list of potential drivers, markers and targets of the disease. The analysis proceeds from a differential meta-analysis of the methylation profiles using an analytical pipeline recently developed by our group [1], through network reconstruction, topological and functional analyses, to finally highlight relevant epigenomic features. Our results show that genes already highlighted for their genetic or transcriptional alteration in colorectal cancer are also differentially methylated, reinforcing -regardless of the level of cellular control- their role in the complex of alterations involved in tumorigenesis.These findings were finally validated in an independent cohort from The Cancer Genome Atlas (TCGA).
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Affiliation(s)
- Danielle Fernandes Durso
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- National Counsel of Technological and Scientific Development (CNPq), ministry of science technology and innovation (MCTI), Brasilia, Brazil
| | | | - Ítalo Faria do Valle
- CAPES Foundation, Ministry of Education of Brazil–Brasília (DF), Brazil
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | | | - Massimiliano Bonafé
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Ana Maria Caetano Faria
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- IRCCS Institute of Neurological Sciences, Bologna, Italy
- Interdepartmental Center “L. Galvani”, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Interdepartmental Center “L. Galvani”, University of Bologna, Bologna, Italy
- Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna, Italy
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15
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16
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Yang Q, Pan W, Qian L. Identification of the miRNA–mRNA regulatory network in multiple sclerosis. Neurol Res 2016; 39:142-151. [PMID: 27809691 DOI: 10.1080/01616412.2016.1250857] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Qinghe Yang
- Department of Neurology, The Second People’s Hospital of Liaocheng, Shandong, China
| | - Wei Pan
- Department of Neurology, The Second People’s Hospital of Liaocheng, Shandong, China
| | - Liwei Qian
- Department of Pediatric, The Second People’s Hospital of Liaocheng, Shandong, China
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17
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Dey P, Panga V, Raghunathan S. A Cytokine Signalling Network for the Regulation of Inducible Nitric Oxide Synthase Expression in Rheumatoid Arthritis. PLoS One 2016; 11:e0161306. [PMID: 27626941 PMCID: PMC5023176 DOI: 10.1371/journal.pone.0161306] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/03/2016] [Indexed: 12/22/2022] Open
Abstract
In rheumatoid arthritis (RA), nitric oxide (NO) is implicated in inflammation, angiogenesis and tissue destruction. The enzyme inducible nitric oxide synthase (iNOS) is responsible for the localised over-production of NO in the synovial joints affected by RA. The pro- and anti-inflammatory cytokines stimulate the synovial macrophages and the fibroblast-like synoviocytes to express iNOS. Therefore, the cytokine signalling network underlying the regulation of iNOS is essential to understand the pathophysiology of the disease. By using information from the literature, we have constructed, for the first time, the cytokine signalling network involved in the regulation of iNOS expression. Using the differential expression patterns obtained by re-analysing the microarray data on the RA synovium and the synovial macrophages available in the Gene Expression Omnibus (GEO) database, we aimed to establish the role played by the network genes towards iNOS regulation in the RA synovium. Our analysis reveals that the network genes belonging to interferon (IFN) and interleukin-10 (IL-10) pathways are always up-regulated in the RA synovium whereas the genes which are part of the anti-inflammatory transforming growth factor-beta (TGF-β) signalling pathway are mostly down-regulated. We observed a consistent up-regulation of the transcription factor signal transducers and activators of transcription 1 (STAT1) in the RA synovium and the macrophages. Interestingly, we found a consistent up-regulation of the iNOS interacting protein ras-related C3 botulinum toxin substrate 2 (RAC2) in the RA synovium as well as the macrophages. Importantly, we have constructed a model to explain the impact of IFN and IL-10 pathways on Rac2-iNOS interaction leading to over-production of NO and thereby causing chronic inflammation in the RA synovium. The interplay between STAT1 and RAC2 in the regulation of NO could have implications for the identification of therapeutic targets for RA.
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Affiliation(s)
- Poulami Dey
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronics City Phase I, Bengaluru 560 100, Karnataka, India
- Manipal University, Manipal, 576104, Karnataka, India
| | - Venugopal Panga
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronics City Phase I, Bengaluru 560 100, Karnataka, India
- Manipal University, Manipal, 576104, Karnataka, India
| | - Srivatsan Raghunathan
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronics City Phase I, Bengaluru 560 100, Karnataka, India
- * E-mail:
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18
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Jagannadham J, Jaiswal HK, Agrawal S, Rawal K. Comprehensive Map of Molecules Implicated in Obesity. PLoS One 2016; 11:e0146759. [PMID: 26886906 PMCID: PMC4757102 DOI: 10.1371/journal.pone.0146759] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 12/22/2015] [Indexed: 01/22/2023] Open
Abstract
Obesity is a global epidemic affecting over 1.5 billion people and is one of the risk factors for several diseases such as type 2 diabetes mellitus and hypertension. We have constructed a comprehensive map of the molecules reported to be implicated in obesity. A deep curation strategy was complemented by a novel semi-automated text mining system in order to screen 1,000 full-length research articles and over 90,000 abstracts that are relevant to obesity. We obtain a scale free network of 804 nodes and 971 edges, composed of 510 proteins, 115 genes, 62 complexes, 23 RNA molecules, 83 simple molecules, 3 phenotype and 3 drugs in "bow-tie" architecture. We classify this network into 5 modules and identify new links between the recently discovered fat mass and obesity associated FTO gene with well studied examples such as insulin and leptin. We further built an automated docking pipeline to dock orlistat as well as other drugs against the 24,000 proteins in the human structural proteome to explain the therapeutics and side effects at a network level. Based upon our experiments, we propose that therapeutic effect comes through the binding of one drug with several molecules in target network, and the binding propensity is both statistically significant and different in comparison with any other part of human structural proteome.
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Affiliation(s)
- Jaisri Jagannadham
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida [UP]-201 307, India
| | - Hitesh Kumar Jaiswal
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida [UP]-201 307, India
| | - Stuti Agrawal
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida [UP]-201 307, India
| | - Kamal Rawal
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida [UP]-201 307, India
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19
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Kuperstein I, Bonnet E, Nguyen HA, Cohen D, Viara E, Grieco L, Fourquet S, Calzone L, Russo C, Kondratova M, Dutreix M, Barillot E, Zinovyev A. Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps. Oncogenesis 2015; 4:e160. [PMID: 26192618 PMCID: PMC4521180 DOI: 10.1038/oncsis.2015.19] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 05/29/2015] [Accepted: 06/08/2015] [Indexed: 02/07/2023] Open
Abstract
Cancerogenesis is driven by mutations leading to aberrant functioning of a complex network of molecular interactions and simultaneously affecting multiple cellular functions. Therefore, the successful application of bioinformatics and systems biology methods for analysis of high-throughput data in cancer research heavily depends on availability of global and detailed reconstructions of signalling networks amenable for computational analysis. We present here the Atlas of Cancer Signalling Network (ACSN), an interactive and comprehensive map of molecular mechanisms implicated in cancer. The resource includes tools for map navigation, visualization and analysis of molecular data in the context of signalling network maps. Constructing and updating ACSN involves careful manual curation of molecular biology literature and participation of experts in the corresponding fields. The cancer-oriented content of ACSN is completely original and covers major mechanisms involved in cancer progression, including DNA repair, cell survival, apoptosis, cell cycle, EMT and cell motility. Cell signalling mechanisms are depicted in detail, together creating a seamless ‘geographic-like' map of molecular interactions frequently deregulated in cancer. The map is browsable using NaviCell web interface using the Google Maps engine and semantic zooming principle. The associated web-blog provides a forum for commenting and curating the ACSN content. ACSN allows uploading heterogeneous omics data from users on top of the maps for visualization and performing functional analyses. We suggest several scenarios for ACSN application in cancer research, particularly for visualizing high-throughput data, starting from small interfering RNA-based screening results or mutation frequencies to innovative ways of exploring transcriptomes and phosphoproteomes. Integration and analysis of these data in the context of ACSN may help interpret their biological significance and formulate mechanistic hypotheses. ACSN may also support patient stratification, prediction of treatment response and resistance to cancer drugs, as well as design of novel treatment strategies.
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Affiliation(s)
- I Kuperstein
- 1] Institut Curie, Paris, France [2] INSERM, U900, Paris, France [3] Mines ParisTech, Fontainebleau, France
| | - E Bonnet
- 1] Institut Curie, Paris, France [2] INSERM, U900, Paris, France [3] Mines ParisTech, Fontainebleau, France
| | - H-A Nguyen
- 1] Institut Curie, Paris, France [2] INSERM, U900, Paris, France [3] Mines ParisTech, Fontainebleau, France
| | - D Cohen
- 1] Institut Curie, Paris, France [2] INSERM, U900, Paris, France [3] Mines ParisTech, Fontainebleau, France
| | | | - L Grieco
- 1] Institut Curie, Paris, France [2] INSERM, U900, Paris, France [3] Mines ParisTech, Fontainebleau, France [4] Ecole Normale Supérieure, IBENS, Paris, France [5] CNRS, UMR8197, Paris, France [6] INSERM, U1024, Paris, France
| | - S Fourquet
- 1] Institut Curie, Paris, France [2] INSERM, U900, Paris, France [3] Mines ParisTech, Fontainebleau, France
| | - L Calzone
- 1] Institut Curie, Paris, France [2] INSERM, U900, Paris, France [3] Mines ParisTech, Fontainebleau, France
| | - C Russo
- 1] Institut Curie, Paris, France [2] INSERM, U900, Paris, France [3] Mines ParisTech, Fontainebleau, France
| | - M Kondratova
- 1] Institut Curie, Paris, France [2] INSERM, U900, Paris, France [3] Mines ParisTech, Fontainebleau, France
| | - M Dutreix
- 1] Institut Curie, Paris, France [2] CNRS, UMR3347, Orsay, France [3] INSERM, U1021, Orsay, France
| | - E Barillot
- 1] Institut Curie, Paris, France [2] INSERM, U900, Paris, France [3] Mines ParisTech, Fontainebleau, France
| | - A Zinovyev
- 1] Institut Curie, Paris, France [2] INSERM, U900, Paris, France [3] Mines ParisTech, Fontainebleau, France
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20
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Kim KJ, Lee S, Kim WU. Applications of systems approaches in the study of rheumatic diseases. Korean J Intern Med 2015; 30:148-60. [PMID: 25750554 PMCID: PMC4351319 DOI: 10.3904/kjim.2015.30.2.148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/23/2014] [Indexed: 12/27/2022] Open
Abstract
The complex interaction of molecules within a biological system constitutes a functional module. These modules are then acted upon by both internal and external factors, such as genetic and environmental stresses, which under certain conditions can manifest as complex disease phenotypes. Recent advances in high-throughput biological analyses, in combination with improved computational methods for data enrichment, functional annotation, and network visualization, have enabled a much deeper understanding of the mechanisms underlying important biological processes by identifying functional modules that are temporally and spatially perturbed in the context of disease development. Systems biology approaches such as these have produced compelling observations that would be impossible to replicate using classical methodologies, with greater insights expected as both the technology and methods improve in the coming years. Here, we examine the use of systems biology and network analysis in the study of a wide range of rheumatic diseases to better understand the underlying molecular and clinical features.
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Affiliation(s)
- Ki-Jo Kim
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Suwon, Korea
| | - Saseong Lee
- POSTECH-CATHOLIC BioMedical Engineering Institute, The Catholic University of Korea, Seoul, Korea
| | - Wan-Uk Kim
- POSTECH-CATHOLIC BioMedical Engineering Institute, The Catholic University of Korea, Seoul, Korea
- Division of Rheumatology, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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21
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Kamide T, Okumura S, Ghosh S, Shinoda Y, Mototani Y, Ohnuki Y, Jin H, Cai W, Suita K, Sato I, Umemura M, Fujita T, Yokoyama U, Sato M, Furutani K, Kitano H, Ishikawa Y. Oscillation of cAMP and Ca(2+) in cardiac myocytes: a systems biology approach. J Physiol Sci 2015; 65:195-200. [PMID: 25585963 PMCID: PMC10717207 DOI: 10.1007/s12576-014-0354-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/18/2014] [Indexed: 12/19/2022]
Abstract
Cyclic adenosine monophosphate (cAMP) and Ca(2+) levels may oscillate in harmony within excitable cells; a mathematical oscillation loop model, the Cooper model, of these oscillations was developed two decades ago. However, in that model all adenylyl cyclase (AC) isoforms were assumed to be inhibited by Ca(2+), and it is now known that the heart expresses multiple AC isoforms, among which the type 5/6 isoforms are Ca(2+)-inhibitable whereas the other five (AC2, 3, 4, 7, and 9) are not. We used a computational systems biology approach with CellDesigner simulation software to develop a comprehensive graphical map and oscillation loop model for cAMP and Ca(2+). This model indicated that Ca(2+)-mediated inhibition of AC is essential to create oscillations of Ca(2+) and cAMP, and the oscillations were not altered by incorporation of phosphodiesterase-mediated cAMP hydrolysis or PKA-mediated inhibition of AC into the model. More importantly, they were created but faded out immediately in the co-presence of Ca(2+)-noninhibitable AC isoforms. Because the subcellular locations of AC isoforms are different, spontaneous cAMP and Ca(2+) oscillations may occur within microdomains containing only Ca(2+)-inhibitable isoforms in cardiac myocytes, which might be necessary for fine tuning of excitation-contraction coupling.
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Affiliation(s)
- Takehisa Kamide
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Satoshi Okumura
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
- Department of Physiology, Tsurumi University School of Dental Medicine, 2-1-2 Tsurumi, Tsurumi-ku, Yokohama, 230-8501 Japan
| | - Samik Ghosh
- The Systems Biology Institute, Minato, Tokyo, 108-0071 Japan
| | - Yoko Shinoda
- Department of Physiology, Tsurumi University School of Dental Medicine, 2-1-2 Tsurumi, Tsurumi-ku, Yokohama, 230-8501 Japan
| | - Yasumasa Mototani
- Department of Physiology, Tsurumi University School of Dental Medicine, 2-1-2 Tsurumi, Tsurumi-ku, Yokohama, 230-8501 Japan
| | - Yoshiki Ohnuki
- Department of Physiology, Tsurumi University School of Dental Medicine, 2-1-2 Tsurumi, Tsurumi-ku, Yokohama, 230-8501 Japan
| | - Huiling Jin
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Wenqian Cai
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Kenji Suita
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Itaru Sato
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Masanari Umemura
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Takayuki Fujita
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Utako Yokoyama
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
| | - Motohiko Sato
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
- Department of Physiology, Aichi Medical University, Nagakute, Aichi 480-1195 Japan
| | - Kazuharu Furutani
- Department of Pharmacology, Graduate School of Medicine, Osaka University, Osaka, 565-0871 Japan
- Center for Advanced Medical Engineering and Informatics, Osaka University, Osaka, 565-0871 Japan
| | - Hiroaki Kitano
- The Systems Biology Institute, Minato, Tokyo, 108-0071 Japan
- Okinawa Institute of Science and Technology Graduate School, Onna-Son, Okinawa, 904-0412 Japan
- Laboratory for Disease Systems Modeling, Riken Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Yoshihiro Ishikawa
- Cardiovascular Research Institute, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004 Japan
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Dent JE, Devescovi V, Li H, Di Lena P, Lu Y, Liu Y, Nardini C. Mechanotransduction map: simulation model, molecular pathway, gene set. ACTA ACUST UNITED AC 2014; 31:1053-9. [PMID: 25429059 DOI: 10.1093/bioinformatics/btu776] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 11/17/2014] [Indexed: 01/07/2023]
Abstract
MOTIVATION Mechanotransduction--the ability to output a biochemical signal from a mechanical input--is related to the initiation and progression of a broad spectrum of molecular events. Yet, the characterization of mechanotransduction lacks some of the most basic tools as, for instance, it can hardly be recognized by enrichment analysis tools, nor could we find any pathway representation. This greatly limits computational testing and hypothesis generation on mechanotransduction biological relevance and involvement in disease or physiological mechanisms. RESULTS We here present a molecular map of mechanotransduction, built in CellDesigner to warrant that maximum information is embedded in a compact network format. To validate the map's necessity we tested its redundancy in comparison with existing pathways, and to estimate its sufficiency, we quantified its ability to reproduce biological events with dynamic simulations, using Signaling Petri Networks. AVAILABILITY AND IMPLEMENTATION SMBL language map is available in the Supplementary Data: core_map.xml, basic_map.xml. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jennifer E Dent
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
| | - Valentina Devescovi
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
| | - Han Li
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
| | - Pietro Di Lena
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
| | - Youtao Lu
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
| | - Yuanhua Liu
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
| | - Christine Nardini
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, People's Republic of China, Quintiles, Global Biostatistics, Reading, Berkshire, UK and Department of Computer Science and Engineering - DISI, University of Bologna, Bologna, Italy
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Tieri P, Zhou X, Zhu L, Nardini C. Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects. Front Cell Dev Biol 2014; 2:59. [PMID: 25414848 PMCID: PMC4220167 DOI: 10.3389/fcell.2014.00059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/26/2014] [Indexed: 12/19/2022] Open
Abstract
Objective: To provide a frame to estimate the systemic impact (side/adverse events) of (novel) therapeutic targets by taking into consideration drugs potential on the numerous districts involved in rheumatoid arthritis (RA) from the inflammatory and immune response to the gut-intestinal (GI) microbiome. Methods: We curated the collection of molecules from high-throughput screens of diverse (multi-omic) biochemical origin, experimentally associated to RA. Starting from such collection we generated RA-related protein-protein interaction (PPI) networks (interactomes) based on experimental PPI data. Pharmacological treatment simulation, topological and functional analyses were further run to gain insight into the proteins most affected by therapy and by multi-omic modeling. Results: Simulation on the administration of MTX results in the activation of expected (apoptosis) and adverse (nitrogenous metabolism alteration) effects. Growth factor receptor-bound protein 2 (GRB2) and Interleukin-1 Receptor Associated Kinase-4 (IRAK4, already an RA target) emerge as relevant nodes. The former controls the activation of inflammatory, proliferative and degenerative pathways in host and pathogens. The latter controls immune alterations and blocks innate response to pathogens. Conclusions: This multi-omic map properly recollects in a single analytical picture known, yet complex, information like the adverse/side effects of MTX, and provides a reliable platform for in silico hypothesis testing or recommendation on novel therapies. These results can support the development of RA translational research in the design of validation experiments and clinical trials, as such we identify GRB2 as a robust potential new target for RA for its ability to control both synovial degeneracy and dysbiosis, and, conversely, warn on the usage of IRAK4-inhibitors recently promoted, as this involves potential adverse effects in the form of impaired innate response to pathogens.
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Affiliation(s)
- Paolo Tieri
- IAC - Istituto per le Applicazioni del Calcolo "Mauro Picone," CNR - Consiglio Nazionale delle Ricerche Rome, Italy ; Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, Chinese Academy of Sciences - Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences Shanghai, China
| | - XiaoYuan Zhou
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, Chinese Academy of Sciences - Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences Shanghai, China
| | - Lisha Zhu
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, Chinese Academy of Sciences - Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences Shanghai, China
| | - Christine Nardini
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, Chinese Academy of Sciences - Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences Shanghai, China
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Artificial neural network inference (ANNI): a study on gene-gene interaction for biomarkers in childhood sarcomas. PLoS One 2014; 9:e102483. [PMID: 25025207 PMCID: PMC4099183 DOI: 10.1371/journal.pone.0102483] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 06/19/2014] [Indexed: 01/31/2023] Open
Abstract
Objective To model the potential interaction between previously identified biomarkers in children sarcomas using artificial neural network inference (ANNI). Method To concisely demonstrate the biological interactions between correlated genes in an interaction network map, only 2 types of sarcomas in the children small round blue cell tumors (SRBCTs) dataset are discussed in this paper. A backpropagation neural network was used to model the potential interaction between genes. The prediction weights and signal directions were used to model the strengths of the interaction signals and the direction of the interaction link between genes. The ANN model was validated using Monte Carlo cross-validation to minimize the risk of over-fitting and to optimize generalization ability of the model. Results Strong connection links on certain genes (TNNT1 and FNDC5 in rhabdomyosarcoma (RMS); FCGRT and OLFM1 in Ewing’s sarcoma (EWS)) suggested their potency as central hubs in the interconnection of genes with different functionalities. The results showed that the RMS patients in this dataset are likely to be congenital and at low risk of cardiomyopathy development. The EWS patients are likely to be complicated by EWS-FLI fusion and deficiency in various signaling pathways, including Wnt, Fas/Rho and intracellular oxygen. Conclusions The ANN network inference approach and the examination of identified genes in the published literature within the context of the disease highlights the substantial influence of certain genes in sarcomas.
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Tieri P, Nardini C. Signalling pathway database usability: lessons learned. MOLECULAR BIOSYSTEMS 2014; 9:2401-7. [PMID: 23942525 DOI: 10.1039/c3mb70242a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND issues and limitations related to accessibility, understandability and ease of use of signalling pathway databases may hamper or divert research workflow, leading, in the worst case, to the generation of confusing reference frameworks and misinterpretation of experimental results. In an attempt to retrieve signalling pathway data related to a specific set of test genes, we queried and analysed the results from six of the major curated signalling pathway databases: Reactome, PathwayCommons, KEGG, InnateDB, PID, and Wikipathways. FINDINGS although we expected differences - often a desirable feature for the integration of each individual query, we observed variations of exceptional magnitude, with disproportionate quality and quantity of the results. Some of the more remarkable differences can be explained by the diverse conceptual designs and purposes of the databases, the types of data stored and the structure of the query, as well as by missing or erroneous descriptions of the search procedure. To go beyond the mere enumeration of these problems, we identified a number of operational features, in particular inner and cross coherence, which, once quantified, offer objective criteria to choose the best source of information. CONCLUSIONS in silico biology heavily relies on the information stored in databases. To ensure that computational biology mirrors biological reality and offers focused hypotheses to be experimentally validated, coherence of data codification is crucial and yet highly underestimated. We make practical recommendations for the end-user to cope with the current state of the databases as well as for the maintainers of those databases to contribute to the goal of the full enactment of the open data paradigm.
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Affiliation(s)
- Paolo Tieri
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Yue Yang Road 320, Shanghai, P. R. China
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Nacher JC, Keith B, Schwartz JM. Network medicine analysis of chondrocyte proteins towards new treatments of osteoarthritis. Proc Biol Sci 2014; 281:20132907. [PMID: 24430851 DOI: 10.1098/rspb.2013.2907] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Osteoarthritis (OA) is a progressive disorder with high incidence in the ageing human population that still has no treatment currently. This disorder induces the breakdown of articular cartilage, leading to the exposure and damage of bone surfaces. For a global understanding of OA development, the systematic integration of known OA-related proteins with protein-protein interaction (PPI) networks is required. In this work, the OA-related interactome was reconstructed using multiple data sources to have the most up-to-date information on OA-related proteins and their interactions. We then combined emergent concepts in network medicine to detect new unclassified OA-related proteins. The mapping of known OA-related proteins with PPI networks showed that these proteins are locally connected to each other and agglomerated in a large component. To expand this module, we applied a diffusion-based algorithm that probabilistically induces more searches in the vicinity of the seed OA-related proteins. As a result, the 10 topmost ranked proteins were connected to the OA disease module, supporting the local hypothesis. We computed structural modules and selected those that had the highest enrichment of OA-related proteins. The identified molecules show a link between structural topology and disease dysfunctionality. Interestingly, the protein Q6EEV6 was highlighted for OA association by both methods, reinforcing the potential involvement of this protein. These results suggest that similar disease-connected modules may exist in different human disorders, which could lead to systematic identification of genes or proteins that have a joint role in specific disease phenotypes.
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Affiliation(s)
- Jose C Nacher
- Department of Information Science, Faculty of Science, Toho University, , Miyama 2-2-1, Funabashi, Chiba 274-8510, Japan, Faculty of Life Sciences, University of Manchester, , Manchester M13 9PT, UK
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Gupta MK, Singh DB, Shukla R, Misra K. A comprehensive metabolic modeling of thyroid pathway in relation to thyroid pathophysiology and therapeutics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:584-93. [PMID: 24044365 DOI: 10.1089/omi.2013.0007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The thyroid pathway represents a complex interaction of different glands for thyroid hormone synthesis. Thyrotropin releasing hormone is synthesized in the hypothalamus and regulates thyrotropin stimulating hormone gene expression in the pituitary gland. In order to understand the complexity of the thyroid pathways, and using experimental data retrieved from the biomedical literature (e.g., NCBI, HuGE Navigator, Protein Data Bank, and KEGG), we constructed a metabolic map of the thyroid hormone pathway at a molecular level and analyzed it topologically. A total of five hub nodes were predicted in regards to the transcription thyroid receptor (TR), cAMP response element-binding protein (CREB), signal transducer and activator of transcription 3 (STAT 3), nuclear factor kappa-light-chain-enhancer of activated B cells (NFkB), and activator protein 1 (AP-1) as being potentially important in study of thyroid disorders and as novel putative therapeutic drug targets. Notably, the thyroid receptor is a highly connected hub node and currently used as a therapeutic target in hypothyroidism. Our analysis represents the first comprehensive description of the thyroid pathway, which pertains to understanding the function of the protein and gene interaction networks. The findings from this study are therefore informative for pathophysiology and rational therapeutics of thyroid disorders.
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Affiliation(s)
- Manish Kumar Gupta
- 1 Department of Bioinformatics, University Institute of Engineering and Technology, Chhatrapati Shahu Ji Maharaj University, Kanpur, 208024, Uttar Pradesh, India
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Dent JE, Yang X, Nardini C. SPNConverter: a new link between static and dynamic complex network analysis. Bioinformatics 2013; 29:2507-8. [DOI: 10.1093/bioinformatics/btt421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Di Lena P, Wu G, Martelli PL, Casadio R, Nardini C. MIMO: an efficient tool for molecular interaction maps overlap. BMC Bioinformatics 2013; 14:159. [PMID: 23672344 PMCID: PMC3680968 DOI: 10.1186/1471-2105-14-159] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 05/01/2013] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. RESULTS Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. CONCLUSIONS MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways.
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Affiliation(s)
- Pietro Di Lena
- CAS Key Laboratory For Computational Biology Chinese Academy of Sciences - Max Plank Institute Partner Institute for Computational Biology, Yue Yang Road 320, Shanghai, 200031, P.R.C
- Department of Computer Science and Engineering - DISIUniversity of Bologna, Mura Anteo Zamboni 7, Bologna, 40126, Italy
| | - Gang Wu
- CAS Key Laboratory For Computational Biology Chinese Academy of Sciences - Max Plank Institute Partner Institute for Computational Biology, Yue Yang Road 320, Shanghai, 200031, P.R.C
| | - Pier Luigi Martelli
- Biocomputing Group, University of Bologna, Via San Giacomo 9/2, Bologna, 40126, Italy
| | - Rita Casadio
- Biocomputing Group, University of Bologna, Via San Giacomo 9/2, Bologna, 40126, Italy
| | - Christine Nardini
- CAS Key Laboratory For Computational Biology Chinese Academy of Sciences - Max Plank Institute Partner Institute for Computational Biology, Yue Yang Road 320, Shanghai, 200031, P.R.C
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Understanding human diseases with high-throughput quantitative measurement and analysis of molecular signatures. SCIENCE CHINA-LIFE SCIENCES 2013; 56:213-9. [DOI: 10.1007/s11427-013-4445-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 11/19/2012] [Indexed: 12/23/2022]
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Gupta MK, Misra K. Modeling and simulation analysis of propyl-thiouracil (PTU), an anti-thyroid drug on thyroid peroxidase (TPO), thyroid stimulating hormone receptor (TSHR), and sodium iodide (NIS) symporter based on systems biology approach. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s13721-013-0023-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Donate PB, Fornari TA, Macedo C, Cunha TM, Nascimento DCB, Sakamoto-Hojo ET, Donadi EA, Cunha FQ, Passos GA. T cell post-transcriptional miRNA-mRNA interaction networks identify targets associated with susceptibility/resistance to collagen-induced arthritis. PLoS One 2013; 8:e54803. [PMID: 23359619 PMCID: PMC3554629 DOI: 10.1371/journal.pone.0054803] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 12/17/2012] [Indexed: 01/09/2023] Open
Abstract
Background Due to recent studies indicating that the deregulation of microRNAs (miRNAs) in T cells contributes to increased severity of rheumatoid arthritis, we hypothesized that deregulated miRNAs may interact with key mRNA targets controlling the function or differentiation of these cells in this disease. Methodology/Principal Findings To test our hypothesis, we used microarrays to survey, for the first time, the expression of all known mouse miRNAs in parallel with genome-wide mRNAs in thymocytes and naïve and activated peripheral CD3+ T cells from two mouse strains the DBA-1/J strain (MHC-H2q), which is susceptible to collagen induced arthritis (CIA), and the DBA-2/J strain (MHC-H2d), which is resistant. Hierarchical clustering of data showed the several T cell miRNAs and mRNAs differentially expressed between the mouse strains in different stages of immunization with collagen. Bayesian statistics using the GenMir++ algorithm allowed reconstruction of post-transcriptional miRNA-mRNA interaction networks for target prediction. We revealed the participation of miR-500, miR-202-3p and miR-30b*, which established interactions with at least one of the following mRNAs: Rorc, Fas, Fasl, Il-10 and Foxo3. Among the interactions that were validated by calculating the minimal free-energy of base pairing between the miRNA and the 3′UTR of the mRNA target and luciferase assay, we highlight the interaction of miR-30b*-Rorc mRNA because the mRNA encodes a protein implicated in pro-inflammatory Th17 cell differentiation (Rorγt). FACS analysis revealed that Rorγt protein levels and Th17 cell counts were comparatively reduced in the DBA-2/J strain. Conclusions/Significance This result showed that the miRNAs and mRNAs identified in this study represent new candidates regulating T cell function and controlling susceptibility and resistance to CIA.
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Affiliation(s)
- Paula B. Donate
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Thais A. Fornari
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Claudia Macedo
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Thiago M. Cunha
- Inflammation and Pain Group, Department of Pharmacology, Faculty of Medicine of Ribeirão Preto, Ribeirão Preto, Brazil
| | - Daniele C. B. Nascimento
- Inflammation and Pain Group, Department of Pharmacology, Faculty of Medicine of Ribeirão Preto, Ribeirão Preto, Brazil
| | - Elza T. Sakamoto-Hojo
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, Ribeirão Preto, Brazil
| | - Eduardo A. Donadi
- Division of Clinical Immunology, Department of Medicine, Faculty of Medicine of Ribeirão Preto, Ribeirão Preto, Brazil
| | - Fernando Q. Cunha
- Inflammation and Pain Group, Department of Pharmacology, Faculty of Medicine of Ribeirão Preto, Ribeirão Preto, Brazil
| | - Geraldo A. Passos
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- Disciplines of Genetics and Molecular Biology, Department of Morphology, Faculty of Dentistry of Ribeirão Preto, Ribeirão Preto, Brazil
- * E-mail:
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Dent JE, Nardini C. From desk to bed: computational simulations provide indication for rheumatoid arthritis clinical trials. BMC SYSTEMS BIOLOGY 2013; 7:10. [PMID: 23339423 PMCID: PMC3653749 DOI: 10.1186/1752-0509-7-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Accepted: 01/18/2013] [Indexed: 12/19/2022]
Abstract
Background Rheumatoid arthritis (RA) is among the most common human systemic autoimmune diseases, affecting approximately 1% of the population worldwide. To date, there is no cure for the disease and current treatments show undesirable side effects. As the disease affects a growing number of individuals, and during their working age, the gathering of all information able to improve therapies -by understanding their and the disease mechanisms of action- represents an important area of research, benefiting not only patients but also societies. In this direction, network analysis methods have been used in previous work to further our understanding of this complex disease, leading to the identification of CRKL as a potential drug target for treatment of RA. Here, we use computational methods to expand on this work, testing the hypothesis in silico. Results Analysis of the CRKL network -available at http://www.picb.ac.cn/ClinicalGenomicNTW/software.html- allows for investigation of the potential effect of perturbing genes of interest. Within the group of genes that are significantly affected by simulated perturbation of CRKL, we are lead to further investigate the importance of PXN. Our results allow us to (1) refine the hypothesis on CRKL as a novel drug target (2) indicate potential causes of side effects in on-going trials and (3) importantly, provide recommendations with impact on on-going clinical studies. Conclusions Based on a virtual network that collects and connects a large number of the molecules known to be involved in a disease, one can simulate the effects of controlling molecules, allowing for the observation of how this affects the rest of the network. This is important to mimic the effect of a drug, but also to be aware of -and possibly control- its side effects. Using this approach in RA research we have been able to contribute to the field by suggesting molecules to be targeted in new therapies and more importantly, to warrant efficacy, to hypothesise novel recommendations on existing drugs currently under test.
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Affiliation(s)
- Jennifer E Dent
- Group of Clinical Genomic Networks, Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China.
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Kim KJ, Hwang D, Kim WU. Systems Approach to Rheumatoid Arthritis. JOURNAL OF RHEUMATIC DISEASES 2013. [DOI: 10.4078/jrd.2013.20.6.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Ki-Jo Kim
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, The Catholic University of Korea, Suwon, Korea
| | - Daehee Hwang
- Center for Systems Biology of Plant Senescence and Life History, Daegu Gyeongbuk Institute of Science & Technology, Daegu, Korea
| | - Wan-Uk Kim
- Division of Rheumatology, Department of Internal Medicine, St. Vincent's Hospital, The Catholic University of Korea, Suwon, Korea
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Traditional chinese medicine-based network pharmacology could lead to new multicompound drug discovery. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2012; 2012:149762. [PMID: 23346189 PMCID: PMC3541710 DOI: 10.1155/2012/149762] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 10/18/2012] [Indexed: 12/20/2022]
Abstract
Current strategies for drug discovery have reached a bottleneck where the paradigm is generally “one gene, one drug, one disease.” However, using holistic and systemic views, network pharmacology may be the next paradigm in drug discovery. Based on network pharmacology, a combinational drug with two or more compounds could offer beneficial synergistic effects for complex diseases. Interestingly, traditional chinese medicine (TCM) has been practicing holistic views for over 3,000 years, and its distinguished feature is using herbal formulas to treat diseases based on the unique pattern classification. Though TCM herbal formulas are acknowledged as a great source for drug discovery, no drug discovery strategies compatible with the multidimensional complexities of TCM herbal formulas have been developed. In this paper, we highlighted some novel paradigms in TCM-based network pharmacology and new drug discovery. A multiple compound drug can be discovered by merging herbal formula-based pharmacological networks with TCM pattern-based disease molecular networks. Herbal formulas would be a source for multiple compound drug candidates, and the TCM pattern in the disease would be an indication for a new drug.
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Understanding the molecular mechanism of interventions in treating rheumatoid arthritis patients with corresponding traditional chinese medicine patterns based on bioinformatics approach. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2012; 2012:129452. [PMID: 23118783 PMCID: PMC3480696 DOI: 10.1155/2012/129452] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 09/02/2012] [Indexed: 12/22/2022]
Abstract
Better effectiveness would be achieved when interventions are used in treating patients with a specific traditional Chinese medicine (TCM) pattern. In this paper, the effectiveness in treating rheumatoid arthritis (RA) patients in a randomized clinical trial as reanalyzed after the patients were classified into different TCM patterns and the underlying mechanism of how the TCM pattern influences the clinical effectiveness of interventions (TCM and biomedicine therapy) was explored. The pharmacological networks of interventions were builtup with protein and protein interaction analyses based on all the related targeted proteins obtained from PubChem. The underlying mechanism was explored by merging the pharmacological networks with the molecular networks of TCM cold and hot patterns in RA. The results show that the TCM therapy is better in treating the RA patients with TCM hot pattern, and the biomedical therapy is better in the RA patients with cold pattern. The pharmacological network of TCM intervention is merged well with the molecular network of TCM hot pattern, and the pharmacological network of biomedical therapy is merged well with the network of cold pattern. The finding indicates that molecular network analysis could give insight into the full understanding of the underlying mechanism of how TCM pattern impacts the efficacy.
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Jiang M, Lu C, Zhang C, Yang J, Tan Y, Lu A, Chan K. Syndrome differentiation in modern research of traditional Chinese medicine. JOURNAL OF ETHNOPHARMACOLOGY 2012; 140:634-642. [PMID: 22322251 DOI: 10.1016/j.jep.2012.01.033] [Citation(s) in RCA: 238] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/22/2012] [Accepted: 01/22/2012] [Indexed: 05/31/2023]
Abstract
Syndrome differentiation (Bian Zheng) in traditional Chinese medicine (TCM) is the comprehensive analysis of clinical information gained by the four main diagnostic TCM procedures: observation, listening, questioning, and pulse analysis, and it is used to guide the choice of treatment either by acupuncture and/or TCM herbal formulae, that is, Fufang. TCM syndrome differentiation can be used for further stratification of the patients' conditions with certain disease, identified by orthodox medical diagnosis, which could help the improvement of efficacy of the selected intervention. In modern TCM research it is possible to integrate syndrome differentiation with orthodox medical diagnosis leading to new scientific findings in overall medical diagnosis and treatment. In this review, the focus is to screen published evidence on the role of syndrome differentiation in modern TCM research with particular emphasis on basic and clinical research as well as, pharmacological evaluation of TCM herbal formulary for drug discovery.
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Affiliation(s)
- Miao Jiang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
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Tieri P, Termanini A, Bellavista E, Salvioli S, Capri M, Franceschi C. Charting the NF-κB pathway interactome map. PLoS One 2012; 7:e32678. [PMID: 22403694 PMCID: PMC3293857 DOI: 10.1371/journal.pone.0032678] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/28/2012] [Indexed: 01/05/2023] Open
Abstract
Inflammation is part of a complex physiological response to harmful stimuli and pathogenic stress. The five components of the Nuclear Factor κB (NF-κB) family are prominent mediators of inflammation, acting as key transcriptional regulators of hundreds of genes. Several signaling pathways activated by diverse stimuli converge on NF-κB activation, resulting in a regulatory system characterized by high complexity. It is increasingly recognized that the number of components that impinges upon phenotypic outcomes of signal transduction pathways may be higher than those taken into consideration from canonical pathway representations. Scope of the present analysis is to provide a wider, systemic picture of the NF-κB signaling system. Data from different sources such as literature, functional enrichment web resources, protein-protein interaction and pathway databases have been gathered, curated, integrated and analyzed in order to reconstruct a single, comprehensive picture of the proteins that interact with, and participate to the NF-κB activation system. Such a reconstruction shows that the NF-κB interactome is substantially different in quantity and quality of components with respect to canonical representations. The analysis highlights that several neglected but topologically central proteins may play a role in the activation of NF-κB mediated responses. Moreover the interactome structure fits with the characteristics of a bow tie architecture. This interactome is intended as an open network resource available for further development, refinement and analysis.
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Affiliation(s)
- Paolo Tieri
- CIG Luigi Galvani Interdept Center, University of Bologna, Bologna, Italy.
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Abstract
Understanding complex biological systems requires extensive support from software tools. Such tools are needed at each step of a systems biology computational workflow, which typically consists of data handling, network inference, deep curation, dynamical simulation and model analysis. In addition, there are now efforts to develop integrated software platforms, so that tools that are used at different stages of the workflow and by different researchers can easily be used together. This Review describes the types of software tools that are required at different stages of systems biology research and the current options that are available for systems biology researchers. We also discuss the challenges and prospects for modelling the effects of genetic changes on physiology and the concept of an integrated platform.
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Bakir-Gungor B, Sezerman OU. A new methodology to associate SNPs with human diseases according to their pathway related context. PLoS One 2011; 6:e26277. [PMID: 22046267 PMCID: PMC3201947 DOI: 10.1371/journal.pone.0026277] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 09/23/2011] [Indexed: 11/18/2022] Open
Abstract
Genome-wide association studies (GWAS) with hundreds of żthousands of single nucleotide polymorphisms (SNPs) are popular strategies to reveal the genetic basis of human complex diseases. Despite many successes of GWAS, it is well recognized that new analytical approaches have to be integrated to achieve their full potential. Starting with a list of SNPs, found to be associated with disease in GWAS, here we propose a novel methodology to devise functionally important KEGG pathways through the identification of genes within these pathways, where these genes are obtained from SNP analysis. Our methodology is based on functionalization of important SNPs to identify effected genes and disease related pathways. We have tested our methodology on WTCCC Rheumatoid Arthritis (RA) dataset and identified: i) previously known RA related KEGG pathways (e.g., Toll-like receptor signaling, Jak-STAT signaling, Antigen processing, Leukocyte transendothelial migration and MAPK signaling pathways); ii) additional KEGG pathways (e.g., Pathways in cancer, Neurotrophin signaling, Chemokine signaling pathways) as associated with RA. Furthermore, these newly found pathways included genes which are targets of RA-specific drugs. Even though GWAS analysis identifies 14 out of 83 of those drug target genes; newly found functionally important KEGG pathways led to the discovery of 25 out of 83 genes, known to be used as drug targets for the treatment of RA. Among the previously known pathways, we identified additional genes associated with RA (e.g. Antigen processing and presentation, Tight junction). Importantly, within these pathways, the associations between some of these additionally found genes, such as HLA-C, HLA-G, PRKCQ, PRKCZ, TAP1, TAP2 and RA were verified by either OMIM database or by literature retrieved from the NCBI PubMed module. With the whole-genome sequencing on the horizon, we show that the full potential of GWAS can be achieved by integrating pathway and network-oriented analysis and prior knowledge from functional properties of a SNP.
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Affiliation(s)
- Burcu Bakir-Gungor
- Biological Sciences and Bioengineering, Faculty of Engineering, Sabancı University, İstanbul, Turkey.
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Yang X, Ye Y, Wang G, Huang H, Yu D, Liang S. VeryGene: linking tissue-specific genes to diseases, drugs, and beyond for knowledge discovery. Physiol Genomics 2011; 43:457-60. [PMID: 21245417 DOI: 10.1152/physiolgenomics.00178.2010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
In addition to many other genes, tissue-specific genes (TSGs) represent a set of genes of great importance for human physiology. However, the links among TSGs, diseases, and potential therapeutic agents are often missing, hidden, or too scattered to find. There is a need to establish a knowledgebase for researchers to share this and additional information in order to speed up discovery and clinical practice. As an initiative toward systems biology, the VeryGene web server was developed to fill this gap. A significant effort has been made to integrate TSGs from two large-scale data analyses with respective information on subcellular localization, Gene Ontology, Reactome, KEGG pathway, Mouse Genome Informatics (MGI) Mammalian Phenotype, disease association, and targeting drugs. The current release carefully selected 3,960 annotated TSGs derived from 127 normal human tissues and cell types, including 5,672 gene-disease and 2,171 drug-target relationships. In addition to being a specialized source for TSGs, VeryGene can be used as a discovery tool by generating novel inferences. Some inherently useful but hidden relations among genes, diseases, drugs, and other important aspects can be inferred to form testable hypotheses. VeryGene is available online at http://www.verygene.com.
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Affiliation(s)
- Xiaoqin Yang
- Institute of Genetic Engineering, Southern Medical University, Guangzhou, Guangdong Province, China
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Rossin EJ, Lage K, Raychaudhuri S, Xavier RJ, Tatar D, Benita Y, Cotsapas C, Daly MJ. Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet 2011; 7:e1001273. [PMID: 21249183 PMCID: PMC3020935 DOI: 10.1371/journal.pgen.1001273] [Citation(s) in RCA: 407] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 12/09/2010] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) have defined over 150 genomic regions unequivocally containing variation predisposing to immune-mediated disease. Inferring disease biology from these observations, however, hinges on our ability to discover the molecular processes being perturbed by these risk variants. It has previously been observed that different genes harboring causal mutations for the same Mendelian disease often physically interact. We sought to evaluate the degree to which this is true of genes within strongly associated loci in complex disease. Using sets of loci defined in rheumatoid arthritis (RA) and Crohn's disease (CD) GWAS, we build protein-protein interaction (PPI) networks for genes within associated loci and find abundant physical interactions between protein products of associated genes. We apply multiple permutation approaches to show that these networks are more densely connected than chance expectation. To confirm biological relevance, we show that the components of the networks tend to be expressed in similar tissues relevant to the phenotypes in question, suggesting the network indicates common underlying processes perturbed by risk loci. Furthermore, we show that the RA and CD networks have predictive power by demonstrating that proteins in these networks, not encoded in the confirmed list of disease associated loci, are significantly enriched for association to the phenotypes in question in extended GWAS analysis. Finally, we test our method in 3 non-immune traits to assess its applicability to complex traits in general. We find that genes in loci associated to height and lipid levels assemble into significantly connected networks but did not detect excess connectivity among Type 2 Diabetes (T2D) loci beyond chance. Taken together, our results constitute evidence that, for many of the complex diseases studied here, common genetic associations implicate regions encoding proteins that physically interact in a preferential manner, in line with observations in Mendelian disease.
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Affiliation(s)
- Elizabeth J. Rossin
- Center for Human Genetics Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Health Science and Technology MD Program, Harvard University and Massachusetts Institute of Technology, Boston, Massachusetts, United States of America
- Harvard Biological and Biomedical Sciences Program, Harvard University, Boston, Massachusetts, United States of America
| | - Kasper Lage
- Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Soumya Raychaudhuri
- Center for Human Genetics Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts, United States of America
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Ramnik J. Xavier
- Center for Human Genetics Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Diana Tatar
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Yair Benita
- Center for Human Genetics Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | | | - Chris Cotsapas
- Center for Human Genetics Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Mark J. Daly
- Center for Human Genetics Research and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, The Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Health Science and Technology MD Program, Harvard University and Massachusetts Institute of Technology, Boston, Massachusetts, United States of America
- Harvard Biological and Biomedical Sciences Program, Harvard University, Boston, Massachusetts, United States of America
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Zhu Y, Zhong Z, Liu Z. Lentiviral vector-mediated upregulation of let-7a inhibits gastric carcinoma cell growth in vitro and in vivo. Scand J Gastroenterol 2011; 46:53-9. [PMID: 20809749 DOI: 10.3109/00365521.2010.510566] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Let-7a, a molecule that is reduced in various cancers, has been associated with cell growth and proliferation. Upregulation of let-7a may inhibit tumor cell growth. To verify this hypothesis, let-7a gene overexpression was studied in gastric cancer cells in vitro and in vivo. MATERIAL AND METHODS A lentiviral system harboring both enhanced green fluorescent protein reporter gene and the let-7a short hairpin RNA expression cassette was firstly constructed. Then the stable let-7a gene overexpression SGC-7901 cells were established and real-time RT-PCR analysis was used to evaluate the expression of the let-7a gene. Their growth-inhibiting, cell cycle arrest characteristics were identified. RESULTS In SGC-7901/let-7a cells, let-7a expression was significantly increased. Their proliferation was obviously retarded and the cell cycle changed with increased G0/G1 arrest and decreased S phase. In animal experiments, SGC-7901/let-7a cell xenografts demonstrated growth suppression compared to parental or control gastric cancer cell xenografts. CONCLUSION The results demonstrated that lentiviral vector was capable of upregulating let-7a, resulting in impressive anticancer effects. It offers a powerful new strategy for the development of novel therapeutic interventions to treat human gastric carcinomas.
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Affiliation(s)
- Yimin Zhu
- Department of General Surgery, The Second Hospital of Jiaxing, Jiaxing, PR China
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