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Costa H, Xu X, Overbeek G, Vasaikar S, Patro CPK, Kostopoulou ON, Jung M, Shafi G, Ananthaseshan S, Tsipras G, Davoudi B, Mohammad AA, Lam H, Strååt K, Wilhelmi V, Shang M, Tegner J, Tong JC, Wong KT, Söderberg-Naucler C, Yaiw KC. Human cytomegalovirus may promote tumour progression by upregulating arginase-2. Oncotarget 2018; 7:47221-47231. [PMID: 27363017 PMCID: PMC5216936 DOI: 10.18632/oncotarget.9722] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 05/14/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Both arginase (ARG2) and human cytomegalovirus (HCMV) have been implicated in tumorigenesis. However, the role of ARG2 in the pathogenesis of glioblastoma (GBM) and the HCMV effects on ARG2 are unknown. We hypothesize that HCMV may contribute to tumorigenesis by increasing ARG2 expression. RESULTS ARG2 promotes tumorigenesis by increasing cellular proliferation, migration, invasion and vasculogenic mimicry in GBM cells, at least in part due to overexpression of MMP2/9. The nor-NOHA significantly reduced migration and tube formation of ARG2-overexpressing cells. HCMV immediate-early proteins (IE1/2) or its downstream pathways upregulated the expression of ARG2 in U-251 MG cells. Immunostaining of GBM tissue sections confirmed the overexpression of ARG2, consistent with data from subsets of Gene Expression Omnibus. Moreover, higher levels of ARG2 expression tended to be associated with poorer survival in GBM patient by analyzing data from TCGA. METHODS The role of ARG2 in tumorigenesis was examined by proliferation-, migration-, invasion-, wound healing- and tube formation assays using an ARG2-overexpressing cell line and ARG inhibitor, N (omega)-hydroxy-nor-L-arginine (nor-NOHA) and siRNA against ARG2 coupled with functional assays measuring MMP2/9 activity, VEGF levels and nitric oxide synthase activity. Association between HCMV and ARG2 were examined in vitro with 3 different GBM cell lines, and ex vivo with immunostaining on GBM tissue sections. The viral mechanism mediating ARG2 induction was examined by siRNA approach. Correlation between ARG2 expression and patient survival was extrapolated from bioinformatics analysis on data from The Cancer Genome Atlas (TCGA). CONCLUSIONS ARG2 promotes tumorigenesis, and HCMV may contribute to GBM pathogenesis by upregulating ARG2.
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Affiliation(s)
- Helena Costa
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Xinling Xu
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Gitta Overbeek
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Suhas Vasaikar
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - C Pawan K Patro
- Social & Cognitive Computing Department, Institute of High Performance Computing, Agency for Science, Technology and Research, Singapore
| | - Ourania N Kostopoulou
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Masany Jung
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Gowhar Shafi
- Department of Genomics and Bioinformatics, Positive Bioscience, Mumbai, India
| | - Sharan Ananthaseshan
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Giorgos Tsipras
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Belghis Davoudi
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Abdul-Aleem Mohammad
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Hoyin Lam
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden.,Present affiliation: Division of Cancer Studies, King's College London, London, UK
| | - Klas Strååt
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden.,Division of Gene Technology, School of Biotechnology, Science for Life Laboratory, Royal Institute of Technology (KTH), Solna, Sweden
| | - Vanessa Wilhelmi
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Mingmei Shang
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Tegner
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Joo Chuan Tong
- Social & Cognitive Computing Department, Institute of High Performance Computing, Agency for Science, Technology and Research, Singapore
| | - Kum Thong Wong
- Department of Pathology, Faculty of Medicine, University of Malaya, Malaysia
| | - Cecilia Söderberg-Naucler
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
| | - Koon-Chu Yaiw
- Cell and Molecular Immunology, Department of Medicine, Center for Molecular Medicine, Unit for Experimental Cardiovascular Research and Department of Neurology, Karolinska Institutet, Stockholm, Sweden
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Vasaikar S, Tsipras G, Landázuri N, Costa H, Wilhelmi V, Scicluna P, Cui HL, Mohammad AA, Davoudi B, Shang M, Ananthaseshan S, Strååt K, Stragliotto G, Rahbar A, Wong KT, Tegner J, Yaiw KC, Söderberg-Naucler C. Overexpression of endothelin B receptor in glioblastoma: a prognostic marker and therapeutic target? BMC Cancer 2018; 18:154. [PMID: 29409474 PMCID: PMC5801893 DOI: 10.1186/s12885-018-4012-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 01/22/2018] [Indexed: 01/07/2023] Open
Abstract
Background Glioblastoma (GBM) is the most common malignant brain tumor with median survival of 12-15 months. Owing to uncertainty in clinical outcome, additional prognostic marker(s) apart from existing markers are needed. Since overexpression of endothelin B receptor (ETBR) has been demonstrated in gliomas, we aimed to test whether ETBR is a useful prognostic marker in GBM and examine if the clinically available endothelin receptor antagonists (ERA) could be useful in the disease treatment. Methods Data from The Cancer Genome Atlas and the Gene Expression Omnibus database were analyzed to assess ETBR expression. For survival analysis, glioblastoma samples from 25 Swedish patients were immunostained for ETBR, and the findings were correlated with clinical history. The druggability of ETBR was assessed by protein-protein interaction network analysis. ERAs were analyzed for toxicity in in vitro assays with GBM and breast cancer cells. Results By bioinformatics analysis, ETBR was found to be upregulated in glioblastoma patients, and its expression levels were correlated with reduced survival. ETBR interacts with key proteins involved in cancer pathogenesis, suggesting it as a druggable target. In vitro viability assays showed that ERAs may hold promise to treat glioblastoma and breast cancer. Conclusions ETBR is overexpressed in glioblastoma and other cancers and may be a prognostic marker in glioblastoma. ERAs may be useful for treating cancer patients. Electronic supplementary material The online version of this article (10.1186/s12885-018-4012-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suhas Vasaikar
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Giorgos Tsipras
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Natalia Landázuri
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Helena Costa
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Vanessa Wilhelmi
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Patrick Scicluna
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Huanhuan L Cui
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Abdul-Aleem Mohammad
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Belghis Davoudi
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Mingmei Shang
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sharan Ananthaseshan
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Klas Strååt
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Afsar Rahbar
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden
| | - Kum Thong Wong
- Department of Pathology, University of Malaya, Kuala Lumpur, Malaysia
| | - Jesper Tegner
- Unit of Computational Medicine, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden.,Biological and Environmental Sciences and Engineering Division (BESE), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Koon-Chu Yaiw
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden.
| | - Cecilia Söderberg-Naucler
- Cell and Molecular Immunology, Experimental Cardiovascular Unit, Departments of Medicine and Neurology, Center for Molecular Medicine, Karolinska Institutet, SE-171 76, Stockholm, Sweden.
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Kannan V, Swartz F, Kiani NA, Silberberg G, Tsipras G, Gomez-Cabrero D, Alexanderson K, Tegnèr J. Conditional Disease Development extracted from Longitudinal Health Care Cohort Data using Layered Network Construction. Sci Rep 2016; 6:26170. [PMID: 27211115 PMCID: PMC4876508 DOI: 10.1038/srep26170] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 04/27/2016] [Indexed: 11/16/2022] Open
Abstract
Health care data holds great promise to be used in clinical decision support systems. However, frequent near-synonymous diagnoses recorded separately, as well as the sheer magnitude and complexity of the disease data makes it challenging to extract non-trivial conclusions beyond confirmatory associations from such a web of interactions. Here we present a systematic methodology to derive statistically valid conditional development of diseases. To this end we utilize a cohort of 5,512,469 individuals followed over 13 years at inpatient care, including data on disability pension and cause of death. By introducing a causal information fraction measure and taking advantage of the composite structure in the ICD codes, we extract an effective directed lower dimensional network representation (100 nodes and 130 edges) of our cohort. Unpacking composite nodes into bipartite graphs retrieves, for example, that individuals with behavioral disorders are more likely to be followed by prescription drug poisoning episodes, whereas women with leiomyoma were more likely to subsequently experience endometriosis. The conditional disease development represent putative causal relations, indicating possible novel clinical relationships and pathophysiological associations that have not been explored yet.
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Affiliation(s)
- Venkateshan Kannan
- Computational Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, SE-17176, Stockholm, Sweden.,Center for Molecular Medicine, L8:05, SE-17176, Stockholm, Karolinska Institutet, Sweden
| | - Fredrik Swartz
- Computational Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, SE-17176, Stockholm, Sweden.,Center for Molecular Medicine, L8:05, SE-17176, Stockholm, Karolinska Institutet, Sweden.,Division of Insurance Medicine, Department of Clinical Neuroscience, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Narsis A Kiani
- Computational Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, SE-17176, Stockholm, Sweden.,Center for Molecular Medicine, L8:05, SE-17176, Stockholm, Karolinska Institutet, Sweden
| | - Gilad Silberberg
- Computational Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, SE-17176, Stockholm, Sweden.,Center for Molecular Medicine, L8:05, SE-17176, Stockholm, Karolinska Institutet, Sweden
| | - Giorgos Tsipras
- Computational Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, SE-17176, Stockholm, Sweden.,Center for Molecular Medicine, L8:05, SE-17176, Stockholm, Karolinska Institutet, Sweden
| | - David Gomez-Cabrero
- Computational Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, SE-17176, Stockholm, Sweden.,Center for Molecular Medicine, L8:05, SE-17176, Stockholm, Karolinska Institutet, Sweden
| | - Kristina Alexanderson
- Division of Insurance Medicine, Department of Clinical Neuroscience, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Jesper Tegnèr
- Computational Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, SE-17176, Stockholm, Sweden.,Center for Molecular Medicine, L8:05, SE-17176, Stockholm, Karolinska Institutet, Sweden.,Unit of Clinical Epidemiology, Department of Medicine, Karolinska University Hospital L8, SE-17176, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
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Abugessaisa I, Saevarsdottir S, Tsipras G, Lindblad S, Sandin C, Nikamo P, Ståhle M, Malmström V, Klareskog L, Tegnér J. Accelerating translational research by clinically driven development of an informatics platform--a case study. PLoS One 2014; 9:e104382. [PMID: 25203647 PMCID: PMC4159182 DOI: 10.1371/journal.pone.0104382] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 07/14/2014] [Indexed: 12/21/2022] Open
Abstract
Translational medicine is becoming increasingly dependent upon data generated from health care, clinical research, and molecular investigations. This increasing rate of production and diversity in data has brought about several challenges, including the need to integrate fragmented databases, enable secondary use of patient clinical data from health care in clinical research, and to create information systems that clinicians and biomedical researchers can readily use. Our case study effectively integrates requirements from the clinical and biomedical researcher perspectives in a translational medicine setting. Our three principal achievements are (a) a design of a user-friendly web-based system for management and integration of clinical and molecular databases, while adhering to proper de-identification and security measures; (b) providing a real-world test of the system functionalities using clinical cohorts; and (c) system integration with a clinical decision support system to demonstrate system interoperability. We engaged two active clinical cohorts, 747 psoriasis patients and 2001 rheumatoid arthritis patients, to demonstrate efficient query possibilities across the data sources, enable cohort stratification, extract variation in antibody patterns, study biomarker predictors of treatment response in RA patients, and to explore metabolic profiles of psoriasis patients. Finally, we demonstrated system interoperability by enabling integration with an established clinical decision support system in health care. To assure the usefulness and usability of the system, we followed two approaches. First, we created a graphical user interface supporting all user interactions. Secondly we carried out a system performance evaluation study where we measured the average response time in seconds for active users, http errors, and kilobits per second received and sent. The maximum response time was found to be 0.12 seconds; no server or client errors of any kind were detected. In conclusion, the system can readily be used by clinicians and biomedical researchers in a translational medicine setting.
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Affiliation(s)
- Imad Abugessaisa
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Saedis Saevarsdottir
- Rheumatology Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Giorgos Tsipras
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Staffan Lindblad
- Medical Management Center, Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, Stockholm, Sweden
| | - Charlotta Sandin
- Rheumatology Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pernilla Nikamo
- Dermatology and Venereology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Mona Ståhle
- Dermatology and Venereology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Vivianne Malmström
- Rheumatology Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Tegnér
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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