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Uzuner D, Akkoç Y, Peker N, Pir P, Gözüaçık D, Çakır T. Transcriptional landscape of cellular networks reveal interactions driving the dormancy mechanisms in cancer. Sci Rep 2021; 11:15806. [PMID: 34349126 PMCID: PMC8339123 DOI: 10.1038/s41598-021-94005-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/28/2021] [Indexed: 11/22/2022] Open
Abstract
Primary cancer cells exert unique capacity to disseminate and nestle in distant organs. Once seeded in secondary sites, cancer cells may enter a dormant state, becoming resistant to current treatment approaches, and they remain silent until they reactivate and cause overt metastases. To illuminate the complex mechanisms of cancer dormancy, 10 transcriptomic datasets from the literature enabling 21 dormancy–cancer comparisons were mapped on protein–protein interaction networks and gene-regulatory networks to extract subnetworks that are enriched in significantly deregulated genes. The genes appearing in the subnetworks and significantly upregulated in dormancy with respect to proliferative state were scored and filtered across all comparisons, leading to a dormancy–interaction network for the first time in the literature, which includes 139 genes and 1974 interactions. The dormancy interaction network will contribute to the elucidation of cellular mechanisms orchestrating cancer dormancy, paving the way for improvements in the diagnosis and treatment of metastatic cancer.
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Affiliation(s)
- Dilara Uzuner
- Department of Bioengineering, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Yunus Akkoç
- Koç University Research Center for Translational Medicine (KUTTAM), Zeytinburnu, 34010, Istanbul, Turkey
| | - Nesibe Peker
- Koç University Research Center for Translational Medicine (KUTTAM), Zeytinburnu, 34010, Istanbul, Turkey
| | - Pınar Pir
- Department of Bioengineering, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Devrim Gözüaçık
- Koç University Research Center for Translational Medicine (KUTTAM), Zeytinburnu, 34010, Istanbul, Turkey.,Koç University School of Medicine, Sarıyer , 34450, Istanbul, Turkey.,SUNUM Nanotechnology Research and Application Center, Tuzla, 34956, Istanbul, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, 41400, Kocaeli, Turkey.
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2
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Ehmsen S, Ditzel HJ. Signaling pathways essential for triple-negative breast cancer stem-like cells. Stem Cells 2020; 39:133-143. [PMID: 33211379 DOI: 10.1002/stem.3301] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/31/2020] [Indexed: 12/24/2022]
Abstract
Since the discovery of breast cancer stem cells (CSCs), a significant effort has been made to identify and characterize these cells. It is a generally believe that CSCs play an important role in cancer initiation, therapy resistance, and progression of triple-negative breast cancer (TNBC), an aggressive breast cancer subtype with poor prognosis. Thus, therapies targeting these cells would be a valuable addition to standard treatments that primarily target more differentiated, rapidly dividing TNBC cells. Although several cell surface and intracellular proteins have been described as biomarkers for CSCs, none of these are specific to this population of cells. Recent research is moving toward cellular signaling pathways as targets and biomarkers for CSCs. The WNT pathway, the nuclear factor-kappa B (NF-κB) pathway, and the cholesterol biosynthesis pathway have recently been identified to play a key role in proliferation, survival, and differentiation of CSCs, including those of breast cancer. In this review, we assess recent findings related to these three pathways in breast CSC, with particular focus on TNBC CSCs, and discuss how targeting these pathways, in combination with current standard of care, might prove effective and improve the prognosis of TNBC patients.
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Affiliation(s)
- Sidse Ehmsen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark.,Research Unit of Oncology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Academy of Geriatric Cancer Research (AgeCare), Odense University Hospital, Odense, Denmark
| | - Henrik J Ditzel
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.,Department of Oncology, Odense University Hospital, Odense, Denmark.,Research Unit of Oncology, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Academy of Geriatric Cancer Research (AgeCare), Odense University Hospital, Odense, Denmark
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3
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Flosbach M, Oberle SG, Scherer S, Zecha J, von Hoesslin M, Wiede F, Chennupati V, Cullen JG, List M, Pauling JK, Baumbach J, Kuster B, Tiganis T, Zehn D. PTPN2 Deficiency Enhances Programmed T Cell Expansion and Survival Capacity of Activated T Cells. Cell Rep 2020; 32:107957. [PMID: 32726622 PMCID: PMC7408006 DOI: 10.1016/j.celrep.2020.107957] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/20/2020] [Accepted: 07/02/2020] [Indexed: 01/18/2023] Open
Abstract
Manipulating molecules that impact T cell receptor (TCR) or cytokine signaling, such as the protein tyrosine phosphatase non-receptor type 2 (PTPN2), has significant potential for advancing T cell-based immunotherapies. Nonetheless, it remains unclear how PTPN2 impacts the activation, survival, and memory formation of T cells. We find that PTPN2 deficiency renders cells in vivo and in vitro less dependent on survival-promoting cytokines, such as interleukin (IL)-2 and IL-15. Remarkably, briefly ex vivo-activated PTPN2-deficient T cells accumulate in 3- to 11-fold higher numbers following transfer into unmanipulated, antigen-free mice. Moreover, the absence of PTPN2 augments the survival of short-lived effector T cells and allows them to robustly re-expand upon secondary challenge. Importantly, we find no evidence for impaired effector function or memory formation. Mechanistically, PTPN2 deficiency causes broad changes in the expression and phosphorylation of T cell expansion and survival-associated proteins. Altogether, our data underline the therapeutic potential of targeting PTPN2 in T cell-based therapies to augment the number and survival capacity of antigen-specific T cells.
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Affiliation(s)
- Markus Flosbach
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Susanne G Oberle
- Division of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Stefanie Scherer
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany; Division of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Madlaina von Hoesslin
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Florian Wiede
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Vijaykumar Chennupati
- Division of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Jolie G Cullen
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Josch K Pauling
- ZD.B Junior Research Group LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Tony Tiganis
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Dietmar Zehn
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany; Division of Immunology and Allergy, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland.
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4
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Stalidzans E, Zanin M, Tieri P, Castiglione F, Polster A, Scheiner S, Pahle J, Stres B, List M, Baumbach J, Lautizi M, Van Steen K, Schmidt HH. Mechanistic Modeling and Multiscale Applications for Precision Medicine: Theory and Practice. NETWORK AND SYSTEMS MEDICINE 2020. [DOI: 10.1089/nsm.2020.0002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Egils Stalidzans
- Computational Systems Biology Group, University of Latvia, Riga, Latvia
- Latvian Biomedical Reasearch and Study Centre, Riga, Latvia
| | - Massimiliano Zanin
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
| | - Paolo Tieri
- CNR National Research Council, IAC Institute for Applied Computing, Rome, Italy
| | - Filippo Castiglione
- CNR National Research Council, IAC Institute for Applied Computing, Rome, Italy
| | | | - Stefan Scheiner
- Institute for Mechanics of Materials and Structures, Vienna University of Technology, Vienna, Austria
| | - Jürgen Pahle
- BioQuant, Heidelberg University, Heidelberg, Germany
| | - Blaž Stres
- Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia
- Department of Automation, Biocybernetics and Robotics, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Markus List
- Big Data in BioMedicine Research Group, Chair of Experimental Bioinformatics, TUM School of Weihenstephan, Technical University of Munich, Freising, Germany
| | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Weihenstephan, Technical University of Munich, Freising, Germany
| | - Manuela Lautizi
- Computational Systems Medicine Research Group, Chair of Experimental Bioinformatics, TUM School of Weihenstephan, Technical University of Munich, Freising, Germany
| | - Kristel Van Steen
- BIO-Systems Genetics, GIGA-R, University of Liège, Liège, Belgium
- BIO3—Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Harald H.H.W. Schmidt
- Department of Pharmacology and Personalised Medicine, Faculty of Health, Medicine and Life Science, Maastricht University, Maastricht, The Netherlands
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5
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Yu Y, Zhou J, Gong C, Long Z, Tian J, Zhu L, Li J, Yu H, Wang F, Zhao Y. Dietary factors and microRNA-binding site polymorphisms in the IL13 gene: risk and prognosis analysis of colorectal cancer. Oncotarget 2018; 8:47379-47388. [PMID: 28537887 PMCID: PMC5564572 DOI: 10.18632/oncotarget.17649] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/21/2017] [Indexed: 02/06/2023] Open
Abstract
Long-term dietary intake influences the structure and activity of microorganisms residing in the human gut. The immune response and gut microbiota have a mutual influence on the risk of colorectal cancer (CRC). This study examines the association of gut microbiota–related dietary factors and polymorphisms in the microRNA-binding site of the interleukin 13 gene (IL13) with the risk and prognosis of CRC. Three polymorphisms (rs847, rs848, and rs1295685) were selected for genotyping in a case–control study (513 cases, 572 controls), and 386 CRC patients were followed up. Two dietary factors closely related with gut microbiota (allium vegetables, overnight meal) were significantly associated with CRC development. Although the three SNPs showed no statistically significant associations with the risk and prognosis of CRC, a significant antagonistic interaction was found between rs848 (G–T) and allium vegetable intake (ORi (odds ratio of interaction), 0.92; 95% CI (confidence interval): 0.86, 0.99; P = 0.03); moreover, significant combined and synergistic interactions were observed for all three SNPs and overnight meal intake. This is the first report of significant combined and interactive effects between dietary factors and polymorphisms in the microRNA binding site of IL13 in CRC and may provide direct guidance on intake of allium vegetable and overnight meals for individuals with specific genetic variants of IL13 to modify their susceptibility to CRC.
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Affiliation(s)
- Yanming Yu
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Junde Zhou
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Chen Gong
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Zhiping Long
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Jingshen Tian
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Lin Zhu
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Jing Li
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Hongyuan Yu
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Fan Wang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
| | - Yashuang Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, P. R. China
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6
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Stefania DD, Vergara D. The Many-Faced Program of Epithelial-Mesenchymal Transition: A System Biology-Based View. Front Oncol 2017; 7:274. [PMID: 29181337 PMCID: PMC5694026 DOI: 10.3389/fonc.2017.00274] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 10/31/2017] [Indexed: 12/16/2022] Open
Abstract
System biology uses a range of experimental and statistical methods to dissect complex processes that results from alterations in biological models. Given the complexity of the epithelial–mesenchymal transition (EMT) program, system biology represents a promising approach to understanding its fine molecular regulation by the interpretation of high-throughput datasets. Herein, we review recent contributions of system biology applied to the field of EMT physiology and illustrate the importance of these approaches to model biological networks that are perturbed during the transition. Together, these results allowed the definition of an EMT signature across different tumor types, the identification of dysregulated processes and new modules of regulation, making possible to reveal the EMT molecular visage underneath.
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Affiliation(s)
- De Domenico Stefania
- Biotecgen, Department of Biological and Environmental Sciences and Technologies, Lecce, Italy.,Institute of Sciences of Food Production, National Research Council, Lecce, Italy
| | - Daniele Vergara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
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7
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Christensen AG, Ehmsen S, Terp MG, Batra R, Alcaraz N, Baumbach J, Noer JB, Moreira J, Leth-Larsen R, Larsen MR, Ditzel HJ. Elucidation of Altered Pathways in Tumor-Initiating Cells of Triple-Negative Breast Cancer: A Useful Cell Model System for Drug Screening. Stem Cells 2017; 35:1898-1912. [DOI: 10.1002/stem.2654] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 05/31/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Anne G. Christensen
- Department of Cancer and Inflammation Research; Institute of Molecular Medicine, University of Southern Denmark; Odense Denmark
| | - Sidse Ehmsen
- Department of Cancer and Inflammation Research; Institute of Molecular Medicine, University of Southern Denmark; Odense Denmark
| | - Mikkel G. Terp
- Department of Cancer and Inflammation Research; Institute of Molecular Medicine, University of Southern Denmark; Odense Denmark
| | - Richa Batra
- Department of Mathematics and Computer Science; Faculty of Science, University of Southern Denmark; Odense Denmark
| | - Nicolas Alcaraz
- Department of Mathematics and Computer Science; Faculty of Science, University of Southern Denmark; Odense Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science; Faculty of Science, University of Southern Denmark; Odense Denmark
| | - Julie B. Noer
- Section for Molecular Disease Biology, Department of Veterinary Disease Biology; Section for Molecular Disease Biology, University of Copenhagen; Frederiksberg C Denmark
| | - José Moreira
- Section for Molecular Disease Biology, Department of Veterinary Disease Biology; Section for Molecular Disease Biology, University of Copenhagen; Frederiksberg C Denmark
| | - Rikke Leth-Larsen
- Department of Cancer and Inflammation Research; Institute of Molecular Medicine, University of Southern Denmark; Odense Denmark
| | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Odense Denmark
- Department of Clinical Biochemistry and Pharmacology; Centre for Clinical Proteomics, Odense University Hospital; Odense Denmark
| | - Henrik J. Ditzel
- Department of Cancer and Inflammation Research; Institute of Molecular Medicine, University of Southern Denmark; Odense Denmark
- Department of Oncology; Odense University Hospital; Odense Denmark
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8
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Girotra S, Yeghiazaryan K, Golubnitschaja O. Potential biomarker panels in overall breast cancer management: advancements by multilevel diagnostics. Per Med 2016; 13:469-484. [PMID: 29767597 DOI: 10.2217/pme-2016-0020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Breast cancer (BC) prevalence has reached an epidemic scale with half a million deaths annually. Current deficits in BC management include predictive and preventive approaches, optimized screening programs, individualized patient profiling, highly sensitive detection technologies for more precise diagnostics and therapy monitoring, individualized prediction and effective treatment of BC metastatic disease. To advance BC management, paradigm shift from delayed to predictive, preventive and personalized medical services is essential. Corresponding step forwards requires innovative multilevel diagnostics procuring specific panels of validated biomarkers. Here, we discuss current instrumental advancements including genomics, proteomics, epigenetics, miRNA, metabolomics, circulating tumor cells and cancer stem cells with a focus on biomarker discovery and multilevel diagnostic panels. A list of the recommended biomarker candidates is provided.
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List M, Alcaraz N, Dissing-Hansen M, Ditzel HJ, Mollenhauer J, Baumbach J. KeyPathwayMinerWeb: online multi-omics network enrichment. Nucleic Acids Res 2016; 44:W98-W104. [PMID: 27150809 PMCID: PMC4987922 DOI: 10.1093/nar/gkw373] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/25/2016] [Indexed: 01/25/2023] Open
Abstract
We present KeyPathwayMinerWeb, the first online platform for de novo pathway enrichment analysis directly in the browser. Given a biological interaction network (e.g. protein–protein interactions) and a series of molecular profiles derived from one or multiple OMICS studies (gene expression, for instance), KeyPathwayMiner extracts connected sub-networks containing a high number of active or differentially regulated genes (proteins, metabolites) in the molecular profiles. The web interface at (http://keypathwayminer.compbio.sdu.dk) implements all core functionalities of the KeyPathwayMiner tool set such as data integration, input of background knowledge, batch runs for parameter optimization and visualization of extracted pathways. In addition to an intuitive web interface, we also implemented a RESTful API that now enables other online developers to integrate network enrichment as a web service into their own platforms.
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Affiliation(s)
- Markus List
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark Institute of Clinical Research, University of Southern Denmark, 5000 Odense, Denmark Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Nicolas Alcaraz
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Martin Dissing-Hansen
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
| | - Henrik J Ditzel
- Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark Department of Oncology, Odense University Hospital, 5000 Odense, Denmark
| | - Jan Mollenhauer
- Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, University of Southern Denmark, 5000 Odense, Denmark Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
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10
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Computational and statistical methods for high-throughput analysis of post-translational modifications of proteins. J Proteomics 2015. [PMID: 26216596 DOI: 10.1016/j.jprot.2015.07.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The investigation of post-translational modifications (PTMs) represents one of the main research focuses for the study of protein function and cell signaling. Mass spectrometry instrumentation with increasing sensitivity improved protocols for PTM enrichment and recently established pipelines for high-throughput experiments allow large-scale identification and quantification of several PTM types. This review addresses the concurrently emerging challenges for the computational analysis of the resulting data and presents PTM-centered approaches for spectra identification, statistical analysis, multivariate analysis and data interpretation. We furthermore discuss the potential of future developments that will help to gain deep insight into the PTM-ome and its biological role in cells. This article is part of a Special Issue entitled: Computational Proteomics.
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11
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Jeong HH, Leem S, Wee K, Sohn KA. Integrative network analysis for survival-associated gene-gene interactions across multiple genomic profiles in ovarian cancer. J Ovarian Res 2015; 8:42. [PMID: 26138921 PMCID: PMC4491426 DOI: 10.1186/s13048-015-0171-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 06/24/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Recent advances in high-throughput technology and the emergence of large-scale genomic datasets have enabled detection of genomic features that affect clinical outcomes. Although many previous computational studies have analysed the effect of each single gene or the additive effects of multiple genes on the clinical outcome, less attention has been devoted to the identification of gene-gene interactions of general type that are associated with the clinical outcome. Moreover, the integration of information from multiple molecular profiles adds another challenge to this problem. Recently, network-based approaches have gained huge popularity. However, previous network construction methods have been more concerned with the relationship between features only, rather than the effect of feature interactions on clinical outcome. METHODS We propose a mutual information-based integrative network analysis framework (MINA) that identifies gene pairs associated with clinical outcome and systematically analyses the resulting networks over multiple genomic profiles. We implement an efficient non-parametric testing scheme that ensures the significance of detected gene interactions. We develop a tool named MINA that automates the proposed analysis scheme of identifying outcome-associated gene interactions and generating various networks from those interacting pairs for downstream analysis. RESULTS We demonstrate the proposed framework using real data from ovarian cancer patients in The Cancer Genome Atlas (TCGA). Statistically significant gene pairs associated with survival were identified from multiple genomic profiles, which include many individual genes that have weak or no effect on survival. Moreover, we also show that integrated networks, constructed by merging networks from multiple genomic profiles, demonstrate better topological properties and biological significance than individual networks. CONCLUSIONS We have developed a simple but powerful analysis tool that is able to detect gene-gene interactions associated with clinical outcome on multiple genomic profiles. By being network-based, our approach provides a better insight into the underlying gene-gene interaction mechanisms that affect the clinical outcome of cancer patients.
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Affiliation(s)
- Hyun-Hwan Jeong
- Department of Information and Computer Engineering, Ajou University, Suwon, 443-749, Republic of Korea.
| | - Sangseob Leem
- Department of Information and Computer Engineering, Ajou University, Suwon, 443-749, Republic of Korea.
| | - Kyubum Wee
- Department of Information and Computer Engineering, Ajou University, Suwon, 443-749, Republic of Korea.
| | - Kyung-Ah Sohn
- Department of Information and Computer Engineering, Ajou University, Suwon, 443-749, Republic of Korea.
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