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Aghakhani S, Niarakis A, Soliman S. MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps. J Integr Bioinform 2024; 21:jib-2023-0048. [PMID: 38314776 PMCID: PMC11293895 DOI: 10.1515/jib-2023-0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Molecular interaction maps (MIMs) are static graphical representations depicting complex biochemical networks that can be formalized using one of the Systems Biology Graphical Notation languages. Regardless of their extensive coverage of various biological processes, they are limited in terms of dynamic insights. However, MIMs can serve as templates for developing dynamic computational models. We present MetaLo, an open-source Python package that enables the coupling of Boolean models inferred from process description MIMs with generic core metabolic networks. MetaLo provides a framework to study the impact of signaling cascades, gene regulation processes, and metabolic flux distribution of central energy production pathways. MetaLo computes the Boolean model's asynchronous asymptotic behavior, through the identification of trap-spaces, and extracts metabolic constraints to contextualize the generic metabolic network. MetaLo is able to handle large-scale Boolean models and genome-scale metabolic models without requiring kinetic information or manual tuning. The framework behind MetaLo enables in depth analysis of the regulatory model, and may allow tackling a lack of omics data in poorly addressed biological fields to contextualize generic metabolic networks along with improper automatic reconstructions of cell- and/or disease-specific metabolic networks. MetaLo is available at https://pypi.org/project/metalo/ under the terms of the GNU General Public License v3.
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Affiliation(s)
- Sahar Aghakhani
- GenHotel - European Research Laboratory for Rheumatoid Arthritis, Univ. Evry, Univ. Paris-Saclay, Evry, France
- Lifeware Group, Inria Saclay, Palaiseau, France
| | - Anna Niarakis
- GenHotel - European Research Laboratory for Rheumatoid Arthritis, Univ. Evry, Univ. Paris-Saclay, Evry, France
- Lifeware Group, Inria Saclay, Palaiseau, France
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2
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Koole L, Martinez-Martinez P, Amelsvoort TV, Evelo CT, Ehrhart F. Interactive neuroinflammation pathways and transcriptomics-based identification of drugs and chemical compounds for schizophrenia. World J Biol Psychiatry 2024; 25:116-129. [PMID: 37961844 DOI: 10.1080/15622975.2023.2281514] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
OBJECTIVES Schizophrenia is a psychiatric disorder affecting 1% of the population. Accumulating evidence indicates that neuroinflammation is involved in the pathology of these disorders by altering neurodevelopmental processes and specifically affecting glutamatergic signalling and astrocytic functioning. The aim of this study was to curate interactive biological pathways involved in schizophrenia for the identification of novel pharmacological targets implementing pathway, gene ontology, and network analysis. METHODS Neuroinflammatory pathways were created using PathVisio and published in WikiPathways. A transcriptomics dataset, originally created by Narla et al. was selected for data visualisation and analysis. Transcriptomics data was visualised within pathways and networks, extended with transcription factors, pathways, and drugs. Network hubs were determined based on degrees of connectivity. RESULTS Glutamatergic, immune, and astrocytic signalling as well as extracellular matrix reorganisation were altered in schizophrenia while we did not find an effect on the complement system. Pharmacological agents that target the glutamate receptor subunits, inflammatory mediators, and metabolic enzymes were identified. CONCLUSIONS New neuroinflammatory pathways incorporating the extracellular matrix, glutamatergic neurons, and astrocytes in the aetiology of schizophrenia were established. Transcriptomics based network analysis provided novel targets, including extra-synaptic glutamate receptors, glutamate transporters and extracellular matrix molecules that can be evaluated for therapeutic strategies.
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Affiliation(s)
- Lisa Koole
- Department of Bioinformatics - BiGCaT, NUTRIM, FHML, Maastricht University, Maastricht, The Netherlands
- Department of Psychiatry and Neuropsychology, MHeNs, FHML, Maastricht University, Maastricht, The Netherlands
| | - Pilar Martinez-Martinez
- Department of Psychiatry and Neuropsychology, MHeNs, FHML, Maastricht University, Maastricht, The Netherlands
| | - Therese van Amelsvoort
- Department of Psychiatry and Neuropsychology, MHeNs, FHML, Maastricht University, Maastricht, The Netherlands
| | - Chris T Evelo
- Department of Bioinformatics - BiGCaT, NUTRIM, FHML, Maastricht University, Maastricht, The Netherlands
| | - Friederike Ehrhart
- Department of Bioinformatics - BiGCaT, NUTRIM, FHML, Maastricht University, Maastricht, The Netherlands
- Department of Psychiatry and Neuropsychology, MHeNs, FHML, Maastricht University, Maastricht, The Netherlands
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3
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Sommariva S, Caviglia G, Piana M. Gain and loss of function mutations in biological chemical reaction networks: a mathematical model with application to colorectal cancer cells. J Math Biol 2021; 82:55. [PMID: 33945019 PMCID: PMC8096774 DOI: 10.1007/s00285-021-01607-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 03/20/2021] [Accepted: 04/13/2021] [Indexed: 12/19/2022]
Abstract
This paper studies a system of Ordinary Differential Equations modeling a chemical reaction network and derives from it a simulation tool mimicking Loss of Function and Gain of Function mutations found in cancer cells. More specifically, from a theoretical perspective, our approach focuses on the determination of moiety conservation laws for the system and their relation with the corresponding stoichiometric surfaces. Then we show that Loss of Function mutations can be implemented in the model via modification of the initial conditions in the system, while Gain of Function mutations can be implemented by eliminating specific reactions. Finally, the model is utilized to examine in detail the G1-S phase of a colorectal cancer cell.
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Affiliation(s)
- Sara Sommariva
- Dipartimento di Matematica, Universitá di Genova, Via Dodecaneso, 35 16146, Genoa, Italy
| | - Giacomo Caviglia
- Dipartimento di Matematica, Universitá di Genova, Via Dodecaneso, 35 16146, Genoa, Italy
| | - Michele Piana
- Dipartimento di Matematica, Universitá di Genova, Via Dodecaneso, 35 16146, Genoa, Italy. .,CNR - SPIN GENOVA, Via Dodecaneso, 35 16146, Genoa, Italy.
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4
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Tlemsani C, Pongor L, Elloumi F, Girard L, Huffman KE, Roper N, Varma S, Luna A, Rajapakse VN, Sebastian R, Kohn KW, Krushkal J, Aladjem MI, Teicher BA, Meltzer PS, Reinhold WC, Minna JD, Thomas A, Pommier Y. SCLC-CellMiner: A Resource for Small Cell Lung Cancer Cell Line Genomics and Pharmacology Based on Genomic Signatures. Cell Rep 2020; 33:108296. [PMID: 33086069 PMCID: PMC7643325 DOI: 10.1016/j.celrep.2020.108296] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/06/2020] [Accepted: 09/30/2020] [Indexed: 01/23/2023] Open
Abstract
CellMiner-SCLC (https://discover.nci.nih.gov/SclcCellMinerCDB/) integrates drug sensitivity and genomic data, including high-resolution methylome and transcriptome from 118 patient-derived small cell lung cancer (SCLC) cell lines, providing a resource for research into this "recalcitrant cancer." We demonstrate the reproducibility and stability of data from multiple sources and validate the SCLC consensus nomenclature on the basis of expression of master transcription factors NEUROD1, ASCL1, POU2F3, and YAP1. Our analyses reveal transcription networks linking SCLC subtypes with MYC and its paralogs and the NOTCH and HIPPO pathways. SCLC subsets express specific surface markers, providing potential opportunities for antibody-based targeted therapies. YAP1-driven SCLCs are notable for differential expression of the NOTCH pathway, epithelial-mesenchymal transition (EMT), and antigen-presenting machinery (APM) genes and sensitivity to mTOR and AKT inhibitors. These analyses provide insights into SCLC biology and a framework for future investigations into subtype-specific SCLC vulnerabilities.
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Affiliation(s)
- Camille Tlemsani
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Lorinc Pongor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Fathi Elloumi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenneth E Huffman
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nitin Roper
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sudhir Varma
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Augustin Luna
- cBio Center, Division of Biostatistics, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Robin Sebastian
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Kurt W Kohn
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Beverly A Teicher
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anish Thomas
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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5
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Beal J, Nguyen T, Gorochowski TE, Goñi-Moreno A, Scott-Brown J, McLaughlin JA, Madsen C, Aleritsch B, Bartley B, Bhakta S, Bissell M, Castillo Hair S, Clancy K, Luna A, Le Novère N, Palchick Z, Pocock M, Sauro H, Sexton JT, Tabor JJ, Voigt CA, Zundel Z, Myers C, Wipat A. Communicating Structure and Function in Synthetic Biology Diagrams. ACS Synth Biol 2019; 8:1818-1825. [PMID: 31348656 PMCID: PMC8023477 DOI: 10.1021/acssynbio.9b00139] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Biological engineers often find it useful to communicate using diagrams. These diagrams can include information both about the structure of the nucleic acid sequences they are engineering and about the functional relationships between features of these sequences and/or other molecular species. A number of conventions and practices have begun to emerge within synthetic biology for creating such diagrams, and the Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard to organize, systematize, and extend such conventions in order to produce a coherent visual language. Here, we describe SBOL Visual version 2, which expands previous diagram standards to include new functional interactions, categories of molecular species, support for families of glyph variants, and the ability to indicate modular structure and mappings between elements of a system. SBOL Visual 2 also clarifies a number of requirements and best practices, significantly expands the collection of glyphs available to describe genetic features, and can be readily applied using a wide variety of software tools, both general and bespoke.
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Affiliation(s)
- Jacob Beal
- BioCoder Consulting , Carlsbad 92008 , California , United States
- Raytheon BBN Technologies , Arlington , Virginia 22209 , United States
| | - Tramy Nguyen
- University of Utah , Salt Lake City , Utah 84112 , United States
| | | | | | | | | | - Curtis Madsen
- Boston University , Boston , Massachusetts 02215 , United States
| | | | - Bryan Bartley
- Raytheon BBN Technologies , Arlington , Virginia 22209 , United States
| | - Shyam Bhakta
- Rice University , Houston , Texas 77005 , United States
| | - Mike Bissell
- Amyris, Inc. , Emeryville , California 94608 , United States
| | | | - Kevin Clancy
- BioCoder Consulting , Carlsbad 92008 , California , United States
| | - Augustin Luna
- Harvard Medical School , Boston , Massachusetts 02115 , United States
| | | | - Zach Palchick
- Zymergen , Emeryville , California 94608 , United States
| | - Matthew Pocock
- Turing Ate My Hamster, Ltd. , Tyne And Wear NE27 0RT , U.K
| | - Herbert Sauro
- University of Washington , Seattle , Washington 98195 , United States
| | - John T Sexton
- Rice University , Houston , Texas 77005 , United States
| | | | | | - Zach Zundel
- University of Utah , Salt Lake City , Utah 84112 , United States
| | - Chris Myers
- University of Utah , Salt Lake City , Utah 84112 , United States
| | - Anil Wipat
- Newcastle University , Newcastle upon Tyne NE1 7RU , U.K
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Abstract
The LRRK2 gene is a major contributor to genetic risk for Parkinson's disease and understanding the biology of the leucine-rich repeat kinase 2 (LRRK2, the protein product of this gene) is an important goal in Parkinson's research. LRRK2 is a multi-domain, multi-activity enzyme and has been implicated in a wide range of signalling events within the cell. Because of the complexities of the signal transduction pathways in which LRRK2 is involved, it has been challenging to generate a clear idea as to how mutations and disease associated variants in this gene are altered in disease. Understanding the events in which LRRK2 is involved at a systems level is therefore critical to fully understand the biology and pathobiology of this protein and is the subject of this review.
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Affiliation(s)
- Alice Price
- School of Pharmacy, University of Reading, Whiteknights, Reading, RG6 6AP, UK
| | - Claudia Manzoni
- School of Pharmacy, University of Reading, Whiteknights, Reading, RG6 6AP, UK
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Building. 35, 35 Convent Drive, Bethesda, MD, 20892, USA
| | - Patrick A Lewis
- School of Pharmacy, University of Reading, Whiteknights, Reading, RG6 6AP, UK.
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
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7
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Tan Z, Li J, Zhang X, Yang X, Zhang Z, Yin KJ, Huang H. P53 Promotes Retinoid Acid-induced Smooth Muscle Cell Differentiation by Targeting Myocardin. Stem Cells Dev 2018; 27:534-544. [PMID: 29482449 DOI: 10.1089/scd.2017.0244] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
TP53 is a widely studied tumor suppressor gene that controls various cellular functions, including cell differentiation. However, little is known about its functional roles in smooth muscle cells (SMCs) differentiation from embryonic stem cells (ESCs). SMC differentiation is at the heart of our understanding of vascular development, normal blood pressure homeostasis, and the pathogenesis of vascular diseases such as atherosclerosis, hypertension, restenosis, as well as aneurysm. Using retinoid acid (RA)-induced SMC differentiation models, we observed that p53 expression is increased during in vitro differentiation of mouse ESCs into SMCs. Meanwhile, suppression of p53 by shRNA reduced RA-induced SMC differentiation. Mechanistically, we have identified for the first time that Myocardin, a transcription factor that induces muscle cell differentiation and muscle-specific gene expression, is the direct target of p53 by bioinformatic analysis, luciferase reporter assay, and chromatin immunoprecipitation approaches. Moreover, in vivo SMC-selective p53 transgenic overexpression inhibited injury-induced neointimal formation. Taken together, our data demonstrate that p53 and its target gene, Myocardin, play regulatory roles in SMC differentiation. This study may lead to the identification of novel target molecules that may, in turn, lead to novel drug discoveries for the treatment of vascular diseases.
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Affiliation(s)
- Zhou Tan
- 1 Key Laboratory of Organ Development and Regeneration of Zhejiang Province, Institute of Life Sciences, College of Life Sciences, Hangzhou Normal University , Hangzhou, China
| | - Jingya Li
- 1 Key Laboratory of Organ Development and Regeneration of Zhejiang Province, Institute of Life Sciences, College of Life Sciences, Hangzhou Normal University , Hangzhou, China
| | - Xuejing Zhang
- 2 Department of Neurology, Pittsburgh Institute of Brain Disorders & Recovery, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Xueqin Yang
- 1 Key Laboratory of Organ Development and Regeneration of Zhejiang Province, Institute of Life Sciences, College of Life Sciences, Hangzhou Normal University , Hangzhou, China
| | - Zunyi Zhang
- 1 Key Laboratory of Organ Development and Regeneration of Zhejiang Province, Institute of Life Sciences, College of Life Sciences, Hangzhou Normal University , Hangzhou, China
| | - Ke-Jie Yin
- 2 Department of Neurology, Pittsburgh Institute of Brain Disorders & Recovery, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Huarong Huang
- 1 Key Laboratory of Organ Development and Regeneration of Zhejiang Province, Institute of Life Sciences, College of Life Sciences, Hangzhou Normal University , Hangzhou, China
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8
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Abstract
A major endeavor of systems biology is the construction of graphical and computational models of biological pathways as a means to better understand their structure and function. Here, we present a protocol for a biologist-friendly graphical modeling scheme that facilitates the construction of detailed network diagrams, summarizing the components of a biological pathway (such as proteins and biochemicals) and illustrating how they interact. These diagrams can then be used to simulate activity flow through a pathway, thereby modeling its dynamic behavior. The protocol is divided into four sections: (i) assembly of network diagrams using the modified Edinburgh Pathway Notation (mEPN) scheme and yEd network editing software with pathway information obtained from published literature and databases of molecular interaction data; (ii) parameterization of the pathway model within yEd through the placement of 'tokens' on the basis of the known or imputed amount or activity of a component; (iii) model testing through visualization and quantitative analysis of the movement of tokens through the pathway, using the network analysis tool Graphia Professional and (iv) optimization of model parameterization and experimentation. This is the first modeling approach that combines a sophisticated notation scheme for depicting biological events at the molecular level with a Petri net-based flow simulation algorithm and a powerful visualization engine with which to observe the dynamics of the system being modeled. Unlike many mathematical approaches to modeling pathways, it does not require the construction of a series of equations or rate constants for model parameterization. Depending on a model's complexity and the availability of information, its construction can take days to months, and, with refinement, possibly years. However, once assembled and parameterized, a simulation run, even on a large model, typically takes only seconds. Models constructed using this approach provide a means of knowledge management, information exchange and, through the computation simulation of their dynamic activity, generation and testing of hypotheses, as well as prediction of a system's behavior when perturbed.
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9
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Dawood M, Hamdoun S, Efferth T. Multifactorial Modes of Action of Arsenic Trioxide in Cancer Cells as Analyzed by Classical and Network Pharmacology. Front Pharmacol 2018; 9:143. [PMID: 29535630 PMCID: PMC5835320 DOI: 10.3389/fphar.2018.00143] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/09/2018] [Indexed: 12/13/2022] Open
Abstract
Arsenic trioxide is a traditional remedy in Chinese Medicine since ages. Nowadays, it is clinically used to treat acute promyelocytic leukemia (APL) by targeting PML/RARA. However, the drug's activity is broader and the mechanisms of action in other tumor types remain unclear. In this study, we investigated molecular modes of action by classical and network pharmacological approaches. CEM/ADR5000 resistance leukemic cells were similar sensitive to As2O3 as their wild-type counterpart CCRF-CEM (resistance ratio: 1.88). Drug-resistant U87.MG ΔEGFR glioblastoma cells harboring mutated epidermal growth factor receptor were even more sensitive (collateral sensitive) than wild-type U87.MG cells (resistance ratio: 0.33). HCT-116 colon carcinoma p53-/- knockout cells were 7.16-fold resistant toward As2O3 compared to wild-type cells. Forty genes determining cellular responsiveness to As2O3 were identified by microarray and COMPARE analyses in 58 cell lines of the NCI panel. Hierarchical cluster analysis-based heat mapping revealed significant differences between As2O3 sensitive cell lines and resistant cell lines with p-value: 1.86 × 10-5. The genes were subjected to Galaxy Cistrome gene promoter transcription factor analysis to predict the binding of transcription factors. We have exemplarily chosen NF-kB and AP-1, and indeed As2O3 dose-dependently inhibited the promoter activity of these two transcription factors in reporter cell lines. Furthermore, the genes identified here and those published in the literature were assembled and subjected to Ingenuity Pathway Analysis for comprehensive network pharmacological approaches that included all known factors of resistance of tumor cells to As2O3. In addition to pathways related to the anticancer effects of As2O3, several neurological pathways were identified. As arsenic is well-known to exert neurotoxicity, these pathways might account for neurological side effects. In conclusion, the activity of As2O3 is not restricted to acute promyelocytic leukemia. In addition to PML/RARA, numerous other genes belonging to diverse functional classes may also contribute to its cytotoxicity. Network pharmacology is suited to unravel the multifactorial modes of action of As2O3.
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Affiliation(s)
| | | | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
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10
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Castagnino N, Maffei M, Tortolina L, Zoppoli G, Piras D, Nencioni A, Ballestrero A, Patrone F, Parodi S. Transcription Factors Synergistically Activated at the Crossing of the Restriction Point between G1 and S Cell Cycle Phases. Pathologic Gate Opening during Multi-Hit Malignant Transformation. NUCLEAR RECEPTOR RESEARCH 2016. [DOI: 10.11131/2016/101201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Nicoletta Castagnino
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy; IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
| | - Massimo Maffei
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy; IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
| | - Lorenzo Tortolina
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy; IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy; IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
| | - Daniela Piras
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy; IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
| | - Alessio Nencioni
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy; IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy; IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
| | - Franco Patrone
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy; IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
| | - Silvio Parodi
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy; IRCCS Azienda Ospedaliera Universitaria San Martino - IST, Genoa, Italy
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11
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Abstract
There is a need for formalised diagrams that both summarise current biological pathway knowledge and support modelling approaches that explain and predict their behaviour. Here, we present a new, freely available modelling framework that includes a biologist-friendly pathway modelling language (mEPN), a simple but sophisticated method to support model parameterisation using available biological information; a stochastic flow algorithm that simulates the dynamics of pathway activity; and a 3-D visualisation engine that aids understanding of the complexities of a system’s dynamics. We present example pathway models that illustrate of the power of approach to depict a diverse range of systems. This Community Page presents a biologist-friendly method for compiling detailed graphical models of biological pathways from the literature, including their subsequent parameterization for use in dynamic simulations of their activity.
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12
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Castagnino N, Maffei M, Tortolina L, Zoppoli G, Piras D, Nencioni A, Moran E, Ballestrero A, Patrone F, Parodi S. Systems medicine in colorectal cancer: from a mathematical model toward a new type of clinical trial. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2016; 8:314-36. [PMID: 27240214 PMCID: PMC6680205 DOI: 10.1002/wsbm.1342] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 03/24/2016] [Accepted: 04/06/2016] [Indexed: 12/18/2022]
Abstract
Current colorectal cancer (CRC) treatment guidelines are primarily based on clinical features, such as cancer stage and grade. However, outcomes may be improved using molecular treatment guidelines. Potentially useful biomarkers include driver mutations and somatically inherited alterations, signaling proteins (their expression levels and (post) translational modifications), mRNAs, micro-RNAs and long noncoding RNAs. Moving to an integrated system is potentially very relevant. To implement such an integrated system: we focus on an important region of the signaling network, immediately above the G1-S restriction point, and discuss the reconstruction of a Molecular Interaction Map and interrogating it with a dynamic mathematical model. Extensive model pretraining achieved satisfactory, validated, performance. The model helps to propose future target combination priorities, and restricts drastically the number of drugs to be finally tested at a cellular, in vivo, and clinical-trial level. Our model allows for the inclusion of the unique molecular profiles of each individual patient's tumor. While existing clinical guidelines are well established, dynamic modeling may be used for future targeted combination therapies, which may progressively become part of clinical practice within the near future. WIREs Syst Biol Med 2016, 8:314-336. doi: 10.1002/wsbm.1342 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Nicoletta Castagnino
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Genoa, Italy
- IRCCS Azienda Ospedaliera Universitaria San Martino-IST, Genoa, Italy
| | - Massimo Maffei
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Genoa, Italy
- IRCCS Azienda Ospedaliera Universitaria San Martino-IST, Genoa, Italy
| | - Lorenzo Tortolina
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Genoa, Italy
- IRCCS Azienda Ospedaliera Universitaria San Martino-IST, Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Genoa, Italy
- IRCCS Azienda Ospedaliera Universitaria San Martino-IST, Genoa, Italy
| | - Daniela Piras
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Genoa, Italy
- IRCCS Azienda Ospedaliera Universitaria San Martino-IST, Genoa, Italy
| | - Alessio Nencioni
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Genoa, Italy
- IRCCS Azienda Ospedaliera Universitaria San Martino-IST, Genoa, Italy
| | - Eva Moran
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Genoa, Italy
- IRCCS Azienda Ospedaliera Universitaria San Martino-IST, Genoa, Italy
| | - Franco Patrone
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Genoa, Italy
- IRCCS Azienda Ospedaliera Universitaria San Martino-IST, Genoa, Italy
| | - Silvio Parodi
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Genoa, Italy
- IRCCS Azienda Ospedaliera Universitaria San Martino-IST, Genoa, Italy
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Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PLoS Comput Biol 2016; 12:e1004989. [PMID: 27336457 PMCID: PMC4918977 DOI: 10.1371/journal.pcbi.1004989] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/17/2016] [Indexed: 12/21/2022] Open
Abstract
The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.
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Bohler A, Wu G, Kutmon M, Pradhana LA, Coort SL, Hanspers K, Haw R, Pico AR, Evelo CT. Reactome from a WikiPathways Perspective. PLoS Comput Biol 2016; 12:e1004941. [PMID: 27203685 PMCID: PMC4874630 DOI: 10.1371/journal.pcbi.1004941] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/24/2016] [Indexed: 12/31/2022] Open
Abstract
Reactome and WikiPathways are two of the most popular freely available databases for biological pathways. Reactome pathways are centrally curated with periodic input from selected domain experts. WikiPathways is a community-based platform where pathways are created and continually curated by any interested party. The nascent collaboration between WikiPathways and Reactome illustrates the mutual benefits of combining these two approaches. We created a format converter that converts Reactome pathways to the GPML format used in WikiPathways. In addition, we developed the ComplexViz plugin for PathVisio which simplifies looking up complex components. The plugin can also score the complexes on a pathway based on a user defined criterion. This score can then be visualized on the complex nodes using the visualization options provided by the plugin. Using the merged collection of curated and converted Reactome pathways, we demonstrate improved pathway coverage of relevant biological processes for the analysis of a previously described polycystic ovary syndrome gene expression dataset. Additionally, this conversion allows researchers to visualize their data on Reactome pathways using PathVisio's advanced data visualization functionalities. WikiPathways benefits from the dedicated focus and attention provided to the content converted from Reactome and the wealth of semantic information about interactions. Reactome in turn benefits from the continuous community curation available on WikiPathways. The research community at large benefits from the availability of a larger set of pathways for analysis in PathVisio and Cytoscape. The pathway statistics results obtained from PathVisio are significantly better when using a larger set of candidate pathways for analysis. The conversion serves as a general model for integration of multiple pathway resources developed using different approaches.
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Affiliation(s)
- Anwesha Bohler
- Department of Bioinformatics—BiGCaT, Maastricht University, Maastricht, The Netherlands
- * E-mail:
| | - Guanming Wu
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
| | - Martina Kutmon
- Department of Bioinformatics—BiGCaT, Maastricht University, Maastricht, The Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
| | - Leontius Adhika Pradhana
- Department of Pharmacy, Faculty of Science, National University of Singapore, Singapore, Republic of Singapore
| | - Susan L. Coort
- Department of Bioinformatics—BiGCaT, Maastricht University, Maastricht, The Netherlands
| | - Kristina Hanspers
- Gladstone Institutes, San Francisco, California, United States of America
| | - Robin Haw
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
| | - Alexander R. Pico
- Gladstone Institutes, San Francisco, California, United States of America
| | - Chris T. Evelo
- Department of Bioinformatics—BiGCaT, Maastricht University, Maastricht, The Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
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Parodi S, Riccardi G, Castagnino N, Tortolina L, Maffei M, Zoppoli G, Nencioni A, Ballestrero A, Patrone F. Systems Medicine in Oncology: Signaling Network Modeling and New-Generation Decision-Support Systems. Methods Mol Biol 2016; 1386:181-219. [PMID: 26677185 DOI: 10.1007/978-1-4939-3283-2_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Two different perspectives are the main focus of this book chapter: (1) A perspective that looks to the future, with the goal of devising rational associations of targeted inhibitors against distinct altered signaling-network pathways. This goal implies a sufficiently in-depth molecular diagnosis of the personal cancer of a given patient. A sufficiently robust and extended dynamic modeling will suggest rational combinations of the abovementioned oncoprotein inhibitors. The work toward new selective drugs, in the field of medicinal chemistry, is very intensive. Rational associations of selective drug inhibitors will become progressively a more realistic goal within the next 3-5 years. Toward the possibility of an implementation in standard oncologic structures of technologically sufficiently advanced countries, new (legal) rules probably will have to be established through a consensus process, at the level of both diagnostic and therapeutic behaviors.(2) The cancer patient of today is not the patient of 5-10 years from now. How to support the choice of the most convenient (and already clinically allowed) treatment for an individual cancer patient, as of today? We will consider the present level of artificial intelligence (AI) sophistication and the continuous feeding, updating, and integration of cancer-related new data, in AI systems. We will also report briefly about one of the most important projects in this field: IBM Watson US Cancer Centers. Allowing for a temporal shift, in the long term the two perspectives should move in the same direction, with a necessary time lag between them.
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Affiliation(s)
- Silvio Parodi
- Department of Internal Medicine (DIMI), Genoa University, Viale Benedetto XV n. 6, 16132, Genoa, Italy.
| | - Giuseppe Riccardi
- Signals and Interactive Systems lab, Department of Engineering and Information Science, Trento University, Trento, Italy
| | - Nicoletta Castagnino
- Department of Internal Medicine (DIMI), Genoa University, Viale Benedetto XV n. 6, 16132, Genoa, Italy
| | - Lorenzo Tortolina
- Department of Internal Medicine (DIMI), Genoa University, Viale Benedetto XV n. 6, 16132, Genoa, Italy
| | - Massimo Maffei
- Department of Internal Medicine (DIMI), Genoa University, Viale Benedetto XV n. 6, 16132, Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine (DIMI), Genoa University, Viale Benedetto XV n. 6, 16132, Genoa, Italy
| | - Alessio Nencioni
- Department of Internal Medicine (DIMI), Genoa University, Viale Benedetto XV n. 6, 16132, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine (DIMI), Genoa University, Viale Benedetto XV n. 6, 16132, Genoa, Italy
| | - Franco Patrone
- Department of Internal Medicine (DIMI), Genoa University, Viale Benedetto XV n. 6, 16132, Genoa, Italy
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Activation of RAF1 (c-RAF) by the Marine Alkaloid Lasonolide A Induces Rapid Premature Chromosome Condensation. Mar Drugs 2015; 13:3625-39. [PMID: 26058013 PMCID: PMC4483648 DOI: 10.3390/md13063625] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/18/2015] [Accepted: 05/26/2015] [Indexed: 01/12/2023] Open
Abstract
Lasonolide A (LSA), a potent antitumor polyketide from the marine sponge, Forcepia sp., induces rapid and reversible protein hyperphosphorylation and premature chromosome condensation (PCC) at nanomolar concentrations independent of cyclin-dependent kinases. To identify cellular targets of LSA, we screened 2951 shRNAs targeting a pool of human kinases and phosphatases (1140 RefSeqs) to identify genes that modulate PCC in response to LSA. This led to the identification of RAF1 (C-RAF) as a mediator of LSA-induced PCC, as shRNAs against RAF1 conferred resistance to LSA. We found that LSA induced RAF1 phosphorylation on Serine 338 within minutes in human colorectal carcinoma HCT-116, ovarian carcinoma OVCAR-8, and Burkitt’s lymphoma CA46 cell lines. RAF1 depletion by siRNAs attenuated LSA-induced PCC in HCT-116 and OVCAR-8 cells. Furthermore, mouse embryonic fibroblasts (MEF) with homozygous deletion in Raf1, but not deletion in the related kinase Braf, were resistant to LSA-induced PCC. Complementation of Raf1−/− MEFs with wild-type human RAF1, but not with kinase-dead RAF1 mutant, restored LSA-induced PCC. Finally, the Raf inhibitor sorafenib, but not the MEK inhibitor AZD6244, effectively suppressed LSA-induced PCC. Our findings implicate a previously unknown, MAPK-independent role of RAF1 in chromatin condensation and potent activation of this pathway by LSA.
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Kutmon M, van Iersel MP, Bohler A, Kelder T, Nunes N, Pico AR, Evelo CT. PathVisio 3: an extendable pathway analysis toolbox. PLoS Comput Biol 2015; 11:e1004085. [PMID: 25706687 PMCID: PMC4338111 DOI: 10.1371/journal.pcbi.1004085] [Citation(s) in RCA: 293] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/11/2014] [Indexed: 12/20/2022] Open
Abstract
PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to describe the detailed steps in biological processes. Those powerful, visual representations help researchers to better understand, share and discuss knowledge. Since the first publication of PathVisio in 2008, the original paper was cited more than 170 times and PathVisio was used in many different biological studies. As an online editor PathVisio is also integrated in the community curated pathway database WikiPathways. Here we present the third version of PathVisio with the newest additions and improvements of the application. The core features of PathVisio are pathway drawing, advanced data visualization and pathway statistics. Additionally, PathVisio 3 introduces a new powerful extension systems that allows other developers to contribute additional functionality in form of plugins without changing the core application. PathVisio can be downloaded from http://www.pathvisio.org and in 2014 PathVisio 3 has been downloaded over 5,500 times. There are already more than 15 plugins available in the central plugin repository. PathVisio is a freely available, open-source tool published under the Apache 2.0 license (http://www.apache.org/licenses/LICENSE-2.0). It is implemented in Java and thus runs on all major operating systems. The code repository is available at http://svn.bigcat.unimaas.nl/pathvisio. The support mailing list for users is available on https://groups.google.com/forum/#!forum/wikipathways-discuss and for developers on https://groups.google.com/forum/#!forum/wikipathways-devel.
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Affiliation(s)
- Martina Kutmon
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands
- * E-mail: (MK); (CTE)
| | | | - Anwesha Bohler
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands
| | | | - Nuno Nunes
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands
| | - Alexander R. Pico
- Gladstone Institutes, San Francisco, California, United States of America
| | - Chris T. Evelo
- Department of Bioinformatics - BiGCaT, Maastricht University, Maastricht, The Netherlands
- * E-mail: (MK); (CTE)
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Dräger A, Palsson BØ. Improving collaboration by standardization efforts in systems biology. Front Bioeng Biotechnol 2014; 2:61. [PMID: 25538939 PMCID: PMC4259112 DOI: 10.3389/fbioe.2014.00061] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 11/14/2014] [Indexed: 11/17/2022] Open
Abstract
Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches. Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of granularity in biology. In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies. Thereby, the mathematical description of systems and approaches for their (repeated) simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation. Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to online resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programing languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts. This article gives a brief overview about the current state of the growing number of operation protocols, mark-up languages, graphical descriptions, and fundamental software support with relevance to systems biology.
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Affiliation(s)
- Andreas Dräger
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Cognitive Systems, Center for Bioinformatics Tübingen (ZBIT), Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Bernhard Ø. Palsson
- Systems Biology Research Group, Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
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Kohn KW, Zeeberg BM, Reinhold WC, Pommier Y. Gene expression correlations in human cancer cell lines define molecular interaction networks for epithelial phenotype. PLoS One 2014; 9:e99269. [PMID: 24940735 PMCID: PMC4062414 DOI: 10.1371/journal.pone.0099269] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 05/01/2014] [Indexed: 12/12/2022] Open
Abstract
Using gene expression data to enhance our knowledge of control networks relevant to cancer biology and therapy is a challenging but urgent task. Based on the premise that genes that are expressed together in a variety of cell types are likely to functions together, we derived mutually correlated genes that function together in various processes in epithelial-like tumor cells. Expression-correlated genes were derived from data for the NCI-60 human tumor cell lines, as well as data from the Broad Institute's CCLE cell lines. NCI-60 cell lines that selectively expressed a mutually correlated subset of tight junction genes served as a signature for epithelial-like cancer cells. Those signature cell lines served as a seed to derive other correlated genes, many of which had various other epithelial-related functions. Literature survey yielded molecular interaction and function information about those genes, from which molecular interaction maps were assembled. Many of the genes had epithelial functions unrelated to tight junctions, demonstrating that new function categories were elicited. The most highly correlated genes were implicated in the following epithelial functions: interactions at tight junctions (CLDN7, CLDN4, CLDN3, MARVELD3, MARVELD2, TJP3, CGN, CRB3, LLGL2, EPCAM, LNX1); interactions at adherens junctions (CDH1, ADAP1, CAMSAP3); interactions at desmosomes (PPL, PKP3, JUP); transcription regulation of cell-cell junction complexes (GRHL1 and 2); epithelial RNA splicing regulators (ESRP1 and 2); epithelial vesicle traffic (RAB25, EPN3, GRHL2, EHF, ADAP1, MYO5B); epithelial Ca(+2) signaling (ATP2C2, S100A14, BSPRY); terminal differentiation of epithelial cells (OVOL1 and 2, ST14, PRSS8, SPINT1 and 2); maintenance of apico-basal polarity (RAB25, LLGL2, EPN3). The findings provide a foundation for future studies to elucidate the functions of regulatory networks specific to epithelial-like cancer cells and to probe for anti-cancer drug targets.
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Affiliation(s)
- Kurt W. Kohn
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail:
| | - Barry M. Zeeberg
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - William C. Reinhold
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
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20
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Cheng HC, Angermann BR, Zhang F, Meier-Schellersheim M. NetworkViewer: visualizing biochemical reaction networks with embedded rendering of molecular interaction rules. BMC SYSTEMS BIOLOGY 2014; 8:70. [PMID: 24934175 PMCID: PMC4094451 DOI: 10.1186/1752-0509-8-70] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 06/05/2014] [Indexed: 01/01/2023]
Abstract
Background Network representations of cell-biological signaling processes frequently contain large numbers of interacting molecular and multi-molecular components that can exist in, and switch between, multiple biochemical and/or structural states. In addition, the interaction categories (associations, dissociations and transformations) in such networks cannot satisfactorily be mapped onto simple arrows connecting pairs of components since their specifications involve information such as reaction rates and conditions with regard to the states of the interacting components. This leads to the challenge of having to reconcile competing objectives: providing a high-level overview without omitting relevant information, and showing interaction specifics while not overwhelming users with too much detail displayed simultaneously. This problem is typically addressed by splitting the information required to understand a reaction network model into several categories that are rendered separately through combinations of visualizations and/or textual and tabular elements, requiring modelers to consult several sources to obtain comprehensive insights into the underlying assumptions of the model. Results We report the development of an application, the Simmune NetworkViewer, that visualizes biochemical reaction networks using iconographic representations of protein interactions and the conditions under which the interactions take place using the same symbols that were used to specify the underlying model with the Simmune Modeler. This approach not only provides a coherent model representation but, moreover, following the principle of “overview first, zoom and filter, then details-on-demand,” can generate an overview visualization of the global network and, upon user request, presents more detailed views of local sub-networks and the underlying reaction rules for selected interactions. This visual integration of information would be difficult to achieve with static network representations or approaches that use scripted model specifications without offering simple but detailed symbolic representations of molecular interactions, their conditions and consequences in terms of biochemical modifications. Conclusions The Simmune NetworkViewer provides concise, yet comprehensive visualizations of reaction networks created in the Simmune framework. In the near future, by adopting the upcoming SBML standard for encoding multi-component, multi-state molecular complexes and their interactions as input, the NetworkViewer will, moreover, be able to offer such visualization for any rule-based model that can be exported to that standard.
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Affiliation(s)
- Hsueh-Chien Cheng
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Building 4, 4 Memorial Drive, 20892 Bethesda, USA.
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Mirel B, Görg C. Scientists' sense making when hypothesizing about disease mechanisms from expression data and their needs for visualization support. BMC Bioinformatics 2014; 15:117. [PMID: 24766796 PMCID: PMC4021544 DOI: 10.1186/1471-2105-15-117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 04/08/2014] [Indexed: 02/02/2023] Open
Abstract
A common class of biomedical analysis is to explore expression data from high throughput experiments for the purpose of uncovering functional relationships that can lead to a hypothesis about mechanisms of a disease. We call this analysis expression driven, -omics hypothesizing. In it, scientists use interactive data visualizations and read deeply in the research literature. Little is known, however, about the actual flow of reasoning and behaviors (sense making) that scientists enact in this analysis, end-to-end. Understanding this flow is important because if bioinformatics tools are to be truly useful they must support it. Sense making models of visual analytics in other domains have been developed and used to inform the design of useful and usable tools. We believe they would be helpful in bioinformatics. To characterize the sense making involved in expression-driven, -omics hypothesizing, we conducted an in-depth observational study of one scientist as she engaged in this analysis over six months. From findings, we abstracted a preliminary sense making model. Here we describe its stages and suggest guidelines for developing visualization tools that we derived from this case. A single case cannot be generalized. But we offer our findings, sense making model and case-based tool guidelines as a first step toward increasing interest and further research in the bioinformatics field on scientists' analytical workflows and their implications for tool design.
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Affiliation(s)
- Barbara Mirel
- School of Education, University of Michigan, Ann Arbor, Michigan 48109, USA.
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Das BB, Huang SYN, Murai J, Rehman I, Amé JC, Sengupta S, Das SK, Majumdar P, Zhang H, Biard D, Majumder HK, Schreiber V, Pommier Y. PARP1-TDP1 coupling for the repair of topoisomerase I-induced DNA damage. Nucleic Acids Res 2014; 42:4435-49. [PMID: 24493735 PMCID: PMC3985661 DOI: 10.1093/nar/gku088] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARP) attach poly(ADP-ribose) (PAR) chains to various proteins including themselves and chromatin. Topoisomerase I (Top1) regulates DNA supercoiling and is the target of camptothecin and indenoisoquinoline anticancer drugs, as it forms Top1 cleavage complexes (Top1cc) that are trapped by the drugs. Endogenous and carcinogenic DNA lesions can also trap Top1cc. Tyrosyl-DNA phosphodiesterase 1 (TDP1), a key repair enzyme for trapped Top1cc, hydrolyzes the phosphodiester bond between the DNA 3'-end and the Top1 tyrosyl moiety. Alternative repair pathways for Top1cc involve endonuclease cleavage. However, it is unknown what determines the choice between TDP1 and the endonuclease repair pathways. Here we show that PARP1 plays a critical role in this process. By generating TDP1 and PARP1 double-knockout lymphoma chicken DT40 cells, we demonstrate that TDP1 and PARP1 are epistatic for the repair of Top1cc. The N-terminal domain of TDP1 directly binds the C-terminal domain of PARP1, and TDP1 is PARylated by PARP1. PARylation stabilizes TDP1 together with SUMOylation of TDP1. TDP1 PARylation enhances its recruitment to DNA damage sites without interfering with TDP1 catalytic activity. TDP1-PARP1 complexes, in turn recruit X-ray repair cross-complementing protein 1 (XRCC1). This work identifies PARP1 as a key component driving the repair of trapped Top1cc by TDP1.
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Affiliation(s)
- Benu Brata Das
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA, Laboratory of Molecular Biology, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India, Biotechnology and Cell Signaling, UMR7242 CNRS, Université de Strasbourg, Laboratory of Excellence Medalis, ESBS, Blvd Sébastien Brant, CS 10413, 67412 Illkirch, France, CEA-DSV-iMETI-SEPIA, BP6, 92265 Fontenay-aux-Roses cedex, France and Laboratory of Molecular Parasitology, Indian Institute of Chemical Biology, Kolkata 700032, India
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Tian Z, Fauré A, Mori H, Matsuno H. Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional Petri net model. BMC SYSTEMS BIOLOGY 2013; 7 Suppl 6:S1. [PMID: 24565082 PMCID: PMC4029488 DOI: 10.1186/1752-0509-7-s6-s1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND Glycogen and glucose are two sugar sources available during the lag phase of E. coli, but the mechanism that regulates their utilization is still unclear. METHODS Attempting to unveil the relationship between glucose and glycogen, we propose an integrated hybrid functional Petri net (HFPN) model including glycolysis, PTS, glycogen metabolic pathway, and their internal regulatory systems. RESULTS AND CONCLUSIONS By comparing known biological results to this model, basic necessary regulatory mechanism for utilizing glucose and glycogen were identified as a feedback circuit in which HPr and EIIAGlc play key roles. Based on this regulatory HFPN model, we discuss the process of glycogen utilization in E. coli in the context of a systematic understanding of carbohydrate metabolism.
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Draw it, if you can! Bioessays 2013; 35:581. [DOI: 10.1002/bies.201370073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Omix - A Visualization Tool for Metabolic Networks with Highest Usability and Customizability in Focus. CHEM-ING-TECH 2013. [DOI: 10.1002/cite.201200234] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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De Ambrosi C, Barla A, Tortolina L, Castagnino N, Pesenti R, Verri A, Ballestrero A, Patrone F, Parodi S. Parameter space exploration within dynamic simulations of signaling networks. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2013; 10:103-120. [PMID: 23311364 DOI: 10.3934/mbe.2013.10.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We started offering an introduction to very basic aspects of molecular biology, for the reader coming from computer sciences, information technology, mathematics. Similarly we offered a minimum of information about pathways and networks in graph theory, for a reader coming from the bio-medical sector. At the crossover about the two different types of expertise, we offered some definition about Systems Biology. The core of the article deals with a Molecular Interaction Map (MIM), a network of biochemical interactions involved in a small signaling-network sub-region relevant in breast cancer. We explored robustness/sensitivity to random perturbations. It turns out that our MIM is a non-isomorphic directed graph. For non physiological directions of propagation of the signal the network is quite resistant to perturbations. The opposite happens for biologically significant directions of signal propagation. In these cases we can have no signal attenuation, and even signal amplification. Signal propagation along a given pathway is highly unidirectional, with the exception of signal-feedbacks, that again have a specific biological role and significance. In conclusion, even a relatively small network like our present MIM reveals the preponderance of specific biological functions over unspecific isomorphic behaviors. This is perhaps the consequence of hundreds of millions of years of biological evolution.
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Affiliation(s)
- Cristina De Ambrosi
- DIBRIS Department of Informatics, Bioengineering, Robotics and Systems Engineering, Universita degli Studi di Genova - Via Balbi, 5 - 16126 Genova, Italy.
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A Calculus of Chemical Systems. IN SEARCH OF ELEGANCE IN THE THEORY AND PRACTICE OF COMPUTATION 2013. [DOI: 10.1007/978-3-642-41660-6_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Zaman A, Rahaman MH, Razzaque S. Kaposi's sarcoma: a computational approach through protein-protein interaction and gene regulatory networks analysis. Virus Genes 2012; 46:242-54. [PMID: 23266878 DOI: 10.1007/s11262-012-0865-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 12/07/2012] [Indexed: 12/27/2022]
Abstract
Interactomic data for Kaposi's Sarcoma Associated Herpes virus (KSHV)-the causative agent of vascular origin tumor called Kaposi's sarcoma-is relatively modest to date. The objective of this study was to assign functions to the previously uncharacterized ORFs in the virus using computational approaches and subsequently fit them to the host interactome landscape on protein, gene, and cellular level. On the basis of expression data, predicted RNA interference data, reported experimental data, and sequence based functional annotation we also tried to hypothesize the ORFs role in lytic and latent cycle during viral infection. We studied 17 previously uncharacterized ORFs in KSHV and the host-virus interplay seems to work in three major functional pathways-cell division, transport, metabolic and enzymatic in general. Studying the host-virus crosstalk for lytic phase predicts ORF 10 and ORF 11 as a predicted virus hub whereas PCNA is predicted as a host hub. On the other hand, ORF31 has been predicted as a latent phase inducible protein. KSHV invests a lion's share of its coding potential to suppress host immune response; various inflammatory mediators such as IFN-γ, TNF, IL-6, and IL-8 are negatively regulated by the ORFs while Il-10 secretion is stimulated in contrast. Although, like any other computational prediction, the study requires further validation, keeping into account the reproducibility and vast sample size of the systems biology approach the study allows us to propose an integrated network for host-virus interaction with good confidence. We hope that the study, in the long run, would help us identify effective dug against potential molecular targets.
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Affiliation(s)
- Aubhishek Zaman
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh.
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Smith AM, Xu W, Sun Y, Faeder JR, Marai GE. RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry. BMC Bioinformatics 2012; 13 Suppl 8:S3. [PMID: 22607382 PMCID: PMC3355338 DOI: 10.1186/1471-2105-13-s8-s3] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Rule-based modeling (RBM) is a powerful and increasingly popular approach to modeling cell signaling networks. However, novel visual tools are needed in order to make RBM accessible to a broad range of users, to make specification of models less error prone, and to improve workflows. RESULTS We introduce RuleBender, a novel visualization system for the integrated visualization, modeling and simulation of rule-based intracellular biochemistry. We present the user requirements, visual paradigms, algorithms and design decisions behind RuleBender, with emphasis on visual global/local model exploration and integrated execution of simulations. The support of RBM creation, debugging, and interactive visualization expedites the RBM learning process and reduces model construction time; while built-in model simulation and results with multiple linked views streamline the execution and analysis of newly created models and generated networks. CONCLUSION RuleBender has been adopted as both an educational and a research tool and is available as a free open source tool at http://www.rulebender.org. A development cycle that includes close interaction with expert users allows RuleBender to better serve the needs of the systems biology community.
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Affiliation(s)
- Adam M Smith
- Department of Computer Science, University of Pittsburgh, Pittsburgh, 15260, USA
| | - Wen Xu
- Department of Computer Science, University of Pittsburgh, Pittsburgh, 15260, USA
| | - Yao Sun
- Department of Computer Science, University of Pittsburgh, Pittsburgh, 15260, USA
| | - James R Faeder
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, 15260, USA
| | - G Elisabeta Marai
- Department of Computer Science, University of Pittsburgh, Pittsburgh, 15260, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, 15260, USA
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van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F. Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics 2012; 28:2016-21. [PMID: 22581176 PMCID: PMC3400951 DOI: 10.1093/bioinformatics/bts270] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. Availability and implementation: Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. Contact:sbgn-libsbgn@lists.sourceforge.net
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Kohn KW, Zeeberg BR, Reinhold WC, Sunshine M, Luna A, Pommier Y. Gene expression profiles of the NCI-60 human tumor cell lines define molecular interaction networks governing cell migration processes. PLoS One 2012; 7:e35716. [PMID: 22570691 PMCID: PMC3343048 DOI: 10.1371/journal.pone.0035716] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 03/20/2012] [Indexed: 12/14/2022] Open
Abstract
Although there is extensive information on gene expression and molecular interactions in various cell types, integrating those data in a functionally coherent manner remains challenging. This study explores the premise that genes whose expression at the mRNA level is correlated over diverse cell lines are likely to function together in a network of molecular interactions. We previously derived expression-correlated gene clusters from the database of the NCI-60 human tumor cell lines and associated each cluster with function categories of the Gene Ontology (GO) database. From a cluster rich in genes associated with GO categories related to cell migration, we extracted 15 genes that were highly cross-correlated; prominent among them were RRAS, AXL, ADAM9, FN14, and integrin-beta1. We then used those 15 genes as bait to identify other correlated genes in the NCI-60 database. A survey of current literature disclosed, not only that many of the expression-correlated genes engaged in molecular interactions related to migration, invasion, and metastasis, but that highly cross-correlated subsets of those genes engaged in specific cell migration processes. We assembled this information in molecular interaction maps (MIMs) that depict networks governing 3 cell migration processes: degradation of extracellular matrix, production of transient focal complexes at the leading edge of the cell, and retraction of the rear part of the cell. Also depicted are interactions controlling the release and effects of calcium ions, which may regulate migration in a spaciotemporal manner in the cell. The MIMs and associated text comprise a detailed and integrated summary of what is currently known or surmised about the role of the expression cross-correlated genes in molecular networks governing those processes.
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Affiliation(s)
- Kurt W Kohn
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
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Why and How to Expand the Role of Systems Biology in Pharmaceutical Research and Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 736:533-42. [DOI: 10.1007/978-1-4419-7210-1_31] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci 2011; 5:230-42. [PMID: 22180826 PMCID: PMC3235518 DOI: 10.4056/sigs.2034671] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Computational Modeling in Biology Network (COMBINE), is an initiative to coordinate the development of the various community standards and formats in computational systems biology and related fields. This report summarizes the activities pursued at the first annual COMBINE meeting held in Edinburgh on October 6-9 2010 and the first HARMONY hackathon, held in New York on April 18-22 2011. The first of those meetings hosted 81 attendees. Discussions covered both official COMBINE standards-(BioPAX, SBGN and SBML), as well as emerging efforts and interoperability between different formats. The second meeting, oriented towards software developers, welcomed 59 participants and witnessed many technical discussions, development of improved standards support in community software systems and conversion between the standards. Both meetings were resounding successes and showed that the field is now mature enough to develop representation formats and related standards in a coordinated manner.
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Affiliation(s)
- Nicolas Le Novère
- EMBL-EBI, Hinxton, CB10 1SD, UK
- Contributed equally to the manuscript
| | - Michael Hucka
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA , USA
- Contributed equally to the manuscript
| | | | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, Ontario M5S, Canada
| | - Emek Demir
- MSKCC - Computational Biology Center, New York, NY, USA
| | | | - Anatoly Sorokin
- School of Informatics, University of Edinburgh, Edinburgh, UK
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Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS. Guidelines for visualizing and annotating rule-based models. MOLECULAR BIOSYSTEMS 2011; 7:2779-95. [PMID: 21647530 PMCID: PMC3168731 DOI: 10.1039/c1mb05077j] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Rule-based modeling provides a means to represent cell signaling systems in a way that captures site-specific details of molecular interactions. For rule-based models to be more widely understood and (re)used, conventions for model visualization and annotation are needed. We have developed the concepts of an extended contact map and a model guide for illustrating and annotating rule-based models. An extended contact map represents the scope of a model by providing an illustration of each molecule, molecular component, direct physical interaction, post-translational modification, and enzyme-substrate relationship considered in a model. A map can also illustrate allosteric effects, structural relationships among molecular components, and compartmental locations of molecules. A model guide associates elements of a contact map with annotation and elements of an underlying model, which may be fully or partially specified. A guide can also serve to document the biological knowledge upon which a model is based. We provide examples of a map and guide for a published rule-based model that characterizes early events in IgE receptor (FcεRI) signaling. We also provide examples of how to visualize a variety of processes that are common in cell signaling systems but not considered in the example model, such as ubiquitination. An extended contact map and an associated guide can document knowledge of a cell signaling system in a form that is visual as well as executable. As a tool for model annotation, a map and guide can communicate the content of a model clearly and with precision, even for large models.
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Affiliation(s)
- Lily A Chylek
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Pleil JD, Stiegel MA, Madden MC, Sobus JR. Heat map visualization of complex environmental and biomarker measurements. CHEMOSPHERE 2011; 84:716-23. [PMID: 21492901 DOI: 10.1016/j.chemosphere.2011.03.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Revised: 03/02/2011] [Accepted: 03/14/2011] [Indexed: 05/19/2023]
Abstract
Over the past decade, the assessment of human systems interactions with the environment has permeated all phases of environmental and public health research. We are invoking lessons learned from the broad discipline of Systems Biology research that focuses primarily on molecular and cellular networks and adapting these concepts to Systems Exposure Science which focuses on interpreting the linkage from environmental measurements and biomonitoring to the expression of biological parameters. A primary tool of systems biology is the visualization of complex genomic and proteomic data using "heat maps" which are rectangular color coded arrays indicating the intensity (or amount) of the dependent variable. Heat maps are flexible in that both the x-axis and y-axis can be arranged to explore a particular hypothesis and allow a fast overview of data with a third quantitative dimension captured as different colors. We are now adapting these tools for interpreting cumulative and aggregate environmental exposure measurements as well as the results from human biomonitoring of biological media including blood, breath and urine. This article uses existing EPA measurements of environmental and biomarker concentrations of polycyclic aromatic hydrocarbons (PAHs) to demonstrate the value of the heat map approach for hypothesis development and to link back to stochastic and mixed effects models that were originally used to assess study results.
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Affiliation(s)
- Joachim D Pleil
- Human Exposure and Atmospheric Sciences Division, NERL/ORD, US Environmental Protection Agency, Research Triangle Park, NC 27711, United States.
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Luna A, Sunshine ML, van Iersel MP, Aladjem MI, Kohn KW. PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). ACTA ACUST UNITED AC 2011; 27:2165-6. [PMID: 21636591 DOI: 10.1093/bioinformatics/btr336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION A plugin for the Java-based PathVisio pathway editor has been developed to help users draw diagrams of bioregulatory networks according to the Molecular Interaction Map (MIM) notation. Together with the core PathVisio application, this plugin presents a simple to use and cross-platform application for the construction of complex MIM diagrams with the ability to annotate diagram elements with comments, literature references and links to external databases. This tool extends the capabilities of the PathVisio pathway editor by providing both MIM-specific glyphs and support for a MIM-specific markup language file format for exchange with other MIM-compatible tools and diagram validation. AVAILABILITY The PathVisio-MIM plugin is freely available and works with versions of PathVisio 2.0.11 and later on Windows, Mac OS X and Linux. Information about MIM notation and the MIMML format is available at http://discover.nci.nih.gov/mim. The plugin, along with diagram examples, instructions and Java source code, may be downloaded at http://discover.nci.nih.gov/mim/mim_pathvisio.html.
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Affiliation(s)
- Augustin Luna
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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37
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Luna A, Karac EI, Sunshine M, Chang L, Nussinov R, Aladjem MI, Kohn KW. A formal MIM specification and tools for the common exchange of MIM diagrams: an XML-Based format, an API, and a validation method. BMC Bioinformatics 2011; 12:167. [PMID: 21586134 PMCID: PMC3118169 DOI: 10.1186/1471-2105-12-167] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 05/17/2011] [Indexed: 01/15/2023] Open
Abstract
Background The Molecular Interaction Map (MIM) notation offers a standard set of symbols and rules on their usage for the depiction of cellular signaling network diagrams. Such diagrams are essential for disseminating biological information in a concise manner. A lack of software tools for the notation restricts wider usage of the notation. Development of software is facilitated by a more detailed specification regarding software requirements than has previously existed for the MIM notation. Results A formal implementation of the MIM notation was developed based on a core set of previously defined glyphs. This implementation provides a detailed specification of the properties of the elements of the MIM notation. Building upon this specification, a machine-readable format is provided as a standardized mechanism for the storage and exchange of MIM diagrams. This new format is accompanied by a Java-based application programming interface to help software developers to integrate MIM support into software projects. A validation mechanism is also provided to determine whether MIM datasets are in accordance with syntax rules provided by the new specification. Conclusions The work presented here provides key foundational components to promote software development for the MIM notation. These components will speed up the development of interoperable tools supporting the MIM notation and will aid in the translation of data stored in MIM diagrams to other standardized formats. Several projects utilizing this implementation of the notation are outlined herein. The MIM specification is available as an additional file to this publication. Source code, libraries, documentation, and examples are available at http://discover.nci.nih.gov/mim.
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Affiliation(s)
- Augustin Luna
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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38
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Achcar F, Camadro JM, Mestivier D. A Boolean probabilistic model of metabolic adaptation to oxygen in relation to iron homeostasis and oxidative stress. BMC SYSTEMS BIOLOGY 2011; 5:51. [PMID: 21489274 PMCID: PMC3094212 DOI: 10.1186/1752-0509-5-51] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 04/13/2011] [Indexed: 01/16/2023]
Abstract
Background In aerobically grown cells, iron homeostasis and oxidative stress are tightly linked processes implicated in a growing number of diseases. The deregulation of iron homeostasis due to gene defects or environmental stresses leads to a wide range of diseases with consequences for cellular metabolism that remain poorly understood. The modelling of iron homeostasis in relation to the main features of metabolism, energy production and oxidative stress may provide new clues to the ways in which changes in biological processes in a normal cell lead to disease. Results Using a methodology based on probabilistic Boolean modelling, we constructed the first model of yeast iron homeostasis including oxygen-related reactions in the frame of central metabolism. The resulting model of 642 elements and 1007 reactions was validated by comparing simulations with a large body of experimental results (147 phenotypes and 11 metabolic flux experiments). We removed every gene, thus generating in silico mutants. The simulations of the different mutants gave rise to a remarkably accurate qualitative description of most of the experimental phenotype (overall consistency > 91.5%). A second validation involved analysing the anaerobiosis to aerobiosis transition. Therefore, we compared the simulations of our model with different levels of oxygen to experimental metabolic flux data. The simulations reproducted accurately ten out of the eleven metabolic fluxes. We show here that our probabilistic Boolean modelling strategy provides a useful description of the dynamics of a complex biological system. A clustering analysis of the simulations of all in silico mutations led to the identification of clear phenotypic profiles, thus providing new insights into some metabolic response to stress conditions. Finally, the model was also used to explore several new hypothesis in order to better understand some unexpected phenotypes in given mutants. Conclusions All these results show that this model, and the underlying modelling strategy, are powerful tools for improving our understanding of complex biological problems.
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Affiliation(s)
- Fiona Achcar
- Modelling in Integrative Biology, Institut Jacques Monod - UMR7592 - CNRS - Univ. Paris-Diderot, Paris, France
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Meier-Schellersheim M, Fraser IDC, Klauschen F. Multiscale modeling for biologists. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 1:4-14. [PMID: 20448808 DOI: 10.1002/wsbm.33] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biomedical research frequently involves performing experiments and developing hypotheses that link different scales of biological systems such as, for instance, the scales of intracellular molecular interactions to the scale of cellular behavior and beyond to the behavior of cell populations. Computational modeling efforts that aim at exploring such multiscale systems quantitatively with the help of simulations have to incorporate several different simulation techniques because of the different time and space scales involved. Here, we provide a nontechnical overview of how different scales of experimental research can be combined with the appropriate computational modeling techniques. We also show that current modeling software permits building and simulating multiscale models without having to become involved with the underlying technical details of computational modeling.
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Affiliation(s)
- Martin Meier-Schellersheim
- Program in Systems Immunology and Infectious Disease Modeling (PSIIM), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Iain D C Fraser
- Program in Systems Immunology and Infectious Disease Modeling (PSIIM), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frederick Klauschen
- Program in Systems Immunology and Infectious Disease Modeling (PSIIM), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Hayes JD, McMahon M, Chowdhry S, Dinkova-Kostova AT. Cancer chemoprevention mechanisms mediated through the Keap1-Nrf2 pathway. Antioxid Redox Signal 2010; 13:1713-48. [PMID: 20446772 DOI: 10.1089/ars.2010.3221] [Citation(s) in RCA: 424] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The cap'n'collar (CNC) bZIP transcription factor Nrf2 controls expression of genes for antioxidant enzymes, metal-binding proteins, drug-metabolising enzymes, drug transporters, and molecular chaperones. Many chemicals that protect against carcinogenesis induce Nrf2-target genes. These compounds are all thiol-reactive and stimulate an adaptive response to redox stress in cells. Such agents induce the expression of genes that posses an antioxidant response element (ARE) in their regulatory regions. Under normal homeostatic conditions, Nrf2 activity is restricted through a Keap1-dependent ubiquitylation by Cul3-Rbx1, which targets the CNC-bZIP transcription factor for proteasomal degradation. However, as the substrate adaptor function of Keap1 is redox-sensitive, Nrf2 protein evades ubiquitylation by Cul3-Rbx1 when cells are treated with chemopreventive agents. As a consequence, Nrf2 accumulates in the nucleus where it heterodimerizes with small Maf proteins and transactivates genes regulated through an ARE. In this review, we describe synthetic compounds and phytochemicals from edible plants that induce Nrf2-target genes. We also discuss evidence for the existence of different classes of ARE (a 16-bp 5'-TMAnnRTGABnnnGCR-3' versus an 11-bp 5'-RTGABnnnGCR-3', with or without the embedded activator protein 1-binding site 5'-TGASTCA-3'), species differences in the ARE-gene battery, and the identity of critical Cys residues in Keap1 required for de-repression of Nrf2 by chemopreventive agents.
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Affiliation(s)
- John D Hayes
- Biomedical Research Institute, Ninewells Hospital, University of Dundee, Scotland, United Kingdom.
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Abstract
Motivation: In Systems Biology, an increasing collection of models of various biological processes is currently developed and made available in publicly accessible repositories, such as biomodels.net for instance, through common exchange formats such as SBML. To date, however, there is no general method to relate different models to each other by abstraction or reduction relationships, and this task is left to the modeler for re-using and coupling models. In mathematical biology, model reduction techniques have been studied for a long time, mainly in the case where a model exhibits different time scales, or different spatial phases, which can be analyzed separately. These techniques are however far too restrictive to be applied on a large scale in systems biology, and do not take into account abstractions other than time or phase decompositions. Our purpose here is to propose a general computational method for relating models together, by considering primarily the structure of the interactions and abstracting from their dynamics in a first step. Results: We present a graph-theoretic formalism with node merge and delete operations, in which model reductions can be studied as graph matching problems. From this setting, we derive an algorithm for deciding whether there exists a reduction from one model to another, and evaluate it on the computation of the reduction relations between all SBML models of the biomodels.net repository. In particular, in the case of the numerous models of MAPK signalling, and of the circadian clock, biologically meaningful mappings between models of each class are automatically inferred from the structure of the interactions. We conclude on the generality of our graphical method, on its limits with respect to the representation of the structure of the interactions in SBML, and on some perspectives for dealing with the dynamics. Availability: The algorithms described in this article are implemented in the open-source software modeling platform BIOCHAM available at http://contraintes.inria.fr/biocham The models used in the experiments are available from http://www.biomodels.net/ Contact:francois.fages@inria.fr
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Affiliation(s)
- Steven Gay
- EPI Contraintes, Institut National de Recherche en Informatique et Automatique, INRIA Paris-Rocquencourt, France
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Freeman TC, Raza S, Theocharidis A, Ghazal P. The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways. BMC SYSTEMS BIOLOGY 2010; 4:65. [PMID: 20478018 PMCID: PMC2878301 DOI: 10.1186/1752-0509-4-65] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Accepted: 05/17/2010] [Indexed: 01/15/2023]
Abstract
Background There is general agreement amongst biologists about the need for good pathway diagrams and a need to formalize the way biological pathways are depicted. However, implementing and agreeing how best to do this is currently the subject of some debate. Results The modified Edinburgh Pathway Notation (mEPN) scheme is founded on a notation system originally devised a number of years ago and through use has now been refined extensively. This process has been primarily driven by the author's attempts to produce process diagrams for a diverse range of biological pathways, particularly with respect to immune signaling in mammals. Here we provide a specification of the mEPN notation, its symbols, rules for its use and a comparison to the proposed Systems Biology Graphical Notation (SBGN) scheme. Conclusions We hope this work will contribute to the on-going community effort to develop a standard for depicting pathways and will provide a coherent guide to those planning to construct pathway diagrams of their biological systems of interest.
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Affiliation(s)
- Tom C Freeman
- Division of Pathway Medicine, University of Edinburgh Medical School, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh, UK.
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Kim S, Aladjem MI, McFadden GB, Kohn KW. Predicted functions of MdmX in fine-tuning the response of p53 to DNA damage. PLoS Comput Biol 2010; 6:e1000665. [PMID: 20174603 PMCID: PMC2824598 DOI: 10.1371/journal.pcbi.1000665] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 12/30/2009] [Indexed: 01/06/2023] Open
Abstract
Tumor suppressor protein p53 is regulated by two structurally homologous proteins, Mdm2 and MdmX. In contrast to Mdm2, MdmX lacks ubiquitin ligase activity. Although the essential interactions of MdmX are known, it is not clear how they function to regulate p53. The regulation of tumor suppressor p53 by Mdm2 and MdmX in response to DNA damage was investigated by mathematical modeling of a simplified network. The simplified network model was derived from a detailed molecular interaction map (MIM) that exhibited four coherent DNA damage response pathways. The results suggest that MdmX may amplify or stabilize DNA damage-induced p53 responses via non-enzymatic interactions. Transient effects of MdmX are mediated by reservoirs of p53∶MdmX and Mdm2∶MdmX heterodimers, with MdmX buffering the concentrations of p53 and/or Mdm2. A survey of kinetic parameter space disclosed regions of switch-like behavior stemming from such reservoir-based transients. During an early response to DNA damage, MdmX positively or negatively regulated p53 activity, depending on the level of Mdm2; this led to amplification of p53 activity and switch-like response. During a late response to DNA damage, MdmX could dampen oscillations of p53 activity. A possible role of MdmX may be to dampen such oscillations that otherwise could produce erratic cell behavior. Our study suggests how MdmX may participate in the response of p53 to DNA damage either by increasing dependency of p53 on Mdm2 or by dampening oscillations of p53 activity and presents a model for experimental investigation. A Molecular Interaction Map (MIM) akin to a circuit diagram of an electric device can give a comprehensive view of cellular processes and help understand complex protein functions in cells. To this end, we generated a MIM focused on the p53-Mdm2-MdmX network proteins and performed computer simulations to help understand how Mdm2 and MdmX may regulate p53. Proper regulation of p53 is important for cell survival: elevated levels of p53 can lead to cell death, and decreased levels of p53 can lead to cancer. Mdm2 and MdmX are structurally homologous proteins that regulate p53. Mdm2 negatively regulates p53 by degradation, but MdmX regulation of p53 is not well understood. Recently, Mdm2 and MdmX have been recognized as potential cancer therapeutic targets. In an effort to better understand how MdmX can alter the p53 activity under various conditions, we used mathematical models based on the MIM network to generate hypotheses that can be tested by experiments. Our simulations suggest that MdmX may increase the dependency of p53 on Mdm2 or dampen p53 oscillations during DNA damage response.
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Affiliation(s)
- Sohyoung Kim
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institute of Health, Bethesda, Maryland, United States of America
| | - Mirit I. Aladjem
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institute of Health, Bethesda, Maryland, United States of America
- * E-mail: (MIA); (KWK)
| | - Geoffrey B. McFadden
- Mathematical and Computational Sciences Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
| | - Kurt W. Kohn
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institute of Health, Bethesda, Maryland, United States of America
- * E-mail: (MIA); (KWK)
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Wimalaratne SM, Halstead MDB, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF. A method for visualizing CellML models. ACTA ACUST UNITED AC 2009; 25:3012-9. [PMID: 19703920 DOI: 10.1093/bioinformatics/btp495] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION The Physiome Project was established in 1997 to develop tools to facilitate international collaboration in the physiological sciences and the sharing of biological models and experimental data. The CellML language was developed to represent and exchange mathematical models of biological processes. CellML models can be very complicated, making it difficult to interpret the underlying physical and biological concepts and relationships captured/described in the mathematical model. RESULTS To address this issue a set of ontologies was developed to explicitly annotate the biophysical concepts represented in the CellML models. This article presents a framework that combines a visual language, together with CellML ontologies, to support the visualization of the underlying physical and biological concepts described by the mathematical model and also their relationships with the CellML model. Automated CellML model visualization assists in the interpretation of model concepts and facilitates model communication and exchange between different communities.
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Affiliation(s)
- S M Wimalaratne
- Auckland Bioengineering Institute and Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand.
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Nordlie E, Gewaltig MO, Plesser HE. Towards reproducible descriptions of neuronal network models. PLoS Comput Biol 2009; 5:e1000456. [PMID: 19662159 PMCID: PMC2713426 DOI: 10.1371/journal.pcbi.1000456] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Accepted: 07/01/2009] [Indexed: 11/19/2022] Open
Abstract
Progress in science depends on the effective exchange of ideas among scientists. New ideas can be assessed and criticized in a meaningful manner only if they are formulated precisely. This applies to simulation studies as well as to experiments and theories. But after more than 50 years of neuronal network simulations, we still lack a clear and common understanding of the role of computational models in neuroscience as well as established practices for describing network models in publications. This hinders the critical evaluation of network models as well as their re-use. We analyze here 14 research papers proposing neuronal network models of different complexity and find widely varying approaches to model descriptions, with regard to both the means of description and the ordering and placement of material. We further observe great variation in the graphical representation of networks and the notation used in equations. Based on our observations, we propose a good model description practice, composed of guidelines for the organization of publications, a checklist for model descriptions, templates for tables presenting model structure, and guidelines for diagrams of networks. The main purpose of this good practice is to trigger a debate about the communication of neuronal network models in a manner comprehensible to humans, as opposed to machine-readable model description languages. We believe that the good model description practice proposed here, together with a number of other recent initiatives on data-, model-, and software-sharing, may lead to a deeper and more fruitful exchange of ideas among computational neuroscientists in years to come. We further hope that work on standardized ways of describing—and thinking about—complex neuronal networks will lead the scientific community to a clearer understanding of high-level concepts in network dynamics, and will thus lead to deeper insights into the function of the brain. Scientists make precise, testable statements about their observations and models of nature. Other scientists can then evaluate these statements and attempt to reproduce or extend them. Results that cannot be reproduced will be duly criticized to arrive at better interpretations of experimental results or better models. Over time, this discourse develops our joint scientific knowledge. A crucial condition for this process is that scientists can describe their own models in a manner that is precise and comprehensible to others. We analyze in this paper how well models of neuronal networks are described in the scientific literature and conclude that the wide variety of manners in which network models are described makes it difficult to communicate models successfully. We propose a good model description practice to improve the communication of neuronal network models.
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Affiliation(s)
- Eilen Nordlie
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Aas, Norway
| | | | - Hans Ekkehard Plesser
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Aas, Norway
- Center for Biomedical Computing, Simula Research Laboratory, Lysaker, Norway
- RIKEN Brain Science Institute, Wako-shi, Saitama, Japan
- * E-mail:
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Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. The Systems Biology Graphical Notation. Nat Biotechnol 2009; 27:735-41. [PMID: 19668183 DOI: 10.1038/nbt.1558] [Citation(s) in RCA: 540] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.
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Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Network architecture of signaling from uncoupled helicase-polymerase to cell cycle checkpoints and trans-lesion DNA synthesis. Cell Cycle 2009; 8:2281-99. [PMID: 19556879 DOI: 10.4161/cc.8.14.9102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
When replication is blocked by a template lesion or polymerase inhibitor while helicase continues unwinding the DNA, single stranded DNA (ssDNA) accumulates and becomes coated with RPA, which then initiates signals via PCNA mono-ubiquitination to activate trans-lesion polymerases and via ATR and Chk1 to inhibit Cdk2-dependent cell cycle progression. The signals are conveyed by way of a complex network of molecular interactions. To clarify those complexities, we have constructed a molecular interaction map (MIM) using a novel hierarchical assembly procedure. Molecules were arranged on the map in hierarchical levels according to interaction step distance from the DNA region of stalled replication. The hierarchical MIM allows us to disentangle the network's interlocking pathways and loops and to suggest functionally significant features of network architecture. The MIM shows how parallel pathways and multiple feedback loops can provide failsafe and robust switch-like responses to replication stress. Within the central level of hierarchy ATR and Claspin together appear to function as a nexus that conveys signals from many sources to many destinations. We noted a division of labor between those two molecules, separating enzymatic and structural roles. In addition, the network architecture disclosed by the hierarchical map, suggested a speculative model for how molecular crowding and the granular localization of network components in the cell nucleus can facilitate function.
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Affiliation(s)
- Kurt W Kohn
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Mallavarapu A, Thomson M, Ullian B, Gunawardena J. Programming with models: modularity and abstraction provide powerful capabilities for systems biology. J R Soc Interface 2009; 6:257-70. [PMID: 18647734 PMCID: PMC2659579 DOI: 10.1098/rsif.2008.0205] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Mathematical models are increasingly used to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations presents a fundamental barrier to progress. Overcoming this requires modularity, enabling sub-systems to be specified independently and combined incrementally, and abstraction, enabling generic properties of biological processes to be specified independently of specific instances. These, in turn, require models to be represented as programs rather than as datatypes. Programmable modularity and abstraction enables libraries of modules to be created, which can be instantiated and reused repeatedly in different contexts with different components. We have developed a computational infrastructure that accomplishes this. We show here why such capabilities are needed, what is required to implement them and what can be accomplished with them that could not be done previously.
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Affiliation(s)
- Aneil Mallavarapu
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Cambridge, MA 02115, USA.
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Heiser LM, Wang NJ, Talcott CL, Laderoute KR, Knapp M, Guan Y, Hu Z, Ziyad S, Weber BL, Laquerre S, Jackson JR, Wooster RF, Kuo WL, Gray JW, Spellman PT. Integrated analysis of breast cancer cell lines reveals unique signaling pathways. Genome Biol 2009; 10:R31. [PMID: 19317917 PMCID: PMC2691002 DOI: 10.1186/gb-2009-10-3-r31] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 01/12/2009] [Accepted: 03/25/2009] [Indexed: 01/21/2023] Open
Abstract
Mapping of sub-networks in the EGFR-MAPK pathway in different breast cancer cell lines reveals that PAK1 may be a marker for sensitivity to MEK inhibitors. Background Cancer is a heterogeneous disease resulting from the accumulation of genetic defects that negatively impact control of cell division, motility, adhesion and apoptosis. Deregulation in signaling along the EgfR-MAPK pathway is common in breast cancer, though the manner in which deregulation occurs varies between both individuals and cancer subtypes. Results We were interested in identifying subnetworks within the EgfR-MAPK pathway that are similarly deregulated across subsets of breast cancers. To that end, we mapped genomic, transcriptional and proteomic profiles for 30 breast cancer cell lines onto a curated Pathway Logic symbolic systems model of EgfR-MAPK signaling. This model was composed of 539 molecular states and 396 rules governing signaling between active states. We analyzed these models and identified several subtype-specific subnetworks, including one that suggested Pak1 is particularly important in regulating the MAPK cascade when it is over-expressed. We hypothesized that Pak1 over-expressing cell lines would have increased sensitivity to Mek inhibitors. We tested this experimentally by measuring quantitative responses of 20 breast cancer cell lines to three Mek inhibitors. We found that Pak1 over-expressing luminal breast cancer cell lines are significantly more sensitive to Mek inhibition compared to those that express Pak1 at low levels. This indicates that Pak1 over-expression may be a useful clinical marker to identify patient populations that may be sensitive to Mek inhibitors. Conclusions All together, our results support the utility of symbolic system biology models for identification of therapeutic approaches that will be effective against breast cancer subsets.
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Affiliation(s)
- Laura M Heiser
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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