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Somers J, Fenner M, Kong G, Thirumalaisamy D, Yashar WM, Thapa K, Kinali M, Nikolova O, Babur Ö, Demir E. A framework for considering prior information in network-based approaches to omics data analysis. Proteomics 2023; 23:e2200402. [PMID: 37986684 DOI: 10.1002/pmic.202200402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 11/22/2023]
Abstract
For decades, molecular biologists have been uncovering the mechanics of biological systems. Efforts to bring their findings together have led to the development of multiple databases and information systems that capture and present pathway information in a computable network format. Concurrently, the advent of modern omics technologies has empowered researchers to systematically profile cellular processes across different modalities. Numerous algorithms, methodologies, and tools have been developed to use prior knowledge networks (PKNs) in the analysis of omics datasets. Interestingly, it has been repeatedly demonstrated that the source of prior knowledge can greatly impact the results of a given analysis. For these methods to be successful it is paramount that their selection of PKNs is amenable to the data type and the computational task they aim to accomplish. Here we present a five-level framework that broadly describes network models in terms of their scope, level of detail, and ability to inform causal predictions. To contextualize this framework, we review a handful of network-based omics analysis methods at each level, while also describing the computational tasks they aim to accomplish.
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Affiliation(s)
- Julia Somers
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA
| | - Madeleine Fenner
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA
| | - Garth Kong
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA
- Division of Oncological Sciences, Oregon Health and Science University, Portland, Oregon, USA
| | - Dharani Thirumalaisamy
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA
| | - William M Yashar
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA
- Division of Oncological Sciences, Oregon Health and Science University, Portland, Oregon, USA
| | - Kisan Thapa
- Computer Science Department, University of Massachusetts Boston, College of Science and Mathematics, Boston, Massachusetts, USA
| | - Meric Kinali
- Computer Science Department, University of Massachusetts Boston, College of Science and Mathematics, Boston, Massachusetts, USA
| | - Olga Nikolova
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA
- Division of Oncological Sciences, Oregon Health and Science University, Portland, Oregon, USA
| | - Özgün Babur
- Computer Science Department, University of Massachusetts Boston, College of Science and Mathematics, Boston, Massachusetts, USA
| | - Emek Demir
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, Oregon, USA
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2
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Boutillier P, Maasha M, Li X, Medina-Abarca HF, Krivine J, Feret J, Cristescu I, Forbes AG, Fontana W. The Kappa platform for rule-based modeling. Bioinformatics 2018; 34:i583-i592. [PMID: 29950016 PMCID: PMC6022607 DOI: 10.1093/bioinformatics/bty272] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Motivation We present an overview of the Kappa platform, an integrated suite of analysis and visualization techniques for building and interactively exploring rule-based models. The main components of the platform are the Kappa Simulator, the Kappa Static Analyzer and the Kappa Story Extractor. In addition to these components, we describe the Kappa User Interface, which includes a range of interactive visualization tools for rule-based models needed to make sense of the complexity of biological systems. We argue that, in this approach, modeling is akin to programming and can likewise benefit from an integrated development environment. Our platform is a step in this direction. Results We discuss details about the computation and rendering of static, dynamic, and causal views of a model, which include the contact map (CM), snaphots at different resolutions, the dynamic influence network (DIN) and causal compression. We provide use cases illustrating how these concepts generate insight. Specifically, we show how the CM and snapshots provide information about systems capable of polymerization, such as Wnt signaling. A well-understood model of the KaiABC oscillator, translated into Kappa from the literature, is deployed to demonstrate the DIN and its use in understanding systems dynamics. Finally, we discuss how pathways might be discovered or recovered from a rule-based model by means of causal compression, as exemplified for early events in EGF signaling. Availability and implementation The Kappa platform is available via the project website at kappalanguage.org. All components of the platform are open source and freely available through the authors' code repositories.
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Affiliation(s)
- Pierre Boutillier
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Mutaamba Maasha
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Xing Li
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Edgewise Networks, Burlington, MA, USA
| | | | - Jean Krivine
- IRIF, Université Paris-Diderot – Paris Paris, France
| | - Jérôme Feret
- Département d’informatique de l’ENS (INRIA/ENS/CNRS), PSL Research University, Paris, France
| | - Ioana Cristescu
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Angus G Forbes
- Department of Computational Media, UC Santa Cruz, Santa Cruz, CA, USA
| | - Walter Fontana
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
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3
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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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4
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Forbes AG, Burks A, Lee K, Li X, Boutillier P, Krivine J, Fontana W. Dynamic Influence Networks for Rule-Based Models. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2018; 24:184-194. [PMID: 28866584 DOI: 10.1109/tvcg.2017.2745280] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.
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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] [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 This article is categorized under:
Biological Mechanisms > Cell Signaling Analytical and Computational Methods > Computational Methods Translational, Genomic, and Systems Medicine > Translational Medicine
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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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6
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Duffy DJ. Problems, challenges and promises: perspectives on precision medicine. Brief Bioinform 2015; 17:494-504. [DOI: 10.1093/bib/bbv060] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Indexed: 12/11/2022] Open
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Tortolina L, Duffy DJ, Maffei M, Castagnino N, Carmody AM, Kolch W, Kholodenko BN, Ambrosi CD, Barla A, Biganzoli EM, Nencioni A, Patrone F, Ballestrero A, Zoppoli G, Verri A, Parodi S. Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies. Oncotarget 2015; 6:5041-58. [PMID: 25671297 PMCID: PMC4467132 DOI: 10.18632/oncotarget.3238] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 12/28/2014] [Indexed: 12/22/2022] Open
Abstract
The interconnected network of pathways downstream of the TGFβ, WNT and EGF-families of receptor ligands play an important role in colorectal cancer pathogenesis.We studied and implemented dynamic simulations of multiple downstream pathways and described the section of the signaling network considered as a Molecular Interaction Map (MIM). Our simulations used Ordinary Differential Equations (ODEs), which involved 447 reactants and their interactions.Starting from an initial "physiologic condition", the model can be adapted to simulate individual pathologic cancer conditions implementing alterations/mutations in relevant onco-proteins. We verified some salient model predictions using the mutated colorectal cancer lines HCT116 and HT29. We measured the amount of MYC and CCND1 mRNAs and AKT and ERK phosphorylated proteins, in response to individual or combination onco-protein inhibitor treatments. Experimental and simulation results were well correlated. Recent independently published results were also predicted by our model.Even in the presence of an approximate and incomplete signaling network information, a predictive dynamic modeling seems already possible. An important long term road seems to be open and can be pursued further, by incremental steps, toward even larger and better parameterized MIMs. Personalized treatment strategies with rational associations of signaling-proteins inhibitors, could become a realistic goal.
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Affiliation(s)
- Lorenzo Tortolina
- Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genoa, Italy
| | - David J. Duffy
- Systems Biology Ireland, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Massimo Maffei
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy
| | - Nicoletta Castagnino
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy
| | - Aimée M. Carmody
- Systems Biology Ireland, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Walter Kolch
- Systems Biology Ireland, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Boris N. Kholodenko
- Systems Biology Ireland, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Cristina De Ambrosi
- Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genoa, Italy
| | - Annalisa Barla
- Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genoa, Italy
| | - Elia M. Biganzoli
- Unit of Medical Statistics, Biometry and Bioinformatics “Giulio A. Maccacaro”, Department of Clinical Sciences and Community Health, University of Milan, Italy
| | - Alessio Nencioni
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy
- Istituto a Carattere di Ricerca Clinic - Scientifico (IRCCS), Azienda Ospedaliera Universitaria San Martino, Istituto Nazionale Tumori (IST), Genoa, Italy
| | - Franco Patrone
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy
- Istituto a Carattere di Ricerca Clinic - Scientifico (IRCCS), Azienda Ospedaliera Universitaria San Martino, Istituto Nazionale Tumori (IST), Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy
- Istituto a Carattere di Ricerca Clinic - Scientifico (IRCCS), Azienda Ospedaliera Universitaria San Martino, Istituto Nazionale Tumori (IST), Genoa, Italy
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy
- Istituto a Carattere di Ricerca Clinic - Scientifico (IRCCS), Azienda Ospedaliera Universitaria San Martino, Istituto Nazionale Tumori (IST), Genoa, Italy
| | - Alessandro Verri
- Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genoa, Italy
| | - Silvio Parodi
- Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy
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Reinhold WC, Varma S, Rajapakse VN, Luna A, Sousa FG, Kohn KW, Pommier YG. Using drug response data to identify molecular effectors, and molecular "omic" data to identify candidate drugs in cancer. Hum Genet 2015; 134:3-11. [PMID: 25213708 PMCID: PMC4282979 DOI: 10.1007/s00439-014-1482-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/19/2014] [Indexed: 12/31/2022]
Abstract
The current convergence of molecular and pharmacological data provides unprecedented opportunities to gain insights into the relationships between the two types of data. Multiple forms of large-scale molecular data, including but not limited to gene and microRNA transcript expression, DNA somatic and germline variations from next-generation DNA and RNA sequencing, and DNA copy number from array comparative genomic hybridization are all potentially informative when one attempts to recognize the panoply of potentially influential events both for cancer progression and therapeutic outcome. Concurrently, there has also been a substantial expansion of the pharmacological data being accrued in a systematic fashion. For cancer cell lines, the National Cancer Institute cell line panel (NCI-60), the Cancer Cell Line Encyclopedia (CCLE), and the collaborative Genomics of Drug Sensitivity in Cancer (GDSC) databases all provide subsets of these forms of data. For the patient-derived data, The Cancer Genome Atlas (TCGA) provides analogous forms of genomic information along with treatment histories. Integration of these data in turn relies on the fields of statistics and statistical learning. Multiple algorithmic approaches may be chosen, depending on the data being considered, and the nature of the question being asked. Combining these algorithms with prior biological knowledge, the results of molecular biological studies, and the consideration of genes as pathways or functional groups provides both the challenge and the potential of the field. The ultimate goal is to provide a paradigm shift in the way that drugs are selected to provide a more targeted and efficacious outcome for the patient.
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Affiliation(s)
- William C Reinhold
- Developmental Therapeutic Branch, Center for Cancer Research, NCI, NIH, 9000 Rockville Pike, Building 37, room 5041, Bethesda, MD, 20892, USA,
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Rother M, Münzner U, Thieme S, Krantz M. Information content and scalability in signal transduction network reconstruction formats. MOLECULAR BIOSYSTEMS 2013; 9:1993-2004. [PMID: 23636168 DOI: 10.1039/c3mb00005b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
One of the first steps towards holistic understanding of cellular networks is the integration of the available information in a human and machine readable format. This network reconstruction process is well established for metabolic networks, and numerous genome wide metabolic reconstructions are already available. Extending these strategies to signalling networks has proven difficult, primarily due to the combinatorial nature of regulatory modifications. The combinatorial nature of possible protein-protein interactions and post translational modifications affects both network size and the correspondence between the reconstructed network and the underlying empirical data. Here, we discuss different approaches to reconstruction of signal transduction networks. We divide the current approaches into topological, specific state based and reaction-contingency based, and discuss their different information content and scalability. The discussion focusses on graphical formats but the points are in general applicable also to mathematical models and databases. While the formats have complementary strengths especially for small networks, reaction-contingency based formats have a number of advantages in the light of global network reconstruction. In particular, they minimise the need for assumptions, maximise the congruence with empirical data, and scale efficiently with network size.
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Affiliation(s)
- Magdalena Rother
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
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Blinov ML, Moraru II. Leveraging modeling approaches: reaction networks and rules. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 736:517-30. [PMID: 22161349 DOI: 10.1007/978-1-4419-7210-1_30] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have witnessed an explosive growth in research involving mathematical models and computer simulations of intracellular molecular interactions, ranging from metabolic pathways to signaling and gene regulatory networks. Many software tools have been developed to aid in the study of such biological systems, some of which have a wealth of features for model building and visualization, and powerful capabilities for simulation and data analysis. Novel high-resolution and/or high-throughput experimental techniques have led to an abundance of qualitative and quantitative data related to the spatiotemporal distribution of molecules and complexes, their interactions kinetics, and functional modifications. Based on this information, computational biology researchers are attempting to build larger and more detailed models. However, this has proved to be a major challenge. Traditionally, modeling tools require the explicit specification of all molecular species and interactions in a model, which can quickly become a major limitation in the case of complex networks - the number of ways biomolecules can combine to form multimolecular complexes can be combinatorially large. Recently, a new breed of software tools has been created to address the problems faced when building models marked by combinatorial complexity. These have a different approach for model specification, using reaction rules and species patterns. Here we compare the traditional modeling approach with the new rule-based methods. We make a case for combining the capabilities of conventional simulation software with the unique features and flexibility of a rule-based approach in a single software platform for building models of molecular interaction networks.
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Affiliation(s)
- Michael L Blinov
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT, USA.
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11
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Murai J, Huang SYN, Das BB, Renaud A, Zhang Y, Doroshow JH, Ji J, Takeda S, Pommier Y. Trapping of PARP1 and PARP2 by Clinical PARP Inhibitors. Cancer Res 2012; 72:5588-99. [PMID: 23118055 DOI: 10.1158/0008-5472.can-12-2753] [Citation(s) in RCA: 1488] [Impact Index Per Article: 124.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Small-molecule inhibitors of PARP are thought to mediate their antitumor effects as catalytic inhibitors that block repair of DNA single-strand breaks (SSB). However, the mechanism of action of PARP inhibitors with regard to their effects in cancer cells is not fully understood. In this study, we show that PARP inhibitors trap the PARP1 and PARP2 enzymes at damaged DNA. Trapped PARP-DNA complexes were more cytotoxic than unrepaired SSBs caused by PARP inactivation, arguing that PARP inhibitors act in part as poisons that trap PARP enzyme on DNA. Moreover, the potency in trapping PARP differed markedly among inhibitors with niraparib (MK-4827) > olaparib (AZD-2281) >> veliparib (ABT-888), a pattern not correlated with the catalytic inhibitory properties for each drug. We also analyzed repair pathways for PARP-DNA complexes using 30 genetically altered avian DT40 cell lines with preestablished deletions in specific DNA repair genes. This analysis revealed that, in addition to homologous recombination, postreplication repair, the Fanconi anemia pathway, polymerase β, and FEN1 are critical for repairing trapped PARP-DNA complexes. In summary, our study provides a new mechanistic foundation for the rational application of PARP inhibitors in cancer therapy.
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Affiliation(s)
- Junko Murai
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA
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12
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A framework for mapping, visualisation and automatic model creation of signal-transduction networks. Mol Syst Biol 2012; 8:578. [PMID: 22531118 PMCID: PMC3361003 DOI: 10.1038/msb.2012.12] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
An intuitive formalism for reconstructing cellular networks from empirical data is presented, and used to build a comprehensive yeast MAP kinase network. The accompanying rxncon software tool can convert networks to a range of standard graphical formats and mathematical models. ![]()
Network mapping at the granularity of empirical data that largely avoids combinatorial complexity Automatic visualisation and model generation with the rxncon open source software tool Visualisation in a range of formats, including all three SBGN formats, as well as contingency matrix or regulatory graph Comprehensive and completely references map of the yeast MAP kinase network in the rxncon format
Intracellular signalling systems are highly complex. This complexity makes handling, analysis and visualisation of available knowledge a major challenge in current signalling research. Here, we present a novel framework for mapping signal-transduction networks that avoids the combinatorial explosion by breaking down the network in reaction and contingency information. It provides two new visualisation methods and automatic export to mathematical models. We use this framework to compile the presently most comprehensive map of the yeast MAP kinase network. Our method improves previous strategies by combining (I) more concise mapping adapted to empirical data, (II) individual referencing for each piece of information, (III) visualisation without simplifications or added uncertainty, (IV) automatic visualisation in multiple formats, (V) automatic export to mathematical models and (VI) compatibility with established formats. The framework is supported by an open source software tool that facilitates integration of the three levels of network analysis: definition, visualisation and mathematical modelling. The framework is species independent and we expect that it will have wider impact in signalling research on any system.
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Machado D, Costa RS, Rocha M, Ferreira EC, Tidor B, Rocha I. Modeling formalisms in Systems Biology. AMB Express 2011; 1:45. [PMID: 22141422 PMCID: PMC3285092 DOI: 10.1186/2191-0855-1-45] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 12/05/2011] [Indexed: 12/18/2022] Open
Abstract
Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future.
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Affiliation(s)
- Daniel Machado
- IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Rafael S Costa
- IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Miguel Rocha
- Department of Informatics/CCTC, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Eugénio C Ferreira
- IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Bruce Tidor
- Department of Biological Engineering/Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isabel Rocha
- IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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14
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Puri A, Neelamegham S. Understanding glycomechanics using mathematical modeling: a review of current approaches to simulate cellular glycosylation reaction networks. Ann Biomed Eng 2011; 40:816-27. [PMID: 22090146 DOI: 10.1007/s10439-011-0464-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Accepted: 11/05/2011] [Indexed: 01/07/2023]
Abstract
Following the footsteps of genomics and proteomics, recent years have witnessed the growth of large-scale experimental methods in the field of glycomics. In parallel, there has also been growing interest in developing Systems Biology based methods to study the glycome. The combined goals of these endeavors is to identify glycosylation-dependent mechanisms regulating human physiology, check points that can control the progression of pathophysiology, and modifications to reaction pathways that can result in more uniform biopharmaceutical processes. In these efforts, mathematical models of N- and O-linked glycosylation have emerged as paradigms for the field. While these are relatively few in number, nevertheless, the existing models provide a basic framework that can be used to develop more sophisticated analysis strategies for glycosylation in the future. The current review surveys these computational models with focus on the underlying mathematics and assumptions, and with respect to their ability to generate experimentally testable hypotheses.
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Affiliation(s)
- Apurv Puri
- Department of Chemical and Biological Engineering, and The New York State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA
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15
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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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16
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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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17
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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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18
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Neelamegham S, Liu G. Systems glycobiology: biochemical reaction networks regulating glycan structure and function. Glycobiology 2011; 21:1541-53. [PMID: 21436236 DOI: 10.1093/glycob/cwr036] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is a growing use of bioinformatics based methods in the field of Glycobiology. These have been used largely to curate glycan structures, organize array-based experimental data and display existing knowledge of glycosylation-related pathways in silico. Although the cataloging of vast amounts of data is beneficial, it is often a challenge to gain meaningful mechanistic insight from this exercise alone. The development of specific analysis tools to query the database is necessary. If these queries can integrate existing knowledge of glycobiology, new insights may be gained. Such queries that couple biochemical knowledge and mathematics have been developed in the field of Systems Biology. The current review summarizes the current state of the art in the application of computational modeling in the field of Glycobiology. It provides (i) an overview of experimental and online resources that can be used to construct glycosylation reaction networks, (ii) mathematical methods to formulate the problem including a description of ordinary differential equation and logic-based reaction networks, (iii) optimization techniques that can be applied to fit experimental data for the purpose of model reconstruction and for evaluating unknown model parameters, (iv) post-simulation analysis methods that yield experimentally testable hypotheses and (v) a summary of available software tools that can be used by non-specialists to perform many of the above functions.
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Affiliation(s)
- Sriram Neelamegham
- Department of Chemical and Biological Engineering, and The NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, NY 14260, USA.
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19
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Abstract
We address one of the central issues in devising languages, methods and tools for the modelling and analysis of complex biological systems, that of linking high-level (e.g. intercellular) information with lower-level (e.g. intracellular) information. Adequate ways of dealing with this issue are crucial for understanding biological networks and pathways, which typically contain huge amounts of data that continue to grow as our knowledge and understanding of a system increases. Trying to comprehend such data using the standard methods currently in use is often virtually impossible. We propose a two-tier compound visual language, which we call Biocharts, that is geared towards building fully executable models of biological systems. One of the main goals of our approach is to enable biologists to actively participate in the computational modelling effort, in a natural way. The high-level part of our language is a version of statecharts, which have been shown to be extremely successful in software and systems engineering. The statecharts can be combined with any appropriately well-defined language (preferably a diagrammatic one) for specifying the low-level dynamics of the pathways and networks. We illustrate the language and our general modelling approach using the well-studied process of bacterial chemotaxis.
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Affiliation(s)
- Hillel Kugler
- Computational Biology Group, Microsoft Research, Cambridge, UK.
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20
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Weissmann G. Monumental Revolutions: Scientific, Sanitary and ʼOmicMonumental Revolutions: Scientific, Sanitary and ʼOmic. FASEB J 2009; 23:3639-43. [DOI: 10.1096/fj.09-1101ufm] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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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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Abstract
With the growing importance of computational models in systems biology there has been much interest in recent years to develop standard model interchange languages that permit biologists to easily exchange models between different software tools. In the present chapter two chief model exchange standards, SBML (Systems Biology Markup Language) and CellML are described. In addition, other related features including visual layout initiatives, ontologies and best practices for model annotation are discussed. Software tools such as developer libraries and basic editing tools are also introduced, together with a discussion on the future of modelling languages and visualization tools in systems biology.
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23
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Aune GJ, Takagi K, Sordet O, Guirouilh-Barbat J, Antony S, Bohr VA, Pommier Y. Von Hippel-Lindau-coupled and transcription-coupled nucleotide excision repair-dependent degradation of RNA polymerase II in response to trabectedin. Clin Cancer Res 2008; 14:6449-55. [PMID: 18927284 DOI: 10.1158/1078-0432.ccr-08-0730] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Ecteinascidin 743 (Et743; trabectedin, Yondelis) has recently been approved in Europe for the treatment of soft tissue sarcomas and is undergoing clinical trials for other solid tumors. Et743 selectively targets cells proficient for TC-NER, which sets it apart from other DNA alkylating agents. In the present study, we examined the effects of Et743 on RNA Pol II. EXPERIMENTAL DESIGN AND RESULTS We report that Et743 induces the rapid and massive degradation of transcribing Pol II in various cancer cell lines and normal fibroblasts. Pol II degradation was abrogated by the proteasome inhibitor MG132 and was dependent on TC-NER. Cockayne syndrome (CS) cells and xeroderma pigmentosum (XP) cells (XPD, XPA, XPG, and XPF) were defective in Pol II degradation, whereas XPC cells whose defect is limited to global genome NER in nontranscribing regions were proficient for Pol II degradation. Complementation of the CSB and XPD cells restored Pol II degradation. We also show that cells defective for the VHL complex were defective in Pol II degradation and that complementation of those cells restores Pol II degradation. Moreover, VHL deficiency rendered cells resistant to Et743-induced cell death, a similar effect to that of TC-NER deficiency. CONCLUSION These results suggest that both TC-NER-induced and VHL-mediated Pol II degradation play a role in cell killing by Et743.
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Affiliation(s)
- Gregory J Aune
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
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24
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Tozluoğlu M, Karaca E, Haliloglu T, Nussinov R. Cataloging and organizing p73 interactions in cell cycle arrest and apoptosis. Nucleic Acids Res 2008; 36:5033-49. [PMID: 18660513 PMCID: PMC2528188 DOI: 10.1093/nar/gkn481] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We have compiled the p73-mediated cell cycle arrest and apoptosis pathways. p73 is a member of the p53 family, consisting of p53, p63 and p73. p73 exists in several isoforms, presenting different domain structures. p73 functions not only as a tumor suppressor in apoptosis but also as differentiator in embryo development. p53 mutations are responsible for half of the human cancers; p73 can partially substitute mutant p53 as tumor suppressor. The pathways we assembled create a p73-centered network consisting of 53 proteins and 176 interactions. We clustered our network into five functional categories: Upregulation, Activation, Suppression, Transcriptional Activity and Degradation. Our literature searches led to discovering proteins (c-Jun and pRb) with apparent opposing functional effects; these indicate either currently missing proteins and interactions or experimental misidentification or functional annotation. For convenience, here we present the p73 network using the molecular interaction map (MIM) notation. The p73 MIM is unique amongst MIMs, since it further implements detailed domain features. We highlight shared pathways between p53 and p73. We expect that the compiled and organized network would be useful to p53 family-based studies.
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Affiliation(s)
- Melda Tozluoğlu
- Polymer Research Center and Chemical Engineering Department, Bogazici University, Bebek-Istanbul 80815, Turkey
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25
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Mazumder A, Palma AJF, Wang Y. Validation and integration of gene-expression signatures in cancer. Expert Rev Mol Diagn 2008; 8:125-8. [PMID: 18366298 DOI: 10.1586/14737159.8.2.125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Chromatin challenges during DNA replication: a systems representation. Mol Biol Cell 2007; 19:1-7. [PMID: 17959828 DOI: 10.1091/mbc.e07-06-0528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In a recent review, A. Groth and coworkers presented a comprehensive account of nucleosome disassembly in front of a DNA replication fork, assembly behind the replication fork, and the copying of epigenetic information onto the replicated chromatin. Understanding those processes however would be enhanced by a comprehensive graphical depiction analogous to a circuit diagram. Accordingly, we have constructed a molecular interaction map (MIM) that preserves in essentially complete detail the processes described by Groth et al. The MIM organizes and elucidates the information presented by Groth et al. on the complexities of chromatin replication, thereby providing a tool for system-level comprehension of the effects of genetic mutations, altered gene expression, and pharmacologic intervention.
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Affiliation(s)
- Kurt W Kohn
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Kurata H, Inoue K, Maeda K, Masaki K, Shimokawa Y, Zhao Q. Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis. Nucleic Acids Res 2007; 35:e134. [PMID: 17940089 PMCID: PMC2175333 DOI: 10.1093/nar/gkm769] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Biochemical network maps are helpful for understanding the mechanism of how a collection of biochemical reactions generate particular functions within a cell. We developed a new and computationally feasible notation that enables drawing a wide resolution map from the domain-level reactions to phenomenological events and implemented it as the extended GUI network constructor of CADLIVE (Computer-Aided Design of LIVing systEms). The new notation presents ‘Domain expansion’ for proteins and RNAs, ‘Virtual reaction and nodes’ that are responsible for illustrating domain-based interaction and ‘InnerLink’ that links real complex nodes to virtual nodes to illustrate the exact components of the real complex. A modular box is also presented that packs related reactions as a module or a subnetwork, which gives CADLIVE a capability to draw biochemical maps in a hierarchical modular architecture. Furthermore, we developed a pathway search module for virtual knockout mutants as a built-in application of CADLIVE. This module analyzes gene function in the same way as molecular genetics, which simulates a change in mutant phenotypes or confirms the validity of the network map. The extended CADLIVE with the newly proposed notation is demonstrated to be feasible for computational simulation and analysis.
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Affiliation(s)
- Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, 820-8502, Fukuoka, Japan.
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28
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Hu Z, Mellor J, Wu J, Kanehisa M, Stuart JM, DeLisi C. Towards zoomable multidimensional maps of the cell. Nat Biotechnol 2007; 25:547-54. [PMID: 17483841 DOI: 10.1038/nbt1304] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The detailed structure of molecular networks, including their dependence on conditions and time, are now routinely assayed by various experimental techniques. Visualization is a vital aid in integrating and interpreting such data. We describe emerging approaches for representing and visualizing systems data and for achieving semantic zooming, or changes in information density concordant with scale. A central challenge is to move beyond the display of a static network to visualizations of networks as a function of time, space and cell state, which capture the adaptability of the cell. We consider approaches for representing the role of protein complexes in the cell cycle, displaying modules of metabolism in a hierarchical format, integrating experimental interaction data with structured vocabularies such as Gene Ontology categories and representing conserved interactions among orthologous groups of genes.
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Affiliation(s)
- Zhenjun Hu
- Program in Bioinformatics and Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
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