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Kadelka C, Butrie TM, Hilton E, Kinseth J, Schmidt A, Serdarevic H. A meta-analysis of Boolean network models reveals design principles of gene regulatory networks. SCIENCE ADVANCES 2024; 10:eadj0822. [PMID: 38215198 PMCID: PMC10786419 DOI: 10.1126/sciadv.adj0822] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean networks, which are intuitive, simple to describe, and can yield qualitative results even when data are sparse. We assembled the largest repository of expert-curated Boolean GRN models. A meta-analysis of this diverse set of models reveals several design principles. GRNs exhibit more canalization, redundancy, and stable dynamics than expected. Moreover, they are enriched for certain recurring network motifs. This raises the important question why evolution favors these design mechanisms.
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Affiliation(s)
- Claus Kadelka
- Department of Mathematics, Iowa State University, Ames, IA 50011, USA
| | | | - Evan Hilton
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
| | - Jack Kinseth
- Department of Mathematics, Iowa State University, Ames, IA 50011, USA
| | - Addison Schmidt
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Haris Serdarevic
- Department of Mathematics, Iowa State University, Ames, IA 50011, USA
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2
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Aghamiri SS, Puniya BL, Amin R, Helikar T. A multiscale mechanistic model of human dendritic cells for in-silico investigation of immune responses and novel therapeutics discovery. Front Immunol 2023; 14:1112985. [PMID: 36993954 PMCID: PMC10040975 DOI: 10.3389/fimmu.2023.1112985] [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: 11/30/2022] [Accepted: 02/22/2023] [Indexed: 03/14/2023] Open
Abstract
Dendritic cells (DCs) are professional antigen-presenting cells (APCs) with the unique ability to mediate inflammatory responses of the immune system. Given the critical role of DCs in shaping immunity, they present an attractive avenue as a therapeutic target to program the immune system and reverse immune disease disorders. To ensure appropriate immune response, DCs utilize intricate and complex molecular and cellular interactions that converge into a seamless phenotype. Computational models open novel frontiers in research by integrating large-scale interaction to interrogate the influence of complex biological behavior across scales. The ability to model large biological networks will likely pave the way to understanding any complex system in more approachable ways. We developed a logical and predictive model of DC function that integrates the heterogeneity of DCs population, APC function, and cell-cell interaction, spanning molecular to population levels. Our logical model consists of 281 components that connect environmental stimuli with various layers of the cell compartments, including the plasma membrane, cytoplasm, and nucleus to represent the dynamic processes within and outside the DC, such as signaling pathways and cell-cell interactions. We also provided three sample use cases to apply the model in the context of studying cell dynamics and disease environments. First, we characterized the DC response to Sars-CoV-2 and influenza co-infection by in-silico experiments and analyzed the activity level of 107 molecules that play a role in this co-infection. The second example presents simulations to predict the crosstalk between DCs and T cells in a cancer microenvironment. Finally, for the third example, we used the Kyoto Encyclopedia of Genes and Genomes enrichment analysis against the model's components to identify 45 diseases and 24 molecular pathways that the DC model can address. This study presents a resource to decode the complex dynamics underlying DC-derived APC communication and provides a platform for researchers to perform in-silico experiments on human DC for vaccine design, drug discovery, and immunotherapies.
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Affiliation(s)
| | | | - Rada Amin
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
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3
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Choi SR, Hwang CY, Lee J, Cho KH. Network Analysis Identifies Regulators of Basal-Like Breast Cancer Reprogramming and Endocrine Therapy Vulnerability. Cancer Res 2021; 82:320-333. [PMID: 34845001 DOI: 10.1158/0008-5472.can-21-0621] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/13/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022]
Abstract
Basal-like breast cancer is the most aggressive breast cancer subtype with the worst prognosis. Despite its high recurrence rate, chemotherapy is the only treatment for basal-like breast cancer, which lacks expression of hormone receptors. In contrast, luminal A tumors express ERα and can undergo endocrine therapy for treatment. Previous studies have tried to develop effective treatments for basal-like patients using various therapeutics but failed due to the complex and dynamic nature of the disease. In this study, we performed a transcriptomic analysis of patients with breast cancer to construct a simplified but essential molecular regulatory network model. Network control analysis identified potential targets and elucidated the underlying mechanisms of reprogramming basal-like cancer cells into luminal A cells. Inhibition of BCL11A and HDAC1/2 effectively drove basal-like cells to transition to luminal A cells and increased ERα expression, leading to increased tamoxifen sensitivity. High expression of BCL11A and HDAC1/2 correlated with poor prognosis in patients with breast cancer. These findings identify mechanisms regulating breast cancer phenotypes and suggest the potential to reprogram basal-like breast cancer cells to enhance their targetability. SIGNIFICANCE: A network model enables investigation of mechanisms regulating the basal-to-luminal transition in breast cancer, identifying BCL11A and HDAC1/2 as optimal targets that can induce basal-like breast cancer reprogramming and endocrine therapy sensitivity.
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Affiliation(s)
- Sea R Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Chae Young Hwang
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jonghoon Lee
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Kwang-Hyun Cho
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
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4
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Ruiz TFR, Taboga SR, Leonel ECR. Molecular mechanisms of mammary gland remodeling: A review of the homeostatic versus bisphenol a disrupted microenvironment. Reprod Toxicol 2021; 105:1-16. [PMID: 34343637 DOI: 10.1016/j.reprotox.2021.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/26/2021] [Accepted: 07/29/2021] [Indexed: 12/30/2022]
Abstract
Mammary gland (MG) undergoes critical points of structural changes throughout a woman's life. During the perinatal and pubertal stages, MG develops through growth and differentiation to establish a pre-mature feature. If pregnancy and lactation occur, the epithelial compartment branches and differentiates to create a specialized structure for milk secretion and nurturing of the newborn. However, the ultimate MG modification consists of a regression process aiming to reestablish the smaller and less energy demanding structure until another production cycle happens. The unraveling of these fascinating physiologic cycles has helped the scientific community elucidate aspects of molecular regulation of proliferative and apoptotic events and remodeling of the stromal compartment. However, greater understanding of the hormonal pathways involved in MG developmental stages led to concern that endocrine disruptors such as bisphenol A (BPA), may influence these specific development/involution stages, called "windows of susceptibility". Since it is used in the manufacture of polycarbonate plastics and epoxy resins, BPA is a ubiquitous chemical present in human everyday life, exerting an estrogenic effect. Thus, descriptions of its deleterious effects on the MG, especially in terms of serum hormone concentrations, hormonal receptor expression, molecular pathways, and epigenetic alterations, have been widely published. Therefore, allied to a didactic description of the main physiological mechanisms involved in different critical points of MG development, the current review provides a summary of key mechanisms by which the endocrine disruptor BPA impacts MG homeostasis at different windows of susceptibility, causing short- and long-term effects.
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Affiliation(s)
- Thalles Fernando Rocha Ruiz
- São Paulo State University (Unesp), Department of Biology, Institute of Biosciences, Humanities and Exact Sciences, São José Do Rio Preto, Brazil.
| | - Sebastião Roberto Taboga
- São Paulo State University (Unesp), Department of Biology, Institute of Biosciences, Humanities and Exact Sciences, São José Do Rio Preto, Brazil.
| | - Ellen Cristina Rivas Leonel
- São Paulo State University (Unesp), Department of Biology, Institute of Biosciences, Humanities and Exact Sciences, São José Do Rio Preto, Brazil; Federal University of Goiás (UFG), Department of Histology, Embryology and Cell Biology, Institute of Biological Sciences, Goiânia, Brazil.
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5
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Qu Y, Liu Y, Ding K, Li Y, Hong X, Zhang H. Partial Response to Pyrotinib Plus Capecitabine in an Advanced Breast Cancer Patient with HER2 Amplification and R157W Mutation After Anti- HER2 Treatment: A Case Report and Literature Review. Onco Targets Ther 2021; 14:1581-1588. [PMID: 33688205 PMCID: PMC7936716 DOI: 10.2147/ott.s289876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/07/2021] [Indexed: 01/08/2023] Open
Abstract
Human epidermal growth factor receptor2 (HER2) overexpression/amplification is associated with high malignancy, rapid disease progression and poor overall survival in breast cancer. The application of anti-HER2 drugs has greatly improved the survival of patients with HER2-positive breast cancer, but drug resistance issues affect the long-term efficacy. The HER2 mutation is considered to be one of the reasons for resistance to anti-HER2 therapy, and there is currently no standard treatment. We report for the first time the detection of HER2 amplification with R157W mutation by second-generation sequencing (NGS) in a 57-year-old hormone receptor-negative, HER2-positive woman with advanced breast cancer who was resistant to multi-line anti-HER2 therapies. She subsequently received pyrotinib combined with capecitabine treatment and achieved partial response. The small-molecule pan-HER family irreversible inhibitor pyrotinib combined with capecitabine has shown a promising effect in the treatment of HER2 mutation-induced resistance, but the molecular mechanism and efficacy need to be further verified.
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Affiliation(s)
- Yanchun Qu
- Department of Oncology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, People's Republic of China.,Department of Oncology, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, People's Republic of China.,The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, People's Republic of China
| | - Yufeng Liu
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, People's Republic of China
| | - Kailin Ding
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, People's Republic of China
| | - Yong Li
- Department of Oncology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, People's Republic of China.,Department of Oncology, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, People's Republic of China
| | - Xiaoyu Hong
- Nanjing Geneseeq Technology Inc, Nanjing, People's Republic of China
| | - Haibo Zhang
- Department of Oncology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, People's Republic of China.,Department of Oncology, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, People's Republic of China
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6
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Aguilar B, Fang P, Laubenbacher R, Murrugarra D. A Near-Optimal Control Method for Stochastic Boolean Networks. LETTERS IN BIOMATHEMATICS 2020; 7:67-80. [PMID: 34141873 PMCID: PMC8208226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
One of the ultimate goals in systems biology is to develop control strategies to find efficient medical treatments. One step towards this goal is to develop methods for changing the state of a cell into a desirable state. We propose an efficient method that determines combinations of network perturbations to direct the system towards a predefined state. The method requires a set of control actions such as the silencing of a gene or the disruption of the interaction between two genes. An optimal control policy defined as the best intervention at each state of the system can be obtained using existing methods. However, these algorithms are computationally prohibitive for models with tens of nodes. Our method generates control actions that approximates the optimal control policy with high probability with a computational efficiency that does not depend on the size of the state space. Our C++ code is available at https://github.com/boaguilar/SDDScontrol.
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Affiliation(s)
- Boris Aguilar
- Institute for Systems Biology, Seattle, WA 98109-5263 USA
| | - Pan Fang
- Computer Science Department, Tulane University, New Orleans, LA 70118 USA
| | | | - David Murrugarra
- Mathematics Department, University of Kentucky, Lexington, KY 40506-0027 USA
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7
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Hou X, Li M, Jia C, Zhang X, Wang Y. Attractor - a new turning point in drug discovery. DRUG DESIGN DEVELOPMENT AND THERAPY 2019; 13:2957-2968. [PMID: 31686779 PMCID: PMC6709805 DOI: 10.2147/dddt.s216397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/28/2019] [Indexed: 11/23/2022]
Abstract
Drug discovery for complex diseases can be viewed as a challenging problem in which the influence of compounds on dynamic features of disease system should be considered, especially the strategies escaping from the disease attractors. Moreover, escaping from the disease-related attractors has been proved to be a cue for the treatment of the complex diseases. The drug discovery methodology based on the attractor theory indicates new solutions for target identification, drug discovery and drug combination design. The methodology is based on the holism level of the organism and the features of system dynamics, so it has advantages for the classification of complex diseases and drug discovery. Currently, research results of this method have increased, which expand the insight scope for drug discovery. This article introduces the major drug discovery methods in the history of pharmacy development and their characteristics, so as to illustrate the reasons and inevitability of the appearance of attractor method, its position in the history of pharmacy development, and its advantages for drug discovery and design, thereby to prove that the attractor method can indeed become the next major drug development method. In addition, it provides a comprehensive description about the concept of attractor, the pipeline of attractor analysis, the common methods of each process and its research progress, so as to provide a macroscopic framework and optional methods and tools for the follow-up researchers.
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Affiliation(s)
- Xucan Hou
- Department of Traditional Chinese Medicine Information Fusion and Utilization, Beijing University of Chinese Medicine, Beijing, People's Republic of China
| | - Meng Li
- Department of Traditional Chinese Medicine Information Fusion and Utilization, Beijing University of Chinese Medicine, Beijing, People's Republic of China
| | - Congmin Jia
- Department of Traditional Chinese Medicine Information Fusion and Utilization, Beijing University of Chinese Medicine, Beijing, People's Republic of China
| | - Xianbao Zhang
- Department of Traditional Chinese Medicine Information Fusion and Utilization, Beijing University of Chinese Medicine, Beijing, People's Republic of China
| | - Yun Wang
- Department of Traditional Chinese Medicine Information Fusion and Utilization, Beijing University of Chinese Medicine, Beijing, People's Republic of China
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8
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Shang Z, Verlan S, Petre I, Zhang G. Reaction Systems and Synchronous Digital Circuits. Molecules 2019; 24:E1961. [PMID: 31117321 PMCID: PMC6571626 DOI: 10.3390/molecules24101961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/26/2019] [Accepted: 04/28/2019] [Indexed: 11/16/2022] Open
Abstract
A reaction system is a modeling framework for investigating the functioning of the living cell, focused on capturing cause-effect relationships in biochemical environments. Biochemical processes in this framework are seen to interact with each other by producing the ingredients enabling and/or inhibiting other reactions. They can also be influenced by the environment seen as a systematic driver of the processes through the ingredients brought into the cellular environment. In this paper, the first attempt is made to implement reaction systems in the hardware. We first show a tight relation between reaction systems and synchronous digital circuits, generally used for digital electronics design. We describe the algorithms allowing us to translate one model to the other one, while keeping the same behavior and similar size. We also develop a compiler translating a reaction systems description into hardware circuit description using field-programming gate arrays (FPGA) technology, leading to high performance, hardware-based simulations of reaction systems. This work also opens a novel interesting perspective of analyzing the behavior of biological systems using established industrial tools from electronic circuits design.
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Affiliation(s)
- Zeyi Shang
- School of Electrical Engineering, Southwest Jiaotong University, Chengdu 611756, Sichuan, China.
- Laboratoire d'Algorithmique, Complexité et Logique, Université Paris Est Créteil, 94010 Créteil, France.
| | - Sergey Verlan
- Laboratoire d'Algorithmique, Complexité et Logique, Université Paris Est Créteil, 94010 Créteil, France.
| | - Ion Petre
- Department of Mathematics and Statistics, University of Turku, FI-20014 Turku, Finland.
- National Institute for Research and Development in Biological Sciences, 060031 Bucharest, Romania.
| | - Gexiang Zhang
- School of Electrical Engineering, Southwest Jiaotong University, Chengdu 611756, Sichuan, China.
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9
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Sizek H, Hamel A, Deritei D, Campbell S, Ravasz Regan E. Boolean model of growth signaling, cell cycle and apoptosis predicts the molecular mechanism of aberrant cell cycle progression driven by hyperactive PI3K. PLoS Comput Biol 2019; 15:e1006402. [PMID: 30875364 PMCID: PMC6436762 DOI: 10.1371/journal.pcbi.1006402] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 03/27/2019] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
The PI3K/AKT signaling pathway plays a role in most cellular functions linked to cancer progression, including cell growth, proliferation, cell survival, tissue invasion and angiogenesis. It is generally recognized that hyperactive PI3K/AKT1 are oncogenic due to their boost to cell survival, cell cycle entry and growth-promoting metabolism. That said, the dynamics of PI3K and AKT1 during cell cycle progression are highly nonlinear. In addition to negative feedback that curtails their activity, protein expression of PI3K subunits has been shown to oscillate in dividing cells. The low-PI3K/low-AKT1 phase of these oscillations is required for cytokinesis, indicating that oncogenic PI3K may directly contribute to genome duplication. To explore this, we construct a Boolean model of growth factor signaling that can reproduce PI3K oscillations and link them to cell cycle progression and apoptosis. The resulting modular model reproduces hyperactive PI3K-driven cytokinesis failure and genome duplication and predicts the molecular drivers responsible for these failures by linking hyperactive PI3K to mis-regulation of Polo-like kinase 1 (Plk1) expression late in G2. To do this, our model captures the role of Plk1 in cell cycle progression and accurately reproduces multiple effects of its loss: G2 arrest, mitotic catastrophe, chromosome mis-segregation / aneuploidy due to premature anaphase, and cytokinesis failure leading to genome duplication, depending on the timing of Plk1 inhibition along the cell cycle. Finally, we offer testable predictions on the molecular drivers of PI3K oscillations, the timing of these oscillations with respect to division, and the role of altered Plk1 and FoxO activity in genome-level defects caused by hyperactive PI3K. Our model is an important starting point for the predictive modeling of cell fate decisions that include AKT1-driven senescence, as well as the non-intuitive effects of drugs that interfere with mitosis.
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Affiliation(s)
- Herbert Sizek
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America
| | - Andrew Hamel
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America
| | - Dávid Deritei
- Department of Physics, Pennsylvania State University, State College, PA, United States of America
- Department of Network and Data Science, Central European University, Budapest, Hungary
| | - Sarah Campbell
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America
| | - Erzsébet Ravasz Regan
- Biochemistry and Molecular Biology, The College of Wooster, Wooster, OH, United States of America
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Naldi A. BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks. Front Physiol 2018; 9:1605. [PMID: 30510517 PMCID: PMC6254088 DOI: 10.3389/fphys.2018.01605] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 10/25/2018] [Indexed: 12/13/2022] Open
Abstract
Here we introduce bioLQM, a new Java software toolkit for the conversion, modification, and analysis of Logical Qualitative Models of biological regulatory networks. BioLQM provides core modeling operations as building blocks for the development of integrated modeling software, or for the assembly of heterogeneous analysis workflows involving several complementary tools. Based on the definition of multi-valued logical models, bioLQM implements import and export facilities, notably for the recent SBML qual exchange format, as well as for formats used by several popular tools, facilitating the design of workflows combining these tools. Model modifications enable the definition of various perturbations, as well as model reduction, easing the analysis of large models. Another modification enables the study of multi-valued models with tools limited to the Boolean case. Finally, bioLQM provides a framework for the development of novel analysis tools. The current version implements various updating modes for model simulation (notably synchronous, asynchronous, and random asynchronous), as well as some static analysis features for the identification of attractors. The bioLQM software can be integrated into analysis workflows through command line and scripting interfaces. As a Java library, it further provides core data structures to the GINsim and EpiLog interactive tools, which supply graphical interfaces and additional analysis methods for cellular and multi-cellular qualitative models.
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Affiliation(s)
- Aurélien Naldi
- Computational Systems Biology Team, Institut de Biologie de l'École Normale Supérieure, École Normale Supérieure, CNRS, INSERM, PSL Université, Paris, France
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11
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ATLANTIS - Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming. Sci Rep 2018; 8:3554. [PMID: 29476134 PMCID: PMC5824948 DOI: 10.1038/s41598-018-22031-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 02/15/2018] [Indexed: 12/14/2022] Open
Abstract
Boolean modelling of biological networks is a well-established technique for abstracting dynamical biomolecular regulation in cells. Specifically, decoding linkages between salient regulatory network states and corresponding cell fate outcomes can help uncover pathological foundations of diseases such as cancer. Attractor landscape analysis is one such methodology which converts complex network behavior into a landscape of network states wherein each state is represented by propensity of its occurrence. Towards undertaking attractor landscape analysis of Boolean networks, we propose an Attractor Landscape Analysis Toolbox (ATLANTIS) for cell fate discovery, from biomolecular networks, and reprogramming upon network perturbation. ATLANTIS can be employed to perform both deterministic and probabilistic analyses. It has been validated by successfully reconstructing attractor landscapes from several published case studies followed by reprogramming of cell fates upon therapeutic treatment of network. Additionally, the biomolecular network of HCT-116 colorectal cancer cell line has been screened for therapeutic evaluation of drug-targets. Our results show agreement between therapeutic efficacies reported by ATLANTIS and the published literature. These case studies sufficiently highlight the in silico cell fate prediction and therapeutic screening potential of the toolbox. Lastly, ATLANTIS can also help guide single or combinatorial therapy responses towards reprogramming biomolecular networks to recover cell fates.
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12
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Bloomingdale P, Nguyen VA, Niu J, Mager DE. Boolean network modeling in systems pharmacology. J Pharmacokinet Pharmacodyn 2018; 45:159-180. [PMID: 29307099 PMCID: PMC6531050 DOI: 10.1007/s10928-017-9567-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 12/29/2017] [Indexed: 01/01/2023]
Abstract
Quantitative systems pharmacology (QSP) is an emerging discipline that aims to discover how drugs modulate the dynamics of biological components in molecular and cellular networks and the impact of those perturbations on human pathophysiology. The integration of systems-based experimental and computational approaches is required to facilitate the advancement of this field. QSP models typically consist of a series of ordinary differential equations (ODE). However, this mathematical framework requires extensive knowledge of parameters pertaining to biological processes, which is often unavailable. An alternative framework that does not require knowledge of system-specific parameters, such as Boolean network modeling, could serve as an initial foundation prior to the development of an ODE-based model. Boolean network models have been shown to efficiently describe, in a qualitative manner, the complex behavior of signal transduction and gene/protein regulatory processes. In addition to providing a starting point prior to quantitative modeling, Boolean network models can also be utilized to discover novel therapeutic targets and combinatorial treatment strategies. Identifying drug targets using a network-based approach could supplement current drug discovery methodologies and help to fill the innovation gap across the pharmaceutical industry. In this review, we discuss the process of developing Boolean network models and the various analyses that can be performed to identify novel drug targets and combinatorial approaches. An example for each of these analyses is provided using a previously developed Boolean network of signaling pathways in multiple myeloma. Selected examples of Boolean network models of human (patho-)physiological systems are also reviewed in brief.
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Affiliation(s)
- Peter Bloomingdale
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, The State University of New York, 431 Kapoor Hall, Buffalo, NY, 14214, USA
| | - Van Anh Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, The State University of New York, 431 Kapoor Hall, Buffalo, NY, 14214, USA
| | - Jin Niu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, The State University of New York, 431 Kapoor Hall, Buffalo, NY, 14214, USA
| | - Donald E Mager
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, The State University of New York, 431 Kapoor Hall, Buffalo, NY, 14214, USA.
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13
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Booth L, Roberts JL, Poklepovic A, Avogadri-Connors F, Cutler RE, Lalani AS, Dent P. HDAC inhibitors enhance neratinib activity and when combined enhance the actions of an anti-PD-1 immunomodulatory antibody in vivo. Oncotarget 2017; 8:90262-90277. [PMID: 29163826 PMCID: PMC5685747 DOI: 10.18632/oncotarget.21660] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 09/13/2017] [Indexed: 01/14/2023] Open
Abstract
Patients whose NSCLC tumors become afatinib resistant presently have few effective therapeutic options to extend their survival. Afatinib resistant NSCLC cells were sensitive to clinically relevant concentrations of the irreversible pan-HER inhibitor neratinib, but not by the first generation ERBB1/2/4 inhibitor lapatinib. In multiple afatinib resistant NSCLC clones, HDAC inhibitors reduced the expression of ERBB1/3/4, but activated c-SRC, which resulted in higher total levels of ERBB1/3 phosphorylation. Neratinib also rapidly reduced the expression of ERBB1/2/3/4, c-MET and of mutant K-/N-RAS; K-RAS co-localized with phosphorylated ATG13 and with cathepsin B in vesicles. Combined exposure of cells to [neratinib + HDAC inhibitors] caused inactivation of mTORC1 and mTORC2, enhanced autophagosome and subsequently autolysosome formation, and caused an additive to greater than additive induction of cell death. Knock down of Beclin1 or ATG5 prevented HDAC inhibitors or neratinib from reducing ERBB1/3/4 and K-/N-RAS expression and reduced [neratinib + HDAC inhibitor] lethality. Neratinib and HDAC inhibitors reduced the expression of multiple HDAC proteins via autophagy that was causal in the reduced expression of PD-L1, PD-L2 and ornithine decarboxylase, and increased expression of Class I MHCA. In vivo, neratinib and HDAC inhibitors interacted to suppress the growth of 4T1 mammary tumors, an effect that was enhanced by an anti-PD-1 antibody. Our data support the premises that neratinib lethality can be enhanced by HDAC inhibitors, that neratinib may be a useful therapeutic tool in afatinib resistant NSCLC, and that [neratinib + HDAC inhibitor] exposure facilitates anti-tumor immune responses.
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Affiliation(s)
- Laurence Booth
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jane L. Roberts
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Andrew Poklepovic
- Department of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | | | | | | | - Paul Dent
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23298, USA
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Timmermans-Sprang EPM, Gracanin A, Mol JA. Molecular Signaling of Progesterone, Growth Hormone, Wnt, and HER in Mammary Glands of Dogs, Rodents, and Humans: New Treatment Target Identification. Front Vet Sci 2017; 4:53. [PMID: 28451590 PMCID: PMC5389977 DOI: 10.3389/fvets.2017.00053] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/28/2017] [Indexed: 12/21/2022] Open
Abstract
Mammary tumors are the most common form of neoplasia in the bitch. Female dogs are protected when they are spayed before the first estrus cycle, but this effect readily disappears and is already absent when dogs are spayed after the second heat. As the ovaries are removed during spaying, ovarian steroids are assumed to play an essential role in tumor development. The sensitivity toward tumor development is already present during early life, which may be caused by early mutations in stem cells during the first estrus cycles. Later on in life, tumors arise that are mostly steroid-receptor positive, although a small subset of tumors overexpressing human epidermal growth factor 2 (HER2) and some lacking estrogen receptor, progesterone receptor (PR), and HER2 (triple negative) are present, as is the situation in humans. Progesterone (P4), acting through PR, is the major steroid involved in outgrowth of mammary tissue. PRs are expressed in two forms, the progesterone receptor A (PRA) and progesterone receptor B (PRB) isoforms derived from splice variants from a single gene. The dog and the whole family of canids have only a functional PRA isoform, whereas the PRB isoform, if expressed at all, is devoid of intrinsic biological activity. In human breast cancer, overexpression of the PRA isoform is related to more aggressive carcinomas making the dog a unique model to study PRA-related mammary cancer. Administration of P4 to adult dogs results in local mammary expression of growth hormone (GH) and wing less-type mouse mammary tumor virus integration site family 4 (Wnt4). Both proteins play a role in activation of mammary stem cells. In this review, we summarize what is known on P4, GH, and Wnt signaling in canine mammary cancer, how the family of HER receptors could interact with this signaling, and what this means for comparative and translational oncological aspects of human breast cancer development.
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Affiliation(s)
| | - Ana Gracanin
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, Netherlands
| | - Jan A Mol
- Department of Clinical Sciences of Companion Animals, Utrecht University, Utrecht, Netherlands
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Murrugarra D, Miller J, Mueller AN. Estimating Propensity Parameters Using Google PageRank and Genetic Algorithms. Front Neurosci 2016; 10:513. [PMID: 27891072 PMCID: PMC5104906 DOI: 10.3389/fnins.2016.00513] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/25/2016] [Indexed: 12/03/2022] Open
Abstract
Stochastic Boolean networks, or more generally, stochastic discrete networks, are an important class of computational models for molecular interaction networks. The stochasticity stems from the updating schedule. Standard updating schedules include the synchronous update, where all the nodes are updated at the same time, and the asynchronous update where a random node is updated at each time step. The former produces a deterministic dynamics while the latter a stochastic dynamics. A more general stochastic setting considers propensity parameters for updating each node. Stochastic Discrete Dynamical Systems (SDDS) are a modeling framework that considers two propensity parameters for updating each node and uses one when the update has a positive impact on the variable, that is, when the update causes the variable to increase its value, and uses the other when the update has a negative impact, that is, when the update causes it to decrease its value. This framework offers additional features for simulations but also adds a complexity in parameter estimation of the propensities. This paper presents a method for estimating the propensity parameters for SDDS. The method is based on adding noise to the system using the Google PageRank approach to make the system ergodic and thus guaranteeing the existence of a stationary distribution. Then with the use of a genetic algorithm, the propensity parameters are estimated. Approximation techniques that make the search algorithms efficient are also presented and Matlab/Octave code to test the algorithms are available at http://www.ms.uky.edu/~dmu228/GeneticAlg/Code.html.
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Affiliation(s)
- David Murrugarra
- Department of Mathematics, University of Kentucky Lexington, KY, USA
| | - Jacob Miller
- Department of Mathematics, University of Kentucky Lexington, KY, USA
| | - Alex N Mueller
- Department of Mathematics, University of Kentucky Lexington, KY, USA
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Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C. Logical Modeling and Dynamical Analysis of Cellular Networks. Front Genet 2016; 7:94. [PMID: 27303434 PMCID: PMC4885885 DOI: 10.3389/fgene.2016.00094] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 05/12/2016] [Indexed: 12/28/2022] Open
Abstract
The logical (or logic) formalism is increasingly used to model regulatory and signaling networks. Complementing these applications, several groups contributed various methods and tools to support the definition and analysis of logical models. After an introduction to the logical modeling framework and to several of its variants, we review here a number of recent methodological advances to ease the analysis of large and intricate networks. In particular, we survey approaches to determine model attractors and their reachability properties, to assess the dynamical impact of variations of external signals, and to consistently reduce large models. To illustrate these developments, we further consider several published logical models for two important biological processes, namely the differentiation of T helper cells and the control of mammalian cell cycle.
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Affiliation(s)
- Wassim Abou-Jaoudé
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, PSL Research UniversityParis, France
| | - Pauline Traynard
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, PSL Research UniversityParis, France
| | - Pedro T. Monteiro
- INESC-ID/Instituto Superior Técnico, University of LisbonLisbon, Portugal
- Instituto Gulbenkian de CiênciaOeiras, Portugal
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Joint Research Centre for Computational Biomedicine, RWTH Aachen UniversityAachen, Germany
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-LincolnLincoln, NE, USA
| | - Denis Thieffry
- Computational Systems Biology Team, Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, Ecole Normale Supérieure, PSL Research UniversityParis, France
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Li H, Yu C, Jiang J, Huang C, Yao X, Xu Q, Yu F, Lou L, Fang J. An anti-HER2 antibody conjugated with monomethyl auristatin E is highly effective in HER2-positive human gastric cancer. Cancer Biol Ther 2016; 17:346-54. [PMID: 26853765 DOI: 10.1080/15384047.2016.1139248] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Antibody-drug conjugate (ADC) is a novel class of therapeutics for cancer target therapy. This study assessed antitumor activity of ADC with an antimitotic agent, monomethyl auristatin E (MMAE) and a humanized monoclonal anti-HER2 antibody, hertuzumab, in gastric cancer. The efficacy of hertuzumab-MC-Val-Cit-PAB-MMAE (hertuzumab-vcMMAE) on human epidermal growth factor receptor 2 (HER2) positive human gastric cancer cells, NCI-N87, was evaluated in vitro and in vivo. The cytotoxicity of hertuzumab was significantly enhanced after conjugation with MMAE. Compared to trastuzumab, hertuzumab had a higher affinity to HER2 and had more potent antibody-dependent cell-mediated cytotoxicity (ADCC) activity in vitro. After conjugation with MMAE, the binding specificity for HER2 was not affected. Furthermore, the internalization of hertuzumab-vcMMAE in HER2 positive gastric cancer cells was verified. Although the conjugation of hertuzumab and MMAE decreased the ADCC effect, the overall cytotoxicity was dramatically increased in HER2 positive gastric cancer cells. In vitro data on this hertuzumab-vcMMAE has exerted much stronger antitumor activity compared to trastuzumab-DM1 in HER2 positive gastric cancer cells. A single administration of hertuzumab-vcMMAE at 5 or 10 mg/kg showed high potency and a sustained tumor inhibitory effect on NCI-N87 xenografts in mice. In conclusion, hertuzumab-vcMMAE conjugate is a highly effective anti-HER2 targeted therapy for HER2-positive gastric cancer.
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Affiliation(s)
- Hongwen Li
- a School of Life Sciences and Technology, Tongji University , Shanghai , China
| | - Chao Yu
- b RemeGen, Ltd. , Yantai , Shandong , China
| | - Jing Jiang
- c School of Pharmacy, Binzhou Medical University , Yantai , Shandong , China
| | | | - Xuejing Yao
- a School of Life Sciences and Technology, Tongji University , Shanghai , China
| | - Qiaoyu Xu
- b RemeGen, Ltd. , Yantai , Shandong , China
| | - Fang Yu
- b RemeGen, Ltd. , Yantai , Shandong , China
| | - Liguang Lou
- d Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai , China
| | - Jianmin Fang
- a School of Life Sciences and Technology, Tongji University , Shanghai , China.,e Tongji University Suzhou Institute , Suzhou , Jiangsu , China.,f Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University , Chengdu , Sichuan , China
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Murrugarra D, Dimitrova ES. Molecular network control through boolean canalization. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2015; 2015:9. [PMID: 26752585 PMCID: PMC4699631 DOI: 10.1186/s13637-015-0029-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/22/2015] [Indexed: 01/12/2023]
Abstract
Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of network modeling where each layer of canalization adds a degree of stability in the dynamics of the network. Recently, dynamic network control approaches have been used for the design of new therapeutic interventions and for other applications such as stem cell reprogramming. This work studies the role of canalization in the control of Boolean molecular networks. It provides a method for identifying the potential edges to control in the wiring diagram of a network for avoiding undesirable state transitions. The method is based on identifying appropriate input-output combinations on undesirable transitions that can be modified using the edges in the wiring diagram of the network. Moreover, a method for estimating the number of changed transitions in the state space of the system as a result of an edge deletion in the wiring diagram is presented. The control methods of this paper were applied to a mutated cell-cycle model and to a p53-mdm2 model to identify potential control targets.
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Affiliation(s)
- David Murrugarra
- Department of Mathematics, University of Kentucky, Lexington, 40506-0027 KY USA
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Bhattacharjee S, Brayden DJ. Development of nanotoxicology: implications for drug delivery and medical devices. Nanomedicine (Lond) 2015; 10:2289-305. [DOI: 10.2217/nnm.15.69] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Current nanotoxicology research suffers from suboptimal in vitro models, lack of in vitro–in vivo correlations, variability within in vitro protocols, deficits in both material purity and physicochemical characterization. Reliable nanomaterial toxicity and mechanistic insights are required for health and toxicity risk assessments. Much in vitro toxicological data is inconclusive in designating whether nanomaterials for drug delivery and medical device implants are truly safe. A critique is presented to analyze the interface between toxicology and nanopharmaceuticals. Deficiencies of existing practices in toxicology are reviewed and useful emerging techniques (e.g., lab-on-a-chip, tissue engineering, atomic force microscopy, high-content analysis) are highlighted. Cross-fertilization between disciplines will aid development of biocompatible delivery and implant platforms while improvements are being suggested for better translation of nanotoxicology.
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Affiliation(s)
| | - David J Brayden
- Conway Institute, University College Dublin (UCD), Dublin, Ireland
- School of Veterinary Medicine, University College Dublin (UCD), Dublin, Ireland
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20
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Naldi A, Monteiro PT, Müssel C, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C. Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics 2015; 31:1154-9. [PMID: 25619997 DOI: 10.1093/bioinformatics/btv013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/05/2015] [Indexed: 01/17/2023] Open
Abstract
The identification of large regulatory and signalling networks involved in the control of crucial cellular processes calls for proper modelling approaches. Indeed, models can help elucidate properties of these networks, understand their behaviour and provide (testable) predictions by performing in silico experiments. In this context, qualitative, logical frameworks have emerged as relevant approaches, as demonstrated by a growing number of published models, along with new methodologies and software tools. This productive activity now requires a concerted effort to ensure model reusability and interoperability between tools. Following an outline of the logical modelling framework, we present the most important achievements of the Consortium for Logical Models and Tools, along with future objectives. Our aim is to advertise this open community, which welcomes contributions from all researchers interested in logical modelling or in related mathematical and computational developments.
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Affiliation(s)
- Aurélien Naldi
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Pedro T Monteiro
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Christoph Müssel
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | | | - Hans A Kestler
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Res
| | - Denis Thieffry
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Ioannis Xenarios
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Julio Saez-Rodriguez
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Tomas Helikar
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Claudine Chaouiya
- Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland, Instituto de Engenharia de Sistemas e Computadores-Investigação e Desenvolvimento (INESC-ID), Lisbon, Portugal, Instituto Gulbenkian de Ciência (IGC), Oeiras, Portugal, Medical Systems Biology, Ulm University, Germany, Friedrich-Schiller University Jena, Jena, Germany, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena, Germany, Institut de Biologie de l'École Normale Supérieure (IBENS)-UMR CNRS 8197-INSERM 1024, Paris, France, Swiss-Prot & Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
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Chung BM, Tom E, Zutshi N, Bielecki TA, Band V, Band H. Nexus of signaling and endocytosis in oncogenesis driven by non-small cell lung cancer-associated epidermal growth factor receptor mutants. World J Clin Oncol 2014; 5:806-823. [PMID: 25493220 PMCID: PMC4259944 DOI: 10.5306/wjco.v5.i5.806] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/19/2014] [Accepted: 09/10/2014] [Indexed: 02/06/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) controls a wide range of cellular processes, and aberrant EGFR signaling as a result of receptor overexpression and/or mutation occurs in many types of cancer. Tumor cells in non-small cell lung cancer (NSCLC) patients that harbor EGFR kinase domain mutations exhibit oncogene addiction to mutant EGFR, which confers high sensitivity to tyrosine kinase inhibitors (TKIs). As patients invariably develop resistance to TKIs, it is important to delineate the cell biological basis of mutant EGFR-induced cellular transformation since components of these pathways can serve as alternate therapeutic targets to preempt or overcome resistance. NSCLC-associated EGFR mutants are constitutively-active and induce ligand-independent transformation in nonmalignant cell lines. Emerging data suggest that a number of factors are critical for the mutant EGFR-dependent tumorigenicity, and bypassing the effects of TKIs on these pathways promotes drug resistance. For example, activation of downstream pathways such as Akt, Erk, STAT3 and Src is critical for mutant EGFR-mediated biological processes. It is now well-established that the potency and spatiotemporal features of cellular signaling by receptor tyrosine kinases such as EGFR, as well as the specific pathways activated, is determined by the nature of endocytic traffic pathways through which the active receptors traverse. Recent evidence indicates that NSCLC-associated mutant EGFRs exhibit altered endocytic trafficking and they exhibit reduced Cbl ubiquitin ligase-mediated lysosomal downregulation. More recent work has shown that mutant EGFRs undergo ligand-independent traffic into the endocytic recycling compartment, a behavior that plays a key role in Src pathway activation and oncogenesis. These studies are beginning to delineate the close nexus between signaling and endocytic traffic of EGFR mutants as a key driver of oncogenic processes. Therefore, in this review, we will discuss the links between mutant EGFR signaling and endocytic properties, and introduce potential mechanisms by which altered endocytic properties of mutant EGFRs may alter signaling and vice versa as well as their implications for NSCLC therapy.
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22
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Conroy BD, Herek TA, Shew TD, Latner M, Larson JJ, Allen L, Davis PH, Helikar T, Cutucache CE. Design, Assessment, and in vivo Evaluation of a Computational Model Illustrating the Role of CAV1 in CD4(+) T-lymphocytes. Front Immunol 2014; 5:599. [PMID: 25538703 PMCID: PMC4257089 DOI: 10.3389/fimmu.2014.00599] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/07/2014] [Indexed: 01/08/2023] Open
Abstract
Caveolin-1 (CAV1) is a vital scaffold protein heterogeneously expressed in both healthy and malignant tissue. We focus on the role of CAV1 when overexpressed in T-cell leukemia. Previously, we have shown that CAV1 is involved in cell-to-cell communication, cellular proliferation, and immune synapse formation; however, the molecular mechanisms have not been elucidated. We hypothesize that the role of CAV1 in immune synapse formation contributes to immune regulation during leukemic progression, thereby warranting studies of the role of CAV1 in CD4+ T-cells in relation to antigen-presenting cells. To address this need, we developed a computational model of a CD4+ immune effector T-cell to mimic cellular dynamics and molecular signaling under healthy and immunocompromised conditions (i.e., leukemic conditions). Using the Cell Collective computational modeling software, the CD4+ T-cell model was constructed and simulated under CAV1+/+, CAV1+/−, and CAV1−/− conditions to produce a hypothetical immune response. This model allowed us to predict and examine the heterogeneous effects and mechanisms of CAV1 in silico. Experimental results indicate a signature of molecules involved in cellular proliferation, cell survival, and cytoskeletal rearrangement that were highly affected by CAV1 knock out. With this comprehensive model of a CD4+ T-cell, we then validated in vivo protein expression levels. Based on this study, we modeled a CD4+ T-cell, manipulated gene expression in immunocompromised versus competent settings, validated these manipulations in an in vivo murine model, and corroborated acute T-cell leukemia gene expression profiles in human beings. Moreover, we can model an immunocompetent versus an immunocompromised microenvironment to better understand how signaling is regulated in patients with leukemia.
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Affiliation(s)
- Brittany D Conroy
- Department of Biology, University of Nebraska at Omaha , Omaha, NE , USA
| | - Tyler A Herek
- Department of Biology, University of Nebraska at Omaha , Omaha, NE , USA
| | - Timothy D Shew
- Department of Biology, University of Nebraska at Omaha , Omaha, NE , USA
| | - Matthew Latner
- Department of Biology, University of Nebraska at Omaha , Omaha, NE , USA
| | - Joshua J Larson
- Department of Biology, University of Nebraska at Omaha , Omaha, NE , USA
| | - Laura Allen
- Department of Biology, University of Nebraska at Omaha , Omaha, NE , USA
| | - Paul H Davis
- Department of Biology, University of Nebraska at Omaha , Omaha, NE , USA
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska at Lincoln , Lincoln, NE , USA
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Oyeyemi OJ, Davies O, Robertson DL, Schwartz JM. A logical model of HIV-1 interactions with the T-cell activation signalling pathway. ACTA ACUST UNITED AC 2014; 31:1075-83. [PMID: 25431332 DOI: 10.1093/bioinformatics/btu787] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 11/20/2014] [Indexed: 01/21/2023]
Abstract
MOTIVATION Human immunodeficiency virus type 1 (HIV-1) hijacks host cellular processes to replicate within its host. Through interactions with host proteins, it perturbs and interrupts signaling pathways that alter key cellular functions. Although networks of viral-host interactions have been relatively well characterized, the dynamics of the perturbation process is poorly understood. Dynamic models of infection have the potential to provide insights into the HIV-1 host interaction. RESULTS We employed a logical signal flow network to model the dynamic interactions between HIV-1 proteins and key human signal transduction pathways necessary for activation of CD4+ T lymphocytes. We integrated viral-host interaction and host signal transduction data into a dynamic logical model comprised of 137 nodes (16 HIV-1 and 121 human proteins) and 336 interactions collected from the HIV-1 Human Interaction Database. The model reproduced expected patterns of T-cell activation, co-stimulation and co-inhibition. After simulations, we identified 26 host cell factors, including MAPK1&3, Ikkb-Ikky-Ikka and PKA, which contribute to the net activation or inhibition of viral proteins. Through in silico knockouts, the model identified a further nine host cell factors, including members of the PI3K signalling pathway that are essential to viral replication. Simulation results intersected with the findings of three siRNA gene knockout studies and identified potential drug targets. Our results demonstrate how viral infection causes the cell to lose control of its signalling system. Logical Boolean modelling therefore provides a useful approach for analysing the dynamics of host-viral interactions with potential applications for drug discovery. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Oyebode J Oyeyemi
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Oluwafemi Davies
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - David L Robertson
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jean-Marc Schwartz
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
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Bailey TA, Luan H, Tom E, Bielecki TA, Mohapatra B, Ahmad G, George M, Kelly DL, Natarajan A, Raja SM, Band V, Band H. A kinase inhibitor screen reveals protein kinase C-dependent endocytic recycling of ErbB2 in breast cancer cells. J Biol Chem 2014; 289:30443-30458. [PMID: 25225290 DOI: 10.1074/jbc.m114.608992] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ErbB2 overexpression drives oncogenesis in 20-30% cases of breast cancer. Oncogenic potential of ErbB2 is linked to inefficient endocytic traffic into lysosomes and preferential recycling. However, regulation of ErbB2 recycling is incompletely understood. We used a high-content immunofluorescence imaging-based kinase inhibitor screen on SKBR-3 breast cancer cells to identify kinases whose inhibition alters the clearance of cell surface ErbB2 induced by Hsp90 inhibitor 17-AAG. Less ErbB2 clearance was observed with broad-spectrum PKC inhibitor Ro 31-8220. A similar effect was observed with Go 6976, a selective inhibitor of classical Ca(2+)-dependent PKCs (α, β1, βII, and γ). PKC activation by PMA promoted surface ErbB2 clearance but without degradation, and ErbB2 was observed to move into a juxtanuclear compartment where it colocalized with PKC-α and PKC-δ together with the endocytic recycling regulator Arf6. PKC-α knockdown impaired the juxtanuclear localization of ErbB2. ErbB2 transit to the recycling compartment was also impaired upon PKC-δ knockdown. PMA-induced Erk phosphorylation was reduced by ErbB2 inhibitor lapatinib, as well as by knockdown of PKC-δ but not that of PKC-α. Our results suggest that activation of PKC-α and -δ mediates a novel positive feedback loop by promoting ErbB2 entry into the endocytic recycling compartment, consistent with reported positive roles for these PKCs in ErbB2-mediated tumorigenesis. As the endocytic recycling compartment/pericentrion has emerged as a PKC-dependent signaling hub for G-protein-coupled receptors, our findings raise the possibility that oncogenesis by ErbB2 involves previously unexplored PKC-dependent endosomal signaling.
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Affiliation(s)
- Tameka A Bailey
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950
| | - Haitao Luan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950; Departments of Genetics, Cell Biology, and Anatomy, and University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950
| | - Eric Tom
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950; Departments of Biochemistry & Molecular Biology, College of Medicine, and University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950
| | - Timothy Alan Bielecki
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950
| | - Bhopal Mohapatra
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950; Departments of Biochemistry & Molecular Biology, College of Medicine, and University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950
| | - Gulzar Ahmad
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950
| | - Manju George
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950
| | - David L Kelly
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950
| | - Srikumar M Raja
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950
| | - Vimla Band
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950; Departments of Genetics, Cell Biology, and Anatomy, and University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950
| | - Hamid Band
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950; Departments of Genetics, Cell Biology, and Anatomy, and University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950; Departments of Biochemistry & Molecular Biology, College of Medicine, and University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950; Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, 985950 Nebraska Medical Center, Omaha, Nebraska 68198-5950.
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25
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Kochi N, Helikar T, Allen L, Rogers JA, Wang Z, Matache MT. Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions. BMC SYSTEMS BIOLOGY 2014; 8:92. [PMID: 25189194 PMCID: PMC4363947 DOI: 10.1186/s12918-014-0092-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 07/21/2014] [Indexed: 11/16/2022]
Abstract
Background An algebraic method for information fusion based on nonadditive set functions is used to assess the joint contribution of Boolean network attributes to the sensitivity of the network to individual node mutations. The node attributes or characteristics under consideration are: in-degree, out-degree, minimum and average path lengths, bias, average sensitivity of Boolean functions, and canalizing degrees. The impact of node mutations is assessed using as target measure the average Hamming distance between a non-mutated/wild-type network and a mutated network. Results We find that for a biochemical signal transduction network consisting of several main signaling pathways whose nodes represent signaling molecules (mainly proteins), the algebraic method provides a robust classification of attribute contributions. This method indicates that for the biochemical network, the most significant impact is generated mainly by the combined effects of two attributes: out-degree, and average sensitivity of nodes. Conclusions The results support the idea that both topological and dynamical properties of the nodes need to be under consideration. The algebraic method is robust against the choice of initial conditions and partition of data sets in training and testing sets for estimation of the nonadditive set functions of the information fusion procedure.
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Affiliation(s)
- Naomi Kochi
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha NE 68198, USA.
| | - Tomáš Helikar
- Department of Mathematics, University of Nebraska at Omaha, Omaha NE 68182, USA. .,Department of Biochemistry, University of Nebraska-Lincoln, Lincoln NE 68588, USA.
| | - Laura Allen
- Department of Mathematics, University of Nebraska at Omaha, Omaha NE 68182, USA.
| | - Jim A Rogers
- Department of Mathematics, University of Nebraska at Omaha, Omaha NE 68182, USA.
| | - Zhenyuan Wang
- Department of Mathematics, University of Nebraska at Omaha, Omaha NE 68182, USA.
| | - Mihaela T Matache
- Department of Mathematics, University of Nebraska at Omaha, Omaha NE 68182, USA.
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26
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Veliz-Cuba A, Aguilar B, Hinkelmann F, Laubenbacher R. Steady state analysis of Boolean molecular network models via model reduction and computational algebra. BMC Bioinformatics 2014; 15:221. [PMID: 24965213 PMCID: PMC4230806 DOI: 10.1186/1471-2105-15-221] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/17/2014] [Indexed: 01/09/2023] Open
Abstract
Background A key problem in the analysis of mathematical models of molecular networks is the determination of their steady states. The present paper addresses this problem for Boolean network models, an increasingly popular modeling paradigm for networks lacking detailed kinetic information. For small models, the problem can be solved by exhaustive enumeration of all state transitions. But for larger models this is not feasible, since the size of the phase space grows exponentially with the dimension of the network. The dimension of published models is growing to over 100, so that efficient methods for steady state determination are essential. Several methods have been proposed for large networks, some of them heuristic. While these methods represent a substantial improvement in scalability over exhaustive enumeration, the problem for large networks is still unsolved in general. Results This paper presents an algorithm that consists of two main parts. The first is a graph theoretic reduction of the wiring diagram of the network, while preserving all information about steady states. The second part formulates the determination of all steady states of a Boolean network as a problem of finding all solutions to a system of polynomial equations over the finite number system with two elements. This problem can be solved with existing computer algebra software. This algorithm compares favorably with several existing algorithms for steady state determination. One advantage is that it is not heuristic or reliant on sampling, but rather determines algorithmically and exactly all steady states of a Boolean network. The code for the algorithm, as well as the test suite of benchmark networks, is available upon request from the corresponding author. Conclusions The algorithm presented in this paper reliably determines all steady states of sparse Boolean networks with up to 1000 nodes. The algorithm is effective at analyzing virtually all published models even those of moderate connectivity. The problem for large Boolean networks with high average connectivity remains an open problem.
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Affiliation(s)
- Alan Veliz-Cuba
- Department of Mathematics, University of Houston, 651 PGH Building, Houston TX, USA.
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27
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Niarakis A, Bounab Y, Grieco L, Roncagalli R, Hesse AM, Garin J, Malissen B, Daëron M, Thieffry D. Computational modeling of the main signaling pathways involved in mast cell activation. Curr Top Microbiol Immunol 2014; 382:69-93. [PMID: 25116096 DOI: 10.1007/978-3-319-07911-0_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A global and rigorous understanding of the signaling pathways and cross-regulatory processes involved in mast cell activation requires the integration of published information with novel functional datasets into a comprehensive computational model. Based on an exhaustive curation of the existing literature and using the software CellDesigner, we have built and annotated a comprehensive molecular map for the FcεRI signaling network. This map can be used to visualize and interpret high-throughput expression data. Furthermore, leaning on this map and using the logical modeling software GINsim, we have derived a qualitative dynamical model, which recapitulates the most salient features of mast cell activation. The resulting logical model can be used to explore the dynamical properties of the system and its responses to different stimuli, in normal or mutant conditions.
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Affiliation(s)
- Anna Niarakis
- Institut de Biologie de l'ENS (IBENS), Ecole Normale Supérieure, Paris, France
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Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC SYSTEMS BIOLOGY 2013; 7:135. [PMID: 24321545 PMCID: PMC3892043 DOI: 10.1186/1752-0509-7-135] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/26/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise quantitative data, and that they are well-suited for studies of large networks. While numerous groups have developed specific computational tools that provide original methods to analyse qualitative models, a standard format to exchange qualitative models has been missing. RESULTS We present the Systems Biology Markup Language (SBML) Qualitative Models Package ("qual"), an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks. We demonstrate the interoperability of models via SBML qual through the analysis of a specific signalling network by three independent software tools. Furthermore, the collective effort to define the SBML qual format paved the way for the development of LogicalModel, an open-source model library, which will facilitate the adoption of the format as well as the collaborative development of algorithms to analyse qualitative models. CONCLUSIONS SBML qual allows the exchange of qualitative models among a number of complementary software tools. SBML qual has the potential to promote collaborative work on the development of novel computational approaches, as well as on the specification and the analysis of comprehensive qualitative models of regulatory and signalling networks.
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Affiliation(s)
- Claudine Chaouiya
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Duncan Bérenguier
- Institut de Mathématiques de Luminy, Campus de Luminy, Case 907, 13288 Marseille Cedex 9, France
| | - Sarah M Keating
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Aurélien Naldi
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Martijn P van Iersel
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nicolas Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Andreas Dräger
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093-0412, USA
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 Tübingen, Germany
| | - Finja Büchel
- Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 Tübingen, Germany
| | - Thomas Cokelaer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bryan Kowal
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Benjamin Wicks
- College of Information Science and Technology, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Emanuel Gonçalves
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Julien Dorier
- Swiss-Prot & Vital-IT group, SIB- Swiss Institute of Bioinformatics, Center for Integrative Genomics, University of Lausanne, Quartier Sorge - Batiment Genopode, CH-1015 Lausanne, Switzerland
| | - Michel Page
- INRIA Grenoble – Rhône-Alpes, 655 avenue de l’Europe, Montbonnot, 38334 Saint-Ismier Cedex, France
- IAE Grenoble, Université Pierre-Mendès-France, Domaine universitaire BP 47, 38040 Grenoble Cedex 9, France
| | - Pedro T Monteiro
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
- Instituto de Engenharia de Sistemas e Computadores - Investigação e Desenvolvimento (INESC-ID), Rua Alves Redol 9, 1000-029 Lisbon, Portugal
| | - Axel von Kamp
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, D-39106 Magdeburg, Germany
| | - Ioannis Xenarios
- Swiss-Prot & Vital-IT group, SIB- Swiss Institute of Bioinformatics, Center for Integrative Genomics, University of Lausanne, Quartier Sorge - Batiment Genopode, CH-1015 Lausanne, Switzerland
| | - Hidde de Jong
- INRIA Grenoble – Rhône-Alpes, 655 avenue de l’Europe, Montbonnot, 38334 Saint-Ismier Cedex, France
| | - Michael Hucka
- Computing and Mathematical sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Steffen Klamt
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, D-39106 Magdeburg, Germany
| | - Denis Thieffry
- Institut de Biologie de l’Ecole Normale Supérieure (IBENS) - UMR CNRS 8197 - INSERM 1024 46 rue d’Ulm, 75230 Paris Cedex 05, France
| | - Nicolas Le Novère
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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Kariya Y, Honma M, Suzuki H. Systems-based understanding of pharmacological responses with combinations of multidisciplinary methodologies. Biopharm Drug Dispos 2013; 34:489-507. [DOI: 10.1002/bdd.1865] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 10/06/2013] [Indexed: 12/25/2022]
Affiliation(s)
- Yoshiaki Kariya
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine; The University of Tokyo; 113-8655 Tokyo Japan
| | - Masashi Honma
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine; The University of Tokyo; 113-8655 Tokyo Japan
| | - Hiroshi Suzuki
- Department of Pharmacy, The University of Tokyo Hospital, Faculty of Medicine; The University of Tokyo; 113-8655 Tokyo Japan
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