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Nanda P, Budak M, Michael CT, Krupinsky K, Kirschner DE. Development and Analysis of Multiscale Models for Tuberculosis: From Molecules to Populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566861. [PMID: 38014103 PMCID: PMC10680629 DOI: 10.1101/2023.11.13.566861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Although infectious disease dynamics are often analyzed at the macro-scale, increasing numbers of drug-resistant infections highlight the importance of within-host modeling that simultaneously solves across multiple scales to effectively respond to epidemics. We review multiscale modeling approaches for complex, interconnected biological systems and discuss critical steps involved in building, analyzing, and applying such models within the discipline of model credibility. We also present our two tools: CaliPro, for calibrating multiscale models (MSMs) to datasets, and tunable resolution, for fine- and coarse-graining sub-models while retaining insights. We include as an example our work simulating infection with Mycobacterium tuberculosis to demonstrate modeling choices and how predictions are made to generate new insights and test interventions. We discuss some of the current challenges of incorporating novel datasets, rigorously training computational biologists, and increasing the reach of MSMs. We also offer several promising future research directions of incorporating within-host dynamics into applications ranging from combinatorial treatment to epidemic response.
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Darragh LB, Knitz MM, Hu J, Clambey ET, Backus J, Dumit A, Samedi V, Bubak A, Greene C, Waxweiler T, Mehrotra S, Bhatia S, Gadwa J, Bickett T, Piper M, Fakhoury K, Liu A, Petit J, Bowles D, Thaker A, Atiyeh K, Goddard J, Hoyer R, Van Bokhoven A, Jordan K, Jimeno A, D'Alessandro A, Raben D, McDermott JD, Karam SD. A phase I/Ib trial and biological correlate analysis of neoadjuvant SBRT with single-dose durvalumab in HPV-unrelated locally advanced HNSCC. NATURE CANCER 2022; 3:1300-1317. [PMID: 36434392 PMCID: PMC9701140 DOI: 10.1038/s43018-022-00450-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 09/21/2022] [Indexed: 11/27/2022]
Abstract
Five-year survival for human papilloma virus-unrelated head and neck squamous cell carcinomas remain below 50%. We assessed the safety of administering combination hypofractionated stereotactic body radiation therapy with single-dose durvalumab (anti-PD-L1) neoadjuvantly (n = 21) ( NCT03635164 ). The primary endpoint of the study was safety, which was met. Secondary endpoints included radiographic, pathologic and objective response; locoregional control; progression-free survival; and overall survival. Among evaluable patients at an early median follow-up of 16 months (448 d or 64 weeks), overall survival was 80.1% with 95% confidence interval (95% CI) (62.0%, 100.0%), locoregional control and progression-free survival were 75.8% with 95% CI (57.5%, 99.8%), and major pathological response or complete response was 75% with 95% exact CI (51.6%, 100.0%). For patients treated with 24 Gy, 89% with 95% CI (57.1%, 100.0%) had MPR or CR. Using high-dimensional multi-omics and spatial data as well as biological correlatives, we show that responders had: (1) an increase in effector T cells; (2) a decrease in immunosuppressive cells; and (3) an increase in antigen presentation post-treatment.
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Affiliation(s)
- Laurel B Darragh
- Radiation Oncology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
- Department of Immunology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Michael M Knitz
- Radiation Oncology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Junxiao Hu
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Eric T Clambey
- Department of Anesthesiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jennifer Backus
- Radiation Oncology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew Dumit
- Radiation Oncology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Von Samedi
- Department of Pathology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Andrew Bubak
- Department of Neurology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Casey Greene
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Timothy Waxweiler
- Radiation Oncology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Sanjana Mehrotra
- Department of Pathology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Shilpa Bhatia
- Radiation Oncology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Jacob Gadwa
- Radiation Oncology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas Bickett
- Radiation Oncology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Miles Piper
- Radiation Oncology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Kareem Fakhoury
- Radiation Oncology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Arthur Liu
- Department of Radiation Oncology, University of Colorado, Poudre Valley Hospital, Fort Collins, CO, USA
| | - Joshua Petit
- Department of Radiation Oncology, University of Colorado, Poudre Valley Hospital, Fort Collins, CO, USA
| | - Daniel Bowles
- Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Ashesh Thaker
- Department of Radiology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Kimberly Atiyeh
- Department of Otolaryngology Head and Neck Surgery, University of Colorado, Memorial South Hospital, Colorado Springs, CO, USA
| | - Julie Goddard
- Department of Otolaryngology Head and Neck Surgery, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Robert Hoyer
- Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Adrie Van Bokhoven
- Department of Pathology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Kimberly Jordan
- Department of Immunology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Antonio Jimeno
- Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - David Raben
- Radiation Oncology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Jessica D McDermott
- Division of Medical Oncology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sana D Karam
- Radiation Oncology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA.
- Department of Immunology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA.
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Bergman D, Sweis RF, Pearson AT, Nazari F, Jackson TL. A global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues. iScience 2022; 25:104387. [PMID: 35637730 PMCID: PMC9142654 DOI: 10.1016/j.isci.2022.104387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 03/30/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Agent-based models (ABMs) are a natural platform for capturing the multiple time and spatial scales in biological processes. However, these models are computationally expensive, especially when including molecular-level effects. The traditional approach to simulating this type of multiscale ABM is to solve a system of ordinary differential equations for the molecular events per cell. This significantly adds to the computational cost of simulations as the number of agents grows, which contributes to many ABMs being limited to around10 5 cells. We propose an approach that requires the same computational time independent of the number of agents. This speeds up the entire simulation by orders of magnitude, allowing for more thorough explorations of ABMs with even larger numbers of agents. We use two systems to show that the new method strongly agrees with the traditionally used approach. This computational strategy can be applied to a wide range of biological investigations.
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Affiliation(s)
- Daniel Bergman
- Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Randy F. Sweis
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, 5841 S Maryland Avenue, MC 2115, Chicago, IL 60605, USA
| | - Alexander T. Pearson
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, 5841 S Maryland Avenue, MC 2115, Chicago, IL 60605, USA
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Shou Y, Johnson SC, Quek YJ, Li X, Tay A. Integrative lymph node-mimicking models created with biomaterials and computational tools to study the immune system. Mater Today Bio 2022; 14:100269. [PMID: 35514433 PMCID: PMC9062348 DOI: 10.1016/j.mtbio.2022.100269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 11/17/2022]
Abstract
The lymph node (LN) is a vital organ of the lymphatic and immune system that enables timely detection, response, and clearance of harmful substances from the body. Each LN comprises of distinct substructures, which host a plethora of immune cell types working in tandem to coordinate complex innate and adaptive immune responses. An improved understanding of LN biology could facilitate treatment in LN-associated pathologies and immunotherapeutic interventions, yet at present, animal models, which often have poor physiological relevance, are the most popular experimental platforms. Emerging biomaterial engineering offers powerful alternatives, with the potential to circumvent limitations of animal models, for in-depth characterization and engineering of the lymphatic and adaptive immune system. In addition, mathematical and computational approaches, particularly in the current age of big data research, are reliable tools to verify and complement biomaterial works. In this review, we first discuss the importance of lymph node in immunity protection followed by recent advances using biomaterials to create in vitro/vivo LN-mimicking models to recreate the lymphoid tissue microstructure and microenvironment, as well as to describe the related immuno-functionality for biological investigation. We also explore the great potential of mathematical and computational models to serve as in silico supports. Furthermore, we suggest how both in vitro/vivo and in silico approaches can be integrated to strengthen basic patho-biological research, translational drug screening and clinical personalized therapies. We hope that this review will promote synergistic collaborations to accelerate progress of LN-mimicking systems to enhance understanding of immuno-complexity.
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Lawton ML, Emili A. Mass Spectrometry-Based Phosphoproteomics and Systems Biology: Approaches to Study T Lymphocyte Activation and Exhaustion. J Mol Biol 2021; 433:167318. [PMID: 34687714 DOI: 10.1016/j.jmb.2021.167318] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/04/2021] [Accepted: 10/15/2021] [Indexed: 11/24/2022]
Abstract
T lymphocytes respond to extracellular cues and recognize and clear foreign bodies. These functions are tightly regulated by receptor-mediated intracellular signal transduction pathways and phosphorylation cascades resulting in rewiring of transcription, cell adhesion, and metabolic pathways, which leads to changes in downstream effector functions including cytokine secretion and target-cell killing. Given that these pathways become dysregulated in chronic diseases such as cancer, auto-immunity, diabetes, and persistent infections, mapping T cell signaling dynamics in normal and pathological states is central to understanding and modulating immune system behavior. Despite recent advances, there remains much to be learned from the study of T cell signaling at a systems level. The application of global phospho-proteomic profiling technology has the potential to provide unprecedented insights into the molecular networks that govern T cell function. These include capturing the spatiotemporal dynamics of the T cell responses as an ensemble of interacting components, rather than a static view at a single point in time. In this review, we describe innovative experimental approaches to study signaling mechanisms in the TCR, co-stimulatory receptors, synthetic signaling molecules such as chimeric antigen receptors, inhibitory receptors, and T cell exhaustion. Technical advances in mass spectrometry and systems biology frameworks are emphasized as these are poised to identify currently unknown functional relationships and dependencies to create causal predictive models that expand from the traditional narrow reductionist lens of singular components in isolation.
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Affiliation(s)
- Matthew L Lawton
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA.
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Johnson SC, Frattolin J, Edgar LT, Jafarnejad M, Moore Jr JE. Lymph node swelling combined with temporary effector T cell retention aids T cell response in a model of adaptive immunity. J R Soc Interface 2021; 18:20210464. [PMID: 34847790 PMCID: PMC8633806 DOI: 10.1098/rsif.2021.0464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 11/02/2021] [Indexed: 12/19/2022] Open
Abstract
Swelling of lymph nodes (LNs) is commonly observed during the adaptive immune response, yet the impact on T cell (TC) trafficking and subsequent immune response is not well known. To better understand the effect of macro-scale alterations, we developed an agent-based model of the LN paracortex, describing the TC proliferative response to antigen-presenting dendritic cells alongside inflammation-driven and swelling-induced changes in TC recruitment and egress, while also incorporating regulation of the expression of egress-modulating TC receptor sphingosine-1-phosphate receptor-1. Analysis of the effector TC response under varying swelling conditions showed that swelling consistently aided TC activation. However, subsequent effector CD8+ TC production was reduced in scenarios where swelling occurred too early in the TC proliferative phase or when TC cognate frequency was low due to increased opportunity for TC exit. Temporarily extending retention of newly differentiated effector TCs, mediated by sphingosine-1-phosphate receptor-1 expression, mitigated any negative effects of swelling by allowing facilitation of activation to outweigh increased access to exit areas. These results suggest that targeting temporary effector TC retention and egress associated with swelling offers new ways to modulate effector TC responses in, for example, immuno-suppressed patients and to optimize of vaccine design.
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Affiliation(s)
- Sarah C. Johnson
- Department of Bioengineering, Imperial College London, London, UK
| | | | - Lowell T. Edgar
- Department of Bioengineering, Imperial College London, London, UK
| | - Mohammad Jafarnejad
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Vodovotz Y, An G. Agent-based models of inflammation in translational systems biology: A decade later. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2019; 11:e1460. [PMID: 31260168 PMCID: PMC8140858 DOI: 10.1002/wsbm.1460] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/14/2019] [Accepted: 06/15/2019] [Indexed: 12/11/2022]
Abstract
Agent-based modeling is a rule-based, discrete-event, and spatially explicit computational modeling method that employs computational objects that instantiate the rules and interactions among the individual components ("agents") of system. Agent-based modeling is well suited to translating into a computational model the knowledge generated from basic science research, particularly with respect to translating across scales the mechanisms of cellular behavior into aggregated cell population dynamics manifesting at the tissue and organ level. This capacity has made agent-based modeling an integral method in translational systems biology (TSB), an approach that uses multiscale dynamic computational modeling to explicitly represent disease processes in a clinically relevant fashion. The initial work in the early 2000s using agent-based models (ABMs) in TSB focused on examining acute inflammation and its intersection with wound healing; the decade since has seen vast growth in both the application of agent-based modeling to a wide array of disease processes as well as methodological advancements in the use and analysis of ABM. This report presents an update on an earlier review of ABMs in TSB and presents examples of exciting progress in the modeling of various organs and diseases that involve inflammation. This review also describes developments that integrate the use of ABMs with cutting-edge technologies such as high-performance computing, machine learning, and artificial intelligence, with a view toward the future integration of these methodologies. This article is categorized under: Translational, Genomic, and Systems Medicine > Translational Medicine Models of Systems Properties and Processes > Mechanistic Models Models of Systems Properties and Processes > Organ, Tissue, and Physiological Models Models of Systems Properties and Processes > Organismal Models.
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Affiliation(s)
- Yoram Vodovotz
- Department of Surgery, Immunology, Computational & Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Gary An
- Department of Surgery, University of Vermont, Burlington, Vermont
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Renardy M, Hult C, Evans S, Linderman JJ, Kirschner DE. Global sensitivity analysis of biological multi-scale models. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019; 11:109-116. [PMID: 32864523 DOI: 10.1016/j.cobme.2019.09.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mathematical models of biological systems need to both reflect and manage the inherent complexities of biological phenomena. Through their versatility and ability to capture behavior at multiple scales, multi-scale models offer a valuable approach. Due to the typically nonlinear and stochastic nature of multi-scale models as well as unknown parameter values, various types of uncertainty are present; thus, effective assessment and quantification of such uncertainty through sensitivity analysis is important. In this review, we discuss global sensitivity analysis in the context of multi-scale and multi-compartment models and highlight its value in model development and analysis. We present an overview of sensitivity analysis methods, approaches for extending such methods to a multi-scale setting, and examples of how sensitivity analysis can inform model reduction. Through schematics and references to past work, we aim to emphasize the advantages and usefulness of such techniques.
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Affiliation(s)
- Marissa Renardy
- University of Michigan Medical School, Department of Microbiology and Immunology
| | - Caitlin Hult
- University of Michigan Medical School, Department of Microbiology and Immunology
- University of Michigan, Department of Chemical Engineering
| | - Stephanie Evans
- University of Michigan Medical School, Department of Microbiology and Immunology
| | | | - Denise E Kirschner
- University of Michigan Medical School, Department of Microbiology and Immunology
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Girel S, Arpin C, Marvel J, Gandrillon O, Crauste F. Model-Based Assessment of the Role of Uneven Partitioning of Molecular Content on Heterogeneity and Regulation of Differentiation in CD8 T-Cell Immune Responses. Front Immunol 2019; 10:230. [PMID: 30842771 PMCID: PMC6392104 DOI: 10.3389/fimmu.2019.00230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/28/2019] [Indexed: 12/16/2022] Open
Abstract
Activation of naive CD8 T-cells can lead to the generation of multiple effector and memory subsets. Multiple parameters associated with activation conditions are involved in generating this diversity that is associated with heterogeneous molecular contents of activated cells. Although naive cell polarisation upon antigenic stimulation and the resulting asymmetric division are known to be a major source of heterogeneity and cell fate regulation, the consequences of stochastic uneven partitioning of molecular content upon subsequent divisions remain unclear yet. Here we aim at studying the impact of uneven partitioning on molecular-content heterogeneity and then on the immune response dynamics at the cellular level. To do so, we introduce a multiscale mathematical model of the CD8 T-cell immune response in the lymph node. In the model, cells are described as agents evolving and interacting in a 2D environment while a set of differential equations, embedded in each cell, models the regulation of intra and extracellular proteins involved in cell differentiation. Based on the analysis of in silico data at the single cell level, we show that immune response dynamics can be explained by the molecular-content heterogeneity generated by uneven partitioning at cell division. In particular, uneven partitioning acts as a regulator of cell differentiation and induces the emergence of two coexisting sub-populations of cells exhibiting antagonistic fates. We show that the degree of unevenness of molecular partitioning, along all cell divisions, affects the outcome of the immune response and can promote the generation of memory cells.
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Affiliation(s)
- Simon Girel
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5208, Institut Camille Jordan, Villeurbanne, France
- Inria, Villeurbanne, France
| | - Christophe Arpin
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Jacqueline Marvel
- CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U111, Université Claude Bernard, Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Olivier Gandrillon
- Inria, Villeurbanne, France
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France
| | - Fabien Crauste
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5208, Institut Camille Jordan, Villeurbanne, France
- Inria, Villeurbanne, France
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Norton KA, Gong C, Jamalian S, Popel AS. Multiscale Agent-Based and Hybrid Modeling of the Tumor Immune Microenvironment. Processes (Basel) 2019; 7:37. [PMID: 30701168 PMCID: PMC6349239 DOI: 10.3390/pr7010037] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Multiscale systems biology and systems pharmacology are powerful methodologies that are playing increasingly important roles in understanding the fundamental mechanisms of biological phenomena and in clinical applications. In this review, we summarize the state of the art in the applications of agent-based models (ABM) and hybrid modeling to the tumor immune microenvironment and cancer immune response, including immunotherapy. Heterogeneity is a hallmark of cancer; tumor heterogeneity at the molecular, cellular, and tissue scales is a major determinant of metastasis, drug resistance, and low response rate to molecular targeted therapies and immunotherapies. Agent-based modeling is an effective methodology to obtain and understand quantitative characteristics of these processes and to propose clinical solutions aimed at overcoming the current obstacles in cancer treatment. We review models focusing on intra-tumor heterogeneity, particularly on interactions between cancer cells and stromal cells, including immune cells, the role of tumor-associated vasculature in the immune response, immune-related tumor mechanobiology, and cancer immunotherapy. We discuss the role of digital pathology in parameterizing and validating spatial computational models and potential applications to therapeutics.
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Affiliation(s)
- Kerri-Ann Norton
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Computer Science Program, Department of Science, Mathematics, and Computing, Bard College, Annandale-on-Hudson, NY 12504, USA
| | - Chang Gong
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Samira Jamalian
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Aleksander S. Popel
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Oncology and the Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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Marino S, Hult C, Wolberg P, Linderman JJ, Kirschner DE. The Role of Dimensionality in Understanding Granuloma Formation. COMPUTATION (BASEL, SWITZERLAND) 2018; 6:58. [PMID: 31258937 PMCID: PMC6599587 DOI: 10.3390/computation6040058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within the first 2-3 months of a Mycobacterium tuberculosis (Mtb) infection, 2-4 mm spherical structures called granulomas develop in the lungs of the infected hosts. These are the hallmark of tuberculosis (TB) infection in humans and non-human primates. A cascade of immunological events occurs in the first 3 months of granuloma formation that likely shapes the outcome of the infection. Understanding the main mechanisms driving granuloma development and function is key to generating treatments and vaccines. In vitro, in vivo, and in silico studies have been performed in the past decades to address the complexity of granuloma dynamics. This study builds on our previous 2D spatio-temporal hybrid computational model of granuloma formation in TB (GranSim) and presents for the first time a more realistic 3D implementation. We use uncertainty and sensitivity analysis techniques to calibrate the new 3D resolution to non-human primate (NHP) experimental data on bacterial levels per granuloma during the first 100 days post infection. Due to the large computational cost associated with running a 3D agent-based model, our major goal is to assess to what extent 2D and 3D simulations differ in predictions for TB granulomas and what can be learned in the context of 3D that is missed in 2D. Our findings suggest that in terms of major mechanisms driving bacterial burden, 2D and 3D models return very similar results. For example, Mtb growth rates and molecular regulation mechanisms are very important both in 2D and 3D, as are cellular movement and modulation of cell recruitment. The main difference we found was that the 3D model is less affected by crowding when cellular recruitment and movement of cells are increased. Overall, we conclude that the use of a 2D resolution in GranSim is warranted when large scale pilot runs are to be performed and if the goal is to determine major mechanisms driving infection outcome (e.g., bacterial load). To comprehensively compare the roles of model dimensionality, further tests and experimental data will be needed to expand our conclusions to molecular scale dynamics and multi-scale resolutions.
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Affiliation(s)
- Simeone Marino
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.M.); (C.H.); (P.W.)
- Statistics Online Computational Resource (SOCR), Department of Health Behavior and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Caitlin Hult
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.M.); (C.H.); (P.W.)
- Statistics Online Computational Resource (SOCR), Department of Health Behavior and Biological Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul Wolberg
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.M.); (C.H.); (P.W.)
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Jennifer J Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Denise E Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; (S.M.); (C.H.); (P.W.)
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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12
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Joslyn LR, Pienaar E, DiFazio RM, Suliman S, Kagina BM, Flynn JL, Scriba TJ, Linderman JJ, Kirschner DE. Integrating Non-human Primate, Human, and Mathematical Studies to Determine the Influence of BCG Timing on H56 Vaccine Outcomes. Front Microbiol 2018; 9:1734. [PMID: 30177914 PMCID: PMC6109686 DOI: 10.3389/fmicb.2018.01734] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/11/2018] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death by an infectious agent, and developing an effective vaccine is an important component of the WHO's EndTB Strategy. Non-human primate (NHP) models of vaccination are crucial to TB vaccine development and have informed design of subsequent human trials. However, challenges emerge when translating results from animal models to human applications, and connecting post-vaccination immunological measurements to infection outcomes. The H56:IC31 vaccine is a candidate currently in phase I/IIa trials. H56 is a subunit vaccine that is comprised of 3 mycobacterial antigens: ESAT6, Ag85B, and Rv2660, formulated in IC31 adjuvant. H56, as a boost to Bacillus Calmette-Guérin (BCG, the TB vaccine that is currently used in most countries world-wide) demonstrates improved protection (compared to BCG alone) in mouse and NHP models of TB, and the first human study of H56 reported strong antigen-specific T cell responses to the vaccine. We integrated NHP and human data with mathematical modeling approaches to improve our understanding of NHP and human response to vaccine. We use a mathematical model to describe T-cell priming, proliferation, and differentiation in lymph nodes and blood, and calibrate the model to NHP and human blood data. Using the model, we demonstrate the impact of BCG timing on H56 vaccination response and reveal a general immunogenic response to H56 following BCG prime. Further, we use uncertainty and sensitivity analyses to isolate mechanisms driving differences in vaccination response observed between NHP and human datasets. This study highlights the power of a systems biology approach: integration of multiple modalities to better understand a complex biological system.
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Affiliation(s)
- Louis R. Joslyn
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, United States
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Elsje Pienaar
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, United States
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Robert M. DiFazio
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Sara Suliman
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Benjamin M. Kagina
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Jennifer J. Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Denise E. Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States
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Joslyn LR, Pienaar E, DiFazio RM, Suliman S, Kagina BM, Flynn JL, Scriba TJ, Linderman JJ, Kirschner DE. Integrating Non-human Primate, Human, and Mathematical Studies to Determine the Influence of BCG Timing on H56 Vaccine Outcomes. Front Microbiol 2018; 9:1898. [PMID: 30177934 PMCID: PMC6110197 DOI: 10.3389/fimmu.2018.01898] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/31/2018] [Indexed: 12/21/2022] Open
Abstract
Background Acute lung injury (ALI) is characterized by suppressed fibrinolytic activity in bronchoalveolar lavage fluid (BALF) attributed to elevated plasminogen activator inhibitor-1 (PAI-1). Restoring pulmonary fibrinolysis by delivering tissue-type plasminogen activator (tPA), urokinase plasminogen activator (uPA), and plasmin could be a promising approach. Objectives To systematically analyze the overall benefit of fibrinolytic therapy for ALI reported in preclinical studies. Methods We searched PubMed, Embase, Web of Science, and CNKI Chinese databases, and analyzed data retrieved from 22 studies for the beneficial effects of fibrinolytics on animal models of ALI. Results Both large and small animals were used with five routes for delivering tPA, uPA, and plasmin. Fibrinolytics significantly increased the fibrinolytic activity both in the plasma and BALF. Fibrin degradation products in BALF had a net increase of 408.41 ng/ml vs controls (P < 0.00001). In addition, plasma thrombin–antithrombin complexes increased 1.59 ng/ml over controls (P = 0.0001). In sharp contrast, PAI-1 level in BALF decreased 21.44 ng/ml compared with controls (P < 0.00001). Arterial oxygen tension was improved by a net increase of 15.16 mmHg, while carbon dioxide pressure was significantly reduced (11.66 mmHg, P = 0.0001 vs controls). Additionally, fibrinolytics improved lung function and alleviated inflammation response: the lung wet/dry ratio was decreased 1.49 (P < 0.0001 vs controls), lung injury score was reduced 1.83 (P < 0.00001 vs controls), and BALF neutrophils were lesser (3 × 104/ml, P < 0.00001 vs controls). The mortality decreased significantly within defined study periods (6 h to 30 days for mortality), as the risk ratio of death was 0.2-fold of controls (P = 0.0008). Conclusion We conclude that fibrinolytic therapy may be effective pharmaceutic strategy for ALI in animal models.
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Affiliation(s)
- Louis R Joslyn
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, United States.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Elsje Pienaar
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, United States.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Robert M DiFazio
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Sara Suliman
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Benjamin M Kagina
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - JoAnne L Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Jennifer J Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, United States
| | - Denise E Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, United States
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Hickey JW, Kosmides AK, Schneck JP. Engineering Platforms for T Cell Modulation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 341:277-362. [PMID: 30262034 DOI: 10.1016/bs.ircmb.2018.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
T cells are crucial contributors to mounting an effective immune response and increasingly the focus of therapeutic interventions in cancer, infectious disease, and autoimmunity. Translation of current T cell immunotherapies has been hindered by off-target toxicities, limited efficacy, biological variability, and high costs. As T cell therapeutics continue to develop, the application of engineering concepts to control their delivery and presentation will be critical for their success. Here, we outline the engineer's toolbox and contextualize it with the biology of T cells. We focus on the design principles of T cell modulation platforms regarding size, shape, material, and ligand choice. Furthermore, we review how application of these design principles has already impacted T cell immunotherapies and our understanding of T cell biology. Recent, salient examples from protein engineering, synthetic particles, cellular and genetic engineering, and scaffolds and surfaces are provided to reinforce the importance of design considerations. Our aim is to provide a guide for immunologists, engineers, clinicians, and the pharmaceutical sector for the design of T cell-targeting platforms.
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Affiliation(s)
- John W Hickey
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Institute for NanoBiotechnology, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Alyssa K Kosmides
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Institute for NanoBiotechnology, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jonathan P Schneck
- Institute for NanoBiotechnology, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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Bhurani V, Mohankrishnan A, Morrot A, Dalai SK. Developing effective vaccines: Cues from natural infection. Int Rev Immunol 2018; 37:249-265. [PMID: 29927676 DOI: 10.1080/08830185.2018.1471479] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ultimate goal of any vaccine is to generate a heterogeneous and stable pool of memory lymphocytes. Vaccine are designed with the hope to generate antigen specific long-lived T cell responses, as it may be the case in natural infection; however, inducing such response by sub-unit vaccine has been a challenge. Although significant progress has been made, there is lot of scope for designing novel vaccine strategies by taking cues from the natural infection. This review focuses upon the roadblocks and the possible ways to overcome them leading to developing effective vaccines. Here we propose that mimicking the natural course of infection as well as the inclusion of non-target antigens in vaccine formulations might generate heterogeneous pool of memory T cells to ensure long-lived protection.
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Affiliation(s)
- Vishakha Bhurani
- a Institute of Science , Nirma University , Ahmedabad , Gujarat , India
| | | | - Alexandre Morrot
- b Faculdade de Medicina , Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil.,c Instituto Oswaldo Cruz , Fiocruz , Rio de Janeiro , Brazil
| | - Sarat Kumar Dalai
- a Institute of Science , Nirma University , Ahmedabad , Gujarat , India
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Tarca AL, Fitzgerald W, Chaemsaithong P, Xu Z, Hassan SS, Grivel J, Gomez‐Lopez N, Panaitescu B, Pacora P, Maymon E, Erez O, Margolis L, Romero R. The cytokine network in women with an asymptomatic short cervix and the risk of preterm delivery. Am J Reprod Immunol 2017; 78:e12686. [PMID: 28585708 PMCID: PMC5575567 DOI: 10.1111/aji.12686] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 03/20/2017] [Indexed: 01/06/2023] Open
Abstract
PROBLEM To characterize the amniotic fluid (AF) inflammatory-related protein (IRP) network in patients with a sonographic short cervix (SCx) and to determine its relation to early preterm delivery (ePTD). METHOD OF STUDY A retrospective cohort study included women with a SCx (≤25 mm; n=223) who had amniocentesis and were classified according to gestational age (GA) at diagnosis and delivery (ePTD <32 weeks of gestation). RESULTS (i) In women with a SCx ≤ 22 1/7 weeks, the concentration of most IRPs increased as the cervix shortened; those with ePTD had a higher rate of increase in MIP-1α, MCP-1, and IL-6 concentrations than those delivering later; and (ii) the concentration of most IRPs and the correlation between several IRP pairs were higher in the ePTD group than for those delivering later. CONCLUSION Women with a SCx at 16-22 1/7 weeks have a unique AF cytokine network that correlates with cervical length at diagnosis and GA at delivery. This network may aid in predicting ePTD.
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Affiliation(s)
- Adi L. Tarca
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Wendy Fitzgerald
- Section on Intercellular InteractionsProgram on Physical BiologyEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMDUSA
| | - Piya Chaemsaithong
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Zhonghui Xu
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
| | - Sonia S. Hassan
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Jean‐Charles Grivel
- Division of Translational MedicineSidra Medical and Research CenterDohaQatar
| | - Nardhy Gomez‐Lopez
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
- Department of ImmunologyMicrobiology and BiochemistryWayne State University School of MedicineDetroitMIUSA
| | - Bogdan Panaitescu
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Percy Pacora
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Eli Maymon
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Offer Erez
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyWayne State University School of MedicineDetroitMIUSA
| | - Leonid Margolis
- Section on Intercellular InteractionsProgram on Physical BiologyEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMDUSA
| | - Roberto Romero
- Perinatology Research BranchProgram for Perinatal Research and ObstetricsDivision of Intramural ResearchEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentNational Institutes of HealthU.S. Department of Health and Human ServicesBethesdaMD, and Detroit, MIUSA
- Department of Obstetrics and GynecologyUniversity of MichiganAnn ArborMIUSA
- Department of Epidemiology and BiostatisticsMichigan State UniversityEast LansingMIUSA
- Center for Molecular Medicine and GeneticsWayne State UniversityDetroitMIUSA
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Kirschner D, Pienaar E, Marino S, Linderman JJ. A review of computational and mathematical modeling contributions to our understanding of Mycobacterium tuberculosis within-host infection and treatment. ACTA ACUST UNITED AC 2017; 3:170-185. [PMID: 30714019 DOI: 10.1016/j.coisb.2017.05.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Tuberculosis (TB) is an ancient and deadly disease characterized by complex host-pathogen dynamics playing out over multiple time and length scales and physiological compartments. Computational modeling can be used to integrate various types of experimental data and suggest new hypotheses, mechanisms, and therapeutic approaches to TB. Here, we offer a first-time comprehensive review of work on within-host TB models that describe the immune response of the host to infection, including the formation of lung granulomas. The models include systems of ordinary and partial differential equations and agent-based models as well as hybrid and multi-scale models that are combinations of these. Many aspects of M. tuberculosis infection, including host dynamics in the lung (typical site of infection for TB), granuloma formation, roles of cytokine and chemokine dynamics, and bacterial nutrient availability have been explored. Finally, we survey applications of these within-host models to TB therapy and prevention and suggest future directions to impact this global disease.
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Affiliation(s)
- Denise Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
| | - Elsje Pienaar
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI
| | - Simeone Marino
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
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Schmiel SE, Yang JA, Jenkins MK, Mueller DL. Cutting Edge: Adenosine A2a Receptor Signals Inhibit Germinal Center T Follicular Helper Cell Differentiation during the Primary Response to Vaccination. THE JOURNAL OF IMMUNOLOGY 2016; 198:623-628. [PMID: 27986907 DOI: 10.4049/jimmunol.1601686] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/27/2016] [Indexed: 12/15/2022]
Abstract
Adenosine A2a receptor (A2aR) signaling acts as a barrier to autoimmunity by promoting anergy, inducing regulatory T cells, and inhibiting effector T cells. However, in vivo effects of A2aR signaling on polyclonal CD4 T cells during a primary response to foreign Ag has yet to be determined. To address this problem, we immunized mice with peptide Ag 2W1S coupled to PE in CFA and treated with the selective A2aR agonist CGS-21680 (CGS). 2W1S:I-Ab-specific tetramer-binding CD4 T cells did not become anergic or differentiate into Foxp3+ regulatory T cells. Additionally, CGS treatment did not inhibit Th1 or Th17 differentiation. However, CGS did abrogate germinal center T follicular helper cells, and blunted PE-specific germinal center B cell responses. The use of A2aR-deficient CD4 T cells established that this CGS effect was T cell intrinsic. Therefore, this study has identified a unique role for A2aRs in regulating CD4 T cell differentiation during vaccination.
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Affiliation(s)
- Shirdi E Schmiel
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455; and
| | - Jessica A Yang
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Marc K Jenkins
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Daniel L Mueller
- Department of Medicine, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455; and
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Morel PA, Lee REC, Faeder JR. Demystifying the cytokine network: Mathematical models point the way. Cytokine 2016; 98:115-123. [PMID: 27919524 DOI: 10.1016/j.cyto.2016.11.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 11/21/2016] [Indexed: 12/22/2022]
Abstract
Cytokines provide the means by which immune cells communicate with each other and with parenchymal cells. There are over one hundred cytokines and many exist in families that share receptor components and signal transduction pathways, creating complex networks. Reductionist approaches to understanding the role of specific cytokines, through the use of gene-targeted mice, have revealed further complexity in the form of redundancy and pleiotropy in cytokine function. Creating an understanding of the complex interactions between cytokines and their target cells is challenging experimentally. Mathematical and computational modeling provides a robust set of tools by which complex interactions between cytokines can be studied and analyzed, in the process creating novel insights that can be further tested experimentally. This review will discuss and provide examples of the different modeling approaches that have been used to increase our understanding of cytokine networks. This includes discussion of knowledge-based and data-driven modeling approaches and the recent advance in single-cell analysis. The use of modeling to optimize cytokine-based therapies will also be discussed.
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Affiliation(s)
- Penelope A Morel
- Department of Immunology, University of Pittsburgh, Pittsburgh, USA.
| | - Robin E C Lee
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
| | - James R Faeder
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
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A Multi-Compartment Hybrid Computational Model Predicts Key Roles for Dendritic Cells in Tuberculosis Infection. COMPUTATION 2016; 4. [PMID: 28989808 PMCID: PMC5627612 DOI: 10.3390/computation4040039] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Tuberculosis (TB) is a world-wide health problem with approximately 2 billion people infected with Mycobacterium tuberculosis (Mtb, the causative bacterium of TB). The pathologic hallmark of Mtb infection in humans and Non-Human Primates (NHPs) is the formation of spherical structures, primarily in lungs, called granulomas. Infection occurs after inhalation of bacteria into lungs, where resident antigen-presenting cells (APCs), take up bacteria and initiate the immune response to Mtb infection. APCs traffic from the site of infection (lung) to lung-draining lymph nodes (LNs) where they prime T cells to recognize Mtb. These T cells, circulating back through blood, migrate back to lungs to perform their immune effector functions. We have previously developed a hybrid agent-based model (ABM, labeled GranSim) describing in silico immune cell, bacterial (Mtb) and molecular behaviors during tuberculosis infection and recently linked that model to operate across three physiological compartments: lung (infection site where granulomas form), lung draining lymph node (LN, site of generation of adaptive immunity) and blood (a measurable compartment). Granuloma formation and function is captured by a spatio-temporal model (i.e., ABM), while LN and blood compartments represent temporal dynamics of the whole body in response to infection and are captured with ordinary differential equations (ODEs). In order to have a more mechanistic representation of APC trafficking from the lung to the lymph node, and to better capture antigen presentation in a draining LN, this current study incorporates the role of dendritic cells (DCs) in a computational fashion into GranSim.
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Mathematical Models for Immunology: Current State of the Art and Future Research Directions. Bull Math Biol 2016; 78:2091-2134. [PMID: 27714570 PMCID: PMC5069344 DOI: 10.1007/s11538-016-0214-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 09/26/2016] [Indexed: 01/01/2023]
Abstract
The advances in genetics and biochemistry that have taken place over the last 10 years led to significant advances in experimental and clinical immunology. In turn, this has led to the development of new mathematical models to investigate qualitatively and quantitatively various open questions in immunology. In this study we present a review of some research areas in mathematical immunology that evolved over the last 10 years. To this end, we take a step-by-step approach in discussing a range of models derived to study the dynamics of both the innate and immune responses at the molecular, cellular and tissue scales. To emphasise the use of mathematics in modelling in this area, we also review some of the mathematical tools used to investigate these models. Finally, we discuss some future trends in both experimental immunology and mathematical immunology for the upcoming years.
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22
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de Jonge J, Isakova-Sivak I, van Dijken H, Spijkers S, Mouthaan J, de Jong R, Smolonogina T, Roholl P, Rudenko L. H7N9 Live Attenuated Influenza Vaccine Is Highly Immunogenic, Prevents Virus Replication, and Protects Against Severe Bronchopneumonia in Ferrets. Mol Ther 2016; 24:991-1002. [PMID: 26796670 PMCID: PMC4881767 DOI: 10.1038/mt.2016.23] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/22/2015] [Indexed: 12/19/2022] Open
Abstract
Avian influenza viruses continue to cross the species barrier, and if such viruses become transmissible among humans, it would pose a great threat to public health. Since its emergence in China in 2013, H7N9 has caused considerable morbidity and mortality. In the absence of a universal influenza vaccine, preparedness includes development of subtype-specific vaccines. In this study, we developed and evaluated in ferrets an intranasal live attenuated influenza vaccine (LAIV) against H7N9 based on the A/Leningrad/134/17/57 (H2N2) cold-adapted master donor virus. We demonstrate that the LAIV is attenuated and safe in ferrets and induces high hemagglutination- and neuraminidase-inhibiting and virus-neutralizing titers. The antibodies against hemagglutinin were also cross-reactive with divergent H7 strains. To assess efficacy, we used an intratracheal challenge ferret model in which an acute severe viral pneumonia is induced that closely resembles viral pneumonia observed in severe human cases. A single- and two-dose strategy provided complete protection against severe pneumonia and prevented virus replication. The protective effect of the two-dose strategy appeared better than the single dose only on the microscopic level in the lungs. We observed, however, an increased lymphocytic infiltration after challenge in single-vaccinated animals and hypothesize that this a side effect of the model.
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Affiliation(s)
- Jørgen de Jonge
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Irina Isakova-Sivak
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Harry van Dijken
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Sanne Spijkers
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Current address: BioNovion, Oss, the Netherlands
| | - Justin Mouthaan
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Current address: Genmab, Utrecht, the Netherlands
| | - Rineke de Jong
- Department of Virology, Central Veterinary Institute of Wageningen UR, Lelystad, the Netherlands
| | - Tatiana Smolonogina
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg, Russia
| | - Paul Roholl
- Microscope Consultancy, Weesp, the Netherlands
| | - Larisa Rudenko
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg, Russia
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23
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Marino S, Gideon HP, Gong C, Mankad S, McCrone JT, Lin PL, Linderman JJ, Flynn JL, Kirschner DE. Computational and Empirical Studies Predict Mycobacterium tuberculosis-Specific T Cells as a Biomarker for Infection Outcome. PLoS Comput Biol 2016; 12:e1004804. [PMID: 27065304 PMCID: PMC4827839 DOI: 10.1371/journal.pcbi.1004804] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 02/10/2016] [Indexed: 11/18/2022] Open
Abstract
Identifying biomarkers for tuberculosis (TB) is an ongoing challenge in developing immunological correlates of infection outcome and protection. Biomarker discovery is also necessary for aiding design and testing of new treatments and vaccines. To effectively predict biomarkers for infection progression in any disease, including TB, large amounts of experimental data are required to reach statistical power and make accurate predictions. We took a two-pronged approach using both experimental and computational modeling to address this problem. We first collected 200 blood samples over a 2- year period from 28 non-human primates (NHP) infected with a low dose of Mycobacterium tuberculosis. We identified T cells and the cytokines that they were producing (single and multiple) from each sample along with monkey status and infection progression data. Machine learning techniques were used to interrogate the experimental NHP datasets without identifying any potential TB biomarker. In parallel, we used our extensive novel NHP datasets to build and calibrate a multi-organ computational model that combines what is occurring at the site of infection (e.g., lung) at a single granuloma scale with blood level readouts that can be tracked in monkeys and humans. We then generated a large in silico repository of in silico granulomas coupled to lymph node and blood dynamics and developed an in silico tool to scale granuloma level results to a full host scale to identify what best predicts Mycobacterium tuberculosis (Mtb) infection outcomes. The analysis of in silico blood measures identifies Mtb-specific frequencies of effector T cell phenotypes at various time points post infection as promising indicators of infection outcome. We emphasize that pairing wetlab and computational approaches holds great promise to accelerate TB biomarker discovery. Tuberculosis (TB) is a disease that is caused by infection after inhaling the bacterium Mycobacterium tuberculosis. Not everyone infected with TB bacteria becomes sick. As a result, two TB-related conditions have been categorized: latent TB infection (not sick but still harboring the bacteria) and active TB disease. If not treated properly, active TB disease can be fatal. Almost 1.3 million die of TB worldwide each year, with ~8,6 million new infections in 2013. No effective vaccine is available to protect against TB and treatment of infection with multiple antibiotics is lengthy (6–9 months), with non-compliance being a major factor for the emergence of drug-resistant strains. A key step in developing effective vaccines and possibly shorter treatment regimens is the ability to identify biomarkers that correlate prognosis and progression to infection (similar to how cholesterol levels are a measure of heart health). In this study we show how pairing computer modeling, statistics and mathematics with datasets derived from non-human primate studies can accelerate biomarker discovery, and offer a new approach to identifying correlates of protection that will be useful in clinical practice, particularly in developing countries where TB is most prevalent.
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Affiliation(s)
- Simeone Marino
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
| | - Hannah P. Gideon
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chang Gong
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Shawn Mankad
- Robert H. Smith School of Business, University of Maryland, College Park, Maryland, United States of America
| | - John T. McCrone
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Philana Ling Lin
- Department of Pediatrics, Children’s Hospital of the University of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America
| | - Jennifer J. Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Denise E. Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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Ziraldo C, Gong C, Kirschner DE, Linderman JJ. Strategic Priming with Multiple Antigens can Yield Memory Cell Phenotypes Optimized for Infection with Mycobacterium tuberculosis: A Computational Study. Front Microbiol 2016; 6:1477. [PMID: 26779136 PMCID: PMC4701940 DOI: 10.3389/fmicb.2015.01477] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/08/2015] [Indexed: 12/16/2022] Open
Abstract
Lack of an effective vaccine results in 9 million new cases of tuberculosis (TB) every year and 1.8 million deaths worldwide. Although many infants are vaccinated at birth with BCG (an attenuated M. bovis), this does not prevent infection or development of TB after childhood. Immune responses necessary for prevention of infection or disease are still unknown, making development of effective vaccines against TB challenging. Several new vaccines are ready for human clinical trials, but these trials are difficult and expensive; especially challenging is determining the appropriate cellular response necessary for protection. The magnitude of an immune response is likely key to generating a successful vaccine. Characteristics such as numbers of central memory (CM) and effector memory (EM) T cells responsive to a diverse set of epitopes are also correlated with protection. Promising vaccines against TB contain mycobacterial subunit antigens (Ag) present during both active and latent infection. We hypothesize that protection against different key immunodominant antigens could require a vaccine that produces different levels of EM and CM for each Ag-specific memory population. We created a computational model to explore EM and CM values, and their ratio, within what we term Memory Design Space. Our model captures events involved in T cell priming within lymph nodes and tracks their circulation through blood to peripheral tissues. We used the model to test whether multiple Ag-specific memory cell populations could be generated with distinct locations within Memory Design Space at a specific time point post vaccination. Boosting can further shift memory populations to memory cell ratios unreachable by initial priming events. By strategically varying antigen load, properties of cellular interactions within the LN, and delivery parameters (e.g., number of boosts) of multi-subunit vaccines, we can generate multiple Ag-specific memory populations that cover a wide range of Memory Design Space. Given a set of desired characteristics for Ag-specific memory populations, we can use our model as a tool to predict vaccine formulations that will generate those populations.
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Affiliation(s)
- Cordelia Ziraldo
- Department of Chemical Engineering, University of Michigan, Ann ArborMI, USA; Department of Microbiology and Immunology, University of Michigan Medical School, Ann ArborMI, USA
| | - Chang Gong
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann ArborMI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann ArborMI, USA
| | - Denise E Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor MI, USA
| | - Jennifer J Linderman
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor MI, USA
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25
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Ziraldo C, Solovyev A, Allegretti A, Krishnan S, Henzel MK, Sowa GA, Brienza D, An G, Mi Q, Vodovotz Y. A Computational, Tissue-Realistic Model of Pressure Ulcer Formation in Individuals with Spinal Cord Injury. PLoS Comput Biol 2015; 11:e1004309. [PMID: 26111346 PMCID: PMC4482429 DOI: 10.1371/journal.pcbi.1004309] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 04/30/2015] [Indexed: 12/22/2022] Open
Abstract
People with spinal cord injury (SCI) are predisposed to pressure ulcers (PU). PU remain a significant burden in cost of care and quality of life despite improved mechanistic understanding and advanced interventions. An agent-based model (ABM) of ischemia/reperfusion-induced inflammation and PU (the PUABM) was created, calibrated to serial images of post-SCI PU, and used to investigate potential treatments in silico. Tissue-level features of the PUABM recapitulated visual patterns of ulcer formation in individuals with SCI. These morphological features, along with simulated cell counts and mediator concentrations, suggested that the influence of inflammatory dynamics caused simulations to be committed to "better" vs. "worse" outcomes by 4 days of simulated time and prior to ulcer formation. Sensitivity analysis of model parameters suggested that increasing oxygen availability would reduce PU incidence. Using the PUABM, in silico trials of anti-inflammatory treatments such as corticosteroids and a neutralizing antibody targeted at Damage-Associated Molecular Pattern molecules (DAMPs) suggested that, at best, early application at a sufficiently high dose could attenuate local inflammation and reduce pressure-associated tissue damage, but could not reduce PU incidence. The PUABM thus shows promise as an adjunct for mechanistic understanding, diagnosis, and design of therapies in the setting of PU.
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Affiliation(s)
- Cordelia Ziraldo
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Joint PhD Program in Computational Biology, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Center for Inflammation and Regenerative Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexey Solovyev
- Center for Inflammation and Regenerative Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Mathematics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ana Allegretti
- Department of Rehabilitation Science and Technology, School of Health and Rehabilitation Science, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Shilpa Krishnan
- Department of Rehabilitation Science and Technology, School of Health and Rehabilitation Science, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - M. Kristi Henzel
- Spinal Cord Injury/Disorders Center, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
| | - Gwendolyn A. Sowa
- Department of Physical Medicine and Rehabilitation, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - David Brienza
- Department of Rehabilitation Science and Technology, School of Health and Rehabilitation Science, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Gary An
- Center for Inflammation and Regenerative Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Surgery, University of Chicago, Chicago, Illinois, United States of America
| | - Qi Mi
- Center for Inflammation and Regenerative Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Sports Medicine and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Yoram Vodovotz
- Center for Inflammation and Regenerative Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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26
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Linderman JJ, Cilfone NA, Pienaar E, Gong C, Kirschner DE. A multi-scale approach to designing therapeutics for tuberculosis. Integr Biol (Camb) 2015; 7:591-609. [PMID: 25924949 DOI: 10.1039/c4ib00295d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Approximately one third of the world's population is infected with Mycobacterium tuberculosis. Limited information about how the immune system fights M. tuberculosis and what constitutes protection from the bacteria impact our ability to develop effective therapies for tuberculosis. We present an in vivo systems biology approach that integrates data from multiple model systems and over multiple length and time scales into a comprehensive multi-scale and multi-compartment view of the in vivo immune response to M. tuberculosis. We describe computational models that can be used to study (a) immunomodulation with the cytokines tumor necrosis factor and interleukin 10, (b) oral and inhaled antibiotics, and
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Affiliation(s)
- Jennifer J Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA.
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Cilfone NA, Kirschner DE, Linderman JJ. Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems. Cell Mol Bioeng 2015; 8:119-136. [PMID: 26366228 PMCID: PMC4564133 DOI: 10.1007/s12195-014-0363-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Biologically related processes operate across multiple spatiotemporal scales. For computational modeling methodologies to mimic this biological complexity, individual scale models must be linked in ways that allow for dynamic exchange of information across scales. A powerful methodology is to combine a discrete modeling approach, agent-based models (ABMs), with continuum models to form hybrid models. Hybrid multi-scale ABMs have been used to simulate emergent responses of biological systems. Here, we review two aspects of hybrid multi-scale ABMs: linking individual scale models and efficiently solving the resulting model. We discuss the computational choices associated with aspects of linking individual scale models while simultaneously maintaining model tractability. We demonstrate implementations of existing numerical methods in the context of hybrid multi-scale ABMs. Using an example model describing Mycobacterium tuberculosis infection, we show relative computational speeds of various combinations of numerical methods. Efficient linking and solution of hybrid multi-scale ABMs is key to model portability, modularity, and their use in understanding biological phenomena at a systems level.
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Affiliation(s)
- Nicholas A. Cilfone
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Denise E. Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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28
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Affiliation(s)
- Ramit Mehr
- Computational Immunology Lab, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University , Ramat-Gan , Israel
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29
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Morel PA, Faeder JR, Hawse WF, Miskov-Zivanov N. Modeling the T cell immune response: a fascinating challenge. J Pharmacokinet Pharmacodyn 2014; 41:401-13. [PMID: 25155903 PMCID: PMC4210366 DOI: 10.1007/s10928-014-9376-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 08/13/2014] [Indexed: 12/11/2022]
Abstract
The immune system is designed to protect the organism from infection and to repair damaged tissue. An effective response requires recognition of the threat, the appropriate effector mechanism to clear the pathogen and a return to homeostasis with minimal damage to self-tissues. T cells play a central role in orchestrating the immune response at all stages of the response and have been the subject of intense study by both experimental immunologists and modelers. This review examines some of the more critical questions in T cell biology and describes the latest attempts to address those questions using approaches that combine mathematical modeling and experiments.
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Affiliation(s)
- Penelope A Morel
- Departments of Immunology, University of Pittsburgh, 200 Lothrop Street, BST E1055, Pittsburgh, PA, 15261, USA,
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Kirschner DE, Hunt CA, Marino S, Fallahi-Sichani M, Linderman JJ. Tuneable resolution as a systems biology approach for multi-scale, multi-compartment computational models. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2014; 6:289-309. [PMID: 24810243 PMCID: PMC4102180 DOI: 10.1002/wsbm.1270] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 03/14/2014] [Accepted: 03/19/2014] [Indexed: 01/19/2023]
Abstract
The use of multi-scale mathematical and computational models to study complex biological processes is becoming increasingly productive. Multi-scale models span a range of spatial and/or temporal scales and can encompass multi-compartment (e.g., multi-organ) models. Modeling advances are enabling virtual experiments to explore and answer questions that are problematic to address in the wet-lab. Wet-lab experimental technologies now allow scientists to observe, measure, record, and analyze experiments focusing on different system aspects at a variety of biological scales. We need the technical ability to mirror that same flexibility in virtual experiments using multi-scale models. Here we present a new approach, tuneable resolution, which can begin providing that flexibility. Tuneable resolution involves fine- or coarse-graining existing multi-scale models at the user's discretion, allowing adjustment of the level of resolution specific to a question, an experiment, or a scale of interest. Tuneable resolution expands options for revising and validating mechanistic multi-scale models, can extend the longevity of multi-scale models, and may increase computational efficiency. The tuneable resolution approach can be applied to many model types, including differential equation, agent-based, and hybrid models. We demonstrate our tuneable resolution ideas with examples relevant to infectious disease modeling, illustrating key principles at work. WIREs Syst Biol Med 2014, 6:225–245. doi:10.1002/wsbm.1270 How to cite this article:WIREs Syst Biol Med 2014, 6:289–309. doi:10.1002/wsbm.1270
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Affiliation(s)
- Denise E Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
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