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Pasin C, Consiglio CR, Huisman J, de Lange AMG, Peckham H, Vallejo-Yagüe E, Abela IA, Islander U, Neuner-Jehle N, Pujantell M, Roth O, Schirmer M, Tepekule B, Zeeb M, Hachfeld A, Aebi-Popp K, Kouyos RD, Bonhoeffer S. Sex and gender in infection and immunity: addressing the bottlenecks from basic science to public health and clinical applications. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221628. [PMID: 37416827 PMCID: PMC10320357 DOI: 10.1098/rsos.221628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 06/14/2023] [Indexed: 07/08/2023]
Abstract
Although sex and gender are recognized as major determinants of health and immunity, their role is rarely considered in clinical practice and public health. We identified six bottlenecks preventing the inclusion of sex and gender considerations from basic science to clinical practice, precision medicine and public health policies. (i) A terminology-related bottleneck, linked to the definitions of sex and gender themselves, and the lack of consensus on how to evaluate gender. (ii) A data-related bottleneck, due to gaps in sex-disaggregated data, data on trans/non-binary people and gender identity. (iii) A translational bottleneck, limited by animal models and the underrepresentation of gender minorities in biomedical studies. (iv) A statistical bottleneck, with inappropriate statistical analyses and results interpretation. (v) An ethical bottleneck posed by the underrepresentation of pregnant people and gender minorities in clinical studies. (vi) A structural bottleneck, as systemic bias and discriminations affect not only academic research but also decision makers. We specify guidelines for researchers, scientific journals, funding agencies and academic institutions to address these bottlenecks. Following such guidelines will support the development of more efficient and equitable care strategies for all.
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Affiliation(s)
- Chloé Pasin
- Collegium Helveticum, 8092 Zurich, Switzerland
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Camila R. Consiglio
- Department of Women's and Children's Health, Karolinska Institutet, 17165 Stockholm, Sweden
| | - Jana S. Huisman
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
- Physics of Living Systems, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ann-Marie G. de Lange
- Department of Clinical Neurosciences, Lausanne University Hospital (CHUV) and University of Lausanne, 1011 Lausanne, Switzerland
- Department of Psychology, University of Oslo, 0373 Oslo, Norway
- Department of Psychiatry, University of Oxford, Oxford OX3 7JX, UK
| | - Hannah Peckham
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCLH and GOSH, London WC1E 6JF, UK
| | | | - Irene A. Abela
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Ulrika Islander
- Department of Rheumatology and Inflammation Research, University of Gothenburg, 40530 Gothenburg, Sweden
- SciLifeLab, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Nadia Neuner-Jehle
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Maria Pujantell
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Olivia Roth
- Marine Evolutionary Biology, Zoological Institute, Christian-Albrechts-University Kiel, 24118 Kiel, Germany
| | - Melanie Schirmer
- Emmy Noether Group for Computational Microbiome Research, ZIEL – Institute for Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Burcu Tepekule
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Marius Zeeb
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Anna Hachfeld
- Department of Infectious Diseases, University Hospital and University of Bern, 3012 Bern, Switzerland
| | - Karoline Aebi-Popp
- Department of Infectious Diseases, University Hospital and University of Bern, 3012 Bern, Switzerland
- Department of Obstetrics and Gynecology, Lindenhofspital, 3012 Bern, Switzerland
| | - Roger D. Kouyos
- Institute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Sebastian Bonhoeffer
- Collegium Helveticum, 8092 Zurich, Switzerland
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
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Linden NJ, Kramer B, Rangamani P. Bayesian parameter estimation for dynamical models in systems biology. PLoS Comput Biol 2022; 18:e1010651. [PMID: 36269772 PMCID: PMC9629650 DOI: 10.1371/journal.pcbi.1010651] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 11/02/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
Dynamical systems modeling, particularly via systems of ordinary differential equations, has been used to effectively capture the temporal behavior of different biochemical components in signal transduction networks. Despite the recent advances in experimental measurements, including sensor development and '-omics' studies that have helped populate protein-protein interaction networks in great detail, modeling in systems biology lacks systematic methods to estimate kinetic parameters and quantify associated uncertainties. This is because of multiple reasons, including sparse and noisy experimental measurements, lack of detailed molecular mechanisms underlying the reactions, and missing biochemical interactions. Additionally, the inherent nonlinearities with respect to the states and parameters associated with the system of differential equations further compound the challenges of parameter estimation. In this study, we propose a comprehensive framework for Bayesian parameter estimation and complete quantification of the effects of uncertainties in the data and models. We apply these methods to a series of signaling models of increasing mathematical complexity. Systematic analysis of these dynamical systems showed that parameter estimation depends on data sparsity, noise level, and model structure, including the existence of multiple steady states. These results highlight how focused uncertainty quantification can enrich systems biology modeling and enable additional quantitative analyses for parameter estimation.
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Affiliation(s)
- Nathaniel J. Linden
- Department of Mechanical and Aerospace Engineering, University of California San Diego, San Diego, California, United States of America
| | - Boris Kramer
- Department of Mechanical and Aerospace Engineering, University of California San Diego, San Diego, California, United States of America
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, San Diego, California, United States of America
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3
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Gangopadhyay K, Roy S, Sen Gupta S, Chandradasan A, Chowdhury S, Das R. Regulating the discriminatory response to antigen by T-cell receptor. Biosci Rep 2022; 42:BSR20212012. [PMID: 35260878 PMCID: PMC8965820 DOI: 10.1042/bsr20212012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 11/17/2022] Open
Abstract
The cell-mediated immune response constitutes a robust host defense mechanism to eliminate pathogens and oncogenic cells. T cells play a central role in such a defense mechanism and creating memories to prevent any potential infection. T cell recognizes foreign antigen by its surface receptors when presented through antigen-presenting cells (APCs) and calibrates its cellular response by a network of intracellular signaling events. Activation of T-cell receptor (TCR) leads to changes in gene expression and metabolic networks regulating cell development, proliferation, and migration. TCR does not possess any catalytic activity, and the signaling initiates with the colocalization of several enzymes and scaffold proteins. Deregulation of T cell signaling is often linked to autoimmune disorders like severe combined immunodeficiency (SCID), rheumatoid arthritis, and multiple sclerosis. The TCR remarkably distinguishes the minor difference between self and non-self antigen through a kinetic proofreading mechanism. The output of TCR signaling is determined by the half-life of the receptor antigen complex and the time taken to recruit and activate the downstream enzymes. A longer half-life of a non-self antigen receptor complex could initiate downstream signaling by activating associated enzymes. Whereas, the short-lived, self-peptide receptor complex disassembles before the downstream enzymes are activated. Activation of TCR rewires the cellular metabolic response to aerobic glycolysis from oxidative phosphorylation. How does the early event in the TCR signaling cross-talk with the cellular metabolism is an open question. In this review, we have discussed the recent developments in understanding the regulation of TCR signaling, and then we reviewed the emerging role of metabolism in regulating T cell function.
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Affiliation(s)
- Kaustav Gangopadhyay
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
| | - Swarnendu Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
| | - Soumee Sen Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
| | - Athira C. Chandradasan
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
| | - Subhankar Chowdhury
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
| | - Rahul Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur 741246, India
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4
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Affinity maturation for an optimal balance between long-term immune coverage and short-term resource constraints. Proc Natl Acad Sci U S A 2022; 119:2113512119. [PMID: 35177475 PMCID: PMC8872716 DOI: 10.1073/pnas.2113512119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 12/15/2022] Open
Abstract
Humoral immunity relies on the mutation and selection of B cells to better recognize pathogens. This affinity maturation process produces cells with diverse recognition capabilities. Examining optimal immune strategies that maximize the long-term immune coverage at a minimal metabolic cost, we show when the immune system should mount a de novo response rather than rely on existing memory cells. Our theory recapitulates known modes of the B cell response, predicts the empirical form of the distribution of clone sizes, and rationalizes as a trade-off between metabolic and immune costs the antigenic imprinting effects that limit the efficacy of vaccines (original antigenic sin). Our predictions provide a framework to interpret experimental results that could be used to inform vaccination strategies. In order to target threatening pathogens, the adaptive immune system performs a continuous reorganization of its lymphocyte repertoire. Following an immune challenge, the B cell repertoire can evolve cells of increased specificity for the encountered strain. This process of affinity maturation generates a memory pool whose diversity and size remain difficult to predict. We assume that the immune system follows a strategy that maximizes the long-term immune coverage and minimizes the short-term metabolic costs associated with affinity maturation. This strategy is defined as an optimal decision process on a finite dimensional phenotypic space, where a preexisting population of cells is sequentially challenged with a neutrally evolving strain. We show that the low specificity and high diversity of memory B cells—a key experimental result—can be explained as a strategy to protect against pathogens that evolve fast enough to escape highly potent but narrow memory. This plasticity of the repertoire drives the emergence of distinct regimes for the size and diversity of the memory pool, depending on the density of de novo responding cells and on the mutation rate of the strain. The model predicts power-law distributions of clonotype sizes observed in data and rationalizes antigenic imprinting as a strategy to minimize metabolic costs while keeping good immune protection against future strains.
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5
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Corral-Jara KF, Rosas da Silva G, Fierro NA, Soumelis V. Modeling the Th17 and Tregs Paradigm: Implications for Cancer Immunotherapy. Front Cell Dev Biol 2021; 9:675099. [PMID: 34026764 PMCID: PMC8137995 DOI: 10.3389/fcell.2021.675099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
CD4 + T cell differentiation is governed by gene regulatory and metabolic networks, with both networks being highly interconnected and able to adapt to external stimuli. Th17 and Tregs differentiation networks play a critical role in cancer, and their balance is affected by the tumor microenvironment (TME). Factors from the TME mediate recruitment and expansion of Th17 cells, but these cells can act with pro or anti-tumor immunity. Tregs cells are also involved in tumor development and progression by inhibiting antitumor immunity and promoting immunoevasion. Due to the complexity of the underlying molecular pathways, the modeling of biological systems has emerged as a promising solution for better understanding both CD4 + T cell differentiation and cancer cell behavior. In this review, we present a context-dependent vision of CD4 + T cell transcriptomic and metabolic network adaptability. We then discuss CD4 + T cell knowledge-based models to extract the regulatory elements of Th17 and Tregs differentiation in multiple CD4 + T cell levels. We highlight the importance of complementing these models with data from omics technologies such as transcriptomics and metabolomics, in order to better delineate existing Th17 and Tregs bifurcation mechanisms. We were able to recompilate promising regulatory components and mechanisms of Th17 and Tregs differentiation under normal conditions, which we then connected with biological evidence in the context of the TME to better understand CD4 + T cell behavior in cancer. From the integration of mechanistic models with omics data, the transcriptomic and metabolomic reprograming of Th17 and Tregs cells can be predicted in new models with potential clinical applications, with special relevance to cancer immunotherapy.
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Affiliation(s)
- Karla F. Corral-Jara
- Computational Systems Biology Team, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR 8197, INSERM U1024, Ecole Normale Supérieure, PSL Research University, Paris, France
| | | | - Nora A. Fierro
- Department of Immunology, Biomedical Research Institute, National Autonomous University of Mexico, Mexico City, Mexico
| | - Vassili Soumelis
- Université de Paris, INSERM U976, France and AP-HP, Hôpital Saint-Louis, Immunology-Histocompatibility Department, Paris, France
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6
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Molari M, Monasson R, Cocco S. Survival probability and size of lineages in antibody affinity maturation. Phys Rev E 2021; 103:052413. [PMID: 34134280 DOI: 10.1103/physreve.103.052413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/06/2021] [Indexed: 11/07/2022]
Abstract
Affinity maturation (AM) is the process through which the immune system is able to develop potent antibodies against new pathogens it encounters, and is at the base of the efficacy of vaccines. At its core AM is analogous to a Darwinian evolutionary process, where B cells mutate and are selected on the base of their affinity for an antigen (Ag), and Ag availability tunes the selective pressure. In cases when this selective pressure is high, the number of B cells might quickly decrease and the population might risk extinction in what is known as a population bottleneck. Here we study the probability for a B-cell lineage to survive this bottleneck scenario as a function of the progenitor affinity for the Ag. Using recursive relations and probability generating functions we derive expressions for the average extinction time and progeny size for lineages that go extinct. We then extend our results to the full population, both in the absence and presence of competition for T-cell help, and quantify the population survival probability as a function of Ag concentration and initial population size. Our study suggests the population bottleneck phenomenology might represent a limit case in the space of biologically plausible maturation scenarios, whose characterization could help guide the process of vaccine development.
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Affiliation(s)
- Marco Molari
- Laboratoire de Physique de l'École Normale Supérieure, ENS, PSL University, CNRS UMR8023, Sorbonne Université, Université de Paris, 24 rue Lhomond, 75005 Paris, France
| | - Rémi Monasson
- Laboratoire de Physique de l'École Normale Supérieure, ENS, PSL University, CNRS UMR8023, Sorbonne Université, Université de Paris, 24 rue Lhomond, 75005 Paris, France
| | - Simona Cocco
- Laboratoire de Physique de l'École Normale Supérieure, ENS, PSL University, CNRS UMR8023, Sorbonne Université, Université de Paris, 24 rue Lhomond, 75005 Paris, France
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7
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Jones E, Sheng J, Carlson J, Wang S. Aging-induced fragility of the immune system. J Theor Biol 2021; 510:110473. [PMID: 32941914 PMCID: PMC7487974 DOI: 10.1016/j.jtbi.2020.110473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 01/03/2023]
Abstract
The adaptive and innate branches of the vertebrate immune system work in close collaboration to protect organisms from harmful pathogens. As an organism ages its immune system undergoes immunosenescence, characterized by declined performance or malfunction in either immune branch, which can lead to disease and death. In this study we develop a mathematical framework of coupled innate and adaptive immune responses, namely the integrated immune branch (IIB) model. This model describes dynamics of immune components in both branches, uses a shape-space representation to encode pathogen-specific immune memory, and exhibits three steady states - health, septic death, and chronic inflammation - qualitatively similar to clinically-observed immune outcomes. In this model, the immune system (initialized in the health state) is subjected to a sequence of pathogen encounters, and we use the number of prior pathogen encounters as a proxy for the "age" of the immune system. We find that repeated pathogen encounters may trigger a fragility in which any encounter with a novel pathogen will cause the system to irreversibly switch from health to chronic inflammation. This transition is consistent with the onset of "inflammaging", a condition observed in aged individuals who experience chronic low-grade inflammation even in the absence of pathogens. The IIB model predicts that the onset of chronic inflammation strongly depends on the history of encountered pathogens; the timing of onset differs drastically when the same set of infections occurs in a different order. Lastly, the coupling between the innate and adaptive immune branches generates a trade-off between rapid pathogen clearance and a delayed onset of immunosenescence. Overall, by considering the complex feedback between immune compartments, our work suggests potential mechanisms for immunosenescence and provides a theoretical framework at the system level and on the scale of an organism's lifetime to account for clinical observations.
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Affiliation(s)
- Eric Jones
- Department of Physics, University of California, Santa Barbara, CA 93106, USA.
| | - Jiming Sheng
- Department of Physics & Astronomy, University of California, Los Angeles, CA 90095, USA
| | - Jean Carlson
- Department of Physics, University of California, Santa Barbara, CA 93106, USA
| | - Shenshen Wang
- Department of Physics & Astronomy, University of California, Los Angeles, CA 90095, USA.
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8
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Directed attenuation to enhance vaccine immunity. PLoS Comput Biol 2021; 17:e1008602. [PMID: 33524036 PMCID: PMC7877766 DOI: 10.1371/journal.pcbi.1008602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 02/11/2021] [Accepted: 12/02/2020] [Indexed: 12/24/2022] Open
Abstract
Many viral infections can be prevented by immunizing with live, attenuated vaccines. Early methods of attenuation were hit-and-miss, now much improved by genetic engineering. However, even current methods operate on the principle of genetic harm, reducing the virus’s ability to grow. Reduced viral growth has the undesired side-effect of reducing the host immune response below that of infection with wild-type. Might some methods of attenuation instead lead to an increased immune response? We use mathematical models of the dynamics of virus with innate and adaptive immunity to explore the tradeoff between attenuation of virus pathology and immunity. We find that modification of some virus immune-evasion pathways can indeed reduce pathology yet enhance immunity. Thus, attenuated vaccines can, in principle, be directed to be safe yet create better immunity than is elicited by the wild-type virus. Live attenuated virus vaccines are among the most effective interventions to combat viral infections. Historically, the mechanism of attenuation has involved genetically reducing the viral growth rate, often achieved by adapting the virus to grow in a novel condition. More recent attenuation methods use genetic engineering but also are thought to impair viral growth rate. These classical attenuations typically result in a tradeoff whereby attenuation depresses the within-host viral load and pathology (which is beneficial to vaccine design), but reduces immunity (which is not beneficial). We use models to explore ways of directing the attenuation of a virus to avoid this tradeoff. We show that directed attenuation by interfering with (some) viral immune-evasion pathways can yield a mild infection but elicit higher levels of immunity than of the wild-type virus.
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9
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Ciabattini A, Garagnani P, Santoro F, Rappuoli R, Franceschi C, Medaglini D. Shelter from the cytokine storm: pitfalls and prospects in the development of SARS-CoV-2 vaccines for an elderly population. Semin Immunopathol 2020; 42:619-634. [PMID: 33159214 PMCID: PMC7646713 DOI: 10.1007/s00281-020-00821-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
The SARS-CoV-2 pandemic urgently calls for the development of effective preventive tools. COVID-19 hits greatly the elder and more fragile fraction of the population boosting the evergreen issue of the vaccination of older people. The development of a vaccine against SARS-CoV-2 tailored for the elderly population faces the challenge of the poor immune responsiveness of the older population due to immunosenescence, comorbidities, and pharmacological treatments. Moreover, it is likely that the inflammaging phenotype associated with age could both influence vaccination efficacy and exacerbate the risk of COVID-19-related "cytokine storm syndrome" with an overlap between the factors which impact vaccination effectiveness and those that boost virulence and worsen the prognosis of SARS-CoV-2 infection. The complex and still unclear immunopathological mechanisms of SARS-CoV-2 infection, together with the progressive age-related decline of immune responses, and the lack of clear correlates of protection, make the design of vaccination strategies for older people extremely challenging. In the ongoing effort in vaccine development, different SARS-CoV-2 vaccine candidates have been developed, tested in pre-clinical and clinical studies and are undergoing clinical testing, but only a small fraction of these are currently being tested in the older fraction of the population. Recent advances in systems biology integrating clinical, immunologic, and omics data can help to identify stable and robust markers of vaccine response and move towards a better understanding of SARS-CoV-2 vaccine responses in the elderly.
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Affiliation(s)
- Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Paolo Garagnani
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institute at Huddinge University Hospital, SE-171 77, Stockholm, Sweden
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40139, Bologna, Italy
- Interdepartmental Centre 'L. Galvan' (CIG), University of Bologna, Via G. Petroni 26, 40139, Bologna, Italy
| | - Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Rino Rappuoli
- GSK, Siena, Italy
- vAMRes Lab, Toscana Life Sciences, Siena, Italy
- Faculty of Medicine, Imperial College, London, UK
| | | | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology (LA.M.M.B.), Department of Medical Biotechnologies, University of Siena, Siena, Italy.
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10
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Hernandez C, Thomas-Chollier M, Naldi A, Thieffry D. Computational Verification of Large Logical Models-Application to the Prediction of T Cell Response to Checkpoint Inhibitors. Front Physiol 2020; 11:558606. [PMID: 33101049 PMCID: PMC7554341 DOI: 10.3389/fphys.2020.558606] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 08/19/2020] [Indexed: 12/31/2022] Open
Abstract
At the crossroad between biology and mathematical modeling, computational systems biology can contribute to a mechanistic understanding of high-level biological phenomenon. But as knowledge accumulates, the size and complexity of mathematical models increase, calling for the development of efficient dynamical analysis methods. Here, we propose the use of two approaches for the development and analysis of complex cellular network models. A first approach, called "model verification" and inspired by unitary testing in software development, enables the formalization and automated verification of validation criteria for whole models or selected sub-parts. When combined with efficient analysis methods, this approach is suitable for continuous testing, thereby greatly facilitating model development. A second approach, called "value propagation," enables efficient analytical computation of the impact of specific environmental or genetic conditions on the dynamical behavior of some models. We apply these two approaches to the delineation and the analysis of a comprehensive model for T cell activation, taking into account CTLA4 and PD-1 checkpoint inhibitory pathways. While model verification greatly eases the delineation of logical rules complying with a set of dynamical specifications, propagation provides interesting insights into the different potential of CTLA4 and PD-1 immunotherapies. Both methods are implemented and made available in the all-inclusive CoLoMoTo Docker image, while the different steps of the model analysis are fully reported in two companion interactive jupyter notebooks, thereby ensuring the reproduction of our results.
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Affiliation(s)
- Céline Hernandez
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Morgane Thomas-Chollier
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Institut Universitaire de France, Paris, France
| | - Aurélien Naldi
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Denis Thieffry
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
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11
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Abstract
A major problem in the analysis of vaccine candidates is the lack of any agreed upon surrogates of efficacy, which means that for diseases that depend on a strong T cell response (HIV, TB especially) the only option is to perform an efficacy trial, involving thousands of subjects, enormous costs, and years before the results are known [1]. We also know that T cell responses are an important part of most pathogen responses, and so identifying key T cell response metrics in early vaccine trials would be generally useful. Given our ignorance of what the most important variables are, what would we like to measure and how can this be accomplished, especially given the explosion of new technologies that are available? What follows is a consideration of what should be measured, with the caveat that some of these will be more important than others.
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Affiliation(s)
- Mark M Davis
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, United States; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United States; Immunology Program, Stanford University School of Medicine, Stanford, CA, United States; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States.
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12
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Companion vaccines for CAR T-cell therapy: applying basic immunology to enhance therapeutic efficacy. Future Med Chem 2020; 12:1359-1362. [PMID: 32597219 DOI: 10.4155/fmc-2020-0081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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13
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Mitra ED, Hlavacek WS. Parameter Estimation and Uncertainty Quantification for Systems Biology Models. CURRENT OPINION IN SYSTEMS BIOLOGY 2019; 18:9-18. [PMID: 32719822 PMCID: PMC7384601 DOI: 10.1016/j.coisb.2019.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mathematical models can provide quantitative insights into immunoreceptor signaling, and other biological processes, but require parameterization and uncertainty quantification before reliable predictions become possible. We review currently available methods and software tools to address these problems. We consider gradient-based and gradient-free methods for point estimation of parameter values, and methods of profile likelihood, bootstrapping, and Bayesian inference for uncertainty quantification. We consider recent and potential future applications of these methods to systems-level modeling of immune-related phenomena.
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Affiliation(s)
- Eshan D. Mitra
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - William S. Hlavacek
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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14
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Grebennikov DS, Donets DO, Orlova OG, Argilaguet J, Meyerhans A, Bocharov GA. Mathematical Modeling of the Intracellular Regulation of Immune Processes. Mol Biol 2019. [DOI: 10.1134/s002689331905008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Andreotti AH, Joseph RE, Conley JM, Iwasa J, Berg LJ. Multidomain Control Over TEC Kinase Activation State Tunes the T Cell Response. Annu Rev Immunol 2019; 36:549-578. [PMID: 29677469 DOI: 10.1146/annurev-immunol-042617-053344] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Signaling through the T cell antigen receptor (TCR) activates a series of tyrosine kinases. Directly associated with the TCR, the SRC family kinase LCK and the SYK family kinase ZAP-70 are essential for all downstream responses to TCR stimulation. In contrast, the TEC family kinase ITK is not an obligate component of the TCR cascade. Instead, ITK functions as a tuning dial, to translate variations in TCR signal strength into differential programs of gene expression. Recent insights into TEC kinase structure have provided a view into the molecular mechanisms that generate different states of kinase activation. In resting lymphocytes, TEC kinases are autoinhibited, and multiple interactions between the regulatory and kinase domains maintain low activity. Following TCR stimulation, newly generated signaling modules compete with the autoinhibited core and shift the conformational ensemble to the fully active kinase. This multidomain control over kinase activation state provides a structural mechanism to account for ITK's ability to tune the TCR signal.
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Affiliation(s)
- Amy H Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA; ,
| | - Raji E Joseph
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA; ,
| | - James M Conley
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA; ,
| | - Janet Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA;
| | - Leslie J Berg
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA; ,
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16
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Abstract
Given the many cell types and molecular components of the human immune system, along with vast variations across individuals, how should we go about developing causal and predictive explanations of immunity? A central strategy in human studies is to leverage natural variation to find relationships among variables, including DNA variants, epigenetic states, immune phenotypes, clinical descriptors, and others. Here, we focus on how natural variation is used to find patterns, infer principles, and develop predictive models for two areas: (a) immune cell activation-how single-cell profiling boosts our ability to discover immune cell types and states-and (b) antigen presentation and recognition-how models can be generated to predict presentation of antigens on MHC molecules and their detection by T cell receptors. These are two examples of a shift in how we find the drivers and targets of immunity, especially in the human system in the context of health and disease.
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Affiliation(s)
- Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02129, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Siranush Sarkizova
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02142, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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17
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Barton JP, Rajkoomar E, Mann JK, Murakowski DK, Toyoda M, Mahiti M, Mwimanzi P, Ueno T, Chakraborty AK, Ndung'u T. Modelling and in vitro testing of the HIV-1 Nef fitness landscape. Virus Evol 2019; 5:vez029. [PMID: 31392033 PMCID: PMC6680064 DOI: 10.1093/ve/vez029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
An effective vaccine is urgently required to curb the HIV-1 epidemic. We have previously described an approach to model the fitness landscape of several HIV-1 proteins, and have validated the results against experimental and clinical data. The fitness landscape may be used to identify mutation patterns harmful to virus viability, and consequently inform the design of immunogens that can target such regions for immunological control. Here we apply such an analysis and complementary experiments to HIV-1 Nef, a multifunctional protein which plays a key role in HIV-1 pathogenesis. We measured Nef-driven replication capacities as well as Nef-mediated CD4 and HLA-I down-modulation capacities of thirty-two different Nef mutants, and tested model predictions against these results. Furthermore, we evaluated the models using 448 patient-derived Nef sequences for which several Nef activities were previously measured. Model predictions correlated significantly with Nef-driven replication and CD4 down-modulation capacities, but not HLA-I down-modulation capacities, of the various Nef mutants. Similarly, in our analysis of patient-derived Nef sequences, CD4 down-modulation capacity correlated the most significantly with model predictions, suggesting that of the tested Nef functions, this is the most important in vivo. Overall, our results highlight how the fitness landscape inferred from patient-derived sequences captures, at least in part, the in vivo functional effects of mutations to Nef. However, the correlation between predictions of the fitness landscape and measured parameters of Nef function is not as accurate as the correlation observed in past studies for other proteins. This may be because of the additional complexity associated with inferring the cost of mutations on the diverse functions of Nef.
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Affiliation(s)
- John P Barton
- Departments of Chemical Engineering, Physics, and Chemistry, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Erasha Rajkoomar
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jaclyn K Mann
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Dariusz K Murakowski
- Departments of Chemical Engineering, Physics, and Chemistry, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mako Toyoda
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | | | | | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Arup K Chakraborty
- Departments of Chemical Engineering, Physics, and Chemistry, Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, USA
| | - Thumbi Ndung'u
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, USA.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute, Durban, South Africa.,Max Planck Institute for Infection Biology, Chariteplatz, D-10117 Berlin, Germany
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18
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Fischer CL, Bates AM, Lanzel EA, Guthmiller JM, Johnson GK, Singh NK, Kumar A, Vidva R, Abbasi T, Vali S, Xie XJ, Zeng E, Brogden KA. Computational Models Accurately Predict Multi-Cell Biomarker Profiles in Inflammation and Cancer. Sci Rep 2019; 9:10877. [PMID: 31350446 PMCID: PMC6659691 DOI: 10.1038/s41598-019-47381-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/15/2019] [Indexed: 01/28/2023] Open
Abstract
Individual computational models of single myeloid, lymphoid, epithelial, and cancer cells were created and combined into multi-cell computational models and used to predict the collective chemokine, cytokine, and cellular biomarker profiles often seen in inflamed or cancerous tissues. Predicted chemokine and cytokine output profiles from multi-cell computational models of gingival epithelial keratinocytes (GE KER), dendritic cells (DC), and helper T lymphocytes (HTL) exposed to lipopolysaccharide (LPS) or synthetic triacylated lipopeptide (Pam3CSK4) as well as multi-cell computational models of multiple myeloma (MM) and DC were validated using the observed chemokine and cytokine responses from the same cell type combinations grown in laboratory multi-cell cultures with accuracy. Predicted and observed chemokine and cytokine responses of GE KER + DC + HTL exposed to LPS and Pam3CSK4 matched 75% (15/20, p = 0.02069) and 80% (16/20, P = 0.005909), respectively. Multi-cell computational models became ‘personalized’ when cell line-specific genomic data were included into simulations, again validated with the same cell lines grown in laboratory multi-cell cultures. Here, predicted and observed chemokine and cytokine responses of MM cells lines MM.1S and U266B1 matched 75% (3/4) and MM.1S and U266B1 inhibition of DC marker expression in co-culture matched 100% (6/6). Multi-cell computational models have the potential to identify approaches altering the predicted disease-associated output profiles, particularly as high throughput screening tools for anti-inflammatory or immuno-oncology treatments of inflamed multi-cellular tissues and the tumor microenvironment.
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Affiliation(s)
- Carol L Fischer
- Department of Biology, Waldorf University, Forest City, IA, 50436, USA
| | - Amber M Bates
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Emily A Lanzel
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Janet M Guthmiller
- College of Dentistry, University of Nebraska Medical Center, Lincoln, NE, 68583, USA
| | - Georgia K Johnson
- Department of Periodontics, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Neeraj Kumar Singh
- Cellworks Group Inc., San Jose, CA, 95110, USA.,Cellworks Research India Pvt. Ltd (Wholly owned subsidiary of Cellworks Group Inc.), Bangalore, India
| | - Ansu Kumar
- Cellworks Group Inc., San Jose, CA, 95110, USA.,Cellworks Research India Pvt. Ltd (Wholly owned subsidiary of Cellworks Group Inc.), Bangalore, India
| | - Robinson Vidva
- Cellworks Group Inc., San Jose, CA, 95110, USA.,Cellworks Research India Pvt. Ltd (Wholly owned subsidiary of Cellworks Group Inc.), Bangalore, India
| | - Taher Abbasi
- Cellworks Group Inc., San Jose, CA, 95110, USA.,Cellworks Research India Pvt. Ltd (Wholly owned subsidiary of Cellworks Group Inc.), Bangalore, India
| | - Shireen Vali
- Cellworks Group Inc., San Jose, CA, 95110, USA.,Cellworks Research India Pvt. Ltd (Wholly owned subsidiary of Cellworks Group Inc.), Bangalore, India
| | - Xian Jin Xie
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Erliang Zeng
- Division of Biostatistics and Computational Biology, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Kim A Brogden
- Department of Periodontics, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA. .,Iowa Institute for Oral Health Research, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA.
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19
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Moses ME, Cannon JL, Gordon DM, Forrest S. Distributed Adaptive Search in T Cells: Lessons From Ants. Front Immunol 2019; 10:1357. [PMID: 31263465 PMCID: PMC6585175 DOI: 10.3389/fimmu.2019.01357] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/29/2019] [Indexed: 11/13/2022] Open
Abstract
There are striking similarities between the strategies ant colonies use to forage for food and immune systems use to search for pathogens. Searchers (ants and cells) use the appropriate combination of random and directed motion, direct and indirect agent-agent interactions, and traversal of physical structures to solve search problems in a variety of environments. An effective immune response requires immune cells to search efficiently and effectively for diverse types of pathogens in different tissues and organs, just as different species of ants have evolved diverse search strategies to forage effectively for a variety of resources in a variety of habitats. Successful T cell search is required to initiate the adaptive immune response in lymph nodes and to eradicate pathogens at sites of infection in peripheral tissue. Ant search strategies suggest novel predictions about T cell search. In both systems, the distribution of targets in time and space determines the most effective search strategy. We hypothesize that the ability of searchers to sense and adapt to dynamic targets and environmental conditions enhances search effectiveness through adjustments to movement and communication patterns. We also suggest that random motion is a more important component of search strategies than is generally recognized. The behavior we observe in ants reveals general design principles and constraints that govern distributed adaptive search in a wide variety of complex systems, particularly the immune system.
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Affiliation(s)
- Melanie E Moses
- Moses Biological Computation Laboratory, Department of Computer Science, University of New Mexico, Albuquerque, NM, United States.,Biology Department, University of New Mexico, Albuquerque, NM, United States.,Santa Fe Institute, Santa Fe, NM, United States
| | - Judy L Cannon
- The Cannon Laboratory, Department of Molecular Genetics & Microbiology, University of New Mexico School of Medicine, Albuquerque, NM, United States.,Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, United States.,Autophagy, Inflammation, and Metabolism Center of Biomedical Research Excellence, University of New Mexico School of Medicine, Albuquerque, NM, United States
| | - Deborah M Gordon
- Santa Fe Institute, Santa Fe, NM, United States.,Department of Biology, Stanford University, Stanford, CA, United States
| | - Stephanie Forrest
- Santa Fe Institute, Santa Fe, NM, United States.,Biodesign Institute and School for Computing, Informatics, and Decision Sciences Engineering, Arizona State University, Tempe, AZ, United States
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20
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Das J, Lanier LL. Data analysis to modeling to building theory in NK cell biology and beyond: How can computational modeling contribute? J Leukoc Biol 2019; 105:1305-1317. [PMID: 31063614 DOI: 10.1002/jlb.6mr1218-505r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 03/25/2019] [Accepted: 04/03/2019] [Indexed: 12/31/2022] Open
Abstract
The use of mathematical and computational tools in investigating Natural Killer (NK) cell biology and in general the immune system has increased steadily in the last few decades. However, unlike the physical sciences, there is a persistent ambivalence, which however is increasingly diminishing, in the biology community toward appreciating the utility of quantitative tools in addressing questions of biological importance. We survey some of the recent developments in the application of quantitative approaches for investigating different problems in NK cell biology and evaluate opportunities and challenges of using quantitative methods in providing biological insights in NK cell biology.
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Affiliation(s)
- Jayajit Das
- Battelle Center for Mathematical Medicine, Research Institute at the Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA.,Department of Physics, The Ohio State University, Columbus, Ohio, USA.,Biophysics Program, The Ohio State University, Columbus, Ohio, USA
| | - Lewis L Lanier
- Department of Microbiology and Immunology and the Parker Institute for Cancer Immunotherapy, University of California, San Francisco, California, USA
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21
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Abstract
The adaptive immune system is able to protect us from a large variety of pathogens, even ones it has not seen yet. Can predicting the future pathogen distribution help in protection? We find that a combination of probabilistic forecasting and occasional sampling of the current environment reduces infection costs—a scheme easily implemented by the memory repertoire. The proposed theoretical framework offers a modular recipe for updating the memory repertoire, which quantitatively predicts the strength of the immune response in flu-vaccination experiments, unlike other update schemes. It also links the observed early life dynamics of the memory pool to the sparseness properties of the pathogen distribution and competitive receptor dynamics for pathogens. An adaptive agent predicting the future state of an environment must weigh trust in new observations against prior experiences. In this light, we propose a view of the adaptive immune system as a dynamic Bayesian machinery that updates its memory repertoire by balancing evidence from new pathogen encounters against past experience of infection to predict and prepare for future threats. This framework links the observed initial rapid increase of the memory pool early in life followed by a midlife plateau to the ease of learning salient features of sparse environments. We also derive a modulated memory pool update rule in agreement with current vaccine-response experiments. Our results suggest that pathogenic environments are sparse and that memory repertoires significantly decrease infection costs, even with moderate sampling. The predicted optimal update scheme maps onto commonly considered competitive dynamics for antigen receptors.
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22
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Palma A, Jarrah AS, Tieri P, Cesareni G, Castiglione F. Gene Regulatory Network Modeling of Macrophage Differentiation Corroborates the Continuum Hypothesis of Polarization States. Front Physiol 2018; 9:1659. [PMID: 30546316 PMCID: PMC6278720 DOI: 10.3389/fphys.2018.01659] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/02/2018] [Indexed: 01/22/2023] Open
Abstract
Macrophages derived from monocyte precursors undergo specific polarization processes which are influenced by the local tissue environment: classically activated (M1) macrophages, with a pro-inflammatory activity and a role of effector cells in Th1 cellular immune responses, and alternatively activated (M2) macrophages, with anti-inflammatory functions and involved in immunosuppression and tissue repair. At least three different subsets of M2 macrophages, namely, M2a, M2b, and M2c, are characterized in the literature based on their eliciting signals. The activation and polarization of macrophages is achieved through many, often intertwined, signaling pathways. To describe the logical relationships among the genes involved in macrophage polarization, we used a computational modeling methodology, namely, logical (Boolean) modeling of gene regulation. We integrated experimental data and knowledge available in the literature to construct a logical network model for the gene regulation driving macrophage polarization to the M1, M2a, M2b, and M2c phenotypes. Using the software GINsim and BoolNet, we analyzed the network dynamics under different conditions and perturbations to understand how they affect cell polarization. Dynamic simulations of the network model, enacting the most relevant biological conditions, showed coherence with the observed behavior of in vivo macrophages. The model could correctly reproduce the polarization toward the four main phenotypes as well as to several hybrid phenotypes, which are known to be experimentally associated to physiological and pathological conditions. We surmise that shifts among different phenotypes in the model mimic the hypothetical continuum of macrophage polarization, with M1 and M2 being the extremes of an uninterrupted sequence of states. Furthermore, model simulations suggest that anti-inflammatory macrophages are resilient to shift back to the pro-inflammatory phenotype.
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Affiliation(s)
- Alessandro Palma
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Abdul Salam Jarrah
- Department of Mathematics and Statistics, American University of Sharjah, Sharjah, United Arab Emirates
| | - Paolo Tieri
- Institute for Applied Computing, National Research Council of Italy, Rome, Italy.,Data Science Program, Sapienza University of Rome, Rome, Italy
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.,Fondazione Santa Lucia Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Filippo Castiglione
- Institute for Applied Computing, National Research Council of Italy, Rome, Italy
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23
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Ebrahimi Z, Asgari S, Ahangari Cohan R, Hosseinzadeh R, Hosseinzadeh G, Arezumand R. Rational affinity enhancement of fragmented antibody by ligand-based affinity improvement approach. Biochem Biophys Res Commun 2018; 506:653-659. [DOI: 10.1016/j.bbrc.2018.10.127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 10/21/2018] [Indexed: 11/28/2022]
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24
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Wagar LE, DiFazio RM, Davis MM. Advanced model systems and tools for basic and translational human immunology. Genome Med 2018; 10:73. [PMID: 30266097 PMCID: PMC6162943 DOI: 10.1186/s13073-018-0584-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/17/2018] [Indexed: 12/31/2022] Open
Abstract
There are fundamental differences between humans and the animals we typically use to study the immune system. We have learned much from genetically manipulated and inbred animal models, but instances in which these findings have been successfully translated to human immunity have been rare. Embracing the genetic and environmental diversity of humans can tell us about the fundamental biology of immune cell types and the elasticity of the immune system. Although people are much more immunologically diverse than conventionally housed animal models, tools and technologies are now available that permit high-throughput analysis of human samples, including both blood and tissues, which will give us deep insights into human immunity in health and disease. As we gain a more detailed picture of the human immune system, we can build more sophisticated models to better reflect this complexity, both enabling the discovery of new immunological mechanisms and facilitating translation into the clinic.
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Affiliation(s)
- Lisa E Wagar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Robert M DiFazio
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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