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Grootveld AK, Kyaw W, Panova V, Lau AWY, Ashwin E, Seuzaret G, Dhenni R, Bhattacharyya ND, Khoo WH, Biro M, Mitra T, Meyer-Hermann M, Bertolino P, Tanaka M, Hume DA, Croucher PI, Brink R, Nguyen A, Bannard O, Phan TG. Apoptotic cell fragments locally activate tingible body macrophages in the germinal center. Cell 2023; 186:1144-1161.e18. [PMID: 36868219 PMCID: PMC7614509 DOI: 10.1016/j.cell.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/04/2023] [Accepted: 01/31/2023] [Indexed: 03/05/2023]
Abstract
Germinal centers (GCs) that form within lymphoid follicles during antibody responses are sites of massive cell death. Tingible body macrophages (TBMs) are tasked with apoptotic cell clearance to prevent secondary necrosis and autoimmune activation by intracellular self antigens. We show by multiple redundant and complementary methods that TBMs derive from a lymph node-resident, CD169-lineage, CSF1R-blockade-resistant precursor that is prepositioned in the follicle. Non-migratory TBMs use cytoplasmic processes to chase and capture migrating dead cell fragments using a "lazy" search strategy. Follicular macrophages activated by the presence of nearby apoptotic cells can mature into TBMs in the absence of GCs. Single-cell transcriptomics identified a TBM cell cluster in immunized lymph nodes which upregulated genes involved in apoptotic cell clearance. Thus, apoptotic B cells in early GCs trigger activation and maturation of follicular macrophages into classical TBMs to clear apoptotic debris and prevent antibody-mediated autoimmune diseases.
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Affiliation(s)
- Abigail K Grootveld
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
| | - Wunna Kyaw
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Veera Panova
- MRC Human Immunology Unit, Nuffield Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Angelica W Y Lau
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Emily Ashwin
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Guillaume Seuzaret
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; Département de Biologie, Université de Lyon, Lyon, France
| | - Rama Dhenni
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | | | - Weng Hua Khoo
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Maté Biro
- EMBL Australia, Single Molecule Science Node, School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Tanmay Mitra
- Department of Systems Biology and Braunschweig Integrated Center for Systems Biology (BRICS), Helmholtz Center for Infection Research, Rebenring 56, D-38106 Braunschweig, Germany
| | - Michael Meyer-Hermann
- Department of Systems Biology and Braunschweig Integrated Center for Systems Biology (BRICS), Helmholtz Center for Infection Research, Rebenring 56, D-38106 Braunschweig, Germany; Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Patrick Bertolino
- Centenary Institute and University of Sydney, AW Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Masato Tanaka
- Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - David A Hume
- Mater Research Institute, University of Queensland, Brisbane, QLD, Australia
| | - Peter I Croucher
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Robert Brink
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Akira Nguyen
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia
| | - Oliver Bannard
- MRC Human Immunology Unit, Nuffield Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Tri Giang Phan
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, Australia; St Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, NSW, Australia.
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Furze JN, Mayad EH. Harmonics, evolutionary generators, DANCE, and HEAR-functional dimensions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:64181-64190. [PMID: 33846914 DOI: 10.1007/s11356-021-13159-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Evolution of the major kingdoms of life has spanned over the last 4 billion years on Earth. Studies of the process comprise different fields of study with alternative perspectives. This paper focuses on mathematic unification of the subject area; enriching an engineering based structure to advance our understanding of pathways which lead to distinct constructs in life, furthering geographic bordering processes with biological context. Application of logistic regression requires partitioning of variance within cellular and molecular systems; use of higher mathematic technique (multi-objective genetic algorithm) generates variance within the different scales of evolution, the result of which is analogous with the Fisher equation model of gene distribution within populations. Laboratory and field studies were integrated to illustrate emergence in evolutionary processes in the terrestrial/soil environment. Nematological field and laboratory trials validate the existence of triangular relationships within biological communities; further harmonic constants between interacting species may be found with emergent consequence. We distinguish different strategical groupings in the soil community, with the core groupings recognized with Meloidogyne spp. illustrating positive (emergent) growth; Radopholus similis (neutral growth), and Helicotylenchus pseudorobustus (negative growth). The patterns of emergent systems are shown in the extremes of Morocco's dynamic soil environment. Fuzzy classification methods: Mamdani, Takugi-Sugeno-Kang; additional novel DANCE (Differential Algorithmic Network Centered Emergence) and functional expressions HEAR (Harmonic Evolutionary Algorithmic Resilience), are recommended to give a basis for development of constructs covering different categories of life.
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Affiliation(s)
- James Nicholas Furze
- Laboratory of Biotechnology and Valorization of Natural Resources, Faculty of Sciences of Agadir, Department of Biology, Ibn Zohr University, BP 8106, Agadir, 80000, Morocco.
- Control and Systems Engineering Department, University of Technology, Alsinaah Street, P.O. Box: 19006, Baghdad, 10066, Iraq.
- Royal Geographical Society with the Institute of British Geographers, 1 Kensington Gore, London, SW7 2AR, UK.
| | - El Hassan Mayad
- Control and Systems Engineering Department, University of Technology, Alsinaah Street, P.O. Box: 19006, Baghdad, 10066, Iraq
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Putri GH, Koprinska I, Ashhurst TM, King NJC, Read MN. Using single-cell cytometry to illustrate integrated multi-perspective evaluation of clustering algorithms using Pareto fronts. Bioinformatics 2021; 37:btab038. [PMID: 33508103 DOI: 10.1093/bioinformatics/btab038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 12/21/2022] Open
Abstract
MOTIVATION Many 'automated gating' algorithms now exist to cluster cytometry and single cell sequencing data into discrete populations. Comparative algorithm evaluations on benchmark datasets rely either on a single performance metric, or a few metrics considered independently of one another. However, single metrics emphasise different aspects of clustering performance and do not rank clustering solutions in the same order. This underlies the lack of consensus between comparative studies regarding optimal clustering algorithms and undermines the translatability of results onto other non-benchmark datasets. RESULTS We propose the Pareto fronts framework as an integrative evaluation protocol, wherein individual metrics are instead leveraged as complementary perspectives. Judged superior are algorithms that provide the best trade-off between the multiple metrics considered simultaneously. This yields a more comprehensive and complete view of clustering performance. Moreover, by broadly and systematically sampling algorithm parameter values using the Latin Hypercube sampling method, our evaluation protocol minimises (un)fortunate parameter value selections as confounding factors. Furthermore, it reveals how meticulously each algorithm must be tuned in order to obtain good results, vital knowledge for users with novel data. We exemplify the protocol by conducting a comparative study between three clustering algorithms (ChronoClust, FlowSOM and Phenograph) using four common performance metrics applied across four cytometry benchmark datasets. To our knowledge, this is the first time Pareto fronts have been used to evaluate the performance of clustering algorithms in any application domain. AVAILABILITY Implementation of our Pareto front methodology and all scripts to reproduce this article are available at https://github.com/ghar1821/ParetoBench.
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Affiliation(s)
- Givanna H Putri
- School of Computer Science, The University of Sydney, Sydney, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, 2006, Australia
| | - Irena Koprinska
- School of Computer Science, The University of Sydney, Sydney, 2006, Australia
| | - Thomas M Ashhurst
- Sydney Cytometry Facility, The University of Sydney and Centenary Institute, Sydney, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, 2006, Australia
| | - Nicholas J C King
- Sydney Cytometry Facility, The University of Sydney and Centenary Institute, Sydney, 2006, Australia
- Discipline of Pathology, The University of Sydney, Sydney, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, 2006, Australia
| | - Mark N Read
- School of Computer Science, The University of Sydney, Sydney, 2006, Australia
- Westmead Initiative, The University of Sydney, Sydney, 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, 2006, Australia
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Molina Ortiz JP, McClure DD, Shanahan ER, Dehghani F, Holmes AJ, Read MN. Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models. Gut Microbes 2021; 13:1965698. [PMID: 34455914 PMCID: PMC8432618 DOI: 10.1080/19490976.2021.1965698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/01/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiome has emerged as a contributing factor in non-communicable disease, rendering it a target of health-promoting interventions. Yet current understanding of the host-microbiome dynamic is insufficient to predict the variation in intervention outcomes across individuals. We explore the mechanisms that underpin the gut bacterial ecosystem and highlight how a more complete understanding of this ecology will enable improved intervention outcomes. This ecology varies within the gut over space and time. Interventions disrupt these processes, with cascading consequences throughout the ecosystem. In vivo studies cannot isolate and probe these processes at the required spatiotemporal resolutions, and in vitro studies lack the representative complexity required. However, we highlight that, together, both approaches can inform in silico models that integrate cellular-level dynamics, can extrapolate to explain bacterial community outcomes, permit experimentation and observation over ecological processes at high spatiotemporal resolution, and can serve as predictive platforms on which to prototype interventions. Thus, it is a concerted integration of these techniques that will enable rational targeted manipulations of the gut ecosystem.
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Affiliation(s)
- Juan P. Molina Ortiz
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Dale D. McClure
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Erin R. Shanahan
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Andrew J. Holmes
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Mark N. Read
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Computer Science, Faculty of Engineering, The University of Sydney, Sydney, Australia
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Wessler T, Joslyn LR, Borish HJ, Gideon HP, Flynn JL, Kirschner DE, Linderman JJ. A computational model tracks whole-lung Mycobacterium tuberculosis infection and predicts factors that inhibit dissemination. PLoS Comput Biol 2020; 16:e1007280. [PMID: 32433646 PMCID: PMC7239387 DOI: 10.1371/journal.pcbi.1007280] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 02/26/2020] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative infectious agent of tuberculosis (TB), kills more individuals per year than any other infectious agent. Granulomas, the hallmark of Mtb infection, are complex structures that form in lungs, composed of immune cells surrounding bacteria, infected cells, and a caseous necrotic core. While granulomas serve to physically contain and immunologically restrain bacteria growth, some granulomas are unable to control Mtb growth, leading to bacteria and infected cells leaving the granuloma and disseminating, either resulting in additional granuloma formation (local or non-local) or spread to airways or lymph nodes. Dissemination is associated with development of active TB. It is challenging to experimentally address specific mechanisms driving dissemination from TB lung granulomas. Herein, we develop a novel hybrid multi-scale computational model, MultiGran, that tracks Mtb infection within multiple granulomas in an entire lung. MultiGran follows cells, cytokines, and bacterial populations within each lung granuloma throughout the course of infection and is calibrated to multiple non-human primate (NHP) cellular, granuloma, and whole-lung datasets. We show that MultiGran can recapitulate patterns of in vivo local and non-local dissemination, predict likelihood of dissemination, and predict a crucial role for multifunctional CD8+ T cells and macrophage dynamics for preventing dissemination. Tuberculosis (TB) is caused by infection with Mycobacterium tuberculosis (Mtb) and kills 3 people per minute worldwide. Granulomas, spherical structures composed of immune cells surrounding bacteria, are the hallmark of Mtb infection and sometimes fail to contain the bacteria and disseminate, leading to further granuloma growth within the lung environment. To date, the mechanisms that determine granuloma dissemination events have not been characterized. We present a computational multi-scale model of granuloma formation and dissemination within primate lungs. Our computational model is calibrated to multiple experimental datasets across the cellular, granuloma, and whole-lung scales of non-human primates. We match to both individual granuloma and granuloma-population datasets, predict likelihood of dissemination events, and predict a critical role for multifunctional CD8+ T cells and macrophage-bacteria interactions to prevent infection dissemination.
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Affiliation(s)
- Timothy Wessler
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Louis R. Joslyn
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - H. Jacob Borish
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Hannah P. Gideon
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Denise E. Kirschner
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (DEK); (JJL)
| | - Jennifer J. Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (DEK); (JJL)
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Alden K, Cosgrove J, Coles M, Timmis J. Using Emulation to Engineer and Understand Simulations of Biological Systems. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:302-315. [PMID: 29994223 DOI: 10.1109/tcbb.2018.2843339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Modeling and simulation techniques have demonstrated success in studying biological systems. As the drive to better capture biological complexity leads to more sophisticated simulators, it becomes challenging to perform statistical analyses that help translate predictions into increased understanding. These analyses may require repeated executions and extensive sampling of high-dimensional parameter spaces: analyses that may become intractable due to time and resource limitations. Significant reduction in these requirements can be obtained using surrogate models, or emulators, that can rapidly and accurately predict the output of an existing simulator. We apply emulation to evaluate and enrich understanding of a previously published agent-based simulator of lymphoid tissue organogenesis, showing an ensemble of machine learning techniques can reproduce results obtained using a suite of statistical analyses within seconds. This performance improvement permits incorporation of previously intractable analyses, including multi-objective optimization to obtain parameter sets that yield a desired response, and Approximate Bayesian Computation to assess parametric uncertainty. To facilitate exploitation of emulation in simulation-focused studies, we extend our open source statistical package, spartan, to provide a suite of tools for emulator development, validation, and application. Overcoming resource limitations permits enriched evaluation and refinement, easing translation of simulator insights into increased biological understanding.
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Fois CAM, Le TYL, Schindeler A, Naficy S, McClure DD, Read MN, Valtchev P, Khademhosseini A, Dehghani F. Models of the Gut for Analyzing the Impact of Food and Drugs. Adv Healthc Mater 2019; 8:e1900968. [PMID: 31592579 DOI: 10.1002/adhm.201900968] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 08/30/2019] [Indexed: 12/16/2022]
Abstract
Models of the human gastrointestinal tract (GIT) can be powerful tools for examining the biological interactions of food products and pharmaceuticals. This can be done under normal healthy conditions or using models of disease-many of which have no curative therapy. This report outlines the field of gastrointestinal modeling, with a particular focus on the intestine. Traditional in vivo animal models are compared to a range of in vitro models. In vitro systems are elaborated over time, recently culminating with microfluidic intestines-on-chips (IsOC) and 3D bioengineered models. Macroscale models are also reviewed for their important contribution in the microbiota studies. Lastly, it is discussed how in silico approaches may have utility in predicting and interpreting experimental data. The various advantages and limitations of the different systems are contrasted. It is posited that only through complementary use of these models will salient research questions be able to be addressed.
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Affiliation(s)
- Chiara Anna Maria Fois
- School of Chemical and Biomolecular Engineering Centre for Advanced Food Enginomics University of Sydney Sydney NSW 2006 Australia
| | - Thi Yen Loan Le
- School of Chemical and Biomolecular Engineering Centre for Advanced Food Enginomics University of Sydney Sydney NSW 2006 Australia
| | - Aaron Schindeler
- School of Chemical and Biomolecular Engineering Centre for Advanced Food Enginomics University of Sydney Sydney NSW 2006 Australia
| | - Sina Naficy
- School of Chemical and Biomolecular Engineering Centre for Advanced Food Enginomics University of Sydney Sydney NSW 2006 Australia
| | - Dale David McClure
- School of Chemical and Biomolecular Engineering Centre for Advanced Food Enginomics University of Sydney Sydney NSW 2006 Australia
| | - Mark Norman Read
- School of Chemical and Biomolecular Engineering Centre for Advanced Food Enginomics University of Sydney Sydney NSW 2006 Australia
| | - Peter Valtchev
- School of Chemical and Biomolecular Engineering Centre for Advanced Food Enginomics University of Sydney Sydney NSW 2006 Australia
| | - Ali Khademhosseini
- Department of Chemical and Biomolecular Engineering Department of Bioengineering Department of Radiology California NanoSystems Institute (CNSI) University of California Los Angeles CA 90095 USA
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering Centre for Advanced Food Enginomics University of Sydney Sydney NSW 2006 Australia
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Read MN, Alden K, Timmis J, Andrews PS. Strategies for calibrating models of biology. Brief Bioinform 2018; 21:24-35. [PMID: 30239570 DOI: 10.1093/bib/bby092] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 08/10/2018] [Accepted: 08/27/2018] [Indexed: 11/14/2022] Open
Abstract
Computational and mathematical modelling has become a valuable tool for investigating biological systems. Modelling enables prediction of how biological components interact to deliver system-level properties and extrapolation of biological system performance to contexts and experimental conditions where this is unknown. A model's value hinges on knowing that it faithfully represents the biology under the contexts of use, or clearly ascertaining otherwise and thus motivating further model refinement. These qualities are evaluated through calibration, typically formulated as identifying model parameter values that align model and biological behaviours as measured through a metric applied to both. Calibration is critical to modelling but is often underappreciated. A failure to appropriately calibrate risks unrepresentative models that generate erroneous insights. Here, we review a suite of strategies to more rigorously challenge a model's representation of a biological system. All are motivated by features of biological systems, and illustrative examples are drawn from the modelling literature. We examine the calibration of a model against distributions of biological behaviours or outcomes, not only average values. We argue for calibration even where model parameter values are experimentally ascertained. We explore how single metrics can be non-distinguishing for complex systems, with multiple-component dynamic and interaction configurations giving rise to the same metric output. Under these conditions, calibration is insufficiently constraining and the model non-identifiable: multiple solutions to the calibration problem exist. We draw an analogy to curve fitting and argue that calibrating a biological model against a single experiment or context is akin to curve fitting against a single data point. Though useful for communicating model results, we explore how metrics that quantify heavily emergent properties may not be suitable for use in calibration. Lastly, we consider the role of sensitivity and uncertainty analysis in calibration and the interpretation of model results. Our goal in this manuscript is to encourage a deeper consideration of calibration, and how to increase its capacity to either deliver faithful models or demonstrate them otherwise.
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Affiliation(s)
| | | | | | - Paul S Andrews
- SimOmics Ltd, Suite 10 IT Centre, Innovation Way, York, UK
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Haridas P, Browning AP, McGovern JA, Sean McElwain DL, Simpson MJ. Three-dimensional experiments and individual based simulations show that cell proliferation drives melanoma nest formation in human skin tissue. BMC SYSTEMS BIOLOGY 2018; 12:34. [PMID: 29587750 PMCID: PMC5872522 DOI: 10.1186/s12918-018-0559-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/06/2018] [Indexed: 02/07/2023]
Abstract
Background Melanoma can be diagnosed by identifying nests of cells on the skin surface. Understanding the processes that drive nest formation is important as these processes could be potential targets for new cancer drugs. Cell proliferation and cell migration are two potential mechanisms that could conceivably drive melanoma nest formation. However, it is unclear which one of these two putative mechanisms plays a dominant role in driving nest formation. Results We use a suite of three-dimensional (3D) experiments in human skin tissue and a parallel series of 3D individual-based simulations to explore whether cell migration or cell proliferation plays a dominant role in nest formation. In the experiments we measure nest formation in populations of irradiated (non-proliferative) and non-irradiated (proliferative) melanoma cells, cultured together with primary keratinocyte and fibroblast cells on a 3D experimental human skin model. Results show that nest size depends on initial cell number and is driven primarily by cell proliferation rather than cell migration. Conclusions Nest size depends on cell number, and is driven primarily by cell proliferation rather than cell migration. All experimental results are consistent with simulation data from a 3D individual based model (IBM) of cell migration and cell proliferation. Electronic supplementary material The online version of this article (10.1186/s12918-018-0559-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Parvathi Haridas
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, 4059, Australia.,School of Mathematical Sciences, QUT, Brisbane, 4001, Australia
| | | | - Jacqui A McGovern
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, 4059, Australia
| | - D L Sean McElwain
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, 4059, Australia.,School of Mathematical Sciences, QUT, Brisbane, 4001, Australia
| | - Matthew J Simpson
- Institute of Health and Biomedical Innovation, Queensland University of Technology (QUT), Kelvin Grove, 4059, Australia. .,School of Mathematical Sciences, QUT, Brisbane, 4001, Australia.
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