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Korkmaz HI, Niessen FB, Pijpe A, Sheraton VM, Vermolen FJ, Krijnen PA, Niessen HW, Sloot PM, Middelkoop E, Gibbs S, van Zuijlen PP. Scar formation from the perspective of complexity science: a new look at the biological system as a whole. J Wound Care 2022; 31:178-184. [PMID: 35148632 DOI: 10.12968/jowc.2022.31.2.178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A burn wound is a complex systemic disease at multiple levels. Current knowledge of scar formation after burn injury has come from traditional biological and clinical studies. These are normally focused on just a small part of the entire process, which has limited our ability to sufficiently understand the underlying mechanisms and to predict systems behaviour. Scar formation after burn injury is a result of a complex biological system-wound healing. It is a part of a larger whole. In this self-organising system, many components form networks of interactions with each other. These networks of interactions are typically non-linear and change their states dynamically, responding to the environment and showing emergent long-term behaviour. How molecular and cellular data relate to clinical phenomena, especially regarding effective therapies of burn wounds to achieve minimal scarring, is difficult to unravel and comprehend. Complexity science can help bridge this gap by integrating small parts into a larger whole, such that relevant biological mechanisms and data are combined in a computational model to better understand the complexity of the entire biological system. A better understanding of the complex biological system of post-burn scar formation could bring research and treatment regimens to the next level. The aim of this review/position paper is to create more awareness of complexity in scar formation after burn injury by describing the basic principles of complexity science and its potential for burn care professionals.
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Affiliation(s)
- H Ibrahim Korkmaz
- Department of Plastic Reconstructive and Hand Surgery, Amsterdam Movement Sciences (AMS) Institute, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands.,Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands.,Burn Center and Department of Plastic and Reconstructive Surgery, Red Cross Hospital, Beverwijk, The Netherlands.,Association of Dutch Burn Centres (ADBC), Beverwijk, The Netherlands
| | - Frank B Niessen
- Department of Plastic Reconstructive and Hand Surgery, Amsterdam Movement Sciences (AMS) Institute, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands
| | - Anouk Pijpe
- Burn Center and Department of Plastic and Reconstructive Surgery, Red Cross Hospital, Beverwijk, The Netherlands
| | - Vivek M Sheraton
- Institute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands
| | - Fred J Vermolen
- Delft Institute of Applied Mathematics, Delft University of Technology, Delft, The Netherlands.,Computational Mathematics, Hasselt University, Diepenbeek, Belgium
| | - Paul Aj Krijnen
- Department of Pathology and Cardiac Surgery, Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands
| | - Hans Wm Niessen
- Department of Pathology and Cardiac Surgery, Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands
| | - Peter Ma Sloot
- Institute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands.,Complexity Institute, Nanyang Technological University, Singapore.,ITMO University, Saint Petersburg, Russian Federation
| | - Esther Middelkoop
- Department of Plastic Reconstructive and Hand Surgery, Amsterdam Movement Sciences (AMS) Institute, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands.,Burn Center and Department of Plastic and Reconstructive Surgery, Red Cross Hospital, Beverwijk, The Netherlands.,Association of Dutch Burn Centres (ADBC), Beverwijk, The Netherlands
| | - Susan Gibbs
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands.,Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Paul Pm van Zuijlen
- Department of Plastic Reconstructive and Hand Surgery, Amsterdam Movement Sciences (AMS) Institute, Amsterdam UMC, Location VUmc, Amsterdam, The Netherlands.,Burn Center and Department of Plastic and Reconstructive Surgery, Red Cross Hospital, Beverwijk, The Netherlands.,Paediatric Surgical Centre, Emma Children's Hospital, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
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Rao RT, Scherholz ML, Hartmanshenn C, Bae SA, Androulakis IP. On the analysis of complex biological supply chains: From Process Systems Engineering to Quantitative Systems Pharmacology. Comput Chem Eng 2017; 107:100-110. [PMID: 29353945 DOI: 10.1016/j.compchemeng.2017.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The use of models in biology has become particularly relevant as it enables investigators to develop a mechanistic framework for understanding the operating principles of living systems as well as in quantitatively predicting their response to both pathological perturbations and pharmacological interventions. This application has resulted in a synergistic convergence of systems biology and pharmacokinetic-pharmacodynamic modeling techniques that has led to the emergence of quantitative systems pharmacology (QSP). In this review, we discuss how the foundational principles of chemical process systems engineering inform the progressive development of more physiologically-based systems biology models.
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Affiliation(s)
- Rohit T Rao
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, NJ 08854
| | - Megerle L Scherholz
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, NJ 08854
| | - Clara Hartmanshenn
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, NJ 08854
| | - Seul-A Bae
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, NJ 08854
| | - Ioannis P Androulakis
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, 98 Brett Road, Piscataway, NJ 08854.,Department of Biomedical Engineering, Rutgers The State University of New Jersey, 599 Taylor Road, Piscataway, NJ 08854
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Bielekova B, Vodovotz Y, An G, Hallenbeck J. How implementation of systems biology into clinical trials accelerates understanding of diseases. Front Neurol 2014; 5:102. [PMID: 25018747 PMCID: PMC4073421 DOI: 10.3389/fneur.2014.00102] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/05/2014] [Indexed: 01/12/2023] Open
Abstract
Systems biology comprises a series of concepts and approaches that have been used successfully both to delineate novel biological mechanisms and to drive translational advances. The goal of systems biology is to re-integrate putatively critical elements extracted from multi-modality datasets in order to understand how interactions among multiple components form functional networks at the organism/patient-level, and how dysfunction of these networks underlies a particular disease. Due to the genetic and environmental diversity of human subjects, identification of critical elements related to a particular disease process from cross-sectional studies requires prohibitively large cohorts. Alternatively, implementation of systems biology principles to interventional clinical trials represents a unique opportunity to gain predictive understanding of complex diseases in comparatively small cohorts of patients. This paper reviews systems biology principles applicable to translational research, focusing on lessons from systems approaches to inflammation applied to multiple sclerosis. We suggest that employing systems biology methods in the design and execution of biomarker-supported, proof-of-principle clinical trials provides a singular opportunity to merge therapeutic development with a basic understanding of disease processes. The ultimate goal is to develop predictive computational models of the disease, which will revolutionize diagnostic process and provide mechanistic understanding necessary for personalized therapeutic approaches. Added, biologically meaningful information can be derived from diagnostic tests, if they are interpreted in functional relationships, rather than as independent measurements. Such systems biology based diagnostics will transform disease taxonomies from phenotypical to molecular and will allow physicians to select optimal therapeutic regimens for individual patients.
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Affiliation(s)
- Bibiana Bielekova
- Neuroimmunological Diseases Unit, National Institute of Neurological Disorder and Stroke, National Institutes of Health , Bethesda, MD , USA ; Center for Human Immunology of the National Institutes of Health , Bethesda, MD , USA
| | - Yoram Vodovotz
- Department of Surgery, University of Pittsburgh , Pittsburgh, PA , USA ; Center for Inflammation and Regenerative Modeling, McGowan Institute of Regenerative Medicine , Pittsburgh, PA , USA
| | - Gary An
- Center for Inflammation and Regenerative Modeling, McGowan Institute of Regenerative Medicine , Pittsburgh, PA , USA ; Department of Surgery, Northwestern University , Chicago, IL , USA
| | - John Hallenbeck
- Stroke Branch, National Institute of Neurological Disorder and Stroke, National Institutes of Health , Bethesda, MD , USA
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Investigation of inflammation and tissue patterning in the gut using a Spatially Explicit General-purpose Model of Enteric Tissue (SEGMEnT). PLoS Comput Biol 2014; 10:e1003507. [PMID: 24675765 PMCID: PMC3967920 DOI: 10.1371/journal.pcbi.1003507] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 01/10/2014] [Indexed: 01/22/2023] Open
Abstract
The mucosa of the intestinal tract represents a finely tuned system where tissue structure strongly influences, and is turn influenced by, its function as both an absorptive surface and a defensive barrier. Mucosal architecture and histology plays a key role in the diagnosis, characterization and pathophysiology of a host of gastrointestinal diseases. Inflammation is a significant factor in the pathogenesis in many gastrointestinal diseases, and is perhaps the most clinically significant control factor governing the maintenance of the mucosal architecture by morphogenic pathways. We propose that appropriate characterization of the role of inflammation as a controller of enteric mucosal tissue patterning requires understanding the underlying cellular and molecular dynamics that determine the epithelial crypt-villus architecture across a range of conditions from health to disease. Towards this end we have developed the Spatially Explicit General-purpose Model of Enteric Tissue (SEGMEnT) to dynamically represent existing knowledge of the behavior of enteric epithelial tissue as influenced by inflammation with the ability to generate a variety of pathophysiological processes within a common platform and from a common knowledge base. In addition to reproducing healthy ileal mucosal dynamics as well as a series of morphogen knock-out/inhibition experiments, SEGMEnT provides insight into a range of clinically relevant cellular-molecular mechanisms, such as a putative role for Phosphotase and tensin homolog/phosphoinositide 3-kinase (PTEN/PI3K) as a key point of crosstalk between inflammation and morphogenesis, the protective role of enterocyte sloughing in enteric ischemia-reperfusion and chronic low level inflammation as a driver for colonic metaplasia. These results suggest that SEGMEnT can serve as an integrating platform for the study of inflammation in gastrointestinal disease.
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Gopalakrishnan V, Kim M, An G. Using an Agent-Based Model to Examine the Role of Dynamic Bacterial Virulence Potential in the Pathogenesis of Surgical Site Infection. Adv Wound Care (New Rochelle) 2013; 2:510-526. [PMID: 24761337 PMCID: PMC3842882 DOI: 10.1089/wound.2012.0400] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 01/11/2013] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE Despite clinical advances, surgical site infections (SSIs) remain a problem. The development of SSIs involves a complex interplay between the cellular and molecular mechanisms of wound healing and contaminating bacteria, and here, we utilize an agent-based model (ABM) to investigate the role of bacterial virulence potential in the pathogenesis of SSI. APPROACH The Muscle Wound ABM (MWABM) incorporates muscle cells, neutrophils, macrophages, myoblasts, abstracted blood vessels, and avirulent/virulent bacteria to simulate the pathogenesis of SSIs. Simulated bacteria with virulence potential can mutate to possess resistance to reactive oxygen species and increased invasiveness. Simulated experiments (t=7 days) involved parameter sweeps of initial wound size to identify transition zones between healed and nonhealed wounds/SSIs, and to evaluate the effect of avirulent/virulent bacteria. RESULTS The MWABM reproduced the dynamics of normal successful healing, including a transition zone in initial wound size beyond which healing was significantly impaired. Parameter sweeps with avirulent bacteria demonstrated that smaller wound sizes were associated with healing failure. This effect was even more pronounced with the addition of virulence potential to the contaminating bacteria. INNOVATION The MWABM integrates the myriad factors involved in the healing of a normal wound and the pathogenesis of SSIs. This type of model can serve as a useful framework into which more detailed mechanistic knowledge can be embedded. CONCLUSION Future work will involve more comprehensive representation of host factors, and especially the ability of those host factors to activate virulence potential in the microbes involved.
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Affiliation(s)
| | - Moses Kim
- Department of Surgery, University of Chicago, Chicago, Illinois
| | - Gary An
- Department of Surgery, University of Chicago, Chicago, Illinois
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Kim M, Christley S, Alverdy JC, Liu D, An G. Immature oxidative stress management as a unifying principle in the pathogenesis of necrotizing enterocolitis: insights from an agent-based model. Surg Infect (Larchmt) 2012; 13:18-32. [PMID: 22217195 DOI: 10.1089/sur.2011.057] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Necrotizing enterocolitis (NEC) is a complex disease involving prematurity, enteral feeding, and bacterial effects. We propose that the underlying initial condition in its pathogenesis is reduced ability of the neonatal gut epithelial cells (NGECs) to clear oxidative stress (OS), and that when such a NGEC population is exposed to enteral feeding, the increased metabolic OS tips the population toward apoptosis, inflammation, bacterial activation, and eventual necrosis. The multi-factorial complexity of NEC requires characterization with computational modeling, and herein, we used an agent-based model (ABM) to instantiate and examine our unifying hypothesis of the pathogenesis of NEC. METHODS An ABM of the neonatal gut was created with NGEC computational agents incorporating rules for pathways for OS, p53, tight junctions, Toll-like receptor (TLR)-4, nitric oxide, and nuclear factor-kappa beta (NF-κB). The modeled bacteria activated TLR-4 on contact with NGECs. Simulations included parameter sweeps of OS response, response to feeding, addition of bacteria, and alterations in gut mucus production. RESULTS The ABM reproduced baseline cellular respiration and clearance of OS. Reduction in OS clearance consistent with clinical NEC led to senescence, apoptosis, or inflammation, with disruption of tight junctions, but rarely to NGEC necrosis. An additional "hit" of bacteria activating TLR-4 potentiated a shift to NGEC necrosis across the entire population. The mucus layer was modeled to limit bacterial-NGEC interactions and reduce this effect, but concomitant apoptosis in the goblet cell population reduced the efficacy of the mucus layer and limited its protective effect in simulated experiments. This finding suggests a means by which increased apoptosis at the cellular population level can lead to a transition to the necrosis outcome. CONCLUSIONS Our ABM incorporates known components of NEC and demonstrates that impaired OS management can lead to apoptosis and inflammation of NGECs, rendering the system susceptible to an additional insult involving regionalized mucus barrier failure and TLR-4 activation, which potentiates the necrosis outcome. This type of integrative dynamic knowledge representation can be a useful adjunct to help guide and contextualize research.
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Affiliation(s)
- Moses Kim
- Department of Surgery, University of Chicago, Chicago, Illinois 60637, USA
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Abstract
Translational bioinformatics plays an indispensable role in transforming psychoneuroimmunology (PNI) into personalized medicine. It provides a powerful method to bridge the gaps between various knowledge domains in PNI and systems biology. Translational bioinformatics methods at various systems levels can facilitate pattern recognition, and expedite and validate the discovery of systemic biomarkers to allow their incorporation into clinical trials and outcome assessments. Analysis of the correlations between genotypes and phenotypes including the behavioral-based profiles will contribute to the transition from the disease-based medicine to human-centered medicine. Translational bioinformatics would also enable the establishment of predictive models for patient responses to diseases, vaccines, and drugs. In PNI research, the development of systems biology models such as those of the neurons would play a critical role. Methods based on data integration, data mining, and knowledge representation are essential elements in building health information systems such as electronic health records and computerized decision support systems. Data integration of genes, pathophysiology, and behaviors are needed for a broad range of PNI studies. Knowledge discovery approaches such as network-based systems biology methods are valuable in studying the cross-talks among pathways in various brain regions involved in disorders such as Alzheimer's disease.
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Seal JB, Alverdy JC, Zaborina O, An G. Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis. Theor Biol Med Model 2011; 8:33. [PMID: 21929759 PMCID: PMC3184268 DOI: 10.1186/1742-4682-8-33] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 09/19/2011] [Indexed: 01/07/2023] Open
Abstract
Background There is a growing realization that alterations in host-pathogen interactions (HPI) can generate disease phenotypes without pathogen invasion. The gut represents a prime region where such HPI can arise and manifest. Under normal conditions intestinal microbial communities maintain a stable, mutually beneficial ecosystem. However, host stress can lead to changes in environmental conditions that shift the nature of the host-microbe dialogue, resulting in escalation of virulence expression, immune activation and ultimately systemic disease. Effective modulation of these dynamics requires the ability to characterize the complexity of the HPI, and dynamic computational modeling can aid in this task. Agent-based modeling is a computational method that is suited to representing spatially diverse, dynamical systems. We propose that dynamic knowledge representation of gut HPI with agent-based modeling will aid in the investigation of the pathogenesis of gut-derived sepsis. Methodology/Principal Findings An agent-based model (ABM) of virulence regulation in Pseudomonas aeruginosa was developed by translating bacterial and host cell sense-and-response mechanisms into behavioral rules for computational agents and integrated into a virtual environment representing the host-microbe interface in the gut. The resulting gut milieu ABM (GMABM) was used to: 1) investigate a potential clinically relevant laboratory experimental condition not yet developed - i.e. non-lethal transient segmental intestinal ischemia, 2) examine the sufficiency of existing hypotheses to explain experimental data - i.e. lethality in a model of major surgical insult and stress, and 3) produce behavior to potentially guide future experimental design - i.e. suggested sample points for a potential laboratory model of non-lethal transient intestinal ischemia. Furthermore, hypotheses were generated to explain certain discrepancies between the behaviors of the GMABM and biological experiments, and new investigatory avenues proposed to test those hypotheses. Conclusions/Significance Agent-based modeling can account for the spatio-temporal dynamics of an HPI, and, even when carried out with a relatively high degree of abstraction, can be useful in the investigation of system-level consequences of putative mechanisms operating at the individual agent level. We suggest that an integrated and iterative heuristic relationship between computational modeling and more traditional laboratory and clinical investigations, with a focus on identifying useful and sufficient degrees of abstraction, will enhance the efficiency and translational productivity of biomedical research.
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Affiliation(s)
- John B Seal
- Department of Surgery, University of Chicago, 5841 South Maryland Ave, MC 5031, Chicago, IL 60637, USA
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Yan Q. Toward the integration of personalized and systems medicine: challenges, opportunities and approaches. Per Med 2011; 8:1-4. [PMID: 29768783 DOI: 10.2217/pme.10.77] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Qing Yan
- PharmTao, PO Box 5672, Santa Clara, CA 95056, USA.
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