1
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Wirth D, Özdemir E, Hristova K. Probing phosphorylation events in biological membranes: The transducer function. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184362. [PMID: 38885782 DOI: 10.1016/j.bbamem.2024.184362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/26/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
The extracellular environment is sensed by receptors in the plasma membrane. Some of these receptors initiate cytoplasmic signaling cascades involving phosphorylation: the addition of a phosphate group to a specific amino acid, such as tyrosine, in a protein. Receptor Tyrosine Kinases (RTKs) are one large class of membrane receptors that can directly initiate signaling cascades through their intracellular kinase domains, which both catalyze tyrosine phosphorylation and get phosphorylated. In the first step of signaling, the ligands stabilize phosphorylation-competent RTK dimers and oligomers, which leads to the phosphorylation of specific tyrosine residues in the activation loop of the kinases. Here we discuss quantitative measurements of tyrosine phosphorylation efficiencies for RTKs, described by the "transducer function". The transducer function links the phosphorylation (the response) and the binding of the activating ligand to the receptor (the stimulus). We overview a methodology that allows such measurements in direct response to ligand binding. We discuss experiments which demonstrate that EGF is a partial agonist, and that two tyrosines in the intracellular domain of EGFR, Y1068 and Y1173, are differentially phosphorylated in the EGF-bound EGFR dimers.
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Affiliation(s)
- Daniel Wirth
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America
| | - Ece Özdemir
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America
| | - Kalina Hristova
- Department of Materials Science and Engineering and Institute for NanoBioTechnology, Johns Hopkins University, 3400 Charles Street, Baltimore, MD 21218, United States of America.
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2
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Haase M, Comlekoglu T, Petrucciani A, Peirce SM, Blemker SS. Agent-based model demonstrates the impact of nonlinear, complex interactions between cytokinces on muscle regeneration. eLife 2024; 13:RP91924. [PMID: 38828844 PMCID: PMC11147512 DOI: 10.7554/elife.91924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Abstract
Muscle regeneration is a complex process due to dynamic and multiscale biochemical and cellular interactions, making it difficult to identify microenvironmental conditions that are beneficial to muscle recovery from injury using experimental approaches alone. To understand the degree to which individual cellular behaviors impact endogenous mechanisms of muscle recovery, we developed an agent-based model (ABM) using the Cellular-Potts framework to simulate the dynamic microenvironment of a cross-section of murine skeletal muscle tissue. We referenced more than 100 published studies to define over 100 parameters and rules that dictate the behavior of muscle fibers, satellite stem cells (SSCs), fibroblasts, neutrophils, macrophages, microvessels, and lymphatic vessels, as well as their interactions with each other and the microenvironment. We utilized parameter density estimation to calibrate the model to temporal biological datasets describing cross-sectional area (CSA) recovery, SSC, and fibroblast cell counts at multiple timepoints following injury. The calibrated model was validated by comparison of other model outputs (macrophage, neutrophil, and capillaries counts) to experimental observations. Predictions for eight model perturbations that varied cell or cytokine input conditions were compared to published experimental studies to validate model predictive capabilities. We used Latin hypercube sampling and partial rank correlation coefficient to identify in silico perturbations of cytokine diffusion coefficients and decay rates to enhance CSA recovery. This analysis suggests that combined alterations of specific cytokine decay and diffusion parameters result in greater fibroblast and SSC proliferation compared to individual perturbations with a 13% increase in CSA recovery compared to unaltered regeneration at 28 days. These results enable guided development of therapeutic strategies that similarly alter muscle physiology (i.e. converting extracellular matrix [ECM]-bound cytokines into freely diffusible forms as studied in cancer therapeutics or delivery of exogenous cytokines) during regeneration to enhance muscle recovery after injury.
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Affiliation(s)
- Megan Haase
- University of VirginiaCharlottesvilleUnited States
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3
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Fan L, Wang H, Kassab GS, Lee LC. Review of cardiac-coronary interaction and insights from mathematical modeling. WIREs Mech Dis 2024; 16:e1642. [PMID: 38316634 PMCID: PMC11081852 DOI: 10.1002/wsbm.1642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/10/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024]
Abstract
Cardiac-coronary interaction is fundamental to the function of the heart. As one of the highest metabolic organs in the body, the cardiac oxygen demand is met by blood perfusion through the coronary vasculature. The coronary vasculature is largely embedded within the myocardial tissue which is continually contracting and hence squeezing the blood vessels. The myocardium-coronary vessel interaction is two-ways and complex. Here, we review the different types of cardiac-coronary interactions with a focus on insights gained from mathematical models. Specifically, we will consider the following: (1) myocardial-vessel mechanical interaction; (2) metabolic-flow interaction and regulation; (3) perfusion-contraction matching, and (4) chronic interactions between the myocardium and coronary vasculature. We also provide a discussion of the relevant experimental and clinical studies of different types of cardiac-coronary interactions. Finally, we highlight knowledge gaps, key challenges, and limitations of existing mathematical models along with future research directions to understand the unique myocardium-coronary coupling in the heart. This article is categorized under: Cardiovascular Diseases > Computational Models Cardiovascular Diseases > Biomedical Engineering Cardiovascular Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Lei Fan
- Joint Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Haifeng Wang
- Department of Mechanical Engineering, Michigan State University, East Lansing, Michigan, USA
| | - Ghassan S Kassab
- California Medical Innovations Institute, San Diego, California, USA
| | - Lik Chuan Lee
- Department of Mechanical Engineering, Michigan State University, East Lansing, Michigan, USA
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4
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Haase M, Comlekoglu T, Petrucciani A, Peirce SM, Blemker SS. Agent-based model demonstrates the impact of nonlinear, complex interactions between cytokines on muscle regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.14.553247. [PMID: 37645968 PMCID: PMC10462020 DOI: 10.1101/2023.08.14.553247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Muscle regeneration is a complex process due to dynamic and multiscale biochemical and cellular interactions, making it difficult to identify microenvironmental conditions that are beneficial to muscle recovery from injury using experimental approaches alone. To understand the degree to which individual cellular behaviors impact endogenous mechanisms of muscle recovery, we developed an agent-based model (ABM) using the Cellular Potts framework to simulate the dynamic microenvironment of a cross-section of murine skeletal muscle tissue. We referenced more than 100 published studies to define over 100 parameters and rules that dictate the behavior of muscle fibers, satellite stem cells (SSC), fibroblasts, neutrophils, macrophages, microvessels, and lymphatic vessels, as well as their interactions with each other and the microenvironment. We utilized parameter density estimation to calibrate the model to temporal biological datasets describing cross-sectional area (CSA) recovery, SSC, and fibroblast cell counts at multiple time points following injury. The calibrated model was validated by comparison of other model outputs (macrophage, neutrophil, and capillaries counts) to experimental observations. Predictions for eight model perturbations that varied cell or cytokine input conditions were compared to published experimental studies to validate model predictive capabilities. We used Latin hypercube sampling and partial rank correlation coefficient to identify in silico perturbations of cytokine diffusion coefficients and decay rates to enhance CSA recovery. This analysis suggests that combined alterations of specific cytokine decay and diffusion parameters result in greater fibroblast and SSC proliferation compared to individual perturbations with a 13% increase in CSA recovery compared to unaltered regeneration at 28 days. These results enable guided development of therapeutic strategies that similarly alter muscle physiology (i.e. converting ECM-bound cytokines into freely diffusible forms as studied in cancer therapeutics or delivery of exogenous cytokines) during regeneration to enhance muscle recovery after injury.
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5
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Stepanova D, Byrne HM, Maini PK, Alarcón T. Computational modeling of angiogenesis: The importance of cell rearrangements during vascular growth. WIREs Mech Dis 2024; 16:e1634. [PMID: 38084799 DOI: 10.1002/wsbm.1634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 03/16/2024]
Abstract
Angiogenesis is the process wherein endothelial cells (ECs) form sprouts that elongate from the pre-existing vasculature to create new vascular networks. In addition to its essential role in normal development, angiogenesis plays a vital role in pathologies such as cancer, diabetes and atherosclerosis. Mathematical and computational modeling has contributed to unraveling its complexity. Many existing theoretical models of angiogenic sprouting are based on the "snail-trail" hypothesis. This framework assumes that leading ECs positioned at sprout tips migrate toward low-oxygen regions while other ECs in the sprout passively follow the leaders' trails and proliferate to maintain sprout integrity. However, experimental results indicate that, contrary to the snail-trail assumption, ECs exchange positions within developing vessels, and the elongation of sprouts is primarily driven by directed migration of ECs. The functional role of cell rearrangements remains unclear. This review of the theoretical modeling of angiogenesis is the first to focus on the phenomenon of cell mixing during early sprouting. We start by describing the biological processes that occur during early angiogenesis, such as phenotype specification, cell rearrangements and cell interactions with the microenvironment. Next, we provide an overview of various theoretical approaches that have been employed to model angiogenesis, with particular emphasis on recent in silico models that account for the phenomenon of cell mixing. Finally, we discuss when cell mixing should be incorporated into theoretical models and what essential modeling components such models should include in order to investigate its functional role. This article is categorized under: Cardiovascular Diseases > Computational Models Cancer > Computational Models.
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Affiliation(s)
- Daria Stepanova
- Laboratorio Subterráneo de Canfranc, Canfranc-Estación, Huesca, Spain
| | - Helen M Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Tomás Alarcón
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Centre de Recerca Matemàtica, Bellaterra, Barcelona, Spain
- Departament de Matemàtiques, Universitat Autònoma de Barcelona, Bellaterra, Spain
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6
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Mahmoodi M, Pishevar A, Azargoshasbi F. Numerical investigation of the pharmacokinetics and pharmacodynamics of the chemotherapeutic drug in avascular and vascular stages of a brain tumor. J Theor Biol 2023; 575:111633. [PMID: 37839585 DOI: 10.1016/j.jtbi.2023.111633] [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: 08/03/2023] [Accepted: 10/05/2023] [Indexed: 10/17/2023]
Abstract
One of the most commonly used approaches for treating solid tumors is the systemic delivery of chemotherapeutic drugs. However, our understanding of the factors influencing treatment efficacy through this method is still limited. This study presents a comprehensive and realistic mathematical model that incorporates the dynamics of tumor growth, capillary network extension, and drug delivery in a coupled and simultaneous manner. The model covers two stages of tumor growth: avascular and vascular. For tumor growth, a continuum model is employed using the phase field interface-capturing method. The neo-vascularization process is modeled using a hybrid discrete-continuum approach. Additionally, a multi-scale model is used to describe the pharmacokinetics of doxorubicin, considering various agents. The study investigates the effect of haptotaxis and reveals that a higher haptotaxis coefficient leads to faster tumor growth (up to 2.6 times) and a quicker progression to angiogenesis. The impact of tumor-related and drug-related parameters is also examined, including tumor size, tumor sensitivity to the drug, chemotherapy initialization, treatment cycle duration, drug affinity to cells, and drug dose. The findings indicate that chemotherapy is more effective during the angiogenesis stage when active loops have formed. Other clinical methods such as radiotherapy and surgery may be more appropriate during the avascular stage or the transition period between angiogenesis initialization and loop formation. The penetration depth of the drug decreases by approximately 50% with an increase in the drug binding rate to surface-cell receptors. As a result, high-associate-rate drugs are preferred for chemotherapy after active loops have formed, while low-associate-rate drugs are suitable for earlier stages.
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Affiliation(s)
- Mohammad Mahmoodi
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran
| | - Ahmadreza Pishevar
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran.
| | - Farzaneh Azargoshasbi
- Department of Mechanical Engineering, Isfahan University of Technology, Isfahan 84156-83111, Iran
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7
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Terragni F, Martinson WD, Carretero M, Maini PK, Bonilla LL. Soliton approximation in continuum models of leader-follower behavior. Phys Rev E 2023; 108:054407. [PMID: 38115402 DOI: 10.1103/physreve.108.054407] [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: 07/28/2023] [Accepted: 10/17/2023] [Indexed: 12/21/2023]
Abstract
Complex biological processes involve collective behavior of entities (bacteria, cells, animals) over many length and time scales and can be described by discrete models that track individuals or by continuum models involving densities and fields. We consider hybrid stochastic agent-based models of branching morphogenesis and angiogenesis (new blood vessel creation from preexisting vasculature), which treat cells as individuals that are guided by underlying continuous chemical and/or mechanical fields. In these descriptions, leader (tip) cells emerge from existing branches and follower (stalk) cells build the new sprout in their wake. Vessel branching and fusion (anastomosis) occur as a result of tip and stalk cell dynamics. Coarse graining these hybrid models in appropriate limits produces continuum partial differential equations (PDEs) for endothelial cell densities that are more analytically tractable. While these models differ in nonlinearity, they produce similar equations at leading order when chemotaxis is dominant. We analyze this leading order system in a simple quasi-one-dimensional geometry and show that the numerical solution of the leading order PDE is well described by a soliton wave that evolves from vessel to source. This wave is an attractor for intermediate times until it arrives at the hypoxic region releasing the growth factor. The mathematical techniques used here thus identify common features of discrete and continuum approaches and provide insight into general biological mechanisms governing their collective dynamics.
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Affiliation(s)
- F Terragni
- Gregorio Millán Institute for Fluid Dynamics, Nanoscience and Industrial Mathematics, Universidad Carlos III de Madrid, 28911 Leganés, Spain
- Department of Mathematics, Universidad Carlos III de Madrid, 28911 Leganés, Spain
| | - W D Martinson
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom
| | - M Carretero
- Gregorio Millán Institute for Fluid Dynamics, Nanoscience and Industrial Mathematics, Universidad Carlos III de Madrid, 28911 Leganés, Spain
- Department of Mathematics, Universidad Carlos III de Madrid, 28911 Leganés, Spain
| | - P K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG, United Kingdom
| | - L L Bonilla
- Gregorio Millán Institute for Fluid Dynamics, Nanoscience and Industrial Mathematics, Universidad Carlos III de Madrid, 28911 Leganés, Spain
- Department of Mathematics, Universidad Carlos III de Madrid, 28911 Leganés, Spain
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8
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Dazzi C, Mehl J, Benamar M, Gerhardt H, Knaus P, Duda GN, Checa S. External mechanical loading overrules cell-cell mechanical communication in sprouting angiogenesis during early bone regeneration. PLoS Comput Biol 2023; 19:e1011647. [PMID: 37956208 PMCID: PMC10681321 DOI: 10.1371/journal.pcbi.1011647] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 11/27/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Sprouting angiogenesis plays a key role during bone regeneration. For example, insufficient early revascularization of the injured site can lead to delayed or non-healing. During sprouting, endothelial cells are known to be mechano-sensitive and respond to local mechanical stimuli. Endothelial cells interact and communicate mechanically with their surroundings, such as outer-vascular stromal cells, through cell-induced traction forces. In addition, external physiological loads act at the healing site, resulting in tissue deformations and impacting cellular arrangements. How these two distinct mechanical cues (cell-induced and external) impact angiogenesis and sprout patterning in early bone healing remains however largely unknown. Therefore, the aim of this study was to investigate the relative role of externally applied and cell-induced mechanical signals in driving sprout patterning at the onset of bone healing. To investigate cellular self-organisation in early bone healing, an in silico model accounting for the mechano-regulation of sprouting angiogenesis and stromal cell organization was developed. Computer model predictions were compared to in vivo experiments of a mouse osteotomy model stabilized with a rigid or a semirigid fixation system. We found that the magnitude and orientation of principal strains within the healing region can explain experimentally observed sprout patterning, under both fixation conditions. Furthermore, upon simulating the selective inhibition of either cell-induced or externally applied mechanical cues, external mechanical signals appear to overrule the mechanical communication acting on a cell-cell interaction level. Such findings illustrate the relevance of external mechanical signals over the local cell-mediated mechanical cues and could be used in the design of fracture treatment strategies for bone regeneration.
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Affiliation(s)
- Chiara Dazzi
- Julius Wolff Institute for Biomechanics and Musculoskeletal Regeneration, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Julia Mehl
- Julius Wolff Institute for Biomechanics and Musculoskeletal Regeneration, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Mounir Benamar
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Holger Gerhardt
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Petra Knaus
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Georg N. Duda
- Julius Wolff Institute for Biomechanics and Musculoskeletal Regeneration, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health Centre for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Sara Checa
- Julius Wolff Institute for Biomechanics and Musculoskeletal Regeneration, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
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9
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Ghasemi Nasab MS, Niroomand-Oscuii H, Bazmara H, Soltani M. Multi-scale model of lumen formation via inverse membrane blebbing mechanism during sprouting angiogenesis process. J Theor Biol 2023; 556:111312. [PMID: 36279960 DOI: 10.1016/j.jtbi.2022.111312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/04/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022]
Abstract
Cancer is one of the leading causes of mortality and morbidity among people worldwide. Cancer appears as solid tumors in many cases. Angiogenesis is the growth of blood vessels from the existing vasculature and is one of the imperative processes in tumor growth. Another vital phenomenon for formation and functionality of this vasculature network is lumen formation. The results of recent studies indicate the importance of blood pressure in this mechanism. Computational modeling can study these processes in different scales. Hence, wide varieties of these models have been proposed during recent years. In this research, a multi-scale model is developed for the angiogenesis process. In the extracellular scale, the growth factor concentration is calculated via the reaction diffusion equation. At the cellular scale, growth, migration, and the adhesion of endothelial cells are modeled by the Potts cellular model. At the intra-cellular scale by considering biochemical signals, a Boolean network model describes migration, division, or apoptosis of endothelial cells. A stochastic model developed for lumen formation via inverse membrane blebbing mechanism. A CFD simulation was also used to investigate the role of pulsated blood pressure in the inverse membrane blebbing mechanism. The lumen formation model shows stochastic behavior in blebs expansion and lumen expansion. Comparing the stochastic model's results with the CFD simulation also shows the vital role of pressure pulse and the topology of the blebs in bleb retraction.
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Affiliation(s)
| | | | | | - Majid Soltani
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Iran; Advanced Bioengineering Initiative Center, Computational Medicine Center, K. N. Toosi University of Technology, Tehran, Iran; Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran; Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, Ontario, Canada; Centre for Biotechnology and Bioengineering (CBB), University of Waterloo, Waterloo, Ontario, Canada
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10
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Bergman D, Sweis RF, Pearson AT, Nazari F, Jackson TL. A global method for fast simulations of molecular dynamics in multiscale agent-based models of biological tissues. iScience 2022; 25:104387. [PMID: 35637730 PMCID: PMC9142654 DOI: 10.1016/j.isci.2022.104387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 03/30/2022] [Accepted: 05/05/2022] [Indexed: 11/18/2022] Open
Abstract
Agent-based models (ABMs) are a natural platform for capturing the multiple time and spatial scales in biological processes. However, these models are computationally expensive, especially when including molecular-level effects. The traditional approach to simulating this type of multiscale ABM is to solve a system of ordinary differential equations for the molecular events per cell. This significantly adds to the computational cost of simulations as the number of agents grows, which contributes to many ABMs being limited to around10 5 cells. We propose an approach that requires the same computational time independent of the number of agents. This speeds up the entire simulation by orders of magnitude, allowing for more thorough explorations of ABMs with even larger numbers of agents. We use two systems to show that the new method strongly agrees with the traditionally used approach. This computational strategy can be applied to a wide range of biological investigations.
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Affiliation(s)
- Daniel Bergman
- Department of Mathematics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Randy F. Sweis
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, 5841 S Maryland Avenue, MC 2115, Chicago, IL 60605, USA
| | - Alexander T. Pearson
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, 5841 S Maryland Avenue, MC 2115, Chicago, IL 60605, USA
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11
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In silico optimization of heparin microislands in microporous annealed particle (MAP) hydrogel for endothelial cell migration. Acta Biomater 2022; 148:171-180. [PMID: 35660016 DOI: 10.1016/j.actbio.2022.05.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/03/2022] [Accepted: 05/27/2022] [Indexed: 11/24/2022]
Abstract
Biomaterials capable of generating growth factor gradients have shown success in guiding tissue regeneration, as growth factor gradients are a physiologic driver of cell migration. Of particular importance, a focus on promoting endothelial cell migration is vital to angiogenesis and new tissue formation. Microporous Annealed Particle (MAP) scaffolds represent a unique niche in the field of regenerative biomaterials research as an injectable biomaterial with an open porosity that allows cells to freely migrate independent of material degradation. Recently, we have used the MAP platform to heterogeneously include spatially isolated heparin-modified microgels (heparin microislands) which can sequester growth factors and guide cell migration. In in vitro sprouting angiogenesis assays, we observed a parabolic relationship between the percentage of heparin microislands and cell migration, where 10% heparin microislands had more endothelial cell migration compared to 1% and 100%. Due to the low number of heparin microisland ratios tested, we hypothesize the spacing between microgels can be further optimized. Rather than use purely empirical methods, which are both expensive and time intensive, we believe this challenge represents an opportunity to use computational modeling. Here we present the first agent-based model of a MAP scaffold to optimize the ratio of heparin microislands. Specifically, we develop a two-dimensional model in Hybrid Automata Library (HAL) of endothelial cell migration within the unique MAP scaffold geometry. Finally, we present how our model can accurately predict cell migration trends in vitro, and these studies provide insight on how computational modeling can be used to design particle-based biomaterials. STATEMENT OF SIGNIFICANCE: : While the combination of experimental and computational approaches is increasingly being used to gain a better understanding of cellular processes, their combination in biomaterials development has been relatively limited. Heparin microislands are spatially isolated heparin microgels; when located within a microporous annealed particle (MAP) scaffold, they can sequester and release growth factors. Importantly, we present the first agent-based model of MAP scaffolds to optimize the ratio of heparin microislands within the scaffold to promote endothelial cell migration. We demonstrate this model can accurately predict trends in vitro, thus opening a new avenue of research to aid in the design of MAP scaffolds.
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12
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Bekisz S, Baudin L, Buntinx F, Noël A, Geris L. In Vitro, In Vivo, and In Silico Models of Lymphangiogenesis in Solid Malignancies. Cancers (Basel) 2022; 14:1525. [PMID: 35326676 PMCID: PMC8946816 DOI: 10.3390/cancers14061525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/24/2022] [Accepted: 03/08/2022] [Indexed: 12/04/2022] Open
Abstract
Lymphangiogenesis (LA) is the formation of new lymphatic vessels by lymphatic endothelial cells (LECs) sprouting from pre-existing lymphatic vessels. It is increasingly recognized as being involved in many diseases, such as in cancer and secondary lymphedema, which most often results from cancer treatments. For some cancers, excessive LA is associated with cancer progression and metastatic dissemination to the lymph nodes (LNs) through lymphatic vessels. The study of LA through in vitro, in vivo, and, more recently, in silico models is of paramount importance in providing novel insights and identifying the key molecular actors in the biological dysregulation of this process under pathological conditions. In this review, the different biological (in vitro and in vivo) models of LA, especially in a cancer context, are explained and discussed, highlighting their principal modeled features as well as their advantages and drawbacks. Imaging techniques of the lymphatics, complementary or even essential to in vivo models, are also clarified and allow the establishment of the link with computational approaches. In silico models are introduced, theoretically described, and illustrated with examples specific to the lymphatic system and the LA. Together, these models constitute a toolbox allowing the LA research to be brought to the next level.
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Affiliation(s)
- Sophie Bekisz
- Biomechanics Research Unit, GIGA In silico Medicine, ULiège, 4000 Liège, Belgium;
| | - Louis Baudin
- Laboratory of Biology of Tumor and Development, GIGA Cancer, ULiège, 4000 Liège, Belgium; (L.B.); (F.B.); (A.N.)
| | - Florence Buntinx
- Laboratory of Biology of Tumor and Development, GIGA Cancer, ULiège, 4000 Liège, Belgium; (L.B.); (F.B.); (A.N.)
| | - Agnès Noël
- Laboratory of Biology of Tumor and Development, GIGA Cancer, ULiège, 4000 Liège, Belgium; (L.B.); (F.B.); (A.N.)
| | - Liesbet Geris
- Biomechanics Research Unit, GIGA In silico Medicine, ULiège, 4000 Liège, Belgium;
- Biomechanics Section, KU Leuven, 3000 Leuven, Belgium
- Skeletal Biology and Engineering Research Center, KU Leuven, 3000 Leuven, Belgium
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13
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Jafari Nivlouei S, Soltani M, Shirani E, Salimpour MR, Travasso R, Carvalho J. A multiscale cell-based model of tumor growth for chemotherapy assessment and tumor-targeted therapy through a 3D computational approach. Cell Prolif 2022; 55:e13187. [PMID: 35132721 PMCID: PMC8891571 DOI: 10.1111/cpr.13187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/09/2021] [Accepted: 01/03/2022] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Computational modeling of biological systems is a powerful tool to clarify diverse processes contributing to cancer. The aim is to clarify the complex biochemical and mechanical interactions between cells, the relevance of intracellular signaling pathways in tumor progression and related events to the cancer treatments, which are largely ignored in previous studies. MATERIALS AND METHODS A three-dimensional multiscale cell-based model is developed, covering multiple time and spatial scales, including intracellular, cellular, and extracellular processes. The model generates a realistic representation of the processes involved from an implementation of the signaling transduction network. RESULTS Considering a benign tumor development, results are in good agreement with the experimental ones, which identify three different phases in tumor growth. Simulating tumor vascular growth, results predict a highly vascularized tumor morphology in a lobulated form, a consequence of cells' motile behavior. A novel systematic study of chemotherapy intervention, in combination with targeted therapy, is presented to address the capability of the model to evaluate typical clinical protocols. The model also performs a dose comparison study in order to optimize treatment efficacy and surveys the effect of chemotherapy initiation delays and different regimens. CONCLUSIONS Results not only provide detailed insights into tumor progression, but also support suggestions for clinical implementation. This is a major step toward the goal of predicting the effects of not only traditional chemotherapy but also tumor-targeted therapies.
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Affiliation(s)
- Sahar Jafari Nivlouei
- Department of Mechanical Engineering, Isfahan University of Technology, Isafahan, Iran.,Department of Physics, CFisUC, University of Coimbra, Coimbra, Portugal
| | - Madjid Soltani
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Iran.,Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON, Canada.,Centre for Biotechnology and Bioengineering (CBB), University of Waterloo, Waterloo, ON, Canada.,Advanced Bioengineering Initiative Center, Computational Medicine Center, K. N. Toosi University of Technology, Tehran, Iran.,Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Ebrahim Shirani
- Department of Mechanical Engineering, Isfahan University of Technology, Isafahan, Iran.,Department of Mechanical Engineering, Foolad Institute of Technology, Fooladshahr, Iran
| | | | - Rui Travasso
- Department of Physics, CFisUC, University of Coimbra, Coimbra, Portugal
| | - João Carvalho
- Department of Physics, CFisUC, University of Coimbra, Coimbra, Portugal
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14
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Zhang Y, Wang H, Oliveira RHM, Zhao C, Popel AS. Systems biology of angiogenesis signaling: Computational models and omics. WIREs Mech Dis 2021; 14:e1550. [PMID: 34970866 PMCID: PMC9243197 DOI: 10.1002/wsbm.1550] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 01/10/2023]
Abstract
Angiogenesis is a highly regulated multiscale process that involves a plethora of cells, their cellular signal transduction, activation, proliferation, differentiation, as well as their intercellular communication. The coordinated execution and integration of such complex signaling programs is critical for physiological angiogenesis to take place in normal growth, development, exercise, and wound healing, while its dysregulation is critically linked to many major human diseases such as cancer, cardiovascular diseases, and ocular disorders; it is also crucial in regenerative medicine. Although huge efforts have been devoted to drug development for these diseases by investigation of angiogenesis‐targeted therapies, only a few therapeutics and targets have proved effective in humans due to the innate multiscale complexity and nonlinearity in the process of angiogenic signaling. As a promising approach that can help better address this challenge, systems biology modeling allows the integration of knowledge across studies and scales and provides a powerful means to mechanistically elucidate and connect the individual molecular and cellular signaling components that function in concert to regulate angiogenesis. In this review, we summarize and discuss how systems biology modeling studies, at the pathway‐, cell‐, tissue‐, and whole body‐levels, have advanced our understanding of signaling in angiogenesis and thereby delivered new translational insights for human diseases. This article is categorized under:Cardiovascular Diseases > Computational Models Cancer > Computational Models
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Affiliation(s)
- Yu Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hanwen Wang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rebeca Hannah M Oliveira
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chen Zhao
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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15
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Soltani M. Capillary network formation and structure in a modified discrete mathematical model of angiogenesis. Biomed Phys Eng Express 2021; 8. [PMID: 34883475 DOI: 10.1088/2057-1976/ac4175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/09/2021] [Indexed: 01/01/2023]
Abstract
Angiogenesis, as part of cancer development, involves hierarchical complicated events and processes. Multiple studies have revealed the significance of the formation and structure of tumor-induced capillary networks. In this study, a discrete mathematical model of angiogenesis is studied and modified to capture the realistic physics of capillary network formation. Modifications are performed on the mathematical foundations of an existing discrete model of angiogenesis. The main modifications are the imposition of the matrix density effect, implementation of realistic boundary and initial conditions, and improvement of the method of governing equations based on physical observation. Results show that endothelial cells accelerate angiogenesis and capillary formation as they migrate toward the tumor and clearly exhibit the physical concept of haptotactic movement. On the other hand, consideration of blood flow-induced stress leads to a dynamic adaptive vascular network of capillaries which intelligibly reflects the brush border effect . The present modified model of capillary network formation is based on the physical rationale that defines a clear mathematical and physical interpretation of angiogenesis, which is likely to be used in cancer development modeling and anti-angiogenic therapies.
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Affiliation(s)
- M Soltani
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Iran.,Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, Ontario, Canada.,Centre for Biotechnology and Bioengineering (CBB), University of Waterloo, Waterloo, Ontario, Canada.,Advanced Bioengineering Initiative Center, Computational Medicine Center, K. N. Toosi University of Technology, Tehran, Tehran Province, Iran
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16
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Dornhaus A, Smith B, Hristova K, Buckley LB. How can we fully realize the potential of mathematical and biological models to reintegrate biology? Integr Comp Biol 2021; 61:2244-2254. [PMID: 34160617 DOI: 10.1093/icb/icab142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Both mathematical models and biological model systems stand as tractable representations of complex biological systems or behaviors. They facilitate research and provide insights, and they can describe general rules. Models that represent biological processes or formalize general hypotheses are essential to any broad understanding. Mathematical or biological models necessarily omit details of the natural systems and thus may ultimately be "incorrect" representations. A key challenge is that tractability requires relatively simple models but simplification can result in models that are incorrect in their qualitative, broad implications if the abstracted details matter. Our paper discusses this tension, and how we can improve our inferences from models. We advocate for further efforts dedicated to model development, improvement, and acceptance by the scientific community, all of which may necessitate a more explicit discussion of the purpose and power of models. We argue that models should play a central role in reintegrating biology as a way to test our integrated understanding of how molecules, cells, organs, organisms, populations, and ecosystems function.
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Affiliation(s)
- Anna Dornhaus
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | - Brian Smith
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Kalina Hristova
- Department of Materials Science and Engineering, and Program in Molecular Biology, John Hopkins University, Baltimore, MD 21218
| | - Lauren B Buckley
- Department of Biology, University of Washington, Seattle, WA 98115
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17
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Hormuth DA, Phillips CM, Wu C, Lima EABF, Lorenzo G, Jha PK, Jarrett AM, Oden JT, Yankeelov TE. Biologically-Based Mathematical Modeling of Tumor Vasculature and Angiogenesis via Time-Resolved Imaging Data. Cancers (Basel) 2021; 13:3008. [PMID: 34208448 PMCID: PMC8234316 DOI: 10.3390/cancers13123008] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 01/03/2023] Open
Abstract
Tumor-associated vasculature is responsible for the delivery of nutrients, removal of waste, and allowing growth beyond 2-3 mm3. Additionally, the vascular network, which is changing in both space and time, fundamentally influences tumor response to both systemic and radiation therapy. Thus, a robust understanding of vascular dynamics is necessary to accurately predict tumor growth, as well as establish optimal treatment protocols to achieve optimal tumor control. Such a goal requires the intimate integration of both theory and experiment. Quantitative and time-resolved imaging methods have emerged as technologies able to visualize and characterize tumor vascular properties before and during therapy at the tissue and cell scale. Parallel to, but separate from those developments, mathematical modeling techniques have been developed to enable in silico investigations into theoretical tumor and vascular dynamics. In particular, recent efforts have sought to integrate both theory and experiment to enable data-driven mathematical modeling. Such mathematical models are calibrated by data obtained from individual tumor-vascular systems to predict future vascular growth, delivery of systemic agents, and response to radiotherapy. In this review, we discuss experimental techniques for visualizing and quantifying vascular dynamics including magnetic resonance imaging, microfluidic devices, and confocal microscopy. We then focus on the integration of these experimental measures with biologically based mathematical models to generate testable predictions.
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Affiliation(s)
- David A. Hormuth
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA; (C.M.P.); (C.W.); (E.A.B.F.L.); (G.L.); (P.K.J.); (J.T.O.); (T.E.Y.)
- Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Caleb M. Phillips
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA; (C.M.P.); (C.W.); (E.A.B.F.L.); (G.L.); (P.K.J.); (J.T.O.); (T.E.Y.)
| | - Chengyue Wu
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA; (C.M.P.); (C.W.); (E.A.B.F.L.); (G.L.); (P.K.J.); (J.T.O.); (T.E.Y.)
| | - Ernesto A. B. F. Lima
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA; (C.M.P.); (C.W.); (E.A.B.F.L.); (G.L.); (P.K.J.); (J.T.O.); (T.E.Y.)
- Texas Advanced Computing Center, The University of Texas at Austin, Austin, TX 78758, USA
| | - Guillermo Lorenzo
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA; (C.M.P.); (C.W.); (E.A.B.F.L.); (G.L.); (P.K.J.); (J.T.O.); (T.E.Y.)
- Department of Civil Engineering and Architecture, University of Pavia, Via Ferrata 3, 27100 Pavia, Italy
| | - Prashant K. Jha
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA; (C.M.P.); (C.W.); (E.A.B.F.L.); (G.L.); (P.K.J.); (J.T.O.); (T.E.Y.)
| | - Angela M. Jarrett
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA;
| | - J. Tinsley Oden
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA; (C.M.P.); (C.W.); (E.A.B.F.L.); (G.L.); (P.K.J.); (J.T.O.); (T.E.Y.)
- Department of Aerospace Engineering and Engineering Mechanics, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Mathematics, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Computer Science, The University of Texas at Austin, Austin, TX 78712, USA
| | - Thomas E. Yankeelov
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA; (C.M.P.); (C.W.); (E.A.B.F.L.); (G.L.); (P.K.J.); (J.T.O.); (T.E.Y.)
- Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA;
- Department of Diagnostic Medicine, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Oncology, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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18
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Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model. Cell Syst 2021; 12:795-809.e9. [PMID: 34139155 DOI: 10.1016/j.cels.2021.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/06/2020] [Accepted: 05/11/2021] [Indexed: 12/24/2022]
Abstract
Cells do not exist in isolation; they continuously act within and react to their environment. And this environment is not static; it continuously adapts and responds to cells. Here, we investigate how vascular structure and function impact emergent cell population behavior using an agent-based model (ABM). Our ABM enables researchers to "mix and match" cell agents, subcellular modules, and microenvironment components ranging from simple nutrient sources to complex, realistic vascular architectures that accurately capture hemodynamics. We use this ABM to highlight the bilateral relationship between cells and nearby vasculature, demonstrate the effect of vascular structure on environmental heterogeneity, and emphasize the non-linear, non-intuitive relationship between vascular function and the behavior of cell populations over time. Our ABM is well suited to characterizing in vitro and in vivo studies, with applications from basic science to translational synthetic biology and medicine. The model is freely available at https://github.com/bagherilab/ARCADE. A record of this paper's transparent peer review process is included in the supplemental information.
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19
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Jafari Nivlouei S, Soltani M, Carvalho J, Travasso R, Salimpour MR, Shirani E. Multiscale modeling of tumor growth and angiogenesis: Evaluation of tumor-targeted therapy. PLoS Comput Biol 2021; 17:e1009081. [PMID: 34161319 PMCID: PMC8259971 DOI: 10.1371/journal.pcbi.1009081] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 07/06/2021] [Accepted: 05/14/2021] [Indexed: 12/12/2022] Open
Abstract
The dynamics of tumor growth and associated events cover multiple time and spatial scales, generally including extracellular, cellular and intracellular modifications. The main goal of this study is to model the biological and physical behavior of tumor evolution in presence of normal healthy tissue, considering a variety of events involved in the process. These include hyper and hypoactivation of signaling pathways during tumor growth, vessels' growth, intratumoral vascularization and competition of cancer cells with healthy host tissue. The work addresses two distinctive phases in tumor development-the avascular and vascular phases-and in each stage two cases are considered-with and without normal healthy cells. The tumor growth rate increases considerably as closed vessel loops (anastomoses) form around the tumor cells resulting from tumor induced vascularization. When taking into account the host tissue around the tumor, the results show that competition between normal cells and cancer cells leads to the formation of a hypoxic tumor core within a relatively short period of time. Moreover, a dense intratumoral vascular network is formed throughout the entire lesion as a sign of a high malignancy grade, which is consistent with reported experimental data for several types of solid carcinomas. In comparison with other mathematical models of tumor development, in this work we introduce a multiscale simulation that models the cellular interactions and cell behavior as a consequence of the activation of oncogenes and deactivation of gene signaling pathways within each cell. Simulating a therapy that blocks relevant signaling pathways results in the prevention of further tumor growth and leads to an expressive decrease in its size (82% in the simulation).
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Affiliation(s)
- Sahar Jafari Nivlouei
- Department of Mechanical Engineering, Isfahan University of Technology, Isafahan, Iran
- CFisUC, Department of Physics, University of Coimbra, Coimbra, Portugal
| | - M. Soltani
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Iran
- Department of Electrical and Computer Engineering, University of Waterloo, Ontario, Canada
- Centre for Biotechnology and Bioengineering (CBB), University of Waterloo, Waterloo, Ontario, Canada
- Advanced Bioengineering Initiative Center, Computational Medicine Center, K. N. Toosi University of Technology, Tehran, Iran
- Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - João Carvalho
- CFisUC, Department of Physics, University of Coimbra, Coimbra, Portugal
| | - Rui Travasso
- CFisUC, Department of Physics, University of Coimbra, Coimbra, Portugal
| | | | - Ebrahim Shirani
- Department of Mechanical Engineering, Isfahan University of Technology, Isafahan, Iran
- Department of Mechanical Engineering, Foolad Institute of Technology, Fooladshahr, Iran
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20
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Saghian R, Cahill L, Rahman A, Steinman J, Stortz G, Kingdom J, Macgowan C, Sled J. Interpretation of wave reflections in the umbilical arterial segment of the feto-placental circulation: computational modeling of the feto-placental arterial tree. IEEE Trans Biomed Eng 2021; 68:3647-3658. [PMID: 34010124 DOI: 10.1109/tbme.2021.3082064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Placental vascular abnormalities are associated with a host of pregnancy complications including placenta mediated fetal growth restriction (FGR). Umbilical arterial (UA) Doppler ultrasound velocity waveforms are widely used in the diagnosis of underlying placental vascular abnormalities in pregnancies with suspected FGR, which greatly help prevent stillbirth via ongoing fetal monitoring and timely delivery. However, the sensitivity of UA Doppler diagnosis diminishes late in gestation. Our goal was to present a generalized wave decomposition method to compute forward and reflected components from UA waveforms. A detailed anatomical based model was also developed to explain observed UA flow waveform and to explore how vascular properties affect the shape of flow wave components. Using pregnant mice and high frequency ultrasound microscopy, we obtained in utero Doppler and M- mode ultrasound measurements in 15 fetuses UA. Following ultrasound, the placentas were collected and perfused with contrast agent to obtain high-resolution 3D images of the feto-placental arteries. Model results indicate the significant role of terminal load impedance (capillary and/or veins) in creating positive or negative reflected waveforms. A negative reflected waveform is obtained when terminal impedance increases. This is consistent with the elongated and non-branching terminal villi that are proposed cause the highly abnormal UA waveforms found in early-onset FGR. The significance of these findings for the diagnostic utility of UA Doppler in human pregnancy is that the identification and measurement of wave reflections may aid in discriminating between healthy and abnormal placental vasculature in pregnancies with suspected late-onset FGR.
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21
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Mamer SB, Wittenkeller A, Imoukhuede PI. VEGF-A splice variants bind VEGFRs with differential affinities. Sci Rep 2020; 10:14413. [PMID: 32879419 PMCID: PMC7468149 DOI: 10.1038/s41598-020-71484-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 08/04/2020] [Indexed: 12/29/2022] Open
Abstract
Vascular endothelial growth factor A (VEGF-A) and its binding to VEGFRs is an important angiogenesis regulator, especially the earliest-known isoform, VEGF-A165a. Yet several additional splice variants play prominent roles in regulating angiogenesis in health and in vascular disease, including VEGF-A121 and an anti-angiogenic variant, VEGF-A165b. Few studies have attempted to distinguish these forms from their angiogenic counterparts, experimentally. Previous studies of VEGF-A:VEGFR binding have measured binding kinetics for VEGFA165 and VEGF-A121, but binding kinetics of the other two pro- and all anti-angiogenic splice variants are not known. We measured the binding kinetics for VEGF-A165, -A165b, and -A121 with VEGFR1 and VEGF-R2 using surface plasmon resonance. We validated our methods by reproducing the known affinities between VEGF-A165a:VEGFR1 and VEGF-A165a:VEGFR2, 1.0 pM and 10 pM respectively, and validated the known affinity VEGF-A121:VEGFR2 as KD = 0.66 nM. We found that VEGF-A121 also binds VEGFR1 with an affinity KD = 3.7 nM. We further demonstrated that the anti-angiogenic variant, VEGF-A165b selectively prefers VEGFR2 binding at an affinity = 0.67 pM while binding VEGFR1 with a weaker affinity-KD = 1.4 nM. These results suggest that the - A165b anti-angiogenic variant would preferentially bind VEGFR2. These discoveries offer a new paradigm for understanding VEGF-A, while further stressing the need to take care in differentiating the splice variants in all future VEGF-A studies.
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Affiliation(s)
- Spencer B Mamer
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Ashley Wittenkeller
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - P I Imoukhuede
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
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22
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Bocci F, Onuchic JN, Jolly MK. Understanding the Principles of Pattern Formation Driven by Notch Signaling by Integrating Experiments and Theoretical Models. Front Physiol 2020; 11:929. [PMID: 32848867 PMCID: PMC7411240 DOI: 10.3389/fphys.2020.00929] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023] Open
Abstract
Notch signaling is an evolutionary conserved cell-cell communication pathway. Besides regulating cell-fate decisions at an individual cell level, Notch signaling coordinates the emergent spatiotemporal patterning in a tissue through ligand-receptor interactions among transmembrane molecules of neighboring cells, as seen in embryonic development, angiogenesis, or wound healing. Due to its ubiquitous nature, Notch signaling is also implicated in several aspects of cancer progression, including tumor angiogenesis, stemness of cancer cells and cellular invasion. Here, we review experimental and computational models that help understand the operating principles of cell patterning driven by Notch signaling. First, we discuss the basic mechanisms of spatial patterning via canonical lateral inhibition and lateral induction mechanisms, including examples from angiogenesis, inner ear development and cancer metastasis. Next, we analyze additional layers of complexity in the Notch pathway, including the effect of varying cell sizes and shapes, ligand-receptor binding within the same cell, variable binding affinity of different ligand/receptor subtypes, and filopodia. Finally, we discuss some recent evidence of mechanosensitivity in the Notch pathway in driving collective epithelial cell migration and cardiovascular morphogenesis.
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Affiliation(s)
- Federico Bocci
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
- Department of Physics and Astronomy, Rice University, Houston, TX, United States
- Department of Chemistry, Rice University, Houston, TX, United States
- Department of Biosciences, Rice University, Houston, TX, United States
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bengaluru, India
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23
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Mamer SB, Page P, Murphy M, Wang J, Gallerne P, Ansari A, Imoukhuede PI. The Convergence of Cell-Based Surface Plasmon Resonance and Biomaterials: The Future of Quantifying Bio-molecular Interactions-A Review. Ann Biomed Eng 2020; 48:2078-2089. [PMID: 31811474 PMCID: PMC8637426 DOI: 10.1007/s10439-019-02429-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/29/2019] [Indexed: 12/20/2022]
Abstract
Cell biology is driven by complex networks of biomolecular interactions. Characterizing the kinetic and thermodynamic properties of these interactions is crucial to understanding their role in different physiological processes. Surface plasmon resonance (SPR)-based approaches have become a key tool in quantifying biomolecular interactions, however conventional approaches require isolating the interacting components from the cellular system. Cell-based SPR approaches have recently emerged, promising to enable precise measurements of biomolecular interactions within their normal biological context. Two major approaches have been developed, offering their own advantages and limitations. These approaches currently lack a systematic exploration of 'best practices' like those existing for traditional SPR experiments. Toward this end, we describe the two major approaches, and identify the experimental parameters that require exploration, and discuss the experimental considerations constraining the optimization of each. In particular, we discuss the requirements of future biomaterial development needed to advance the cell-based SPR technique.
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Affiliation(s)
- Spencer B Mamer
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | | | - Jiaojiao Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pierrick Gallerne
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Ecole Centrale de Lille, Villeneuve d'Ascq, Hauts-De-France, France
| | - Ali Ansari
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - P I Imoukhuede
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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24
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Stalidzans E, Zanin M, Tieri P, Castiglione F, Polster A, Scheiner S, Pahle J, Stres B, List M, Baumbach J, Lautizi M, Van Steen K, Schmidt HH. Mechanistic Modeling and Multiscale Applications for Precision Medicine: Theory and Practice. NETWORK AND SYSTEMS MEDICINE 2020. [DOI: 10.1089/nsm.2020.0002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Egils Stalidzans
- Computational Systems Biology Group, University of Latvia, Riga, Latvia
- Latvian Biomedical Reasearch and Study Centre, Riga, Latvia
| | - Massimiliano Zanin
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Spain
| | - Paolo Tieri
- CNR National Research Council, IAC Institute for Applied Computing, Rome, Italy
| | - Filippo Castiglione
- CNR National Research Council, IAC Institute for Applied Computing, Rome, Italy
| | | | - Stefan Scheiner
- Institute for Mechanics of Materials and Structures, Vienna University of Technology, Vienna, Austria
| | - Jürgen Pahle
- BioQuant, Heidelberg University, Heidelberg, Germany
| | - Blaž Stres
- Department of Animal Science, University of Ljubljana, Ljubljana, Slovenia
- Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia
- Department of Automation, Biocybernetics and Robotics, Jozef Stefan Institute, Ljubljana, Slovenia
| | - Markus List
- Big Data in BioMedicine Research Group, Chair of Experimental Bioinformatics, TUM School of Weihenstephan, Technical University of Munich, Freising, Germany
| | - Jan Baumbach
- Chair of Experimental Bioinformatics, TUM School of Weihenstephan, Technical University of Munich, Freising, Germany
| | - Manuela Lautizi
- Computational Systems Medicine Research Group, Chair of Experimental Bioinformatics, TUM School of Weihenstephan, Technical University of Munich, Freising, Germany
| | - Kristel Van Steen
- BIO-Systems Genetics, GIGA-R, University of Liège, Liège, Belgium
- BIO3—Systems Medicine, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Harald H.H.W. Schmidt
- Department of Pharmacology and Personalised Medicine, Faculty of Health, Medicine and Life Science, Maastricht University, Maastricht, The Netherlands
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Rubin JB, Lagas JS, Broestl L, Sponagel J, Rockwell N, Rhee G, Rosen SF, Chen S, Klein RS, Imoukhuede P, Luo J. Sex differences in cancer mechanisms. Biol Sex Differ 2020; 11:17. [PMID: 32295632 PMCID: PMC7161126 DOI: 10.1186/s13293-020-00291-x] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
We now know that cancer is many different diseases, with great variation even within a single histological subtype. With the current emphasis on developing personalized approaches to cancer treatment, it is astonishing that we have not yet systematically incorporated the biology of sex differences into our paradigms for laboratory and clinical cancer research. While some sex differences in cancer arise through the actions of circulating sex hormones, other sex differences are independent of estrogen, testosterone, or progesterone levels. Instead, these differences are the result of sexual differentiation, a process that involves genetic and epigenetic mechanisms, in addition to acute sex hormone actions. Sexual differentiation begins with fertilization and continues beyond menopause. It affects virtually every body system, resulting in marked sex differences in such areas as growth, lifespan, metabolism, and immunity, all of which can impact on cancer progression, treatment response, and survival. These organismal level differences have correlates at the cellular level, and thus, males and females can fundamentally differ in their protections and vulnerabilities to cancer, from cellular transformation through all stages of progression, spread, and response to treatment. Our goal in this review is to cover some of the robust sex differences that exist in core cancer pathways and to make the case for inclusion of sex as a biological variable in all laboratory and clinical cancer research. We finish with a discussion of lab- and clinic-based experimental design that should be used when testing whether sex matters and the appropriate statistical models to apply in data analysis for rigorous evaluations of potential sex effects. It is our goal to facilitate the evaluation of sex differences in cancer in order to improve outcomes for all patients.
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Affiliation(s)
- Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA.
- Department of Neuroscience, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA.
| | - Joseph S Lagas
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Lauren Broestl
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Jasmin Sponagel
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Nathan Rockwell
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Gina Rhee
- Department of Pediatrics, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Sarah F Rosen
- Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Si Chen
- Department of Biomedical Engineering, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Robyn S Klein
- Department of Neuroscience, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
- Department of Medicine, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Princess Imoukhuede
- Department of Biomedical Engineering, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
| | - Jingqin Luo
- Department of Surgery, Washington University School of Medicine, 660 South Euclid Avenue, St Louis, MO, 63110, USA
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26
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Zhai X, Larkin JW, Süel GM, Mugler A. Spiral Wave Propagation in Communities with Spatially Correlated Heterogeneity. Biophys J 2020; 118:1721-1732. [PMID: 32105650 DOI: 10.1016/j.bpj.2020.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 12/29/2022] Open
Abstract
Many multicellular communities propagate signals in a directed manner via excitable waves. Cell-to-cell heterogeneity is a ubiquitous feature of multicellular communities, but the effects of heterogeneity on wave propagation are still unclear. Here, we use a minimal FitzHugh-Nagumo-type model to investigate excitable wave propagation in a two-dimensional heterogeneous community. The model shows three dynamic regimes in which waves either propagate directionally, die out, or spiral indefinitely, and we characterize how these regimes depend on the heterogeneity parameters. We find that in some parameter regimes, spatial correlations in the heterogeneity enhance directional propagation and suppress spiraling. However, in other regimes, spatial correlations promote spiraling, a surprising feature that we explain by demonstrating that these spirals form by a second, distinct mechanism. Finally, we characterize the dynamics using techniques from percolation theory. Despite the fact that percolation theory does not completely describe the dynamics quantitatively because it neglects the details of the excitable propagation, we find that it accounts for the transitions between the dynamic regimes and the general dependency of the spiral period on the heterogeneity and thus provides important insights. Our results reveal that the spatial structure of cell-to-cell heterogeneity can have important consequences for signal propagation in cellular communities.
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Affiliation(s)
- Xiaoling Zhai
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana
| | - Joseph W Larkin
- Department of Biology and Department of Physics, Boston University, Boston, Massachusetts
| | - Gürol M Süel
- Division of Biological Sciences and San Diego Center for Systems Biology, University of California, San Diego, La Jolla, California
| | - Andrew Mugler
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana.
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Weinstein N, Mendoza L, Álvarez-Buylla ER. A Computational Model of the Endothelial to Mesenchymal Transition. Front Genet 2020; 11:40. [PMID: 32226439 PMCID: PMC7080988 DOI: 10.3389/fgene.2020.00040] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/14/2020] [Indexed: 12/13/2022] Open
Abstract
Endothelial cells (ECs) form the lining of lymph and blood vessels. Changes in tissue requirements or wounds may cause ECs to behave as tip or stalk cells. Alternatively, they may differentiate into mesenchymal cells (MCs). These processes are known as EC activation and endothelial-to-mesenchymal transition (EndMT), respectively. EndMT, Tip, and Stalk EC behaviors all require SNAI1, SNAI2, and Matrix metallopeptidase (MMP) function. However, only EndMT inhibits the expression of VE-cadherin, PECAM1, and VEGFR2, and also leads to EC detachment. Physiologically, EndMT is involved in heart valve development, while a defective EndMT regulation is involved in the physiopathology of cardiovascular malformations, congenital heart disease, systemic and organ fibrosis, pulmonary arterial hypertension, and atherosclerosis. Therefore, the control of EndMT has many promising potential applications in regenerative medicine. Despite the fact that many molecular components involved in EC activation and EndMT have been characterized, the system-level molecular mechanisms involved in this process have not been elucidated. Toward this end, hereby we present Boolean network model of the molecular involved in the regulation of EC activation and EndMT. The simulated dynamic behavior of our model reaches fixed and cyclic patterns of activation that correspond to the expected EC and MC cell types and behaviors, recovering most of the specific effects of simple gain and loss-of-function mutations as well as the conditions associated with the progression of several diseases. Therefore, our model constitutes a theoretical framework that can be used to generate hypotheses and guide experimental inquiry to comprehend the regulatory mechanisms behind EndMT. Our main findings include that both the extracellular microevironment and the pattern of molecular activity within the cell regulate EndMT. EndMT requires a lack of VEGFA and sufficient oxygen in the extracellular microenvironment as well as no FLI1 and GATA2 activity within the cell. Additionally Tip cells cannot undergo EndMT directly. Furthermore, the specific conditions that are sufficient to trigger EndMT depend on the specific pattern of molecular activation within the cell.
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Affiliation(s)
- Nathan Weinstein
- Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Elena R Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Single-Cell Receptor Quantification of an In Vitro Coculture Angiogenesis Model Reveals VEGFR, NRP1, Tie2, and PDGFR Regulation and Endothelial Heterogeneity. Processes (Basel) 2019. [DOI: 10.3390/pr7060356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Angiogenesis, the formation of new blood vessels from pre-existing ones, is essential for both normal development and numerous pathologies. Systems biology has offered a unique approach to study angiogenesis by profiling tyrosine kinase receptors (RTKs) that regulate angiogenic processes and computationally modeling RTK signaling pathways. Historically, this systems biology approach has been applied on ex vivo angiogenesis assays, however, these assays are difficult to quantify and limited in their potential of temporal analysis. In this study, we adopted a simple two-dimensional angiogenesis assay comprised of human umbilical vein endothelial cells (HUVECs) and human dermal fibroblasts (HDFs) and examined temporal dynamics of a panel of six RTKs and cell heterogeneity up to 17 days. We observed ~2700 VEGFR1 (vascular endothelial growth factor receptor 1) per cell on 24-h-old cocultured HDF plasma membranes, which do not express VEGFR when cultured alone. We observed 4000–8100 VEGFR2 per cell on cocultured HUVEC plasma membranes throughout endothelial tube formation. We showed steady increase of platelet-derived growth factor receptors (PDGFRs) on cocultured HDF plasma membranes, and more interestingly, 1900–2900 PDGFRβ per plasma membrane were found on HUVECs within the first six hours of coculturing. These quantitative findings will offer us insights into molecular regulation during angiogenesis and help assess in vitro tube formation models and their physiological relevance.
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29
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King C, Hristova K. Direct measurements of VEGF–VEGFR2 binding affinities reveal the coupling between ligand binding and receptor dimerization. J Biol Chem 2019; 294:9064-9075. [DOI: 10.1074/jbc.ra119.007737] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/05/2019] [Indexed: 01/13/2023] Open
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Abstract
Receptor tyrosine kinases (RTKs) play important roles in cell growth, motility, differentiation, and survival. These single-pass membrane proteins are grouped into subfamilies based on the similarity of their extracellular domains. They are generally thought to be activated by ligand binding, which promotes homodimerization and then autophosphorylation in trans. However, RTK interactions are more complicated, as RTKs can interact in the absence of ligand and heterodimerize within and across subfamilies. Here, we review the known cross-subfamily RTK heterointeractions and their possible biological implications, as well as the methodologies which have been used to study them. Moreover, we demonstrate how thermodynamic models can be used to study RTKs and to explain many of the complicated biological effects which have been described in the literature. Finally, we discuss the concept of the RTK interactome: a putative, extensive network of interactions between the RTKs. This RTK interactome can produce unique signaling outputs; can amplify, inhibit, and modify signaling; and can allow for signaling backups. The existence of the RTK interactome could provide an explanation for the irreproducibility of experimental data from different studies and for the failure of some RTK inhibitors to produce the desired therapeutic effects. We argue that a deeper knowledge of RTK interactome thermodynamics can lead to a better understanding of fundamental RTK signaling processes in health and disease. We further argue that there is a need for quantitative, thermodynamic studies that probe the strengths of the interactions between RTKs and their ligands and between different RTKs.
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Affiliation(s)
- Michael D. Paul
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore MD 21218
| | - Kalina Hristova
- Department of Materials Science and Engineering, Institute for NanoBioTechnology, and Program in Molecular Biophysics, Johns Hopkins University, Baltimore MD 21218
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31
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Chen Z, Zou Y. A multiscale model for heterogeneous tumor spheroid in vitro. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2018; 15:361-392. [PMID: 29161840 DOI: 10.3934/mbe.2018016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this paper, a novel multiscale method is proposed for the study of heterogeneous tumor spheroid growth in vitro. The entire tumor spheroid is described by an ellipsoid-based model while nutrient and other environmental factors are treated as continua. The ellipsoid-based discrete component is capable of incorporating mechanical effects and deformability, while keeping a minimum set of free variables to describe complex shape variations. Moreover, our purely cell-based description of tumor avoids the complex mutual conversion between a cell-based model and continuum model within a tumor, such as force and mass transformation. This advantage makes it highly suitable for the study of tumor spheroids in vitro whose size are normally less than 800 μm in diameter. In addition, our numerical scheme provides two computational options depending on tumor size. For a small or medium tumor spheroid, a three-dimensional (3D) numerical model can be directly applied. For a large spheroid, we suggest the use of a 3D-adapted 2D cross section configuration, which has not yet been explored in the literature, as an alternative for the theoretical investigation to bridge the gap between the 2D and 3D models. Our model and its implementations have been validated and applied to various studies given in the paper. The simulation results fit corresponding in vitro experimental observations very well.
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Affiliation(s)
- Zhan Chen
- Department of Mathematical Sciences, Georgia Southern University, Statesboro, GA, 30460, United States
| | - Yuting Zou
- Department of Mathematical Sciences, Georgia Southern University, Statesboro, GA, 30460, United States
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32
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Bentley K, Chakravartula S. The temporal basis of angiogenesis. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0522. [PMID: 28348255 PMCID: PMC5379027 DOI: 10.1098/rstb.2015.0522] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2017] [Indexed: 12/12/2022] Open
Abstract
The process of new blood vessel growth (angiogenesis) is highly dynamic, involving complex coordination of multiple cell types. Though the process must carefully unfold over time to generate functional, well-adapted branching networks, we seldom hear about the time-based properties of angiogenesis, despite timing being central to other areas of biology. Here, we present a novel, time-based formulation of endothelial cell behaviour during angiogenesis and discuss a flurry of our recent, integrated in silico/in vivo studies, put in context to the wider literature, which demonstrate that tissue conditions can locally adapt the timing of collective cell behaviours/decisions to grow different vascular network architectures. A growing array of seemingly unrelated ‘temporal regulators’ have recently been uncovered, including tissue derived factors (e.g. semaphorins or the high levels of VEGF found in cancer) and cellular processes (e.g. asymmetric cell division or filopodia extension) that act to alter the speed of cellular decisions to migrate. We will argue that ‘temporal adaptation’ provides a novel account of organ/disease-specific vascular morphology and reveals ‘timing’ as a new target for therapeutics. We therefore propose and explain a conceptual shift towards a ‘temporal adaptation’ perspective in vascular biology, and indeed other areas of biology where timing remains elusive. This article is part of the themed issue ‘Systems morphodynamics: understanding the development of tissue hardware’.
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Affiliation(s)
- Katie Bentley
- Computational Biology Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA .,Cellular Adaptive Behaviour Laboratory, Rudbeck Laboratories, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Shilpa Chakravartula
- Computational Biology Laboratory, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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33
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Weinstein N, Mendoza L, Gitler I, Klapp J. A Network Model to Explore the Effect of the Micro-environment on Endothelial Cell Behavior during Angiogenesis. Front Physiol 2017; 8:960. [PMID: 29230182 PMCID: PMC5711888 DOI: 10.3389/fphys.2017.00960] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/10/2017] [Indexed: 01/07/2023] Open
Abstract
Angiogenesis is an important adaptation mechanism of the blood vessels to the changing requirements of the body during development, aging, and wound healing. Angiogenesis allows existing blood vessels to form new connections or to reabsorb existing ones. Blood vessels are composed of a layer of endothelial cells (ECs) covered by one or more layers of mural cells (smooth muscle cells or pericytes). We constructed a computational Boolean model of the molecular regulatory network involved in the control of angiogenesis. Our model includes the ANG/TIE, HIF, AMPK/mTOR, VEGF, IGF, FGF, PLCγ/Calcium, PI3K/AKT, NO, NOTCH, and WNT signaling pathways, as well as the mechanosensory components of the cytoskeleton. The dynamical behavior of our model recovers the patterns of molecular activation observed in Phalanx, Tip, and Stalk ECs. Furthermore, our model is able to describe the modulation of EC behavior due to extracellular micro-environments, as well as the effect due to loss- and gain-of-function mutations. These properties make our model a suitable platform for the understanding of the molecular mechanisms underlying some pathologies. For example, it is possible to follow the changes in the activation patterns caused by mutations that promote Tip EC behavior and inhibit Phalanx EC behavior, that lead to the conditions associated with retinal vascular disorders and tumor vascularization. Moreover, the model describes how mutations that promote Phalanx EC behavior are associated with the development of arteriovenous and venous malformations. These results suggest that the network model that we propose has the potential to be used in the study of how the modulation of the EC extracellular micro-environment may improve the outcome of vascular disease treatments.
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Affiliation(s)
- Nathan Weinstein
- ABACUS-Laboratorio de Matemáticas Aplicadas y Cómputo de Alto Rendimiento, Departamento de Matemáticas, Centro de Investigación y de Estudios Avanzados CINVESTAV-IPN, Mexico City, Mexico
| | - Luis Mendoza
- CompBioLab, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Isidoro Gitler
- ABACUS-Laboratorio de Matemáticas Aplicadas y Cómputo de Alto Rendimiento, Departamento de Matemáticas, Centro de Investigación y de Estudios Avanzados CINVESTAV-IPN, Mexico City, Mexico
| | - Jaime Klapp
- ABACUS-Laboratorio de Matemáticas Aplicadas y Cómputo de Alto Rendimiento, Departamento de Matemáticas, Centro de Investigación y de Estudios Avanzados CINVESTAV-IPN, Mexico City, Mexico
- Departamento de Física, Instituto Nacional de Investigaciones Nucleares, Mexico City, Mexico
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Discovery of High-Affinity PDGF-VEGFR Interactions: Redefining RTK Dynamics. Sci Rep 2017; 7:16439. [PMID: 29180757 PMCID: PMC5704011 DOI: 10.1038/s41598-017-16610-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/14/2017] [Indexed: 01/15/2023] Open
Abstract
Nearly all studies of angiogenesis have focused on uni-family ligand-receptor binding, e.g., VEGFs bind to VEGF receptors, PDGFs bind to PDGF receptors, etc. The discovery of VEGF-PDGFRs binding challenges this paradigm and calls for investigation of other ligand-receptor binding possibilities. We utilized surface plasmon resonance to identify and measure PDGF-to-VEGFR binding rates, establishing cut-offs for binding and non-binding interactions. We quantified the kinetics of the recent VEGF-A:PDGFRβ interaction for the first time with KD = 340 pM. We discovered new PDGF:VEGFR2 interactions with PDGF-AA:R2 KD = 530 nM, PDGF-AB:R2 KD = 110 pM, PDGF-BB:R2 KD = 40 nM, and PDGF-CC:R2 KD = 70 pM. We computationally predict that cross-family PDGF binding could contribute up to 96% of VEGFR2 ligation in healthy conditions and in cancer. Together the identification, quantification, and simulation of these novel cross-family interactions posits new mechanisms for understanding anti-angiogenic drug resistance and presents an expanded role of growth factor signaling with significance in health and disease.
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35
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Immunophysical analysis of corneal neovascularization: mechanistic insights and implications for pharmacotherapy. Sci Rep 2017; 7:12220. [PMID: 28939878 PMCID: PMC5610330 DOI: 10.1038/s41598-017-12533-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 09/08/2017] [Indexed: 01/28/2023] Open
Abstract
The cornea lacks adaptive immune cells and vasculature under healthy conditions, but is populated by both cell types under pathologic conditions and after transplantation. Here we propose an immunophysical approach to describe postoperative neovascularization in corneal grafts. We develop a simple dynamic model that captures not only the well-established interactions between innate immunity and vascular dynamics but also incorporates the contributions of adaptive immunity to vascular growth. We study how these interactions determine dynamic changes and steady states of the system as well as the clinical outcome, i.e. graft survival. The model allows us to systematically explore the impact of pharmacological inhibitors of vascular growth on the function and survival of transplanted corneas and search for the optimal time to initiatetherapy. Predictions from our models will help ongoing efforts to design therapeutic approaches to modulate alloimmunity and suppress allograft rejection.
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Hosseini F, Naghavi N. Modelling Tumor-induced Angiogenesis: Combination of Stochastic Sprout Spacing and Sprout Progression. J Biomed Phys Eng 2017; 7:233-256. [PMID: 29082215 PMCID: PMC5654130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/01/2015] [Indexed: 06/07/2023]
Abstract
BACKGROUND Angiogenesis initiated by cancerous cells is the process by which new blood vessels are formed to enhance oxygenation and growth of tumor. OBJECTIVE In this paper, we present a new multiscale mathematical model for the formation of a vascular network in tumor angiogenesis process. METHODS Our model couples an improved sprout spacing model as a stochastic mathematical model of sprouting along an existing parent blood vessel, with a mathematical model of sprout progression in the extracellular matrix (ECM) in response to some tumor angiogenic factors (TAFs). We perform simulations of the siting of capillary sprouts on an existing blood vessel using finite difference approximation of the dynamic equations of some angiogenesis activators and inhibitors. Angiogenesis activators are chemicals secreted by hypoxic tumor cells for initiating angiogenesis, and inhibitors of the angiogenesis are chemicals that are produced around every new sprout during tumor angiogenesis to inhibit the formation of further sprouts as a feedback of sprouting in angiogenesis. Moreover, for modelling sprout progression in ECM, we use three equations for the motility of endothelial cells at the tip of the activated sprouts, the consumption of TAF and the production and uptake of Fibronectin by endothelial cells. RESULTS Coupling these two basic models not only does provide a better time estimation of angiogenesis process, but also it is more compatible with reality. CONCLUSION This model can be used to provide basic information for angiogenesis in the related studies. Related simulations can estimate the position and number of sprouts along parent blood vessel during the initial steps of angiogenesis and models the process of sprout progression in ECM until they vascularize a tumor.
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Affiliation(s)
- F Hosseini
- Department of Electrical Engineering, Faculty of Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
| | - N Naghavi
- Department of Electrical Engineering, Faculty of Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
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Morshed A, Dutta P. Hypoxic behavior in cells under controlled microfluidic environment. Biochim Biophys Acta Gen Subj 2017; 1861:759-771. [PMID: 28111315 DOI: 10.1016/j.bbagen.2017.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 01/15/2017] [Accepted: 01/18/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND Depleted oxygen levels, known as hypoxia, causes considerable changes in the cellular metabolism. Hypoxia-inducible factors (HIF) act as the major protagonist in orchestrating manifold hypoxic responses by escaping cellular degradation mechanisms. These complex and dynamic intracellular responses are significantly dependent on the extracellular environment. In this study, we present a detailed model of a hypoxic cellular microenvironment in a microfluidic setting involving HIF hydroxylation. METHODS We have modeled the induction of hypoxia in a microfluidic chip by an unsteady permeation of oxygen from the microchannel through a porous polydimethylsiloxane channel wall. Extracellular and intracellular interactions were modeled with two different mathematical descriptions. Intracellular space is directly coupled to the extracellular environment through uptake and consumption of oxygen and ascorbate similar to cells in vivo. RESULTS Our results indicate a sharp switch in HIF hydroxylation behavior with changing prolyl hydroxylase levels from 0.1 to 4.0μM. Furthermore, we studied the effects of extracellular ascorbate concentration, using a new model, to predict its accumulation inside the cell over a relevant physiological range. In different hypoxic conditions, the cellular environment showed a significant dependence on oxygen levels in resulting intracellular response. CONCLUSIONS Change in hydroxylation behavior and nutrient supplementation can have significant potential in designing novel therapeutic interventions in cancer and ischemia/reperfusion injuries. GENERAL SIGNIFICANCE The hybrid mathematical model can effectively predict intracellular behavior due to external influences providing valuable directions in designing future experiments.
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Affiliation(s)
- Adnan Morshed
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164-2920, United States
| | - Prashanta Dutta
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164-2920, United States.
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Yankeelov TE, An G, Saut O, Luebeck EG, Popel AS, Ribba B, Vicini P, Zhou X, Weis JA, Ye K, Genin GM. Multi-scale Modeling in Clinical Oncology: Opportunities and Barriers to Success. Ann Biomed Eng 2016; 44:2626-41. [PMID: 27384942 DOI: 10.1007/s10439-016-1691-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/29/2016] [Indexed: 12/11/2022]
Abstract
Hierarchical processes spanning several orders of magnitude of both space and time underlie nearly all cancers. Multi-scale statistical, mathematical, and computational modeling methods are central to designing, implementing and assessing treatment strategies that account for these hierarchies. The basic science underlying these modeling efforts is maturing into a new discipline that is close to influencing and facilitating clinical successes. The purpose of this review is to capture the state-of-the-art as well as the key barriers to success for multi-scale modeling in clinical oncology. We begin with a summary of the long-envisioned promise of multi-scale modeling in clinical oncology, including the synthesis of disparate data types into models that reveal underlying mechanisms and allow for experimental testing of hypotheses. We then evaluate the mathematical techniques employed most widely and present several examples illustrating their application as well as the current gap between pre-clinical and clinical applications. We conclude with a discussion of what we view to be the key challenges and opportunities for multi-scale modeling in clinical oncology.
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Affiliation(s)
- Thomas E Yankeelov
- Departments of Biomedical Engineering and Internal Medicine, Institute for Computational and Engineering Sciences, Cockrell School of Engineering, The University of Texas at Austin, 107 W. Dean Keeton, BME Building, 1 University Station, C0800, Austin, TX, 78712, USA.
| | - Gary An
- Department of Surgery and Computation Institute, The University of Chicago, Chicago, IL, USA
| | - Oliver Saut
- Institut de Mathématiques de Bordeaux, Université de Bordeaux and INRIA, Bordeaux, France
| | - E Georg Luebeck
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Aleksander S Popel
- Departments of Biomedical Engineering and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Benjamin Ribba
- Pharma Research and Early Development, Clinical Pharmacology, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Paolo Vicini
- Clinical Pharmacology and DMPK, MedImmune, Gaithersburg, MD, USA
| | - Xiaobo Zhou
- Center for Bioinformatics and Systems Biology, Radiology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jared A Weis
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kaiming Ye
- Department of Biomedical Engineering, Watson School of Engineering and Applied Science, Binghamton University, State University of New York, Binghamton, NY, USA
| | - Guy M Genin
- Departments of Mechanical Engineering and Materials Science, and Neurological Surgery, Washington University in St. Louis, St. Louis, MO, USA
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Apriasari ML, Dachlan YP, Ernawati DS. Effect of Musa acuminata Stem By Immunohistochemistry Test in Ulcer. ACTA ACUST UNITED AC 2016. [DOI: 10.3923/ajb.2016.135.141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Kinstlinger IS, Miller JS. 3D-printed fluidic networks as vasculature for engineered tissue. LAB ON A CHIP 2016; 16:2025-43. [PMID: 27173478 DOI: 10.1039/c6lc00193a] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Fabrication of vascular networks within engineered tissue remains one of the greatest challenges facing the fields of biomaterials and tissue engineering. Historically, the structural complexity of vascular networks has limited their fabrication in tissues engineered in vitro. Recently, however, key advances have been made in constructing fluidic networks within biomaterials, suggesting a strategy for fabricating the architecture of the vasculature. These techniques build on emerging technologies within the microfluidics community as well as on 3D printing. The freeform fabrication capabilities of 3D printing are allowing investigators to fabricate fluidic networks with complex architecture inside biomaterial matrices. In this review, we examine the most exciting 3D printing-based techniques in this area. We also discuss opportunities for using these techniques to address open questions in vascular biology and biophysics, as well as for engineering therapeutic tissue substitutes in vitro.
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Affiliation(s)
| | - Jordan S Miller
- Department of Bioengineering, Rice University, Houston, TX, USA.
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41
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Sarabipour S, Ballmer-Hofer K, Hristova K. VEGFR-2 conformational switch in response to ligand binding. eLife 2016; 5:e13876. [PMID: 27052508 PMCID: PMC4829425 DOI: 10.7554/elife.13876] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/09/2016] [Indexed: 01/02/2023] Open
Abstract
VEGFR-2 is the primary regulator of angiogenesis, the development of new blood vessels from pre-existing ones. VEGFR-2 has been hypothesized to be monomeric in the absence of bound ligand, and to undergo dimerization and activation only upon ligand binding. Using quantitative FRET and biochemical analysis, we show that VEGFR-2 forms dimers also in the absence of ligand when expressed at physiological levels, and that these dimers are phosphorylated. Ligand binding leads to a change in the TM domain conformation, resulting in increased kinase domain phosphorylation. Inter-receptor contacts within the extracellular and TM domains are critical for the establishment of the unliganded dimer structure, and for the transition to the ligand-bound active conformation. We further show that the pathogenic C482R VEGFR-2 mutant, linked to infantile hemangioma, promotes ligand-independent signaling by mimicking the structure of the ligand-bound wild-type VEGFR-2 dimer.
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Affiliation(s)
- Sarvenaz Sarabipour
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, United States
| | - Kurt Ballmer-Hofer
- Laboratory of Biomolecular Research, Molecular Cell Biology, Paul Scherrer Institute, Villigen, Switzerland
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, United States
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42
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Kassab GS, An G, Sander EA, Miga MI, Guccione JM, Ji S, Vodovotz Y. Augmenting Surgery via Multi-scale Modeling and Translational Systems Biology in the Era of Precision Medicine: A Multidisciplinary Perspective. Ann Biomed Eng 2016; 44:2611-25. [PMID: 27015816 DOI: 10.1007/s10439-016-1596-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 03/18/2016] [Indexed: 12/18/2022]
Abstract
In this era of tremendous technological capabilities and increased focus on improving clinical outcomes, decreasing costs, and increasing precision, there is a need for a more quantitative approach to the field of surgery. Multiscale computational modeling has the potential to bridge the gap to the emerging paradigms of Precision Medicine and Translational Systems Biology, in which quantitative metrics and data guide patient care through improved stratification, diagnosis, and therapy. Achievements by multiple groups have demonstrated the potential for (1) multiscale computational modeling, at a biological level, of diseases treated with surgery and the surgical procedure process at the level of the individual and the population; along with (2) patient-specific, computationally-enabled surgical planning, delivery, and guidance and robotically-augmented manipulation. In this perspective article, we discuss these concepts, and cite emerging examples from the fields of trauma, wound healing, and cardiac surgery.
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Affiliation(s)
- Ghassan S Kassab
- California Medical Innovations Institute, San Diego, CA, 92121, USA
| | - Gary An
- Department of Surgery, University of Chicago, Chicago, IL, 60637, USA
| | - Edward A Sander
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
| | - Michael I Miga
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Julius M Guccione
- Department of Surgery, University of California, San Francisco, CA, 94143, USA
| | - Songbai Ji
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA.,Department of Surgery and of Orthopaedic Surgery, Geisel School of Medicine, Dartmouth College, Hanover, NH, 03755, USA
| | - Yoram Vodovotz
- Department of Surgery, University of Pittsburgh, W944 Starzl Biomedical Sciences Tower, 200 Lothrop St., Pittsburgh, PA, 15213, USA. .,Center for Inflammation and Regenerative Modeling, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA.
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43
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Li XL, Oduola WO, Qian L, Dougherty ER. Integrating Multiscale Modeling with Drug Effects for Cancer Treatment. Cancer Inform 2016; 14:21-31. [PMID: 26792977 PMCID: PMC4712979 DOI: 10.4137/cin.s30797] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/08/2015] [Accepted: 11/15/2015] [Indexed: 12/12/2022] Open
Abstract
In this paper, we review multiscale modeling for cancer treatment with the incorporation of drug effects from an applied system's pharmacology perspective. Both the classical pharmacology and systems biology are inherently quantitative; however, systems biology focuses more on networks and multi factorial controls over biological processes rather than on drugs and targets in isolation, whereas systems pharmacology has a strong focus on studying drugs with regard to the pharmacokinetic (PK) and pharmacodynamic (PD) relations accompanying drug interactions with multiscale physiology as well as the prediction of dosage-exposure responses and economic potentials of drugs. Thus, it requires multiscale methods to address the need for integrating models from the molecular levels to the cellular, tissue, and organism levels. It is a common belief that tumorigenesis and tumor growth can be best understood and tackled by employing and integrating a multifaceted approach that includes in vivo and in vitro experiments, in silico models, multiscale tumor modeling, continuous/discrete modeling, agent-based modeling, and multiscale modeling with PK/PD drug effect inputs. We provide an example application of multiscale modeling employing stochastic hybrid system for a colon cancer cell line HCT-116 with the application of Lapatinib drug. It is observed that the simulation results are similar to those observed from the setup of the wet-lab experiments at the Translational Genomics Research Institute.
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Affiliation(s)
- Xiangfang L. Li
- Department of Electrical and Computer Engineering, Prairie View A&M University, Prairie View, TX, USA
| | - Wasiu O. Oduola
- Department of Electrical and Computer Engineering, Prairie View A&M University, Prairie View, TX, USA
| | - Lijun Qian
- Department of Electrical and Computer Engineering, Prairie View A&M University, Prairie View, TX, USA
| | - Edward R. Dougherty
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
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44
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Estrada R, Allingham MJ, Mettu PS, Cousins SW, Tomasi C, Farsiu S. Retinal Artery-Vein Classification via Topology Estimation. IEEE TRANSACTIONS ON MEDICAL IMAGING 2015; 34:2518-34. [PMID: 26068204 PMCID: PMC4685460 DOI: 10.1109/tmi.2015.2443117] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We propose a novel, graph-theoretic framework for distinguishing arteries from veins in a fundus image. We make use of the underlying vessel topology to better classify small and midsized vessels. We extend our previously proposed tree topology estimation framework by incorporating expert, domain-specific features to construct a simple, yet powerful global likelihood model. We efficiently maximize this model by iteratively exploring the space of possible solutions consistent with the projected vessels. We tested our method on four retinal datasets and achieved classification accuracies of 91.0%, 93.5%, 91.7%, and 90.9%, outperforming existing methods. Our results show the effectiveness of our approach, which is capable of analyzing the entire vasculature, including peripheral vessels, in wide field-of-view fundus photographs. This topology-based method is a potentially important tool for diagnosing diseases with retinal vascular manifestation.
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Affiliation(s)
- Rolando Estrada
- Department of Ophthalmology, Duke University, Durham, NC 27708 USA
| | | | | | - Scott W. Cousins
- Department of Ophthalmology, Duke University, Durham, NC 27708 USA
| | - Carlo Tomasi
- Department of Computer Science, Duke University, Durham, NC 27708 USA
| | - Sina Farsiu
- Departments of Biomedical Engineering, Ophthalmology, Electrical and Computer Engineering, and Computer Science, Duke University, Durham, NC, 27708 USA
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Mehdizadeh H, Bayrak ES, Lu C, Somo SI, Akar B, Brey EM, Cinar A. Agent-based modeling of porous scaffold degradation and vascularization: Optimal scaffold design based on architecture and degradation dynamics. Acta Biomater 2015; 27:167-178. [PMID: 26363375 DOI: 10.1016/j.actbio.2015.09.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 08/26/2015] [Accepted: 09/08/2015] [Indexed: 12/11/2022]
Abstract
A multi-layer agent-based model (ABM) of biomaterial scaffold vascularization is extended to consider the effects of scaffold degradation kinetics on blood vessel formation. A degradation model describing the bulk disintegration of porous hydrogels is incorporated into the ABM. The combined degradation-angiogenesis model is used to investigate growing blood vessel networks in the presence of a degradable scaffold structure. Simulation results indicate that higher porosity, larger mean pore size, and rapid degradation allow faster vascularization when not considering the structural support of the scaffold. However, premature loss of structural support results in failure for the material. A strategy using multi-layer scaffold with different degradation rates in each layer was investigated as a way to address this issue. Vascularization was improved with the multi-layered scaffold model compared to the single-layer model. The ABM developed provides insight into the characteristics that influence the selection of optimal geometric parameters and degradation behavior of scaffolds, and enables easy refinement of the model as new knowledge about the underlying biological phenomena becomes available. STATEMENT OF SIGNIFICANCE This paper proposes a multi-layer agent-based model (ABM) of biomaterial scaffold vascularization integrated with a structural-kinetic model describing bulk degradation of porous hydrogels to consider the effects of scaffold degradation kinetics on blood vessel formation. This enables the assessment of scaffold characteristics and in particular the disintegration characteristics of the scaffold on angiogenesis. Simulation results indicate that higher porosity, larger mean pore size, and rapid degradation allow faster vascularization when not considering the structural support of the scaffold. However, premature loss of structural support by scaffold disintegration results in failure of the material and disruption of angiogenesis. A strategy using multi-layer scaffold with different degradation rates in each layer was investigated as away to address this issue. Vascularization was improved with the multi-layered scaffold model compared to the single-layer model. The ABM developed provides insight into the characteristics that influence the selection of optimal geometric and degradation characteristics of tissue engineering scaffolds.
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Affiliation(s)
- Hamidreza Mehdizadeh
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, 10 W 33rd St, Suite 127, Chicago, IL 60616, USA
| | - Elif S Bayrak
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, 10 W 33rd St, Suite 127, Chicago, IL 60616, USA
| | - Chenlin Lu
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, 10 W 33rd St, Suite 127, Chicago, IL 60616, USA
| | - Sami I Somo
- Department of Biomedical Engineering, Illinois Institute of Technology, Suite 314, 3255 S Dearborn St, Chicago, IL 60616, USA
| | - Banu Akar
- Department of Biomedical Engineering, Illinois Institute of Technology, Suite 314, 3255 S Dearborn St, Chicago, IL 60616, USA
| | - Eric M Brey
- Department of Biomedical Engineering, Illinois Institute of Technology, Suite 314, 3255 S Dearborn St, Chicago, IL 60616, USA; Research Service, Hines Veterans Administration Hospital, Hines, IL, USA
| | - Ali Cinar
- Department of Chemical and Biological Engineering, Illinois Institute of Technology, 10 W 33rd St, Suite 127, Chicago, IL 60616, USA; Department of Biomedical Engineering, Illinois Institute of Technology, Suite 314, 3255 S Dearborn St, Chicago, IL 60616, USA.
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46
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Integrative Utilization of Microenvironments, Biomaterials and Computational Techniques for Advanced Tissue Engineering. J Biotechnol 2015; 212:71-89. [DOI: 10.1016/j.jbiotec.2015.08.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 08/02/2015] [Accepted: 08/11/2015] [Indexed: 01/13/2023]
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Datta M, Via LE, Chen W, Baish JW, Xu L, Barry CE, Jain RK. Mathematical Model of Oxygen Transport in Tuberculosis Granulomas. Ann Biomed Eng 2015; 44:863-72. [PMID: 26253038 DOI: 10.1007/s10439-015-1415-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/01/2015] [Indexed: 11/26/2022]
Abstract
Pulmonary granulomas--the hallmark of Mycobacterium tuberculosis (MTB) infection--are dense cellular lesions that often feature regions of hypoxia and necrosis, partially due to limited transport of oxygen. Low oxygen in granulomas can impair the host immune response, while MTB are able to adapt and persist in hypoxic environments. Here, we used a physiologically based mathematical model of oxygen diffusion and consumption to calculate oxygen profiles within the granuloma, assuming Michaelis-Menten kinetics. An approximate analytical solution--using a priori and newly estimated parameters from experimental data in a rabbit model of tuberculosis--was able to predict the size of hypoxic and necrotic regions in agreement with experimental results from the animal model. Such quantitative understanding of transport limitations can inform future tuberculosis therapeutic strategies that may include adjunct host-directed therapies that facilitate oxygen and drug delivery for more effective treatment.
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Affiliation(s)
- Meenal Datta
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Cox 7, 100 Blossom Street, Boston, MA, 02114, USA
- Department of Chemical and Biological Engineering, Tufts University, Medford, MA, 02155, USA
| | - Laura E Via
- Tuberculosis Research Section, Laboratory of Clinical Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
| | - Wei Chen
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Cox 7, 100 Blossom Street, Boston, MA, 02114, USA
- Department of Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - James W Baish
- Departments of Biomedical and Mechanical Engineering, Bucknell University, Lewisburg, PA, 17837, USA
| | - Lei Xu
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Cox 7, 100 Blossom Street, Boston, MA, 02114, USA
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Infectious Disease, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
| | - Rakesh K Jain
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Cox 7, 100 Blossom Street, Boston, MA, 02114, USA.
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48
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Chen S, Guo X, Imarenezor O, Imoukhuede PI. Quantification of VEGFRs, NRP1, and PDGFRs on Endothelial Cells and Fibroblasts Reveals Serum, Intra-Family Ligand, and Cross-Family Ligand Regulation. Cell Mol Bioeng 2015. [DOI: 10.1007/s12195-015-0411-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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49
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Bazmara H, Soltani M, Sefidgar M, Bazargan M, Mousavi Naeenian M, Rahmim A. The Vital Role of Blood Flow-Induced Proliferation and Migration in Capillary Network Formation in a Multiscale Model of Angiogenesis. PLoS One 2015; 10:e0128878. [PMID: 26047145 PMCID: PMC4457864 DOI: 10.1371/journal.pone.0128878] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/01/2015] [Indexed: 01/16/2023] Open
Abstract
Sprouting angiogenesis and capillary network formation are tissue scale phenomena. There are also sub-scale phenomena involved in angiogenesis including at the cellular and intracellular (molecular) scales. In this work, a multiscale model of angiogenesis spanning intracellular, cellular, and tissue scales is developed in detail. The key events that are considered at the tissue scale are formation of closed flow path (that is called loop in this article) and blood flow initiation in the loop. At the cellular scale, growth, migration, and anastomosis of endothelial cells (ECs) are important. At the intracellular scale, cell phenotype determination as well as alteration due to blood flow is included, having pivotal roles in the model. The main feature of the model is to obtain the physical behavior of a closed loop at the tissue scale, relying on the events at the cellular and intracellular scales, and not by imposing physical behavior upon it. Results show that, when blood flow is considered in the loop, the anastomosed sprouts stabilize and elongate. By contrast, when the loop is modeled without consideration of blood flow, the loop collapses. The results obtained in this work show that proper determination of EC phenotype is the key for its survival.
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Affiliation(s)
- Hossein Bazmara
- Department of Mechanical Engineering, K. N. T. University of Technology, Tehran, Iran
| | - Madjid Soltani
- Department of Mechanical Engineering, K. N. T. University of Technology, Tehran, Iran
- Division of Nuclear Medicine, Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, Baltimore, MD, United States of America
- * E-mail:
| | - Mostafa Sefidgar
- Department of Mechanical Engineering, K. N. T. University of Technology, Tehran, Iran
| | - Majid Bazargan
- Department of Mechanical Engineering, K. N. T. University of Technology, Tehran, Iran
| | | | - Arman Rahmim
- Division of Nuclear Medicine, Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, Baltimore, MD, United States of America
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50
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Hu Z, Brooks SA, Dormoy V, Hsu CW, Hsu HY, Lin LT, Massfelder T, Rathmell WK, Xia M, Al-Mulla F, Al-Temaimi R, Amedei A, Brown DG, Prudhomme KR, Colacci A, Hamid RA, Mondello C, Raju J, Ryan EP, Woodrick J, Scovassi AI, Singh N, Vaccari M, Roy R, Forte S, Memeo L, Salem HK, Lowe L, Jensen L, Bisson WH, Kleinstreuer N. Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: focus on the cancer hallmark of tumor angiogenesis. Carcinogenesis 2015; 36 Suppl 1:S184-202. [PMID: 26106137 PMCID: PMC4492067 DOI: 10.1093/carcin/bgv036] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/12/2014] [Accepted: 12/15/2014] [Indexed: 01/09/2023] Open
Abstract
One of the important 'hallmarks' of cancer is angiogenesis, which is the process of formation of new blood vessels that are necessary for tumor expansion, invasion and metastasis. Under normal physiological conditions, angiogenesis is well balanced and controlled by endogenous proangiogenic factors and antiangiogenic factors. However, factors produced by cancer cells, cancer stem cells and other cell types in the tumor stroma can disrupt the balance so that the tumor microenvironment favors tumor angiogenesis. These factors include vascular endothelial growth factor, endothelial tissue factor and other membrane bound receptors that mediate multiple intracellular signaling pathways that contribute to tumor angiogenesis. Though environmental exposures to certain chemicals have been found to initiate and promote tumor development, the role of these exposures (particularly to low doses of multiple substances), is largely unknown in relation to tumor angiogenesis. This review summarizes the evidence of the role of environmental chemical bioactivity and exposure in tumor angiogenesis and carcinogenesis. We identify a number of ubiquitous (prototypical) chemicals with disruptive potential that may warrant further investigation given their selectivity for high-throughput screening assay targets associated with proangiogenic pathways. We also consider the cross-hallmark relationships of a number of important angiogenic pathway targets with other cancer hallmarks and we make recommendations for future research. Understanding of the role of low-dose exposure of chemicals with disruptive potential could help us refine our approach to cancer risk assessment, and may ultimately aid in preventing cancer by reducing or eliminating exposures to synergistic mixtures of chemicals with carcinogenic potential.
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Affiliation(s)
- Zhiwei Hu
- To whom correspondence should be addressed. Tel: +1 614 685 4606; Fax: +1-614-247-7205;
| | - Samira A. Brooks
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Valérian Dormoy
- INSERM U1113, team 3 “Cell Signalling and Communication in Kidney and Prostate Cancer”, University of Strasbourg, Facultée de Médecine, 67085 Strasbourg, France
- Department of Cell and Developmental Biology, University of California, Irvine, CA 92697, USA
| | - Chia-Wen Hsu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-3375, USA
| | - Hsue-Yin Hsu
- Department of Life Sciences, Tzu-Chi University, Taiwan, Republic of China
| | - Liang-Tzung Lin
- Department of Microbiology and Immunology, Taipei Medical University, Taiwan, Republic of China
| | - Thierry Massfelder
- INSERM U1113, team 3 “Cell Signalling and Communication in Kidney and Prostate Cancer”, University of Strasbourg, Facultée de Médecine, 67085 Strasbourg, France
| | - W. Kimryn Rathmell
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892-3375, USA
| | - Fahd Al-Mulla
- Department of Life Sciences, Tzu-Chi University, Taiwan, Republic of China
| | | | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, University of Firenze, Florence 50134, Italy
| | - Dustin G. Brown
- Department of Environmental and Radiological Health Sciences
, Colorado State University/Colorado School of Public Health, Fort Collins, CO 80523, USA
| | - Kalan R. Prudhomme
- Environmental and Molecular Toxicology, Environmental Health Science Center, Oregon State University, Corvallis, OR 97331, USA
| | - Annamaria Colacci
- Center for Environmental Carcinogenesis and Risk Assessment, Environmental Protection and Health Prevention Agency, Bologna, Italy
| | - Roslida A. Hamid
- Faculty of Medicine and Health Sciences, University Putra, Serdang, Selangor, Malaysia
| | - Chiara Mondello
- Institute of Molecular Genetics, National Research Council, Pavia 27100, Italy
| | - Jayadev Raju
- Regulatory Toxicology Research Division, Bureau of Chemical Safety, Food Directorate
, Health Products and Food Branch Health Canada, Ottawa, Ontario K1A0K9, Canada
| | - Elizabeth P. Ryan
- Department of Environmental and Radiological Health Sciences
, Colorado State University/Colorado School of Public Health, Fort Collins, CO 80523, USA
| | - Jordan Woodrick
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, WashingtonDC 20057, USA
| | - A. Ivana Scovassi
- Institute of Molecular Genetics, National Research Council, Pavia 27100, Italy
| | - Neetu Singh
- Advanced Molecular Science Research Centre (Centre for Advance Research), King George’s Medical University, Lucknow, Uttar Pradesh 226003, India
| | - Monica Vaccari
- Center for Environmental Carcinogenesis and Risk Assessment, Environmental Protection and Health Prevention Agency, Bologna, Italy
| | - Rabindra Roy
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, WashingtonDC 20057, USA
| | - Stefano Forte
- Mediterranean Institute of Oncology, Viagrande 95029, Italy
| | - Lorenzo Memeo
- Mediterranean Institute of Oncology, Viagrande 95029, Italy
| | - Hosni K. Salem
- Urology Department, kasr Al-Ainy School of Medicine, Cairo University, El Manial, Cairo 12515, Egypt
| | - Leroy Lowe
- Getting to Know Cancer, Truro, Nova Scotia B2N 1X5, Canada
| | - Lasse Jensen
- Division of Cardiovascular Medicine, Department of Medical and Health Sciences, Linköping University, Linköping, Sweden and
| | - William H. Bisson
- Environmental and Molecular Toxicology, Environmental Health Science Center, Oregon State University, Corvallis, OR 97331, USA
| | - Nicole Kleinstreuer
- Integrated Laboratory Systems, Inc., in support of the National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, NIEHS, MD K2-16, RTP, NC 27709, USA
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