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Arrestin-3 scaffolding of the JNK3 cascade suggests a mechanism for signal amplification.
Perry NA, Kaoud TS, Ortega OO, Kaya AI, Marcus DJ, Pleinis JM, Berndt S, Chen Q, Zhan X, Dalby KN, Lopez CF, Iverson TM, Gurevich VV
(2019) Proc Natl Acad Sci U S A 116: 810-815
MeSH Terms: MAP Kinase Kinase 4, MAP Kinase Kinase 7, MAP Kinase Signaling System, Mitogen-Activated Protein Kinase 10, Models, Biological, Phosphorylation, Software, beta-Arrestin 2
Show Abstract · Added April 1, 2019
Scaffold proteins tether and orient components of a signaling cascade to facilitate signaling. Although much is known about how scaffolds colocalize signaling proteins, it is unclear whether scaffolds promote signal amplification. Here, we used arrestin-3, a scaffold of the ASK1-MKK4/7-JNK3 cascade, as a model to understand signal amplification by a scaffold protein. We found that arrestin-3 exhibited >15-fold higher affinity for inactive JNK3 than for active JNK3, and this change involved a shift in the binding site following JNK3 activation. We used systems biochemistry modeling and Bayesian inference to evaluate how the activation of upstream kinases contributed to JNK3 phosphorylation. Our combined experimental and computational approach suggested that the catalytic phosphorylation rate of JNK3 at Thr-221 by MKK7 is two orders of magnitude faster than the corresponding phosphorylation of Tyr-223 by MKK4 with or without arrestin-3. Finally, we showed that the release of activated JNK3 was critical for signal amplification. Collectively, our data suggest a "conveyor belt" mechanism for signal amplification by scaffold proteins. This mechanism informs on a long-standing mystery for how few upstream kinase molecules activate numerous downstream kinases to amplify signaling.
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Traction Force Microscopy for Noninvasive Imaging of Cell Forces.
Mulligan JA, Bordeleau F, Reinhart-King CA, Adie SG
(2018) Adv Exp Med Biol 1092: 319-349
MeSH Terms: Biomechanical Phenomena, Extracellular Matrix, Humans, Microscopy, Atomic Force, Models, Biological
Show Abstract · Added April 10, 2019
The forces exerted by cells on their surroundings play an integral role in both physiological processes and disease progression. Traction force microscopy is a noninvasive technique that enables the in vitro imaging and quantification of cell forces. Utilizing expertise from a variety of disciplines, recent developments in traction force microscopy are enhancing the study of cell forces in physiologically relevant model systems, and hold promise for further advancing knowledge in mechanobiology. In this chapter, we discuss the methods, capabilities, and limitations of modern approaches for traction force microscopy, and highlight ongoing efforts and challenges underlying future innovations.
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5 MeSH Terms
Endothelial cells on an aged subendothelial matrix display heterogeneous strain profiles in silico.
Kohn JC, Abdalrahman T, Sack KL, Reinhart-King CA, Franz T
(2018) Biomech Model Mechanobiol 17: 1405-1414
MeSH Terms: Animals, Blood Vessels, Computer Simulation, Endothelial Cells, Extracellular Matrix, Male, Mice, Inbred C57BL, Models, Biological, Stress, Mechanical
Show Abstract · Added April 10, 2019
Within the artery intima, endothelial cells respond to mechanical cues and changes in subendothelial matrix stiffness. Recently, we found that the aging subendothelial matrix stiffens heterogeneously and that stiffness heterogeneities are present on the scale of one cell length. However, the impacts of these complex mechanical micro-heterogeneities on endothelial cells have not been fully understood. Here, we simulate the effects of matrices that mimic young and aged vessels on single- and multi-cell endothelial cell models and examine the resulting cell basal strain profiles. Although there are limitations to the model which prohibit the prediction of intracellular strain distributions in alive cells, this model does introduce mechanical complexities to the subendothelial matrix material. More heterogeneous basal strain distributions are present in the single- and multi-cell models on the matrix mimicking an aged artery over those exhibited on the young artery. Overall, our data indicate that increased heterogeneous strain profiles in endothelial cells are displayed in silico when there is an increased presence of microscale arterial mechanical heterogeneities in the matrix.
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Genome Editing and Induced Pluripotent Stem Cell Technologies for Personalized Study of Cardiovascular Diseases.
Chun YW, Durbin MD, Hong CC
(2018) Curr Cardiol Rep 20: 38
MeSH Terms: Cardiovascular Diseases, Cell Differentiation, Gene Editing, Humans, Induced Pluripotent Stem Cells, Models, Biological, Precision Medicine
Show Abstract · Added May 1, 2018
PURPOSE OF REVIEW - The goal of this review is to highlight the potential of induced pluripotent stem cell (iPSC)-based modeling as a tool for studying human cardiovascular diseases. We present some of the current cardiovascular disease models utilizing genome editing and patient-derived iPSCs.
RECENT FINDINGS - The incorporation of genome-editing and iPSC technologies provides an innovative research platform, providing novel insight into human cardiovascular disease at molecular, cellular, and functional level. In addition, genome editing in diseased iPSC lines holds potential for personalized regenerative therapies. The study of human cardiovascular disease has been revolutionized by cellular reprogramming and genome editing discoveries. These exceptional technologies provide an opportunity to generate human cell cardiovascular disease models and enable therapeutic strategy development in a dish. We anticipate these technologies to improve our understanding of cardiovascular disease pathophysiology leading to optimal treatment for heart diseases in the future.
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7 MeSH Terms
3D bone models to study the complex physical and cellular interactions between tumor and the bone microenvironment.
Vanderburgh JP, Guelcher SA, Sterling JA
(2018) J Cell Biochem 119: 5053-5059
MeSH Terms: Animals, Bone Neoplasms, Bone and Bones, Cellular Microenvironment, Humans, Models, Biological, Tissue Engineering, Tissue Scaffolds, Tumor Microenvironment
Show Abstract · Added April 15, 2019
As the complexity of interactions between tumor and its microenvironment has become more evident, a critical need to engineer in vitro models that veritably recapitulate the 3D microenvironment and relevant cell populations has arisen. This need has caused many groups to move away from the traditional 2D, tissue culture plastic paradigms in favor of 3D models with materials that more closely replicate the in vivo milieu. Creating these 3D models remains a difficult endeavor for hard and soft tissues alike as the selection of materials, fabrication processes, and optimal conditions for supporting multiple cell populations makes model development a nontrivial task. Bone tissue in particular is uniquely difficult to model in part because of the limited availability of materials that can accurately capture bone rigidity and architecture, and also due to the dependence of both bone and tumor cell behavior on mechanical signaling. Additionally, the bone is a complex cellular microenvironment with multiple cell types present, including relatively immature, pluripotent cells in the bone marrow. This prospect will focus on the current 3D models in development to more accurately replicate the bone microenvironment, which will help facilitate improved understanding of bone turnover, tumor-bone interactions, and drug response. These studies have demonstrated the importance of accurately modelling the bone microenvironment in order to fully understand signaling and drug response, and the significant effects that model properties such as architecture, rigidity, and dynamic mechanical factors have on tumor and bone cell response.
© 2018 Wiley Periodicals, Inc.
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9 MeSH Terms
Isotopically nonstationary metabolic flux analysis (INST-MFA): putting theory into practice.
Cheah YE, Young JD
(2018) Curr Opin Biotechnol 54: 80-87
MeSH Terms: Autotrophic Processes, Carbon Isotopes, Isotope Labeling, Metabolic Flux Analysis, Models, Biological, Software
Show Abstract · Added March 14, 2018
Typically, C flux analysis relies on assumptions of both metabolic and isotopic steady state. If metabolism is steady but isotope labeling is not allowed to fully equilibrate, isotopically nonstationary metabolic flux analysis (INST-MFA) can be used to estimate fluxes. This requires solution of differential equations that describe the time-dependent labeling of network metabolites, while iteratively adjusting the flux and pool size parameters to match the transient labeling measurements. INST-MFA holds a number of unique advantages over approaches that rely solely upon steady-state isotope enrichments. First, INST-MFA can be applied to estimate fluxes in autotrophic systems, which consume only single-carbon substrates. Second, INST-MFA is ideally suited to systems that label slowly due to the presence of large intermediate pools or pathway bottlenecks. Finally, INST-MFA provides increased measurement sensitivity to estimate reversible exchange fluxes and metabolite pool sizes, which represents a potential framework for integrating metabolomic analysis with C flux analysis. This review highlights the unique capabilities of INST-MFA, describes newly available software tools that automate INST-MFA calculations, presents several practical examples of recent INST-MFA applications, and discusses the technical challenges that lie ahead.
Copyright © 2018 Elsevier Ltd. All rights reserved.
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6 MeSH Terms
Eigenstrain as a mechanical set-point of cells.
Lin S, Lampi MC, Reinhart-King CA, Tsui G, Wang J, Nelson CA, Gu L
(2018) Biomech Model Mechanobiol 17: 951-959
MeSH Terms: Animals, Aorta, Biomechanical Phenomena, Cattle, Cells, Cultured, Endothelial Cells, Models, Biological, Stress, Mechanical
Show Abstract · Added April 10, 2019
Cell contraction regulates how cells sense their mechanical environment. We sought to identify the set-point of cell contraction, also referred to as tensional homeostasis. In this work, bovine aortic endothelial cells (BAECs), cultured on substrates with different stiffness, were characterized using traction force microscopy (TFM). Numerical models were developed to provide insights into the mechanics of cell-substrate interactions. Cell contraction was modeled as eigenstrain which could induce isometric cell contraction without external forces. The predicted traction stresses matched well with TFM measurements. Furthermore, our numerical model provided cell stress and displacement maps for inspecting the fundamental regulating mechanism of cell mechanosensing. We showed that cell spread area, traction force on a substrate, as well as the average stress of a cell were increased in response to a stiffer substrate. However, the cell average strain, which is cell type-specific, was kept at the same level regardless of the substrate stiffness. This indicated that the cell average strain is the tensional homeostasis that each type of cell tries to maintain. Furthermore, cell contraction in terms of eigenstrain was found to be the same for both BAECs and fibroblast cells in different mechanical environments. This implied a potential mechanical set-point across different cell types. Our results suggest that additional measurements of contractility might be useful for monitoring cell mechanosensing as well as dynamic remodeling of the extracellular matrix (ECM). This work could help to advance the understanding of the cell-ECM relationship, leading to better regenerative strategies.
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Biophysical Modeling of In Vivo Glioma Response After Whole-Brain Radiation Therapy in a Murine Model of Brain Cancer.
Hormuth DA, Weis JA, Barnes SL, Miga MI, Quaranta V, Yankeelov TE
(2018) Int J Radiat Oncol Biol Phys 100: 1270-1279
MeSH Terms: Animals, Brain Neoplasms, Cell Death, Cell Proliferation, Contrast Media, Cranial Irradiation, Diffusion Magnetic Resonance Imaging, Disease Models, Animal, Female, Glioma, Magnetic Resonance Imaging, Models, Biological, Radiation Dosage, Rats, Rats, Wistar, Treatment Outcome, Tumor Burden
Show Abstract · Added July 23, 2018
PURPOSE - To develop and investigate a set of biophysical models based on a mechanically coupled reaction-diffusion model of the spatiotemporal evolution of tumor growth after radiation therapy.
METHODS AND MATERIALS - Post-radiation therapy response is modeled using a cell death model (M), a reduced proliferation rate model (M), and cell death and reduced proliferation model (M). To evaluate each model, rats (n = 12) with C6 gliomas were imaged with diffusion-weighted magnetic resonance imaging (MRI) and contrast-enhanced MRI at 7 time points over 2 weeks. Rats received either 20 or 40 Gy between the third and fourth imaging time point. Diffusion-weighted MRI was used to estimate tumor cell number within enhancing regions in contrast-enhanced MRI data. Each model was fit to the spatiotemporal evolution of tumor cell number from time point 1 to time point 5 to estimate model parameters. The estimated model parameters were then used to predict tumor growth at the final 2 imaging time points. The model prediction was evaluated by calculating the error in tumor volume estimates, average surface distance, and voxel-based cell number.
RESULTS - For both the rats treated with either 20 or 40 Gy, significantly lower error in tumor volume, average surface distance, and voxel-based cell number was observed for the M and M models compared with the M model. The M model fit, however, had significantly lower sum squared error compared with the M and M models.
CONCLUSIONS - The results of this study indicate that for both doses, the M and M models result in accurate predictions of tumor growth, whereas the M model poorly describes response to radiation therapy.
Copyright © 2017 Elsevier Inc. All rights reserved.
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17 MeSH Terms
Wnt6 maintains anterior escort cells as an integral component of the germline stem cell niche.
Wang X, Page-McCaw A
(2018) Development 145:
MeSH Terms: Animals, Animals, Genetically Modified, Bone Morphogenetic Proteins, Cadherins, Cell Count, Cell Differentiation, Cell Lineage, Cell Survival, Drosophila Proteins, Drosophila melanogaster, Female, Germ Cells, Ligands, Models, Biological, Ovary, Signal Transduction, Stem Cell Niche, Wnt Proteins
Show Abstract · Added March 20, 2018
Stem cells reside in a niche, a local environment whose cellular and molecular complexity is still being elucidated. In ovaries, germline stem cells depend on cap cells for self-renewing signals and physical attachment. Germline stem cells also contact the anterior escort cells, and here we report that anterior escort cells are absolutely required for germline stem cell maintenance. When escort cells die from impaired Wnt signaling or expression, the loss of anterior escort cells causes loss of germline stem cells. Anterior escort cells function as an integral niche component by promoting DE-cadherin anchorage and by transiently expressing the Dpp ligand to promote full-strength BMP signaling in germline stem cells. Anterior escort cells are maintained by Wnt6 ligands produced by cap cells; without Wnt6 signaling, anterior escort cells die leaving vacancies in the niche, leading to loss of germline stem cells. Our data identify anterior escort cells as constituents of the germline stem cell niche, maintained by a cap cell-produced Wnt6 survival signal.
© 2018. Published by The Company of Biologists Ltd.
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18 MeSH Terms
Mechanically Coupled Reaction-Diffusion Model to Predict Glioma Growth: Methodological Details.
Hormuth DA, Eldridge SL, Weis JA, Miga MI, Yankeelov TE
(2018) Methods Mol Biol 1711: 225-241
MeSH Terms: Algorithms, Animals, Brain, Brain Neoplasms, Computer Simulation, Female, Glioma, Magnetic Resonance Imaging, Models, Biological, Rats, Wistar, Software
Show Abstract · Added July 23, 2018
Biophysical models designed to predict the growth and response of tumors to treatment have the potential to become a valuable tool for clinicians in care of cancer patients. Specifically, individualized tumor forecasts could be used to predict response or resistance early in the course of treatment, thereby providing an opportunity for treatment selection or adaption. This chapter discusses an experimental and modeling framework in which noninvasive imaging data is used to initialize and parameterize a subject-specific model of tumor growth. This modeling approach is applied to an analysis of murine models of glioma growth.
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11 MeSH Terms