Publications

Hamidreza, J., Shi, L., Wolfenson, H., Carlier, A. (2024) YAP phosphorylation within integrin adhesions: insights from a computational model. Biophysical Journal, DOI: 10.1016/j.bpj.2024.09.002

YAP plays an important mechanosignaling role in essential processes such as cell proliferation and apoptosis. Our recent study shows direct recruitment and phosphorylation of YAP (at the Y357 residue) in small adhesions. However, formation of larger adhesions on stiff matrices significantly reduces YAP Y357 phosphorylation. In this study, we explore the dynamic interplay between adhesion properties and YAP phosphorylation with the aim to identify different factors that could lead to the experimentally-observed behavior. Our findings highlight the significance of adhesion size, spatial distribution, and lifetime, as well as the diffusion rate of YAP and the rate of YAP binding to adhesions, in modulating YAP phosphorylation levels. Overall, this work contributes to an improved understanding of YAP mechanotransduction mechanisms.

Hamidreza, J., Khalilimeybodi, A., Barrasa-Fano, J., Fraley, S., Rangamani, P., Carlier, A. (2024) Insights gained from computational modeling of YAP/TAZ signaling for cellular mechanotransduction. NPJ Systems Biology and Applications, https://doi.org/10.1038/s41540-024-00414-9
In this article, we provide a critical review of the current state-of-the-art of computational models that focus on YAP/TAZ signaling. We identify how different models either explain contradictory experimental observations or generate experimentally testable predictions. These models have provided valuable insights into the regulatory mechanisms of YAP/TAZ in diverse cellular contexts and make the case for biophysical modeling as an indispensable tool for deciphering mechanotransduction and its regulation of cell fate.

Donders, Z., Skorupska, I., Willems, E., Mussen, F., Van Broeckhoven, J., Carlier, A., Schepers, M., Vanmierlo, T. (2024) Beyond PDE4 inhibition: a comprehensive review on downstream cAMP signaling in the central nervous system. Biomedicine & Pharmacotherapy,
https://doi.org/10.1016/j.biopha.2024.117009
Cyclic adenosine monophosphate (cAMP) is a key second messenger that regulates signal transduction pathways pivotal for numerous biological functions. It has been shown that increased cAMP levels in the central nervous system (CNS) promote neuroplasticity, neurotransmission, neuronal survival, and myelination while suppressing neuroinflammation. This review provides a comprehensive overview of the existing knowledge regarding downstream mediators of cAMP signaling induced by PDE4 inhibition or cAMP stimulators. Furthermore, we highlight existing gaps and future perspectives that may incentivize additional downstream research concerning PDE(4) inhibition, thereby providing novel therapeutic approaches for CNS disorders.

Honasoge, K., Karagöz, Z., Goult, B., Wolfenson, H., LaPointe, V., Carlier, A. (2023) Force-dependent focal adhesion assembly and disassembly: a computational study. PLoS Computational biology, https://doi.org/10.1371/journal.pcbi.1011500
Although cell–ECM interactions have been studied extensively, it is not completely understood how immature (nascent) adhesions develop into mature (focal) adhesions and how mechanical forces influence this process. Here, we present a simplified mechano-chemical model based on ordinary differential equations with three major proteins involved in adhesions: integrins, talin and vinculin. The model predicts biphasic variation of actin retrograde velocity and maturation fraction with substrate stiffness, with maturation fractions between 18–35%, optimal stiffness of ∼1 pN/nm, and a mechanosensitive range of 1-100 pN/nm, all corresponding to key experimental findings. The model also proposes that signal-dependent disassembly rate variations play an underappreciated role in maturation fraction regulation.

Karagöz, Z., Passanha, F., Robeerst, L., van Griensven, M., LaPointe, V., Carlier, A. (2023) Computational evidence for multi-layer crosstalk between cadherin-11 and PDGF pathways. Scientific Reports, 10.1038/s41598-023-42624-x

Various cell surface receptors play an important role in the differentiation and self-renewal of human mesenchymal stem cells (hMSCs). In this study, we used a computational model to represent the experimentally proven interactions between cadherin-11 and two PDGFRs and we inspected whether the crosstalk also exists downstream of the signaling initiated by the two receptor families. Overall, our predictions suggest the existence of another layer of crosstalk, namely between β-catenin (downstream to cadherin-11) and an ERK inhibitor protein (e.g. DUSP1), different than the crosstalk at the receptor level between cadherin-11 and PDGFR-α and -β. By investigating the multi-level crosstalk between cadherin and PDGFRs computationally, this study contributes to an improved understanding of the effect of cell surface receptors on hMSCs proliferation.

Zhang, X., Karagoz, Z., Swapnasrita, S., Habibovic, P., Carlier, A., van Rijt, S. (2023), Development of Mesoporous Silica Nanoparticle-Based Films with Tunable Arginine-Glycine-Aspartate Peptide Global Density and Clustering Levels to Study Stem Cell Adhesion and Differentiation. ACS Applied Materials & Interface,  https://doi.org/10.1021/acsami.3c04249  

In this study, we developed a series of biointerfaces using arginine-glycine-aspartate (RGD)-functionalized mesoporous silica nanoparticles (MSN-RGD) to study the effect of RGD adhesion ligand global density (ligand coverage over the surface), spacing, and RGD clustering levels on stem cell adhesion and differentiation. In addition, a computational simulation study was performed to analyze nanoparticle distribution and RGD spacing on the resulting surfaces to determine experimental conditions. Our findings indicate that both RGD global density and clustering levels are crucial variables in regulating stem cell behaviors. 

Ruiter, A.A.F., King J., Swapnasrita, S., Giselbrecht, S., Truckenmüller, R., LaPointe, V.L.S., Baker, M., Carlier, A. (2023) Optimization of media change intervals through hydrogels using mathematical models. Biomacromolecules, https://doi.org/10.1021/acs.biomac.2c00961

In this study we combined mathematical modeling, fluorescent recovery after photobleaching, and hydrogel diffusion experiments on cell culture inserts to provide a multiscale practical approach for diffusion. We observed a dampening effect of the hydrogel that slowed the response to concentration changes and the creation of a diffusion gradient in the hydrogel by media refreshment. Our designed model combined with measurements provides a practical point of reference for diffusion coefficients in real-world culture conditions, enabling more informed choices on hydrogel culture conditions.

Mak M., Carlier, A., Spill, F., Malandrino, A., Long, M., Gomez-Benito, MJ (2022) Mechanobiology and the microenvironment: computational and experimental approaches. Editorial article Frontiers in Cell and Developmental Biology,

 https://doi.org/10.3389/fcell.2022.1054135 

The cell microenvironment (ME) varies among a wide range of tissues and influences critical cell processes such as proliferation, differentiation, migration and matrix production. It has been demonstrated that extracellular matrix (ECM) mechanical properties (i.e. stiffness, viscoelasticity, adhesiveness and topography) and the mechanical state of the ME influence the outcome of these cellular processes. In recent years, the influence of the ME on cancer progression has been the focus of extensive research. However, how local cell-ME interactions influence tissue level processes, such as vasculogenesis, tissue morphogenesis and bone healing and remodeling has been understudied. In this research topic collection, exciting new studies shed light on the relationship between the mechanobiology of these processes and the ME, using experimental and computational techniques.

NBTE board: Carlier, A., Yang, F., Lolli, A., Utomo, L., Leijten, J., Rouwkema, J., Daamen, W., and van Rijn, P. (2022) Celebrating 30 Years of Netherlands Society for Biomaterials and Tissue Engineering: Past, Present, and Future. Tissue Engineering part A, 28(11), https://doi.org/10.1089/ten.tea.2022.29029.sri

The field of Biomaterials and Tissue Engineering is, like many other fields, older than one would initially consider. Research in any field starts long before the field is defined. The same holds for the respective scientific societies that are being established to bring together a community of researchers and other relevant parties within a scientific field. This guest editorial and the corresponding special issue on Biomaterials and Tissue Engineering in the Netherlands is a celebration of 30 years of community building in the Netherlands through the Netherlands Society for Biomaterials and Tissue Engineering (NBTE).

Paes, D., Hermans, S., van den Hove, D., Vanmierlo, T., Prickaerts, J., Carlier, A. (2022) Computational investigation of the dynamic control of cAMP signaling by PDE4 isoform types. Biophysical Journal, https://doi.org/10.1016/j.bpj.2022.06.019

Cyclic adenosine monophosphate (cAMP) is a generic signaling molecule that, through precise control of its signaling dynamics, exerts distinct cellular effects. Phosphodiesterase 4 (PDE4) enzymes profoundly control cAMP signaling and comprise different isoform types of which the enzymatic activity is modulated by differential feedback mechanisms. Here, we established a computational model to study how feedback mechanisms on different PDE4 isoform types lead to dynamic, isoform-specific control of cAMP signaling. Simulations indicated that long PDE4 isoforms exert the most profound control on oscillatory cAMP signaling, as opposed to the PDE4-mediated control of single cAMP input pulses. Moreover, elevating cAMP levels or decreasing PDE4 levels revealed different effects on downstream signaling. Together these results underline that cAMP signaling is distinctly regulated by different PDE4 isoform types and that this isoform-specificity should be considered in both computational and experimental follow-up studies to better define PDE4 enzymes as therapeutic targets in diseases in which cAMP signaling is aberrant.

Baptista, D., Moreira Teixeira, L., Barata, D., Tahmasebi Birgani, Z., King, J., van Riet, S., Pasman, T., Poot, A., Stamatialis, D., Rottier, R., Hiemstra, P., Carlier, A., van Blitterswijk, C., Habibovic, P., Giselbrecht, S., Truckenmüller, R. (2022) 3D Lung-on-Chip model based on biomimetically microcurved culture membranes. ACS Biomaterials Science and Engineering, https://doi.org/10.1021/acsbiomaterials.1c01463.

There is increasing evidence that the strongly, microscale curved surfaces that epithelial or endothelial cells experience when lining small body lumens, such as the alveoli or blood vessels, impact their behavior. However, the most commonly used cell culture substrates for modeling of these human tissue barriers in organ-on-a-chip, ion track-etched porous membranes, provide only flat surfaces. Here, we propose a more realistic culture environment for alveolar cells based on biomimetically microcurved track-etched membranes. The microcurved membranes were seeded by infusion with primary human alveolar epithelial cells. The confluent curved epithelial cell monolayers could be cultured successfully at the air−liquid interface for 14 days. The presented 3D lung-on-a-chip model might set the stage for other (micro)anatomically inspired membrane-based organ-on-a-chip in the future

Post, J.N., Loerakker, S., Merks, R.M.H., Carlier, A. (2022) Implementing computational modeling in tissue engineering: where disciplines meet. Tissue Engineering Part A, https://doi.org/10.1089/ten.TEA.2021.0215

In recent years, the mathematical and computational sciences have developed novel methodologies and insights that can aid in designing advanced bioreactors, microfluidic set-ups or organ-on-chip devices, in optimizing culture conditions, or predicting long-term behavior of engineered tissues in vivo. In this review, we introduce the concept of computational models and how they can be integrated in an interdisciplinary workflow for Tissue Engineering and Regenerative Medicine (TERM). We specifically aim this review of general concepts and examples at experimental scientists with little or no computational modeling experience. We also describe the contribution of computational models in understanding TERM processes and in advancing the TERM field by providing novel insights.

Swapnasrita, S., Carlier, A., Layton, A. (2022) Sex-specific computational models of kidney function in patients with diabetes. Frontiers in Physiology, https://doi.org/10.3389/fphys.2022.741121

In this study, we have developed computational models of kidney function, separate for male and female patients with diabetes. The simulation results indicate that diabetes enhances Na+ transport, especially along the proximal tubules and thick ascending limbs, to similar extents in male and female patients, which can be explained by the diabetes-induced increase in glomerular filtration rate. Model simulations also suggest that SGLT2 inhibition raises luminal [Cl–] at the macula densa, twice as much in males as in females, and could indicate activation of the tubuloglomerular feedback signal. By inducing osmotic diuresis in the proximal tubules, SGLT2 inhibition reduces paracellular transport, eventually leading to diuresis and natriuresis. Those effects on urinary excretion are blunted in women, in part due to their higher distal transport capacity.

Tuvshindorj, U., Trouillet, V., Vasilevich, A., Koch, B., Vermeulen, S., Carlier, A., Alexander, M., Giselbrecht, S., Truckenmüller, R., de Boer, J. (2022) The Galapagos Chip platform for high-throughput screening of cell adhesive micropatterns. Small, https://doi.org/10.1002/smll.202105704

In this study a high-throughput screening platform called “Galapagos chip” is developed. It contains a library of 2176 distinct subcellular chemical patterns created using mathematical algorithms and a straightforward UV-induced two-step surface modification. This approach enables the immobilization of ligands in geometrically defined regions onto cell culture substrates. To validate the system, binary RGD/polyethylene glycol patterns are prepared on which human mesenchymal stem cells are cultured, and the authors observe how different patterns affect cell and organelle morphology. As proof of concept, the cells are stained for the mechanosensitive YAP protein, and, using a machine-learning algorithm, it is demonstrated that cell shape and YAP nuclear translocation correlate. In summary, the Galapagos chip is a versatile platform to screen geometrical aspects of cell–ECM interaction.

King, J., Eroumé, K., Truckenmüller, R., Giselbrecht S., Cowan, A.E., Loew, L., Carlier, A. (2021) Teaching mathematical modeling of cellular systems with the VCell MathModel. The Biophysicist, https://doi.org/10.35459/tbp.2021.000198

Mathematical biology has emerged as a powerful approach to describe and understand biological systems. Here, we introduce an interactive teaching tool with a practical hands-on skill session plan to introduce students to the various components of a mathematical model with 4 different mathematical approaches (i.e., ordinary differential equations, partial differential equations, stochastic differential equations, and spatial stochastic differential equations) and their advantages and disadvantages. As such, we provide a didactic summary for instructors and students interested in using VCell MathModels for mathematical modeling; this work is also valuable for mathematics-savvy users who would like to exploit fully the capabilities of the VCell software.

King, J., Giselbrecht, S., Truckenmüller, R., Carlier, A. (2021) Mechanistic computational models of epithelial cell transporters – the adorned heroes of pharmacokinetics. Frontiers in Pharmacology – Drug Metabolism and Transport, https://doi.org/10.3389/fphar.2021.780620y

Epithelial membrane transporter kinetics portray an irrefutable role in solute transport in and out of cells. Mechanistic models are used to investigate the transport of solutes at the organ, tissue, cell or membrane scale. Here, we review the recent advancements in using computational models to investigate epithelial transport kinetics on the cell membrane.

King, J., Swapnasrita, S., Truckenmüller, R., Giselbrecht, S., Masereeuw, R., Carlier, A. (2021) Modeling indoxyl sulfate transport in a bioartificial kidney: two-step binding kinetics or lumped parameters for uremic toxin clearance? Computers in Biology and Medicine, https://doi.org/10.1016/j.compbiomed.2021.104912

Toxin removal by the kidney is deficient in a patient suffering from end-stage kidney disease, and current dialysis therapies are insufficient in subsidizing this loss. This study used mathematical models to compare two types of active toxin transport kinetics. i.e., two-step binding and lumped parameter. The modeling results indicated that the transporter density is the most influential parameter for the indoxyl sulfate clearance. Moreover, a uniform distribution of transporters increases the indoxyl sulfate clearance, highlighting the need for a high-quality, functional proximal tubule monolayer in a bioartificial kidney. In summary, this study contributed to an improved understanding of indoxyl sulfate transport in advanced bioartificial dialysis devices, which can be used along with laboratory experiments to develop promising renal replacement therapies in the future.

Viguerie, A., Swapnasrita, S., Veneziani, A., Carlier, A. (2021) A multi-domain shear-stress dependent diffusive model of cell transport-aided dialysis: analysis and simulation. Mathematical Biosciences and Engineering, 18(6):8188-8200, doi: 10.3934/mbe.2021406

Kidney dialysis is the most widespread treatment method for end-stage renal disease, a debilitating health condition common in industrialized societies. In the present work, we introduce a model for cell-transport aided dialysis, incorporating the effects of the shear stress. We analyze the model mathematically and establish its well-posedness. We then present a series of numerical results, which suggest that a hollow-fiber design with a wavy profile may increase the efficiency of the dialysis treatment. We investigate numerically the shape of the wavy channel to maximize the toxin clearance. These results demonstrate the potential for the use of computational models in the study and advancement of renal therapies.

King, J., Mihaila, S., Ahmed, S., Truckenmüller, R., Giselbrecht, S., Masereeuw, R., Carlier, A. (2021) The influence of OAT1 density and functionality on indoxyl sulfate transport in the human proximal tubule: an integrated computational and in vitro study. Toxins, 13(10), https://www.mdpi.com/2072-6651/13/10/674

Research has shown that traditional dialysis is an insufficient long-term therapy for patients suffering from end-stage kidney disease due to the high retention of uremic toxins in the blood as a result of the absence of the active transport functionality of the proximal tubule (PT). In this integrated experimental–computational study, we developed a PT computational model that focuses on indoxyl sulfate (IS) transport by organic anionic transporter 1 (OAT1), capturing the transporter density in detail along the basolateral cell membrane as well as the activity of the transporter and the inward boundary flux. The results suggest that IS removal in the physiological model was influenced mainly by transporter density and IS dissociation rate from OAT1 and not by the initial albumin concentrationy provide an exciting avenue to help understand the toxin–transporter complexities in the PT and make better-informed decisions on bioartificial kidney designs and the underlining transporter-related issues in uremic patients.

Eroumé, K., Cavill, R., Stankova, K., de Boer, J., Carlier, A. (2021) Exploring the influence of cytosolic and membrane FAK activation on YAP/TAZ nuclear translocation. Biophysical Journal, https://doi.org/10.1016/j.bpj.2021.09.009

Membrane binding and unbinding dynamics play a crucial role in the biological activity of several nonintegral membrane proteins, which have to be recruited to the membrane to perform their functions. The in silico predictions of this study show that when the cell membrane interaction area with the underlying substrate increases, for example, through cell spreading, this leads to more encounters between membrane-bound signaling partners and downstream signal amplification. Because membrane activation is a motif common to many signaling pathways, this study has important implications for understanding the design principles of signaling networks.

Farzin, A., Hassan, S., Moreira Teixeira, L., Gurian, M., Crispim, J., Manhas, V., Carlier, A., Bae, H., Geris, L., Noshadi, I., Shin, S., Leijten, J. (2021) Self-oxygenation of tissues orchestrates full-thickness vascularization of living implants. Advanced Functional Materials, https://doi.org/10.1002/adfm.202100850

Bioengineering of tissues and organs has the potential to generate functional replacement organs. However, achieving the full-thickness vascularization that is required for long-term survival of living implants has remained a grand challenge, especially for clinically sized implants. Here it is reported that this challenge can be addressed by engineering self-oxygenating tissues, which is achieved via the incorporation of hydrophobic oxygen-generating micromaterials into engineered tissues. Numerical simulations predict that self-oxygenation of living tissues will effectively orchestrate rapid full-thickness vascularization of implanted tissues, which is empirically confirmed via in vivo experimentation. Self-oxygenation of tissues thus represents a novel, effective, and widely applicable strategy to enable the vascularization living implants, which is expected to advance organ transplantation and regenerative medicine applications.

Vermeulen, S., Honig, F., Vasilevich, A., Roumans, N., Romero, M., Dede Eren, Aysegul, Tuvshindorj, U., Alexander, M., Carlier, A., Williams, P., Uquillas, J., de Boer, J. (2021) Expanding Biomaterial Surface Topographical Design Space through Natural Surface Reproduction. Advanced Materials, https://doi.org/10.1002/adma.202102084

Surface topography is a tool to endow biomaterials with bioactive properties. However, the large number of possible designs makes it challenging to find the optimal surface structure to induce a specific cell response. Inspired by the diversity of natural surfaces, this study assesses as to what extent the topographical design space and consequently the resulting cellular responses can be expanded using natural surfaces. To this end, 26 plant and insect surfaces are replicated in polystyrene and their surface properties are quantified using white light interferometry. Through machine-learning algorithms, it is demonstrated that natural surfaces result in distinct morphological and focal adhesion profiles in mesenchymal stem cells (MSCs) and Pseudomonas aeruginosa colonization. Furthermore, differentiation experiments reveal the strong potential of the holy lotus to improve osteogenesis in MSCs.

King, J., Eroumé, K., Truckenmüller, R., Giselbrecht S., Cowan, A.E., Loew, L., Carlier, A. (2021) 10 steps to investigate a cellular system with mathematical modeling. PLoS Computational Biology, doi.org/10.1371/journal.pcbi.1008921

Cellular and intracellular processes are inherently complex due to the large number of components and interactions, which are often non-linear and occur at different spatiotemporal scales. Because of this complexity, mathematical modeling is increasingly used to simulate such systems and perform experiments in silico, many orders of magnitude faster than real experiments and often at a higher spatiotemporal resolution. In this article, we focus on the generic modeling process and illustrate it with an example model of membrane lipid turnover.

Karagöz, Z., Geuens, T., LaPointe, V.L.S., van Griensven, M., Carlier, A. (2021) Win, lose or tie: mathematical modeling of ligand competition at the cell-extracellular matrix interface. Frontiers in Bioengineering and Biotechnology, section Tissue Engineering and Regenerative Medicine, https://doi.org/10.3389/fbioe.2021.657244

In this study we developed a mathematical model that enabled us to simulate three main interactions, namely integrin activation, ligand binding and integrin clustering. Different from previously published computational models, we account for the binding of more than one type of ligand to the integrin. This competition between ligands defines the fate of the system. We have demonstrated that an increase in the initial concentration of ligands does not ensure an increase in the steady state concentration of ligand-bound integrins. The ligand with higher binding rate occupies more integrins at the steady state than does the competing ligand. With cell type specific, quantitative input on integrin-ligand binding rates, this model can be used to develop instructive cell culture systems.

Yang, L., Pijuan-Galito, S., Suk Rho, H., Vasilevich, A., Dede Eren, A., Ge, L., Habibovic, P., Alexander, M., de Boer, J., Carlier, A., van Rijn, P., Zhou, Q. (2021) High-throughput methods in the discovery and study of biomaterials and materiobiology. Chemical Reviews, https://doi.org/10.1021/acs.chemrev.0c00752

In this review, we first introduce materiobiology and its high-throughput screening (HTS). Then we present an in-depth of the recent progress of 2D/3D HTS platforms (i.e., gradient and microarray) in the principle, preparation, screening for materiobiology, and combination with other advanced technologies. The Compendium for Biomaterial Transcriptomics and high content imaging, computational simulations, and their translation toward commercial and clinical uses are highlighted. In the final section, current challenges and future perspectives are discussed. High-throughput experimentation within the field of materiobiology enables the elucidation of the relationships between biomaterial properties and biological behavior and thereby serves as a potential tool for accelerating the development of high-performance biomaterials.

Eroumé, K., Vasilevich, A., Vermeulen, S., de Boer, J., Carlier, A. (2021) On the influence of cell shape on dynamic reaction-diffusion polarization patterns. PLoS One, doi:10.1371/journal.pone.0248293

In this study we investigated the influence of cell shape on the Cdc42 patterns using an established computational polarization model. Our simulation results showed that not only cell shape but also Cdc42 and Rho-related (in)activation parameter values affected the distribution of active Cdc42. Despite an initial Cdc42 gradient, the in silico results also showed that the maximal Cdc42 concentration shifts in the opposite direction, a phenomenon we propose to call “reverse polarization”. Future work should focus on a mathematical description of the underpinnings of reverse polarization, in combination with experimental validation of spatiotemporal Rho GTPase patterns.

Karagöz, Z., Rijns, L., Dankers, P., van Griensven, M., Carlier, A. (2021) Towards understanding the messengers of extracellular space: computational models of outside-in integrin reaction networks. Computational and Structural Biotechnology Journal, 19:303-314, https://doi.org/10.1016/j.csbj.2020.12.025

The interactions between cells and their extracellular matrix (ECM) are critically important for homeostatic control of cell growth, proliferation, differentiation and apoptosis. Transmembrane integrin molecules facilitate the communication between ECM and the cell. In this review, we summarize the computational models of integrin signaling while we explain the function of integrins at three main subcellular levels (outside the cell, cell membrane, cytosol). We also discuss how these computational modeling efforts can be helpful in other disciplines such as biomaterial design.

Vasilevich, A., Carlier, A., Winkler, D., Singh, S., de Boer, J. (2020) Evolutionary design of optimal surface topographies for biomaterials. Scientific Reports, 10(1):22160, https://doi.org/10.1038/s41598-020-78777-2.

Natural evolution tackles optimization by producing many genetic variants and exposing these variants to selective pressure, resulting in the survival of the fittest. In this study, we took inspiration from nature to optimize materials surface topographies using evolutionary algorithms. We show that successive cycles of material design, production, and fitness assessment, selection, and mutation results in optimization of biomaterials designs.

Vasilevich, A., Vermeulen, S., Kamphuis M., Roumans, N., Eroumé, S., Hebels, D., van de Peppel, J., Reihs, R., Beijer, N., Carlier, A., Carpenter, A., Singh, S., de Boer, J. (2020) On the correlation between material-induced cel shape and phenotypical response of human mesenchymal stem cells. Scientific Reports, 10(1):18988, doi: 10.1038/s41598-020-76019-z.

In this study we propose an approach to identify a universal set of genes that regulate the material-induced phenotypical response of human mesenchymal stem cells. Hereto we defined the phenotypic response of human bone marrow-derived mesenchymal stem cells (hMSCs) to 2176 randomly generated surface topographies by probing basic functions such as migration, proliferation, protein synthesis, apoptosis, and differentiation using quantitative image analysis. Clustering the surfaces into 28 archetypical cell shapes, we found a very strict correlation between cell shape and physiological response and selected seven cell shapes to describe the molecular mechanism leading to phenotypic diversity. Transcriptomics analysis revealed a tight link between cell shape, molecular signatures, and phenotype.

Vermeulen, M., Roumans, N., Honig, F., Carlier, A., Hebels, D., Dede Eren, A., ten Dijke, P., Vasilevich, A., de Boer, J. (2020) Mechanotransduction is a context-dependent activator of TGF-β signaling in mesenchymal stem cells. Biomaterials, https://doi.org/10.1016/j.biomaterials.2020.120331

In this study we investigated the link between mechanotransduction and TGF-β signaling. We discovered that mesenchymal stem cells exposed to both micro-topographies and TGF-β2 display synergistic induction of SMAD phosphorylation and transcription of the TGF-β target genes SCXA, a-SMA, and SOX9. Pharmacological perturbations revealed that Rho/ROCK/SRF signaling is required for this synergistic response. We further found an activation of the early response genes SRF and EGR1 during the early adaptation phase on micro-topographies, which coincided with higher expression of the TGF-β type-II receptor gene. These findings provide novel insights into the convergence of mechanobiology and TGF-β signaling, which can lead to improved culture protocols and therapeutic applications.

Vassey, M., Figueredo, G.P., Scurr, P., Vasilevich, A., Vermeulen, S., Carlier, A., Luckett, J., Beijer, N., Williams, P., Winkler, D., de Boer, J., Ghaemmaghami, A.M., Alexander, M.R. (2020) Immune modulation by design: using topography to control human monocyte attachment and macrophage differentiation. Advanced Science, https://doi.org/10.1002/advs.201903392

Macrophages play a central role in orchestrating immune responses to foreign materials, which are often responsible for the failure of implanted medical devices. Material topography is known to influence macrophage attachment and phenotype, providing opportunities for the rational design of ‘immune-instructive’ topographies to modulate macrophage function and thus foreign body responses to biomaterials. This study reveals that micropillars 5-10 mm in diameter play a dominant role in driving macrophage attachment, illustrating that materials can potentially be designed to induce pro-inflammatory, anti-inflammatory or regulatory immune responses, for future application in the fight against foreign body rejection of medical devices.

van Gastel, N., Stegen, S., Eelen, G., Schoors, S., Carlier, A., Daniëls, V., Baryawno, N., Przybylzki, D., Depypere, M., Stiers, P-J., Lambrechts, D., Van Looveren, R., Torrekens, S., Sharda, A., Agostinis, P., Lambrechts, D., Maes, F., Swinnen, J., Geris, L., Van Oosterwyck, H., Thienpont, B., Carmeliet P., Scadden, D., Carmeliet, G. (2020) Lipid availability determines fate of skeletal progenitor cells via SOX9. Nature, https://doi.org/10.1038/s41586-020-2050-1

The avascular nature of cartilage makes it a unique tissue, but whether and how the absence of nutrient supply regulates chondrogenesis remain unknown. Here we show that obstruction of vascular invasion during bone healing favours chondrogenic over osteogenic differentiation of skeletal progenitor cells. Our results define lipid scarcity as an important determinant of chondrogenic commitment, reveal a role for FOXO transcription factors during lipid starvation, and identify SOX9 as a critical metabolic mediator. These data highlight the importance of the nutritional microenvironment in the specification of skeletal cell fate.

Grivas, K., Vavva, M., Demosthenes, P., Carlier, A., Geris, L., Van Oosterwyck, H., Fotiadis, D. (2019) Effect of ultrasound on bone fracture healing: a computational mechanobioregulatory model. Journal of the Acoustical Society of America, 145, 1048, https://doi.org/10.1121/1.5089221

In the present work, a mechanobioregulatory model of bone solidification under the US presence incorporating also the mechanical environment on the regeneration process, which is known to affect cellular processes, is presented. An iterative procedure is adopted, where the finite element method is employed to compute the mechanical stimuli at the linear elastic phases of the poroelastic callus region and a coupled system of partial differential equations to simulate the enhancement by the US cell angiogenesis process and thus the oxygen concentration in the fractured area. The numerical simulations demonstrate the salutary effect of US on bone repair.

Vavva, M., Grivas, K., Carlier, A., Demosthenes, P., Geris, L., Van Oosterwyck, H., Fotiadis, D. (2018) Effect of ultrasound on bone fracture healing: a computational bioregulatory model. Computers in Biology and Medicine, https://doi.org/10.1016/j.compbiomed.2018.06.024

In this study a mathematical model predicting bone healing under the presence of ultrasound is demonstrated. The effect of the ultrasound characteristics on angiogenesis and bone healing is investigated by applying different boundary conditions of acoustic pressure at the periosteal region of the bone model, which correspond to different intensity values. The results made clear that ultrasound enhances angiogenesis mechanisms during bone healing. The proposed model could be regarded as a step towards the monitoring of the effect of ultrasound on bone regeneration.

Geris, L., Lambrechts, T., Carlier, A., Papantoniou, I. (2018) The future is digital: in silico tissue engineering. Current Opinion in Biomedical Engeering, https://doi.org/10.1016/j.cobme.2018.04.001

The Industry 4.0 concept refers to automation and data exchange in manufacturing technologies, which includes technologies for cell therapy product manufacturing. An important aspect of this concept is the development and use of Digital Twins. A Digital Twin is a digital representation of a product or process that is used to optimize the design and use of said product or process. In this opinion article, we show that such Digital Twins have already been developed for a variety of tissue engineering processes. Using skeletal tissue engineering as a case study, we discuss a number of models at various stages of use between bench and bedside and ranging from pure data-driven models to models built on known mechanisms and first principles. Finally, we emphasize the importance of data collection and model validation to ensure, amongst others, compliance to regulatory guidelines.

Kumari, S., Vermeulen, S., van der Veer, B., Carlier, A., de Boer, J., Subramanyam, D. (2018) Shaping cell fate: influence of topographical substratum properties on embryonic stem cells. Tissue Engineering part B, doi:10.1089/ten.TEB.2017.0468

In this study we have performed an in silico clinical trial on 200 virtual subjects, generated from a previously established model of murine bone regeneration, to tackle the challenges associated with the small, pediatric patient population. Each virtual subject was simulated to receive no treatment and bone morphogenetic protein (BMP) treatment. We have shown that the degree of severity of CPT is significantly reduced with BMP treatment, although the effect is highly subject-specific. Using machine learning techniques we were also able to stratify the virtual subject population in adverse responders, non-responders, responders and asymptomatic.

Carlier, A., Vasilevich, A., Marechal, M., de Boer, J., Geris, L. (2018) In silico clinical trials for pediatric orphan diseases. Scientific Reports, 6;8(1):2465, doi:10.1038/s41598-018-20737-y

In this study we have performed an in silico clinical trial on 200 virtual subjects, generated from a previously established model of murine bone regeneration, to tackle the challenges associated with the small, pediatric patient population. Each virtual subject was simulated to receive no treatment and bone morphogenetic protein (BMP) treatment. We have shown that the degree of severity of CPT is significantly reduced with BMP treatment, although the effect is highly subject-specific. Using machine learning techniques we were also able to stratify the virtual subject population in adverse responders, non-responders, responders and asymptomatic.

Hebels, D.G.A.J, Carlier, A., Coonen, M.L.J., Theunissen, D.H., de Boer, J. (2017) cBiT: a transcriptomics database for innovative biomaterial engineering. Biomaterials, https://doi.org/10.1016/j.biomaterials.2017.10.008

Creating biomaterials that are suited for clinical application is still hampered by a lack of understanding of the interaction between a cell and the biomaterial surface it grows on. In this paper we present the Compendium for Biomaterial Transcriptomics (cBiT), a publicly accessible data repository directed at collecting transcriptomics data and carefully recorded material properties and other relevant metadata.

Vasilevich, A., Carlier, A., de Boer, J., Singh, S. (2017) Review: How not to drown in data: a guide for biomaterial engineers. Trends in Biotechnology, https://doi.org/10.1016/j.tibtech.2017.05.007

High-throughput assays that produce hundreds of measurements per sample are powerful tools for quantifying cell–material interactions. With advances in automation and miniaturization in material fabrication, hundreds of biomaterial samples can be rapidly produced, which can then be characterized using these assays. However, the resulting deluge of data can be overwhelming. This review describes machine learning and computational simulation approaches that can be brought to bear on the problem of analyzing biomaterial screening data.

Carlier, A., Alsber, E. (2016) Special collection: Harnessing topographical cues for Tissue Engineering. Tissue Engineering part A, 22:15, doi:10.1089/ten.tea.2016.0188; http://online.liebertpub.com/doi/full/10.1089/ten.tea.2016.0188

Despite the fact that it has been extensively shown that surface topographies greatly affect cell behavior, they have only been recently explored for applications in tissue engineering (first publication in Tissue Engineering in 2007). In this special collection, I highlight papers that exploit the power of surface topography for applications in retinal regeneration, nerve regeneration, cartilage repair, bone repair, dermal wound healing, and vascular scaffolds.

Carlier, A., Akdeniz Skvortsov, G., Hafezi, F., Ferraris, E., Patterson, J., Koc, B., Van Oosterwyck, H. (2016) Computational model-informed design and bioprinting of cell-patterned constructs for bone tissue engineering. Biofabrication, 8:2, http://dx.doi.org/10.1088/1758-5090/8/2/025009; http://iopscience.iop.org/article/10.1088/1758-5090/8/2/025009/meta

By using a computational model of bone regeneration we show that particular cell patterns in tissue engineering constructs are able to enhance bone regeneration compared to constructs with a uniform cell distribution. In addition, we demonstrate that the discretization of the pattern, which is required for the bioprinting process, has a substantial effect on bone regeneration. We successfully bioprinted the most promising cell-gradient patterns by using cell-laden hydrogels with varying cell densities. In summary, this publication describes a novel integrated approach for the biofabrication of bone tissue engineering constructs by combining in silico models with bioprinting technology.

Carlier, A., Brems, H., Ashbourn, J.M.A., Nica, I., Legius, E., Geris, L. (2015). Capturing the wide variety of impaired fracture healing phenotypes in Neurofibromatosis Type 1 with eight key factors: a computational study. Sci Rep, 6, 20010, doi:10.1038/srep20010; http://www.nature.com/articles/srep20010

In this publication we used a previously established computational model of bone regeneration to examine the effect of the Nf1 mutation on bone fracture healing by altering the parameter values of eight key factors which describe the aberrant cellular behavior of Nf1 haploinsufficient and Nf1 bi-allelically inactivated cells. We show that the computational model is able to predict the formation of a hamartoma as well as a wide variety of CPT phenotypes through different combinations of altered parameter values. A sensitivity analysis by “Design of Experiments” identified the impaired endochondral ossification process and increased infiltration of fibroblastic cells as key contributors to the degree of severity of CPT.

Carlier, A., Lammens, J., Van Oosterwyck, H., Geris, L. (2015). Computational modeling of bone fracture non-unions: four clinically relevant case studies. In Silico Cell Tissue Sci, 2:1, doi: 10.1186/s40482-015-0004-x; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684906/

This paper reviews four different computational models, each capturing a particular clinical case of non-union: non-union induced by reaming of the marrow canal and periosteal stripping, non-union due to a large interfragmentary gap, non-union due to a genetic disorder (i.e. NF1 related congenital pseudoarthrosis of the tibia (CPT)) and non-union due to mechanical overload. Together, the four computational models are able to capture the etiology of a wide range of fracture non-union types and design novel treatment strategies thereof.

Carlier, A., Geris, L., Lammens, J., Van Oosterwyck, H. (2015). Bringing computational models of bone regeneration to the clinic. WIREs Syst Biol Med, doi:10.1002/wsbm.1299; http://onlinelibrary.wiley.com/doi/10.1002/wsbm.1299/full

This paper reviews the key challenges that limit the translation of computational models of bone regeneration from a research context into clinical practice: the clear mismatch between the scope of the existing and the clinically required models, the limited quantitative information of insufficient quality to determine of patient-specific parameter values and the limited corroboration of the computational models in (small) animal models.

Carlier, A., van Gastel, N., Geris, L., Carmeliet, G., Van Oosterwyck, H. (2014). Size does matter: an integrative in vivo-in silico approach for the treatment of critical size bone defects. PLoS Comput Biol, 10(11), e1003888; http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003888

In this publication we used a previously established computational model of bone regeneration to understand the causes of impaired healing in a critical size bone defect, i.e. the delayed vascularization of the central callus region results in harsh hypoxic conditions, cell death and finally disrupted bone healing. The model was also used to investigate the influence of the host environment on the bone healing process and novel tissue engineering treatment strategies were designed and tested for effectiveness in silico.

Carlier, A., Geris, L., van Gastel, N., Carmeliet, G., Van Oosterwyck, H. (2014). Oxygen as a critical determinant of bone fracture healing – a multiscale model. J Theor Biol, 365, 247-264; http://www.sciencedirect.com/science/article/pii/S0022519314006018

This paper describes the establishment of a computational model of bone regeneration, including a detailed description of the influence of oxygen on the various cellular processes. The predictions of the computational model agreed well with experimental observations and an extensive sensitivity analysis indicated the robustness of the model. When the model was applied to the challenging clinical case of a critical sized bone defect, the predictions highlighted the importance of adequate spatiotemporal oxygen patterns for successful bone healing.

Carlier, A., Geris, L., Bentley, K., Carmeliet, G., Carmeliet, P., Van Oosterwyck, H. (2012). MOSAIC: A Multiscale Model of Osteogenesis and Sprouting Angiogenesis with Lateral Inhibition of Endothelial Cells. PLoS Comput Biol, 8(10), e1002724; http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002724

In this paper we present a new multiscale model of sprouting angiogenesis during bone regeneration, including lateral inhibition of endothelial cells through the Dll4-Notch signaling pathway. In high VEGF concentrations the MOSAIC model predicted the absence of a vascular network and fracture healing. This result was not retrieved for a more phenomenological model, highlighting the importance of implementing the actual signaling pathway rather than a set of phenomenological rules.

Chai, Y.C., Carlier, A., Bolander, J., Roberts, S.J., Geris, L., Schrooten, J., Van Oosterwyck, H., Luyten, F.P. (2012). Current views on calcium phosphate osteogenicity and the translation into effective bone regeneration strategies. Acta Biomaterialia, 8(12), 3876-3887; http://www.sciencedirect.com/science/article/pii/S1742706112003030

This publication reviews the bone biology of CaP biomaterials, their production techniques and existing computational models to simulate CaP-driven osteogenesis in bone tissue engineering. Although numerous studies have been devoted to unravelling the mechanisms of osteoinductivity of CaP scaffolds, many questions still remain unresolved. To overcome this bottleneck and decipher the complex in vivo biological process of bone regeneration inside CaP constructs, it was found to be crucial to combine experimental and computational research efforts.

Carlier, A., Chai, Y., Moesen, M., Theys, T., Schrooten, J., Van Oosterwyck, H., Geris, L. (2011). Designing optimal calcium phosphate scaffold-cell combinations using an integrative model based approach. Acta Biomaterialia, 7, 3573-3585; http://www.sciencedirect.com/science/article/pii/S1742706111002583

In this study, we have developed a new, experimentally informed bioregulatory model of direct, ectopic bone formation inside CaP biomaterials. The model was able to qualitatively predict normal and impaired bone formation and was applied to design optimal combinations of CaP biomaterials and cell culture conditions to maximize the amount of bone formation in tissue engineering applications.