Optimizing the medium refreshment regime during neotissue growth in a perfusion bioreactor described by a reduced computational model capturing curvature and shear stress distribution
Mehrian, Mohammad ; ; et al
Scientific conference (2016, April 15)Detailed reference viewed: 21 (3 ULg)
Capturing the wide variety of impaired fracture healing phenotypes in Neurofibromatosis Type 1 with eight key factors: a computational study.
; ; et al
in Scientific Reports (2016), 7
Congenital pseudarthrosis of the tibia (CPT) is a rare disease which normally presents itself during early childhood by anterolateral bowing of the tibia and spontaneous tibial fractures. Although the ... [more ▼]
Congenital pseudarthrosis of the tibia (CPT) is a rare disease which normally presents itself during early childhood by anterolateral bowing of the tibia and spontaneous tibial fractures. Although the exact etiology of CPT is highly debated, 40-80% of CPT patients are carriers of a mutation in the Neurofibromatosis Type 1 (NF1) gene, which can potentially result in an altered phenotype of the skeletal cells and impaired bone healing. In this study we use a 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 behaviour 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. Hence, the computational model results have added credibility to the experimental hypothesis of a genetic cause (i.e. Nf1 mutation) for CPT. [less ▲]Detailed reference viewed: 16 (4 ULg)
The combined mechanism of bone morphogenetic protein- and calcium phosphate-induced skeletal tissue formation by human periosteum derived cells.
; ; Geris, Liesbet et al
in European Cells and Materials (2016), 31
When combining osteogenic progenitor cells such as human periosteum derived cells (hPDCs) with osteoconductive biomaterials like calcium phosphate (CaP)-scaffolds, in vivo bone formation can be achieved ... [more ▼]
When combining osteogenic progenitor cells such as human periosteum derived cells (hPDCs) with osteoconductive biomaterials like calcium phosphate (CaP)-scaffolds, in vivo bone formation can be achieved. This process is dependent on the early activation of Bone morphogenetic protein (BMP)-signalling. However, the bone forming process is slow and routinely only a limited amount of bone and bone marrow is formed. Therefore, we hypothesised that a robust clinically relevant outcome could be achieved by adding more physiological levels of potent BMP-ligands to these cell- and CaP-based constructs. For this, hPDCs were characterised for their responsiveness to BMP-ligands upon in vitro 2D stimulation. BMP-2, -4, -6 and -9 robustly induced osteochondrogenic differentiation. Subsequently, these ligands were coated onto clinically approved CaP-scaffolds, BioOss(R) and CopiOs(R), followed by hPDC-seeding. Protein lysates and conditioned media were investigated for activation of BMP signalling pathways. Upon in vivo implantation, the most abundant bone formation was found in BMP-2 and BMP-6-coated scaffolds. Implanted cells actively contributed to the newly formed bone. Remnants of cartilage could be observed in BMP-coated CopiOs(R)-constructs. Computational analysis displayed that the type of BMP-ligand as well as the CaP-scaffold affects skeletal tissue formation, observed in a qualitative as well as quantitative manner. Furthermore, the in vitro mechanism appears to predict the in vivo outcome. This study presents further evidence for the potential of BMP-technology in the development of clinically relevant cell-based constructs for bone regenerative strategies. [less ▲]Detailed reference viewed: 9 (2 ULg)
Early BMP, Wnt and Ca(2+)/PKC pathway activation predicts the bone forming capacity of periosteal cells in combination with calcium phosphates.
; ; Geris, Liesbet et al
in Biomaterials (2016), 86
The development of osteoinductive calcium phosphate- (CaP) based biomaterials has, and continues to be, a major focus in the field of bone tissue engineering. However, limited insight into the ... [more ▼]
The development of osteoinductive calcium phosphate- (CaP) based biomaterials has, and continues to be, a major focus in the field of bone tissue engineering. However, limited insight into the spatiotemporal activation of signalling pathways has hampered the optimisation of in vivo bone formation and subsequent clinical translation. To gain further knowledge regarding the early molecular events governing bone tissue formation, we combined human periosteum derived progenitor cells with three types of clinically used CaP-scaffolds, to obtain constructs with a distinct range of bone forming capacity in vivo. Protein phosphorylation together with gene expression for key ligands and target genes were investigated 24 hours after cell seeding in vitro, and 3 and 12 days post ectopic implantation in nude mice. A computational modelling approach was used to deduce critical factors for bone formation 8 weeks post implantation. The combined Ca(2+)-mediated activation of BMP-, Wnt- and PKC signalling pathways 3 days post implantation were able to discriminate the bone forming from the non-bone forming constructs. Subsequently, a mathematical model able to predict in vivo bone formation with 96% accuracy was developed. This study illustrates the importance of defining and understanding CaP-activated signalling pathways that are required and sufficient for in vivo bone formation. Furthermore, we demonstrate the reliability of mathematical modelling as a tool to analyse and deduce key factors within an empirical data set and highlight its relevance to the translation of regenerative medicine strategies. [less ▲]Detailed reference viewed: 10 (0 ULg)
Combinatorial Analysis of Growth Factors Reveals the Contribution of Bone Morphogenetic Proteins to Chondrogenic Differentiation of Human Periosteal Cells.
; ; et al
in Tissue Engineering. Part C, Methods (2016), 22(5), 473-86
Successful application of cell-based strategies in cartilage and bone tissue engineering has been hampered by the lack of robust protocols to efficiently differentiate mesenchymal stem cells into the ... [more ▼]
Successful application of cell-based strategies in cartilage and bone tissue engineering has been hampered by the lack of robust protocols to efficiently differentiate mesenchymal stem cells into the chondrogenic lineage. The development of chemically defined culture media supplemented with growth factors (GFs) has been proposed as a way to overcome this limitation. In this work, we applied a fractional design of experiment (DoE) strategy to screen the effect of multiple GFs (BMP2, BMP6, GDF5, TGF-beta1, and FGF2) on chondrogenic differentiation of human periosteum-derived mesenchymal stem cells (hPDCs) in vitro. In a micromass culture (muMass) system, BMP2 had a positive effect on glycosaminoglycan deposition at day 7 (p < 0.001), which in combination with BMP6 synergistically enhanced cartilage-like tissue formation that displayed in vitro mineralization capacity at day 14 (p < 0.001). Gene expression of muMasses cultured for 7 days with a medium formulation supplemented with 100 ng/mL of BMP2 and BMP6 and a low concentration of GDF5, TGF-beta1, and FGF2 showed increased expression of Sox9 (1.7-fold) and the matrix molecules aggrecan (7-fold increase) and COL2A1 (40-fold increase) compared to nonstimulated control muMasses. The DoE analysis indicated that in GF combinations, BMP2 was the strongest effector for chondrogenic differentiation of hPDCs. When transplanted ectopically in nude mice, the in vitro-differentiated muMasses showed maintenance of the cartilaginous phenotype after 4 weeks in vivo. This study indicates the power of using the DoE approach for the creation of new medium formulations for skeletal tissue engineering approaches. [less ▲]Detailed reference viewed: 6 (0 ULg)
Coupling curvature-dependent and shear stress-stimulated neotissue growth in dynamic bioreactor cultures: a 3D computational model of a complete scaffold.
; ; et al
in Biomechanics & Modeling in Mechanobiology (2016), 15(1), 169-80
The main challenge in tissue engineering consists in understanding and controlling the growth process of in vitro cultured neotissues toward obtaining functional tissues. Computational models can provide ... [more ▼]
The main challenge in tissue engineering consists in understanding and controlling the growth process of in vitro cultured neotissues toward obtaining functional tissues. Computational models can provide crucial information on appropriate bioreactor and scaffold design but also on the bioprocess environment and culture conditions. In this study, the development of a 3D model using the level set method to capture the growth of a microporous neotissue domain in a dynamic culture environment (perfusion bioreactor) was pursued. In our model, neotissue growth velocity was influenced by scaffold geometry as well as by flow- induced shear stresses. The neotissue was modeled as a homogenous porous medium with a given permeability, and the Brinkman equation was used to calculate the flow profile in both neotissue and void space. Neotissue growth was modeled until the scaffold void volume was filled, thus capturing already established experimental observations, in particular the differences between scaffold filling under different flow regimes. This tool is envisaged as a scaffold shape and bioprocess optimization tool with predictive capacities. It will allow controlling fluid flow during long-term culture, whereby neotissue growth alters flow patterns, in order to provide shear stress profiles and magnitudes across the whole scaffold volume influencing, in turn, the neotissue growth. [less ▲]Detailed reference viewed: 5 (0 ULg)
Combining microCT-based characterization with empirical modelling as a robust screening approach for the design of optimized CaP-containing scaffolds for progenitor cell-mediated bone formation.
; ; et al
in Acta Biomaterialia (2016), 35
Biomaterials are a key ingredient to the success of bone tissue engineering (TE), which focuses on the healing of bone defects by combining scaffolds with cells and/or growth factors. Due to the widely ... [more ▼]
Biomaterials are a key ingredient to the success of bone tissue engineering (TE), which focuses on the healing of bone defects by combining scaffolds with cells and/or growth factors. Due to the widely variable material characteristics and patient-specificities, however, current bone TE strategies still suffer from low repeatability and lack of robustness, which hamper clinical translation. Hence, optimal TE construct (i.e. cells and scaffold) characteristics are still under debate. This study aimed to reduce the material-specific variability for cell-based construct design, avoiding trial-and-error, by combining microCT characterization and empirical modelling as an innovative and robust screening approach. Via microCT characterization we have built a quantitative construct library of morphological and compositional properties of six CE approved CaP-based scaffolds (CopiOs(R), BioOss, Integra Mozaik, chronOS Vivify, MBCP and ReproBone), and of their bone forming capacity and in vivo scaffold degradation when combined with human periosteal derived cells (hPDCs). The empirical model, based on the construct library, allowed identification of the construct characteristics driving optimized bone formation, i.e. (a) the percentage of beta-TCP and dibasic calcium phosphate, (b) the concavity of the CaP structure, (c) the average CaP structure thickness and (d) the seeded cell amount (taking into account the seeding efficiency). Additionally, the model allowed to quantitatively predict the bone forming response of different hPDC-CaP scaffold combinations, thus providing input for a more robust design of optimized constructs and avoiding trial-and error. This could improve and facilitate clinical translation. STATEMENT OF SIGNIFICANCE: Biomaterials that support regenerative processes are a key ingredient for successful bone tissue engineering (TE). However, the optimal scaffold structure is still under debate. In this study, we have provided a useful innovative approach for robust screening of potential biomaterials or constructs (i.e. scaffolds seeded with cells and/or growth factors) by combining microCT characterization with empirical modelling. This novel approach leads to a better insight in the scaffold parameters influencing progenitor cell-mediated bone formation. Additionally, it serves as input for more controlled and robust design of optimized CaP-containing bone TE scaffolds. Hence, this novel approach could improve and facilitate clinical translation. [less ▲]Detailed reference viewed: 17 (4 ULg)
In silico regenerative medicine: how computational tools allow regulatory and financial challenges to be addressed in a volatile market.
Geris, Liesbet ; ; et al
in Interface focus (2016), 6(2), 20150105
The cell therapy market is a highly volatile one, due to the use of disruptive technologies, the current economic situation and the small size of the market. In such a market, companies as well as ... [more ▼]
The cell therapy market is a highly volatile one, due to the use of disruptive technologies, the current economic situation and the small size of the market. In such a market, companies as well as academic research institutes are in need of tools to advance their understanding and, at the same time, reduce their R&D costs, increase product quality and productivity, and reduce the time to market. An additional difficulty is the regulatory path that needs to be followed, which is challenging in the case of cell-based therapeutic products and should rely on the implementation of quality by design (QbD) principles. In silico modelling is a tool that allows the above-mentioned challenges to be addressed in the field of regenerative medicine. This review discusses such in silico models and focuses more specifically on the bioprocess. Three (clusters of) examples related to this subject are discussed. The first example comes from the pharmaceutical engineering field where QbD principles and their implementation through the use of in silico models are both a regulatory and economic necessity. The second example is related to the production of red blood cells. The described in silico model is mainly used to investigate the manufacturing process of the cell-therapeutic product, and pays special attention to the economic viability of the process. Finally, we describe the set-up of a model capturing essential events in the development of a tissue-engineered combination product in the context of bone tissue engineering. For each of the examples, a short introduction to some economic aspects is given, followed by a description of the in silico tool or tools that have been developed to allow the implementation of QbD principles and optimal design. [less ▲]Detailed reference viewed: 6 (1 ULg)
A reduced model developed for describing neotissue growth during dynamic bioreactor culture
Mehrian, Mohammad ; ; Geris, Liesbet
Scientific conference (2015, November 26)Detailed reference viewed: 10 (5 ULg)
Uncertainty in biology: a computational modeling approach
Geris, Liesbet ;
Book published by Springer (2015)
Computational modeling of biomedical processes is gaining more and more weight in the current research into the etiology of biomedical problems and potential treatment strategies. Computational modeling ... [more ▼]
Computational modeling of biomedical processes is gaining more and more weight in the current research into the etiology of biomedical problems and potential treatment strategies. Computational modeling allows to reduce, refine and replace animal experimentation as well as to translate findings obtained in these experiments to the human background. However these biomedical problems are inherently complex with a myriad of influencing factors, which strongly complicates the model building and validation process. This book wants to address four main issues related to the building and validation of computational models of biomedical processes: 1. Modeling establishment under uncertainty 2. Model selection and parameter fitting 3. Sensitivity analysis and model adaptation 4. Model predictions under uncertainty In each of the abovementioned areas, the book discusses a number of key-techniques by means of a general theoretical description followed by one or more practical examples. This book is intended for graduate students and researchers active in the field of computational modeling of biomedical processes who seek to acquaint themselves with the different ways in which to study the parameter space of their model as well as its overall behavior. [less ▲]Detailed reference viewed: 65 (7 ULg)
A semiquantitative framework for gene regulatory networks: increasing the time and quantitative resolution of Boolean networks
Kerkhofs, Johan ; Geris, Liesbet
in PLoS ONE (2015), 10(6), 0130033
Boolean models have been instrumental in predicting general features of gene networks and more recently also as explorative tools in specific biological applications. In this study we introduce a basic ... [more ▼]
Boolean models have been instrumental in predicting general features of gene networks and more recently also as explorative tools in specific biological applications. In this study we introduce a basic quantitative and a limited time resolution to a discrete (Boolean) framework. Quantitative resolution is improved through the employ of normalized variables in unison with an additive approach. Increased time resolution stems from the introduction of two distinct priority classes. Through the implementation of a previously published chondrocyte network and T helper cell network, we show that this addition of quantitative and time resolution broadens the scope of biological behaviour that can be captured by the models. Specifically, the quantitative resolution readily allows models to discern qualitative differences in dosage response to growth factors. The limited time resolution, in turn, can influence the reachability of attractors, delineating the likely long term system behaviour. Importantly, the information required for implementation of these features, such as the nature of an interaction, is typically obtainable from the literature. Nonetheless, a trade-off is always present between additional computational cost of this approach and the likelihood of extending the model’s scope. Indeed, in some cases the inclusion of these features does not yield additional insight. This framework, incorporating increased and readily available time and semi-quantitative resolution, can help in substantiating the litmus test of dynamics for gene networks, firstly by excluding unlikely dynamics and secondly by refining falsifiable predictions on qualitative behaviour. [less ▲]Detailed reference viewed: 59 (4 ULg)
In silico screening to predict chondrocyte hypertrophy using a semiquantitative gene network model
Kerkhofs, Johan ; ; et al
Poster (2015, April 30)
PURPOSE: In development, chondrocyte hypertrophy is a crucial and well-studied step in endochondral ossification. Hypertrophy may also play a role in pathophysiological processes, including osteoarthritis ... [more ▼]
PURPOSE: In development, chondrocyte hypertrophy is a crucial and well-studied step in endochondral ossification. Hypertrophy may also play a role in pathophysiological processes, including osteoarthritis. We employ a computational approach to estimate the effect of individual factors in this complex process. METHODS: We have combined information gleaned from a high number of publications on chondrocyte differentiation into a gene regulatory network of 46 factors and over 150 interactions. This network can estimate the stability of proliferative chondrocytes/permanent cartilage (stable state with SOX9 activity) and hypertrophic chondrocytes (stable state with RUNX2 activity) by employing 2 measures. A first measure is a Monte Carlo analysis that assesses stability in the face of random initial conditions, the second modifies stable states to estimate the sensitivity to perturbation. RESULTS: For each factor, these qualitative measures are calculated in silico under knockout and overexpression conditions and compared to the wild type situation. This enables screening of the effects of all incorporated factors on cartilage homeostasis, differentiation and pathogenesis via the initiation of hypertrophy. Indeed, our gene network analysis indicated multiple candidate genes for the development of osteoarthritis. Factors that amplify the SOX9 attractor basin include TGFβ, PPR, IGF-I, and PKA. The presence of RAS, IHH, GLI2 and FGF is required for the Runx2 stable state. Using a literature study, we corroborated several of the proposed factors. CONCLUSIONS: In silico screening of overexpression and knockout presents a novel strategy to improve bone and cartilage tissue engineering approaches, and can be used to propose a list of putative therapeutic targets for e.g. osteoarthritis. [less ▲]Detailed reference viewed: 23 (2 ULg)
Computational modeling of bone fracture non-unions: four clinically relevant case studies.
; ; et al
in In Silico Cell and Tissue Science (2015), 2
The human skeleton has a remarkable regeneration capacity. Nevertheless, 5-10 % of the bone fractures fails to heal and develops into a non-union which is a challenging orthopedic complication requiring ... [more ▼]
The human skeleton has a remarkable regeneration capacity. Nevertheless, 5-10 % of the bone fractures fails to heal and develops into a non-union which is a challenging orthopedic complication requiring complex and expensive treatment. This review paper will discuss 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. Further research is required to corroborate the computational models in both animal and human settings and translate them from bench to bed side. [less ▲]Detailed reference viewed: 2 (0 ULg)
A mechano-regulatory model for bone healing predictions under the influence of ultrasound.
; ; et al
in Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference (2015), 2015
The bone healing process involves a sequence of cellular action and interaction, regulated by biochemical and mechanical signals. Experimental studies have shown that ultrasound accelerates bone ... [more ▼]
The bone healing process involves a sequence of cellular action and interaction, regulated by biochemical and mechanical signals. Experimental studies have shown that ultrasound accelerates bone solidification and enhances the underlying healing mechanisms. An integrated computational model is presented for deriving predictions of bone healing under the presence of ultrasound. [less ▲]Detailed reference viewed: 5 (0 ULg)
A Three-Dimensional Computational Fluid Dynamics Model Of Shear Stress Distribution During Neotissue Growth In A Perfusion Bioreactor.
Guyot, Yann ; ; et al
in Biotechnology and bioengineering (2015)
Bone tissue engineering strategies use flow through perfusion bioreactors to apply mechanical stimuli to cells seeded on porous scaffolds. Cells grow on the scaffold surface but also by bridging the ... [more ▼]
Bone tissue engineering strategies use flow through perfusion bioreactors to apply mechanical stimuli to cells seeded on porous scaffolds. Cells grow on the scaffold surface but also by bridging the scaffold pores leading a fully filled scaffold following the scaffold's geometric characteristics. Current computational fluid dynamic approaches for tissue engineering bioreactor systems have been mostly carried out for empty scaffolds. The effect of 3D cell growth and extracellular matrix formation (termed in this study as neotissue growth), on its surrounding fluid flow field is a challenge yet to be tackled. In this work a combined approach was followed linking curvature driven cell growth to fluid dynamics modeling. The level-set method (LSM) was employed to capture neotissue growth driven by curvature, while the Stokes and Darcy equations, combined in the Brinkman equation, provided information regarding the distribution of the shear stress profile at the neotissue/medium interface and within the neotissue itself during growth. The neotissue was assumed to be micro-porous allowing flow through its structure while at the same time allowing the simulation of complete scaffold filling without numerical convergence issues. The results show a significant difference in the amplitude of shear stress for cells located within the micro-porous neo-tissue or at the neotissue/medium interface, demonstrating the importance of taking along the neotissue in the calculation of the mechanical stimulation of cells during culture.The presented computational framework is used on different scaffold pore geometries demonstrating its potential to be used a design as tool for scaffold architecture taking into account the growing neotissue. This article is protected by copyright. All rights reserved. [less ▲]Detailed reference viewed: 53 (11 ULg)
Cell based advanced therapeutic medicinal products for bone repair: Keep it simple?
; ; et al
in Advanced drug delivery reviews (2015), 84
The development of cell based advanced therapeutic medicinal products (ATMPs) for bone repair has been expected to revolutionize the health care system for the clinical treatment of bone defects. Despite ... [more ▼]
The development of cell based advanced therapeutic medicinal products (ATMPs) for bone repair has been expected to revolutionize the health care system for the clinical treatment of bone defects. Despite this great promise, the clinical outcomes of the few cell based ATMPs that have been translated into clinical treatments have been far from impressive. In part, the clinical outcomes have been hampered because of the simplicity of the first wave of products. In response the field has set-out and amassed a plethora of complexities to alleviate the simplicity induced limitations. Many of these potential second wave products have remained "stuck" in the development pipeline. This is due to a number of reasons including the lack of a regulatory framework that has been evolving in the last years and the shortage of enabling technologies for industrial manufacturing to deal with these novel complexities. In this review, we reflect on the current ATMPs and give special attention to novel approaches that are able to provide complexity to ATMPs in a straightforward manner. Moreover, we discuss the potential tools able to produce or predict 'goldilocks' ATMPs, which are neither too simple nor too complex. [less ▲]Detailed reference viewed: 19 (2 ULg)
Computational modeling under uncertainty: challenges and opportunities
; Geris, Liesbet
in Modeling under uncertainty: a computational modeling approach (2015)
Computational Biology has increasingly become an important tool for biomedical and translational research. In particular, when generating novel hypothesis despite fundamental uncertainties in data and ... [more ▼]
Computational Biology has increasingly become an important tool for biomedical and translational research. In particular, when generating novel hypothesis despite fundamental uncertainties in data and mechanistic understanding of biological processes underpinning diseases. While in the present book, we have reviewed the necessary background and existing novel methodologies that set the basis for dealing with uncertainty, there are still many “grey”, or less well-defined, areas of investigations offering both challenges and opportunities. This final chapter in the book provides some reflections on those areas, namely: (1) the need for novel robust mathematical and statistical methodologies to generate hypothesis under uncertainty; (2) the challenge of aligning those methodologies in a context that requires larger computational resources; (3) the accessibility of modeling tools for less mathematical literate researchers; and (4) the integration of models with –omics data and its application in clinical environments. [less ▲]Detailed reference viewed: 41 (0 ULg)
An introduction to uncertainty in the development of computational models of biological processes
Geris, Liesbet ;
in Modeling under uncertainty: a computational modeling approach (2015)
This chapter aims to provide an introduction to the different ways in which uncertainty can be dealt with computational modelling of biological processes. The first step is model establishment under ... [more ▼]
This chapter aims to provide an introduction to the different ways in which uncertainty can be dealt with computational modelling of biological processes. The first step is model establishment under uncertainty. Once models have been established, data can further be used to select which of the proposed models best meets the predefined criteria. Subsequently, parameter values can be optimized for a specific model configuration. Sensitivity analyses allow to assess the influence of the previous choices on the model output. Additionally, model adaptation permits to focus on specific aspects of the model without losing its global predictive capacity. Finally, predictions with the established models should also consider the effect of uncertainty in the model development process. [less ▲]Detailed reference viewed: 20 (0 ULg)
Computational bone tissue engineering: from carriers and culture to clinics
Conference (2015)Detailed reference viewed: 20 (1 ULg)
Of models and men: recent advances in computational bone tissue engineering
Conference (2015)Detailed reference viewed: 19 (1 ULg)