References of "Geris, Liesbet"
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See detailProtein synthesis at the speed of codons
Joiret, Marc ULiege; Geris, Liesbet ULiege; Close, Pierre ULiege

Speech/Talk (2020)

Introduction to open boundaries transport model on a 1D lattice and presentation of the totally asymmetric simple exclusion process and its application to protein synthesis modeling.

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See detailIn silico tools predict effects of drugs on bone remodelling.
Geris, Liesbet ULiege

in Nature Reviews Rheumatology (2020)

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See detailDevelopmentally Engineered Callus Organoid Bioassemblies Exhibit Predictive In Vivo Long Bone Healing.
Nilsson Hall, Gabriella; Mendes, Luís Freitas; Gklava, Charikleia et al

in Advanced science (2020), 7(2), 1902295

Clinical translation of cell-based products is hampered by their limited predictive in vivo performance. To overcome this hurdle, engineering strategies advocate to fabricate tissue products through ... [more ▼]

Clinical translation of cell-based products is hampered by their limited predictive in vivo performance. To overcome this hurdle, engineering strategies advocate to fabricate tissue products through processes that mimic development and regeneration, a strategy applicable for the healing of large bone defects, an unmet medical need. Natural fracture healing occurs through the formation of a cartilage intermediate, termed "soft callus," which is transformed into bone following a process that recapitulates developmental events. The main contributors to the soft callus are cells derived from the periosteum, containing potent skeletal stem cells. Herein, cells derived from human periosteum are used for the scalable production of microspheroids that are differentiated into callus organoids. The organoids attain autonomy and exhibit the capacity to form ectopic bone microorgans in vivo. This potency is linked to specific gene signatures mimicking those found in developing and healing long bones. Furthermore, callus organoids spontaneously bioassemble in vitro into large engineered tissues able to heal murine critical-sized long bone defects. The regenerated bone exhibits similar morphological properties to those of native tibia. These callus organoids can be viewed as a living "bio-ink" allowing bottom-up manufacturing of multimodular tissues with complex geometric features and inbuilt quality attributes. [less ▲]

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See detailComputational Modeling of Human Mesenchymal Stromal Cell Proliferation and Extra-Cellular Matrix Production in 3D Porous Scaffolds in a Perfusion Bioreactor: The Effect of Growth Factors.
Mehrian, Mohammad; Lambrechts, Toon; Papantoniou, Ioannis et al

in Frontiers in bioengineering and biotechnology (2020), 8

Stem cell expansion on 3D porous scaffolds cultured in bioreactor systems has been shown to be beneficial for maintenance of the original cell functionality in tissue engineering strategies (TE). However ... [more ▼]

Stem cell expansion on 3D porous scaffolds cultured in bioreactor systems has been shown to be beneficial for maintenance of the original cell functionality in tissue engineering strategies (TE). However, the production of extracellular matrix (ECM) makes harvesting the progenitor cell population from 3D scaffolds a challenge. Medium composition plays a role in stimulating cell proliferation over extracellular matrix (ECM) production. In this regard, a computational model describing tissue growth inside 3D scaffolds can be a great tool in designing optimal experimental conditions. In this study, a computational model describing cell and ECM growth in a perfusion bioreactor is developed, including a description of the effect of a (generic) growth factor on the biological processes taking place inside the 3D scaffold. In the model, the speed of cell and ECM growth depends on the flow-induced shear stress, curvature and the concentrations of oxygen, glucose, lactate, and growth factor. The effect of the simulated growth factor is to differentially enhance cell proliferation over ECM production. After model calibration with historic in-house data, a multi-objective optimization procedure is executed aiming to minimize the total experimental cost whilst maximizing cell growth during culture. The obtained results indicate there are multiple optimum points for the medium refreshment regime and the initial growth factor concentration where a trade-off is made between the final amount of cells and the culture cost. Finally, the model is applied to experiments reported in the literature studying the effects of perfusion-based cell culture and/or growth factor supplementation on cell expansion. The qualitative similarities between the simulation and experimental results, even in the absence of proper model calibration, reinforces the generic character of the proposed modeling framework. The model proposed in this study can contribute to the cost efficient production of cell-based TE products, ultimately contributing to their affordability and accessibility. [less ▲]

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See detailUse of Computational Modeling to Study Joint Degeneration: A Review.
Mukherjee, Satanik; Nazemi, Majid; Jonkers, Ilse et al

in Frontiers in bioengineering and biotechnology (2020), 8

Osteoarthritis (OA), a degenerative joint disease, is the most common chronic condition of the joints, which cannot be prevented effectively. Computational modeling of joint degradation allows to estimate ... [more ▼]

Osteoarthritis (OA), a degenerative joint disease, is the most common chronic condition of the joints, which cannot be prevented effectively. Computational modeling of joint degradation allows to estimate the patient-specific progression of OA, which can aid clinicians to estimate the most suitable time window for surgical intervention in osteoarthritic patients. This paper gives an overview of the different approaches used to model different aspects of joint degeneration, thereby focusing mostly on the knee joint. The paper starts by discussing how OA affects the different components of the joint and how these are accounted for in the models. Subsequently, it discusses the different modeling approaches that can be used to answer questions related to OA etiology, progression and treatment. These models are ordered based on their underlying assumptions and technologies: musculoskeletal models, Finite Element models, (gene) regulatory models, multiscale models and data-driven models (artificial intelligence/machine learning). Finally, it is concluded that in the future, efforts should be made to integrate the different modeling techniques into a more robust computational framework that should not only be efficient to predict OA progression but also easily allow a patient's individualized risk assessment as screening tool for use in clinical practice. [less ▲]

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See detailOptimizing neotissue growth inside perfusion bioreactors with respect to culture and labor cost: a multi-objective optimization study using evolutionary algorithms.
Mehrian, Mohammad; Geris, Liesbet ULiege

in Computer methods in biomechanics and biomedical engineering (2020), 23(7), 285-294

Tissue engineering is a fast progressing domain where solutions are provided for organ failure or tissue damage. In this domain, computer models can facilitate the design of optimal production process ... [more ▼]

Tissue engineering is a fast progressing domain where solutions are provided for organ failure or tissue damage. In this domain, computer models can facilitate the design of optimal production process conditions leading to robust and economically viable products. In this study, we use a previously published computationally efficient model, describing the neotissue growth (cells + their extracellular matrix) inside 3D scaffolds in a perfusion bioreactor. In order to find the most cost-effective medium refreshment strategy for the bioreactor culture, a multi-objective optimization strategy was developed aimed at maximizing the neotissue growth while minimizing the total cost of the experiment. Four evolutionary optimization algorithms (NSGAII, MOPSO, MOEA/D and GDEIII) were applied to the problem and the Pareto frontier was computed in all methods. All algorithms led to a similar outcome, albeit with different convergence speeds. The simulation results indicated that, given the actual cost of the labor compared to the medium cost, the most cost-efficient way of refreshing the medium was obtained by minimizing the refreshment frequency and maximizing the refreshment amount. [less ▲]

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See detailPredicting in vitro human mesenchymal stromal cell expansion based on individual donor characteristics using machine learning.
Mehrian, Mohammad; Lambrechts, Toon; Marechal, Marina et al

in Cytotherapy (2020), 22(2), 82-90

BACKGROUND: Human mesenchymal stromal cells (hMSCs) have become attractive candidates for advanced medical cell-based therapies. An in vitro expansion step is routinely used to reach the required clinical ... [more ▼]

BACKGROUND: Human mesenchymal stromal cells (hMSCs) have become attractive candidates for advanced medical cell-based therapies. An in vitro expansion step is routinely used to reach the required clinical quantities. However, this is influenced by many variables including donor characteristics, such as age and gender, and culture conditions, such as cell seeding density and available culture surface area. Computational modeling in general and machine learning in particular could play a significant role in deciphering the relationship between the individual donor characteristics and their growth dynamics. METHODS: In this study, hMSCs obtained from 174 male and female donors, between 3 and 64 years of age with passage numbers ranging from 2 to 27, were studied. We applied a Random Forests (RF) technique to model the cell expansion procedure by predicting the population doubling time (PDT) for each passage, taking into account individual donor-related characteristics. RESULTS: Using the RF model, the mean absolute error between model predictions and experimental results for the PDT in passage 1 to 4 is significantly lower compared with the errors obtained with theoretical estimates or historical data. Moreover, statistical analysis indicate that the PD and PDT in different age categories are significantly different, especially in the youngest group (younger than 10 years of age) compared with the other age groups. DISCUSSION: In summary, we introduce a predictive computational model describing in vitro cell expansion dynamics based on individual donor characteristics, an approach that could greatly assist toward automation of a cell expansion culture process. [less ▲]

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See detailOptimising 3D bioprinter nozzle design through in silico modelling
Mandal, Sourav ULiege; Reina-Romo, Esther; Steenvoort, Nina Van et al

Poster (2019, November 15)

3D bioprinting is a flourishing technology, in addressing tissue-engineering construct manufacturing related challenges. However, the realization of the potential of this developing technique is hindered ... [more ▼]

3D bioprinting is a flourishing technology, in addressing tissue-engineering construct manufacturing related challenges. However, the realization of the potential of this developing technique is hindered by multiple technical hurdles which restrict the printability and cell survivability. In addition, commonly employed experimental trial and error approaches are time consuming and resource intensive, especially when a new material needs to be printed. To address these issues, computational or in silico modelling of specific parts of the system can be a viable option to optimize the relevant design as well as the printing and material parameters. Shear stress is proven to be a crucial factor for cell survivability in extrusion-based 3D bioprinting. Here, we sought to provide the appropriate choice for nozzle design in order to minimize the maximum shear stress occurring in the nozzle during bioprinting. We have modelled three widely used natural and synthetic shear-thinning hydrogel materials, namely alginate, alginate-gelatine and pluronic F127 (PF127) in two different nozzle configurations (conical and blunted). The model started with varying all the design parameters in the range relevant to practical application, using space-filling latin hypercube sampling (LHS) and running computational fluid dynamics (CFD) models to obtain flow profile and shear stress responses for each design. The outcomes from 1200 different in silico tested combinations are fitted into a machine learning method, known as Gaussian process to obtain the response of individual design parameters on the maximum shear stress generated in the hydrogel. It is found that the lower nozzle length and nozzle exit radius are the most important parameters for blunted nozzle designs whereas for conical designs middle and exit radii of the nozzle are crucial factors influencing shear stress. In addition, shear-thinning material properties were also shown to have important effects. In summary, we demonstrate the efficacy of CFD and ML based in silico modelling as a feasible pathway to overcome costly experimental trial and errors. This will help in optimising printing parameters, quantification and cost reduction for the development of new bio-printable materials. [less ▲]

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See detailmRNA translation rate modeling with an extended TASEP incorporating tRNAs modifications
Joiret, Marc ULiege; Rapino, Francesca ULiege; Close, Pierre ULiege et al

Poster (2019, September 05)

Translational regulation through synonymous codon usage has been recently shown to play an important role in health and disease. Modified tRNAs are important actors involved in regulating protein ... [more ▼]

Translational regulation through synonymous codon usage has been recently shown to play an important role in health and disease. Modified tRNAs are important actors involved in regulating protein expression levels by optimizing the decoding of differentially used codons, nevertheless their contribution in protein synthesis dynamics remain unclear. Totally Asymmetric Simple Exclusion Process (TASEP) models have been used to quantify the transcripts translation rate by ribosomes. Our work aims at extending TASEP modeling to accommodate for tRNA modifications effects. We generated a computational stochastic model quantifying protein synthesis rates. The algorithm uses ribosome residence time per codon from transcripts codons sequences, relative transcripts abundance and tables of (modified or not) tRNA relative abundance. Important features in the model include the elongation rate variation caused by charged amino-acids in the ribosomal exit tunnel, proline ring opening delay at the peptide transfer center and optionally transcript secondary structure slow down effects. The model allows to compare relative protein expression levels as well as RiboSeq profiles in different scenarios with a controllable pool of ribosomes. We intend to use our model to help understand how codon usage and tRNA modifications dynamically interact and impact on protein synthesis. [less ▲]

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See detailComputational Modeling of a Growing Fetal Long Bone
Nazemi, Sayed Majid ULiege; Geris, Liesbet ULiege

Conference (2019)

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See detailDigital twins in tissue engineering: from bench to bedside via the computer.
Geris, Liesbet ULiege

in Abstract book of CMBBE2019 (2019)

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See detailUncoupling of in-vitro identity of embryonic limb derived skeletal progenitors and their in-vivo bone forming potential
Verbeeck, L.; Geris, Liesbet ULiege; Tylzanowski, P. et al

in Scientific Reports (2019), 9(1),

The healing of large bone defects remains a major unmet medical need. Our developmental engineering approach consists of the in vitro manufacturing of a living cartilage tissue construct that upon ... [more ▼]

The healing of large bone defects remains a major unmet medical need. Our developmental engineering approach consists of the in vitro manufacturing of a living cartilage tissue construct that upon implantation forms bone by recapitulating an endochondral ossification process. Key to this strategy is the identification of the cells to produce such cartilage intermediates efficiently. We applied a cell selection strategy based on published skeletal stem cell markers using mouse embryonic limb cartilage as cell source and analysed their potential to form bone in an in vivo ectopic assay. FGF2 supplementation to the culture media for expansion blocked dedifferentiation of the embryonic cartilage cells in culture and enriched for stem cells and progenitors as quantified using the recently published CD marker set. However, when the stem cells and progenitors were fractionated from expanded embryonic cartilage cells and assessed in the ectopic assay, a major loss of bone forming potential was observed. We conclude that cell expansion appears to affect the association between cell identity based on CD markers and in vivo bone forming capacity. © 2019, The Author(s). [less ▲]

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See detailThe Third Era of Tissue Engineering: Reversing the Innovation Drivers.
Geris, Liesbet ULiege; Papantoniou, Ioannis

in Tissue engineering. Part A (2019), 25(11-12), 821-826

IMPACT STATEMENT: From this perspective, we discuss the different stages of development the tissue engineering (TE) field has gone through in its relatively young history. We discuss how TE is evolving ... [more ▼]

IMPACT STATEMENT: From this perspective, we discuss the different stages of development the tissue engineering (TE) field has gone through in its relatively young history. We discuss how TE is evolving from a technology-driven, science-focused field toward a patient-driven, manufacturing-focused one where patients' needs are translated into production process requirements, and subsequently into technological and biological innovations needed to meet the regulatory and clinical demands. [less ▲]

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See detailNeurofibromatosis type 1-related pseudarthrosis: Beyond the pseudarthrosis site.
Brekelmans, Carlijn; Hollants, Silke; De Groote, Caroline et al

in Human Mutation (2019)

Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder affecting approximately 1 in 2,000 newborns. Up to 5% of NF1 patients suffer from pseudarthrosis of a long bone (NF1-PA). Current ... [more ▼]

Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder affecting approximately 1 in 2,000 newborns. Up to 5% of NF1 patients suffer from pseudarthrosis of a long bone (NF1-PA). Current treatments are often unsatisfactory, potentially leading to amputation. To gain more insight into the pathogenesis we cultured cells from PA tissue and normal-appearing periosteum of the affected bone for NF1 mutation analysis. PA cells were available from 13 individuals with NF1. Biallelic NF1 inactivation was identified in all investigated PA cells obtained during the first surgery. Three of five cases sampled during a later intervention showed biallelic NF1 inactivation. Also, in three individuals, we examined periosteum-derived cells from normal-appearing periosteum proximal and distal to the PA. We identified the same biallelic NF1 inactivation in the periosteal cells outside the PA region. These results indicate that NF1 inactivation is required but not sufficient for the development of NF1-PA. We observed that late-onset NF1-PA occurs and is not always preceded by congenital bowing. Furthermore, the failure to identify biallelic inactivation in two of five later interventions and one reintervention with a known somatic mutation indicates that NF1-PA can persist after the removal of most NF1 negative cells. [less ▲]

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See detailTowards Self-Regulated Bioprocessing: A Compact Benchtop Bioreactor System for Monitored and Controlled 3D Cell and Tissue Culture.
de Bournonville, Sebastien; Lambrechts, Toon; Vanhulst, Johan et al

in Biotechnology Journal (2019)

Bioreactors are crucial tools for the manufacturing of living cell-based tissue engineered products. However, to reach the market successfully, higher degrees of automation, as well as a decreased ... [more ▼]

Bioreactors are crucial tools for the manufacturing of living cell-based tissue engineered products. However, to reach the market successfully, higher degrees of automation, as well as a decreased footprint still need to be reached. In this study, the use of a benchtop bioreactor for in vitro perfusion culture of scaffold-based tissue engineering constructs is assessed. A low-footprint benchtop bioreactor system is designed, comprising a single-use fluidic components and a bioreactor housing. The bioreactor is operated using an in-house developed program and the culture environment is monitored by specifically designed sensor ports. A gas-exchange module is incorporated allowing for heat and mass transfers. Titanium-based scaffolds are seeded with human periosteum-derived cells and cultured up to 3 weeks. The benchtop bioreactor constructs are compared to benchmark perfusion systems. Live/Dead stainings, DNA quantifications, glucose consumption, and lactate production assays confirm that the constructs cultured in the benchtop bioreactor grew similarly to the benchmark systems. Manual regulation of the system set points enabled efficient alteration of the culture environment in terms of temperature, pH, and dissolved oxygen. This study provides the necessary basis for the development of low-footprint, automated, benchtop perfusion bioreactors and enables the implementation of active environment control. [less ▲]

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See detailHuman Platelet Lysate Improves Bone Forming Potential of Human Progenitor Cells Expanded in Microcarrier-Based Dynamic Culture.
Gupta, Priyanka; Hall, Gabriella Nilsson; Geris, Liesbet ULiege et al

in Stem Cells Translational Medicine (2019)

Xenogeneic-free media are required for translating advanced therapeutic medicinal products to the clinics. In addition, process efficiency is crucial for ensuring cost efficiency, especially when ... [more ▼]

Xenogeneic-free media are required for translating advanced therapeutic medicinal products to the clinics. In addition, process efficiency is crucial for ensuring cost efficiency, especially when considering large-scale production of mesenchymal stem cells (MSCs). Human platelet lysate (HPL) has been increasingly adopted as an alternative for fetal bovine serum (FBS) for MSCs. However, its therapeutic and regenerative potential in vivo is largely unexplored. Herein, we compare the effects of FBS and HPL supplementation for a scalable, microcarrier-based dynamic expansion of human periosteum-derived cells (hPDCs) while assessing their bone forming capacity by subcutaneous implantation in small animal model. We observed that HPL resulted in faster cell proliferation with a total fold increase of 5.2 +/- 0.61 in comparison to 2.7 +/- 02.22-fold in FBS. Cell viability and trilineage differentiation capability were maintained by HPL, although a suppression of adipogenic differentiation potential was observed. Differences in mRNA expression profiles were also observed between the two on several markers. When implanted, we observed a significant difference between the bone forming capacity of cells expanded in FBS and HPL, with HPL supplementation resulting in almost three times more mineralized tissue within calcium phosphate scaffolds. FBS-expanded cells resulted in a fibrous tissue structure, whereas HPL resulted in mineralized tissue formation, which can be classified as newly formed bone, verified by muCT and histological analysis. We also observed the presence of blood vessels in our explants. In conclusion, we suggest that replacing FBS with HPL in bioreactor-based expansion of hPDCs is an optimal solution that increases expansion efficiency along with promoting bone forming capacity of these cells. Stem Cells Translational Medicine 2019. [less ▲]

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