A hybrid physics-based and data-driven framework for cellular biological systems: Application to the morphogenesis of organoids.

How cells orchestrate their cellular functions remains a crucial question to unravel how they organize in different patterns. We present a framework based on artificial intelligence to advance the understanding of how cell functions are coordinated spatially and temporally in biological systems. It consists of a hybrid physics-based model that integrates both mechanical interactions and cell functions with a data-driven model that regulates the cellular decision-making process through a deep learning algorithm trained on image data metrics. To illustrate our approach, we used data from 3D cultures of murine pancreatic ductal adenocarcinoma cells (PDAC) grown in Matrigel as tumor organoids. Our approach allowed us to find the underlying principles through which cells activate different cell processes to self-organize in different patterns according to the specific microenvironmental conditions. The framework proposed here expands the tools for simulating biological systems at the cellular level, providing a novel perspective to unravel morphogenetic patterns.

Tumour growth: An approach to calibrate parameters of a multiphase porous media model based on in vitro observations of Neuroblastoma spheroid growth in a hydrogel microenvironment.

To unravel processes that lead to the growth of solid tumours, it is necessary to link knowledge of cancer biology with the physical properties of the tumour and its interaction with the surrounding microenvironment. Our understanding of the underlying mechanisms is however still imprecise. We therefore developed computational physics-based models, which incorporate the interaction of the tumour with its surroundings based on the theory of porous media. However, the experimental validation of such models represents a challenge to its clinical use as a prognostic tool. This study combines a physics-based model with in vitro experiments based on microfluidic devices used to mimic a three-dimensional tumour microenvironment. By conducting a global sensitivity analysis, we identify the most influential input parameters and infer their posterior distribution based on Bayesian calibration. The resulting probability density is in agreement with the scattering of the experimental data and thus validates the proposed workflow. This study demonstrates the huge challenges associated with determining precise parameters with usually only limited data for such complex processes and models, but also demonstrates in general how to indirectly characterise the mechanical properties of neuroblastoma spheroids that cannot feasibly be measured experimentally.

A 3D multi-agent-based model for lumen morphogenesis: the role of the biophysical properties of the extracellular matrix.

The correct function of many organs depends on proper lumen morphogenesis, which requires the orchestration of both biological and mechanical aspects. However, how these factors coordinate is not yet fully understood. Here, we focus on the development of a mechanistic model for computationally simulating lumen morphogenesis. In particular, we consider the hydrostatic pressure generated by the cells' fluid secretion as the driving force and the density of the extracellular matrix as regulators of the process. For this purpose, we develop a 3D agent-based-model for lumen morphogenesis that includes cells' fluid secretion and the density of the extracellular matrix. Moreover, this computer-based model considers the variation in the biological behavior of cells in response to the mechanical forces that they sense. Then, we study the formation of the lumen under different-mechanical scenarios and conclude that an increase in the matrix density reduces the lumen volume and hinders lumen morphogenesis. Finally, we show that the model successfully predicts normal lumen morphogenesis when the matrix density is physiological and aberrant multilumen formation when the matrix density is excessive. Supplementary Information: The online version contains supplementary material available at 10.1007/s00366-022-01654-1.

A mechanistic protrusive-based model for 3D cell migration.

Cell migration is essential for a variety of biological processes, such as embryogenesis, wound healing, and the immune response. After more than a century of research-mainly on flat surfaces-, there are still many unknowns about cell motility. In particular, regarding how cells migrate within 3D matrices, which more accurately replicate in vivo conditions. We present a novel in silico model of 3D mesenchymal cell migration regulated by the chemical and mechanical profile of the surrounding environment. This in silico model considers cell's adhesive and nuclear phenotypes, the effects of the steric hindrance of the matrix, and cells ability to degradate the ECM. These factors are crucial when investigating the increasing difficulty that migrating cells find to squeeze their nuclei through dense matrices, which may act as physical barriers. Our results agree with previous in vitro observations where fibroblasts cultured in collagen-based hydrogels did not durotax toward regions with higher collagen concentrations. Instead, they exhibited an adurotactic behavior, following a more random trajectory. Overall, cell's migratory response in 3D domains depends on its phenotype, and the properties of the surrounding environment, that is, 3D cell motion is strongly dependent on the context.

Unravelling cell migration: defining movement from the cell surface.

Cell motility is essential for life and development. Unfortunately, cell migration is also linked to several pathological processes, such as cancer metastasis. Cells' ability to migrate relies on many actors. Cells change their migratory strategy based on their phenotype and the properties of the surrounding microenvironment. Cell migration is, therefore, an extremely complex phenomenon. Researchers have investigated cell motility for more than a century. Recent discoveries have uncovered some of the mysteries associated with the mechanisms involved in cell migration, such as intracellular signaling and cell mechanics. These findings involve different players, including transmembrane receptors, adhesive complexes, cytoskeletal components , the nucleus, and the extracellular matrix. This review aims to give a global overview of our current understanding of cell migration.

Time-dependent in silico modelling of orthognathic surgery to support the design of biodegradable bone plates.

Orthognathic surgery is performed to realign the jaws of a patient through several osteotomies. The state-of-the-art bone plates used to maintain the bone fragments in place are made of titanium. The presence of these non-degradable plates can have unwanted side effects on the long term (e.g. higher infection risk) if they are not removed. Using a biodegradable material such as magnesium may be a possible solution to this problem. However, biodegradation leads to a decrease of mechanical strength, therefore a time-dependent computational approach can help to evaluate the performance of such plates. In the present work, a computational framework has been developed to include biodegradation and bone healing algorithms in a finite element model. It includes bone plates and the mandible, which are submitted to masticatory loads during the early healing period (two months following the surgery). Two different bone plate designs with different stiffnesses have been tested. The stiff design exhibited good mechanical stability, with maximum Von Mises stress being less than 40% of the yield strength throughout the simulation. The flexible design shows high stresses when the bone healing has not started in the fracture gaps, indicating possible failure of the plate. However, this design leads to a higher bone healing quality after two months, as more cartilage is formed due to higher strains exerted in fracture gaps. We therefore conclude that in silico modelling can support tuning of the design parameters to ensure mechanical stability and while promoting bone healing.

Multiscale modeling of bone tissue mechanobiology.

Mechanical environment has a crucial role in our organism at the different levels, ranging from cells to tissues and our own organs. This regulatory role is especially relevant for bones, given their importance as load-transmitting elements that allow the movement of our body as well as the protection of vital organs from load impacts. Therefore bone, as living tissue, is continuously adapting its properties, shape and repairing itself, being the mechanical loads one of the main regulatory stimuli that modulate this adaptive behavior. Here we review some key results of bone mechanobiology from computational models, describing the effect that changes associated to the mechanical environment induce in bone response, implant design and scaffold-driven bone regeneration.

A new 3D finite element-based approach for computing cell surface tractions assuming nonlinear conditions.

Advances in methods for determining the forces exerted by cells while they migrate are essential for attempting to understand important pathological processes, such as cancer or angiogenesis, among others. Precise data from three-dimensional conditions are both difficult to obtain and manipulate. For this purpose, it is critical to develop workflows in which the experiments are closely linked to the subsequent computational postprocessing. The work presented here starts from a traction force microscopy (TFM) experiment carried out on microfluidic chips, and this experiment is automatically joined to an inverse problem solver that allows us to extract the traction forces exerted by the cell from the displacements of fluorescent beads embedded in the extracellular matrix (ECM). Therefore, both the reconstruction of the cell geometry and the recovery of the ECM displacements are used to generate the inputs for the resolution of the inverse problem. The inverse problem is solved iteratively by using the finite element method under the hypothesis of finite deformations and nonlinear material formulation. Finally, after mathematical postprocessing is performed, the traction forces on the surface of the cell in the undeformed configuration are obtained. Therefore, in this work, we demonstrate the robustness of our computational-based methodology by testing it under different conditions in an extreme theoretical load problem and then by applying it to a real case based on experimental results. In summary, we have developed a new procedure that adds value to existing methodologies for solving inverse problems in 3D, mainly by allowing for large deformations and not being restricted to any particular material formulation. In addition, it automatically bridges the gap between experimental images and mechanical computations.

Cell biophysical stimuli in lobopodium formation: a computer based approach.

Different cell migration modes have been identified in 3D environments, e.g., modes incorporating lamellopodia or blebs. Recently, a new type of cellular migration has been investigated: lobopodia-based migration, which appears only in three-dimensional matrices under certain conditions. The cell creates a protrusion through which the nucleus slips, dividing the cell into two parts (front and rear) with different hydrostatic pressures. In this work, we elucidate the mechanical conditions that favour this type of migration.One of the hypotheses about this type of migration is that it depends on the mechanical properties of the extracellular matrix. That is, lobopodia-based migration is dependent on whether the extracellular matrix is linearly elastic or non-linearly elastic.To determine whether the mechanical properties of the extracellular matrix are crucial in the choice of cell migration mode and which mechanotransduction mechanism the cell might use, we develop a finite element model. From our simulations, we identify two different possible mechanotransduction mechanisms that could regulate the cell to switch from a lobopodial to a lamellipodial migration mode. The first relies on a differential pressure increase inside the cytoplasm while the cell contracts, and the second relies on a change in the fluid flow direction in non-linearly elastic extracellular matrices but not in linearly elastic matrices. The biphasic nature of the cell has been determined to mediate this mechanism and the different behaviours of cells in linearly elastic and non-linearly elastic matrices.

The role of nuclear mechanics in cell deformation under creeping flows.

Despite the relevant regulatory role that nuclear deformation plays in cell behaviour, a thorough understanding of how fluid flow modulates the deformation of the cell nucleus in non-confined environments is lacking. In this work, we investigated the dynamics of cell deformation under different creeping flows as a general simulation tool for predicting nuclear stresses and strains. Using this solid-fluid modelling interaction framework, we assessed the stress and strain levels that the cell nucleus experiences as a function of different microenvironmental conditions, such as physical constraints, fluid flows, cytosol properties, and nucleus properties and size. Therefore, the simulation methodology proposed here allows the design of deformability-based experiments involving fluid flow, such as real-time deformability cytometry and dynamic cell culture in bioreactors or microfluidic devices.

An Evaluation of Surgical Functional Reconstruction of the Foot Using Kinetic and Kinematic Systems: A Case Report.

Most pedobarographic studies of microsurgical foot reconstruction have been retrospective. In the present study, we report the results from a prospective pedobarographic study of a patient after microsurgical reconstruction of her foot with a latissimus dorsi flap and a cutaneous paddle, with a 42-month follow-up period. We describe the foot reconstruction plan and the pedobarographic measurements and analyzed its functional outcome. The goal of the present study was to demonstrate that pedobarography could have a role in the treatment of foot reconstruction from a quantitative perspective. The pedobarographic measurements were recorded after the initial coverage surgery and 2 subsequent foot remodeling procedures. A total of 4 pedobarographic measurements and 2 gait analyses were recorded and compared for both the noninvolved foot and the injured foot. Furthermore, the progress of the reconstructed foot was critically evaluated using this method. Both static and dynamic patterns were compared at subsequent follow-up visits after the foot reconstruction. The values and progression of the foot shape, peak foot pressure (kPa), average foot pressure (kPa), total contact surface (cm2), loading time (%), and step time (ms) were recorded. Initially, the pressure distribution of the reconstructed foot showed higher peak values at nonanatomic locations, revealing a greater ulceration risk. Over time, we found an improvement in the shape and values of these factors in the involved foot. To homogenize the pressure distribution and correct the imbalance between the 2 feet, patient-specific insoles were designed and fabricated. In our patient, pedobarography provided an objective, repeatable, and recordable method for the evaluation of the reconstructed foot. Pedobarography can therefore provide valuable insights into the prevention of pressure ulcers and optimization of rehabilitation.

In silico Mechano-Chemical Model of Bone Healing for the Regeneration of Critical Defects: The Effect of BMP-2.

The healing of bone defects is a challenge for both tissue engineering and modern orthopaedics. This problem has been addressed through the study of scaffold constructs combined with mechanoregulatory theories, disregarding the influence of chemical factors and their respective delivery devices. Of the chemical factors involved in the bone healing process, bone morphogenetic protein-2 (BMP-2) has been identified as one of the most powerful osteoinductive proteins. The aim of this work is to develop and validate a mechano-chemical regulatory model to study the effect of BMP-2 on the healing of large bone defects in silico. We first collected a range of quantitative experimental data from the literature concerning the effects of BMP-2 on cellular activity, specifically proliferation, migration, differentiation, maturation and extracellular matrix production. These data were then used to define a model governed by mechano-chemical stimuli to simulate the healing of large bone defects under the following conditions: natural healing, an empty hydrogel implanted in the defect and a hydrogel soaked with BMP-2 implanted in the defect. For the latter condition, successful defect healing was predicted, in agreement with previous in vivo experiments. Further in vivo comparisons showed the potential of the model, which accurately predicted bone tissue formation during healing, bone tissue distribution across the defect and the quantity of bone inside the defect. The proposed mechano-chemical model also estimated the effect of BMP-2 on cells and the evolution of healing in large bone defects. This novel in silico tool provides valuable insight for bone tissue regeneration strategies.

Is the callus shape an optimal response to a mechanobiological stimulus?

After bone trauma, the natural response to restore bone function is the formation of a callus around the fracture. Although several bone healing models have been developed, none have effectively perceived early callus formation and shape as the result of an optimal response to a mechanobiological stimulus. In this paper, we investigate which stimulus regulates early callus formation. An optimal design problem is formulated, and several objective functions are defined, each using a different mechanobiological stimulus. The following stimuli were analysed: the interfragmentary strain, the second invariant of the deviatoric strain tensor and a generic inflammatory factor. Different regions for callus formation were also evaluated, such as the gap region, the periosteum and the periosteum border. Each stimulus was computed using the finite element method, and the callus shape was optimised using the steepest descent method. The results demonstrated that the inflammatory factor approach, the interfragmentary strain and the second invariant of the deviatoric strain tensor over the inner gap provided the best results when compared with histological callus shapes. Therefore, this work suggests that callus growth can be an optimal mechanobiological response to either local mechanical instability and/or local inflammatory reaction.

A cell-regulatory mechanism involving feedback between contraction and tissue formation guides wound healing progression.

Wound healing is a process driven by cells. The ability of cells to sense mechanical stimuli from the extracellular matrix that surrounds them is used to regulate the forces that cells exert on the tissue. Stresses exerted by cells play a central role in wound contraction and have been broadly modelled. Traditionally, these stresses are assumed to be dependent on variables such as the extracellular matrix and cell or collagen densities. However, we postulate that cells are able to regulate the healing process through a mechanosensing mechanism regulated by the contraction that they exert. We propose that cells adjust the contraction level to determine the tissue functions regulating all main activities, such as proliferation, differentiation and matrix production. Hence, a closed-regulatory feedback loop is proposed between contraction and tissue formation. The model consists of a system of partial differential equations that simulates the evolution of fibroblasts, myofibroblasts, collagen and a generic growth factor, as well as the deformation of the extracellular matrix. This model is able to predict the wound healing outcome without requiring the addition of phenomenological laws to describe the time-dependent contraction evolution. We have reproduced two in vivo experiments to evaluate the predictive capacity of the model, and we conclude that there is feedback between the level of cell contraction and the tissue regenerated in the wound.

Influence of high-frequency cyclical stimulation on the bone fracture-healing process: mathematical and experimental models.

Mechanical stimulation affects the evolution of healthy and fractured bone. However, the effect of applying cyclical mechanical stimuli on bone healing has not yet been fully clarified. The aim of the present study was to determine the influence of a high-frequency and low-magnitude cyclical displacement of the fractured fragments on the bone-healing process. This subject is studied experimentally and computationally for a sheep long bone. On the one hand, the mathematical computational study indicates that mechanical stimulation at high frequencies can stimulate and accelerate the process of chondrogenesis and endochondral ossification and consequently the bony union of the fracture. This is probably achieved by the interstitial fluid flow, which can move nutrients and waste from one place to another in the callus. This movement of fluid modifies the mechanical stimulus on the cells attached to the extracellular matrix. On the other hand, the experimental study was carried out using two sheep groups. In the first group, static fixators were implanted, while, in the second one, identical devices were used, but with an additional vibrator. This vibrator allowed a cyclic displacement with low magnitude and high frequency (LMHF) to be applied to the fractured zone every day; the frequency of stimulation was chosen from mechano-biological model predictions. Analysing the results obtained for the control and stimulated groups, we observed improvements in the bone-healing process in the stimulated group. Therefore, in this study, we show the potential of computer mechano-biological models to guide and define better mechanical conditions for experiments in order to improve bone fracture healing. In fact, both experimental and computational studies indicated improvements in the healing process in the LMHF mechanically stimulated fractures. In both studies, these improvements could be associated with the promotion of endochondral ossification and an increase in the rate of cell proliferation and tissue synthesis.

ANÁLISIS BIOMECÁNICO DE LA EPIFISIOLISIS DE LA CABEZA FEMORAL: COMPARACIÓN ENTRE FÉMURES SANOS Y ENFERMOS

En este trabajo se desarrolla un análisis por elementos finitos cuyo objetivo principal es determinar las diferencias de tensiones en la placa de crecimiento que se producen entre fémures sanos, con epifisiolisis unilateral y con epifisiolisis bilateral, para evaluar sus posibles causas. Se elaboraron los modelos de elementos finitos correspondientes a 45 pacientes. Los resultados mostraron un patrón de esfuerzos similar en todos los grupos de fémures y, además, la aparición de tensiones mayores en el grupo con epifisiolisis con respecto al grupo control. Se observó también que el valor del ángulo axial-fisis dependía significativamente del tipo de fémur analizado, y, además, una mayor influencia de los factores geométricos en la incidencia de la enfermedad, en comparación con la del índice de masa corporal.

In this work, a finite element analysis (FEA) is accomplished to study the differences of stresses in the growth plate, that are produced in healthy and unhealthy femurs, and to evaluate the possible causes of this illness. Finite element models of 45 patients were developed. The results demonstrated a similar pattern of stresses in all the groups of femurs and also the appearance of greater stresses in the group with slipped capital femoral epiphysis than in the control group. It was also observed a strong dependency on the value of the axial-fisis angle from the group of femur analyzed and a bigger influence of the geometric factors than of the body mass index, in the incidence of the illness.

Computational comparison of reamed versus unreamed intramedullary tibial nails.

We compared, via a computational model, the biomechanical performance of reamed versus unreamed intramedullary tibial nails to treat fractures in three different locations: proximal, mid-diaphyseal, and distal. Two finite element models were analyzed for the two nail types and the three kinds of fractures. Several biomechanical variables were determined: interfragmentary strains in the fracture site, von Mises stresses in nails and bolts, and strain distributions in the tibia and fibula. Although good mechanical stabilization was achieved in all the simulated fractures, the best results were obtained in the proximal fracture for the unreamed nail and in the mid-diaphyseal and distal fractures for the reamed nail. The interlocking bolts, in general, were subjected to higher stresses in the unreamed tibial nail than in the reamed one; thus the former stabilization technique is more likely to fail due to fatigue.