Section: Application Domains
Applicative axis 2: Growth, evolution and regeneration in populations and tissues
Luis Almeida, Pierre-Alexandre Bliman, Marie Doumic, Dirk Drasdo, Benoît Perthame, Diane Peurichard, Nastassia Pouradier Duteil, Philippe Robert
The applications in this category span very different subjects from amyloid diseases, dengue fever, wound healing, liver regeneration and toxicity, up to bacterial growth and development of organisms. As the applications, the methods span a wide range. Those concerning identification of models and parameters with regard to data have partially been outlined in axis 3. Focus in this axis is on the model contribution to the biologically and/or medically relevant insights and aspects.
Liver-related modelling is partially performed within the Inria team MIMESIS (Strasbourg) with the focus on real-time, patient-specific biomechanical liver models to guide surgery and surgeons. Internationally, spatial temporal liver related models are developed in Fraunhofer MEVIS (Bremen), by T. Ricken (TU Dortmund), and P. Segers group (Leuven).
Different from these, Mamba has a strong focus on spatial-temporal modeling on the histological scale, integration of molecular processes in each individual cell, and single-cell (agent) based models . Works by Schliess ,  have been highlighted in editorials.
Mathematical modeling of protein aggregation is a relatively recent domain, only a few other groups have emerged yet; among them we can cite the Inria team Dracula, with whom we are in close contact, and e.g., the work by Jean-Michel Coron (Sorbonne Université) and Monique Chyba (Hawaii, USA) in control, and Suzanne Sindi (USA) for the modeling of the yeast prion. We have interactions with all these groups and organized a workshop in June 2017, gathering both the biophysics and applied mathematics communities.
Application to protein aggregation in amyloid diseases is a long-standing interest of Mamba, dating back to 2010 , and developed through the collaboration with Human Rezaei's team at Inra. More recently, with Wei-Feng Xue in Canterbury, we investigated the intrinsic variability among identical experiments of nucleation , , Sarah Eugène's Ph.D subject (co-supervised by Philippe Robert) .
In collaboration with Tom Banks first ,  and then Philippe Moireau, we developed quantitative comparisons between model and data. Through data assimilation and statistical methods , we proposed new models and mechanisms.
Biological control of arboviroses
Sterile Insect Technique (SIT)  is a biological control method relying on massive releases of sterile male insects into the wild. The latter compete with wild males to mate with the females, and induce no offspring to the latter, thus reducing the next generation's population. This can result in a progressive reduction, or even disparition, of the target population.
A related technique is based on the infection by Wolbachia . This symbiotic bacterium is maternally transmitted from infected females to their offspring, but induces cytoplasmic incompatibility , : mating between infected males and uninfected females gives no offspring. Releases of Wolbachia infected males alone is thus comparable to classical SIT.
On the other hand, releasing both infected males and females in sufficient quantity may result in infection of the wild population. This gives rise to an interesting new control principle, as Wolbachia has been shown to severely reduce the insect vectorial ability to transmit dengue, zika or chikungunya, indirectly by lifespan and fertility reduction, and directly by reducing the ability of the viruses to proliferate within the organism .
We proposed new insights on the practical and theoretical issues raised by the implementation of the previous methods. Concerning the SIT, we obtained control synthesis results through impulsive periodic release of controlled amplitude , and through optimal control approach . Concerning Wolbachia technique, we investigated general control principles  capable of spreading the infection.
Wound healing 1: epithelial tissues
We studied cell motion in epithelial gap closure, a form of collective cell migration that is a very widespread phenomenon both during development and adult life - it is essential for both the formation and for the maintenance of epithelial layers. Due to their importance, in vivo wound healing and morphogenetic movements involving closure of holes in epithelia have been the object of many studies. In our works (ravasio:hal-01245750, vedula:hal-01298859) we considered wound healing and epithelial gap closure in both in vivo (in particular drosophila pupa) and in vitro (MDCK cell and human keratinocytes). We found some similarities in the geometry dependence of the wound closure strategies between these two situations, indicating the existence of conserved mechanisms that should be widespread across living beings. We are concentrating on the study of actin cable formation.
Wound healing 2: adipose tissues
After injury, if regeneration can be observed in hydra, planaria and some vertebrates, regeneration is rare in mammals and particularly in humans. In this research axis, we investigated the mechanisms by which biological tissues recover after injury. We explored this question on adipose tissue, using the mathematical framework recently developed in . Our assumption is that simple mechanical cues between the Extra-Cellular Matrix (ECM) and differentiated cells can explain adipose tissue morphogenesis and that regeneration requires after injury the same mechanisms. We validated this hypothesis by means of a two-dimensional Individual Based Model (IBM) of interacting adipocytes and ECM fiber elements . The model successfully generated regeneration or scar formation as functions of few key parameters, and seemed to indicate that the fate of injury outcome could be mainly due to ECM rigidity.
Following these encouraging results, the team is currently taking a step further in the model validation and confrontation to experimental data. The first direction concerns the development of a 3D framework to validate the mechanisms observed in 2D. In collaboration with S. Merino-Aceituno from the University of Vienna, efforts are being made in the development of a complete synthetic tissue model coupling the ECM and cell modelling with a vascularization model.A PhD project has been started to implement the coupled models and reduce the CPU time with the long-term goal to develop a usable software which would serve to investigate the role of different mechanisms in tissue development (not restricted to adipose tissues). Finally, further developments in collaboration with Imperial College London aim at pursuing the derivation of macroscopic PDE models from the agent-based formalisms.
Mathematical modelling of axolotl regeneration
Tissue response after injury/amputation induces one or two alternatives: scar formation versus regeneration (complete recovery of tissue shape and functions). In most mammals, regeneration is considered largely impaired for the benefit of a fibrotic scar after injury automatically associated with dysfunctions, but complete regeneration has been largely described and investigated in animal models such as zebra fish, salamander, or axolotl. Despite several processes regulating regeneration have been identified at different scales -from diffusing molecules and cellular gene expression patterns up to tissue mechanics-, how these mechanisms individually or collectively play a role in the regulation of regenerative processes remains poorly understood. In order to give insights into the mechanisms of tissue regeneration, Valeria Caliaro started an Inria PhD project in october 2019, in collaboration with Osvaldo Chara, internationally recognized group leader of SysBio in Argentina. This project focuses on the role of cell proliferation in space and time along the two first phases of regeneration after injury: (i) initiation of a regeneration response, (ii) tissue patterning during regenerate growth. The first part of the project aims at building an agent-based model featuring few key mechanisms regulating cell proliferation after injury. The model construction is based on recent works where the authors developed a mathematical model given by ordinary differential equations (ODEs) and a mathematical framework in 1D  showing that acceleration of the cell cycle is the major driver of regenerative spinal cord outgrowth in axolotls. Building on both mathematical models and introducing heuristic rules which rely on Prof O. Chara expertise, we propose a 2D-ABM using methodologies borrowed from socio-dynamics and collective behavior studies (based on many interacting agent systems). While the focus is made on proliferation-based mechanisms, other mechanisms responsible for collective behavior such as volume exclusion, diffusion or aggregation will be tested and compared with experimental data. The resulting model will provide a synthetic tissue model which will serve to investigate regeneration in cellular systems, focusing on cell proliferation properties. The second part of the PhD will be devoted to the derivation of continuous models from the agent-based formalism. This will provide a large scale ‘synthetic tissue’ model to explore the role of large scale effects in general tissue models. Model validation and calibration will be ensured by quantitative comparison with biological data already present in the literature and generated by the SysBio group of O. Chara, particularly the representative images of regenerative spinal cords after tail amputation. By varying the model parameters and observing the resulting alteration of the spinal cord size and architecture as a consequence of these variations, it will be possible to provide ‘in silico’ setting experiments to guide and plan future in vivo or ex vivo experiments. Altogether, the project is expected to provide a mechanistic understanding of the cellular mechanisms driving spinal cord regeneration, and to identify how spatial structuration can influence cell differentiation and growth.
 Rodrigo Albors A, Tazaki A, Rost F, Nowoshilow S, Chara O & Tanaka EM. 2015. Planar cell polarity-mediated induction of neural stem cell expansion during axolotl spinal cord regeneration. Elife. 4:e10230.  Rost F, Rodrigo Albors A, Mazurov V, Brusch L, Deutsch A, Tanaka EM & Chara O. 2016. Accelerated cell divisions drive the outgrowth of the regenerating spinal cord in axolotls. Elife. 5. pii: e20357.  Cura Costa E, Rodrigo Albors A, Tanaka EM & Chara O. Spatiotemporal distribution of cell proliferation rules spinal cord regeneration in the axolotl. MS in preparation.
Quantitative cell-based model predicts mechanical stress response of growing tumor spheroids
Model simulations indicate that the response of growing cell populations on mechanical stress follows the same functional relationship and is predictable over different cell lines and growth conditions despite experimental response curves look largely different. We developed a hybrid model strategy in which cells are represented by coarse-grained individual units calibrated with a high resolution cell model and parameterized by measurable biophysical and cell-biological parameters. Cell cycle progression in our model is controlled by volumetric strain, the latter being derived from a bio-mechanical relation between applied pressure and cell compressibility. After parameter calibration from experiments with mouse colon carcinoma cells growing against the resistance of an elastic alginate capsule, the model adequately predicts the growth curve in i) soft and rigid capsules, ii) in different experimental conditions where the mechanical stress is generated by osmosis via a high molecular weight dextran solution, and iii) for other cell types with different growth kinetics from the growth kinetics in absence of external stress. Our model simulation results suggest a generic, even quantitatively same, growth response of cell populations upon externally applied mechanical stress, as it can be quantitatively predicted using the same growth progression function ()
Modeling of morphogen diffusion in Drosophila oogenesis
In collaboration with a team of developmental biologists of Rutgers University (Camden, New Jersey), we have built a model for the diffusion of the Gurken morphogen during Drosophila oogenesis, taking into account a wide variety of biological mechanisms such as diffusion of the morphogen, reactions of components of the EGFR signaling pathway, movement of the source of morphogen, shift of the overlying follicle cells and growth of the egg chamber. This model, together with a complete numerical code developed in Matlab, provides a tool to understand how each mechanism influences the signal distribution. The overall aim of the project is to use this tool to guide future experiments, and to understand what mechanisms contribute to the different distributions of signal among species.
Bacterial population growth
We exploited all the methods developed to estimate the division rate of a population (see axis 3) to address a seminal question of biology: is it a size-sensing or a timing mechanism which triggers bacterial growth? In , we showed that a sizer model is robust and fits the data well. Several studies from other groups came at the same time, showing a renewed interest on a question dated back to Jacques Monod's PhD thesis (1941). Of special interest is the “adder” model, for which we are currently developing new estimation methods .
A quantitative high resolution computational mechanics cell model for growing and regenerating tissues
Mathematical models are increasingly designed to guide experiments in biology, biotechnology, as well as to assist in medical decision making. They are in particular important to understand emergent collective cell behavior. For this purpose, the models, despite still abstractions of reality, need to be quantitative in all aspects relevant for the question of interest. Considered was as showcase example the regeneration of liver after drug-induced depletion of hepatocytes, in which the surviving and dividing hepatocytes must squeeze in between the blood vessels of a network to refill the emerged lesions. Here, the cells’ response to mechanical stress might significantly impact the regeneration process. We present a 3D high-resolution cell-based model integrating information from measurements in order to obtain a refined and quantitative understanding of the impact of cell-biomechanical effects on the closure of drug-induced lesions in liver. Our model represents each cell individually and is constructed by a discrete, physically scalable network of viscoelastic elements, capable of mimicking realistic cell deformation and supplying information at subcellular scales. The cells have the capability to migrate, grow, and divide, and the nature and parameters of their mechanical elements can be inferred from comparisons with optical stretcher experiments. Due to triangulation of the cell surface, interactions of cells with arbitrarily shaped (triangulated) structures such as blood vessels can be captured naturally. Comparing our simulations with those of so-called center-based models, in which cells have a largely rigid shape and forces are exerted between cell centers, we find that the migration forces a cell needs to exert on its environment to close a tissue lesion, is much smaller than predicted by center-based models. To stress generality of the approach, the liver simulations were complemented by monolayer and multicellular spheroid growth simulations. In summary, our model can give quantitative insight in many tissue organization processes, permits hypothesis testing in silico, and guide experiments in situations in which cell mechanics is considered important .
Liver regeneration and disease: towards a full virtual liver model at histological scale
In our work towards a full virtual liver model at histological level, a number of steps were performed. The models under points (1)-(4) focus on either a single or a few liver lobules. A liver lobule is the smallest repetitive functional and anatomical building block of liver, while (5) addresses a much larger organisational building block of the liver, a liver lobe that consists of thousands to hundreds of thousands of lobules depending on the species. A second strand (6), (7) addresses image analysis, which in most cases forms the entrance to modeling as it provides the data necessary to generate model hypotheses and to parameterize a model.
(1) Cell types: In a former work by Hoehme et. al. ( ) a model of liver regeneration after drug-induced damage was established considering hepatocytes and blood vessels. This model has now been expanded to include all relevant cell types, including hepatocytes, blood vessels, hepatic stellate cells, Kupffer cells, invading macrophages and other immune cells. Thereby it is now possible to study perturbations in the temporal scenario of damage and regeneration after signaling events or cells types are knocked down individually or collectively. This model is currently compared to respective perturbation experiments.
(2) Liver disease: Degenerative liver diseases such as liver fibrosis and cirrhosis develop out of a disturbed balance of degenerative and regenerative processes. The model under (1) has thereby been extended by the formation of extracellular matrix, mimicked as fiber networks, to capture the disease process leading to liver fibrosis. In that process characteristic streets form that modify the mechanics, perfusion behavior and detoxification capacity of the liver.
(3) Consequence of liver fibrosis: Whole-slide scans from fibrotic liver in a mouse model has been analysed at different time points after emergence of the disease with regard to the degree of excess matrix to mimic the possible consequences of fibrotic inclusions on perfusion and function of liver within a multiscale model that considers ammonia detoxification in each individual hepatocyte as well as blood flow and transport processes in the liver lobule.
(4) Bile flux: Bile flux has been for decades believed to be controlled by convection at the level of liver lobules as well as at the level of the entire organ. By a methodology based on correlative imaging for quantitative intravital flux analysis no directed advection was detectable in bile canaliculi at the resolution limit. Instead, after active transport across hepatocyte membranes bile salts within the liver lobules are transported in the canaliculi by a diffusion-dominated process. Only in the interlobular ducts i.e., at super-lobular level, diffusion is augmented by advection. In silico simulations of bile transport in real 3D bile network microarchitectures can quantitatively explain the data assuming diffusive transport as sole mechanism.
(5) Liver regeneration after partial hepatectomy (partial organ removal): Partial hepatectomy is an adequate therapy in case of diseases or events that destructed only part of the liver. A typical case is a primary tumor or a metastasis affecting only a single liver lobe. Within an biophysical agent-based model capturing many aspects of the cell mechanics we studied regrowth of liver after partial organ removal in mouse calibrated with multivariate experimental data. Our model predicts characteristic proliferation pattern that change from small animals (as mouse) to large animals (as pig).
(6) Bile duct ligation: Bile duct ligation (BDL) is an experimental procedure that mimics obstructive cholestatic disease. One of the early consequences of BDL in rodents is the appearance of so-called bile infarcts that correspond to Charcot-Gombault necrosis in human cholestasis. The mechanisms causing bile infarcts and their pathophysiological relevance are unclear. Therefore, intravital two photon–based imaging of BDL mice was performed with fluorescent bile salts (BS) and non-BS organic anion analogues. Key findings were followed up by matrix-assisted laser desorption ionization imaging, clinical chemistry, immunostaining, and gene expression analyses. Our group performed analysis of intravital imaging. The key finding is that bile microinfarcts occur in the acute phase after BDL in a limited number of dispersed hepatocytes followed by larger infarcts involving neighboring hepatocytes, and they allow leakage of bile from the BS-overloaded biliary tract into blood, thereby protecting the liver from BS toxicity; in the chronic phase after BDL, reduced sinusoidal BS uptake is a dominant protective factor, and the kidney contributes to the elimination of BS until cholemic nephropathy sets in .
(7) Periportalisation during liver fibrosis formation: Within a liver lobule, the function of hepatocytes is zonated i.e., certain functions are only executed by either hepatocytes close to the center (pericentral region) or hepatocytes in the periphery of the lobule (periportal region). Little is known about how liver fibrosis influences lobular zonation. To address this question, three mouse models of liver fibrosis were used, CCl4 administration repeated for 2, 6 and 12 months to induce pericentral damage, as well as bile duct ligation (21 days) and a particular mdr2-mouse model to study periportal fibrosis. Analyses were performed by RNA-sequencing, immunostaining of zonated proteins and image analysis. Image analysis was performed by our group. The key result was that liver fibrosis leads to strong alterations of lobular zonation, where the pericentral region adopts periportal features. Beside adverse consequences, periportalization supports adaptation to repeated doses of hepatotoxic compounds .
Toxicity extrapolation from in vitro to in vivo
In vivo toxicity prediction from in vitro data is a major objective in toxicology as it permits bypassing animal experiments, and as the predictive power of animal experiments for human is limited. Objective was the prediction of paracetamol (acetaminophen)-induced hepatotoxicity from in vitro experiments. For this purpose, numerous iterations between in vitro experiments, in vivo experiments and simulations were performed for mouse. Using a recent thesis (Géraldine Cellière'ns PhD thesis ) as a start point, two candidate mechanisms could be identified both explaining the in vivo data after calibration of the in silico model with in vitro toxicity data.
Relating imaging on microscopic scales with imaging on macroscopic scales: From Diffusion-Weighted MRI Calibrated With Histological Data: an Example From Lung Cancer
Diffusion-weighted magnetic resonance imaging (DWI) is a key non-invasive imaging technique for cancer diagnosis and tumor treatment assessment, reflecting Brownian movement of water molecules in tissues. Since densely packed cells restrict molecule mobility, tumor tissues produce usually higher signal (less attenuated signal) on isotropic maps compared with normal tissues. However, no general quantitative relation between DWI data and the cell density has been established. In order to link low-resolution clinical cross-sectional data with high resolution histological information, we developed an image processing and analysis chain, which was used to study the correlation between the diffusion coefficient (D value) estimated from DWI and tumor cellularity from serial histological slides of a resected non-small cell lung cancer tumor. Color deconvolution followed by cell nuclei segmentation was performed on digitized histological images to determine local and cell-type specific 2d (two-dimensional) densities. From these, the 3d cell density was inferred by a model-based sampling technique, which is necessary for the calculation of local and global 3d tumor cell count. Next, DWI sequence information was overlaid with high resolution CT data and the resected histology using prominent anatomical hallmarks for co-registration of histology tissue blocks and non-invasive imaging modalities’ data. The integration of cell numbers information and DWI data derived from different tumor areas revealed a clear negative correlation between cell density and D value. Importantly, spatial tumor cell density can be calculated based on DWI data. In summary, our results demonstrate that tumor cell count and heterogeneity can be predicted from DWI data, which may open new opportunities for personalized diagnosis and therapy optimization . The work of that paper has been further advanced to adapt the procedures for clinical use (in preparation).
Biological control of arboviroses: Nicolas Vauchelet (Université Paris 13); Grégoire Nadin (LJLL, Sorbonne Université); Yannick Privat (Université de Strasbourg); D. Villela, C. Struchiner (Fiocruz, Brazil); Jorge Zubelli (IMPA, Brazil); Alain Rapaport (INRA-Montpellier), Y. Dumont (CIRAD-Montpellier); Ch. Schaerer, P. Pérez-Estigarribia (UNA, Paraguay), O. Vasilieva (Universidad del Valle, Cali, Colombia), D. Cardona-Salgado (Universidad Autónoma de Occidente, Cali, Colombia).
Protein aggregation in amyloid diseases: Human Rezaei's team at Inra Jouy-en-Josas (France) and W-F Xue's team in at university of Kent (Great Britain); Tom Banks at the North Carolina State University (USA) and Philippe Moireau (M3DISIM)
Wound healing: Patrizia Bagnerini (Genova, Numerical methods), Benoît Ladoux (Institut Jacques Monod et Mechanobiology Institute Singapore, Biophysics) and Antonio Jacinto (CEDOC, Lisbon, Biology and Medicine). (Adipose tissue regeneration) team of L. Casteilla (StromaLab, Toulouse). (Axolotl regeneration) team of O. Chara, SysBio group, Argentina.