Section: Application Domains

Applicative axis 1: Focus on cancer

Personnel

Luis Almeida, Cécile Carrère, Jean Clairambault, Marie Doumic, Dirk Drasdo, Benoît Perthame, Diane Peurichard.

Project-team positioning

The MAMBA team designs and analyses mathematical models of tumor growth and therapy, at the cell population level, using agent-based or partial differential equations, with special interest in methodologies for therapeutic optimisation using combined anticancer drug treatments. Rather than, or not only, modeling the effect of drugs on molecular targets, we represent these effects by their functional consequences on the fate of healthy and cancer cell populations: proliferation (velocity of the cell division cycle, decreasing it, e.g., by antagonizing growth factor receptors), apoptosis, cell death or senescence.

Our goal in doing this is to circumvent the two main issues of anticancer therapy in the clinic, namely unwanted toxic side effects in populations of healthy cells and emergence of drug-induced drug resistance in cancer cell populations. This point of view leads us to take into account phenomena of transient and reversible resistance, observed in many cancer cell populations, by designing and analyzing models of cell populations structured in continuous phenotypes, relevant for the description of the behavior of cell populations exposed to drugs: either degree of resistance to a given drug, or potential of resistance to drug-induced stress, proliferation potential, and plasticity.

Such modeling options naturally lead us to to take into account in a continuous way (i.e., by continuous-valued phenotype or relevant gene expression) the wide phenotypic heterogeneity of cancer cell populations. They also lead us to adopt the point of view of adaptive dynamics according to which characteristic traits of cell populations evolve with tumor environmental pressure (drugs, cytokines or metabolic conditions, mechanical stress and spatial conditions), in particular from drug sensitivity to resistance. This position is original on the international scene of teams dealing with drug resistance in cancer.

Scientific achievements

Modeling Acute Myeloid Leukemia (AML) and its control by anticancer drugs by PDEs and Delay Differential equations

In collaboration with Catherine Bonnet (Inria DISCO, Saclay) and François Delhommeau (St Antoine hospital in Paris), together with DISCO PhD students José Luis Avila Alonso and Walid Djema, this theme has led to common published proceedings of conferences: IFAC, ACC, CDC, MTNS  [66], [67], [68], [77], [91], [65]. These works study the stability of the haematopoietic system and its possible restabilization by combinations of anticancer drugs with functional targets on cell populations: proliferation, apoptosis, differentiation.

Adaptive dynamics setting to model and circumvent evolution towards drug resistance in cancer by optimal control

We tackle the problem to represent and inhibit - using optimal control algorithms, in collaboration with Emmanuel Trélat, proposed Inria team CAGE - drug-induced drug resistance in cancer cell populations. This theme, presently at the core of our works on cancer modeling with a evolutionary perspective on tumor heterogeneity, is documented in a series of articles  [88], [89], [115], [116], [118]. Taking into account the two main pitfalls of cancer therapy, unwanted side effects on healthy cells and evolution towards resistance in cancer cells, it has attracted to our team the interest of several teams of biologists, with whom we have undertaken common collaborative works, funded by laureate answers to national calls (see ITMO Cancer HTE call).

This theme is also at the origin of methodological developments (see Research axis 1). In collaboration with Shensi Shen from Institut Gustave Roussy and Francois Vallette from Université de Nantes, we aim to develop simple non-spatial models to understand the mechanisms of drug resistance acquisition -and lost- in melanoma and glioblastoma. The models are systematically compared with in vitro and in vivo data generated by our collaborators and treated via image processing techniques developed in the team.

Senescence modeling by telomere shortening

In many animals, aging tissues accumulate senescent cells, a process which is beneficial to protect from cancer in the young organism. In collaboration with Teresa Teixeira and Zhou Xu from IBCP, we proposed a mathematical model based on the molecular mechanisms of telomere replication and shortening and fitted it on individual lineages of senescent Saccharomyces cerevisiae cells, in order to decipher the causes of heterogeneity in replicative senescence  [79].

Biomechanically mediated growth control of cancer cells

Model simulations indicate that the response of growing cell populations on mechanical stress follows a simple universal functional relationship and is predictable over different cell lines and growth conditions despite the response curves look largely different. We developed a hybrid model strategy in which cells were represented by coarse-grained individual units calibrated in a high resolution cell model and parameterized each model cell 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. Our model simulation results suggest that the growth response of cell population upon externally applied mechanical stress is the same, as it can be quantitatively predicted using the same growth progression function [44].

Collaborations

• AML modelling: Catherine Bonnet, DISCO Inria team, Saclay, and François Delhommeau, INSERM St Antoine (also collaborator in the INSERM HTE laureate project EcoAML, see below).

• INSERM HTE laureate project MoGlImaging, headed by E. Moyal (Toulouse): François Vallette, CRCNA and INSERM Nantes

• INSERM HTE laureate project EcoAML, headed by François Delhommeau, INSERM St Antoine: François Delhommeau, Thierry Jaffredo (IBPS), Delphine Salort (LCQB-IBPS)

• Adaptive dynamics to model drug resistance and optimal control to circumvent it:

  Alexandre Escargueil, Michèle Sabbah (1 PhD thesis in common), St Antoine Hospital, Paris

  Emmanuel Trélat (1 PhD thesis in common) at Inria team CAGE and Laboratoire Jacques-Louis Lions at Sorbonne Université.

  Frédéric Thomas at CREEC, Montpellier.

  Tommaso Lorenzi (Univ. of St Andrews).

• Telomere shortening: Teresa Teixeira and Zhou Xu (IBCP, Paris), Philippe Robert (Inria RAP).

• TRAIL treatment: Gregory Batt, Inria Saclay and Inst. Pasteur (France)

• Biomechanical control of cancer cells: Pierre Nassoy, Bioimaging and Optofluidics Group, LP2N – UMR 5298. IOGS, CNRS & University of Bordeaux