Section: Overall Objectives

Research axis 3: Multi-scale modeling of the immune response

Executive summary

Vaccination represents a worldwide health, social and economical challenge as it has allowed the eradication or the strong containment of several devastating diseases over the past century. However to date, most of the effective vaccines rely on the generation of neutralizing antibody responses and such vaccines have proven largely unsuccessful in the prevention against some pathogens, such as HIV or malaria. In such cases, vaccines geared towards the generation of CD8 T cell immunity may provide a better protection. The generation of memory CD8 T cells following antigenic immunization is a long process (lasting up to month in murine preclinical models), therefore strongly slowing the process of vaccine monitoring in preclinical studies. Thus, the dynamical modeling of the CD8 T cell immune response both at the cellular and molecular levels should provide an important tool to better understand the dynamics of the response and to speed-up the process and reduce costs of vaccine development.

However, currently published cellular models of the immune response are either over-simplified, not predicting important parameters of this response, or too complicated for most of their parameters to be accessible for experimental measurements, thus impeding their biological validation. Dynamical models of the CD8 T cell response at the molecular level are very scarce and there is no multi-scale model of the immune response giving insights into both the regulation at the molecular scale and the consequences on cell population dynamics.

The objective of this research axis is therefore to develop a predictive multi-scale model of the CD8 T cell response, by confronting the model at different stages to in vivo-acquired experimental data, in order to be able to investigate the influence of early molecular events on cell population dynamics few days or weeks later.

Project-team positioning

We are aiming at building and analyzing a multi-scale model of the CD8 T cell immune response, from the molecular to the cellular and potentially organismal scale. This consists in describing the dynamics at each scale with relevant formalisms as well as the careful description of the couplings between scales.

Only few research groups are actually working on the CD8 T cell immune response around the world, and none of them deals with multi-scale modeling of this response. A network developed around Alan Perelson's work in theoretical immunology in the last decades, at Los Alamos National Laboratory, and involves mainly people in various US universities or institutes. In Europe, Rob De Boer's group (http://theory.bio.uu.nl/rdb/) of theoretical immunology in Utrecht, Netherlands, is the historical leader in the CD8 T cell dynamics modeling. We considered the models developed in these groups when we started our project, and we contributed to improve them by using nonlinearities accounting for cell population interactions to regulate the response. Also, our initial focus was on the generation of memory cells associated with vaccine development so we modeled CD8 T cell responses against influenza and vaccinia viruses, whereas other groups usually consider LCMV in its chronic form.

Ron Germain's group at the NIH, and Grégoire Altan-Bonnet in subsequent works, focused on the molecular regulation of the CD4 and CD8 T cell immune responses. In particular, they built the Simmune software, which allows the modeling and simulation of molecular interactions (https://www.niaid.nih.gov/research/simmune-project). This software is not really devoted to multi-scale modeling yet it provides an interesting tool to describe molecular interactions. Since our aim is to couple molecular and cellular scales at the tissue level, and we do not want to consider large networks but rather small-simplified informative interaction networks, we are confident that our approach is complementary of these works.

Within Inria project-teams, NUMED develops multi-scale approaches for biological problems, and MAMBA and MONC (https://www.inria.fr/en/teams/monc) mention models of cancer progression and treatment including immune responses. In the first case the methodology is similar, and collaborations between NUMED and DRACULA already exist (both teams are located in Lyon), but applications differ. In the second case, MAMBA and MONC are mainly focused on cancer modeling and up to now are motivated by including an action of the immune system in the fight against cancer, which is very different from what we are developing. However, both modeling approaches are complementary and could lead to interactions, in particular in the light of recent advances in medical research pointing towards an important role - and high expectations - of the immune reaction in fighting cancers. Finally, SISTM (https://www.inria.fr/en/teams/sistm) also focuses on the modeling of the immune response, mainly against HIV, but the motivation is very similar to ours: the objective is to provide tools and methods in order to efficiently develop vaccines. They consider the CD4 T cell response instead of the CD8 T cell response, and biostatistics to achieve their goals instead of multi-scale models, yet even though there is no interaction between SISTM and DRACULA at this moment our methods and objectives are close enough to foreshadow future collaborations.

Collaborations

On this topic our main collaborators are members of Jacqueline Marvel's team in Lyon in the CIRI (Centre International de Recherche en Infectiologie INSERM U1111): Dr. Jacqueline Marvel, head of the team, Dr. Christophe Arpin (CR CNRS), and other technicians and engineers of the team. They are all immunologists, specialists of the CD8 T cell response and of the generation of memory CD8 T cells.

We also interact with private companies: AltraBio (http://www.altrabio.com/), that provides tools for data analysis, and CosmoTech, that develops a modeling and simulating platform that should allow transferring our model on an easy-to-use platform devoted to commercial uses.