Showing papers by "Philippe Robert published in 2017"

How to Simulate a Germinal Center.

Abstract: Germinal centers host a mini-evolutionary environment where B cells can mutate their receptor and be selected depending on its affinity to target antigens in a process called affinity maturation. Starting from founder cells with a weak B cell receptor affinity, germinal centers release output cells as antibody-secreting cells or memory cells with a very high affinity, a property which is essential for pathogen clearance and immune memory. Therapeutic interventions on the germinal centers are tantalizing approaches to improve vaccines or to support rejection of chronic pathogens such as HIV. However, the complexity of the selection processes makes it very hard to make reliable predictions. Here, we present in detail how to build an agent-based model (hyphasma), accounting for the dynamics of the germinal center. It encompasses the core quantitative traits of affinity maturation, and allowed to make reliable predictions in previous studies.

Multidimensional Analysis Integrating Human T-Cell Signatures in Lymphatic Tissues with Sex of Humanized Mice for Prediction of Responses after Dendritic Cell Immunization.

Abstract: Mice transplanted with human cord blood-derived hematopoietic stem cells (HSCs) became a powerful experimental tool for studying the heterogeneity of human immune reconstitution and immune responses in vivo. Yet, analyses of human T cell maturation in humanized models have been hampered by an overall low immune reactivity and lack of methods to define predictive markers of responsiveness. Long-lived human lentiviral induced dendritic cells expressing the cytomegalovirus pp65 protein (iDCpp65) promoted the development of pp65-specific human CD8+ T cell responses in NOD.Cg-Rag1 tm1Mom -Il2rγ tm1Wj humanized mice through the presentation of immune-dominant antigenic epitopes (signal 1), expression of co-stimulatory molecules (signal 2), and inflammatory cytokines (signal 3). We exploited this validated system to evaluate the effects of mouse sex in the dynamics of T cell homing and maturation status in thymus, blood, bone marrow, spleen, and lymph nodes. Statistical analyses of cell relative frequencies and absolute numbers demonstrated higher CD8+ memory T cell reactivity in spleen and lymph nodes of immunized female mice. In order to understand to which extent the multidimensional relation between organ-specific markers predicted the immunization status, the immunophenotypic profiles of individual mice were used to train an artificial neural network designed to discriminate immunized and non-immunized mice. The highest accuracy of immune reactivity prediction could be obtained from lymph node markers of female mice (77.3%). Principal component analyses further identified clusters of markers best suited to describe the heterogeneity of immunization responses in vivo. A correlation analysis of these markers reflected a tissue-specific impact of immunization. This allowed for an organ-resolved characterization of the immunization status of individual mice based on the identified set of markers. This new modality of multidimensional analyses can be used as a framework for defining minimal but predictive signatures of human immune responses in mice and suggests critical markers to characterize responses to immunization after HSC transplantation.

Mathematical Modeling of Synaptic Patterns.

Abstract: During antigen recognition by T cells, a specific spatial structure is formed at the contact face to an antigen-presenting cell (APC), called an immunological synapse (IS). The IS supports bidirectional signaling and release of effector molecules and is widely studied both biologically and numerically, in order to understand the process of T cell activation and signaling. This specialized structure harbors a central area (central supramolecular activation cluster, cSMAC) populated by T cell receptor-peptide-major histocompatibility complex (TCR-pMHC ) interactions, hedged by a peripheral ring (peripheral supramolecular activation cluster, pSMAC) of integrin lymphocyte function associated-1 interactions with its immunoglobulin superfamily ligand intercellular adhesion molecule-1 (LFA-1-ICAM-1). These two regions form the "bull's eye" pattern characteristic of the mature IS.In theoretical studies, different modeling architectures, including partial differential equations (PDE) and agent-based models , have been developed with the purpose to answer mechanistic questions about the IS dynamics. In this chapter, we explain possible physiological mechanisms that lead to the formation of ISs and technical issues that may occur in the course of development of agent-based models.

Quantitative characterization of CTLA4 trafficking and turnover using a combined in vitro and in silico approach

Abstract: CTLA4 is an essential negative regulator of T cell immune responses and is a key checkpoint regulating autoimmunity and anti-tumour immunity. Genetic mutations resulting in a quantitative defect in CTLA4 are associated with the development of an immune dysregulation syndrome. Endocytosis of CTLA4 is rapid and continuous with subsequent degradation or recycling. CTLA4 has two natural ligands, the surface transmembrane proteins CD80 and CD86 that are shared with the T cell co-stimulatory receptor CD28. Upon ligation with CD80/CD86, CTLA4 can remove these ligands from the opposing cells by transendocytosis. The efficiency of ligand removal is thought to be highly dependent on the processes involved in CTLA4 trafficking. With a combined in vitro-in silico study, we quantify the rates of CTLA4 internalization, recycling and degradation. We incorporate experimental data from cell lines and primary human T cells. Our model provides a framework for exploring the impact of altered affinity of natural ligands or therapeutic anti-CTLA4 antibodies and for predicting the effect of clinically relevant CTLA4 pathway mutations. The presented methodology for extracting trafficking rates can be transferred to the study of other transmembrane proteins.