Scientific background Allogeneic hematopoietic stem cell transplantation (alloHSCT) is the first cellular immunotherapy developed to cure hematologic malignancies. It is based on the anti-tumor allo-immune response (graft versus tumor effect) induced by the donor immune system also transferred during the transplant process. Despite its efficiency, hematologic malignancies relapse accounts for half of deceases and to date, no biomarker allow to predict whose patient will relapse after allogeneic HSCT and to identify these patients early before relapse. Traditional statistical methods used for biomarker identifications are limited, mostly by their parametric nature, and could benefit from advanced machine learning and optimization techniques to select relevant variables and link them to the relapsing process. This unmet medical need is of critical importance to improve prognosis of patients who are currently treated for a hematologic cancer with allo-HSCT and to adapt their treatment before relapse. Hypothesis Here, we assume that integration of clinical data with immune and metabolic variables could provide metadata for a mathematical model to predict relapse occurrence. Aims To characterize circulating immune subsets and metabolome in the donor and to compare them at 3 months and one year after transplantation in patients with or without relapse To build a calibrated stochastic simulator for the relapsing process, accounting for post-transplant events and integrating clinical data with immune and metabolic variables. Methodology This project will rely on a multicentric cohort of 369 patients who received an alloHSCT. We will use mass cytometry and mass spectrometry to decipher circulating immune subsets and metabolites associated with relapse and other post-transplantation events. We will then create a simulator that model the dynamics of post-transplant events to identify relevant biomarkers using advanced optimization techniques and to generate a tool to predict relapse after alloHSCT. Validation in animal model will finally help to identify relevant new therapeutic targets. Expected results and impact This project will use data from an already constituted large cohort of patients to develop a machine learning tool for clinicians to estimate the probability of relapse based on various clinical and immune-metabolic data.

Communication is central to the function of all living systems, at all organizational scales (from cells to organs and organisms). It is also crucial to the immune system, where there is a need to tightly coordinate actions from different cells and cell types in order to maintain the integrity of an organism. Dendritic cells (DC) are at the forefront of innate immunity, and subsequently stimulate T cells to induce the primary adaptive immune response. In that respect, DC-T cell communication is of paramount importance to immunity against pathogens, and can be perturbed in various situations of immunopathology. DC communicate with T cells through over 60 molecular ligands, sensed by specific receptors on T cells. Past studies have mostly analyzed the communication process by focusing on one or two of these molecules. We were the first to establish a multivariate mathematical model of DC-T cell communication, in which 36 DC communication molecules were integrated, together with their collective impact on CD4 T cell activation and T helper cell differentiation. In this proposal, we aim at the next level in the systems analysis of DC-T cell communication, by introducing novel technologies (35 color flow cytometry, nanostring), increasing the number of DC molecules to be integrated (between 50 and 60), comparing DC-T cell communication of different DC subsets (WP1), systematically analyzing context-dependency (WP2), and introducing antigen specificity (WP3). We hope to uncover novel mechanisms and rules governing DC-T cell communication, with implications in immunopathology, cancer, and vaccine design.

The loss of functional ? cells is the root cause for the development of diabetes. Therapies aimed at the replenishment of the pancreatic ? cell are among the most promising strategies to treat diabetes. In this project, we will investigate the effects of new selective Dyrk1A inhibitors developed by a French Biotech, on the proliferation of human ? cells, and the regeneration of ? cell in relevant preclinical models of type 2 diabetes. This translational research program will pave the way for the rapid clinical evaluation of these highly advanced Dyrk1A inhibitors in diabetic patients.

The Epi-Dev project will investigate the epigenetic and transcriptional mechanisms underlying lymphoid lineage specification in mammals. Our consortium will use a comparative human/mouse experimental strategy combining functional analyses and high throughput transcriptomic and epigenomic studies. Human studies will aim to investigate the bases of lymphoid priming in multipotent progenitors and to characterize the signaling pathways and gene networks driving the differential emergence of IL7 receptor (CD127) positive or negative lymphoid progenitors. Mouse studies conducted in parallel will also aim to dissect lymphoid priming and subsequent lymphoid diversification in the fetal liver. Single-cell comparative transcriptomics will then be used to define the developmental trajectories of human and mouse lymphoid progenitors. Overall, the Epi-Dev project will provide a roadmap of the early steps of lymphoid differentiation and will distinguish species-specific regulatory mechanisms from those that have been conserved through evolution. Ultimately, this project will contribute to a better understanding of the developmental plasticity and functional properties of the cells from which hematological malignancies originate and help unravel the perturbations of lymphoid differentiation associated with pathologic conditions and aging.

The thymus provides the environment for the development and selection of T cells. Thymic epithelial cells coordinate virtually all stages of T cell development, providing key cytokines, chemokines and ligands for the commitment, survival and proliferation of thymocytes and also for positive and negative selection of T cell precursors. Work from partner 1 showed that the embryonic thymus is colonize by two consecutive waves of thymic seeding progenitors. The first hematopoietic cells that colonize the thymus display a unique capacity to generate lymphoid tissue inducer cells and invariant gd T cells that together are the first thymocytes to interact with thymic epithelial cells. The second wave produces conventional ab and gd expressing T cells. The first wave of thymic progenitors are of exclusive embryonic origin and induce the differentiation of thymic epithelial progenitors into cortical and medullary epithelial cells as well as their subsequent maturation, which is required for the induction of central tolerance. This project aims to understand the molecular and cellular events that regulate the generation of the first thymic lymphoid cells, their impact in the establishment and maintenance of peripheral tolerance and their involvement in thymic involution. In this project we propose to: (1) Identify the cell-intrinsic molecular mechanisms that regulate the developmental potential of thymic seeding progenitors giving rise to the first invariant T cells and thymic lymphoid tissue inducer cells. For this, we will perform a transcriptomic and epigenomic analysis of the progenitors of thymic seeding cells from both waves, (2) Characterize the role of thymic seeding progenitors in the maturation of medullary thymic epithelial cells and in the development of thymic architecture. This will be carried out using fetal thymic organ cultures of alymphoid (Ragc-/-) thymic lobes colonized with thymic seeding progenitors and (3) Investigate the impact of a deficiency of the first wave thymic seeding progenitors in tolerance induction, autoimmunity and thymic involution. This will be done by reconstituting mice with progenitors that can only generate the second wave of thymic seeding progenitors or by depleting the first wave. This project will lead to a better understanding all conditions of immune deficiencies arising from a compromised thymic function, including the effects of chemotherapy and irradiation in pathological situations of cancer and bone marrow transplantation or during aging. Moreover, since gd T cells are important for the integrity of the alveolar epithelia, understanding the origin and developmental pathways leading to the production of these cells will contribute to cell therapy approaches for the treatment of airway viral infections such as influenza or different types of coronavirus. In this project we will investigate the first interactions between thymocytes and epithelial cells, that are likely to modulate all epithelial compartments for life and thus impact on involution that occurs with ageing or in pathologic conditions. Altogether these experiments will provide new insights in thymic epithelia development and involution and could reveal strategies to maintain or restore thymic function in aging and disease.