Macrophages play key roles in tissue regeneration and inflammation at steady-state, two processes that are essential to maintain tissue homeostasis and, if dis-regulated, can lead to pathology. We have recently discovered a peculiar population of macrophages in the distal colon that is needed to locally maintain the survival of epithelial cells in homeostasis. These macrophages are localized in the stroma, but insert “balloon-like protrusions (BLPs)” through the basement membrane in between epithelial cells. BLPs sample the fluids that are absorbed through the epithelium and instruct epithelial cells to stop absorption if fluids are overloaded with fungal toxins. We here propose a project aiming to identify the key players involved in the tripartite interaction between macrophages, epithelial cells and fungi (Aim 1), unraveling the underlying molecular and cellular mechanisms (Aim 2) and evaluating whether and how failure in this “ménage à trois” can lead to colon pathology (Aim 3).

Mucosal Associated Invariant T cells (MAIT) represent a key immune cell population because of their abundance in humans, their ability to provide immediate responses upon stimulation, and their potential involvement in many pathologies. MAIT cells recognize microbiota-derived metabolites presented by the MHC-related molecule MR1. Both MR1 and the TCR of MAIT cells are conserved in evolution, indicating non-redundant functions linked to antigen recognition. MAIT ligands produced by the microbiota control MAIT cell development. However, mechanisms underlying microbiota production of MAIT antigens remain undefined. Upon thymic egress, MAIT cells migrate to mucosal and liver tissues where they accumulate over time and reach high frequencies in humans (1-10% of T cells in the intestine, 20-45% in liver). MAIT cells are further recruited and activated in the intestinal lesions of patients with inflammatory bowel diseases, suggesting a role in these pathologies. Whether MAIT cell accumulation and function in intestinal tissues rely on the recognition of microbiota-derived antigens is unknown, and the role played by MAIT cells in the gut also remains unclear. The MicrobMAIT proposal aims at addressing the role played by microbiota-derived antigens in the biology of MAIT cells. We will take advantage of innovative genetic tools and reagents to: 1. Explore rules governing MAIT antigen production by the microbiota, in mice and humans 2. Determine the dynamics of MAIT antigens and identify antigen-presenting cells in vivo 3. Define the influence of the microbiota on MAIT cell maintenance and function during intestinal inflammation Based on our sound preliminary data, we expect to identify a new MAIT-dependent mechanism of immune surveillance of the intestinal microbiota. Future manipulation of this interaction may offer innovative therapeutic opportunities against intestinal inflammation as well as colonic carcinogenesis.

Aging is one of the major public health challenge. By impacting hematopoietic stem cells (HSCs) function, aging, exposure to irradiation, chemotherapy or chronic inflammation are highly associated with increased risk of developing cancers, and many other aging-related health disorders such as heart or neurocognitive diseases, through decline in the adaptive immunity and enhanced infections and inflammation. Epigenetic factors are key regulators of HSC function and epigenetic alterations have been observed in aged HSCs. Alteration of heterochromatin in HSCs during age is accompanied by overexpression of transposable elements (TEs) and increased inflammation. TEs are major contributors of gene regulatory networks. They can also be sensed as endogenous genomic parasites, eventually inducing an intrinsic sterile inflammation. Inflammation can in turn induce alterations in heterochromatin and TE expression and worsen the HSC phenotype in a vicious circle. We hypothesize here that heterochromatin alterations and TEs play a central role in the functional alterations of HSCs and in the production / function of myeloid cells during the aging process. Through the association of three partners with complementary expertise in epigenetics, transcription, biology, TEs, myelomonocyte differentiation and inflammatory response, we will explore whether: 1/ Alterations in heterochromatin and TE derepression are common events in age and stress 2/ TE derepression, via transcriptome alterations, act as the driving force behind HSC functional changes and their ability to produce monocytes with age 3/ TEs are involved in the inflammatory properties of aged HSCs and monocytes 4/ These pathways can be manipulated by reprogramming to rejuvenate HSC function This project should identify ways to restore lymphoid/myeloid HSC production and decrease chronic inflammation and immunosenescence by manipulating HSC heterochromatin and TE expression, thereby contributing to healthier aging.

Mucosal-associated invariant T (MAIT) cells are numerous in humans and are implicated in various pathological settings. As such, understanding their biology is essential, and will lead to innovative therapeutic strategies. MAIT cells are selected on double positive thymocytes leading to memory phenotype and immediate effector functions. This original selection process targets MAIT cells to mucosal tissues in which they establish long term residency. MAIT cells are also found in secondary lymphoid organs, possibly providing B and T cell help during immune responses. Recent data suggest that MAIT cells migrate between mucosal tissues and their draining lymph nodes (LNs) at steady state and following inflammation. However, the role and dynamics of MAIT cells in LNs remain poorly understood. A comprehensive phenotypic and functional characterization of MAIT cells in various LNs and the corresponding organs is needed to decipher the specific role of LN MAIT cells within immune responses. Assessing the mechanisms involved in cell pool establishment and exchange will also help characterizing MAIT cell biology. We hypothesize that MAIT cells circulate back and forth between tissues and draining LNs, hence being poised in LNs to tissue-specific immune responses. Following tissue inflammation, this migration may ensure both adaptation of the LN response and mobilization of MAIT cells for rapid effector function in the tissue. Here we will test these hypotheses by 1) characterizing MAIT cells in mesenteric, mediastinal and inguinal/brachial LNs and in the drained tissues; 2) analyzing MAIT cell dynamics between different LNs and tissues at steady state, including pool establishment and mechanisms of migration and retention in LNs; 3) assessing MAIT cell effector functions following various triggers in different LNs and trafficking during inflammation. Building on long term expertise, specifically developed animal models and tools, and state-of-the-art techniques, this project will characterize the dynamics and functions of LN MAIT cells, to provide a conceptual framework that could be broaden to other unconventional T cells and resident memory cells.

The process of aging represents the gradual deterioration of function with time, which affects almost all tissues and organs. In humans, it is the most prevailing risk factor for the morbidity and mortality attributable to numerous acute and chronic diseases. However, the cellular and molecular bases for these phenomena remain largely unknown. Our preliminary work has uncovered a striking build-up of tissue macrophages that carry numerous markers of senescence in multiple organs of aged mice, implicating loss or alteration of macrophage function as a potential driver of aging phenotype including inflammaging. In this project, we will uncover the mechanisms underlying age- and inflammation-induced senescence/senescence-like state of tissue macrophages, we will determine how this shapes tissue inflammation and immune response during aging, and we will explore how modulation of macrophage senescence could be used to impact the aging process.