Optical imaging of the small intestine immune compartment across scales.

The limitations of 2D microscopy constrain our ability to observe and understand tissue-wide networks that are, by nature, 3-dimensional. Optical projection tomography (OPT) enables the acquisition of large volumes (ranging from micrometres to centimetres) in various tissues. We present a multi-modal workflow for the characterization of both structural and quantitative parameters of the mouse small intestine. As proof of principle, we evidence its applicability for imaging the mouse intestinal immune compartment and surrounding mucosal structures. We quantify the volumetric size and spatial distribution of Isolated Lymphoid Follicles (ILFs) and quantify the density of villi throughout centimetre-long segments of intestine. Furthermore, we exhibit the age and microbiota dependence for ILF development, and leverage a technique that we call reverse-OPT for identifying and homing in on regions of interest. Several quantification capabilities are displayed, including villous density in the autofluorescent channel and the size and spatial distribution of the signal of interest at millimetre-scale volumes. The concatenation of 3D imaging with reverse-OPT and high-resolution 2D imaging allows accurate localisation of ROIs and adds value to interpretations made in 3D. Importantly, OPT may be used to identify sparsely-distributed regions of interest in large volumes whilst retaining compatibility with high-resolution microscopy modalities, including confocal microscopy. We believe this pipeline to be approachable for a wide-range of specialties, and to provide a new method for characterisation of the mouse intestinal immune compartment

ILC3s restrict the dissemination of intestinal bacteria to safeguard liver regeneration after surgery.

It is generally believed that environmental or cutaneous bacteria are the main origin of surgical infections. Therefore, measures to prevent postoperative infections focus on optimizing hygiene and improving asepsis and antisepsis. In a large cohort of patients with infections following major surgery, we identified that the causative bacteria are mainly of intestinal origin. Postoperative infections of intestinal origin were also found in mice undergoing partial hepatectomy. CCR6+ group 3 innate lymphoid cells (ILC3s) limited systemic bacterial spread. Such bulwark function against host invasion required the production of interleukin-22 (IL-22), which controlled the expression of antimicrobial peptides in hepatocytes, thereby limiting bacterial spread. Using genetic loss-of-function experiments and punctual depletion of ILCs, we demonstrate that the failure to restrict intestinal commensals by ILC3s results in impaired liver regeneration. Our data emphasize the importance of endogenous intestinal bacteria as a source for postoperative infection and indicate ILC3s as potential new targets

Role of epidermal Langerhans cells in the induction and breakdown of immune tolerance to skin allergens

La tolérance périphérique vis-à-vis de molécules potentiellement allergéniques en contact avec la peau joue un rôle essentiel pour prévenir le développement de l’eczéma allergique de contact (EAC). Au cours de ma thèse, j'ai contribué à l'identification des mécanismes et des acteurs responsables de l'induction de la tolérance par voie cutanée et à préciser le rôle respectif des sous-populations de cellules dendritiques (DC) cutanées dans la rupture de la tolérance et l'induction de lymphocytes T (LT) CD8+ initiant l'EAC. A l'aide d'un modèle murin d'induction de tolérance aux haptènes, j’ai pu montrer que les cellules de Langerhans (LC) épidermiques sont les cellules clés pour induire la tolérance cutanée et empêcher le développement d'un EAC médié par les LT CD8+. En effet, suite à l’application épicutanée d’un allergène/haptène faible, le DNTB, les LC migrent de la peau aux ganglions lymphatiques pour présenter l’antigène aux LT CD8+. Des expériences de déplétion in vivo et de transfert adoptif montrent que les LC sont responsables de la suppression de l’EAC en prévenant la différentiation des LT CD8+ spécifiques de l'allergène en cellules T cytotoxiques via deux mécanismes complémentaires: i) l’anergie/délétion des LT CD8+ et ii) l'activation de LT régulateurs Foxp3+ exprimant ICOS. Après avoir identifié des conditions d'immunisation conduisant au développement d'un EAC au DNTB, j'ai montré que la rupture de tolérance à ce type d'allergène est associée à i) à des modifications phénotypiques des LC épidermiques, ii) au recrutement rapide de monocytes inflammatoires Gr1+ dans la peau et iii) à une capacité équivalente des LC et des DC dermiques Langerin- à présenter l'allergène aux LT CD8+ dans les ganglions. Dans cette situation, les LC jouent un rôle pro-inflammatoire puisque leur déplétion réduit de manière dramatique l'induction de LT CD8+ effecteurs et l'EAC. Ces résultats indiquent que les LC jouent un rôle essentiel à la fois dans la prévention et dans l’induction de l’EAC, et que leur fonction tolérogène ou stimulatrice est vraisemblablement conditionnée par le microenvironnement cutané lors de la pénétration de l’allergèneInduction of peripheral tolerance to potentially allergenic molecules in contact with the skin is essential to prevent the development of allergic contact dermatitis (ACD). During my PhD, I contributed to the identification of the mechanisms and actors responsible for the induction of skin tolerance and clarified the respective roles of dendritic cell (DC) subsets in the breakdown of skin tolerance leading to the priming of cytotoxic CD8+ T cells and developpement of ACD. Using a mouse model of cutaneous tolerance to a model weak allergen, we show that epidermal Langerhans cells (LC) are essential to induce CD8+ T cell tolerance and prevent the development of ACD. Indeed, following the epicutaneous delivery of the weak allergen/hapten DNTB, LC were found to migrate from skin to draining lymph nodes to present the allergen to CD8+ T cells. Depletion and adoptive transfer experiments revealed that LC protect from development of ACD by preventing the priming of allergenspecific cytotoxic CD8+ T cells via two complementary mechanisms: i) anergy/deletion of allergen-specific CD8+ T cells and ii) activation of highly suppressive Foxp3+ regulatory T cells expressing ICOS. We identified DNTB skin delivery conditions that allow for CD8+ T cell priming and initiation of ACD. Breakdown of tolerance to this weak allergen was associated with i) phenotypic modifications of epidermal LC, ii) recruitment of inflammatory monocytes to the skin and iii) allergen presentation to CD8+ T cells by both LC and dermal Langerin- DC. In addition, LC are involved in tolerance breakdown as their depletion prior to skin immunization abrogated induction of CD8+ effector cells and ACD. These results demonstrate that LC are essential for both the induction of skin tolerance to weak skin allergens and for the induction of ACD, and suggest that their tolerogenic versus immuno-stimulatory function is likely dictated by signals from the skin microenvironment after penetration of the allerge