Prevention and regulation of excessive inflammation is a key target to protect against inflammatory pathologies such as autoimmunity and allergy. In a mouse model of acute lung protease hypersensitivity, we assessed the efficacy of immunological cross-regulation to mitigate pathogenic inflammation. We show that induction of a type 1 response using Toll-like receptor ligands or a bacterial lysate efficiently blocks acute eosinophilia and type 2 responses evoked by the cysteine protease papain. Upon rechallenge with papain weeks later, mice displayed enhanced type 2 responses and eosinophilia, whereas this response was absent if the initial inflammation was cross-regulated. Memory of the initial event was stored in adventitial stromal cells expressing CCL11. Accessibility of the Ccl11 locus was increased by papain exposure in an interleukin-4- and interleukin-13-dependent manner and blocked by interferon gamma. Our results show how the nature of an initial inflammation is memorized by tissue-resident cells and shapes subsequent inflammatory responses.

Le microbiote est activement impliqué dans le développement et la régulation du système immunitaire, ainsi que dans la régulation de certaines fonctions du cerveau. La véritable complexité, et la beauté, de ces interactions se révèlent sous le microscope d’une analyse intégrée des échanges entre ces différents compartiments. Ici, je rapporte brièvement, dans un premier temps, nos observations sur l’empreinte immunitaire néonatale induite par le microbiote, empreinte qui détermine la réactivité du système immunitaire à long terme, et ainsi, la susceptibilité de l’individu aux maladies inflammatoires. Dans un deuxième temps, je décris l’influence que le microbiote exerce sur l’état mental et le comportement alimentaire, ainsi que son impact indirect, via le système immunitaire, sur la résilience mentale. Ces résultats sont le fruit d’une recherche transdisciplinaire qui propose une vision holistique de la maladie inflammatoire chronique et de ses conséquences sur le cerveau.

The immune system was historically defined as a system that provides protection from pathogens. Numerous models have been developed to understand how immunity faces a complex world of microbes that includes pathogens and symbionts, as well as cells of our own self that may develop tumors. Based on the classical assumption that survival depends on internal homeostasis, we have developed a formal model of homeostasis for a host interacting with microbes and self. We propose that such a model must include two fundamental functions: a function that counters change (including tissue repair), and a function that counters the agent of change (such as 'immunity' to microbes or self). We show that this elementary model is sufficient to generate symbiosis, and suggest that the conditions leading to symbiosis contribute to eukaryotic evolution and ontogeny. This model may be further applied to symbiotic interactions between organisms and non-microbial or non-cellular agents of change, such as social partners. ### Competing Interest Statement The authors have declared no competing interest.

The microbiota is actively involved in the development and regulation of the immune system, as well as in the regulation of certain brain functions. The true complexity and beauty of these interactions are revealed under the microscope of an integrated analysis of the exchanges between these different compartments. Here, I will first briefly report on our observations on the neonatal immunological imprinting induced by the microbiota, which determines the long-term reactivity of the immune system and, thus, an individual's susceptibility to inflammatory diseases. Second, I describe the influence that the microbiota exerts on mental states and eating behavior, as well as its indirect impact, via the immune system, on mental resilience. These results are the fruit of transdisciplinary research that offers a holistic view of chronic inflammatory disease and its consequences on the brain.

SUMMARY Food provides nutrients that are selectively absorbed by the intestine, but, at the same time, may contain elements that challenge the intestinal barrier and induce post-prandial inflammation (PPI). How PPI is controlled in order to avoid pathological perturbation of homeostasis remains unclear. Here, we report that during fasting, enterocytes increase their absorptive potential and oxidative metabolism, a program that is largely reversed upon food intake of lipids that perturb the intestinal barrier and induce PPI. Such perturbation is countered by ILC3s, in the absence of which PPI increases, program reversal does not occur, and enterocytes engage into excessive oxidative metabolism. This enterocyte state leads to critical hypoglycemia as a consequence of decreased glucose absorption and increased insulinemia, recapitulating the pathological situation found in patients suffering from intestinal damage and sepsis. We hereby uncover a critical function for ILC3s in maintaining enterocyte homeostasis upon challenging food intake.

The gut microbiota, immune system, and enteric nervous system interact to regulate adult gut physiology. However, the mechanisms establishing gut physiology during development remain unknown. We report that in developing zebrafish, enteroendocrine cells produced interleukin-22 (IL-22) in response to microbial signals before lymphocytes populated the gut. In larvae, IL-22 shaped the gut microbiota, increasing Lactobacillaceae abundance and ghrelin expression to promote gut motility. Impaired motility and ghrelin expression were restored in il22-/- zebrafish by transfer of microbiota from wild-type zebrafish or by introducing only Lactobacillus plantarum. IL-22-deficient mice also had impaired gut motility and reduced ghrelin expression in early life, indicating a conserved function. Thus, before immune system maturation, enteroendocrine cells regulate early-life gut function by controlling the microbiota through IL-22.

Innate lymphoid cells (ILCs) include T-bet-dependent NK and ILC1 cells, GATA-3-dependent ILC2 cells, and RORγt-dependent ILC3 cells. Their functional and developmental regulation at the posttranscriptional level remains elusive. The CCR4-NOT complex plays a central role in mRNA decay by mediating deadenylation. To explore the overall impact of mRNA decay on ILCs, we conditionally deleted Cnot3, an essential subunit of the CCR4-NOT complex. Loss of CNOT3 in ILC2 cells led to aberrant expression of T-bet and RORγt, accompanied by upregulation of type 1 and type 3 signature genes. Mechanistically, CNOT3 targeted the 3' untranslated regions of Tbx21 and Rorc mRNAs through interactions with Roquin and ZFP36L1, respectively. Elevated T-bet expression in CNOT3-deficient ILC2 cells suppressed GATA-3 levels, thereby impairing type 2 immune responses in models of airway allergy and helminth infection. Thus, our findings reveal that CNOT3 maintains ILC2 differentiation and function by restricting type 1 and type 3 transcriptional programs.

The gut microbiota, immune system, and enteric nervous system tightly interact to regulate adult gut physiology. Yet the mechanisms establishing gut physiology during development remain unknown. Here, we report that in developing zebrafish, enteroendocrine cells produce IL-22 in response to microbial signals before lymphocytes populate the gut. In larvae, IL-22 is crucial to set gut microbiota composition, and ghrelin hormone expression to promote gut motility. IL-22 developmental function depends on its ability to modulate gut microbiota, as bacterial transfer from wild-type zebrafish restored gut motility in il22 -/- by reestablishing ghrelin hormone expression. Additionally, IL-22-deficient mice show impaired gut motility and reduced ghrelin expression in early life, indicating a conserved function. Altogether, we identify a circuit where enteroendocrine cells regulate gut function via cytokine control of the microbiota, showing how gut physiology is set prior to immune system maturation. ### Competing Interest Statement The authors have declared no competing interest.

Background Perinatal exposure to titanium dioxide (TiO 2 ), as a foodborne particle, may influence the intestinal barrier function and the susceptibility to develop inflammatory bowel diseases (IBD) later in life. Here, we investigate the impact of perinatal foodborne TiO 2 exposure on the intestinal mucosal function and the susceptibility to develop IBD-associated colitis. Pregnant and lactating mother mice were exposed to TiO 2 until pups weaning and the gut microbiota and intestinal barrier function of their offspring was assessed at day 30 post-birth (weaning) and at adult age (50 days). Epigenetic marks was studied by DNA methylation profile measuring the level of 5-methyl-2′-deoxycytosine (5-Me-dC) in DNA from colic epithelial cells. The susceptibility to develop IBD has been monitored using dextran-sulfate sodium (DSS)-induced colitis model. Germ-free mice were used to define whether microbial transfer influence the mucosal homeostasis and subsequent exacerbation of DSS-induced colitis. Results In pregnant and lactating mice, foodborne TiO 2 was able to translocate across the host barriers including gut, placenta and mammary gland to reach embryos and pups, respectively. This passage modified the chemical element composition of foetus, and spleen and liver of mothers and their offspring. We showed that perinatal exposure to TiO 2 early in life alters the gut microbiota composition, increases the intestinal epithelial permeability and enhances the colonic cytokines and myosin light chain kinase expression. Moreover, perinatal exposure to TiO 2 also modifies the abilities of intestinal stem cells to survive, grow and generate a functional epithelium. Maternal TiO 2 exposure increases the susceptibility of offspring mice to develop severe DSS-induced colitis later in life. Finally, transfer of TiO 2 -induced microbiota dysbiosis to pregnant germ-free mice affects the homeostasis of the intestinal mucosal barrier early in life and confers an increased susceptibility to develop colitis in adult offspring. Conclusions Our findings indicate that foodborne TiO 2 consumption during the perinatal period has negative long-lasting consequences on the development of the intestinal mucosal barrier toward higher colitis susceptibility. This demonstrates to which extent environmental factors influence the microbial-host interplay and impact the long-term mucosal homeostasis.

The central nervous system regulates systemic immune responses by integrating the physiological and behavioral constraints faced by an individual. Corticosterone (CS), the release of which is controlled in the hypothalamus by the paraventricular nucleus (PVN), is a potent negative regulator of immune responses. Using the mouse model, we report that the parabrachial nucleus (PB), an important hub linking interoceptive afferent information to autonomic and behavioral responses, also integrates the pro-inflammatory cytokine IL-1β signal to induce the CS response. A subpopulation of PB neurons, directly projecting to the PVN and receiving inputs from the vagal complex (VC), responds to IL-1β to drive the CS response. Pharmacogenetic reactivation of these IL-1β-activated PB neurons is sufficient to induce CS-mediated systemic immunosuppression. Our findings demonstrate an efficient brainstem-encoded modality for the central sensing of cytokines and the regulation of systemic immune responses.

Neurosciences have a long history, tracing back to Antiquity, in the quest for understanding the senses, the mind, and the brain. Immunology, in contrast, was born at the end of the 19th century from the necessity to understand how we survive microbes, just shown to be the source of infectious diseases. The 19th century also gave rise to neuroimmunology, largely to unravel the mechanisms driving pathologies of the nervous system, an aim still shared by most clinical neuroscience departments. Immunology and neurosciences have since grown into rich and complex disciplines. Nevertheless, only on rare occasions have the fields crossed paths to reveal how the two systems crosstalk to maintain health, regulate physiology and alter behavior. Sickness behavior is probably the best-studied effect of the immune system on the brain1Dantzer R O'Connor JC Freund GG Johnson RW Kelley KW From inflammation to sickness and depression: when the immune system subjugates the brain.Nat. Rev. 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Maybe the two systems even share a common memory. The current surge of interest in Neuroimmunology tells us that, indeed, it has entered a new age. It is an evolution that Mucosal Immunology wishes to actively support and welcome within its pages. To imagine how the future may look like in (mucosal) Neuroimmunology, we have invited prominent immunologists, neuroscientists, neuroimmunologists and immunoneurologists to share their visions. Below is my attempt to synthesize their ideas, which I have grouped into five themes. I wish to warmly thank you for your willingness to participate: Aleksandra Deczkowska (Institut Pasteur), Asya Rolls (Technion), Caroline Sokol (Harvard), Daniel Mucida (Rockefeller), Elaine Hsiao (UCLA), Francisco Quintana (Harvard), Gabriel Lepousez (Institut Pasteur), Henrique Veiga-Fernandes (Champallimaud), Isaac Chiu (Harvard), Jun Huh (Harvard), Maria Rescigno (Humanitas, Milan), Marco Prinz (Freiburg University), Michal Schwartz (Weizmann Institute), Michel Neunlist (Université Nantes), Pierre-Marie Lledo (Institut Pasteur), Robert Dantzer (MD Anderson Cancer Center), Sarkis Mazmanian (Caltech), Vassilis Pachnis (Crick Institute) and Yuuki Obata (UT Southwestern Medical Center). 1. Neuronal sensing of the mucosal environment (CS, DM, EH, IC, MN, YO). The intestine is sometimes referred to as the 2nd brain, because of the presence of 108 neurons in the human gut (yet still far less neurons than the 1011 neurons in the 1st brain). Visualization of neuronal fibers in intestinal villi reveals a stunningly dense network20Obata Y Pachnis V The effect of microbiota and the immune system on the development and organization of the enteric nervous system.Gastroenterology. 2016; 151 (1:CAS:528:DC%2BC28XhslKnurnL, 27521479): 836-84410.1053/j.gastro.2016.07.044Abstract Full Text Full Text PDF PubMed Scopus (127) Google Scholar, which makes interactions between the enteric nervous system, the microbiota and the local immune system seem inevitable21Jacobson A Yang D Vella M Chiu IM The intestinal neuro-immune axis: crosstalk between neurons, immune cells, and microbes.Mucosal Immunol. 2021; 14 (8075967, 1:CAS:528:DC%2BB3MXjtFOnt7o%3D, 33542493): 555-56510.1038/s41385-020-00368-1Abstract Full Text Full Text PDF PubMed Scopus (60) Google Scholar22Wang H Foong JPP Harris NL Bornstein JC Enteric neuroimmune interactions coordinate intestinal responses in health and disease.Mucosal Immunol. 2022; 15 (1:CAS:528:DC%2BB3MXhvFegsbbE, 34471248): 27-3910.1038/s41385-021-00443-1Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar. The intestine also harbors two layers of neurons, the submucosal and the myenteric plexi, which coordinate intestinal movements and communicate with the central nervous system (CNS) through the parasympathetic vagal and pelvic nerves, the sympathetic celiac and mesenteric ganglia, and fibers to the spinal cord. A key question is: What do these neurons sense in the intestine (and lung, skin, …) and how do they impact immunity? Food and microbiota are sensed by epithelial cells and immune cells via innate and adaptive receptors. Do neurons sense food and microbes via similar or distinct receptors, how do they connect to immune, epithelial and stromal cells in such sensing processes and how is this information shared with the immune system during homeostasis, defense and pathology? A simplistic view would posit that each system and its cells collect information functionally relevant to itself: the immune system senses pathogens, epithelial cells sense nutrients, the nervous system senses noxious/painful stimuli, temperature, odors, movement. However, we tend to shift away from such system-centric view to a more niche-centric view, where different cell types and receptors sense elements present in a specific niche and process information via the systems they are linked to. For example, intestinal epithelial cells can sense nutrients, microbes and movement, and transfer information to the immune and nervous system via cell-bound and soluble factors23Schneider C O'Leary CE Locksley RM Regulation of immune responses by tuft cells.Nat. Rev. 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The intestinal immune system manufactures large amounts of antibodies “just” to maintain an equilibrium with its resident microbiota31Sansonetti PJ Medzhitov R Learning tolerance while fighting ignorance.Cell. 2009; 138 (1:CAS:528:DC%2BD1MXhsVChs7jP, 19665961): 416-42010.1016/j.cell.2009.07.024Abstract Full Text Full Text PDF PubMed Scopus (116) Google Scholar, and normal brain functions require bacterial products32Nagpal J Cryan JF Microbiota-brain interactions: moving toward mechanisms in model organisms.Neuron. 2021; 109 (1:CAS:528:DC%2BB3MXitlSktbjF, 34653349): 3930-395310.1016/j.neuron.2021.09.036Abstract Full Text Full Text PDF PubMed Scopus (19) Google Scholar. Nevertheless, the question remains open and fascinating: How do the microbiota and mucosae communicate with the brain? 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Memory is nevertheless a broad phenomenon, found in any system that carries traces of the past, such as fingerprints in a crime scene, modifications in cell activation status, rewiring of neuronal networks or editing of the epigenetic code. Since the brain receives information from the microbiota and the immune system, it is tempting to ask whether the brain can encode and memorize information from microbiota and immunity, and therewith modify subsequent immune responses. The brain also receives exteroceptive and interoceptive information of very diverse nature, such as social interaction, vision, stress or hunger, which may contribute to the shaping of immune responses3Schiller M Ben-Shaanan TL Rolls A Neuronal regulation of immunity: why, how and where?.Nat. Rev. Immunol. 2021; 21 (1:CAS:528:DC%2BB3cXhs1aiur3F, 32811994): 20-3610.1038/s41577-020-0387-1Crossref PubMed Scopus (54) Google Scholar. 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In other words, which are the contexts in which, or during which, the local neurons become key players in the immune response. Is a local neuro-immune crosstalk key to maintain local homeostasis, to recruit and activate immune cells (providing signal 2 for the activation of lymphocytes), or to coordinate defense and repair? Is memory encoded in local fibers and neurons that shapes subsequent immune challenges? And ultimately, is the brain involved is such local regulation of immunity, based for example on an immune homunculus? A corollary of such considerations is the role of local neuro-immune interactions in immunopathology, such as inflammatory bowel disease (IBD), with a possible involvement of the brain12Koren T et al.Insular cortex neurons encode and retrieve specific immune responses.Cell. 2021; 184 (1:CAS:528:DC%2BB3MXislajt7zM, 34890554): 621110.1016/j.cell.2021.11.021Abstract Full Text Full Text PDF PubMed Scopus (3) Google Scholar. 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The pro-inflammatory cytokine IL-17a promotes aggregation behaviors and social interactions45Chen C et al.IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses.Nature. 2017; 542 (5503128, 1:CAS:528:DC%2BC2sXht1Oltr0%3D, 28099418): 43-4810.1038/nature20818Crossref PubMed Scopus (61) Google Scholar46Leonardi I et al.Mucosal fungi promote gut barrier function and social behavior via Type 17 immunity.Cell. 2022; 185 (1:CAS:528:DC%2BB38XjvV2lt7Y%3D, 35176228): 831-846 e81410.1016/j.cell.2022.01.017Abstract Full Text Full Text PDF PubMed Scopus (46) Google Scholar, whereas TNFα and IL-1β induce sickness behavior upon infection1Dantzer R O'Connor JC Freund GG Johnson RW Kelley KW From inflammation to sickness and depression: when the immune system subjugates the brain.Nat. Rev. Neurosci. 2008; 9 (2919277, 1:CAS:528:DC%2BD2sXhsVGjsbfJ, 18073775): 46-5610.1038/nrn2297Crossref PubMed Scopus (4760) Google Scholar, forcing withdrawal from social interactions. But what is the impact of chronic activation of the immune and nervous system by a dysbiotic microbiota at mucosae, over weeks, months, or years? Does the common language between the immune and nervous systems provide a basis for crosstalk and cross-regulation, and at the same time, a basis for cross-perturbation and cross-pathology47Rolli-Derkinderen M et al.Is Parkinson's disease a chronic low-grade inflammatory bowel disease?.J. Neurol. 2020; 267 (30989372): 2207-221310.1007/s00415-019-09321-0Crossref PubMed Scopus (38) Google Scholar? I would like to conclude by inviting you to open a new chapter in Mucosal Immunology, and hope that this short discussion will convey the growing excitement in neuroimmunology. I believe that we enter a new age in biological research, where different disciplines are able, more than ever, to crossbreed and generate new physiological concepts. Physiological, because our physical and mental states are, after all, the sum of the interactions of all bodily systems. Towards a genuine understanding (or modeling) of the holobiont48Demas GE Carlton ED Ecoimmunology for psychoneuroimmunologists: considering context in neuroendocrine-immune-behavior interactions.Brain Behav. Immun. 2015; 44 (1:CAS:528:DC%2BC2cXhsFGltLnL, 25218837): 9-1610.1016/j.bbi.2014.09.002Crossref PubMed Scopus (39) Google Scholar, the basis for personalized medicine.

RORγt is a lineage-specifying transcription factor that is expressed by immune cells that are enriched in the gastrointestinal tract and promote immunity, inflammation and tissue homeostasis1–15. However, fundamental questions remain with regard to the cellular heterogeneity among these cell types, the mechanisms that control protective versus inflammatory properties and their functional redundancy. Here we define all RORγt+ immune cells in the intestine at single-cell resolution and identify a subset of group 3 innate lymphoid cells (ILC3s) that expresses ZBTB46, a transcription factor specifying conventional dendritic cells16–20. ZBTB46 is robustly expressed by CCR6+ lymphoid-tissue-inducer-like ILC3s that are developmentally and phenotypically distinct from conventional dendritic cells, and its expression is imprinted by RORγt, fine-tuned by microbiota-derived signals and increased by pro-inflammatory cytokines. ZBTB46 restrains the inflammatory properties of ILC3s, including the OX40L-dependent expansion of T helper 17 cells and the exacerbated intestinal inflammation that occurs after enteric infection. Finally, ZBTB46+ ILC3s are a major source of IL-22, and selective depletion of this population renders mice susceptible to enteric infection and associated intestinal inflammation. These results show that ZBTB46 is a transcription factor that is shared between conventional dendritic cells and ILC3s, and identify a cell-intrinsic function for ZBTB46 in restraining the pro-inflammatory properties of ILC3s and a non-redundant role for ZBTB46+ ILC3s in orchestrating intestinal health. A subset of group 3 innate lymphoid cells (ILC3s) expresses the transcription factor ZBTB46—which was previously thought to be restricted to conventional dendritic cells—and these ILC3s have a role in regulating intestinal health.

Tissue-resident innate lymphoid cells (ILCs) regulate tissue homeostasis, protect against pathogens at mucosal surfaces, and are key players at the interface of innate and adaptive immunity. How ILCs adapt their phenotype and function to environmental cues within tissues remains to be fully understood. Here, we show that Mycobacterium tuberculosis (Mtb) infection alters the phenotype and function of lung IL-18Rα+ ILC toward a protective interferon-γ-producing ILC1-like population. This differentiation is controlled by type 1 cytokines and is associated with a glycolytic program. Moreover, a BCG-driven type I milieu enhances the early generation of ILC1-like cells during secondary challenge with Mtb. Collectively, our data reveal how tissue-resident ILCs adapt to type 1 inflammation toward a pathogen-tailored immune response.

The nervous system and the immune system both rely on an extensive set of modalities to perceive and act on perturbations in the internal and external environments. During feeding, the intestine is exposed to nutrients that may contain noxious substances and pathogens. Here we show that Vasoactive Intestinal Peptide (VIP), produced by the nervous system in response to feeding, potentiates the production of effector cytokines by intestinal type 2 and type 3 innate lymphoid cells (ILC2s and ILC3s). Exposure to VIP alone leads to modest activation of ILCs, but strongly potentiates ILCs to concomitant or subsequent activation by the inducer cytokines IL-33 or IL-23, via mobilization of cAMP and energy by glycolysis. Consequently, VIP increases resistance to intestinal infection by the helminth Trichuris muris and the enterobacteria Citrobacter rodentium. These findings uncover a functional neuro-immune crosstalk unfolding during feeding that increases the reactivity of innate immunity necessary to face potential threats associated with food intake.

Microbial colonization of the mammalian intestine elicits inflammatory or tolerogenic T cell responses, but the mechanisms controlling these distinct outcomes remain poorly understood, and accumulating evidence indicates that aberrant immunity to intestinal microbiota is causally associated with infectious, inflammatory and malignant diseases1–8. Here we define a critical pathway controlling the fate of inflammatory versus tolerogenic T cells that respond to the microbiota and express the transcription factor RORγt. We profiled all RORγt+ immune cells at single-cell resolution from the intestine-draining lymph nodes of mice and reveal a dominant presence of T regulatory (Treg) cells and lymphoid tissue inducer-like group 3 innate lymphoid cells (ILC3s), which co-localize at interfollicular regions. These ILC3s are distinct from extrathymic AIRE-expressing cells, abundantly express major histocompatibility complex class II, and are necessary and sufficient to promote microbiota-specific RORγt+ Treg cells and prevent their expansion as inflammatory T helper 17 cells. This occurs through ILC3-mediated antigen presentation, αV integrin and competition for interleukin-2. Finally, single-cell analyses suggest that interactions between ILC3s and RORγt+ Treg cells are impaired in inflammatory bowel disease. Our results define a paradigm whereby ILC3s select for antigen-specific RORγt+ Treg cells, and against T helper 17 cells, to establish immune tolerance to the microbiota and intestinal health. ILC3s expressing MHC class II control the fate of inflammatory versus tolerogenic T cells that respond to the microbiota by selecting for antigen-specific RORγt+ Treg cells and against TH17 cells, establishing intestinal homoeostasis.

Tumor necrosis factor (TNF) drives chronic inflammation and cell death in the intestine, and blocking TNF is a therapeutic approach in inflammatory bowel disease (IBD). Despite this knowledge, the pathways that protect the intestine from TNF are incompletely understood. Here we demonstrate that group 3 innate lymphoid cells (ILC3s) protect the intestinal epithelium from TNF-induced cell death. This occurs independent of interleukin-22 (IL-22), and we identify that ILC3s are a dominant source of heparin-binding epidermal growth factor–like growth factor (HB-EGF). ILC3s produce HB-EGF in response to prostaglandin E2 (PGE2) and engagement of the EP2 receptor. Mice lacking ILC3-derived HB-EGF exhibit increased susceptibility to TNF-mediated epithelial cell death and experimental intestinal inflammation. Finally, human ILC3s produce HB-EGF and are reduced from the inflamed intestine. These results define an essential role for ILC3-derived HB-EGF in protecting the intestine from TNF and indicate that disruption of this pathway contributes to IBD. TNF is an important driver of many inflammatory diseases. Zhou et al. demonstrate ILC3 production of the growth factor HB-EGF protects against TNF-mediated injury of the gut epithelium in inflammatory bowel disease.

Microbial colonization of the mammalian intestine elicits inflammatory or tolerogenic T cell responses, but the mechanisms controlling these distinct outcomes remain poorly understood and accumulating evidence indicates that aberrant immunity to intestinal microbiota is causally associated with infectious, inflammatory, and malignant diseases 1–8 . Here, we define a critical pathway controlling the fate of inflammatory versus tolerogenic T cells that are specific for the microbiota and express the transcription factor RORγt. We profiled all RORγt + immune cells at single cell resolution from the intestine-draining lymph nodes of mice and reveal a dominant presence of Tregs and lymphoid tissue-induced (LTi)-like group 3 innate lymphoid cells (ILC3s), which co-localize at interfollicular regions. These ILC3s have interconverting potential with RORγt + extrathymic Aire-expressing cells, abundantly express major histocompatibility complex class II, and are necessary and sufficient to promote microbiota-specific RORγt + Tregs and prevent their expansion as inflammatory T helper (Th)17 cells. This occurs through ILC3-mediated antigen-presentation, interleukin-2 gradients, and α v integrin. Finally, single-cell analyses demonstrate that ILC3 and RORγt + Treg interactions are impaired in inflammatory bowel disease. Our results define a novel paradigm whereby ILC3s positively select for antigen specific RORγt + Tregs, and against Th17 cells, to establish immune tolerance to the microbiota and intestinal health.

The spleen contains a myriad of conventional dendritic cell (cDC) subsets that protect against systemic pathogen dissemination by bridging antigen detection to the induction of adaptive immunity. How cDC subsets differentiate in the splenic environment is poorly understood. Here, we report that LTα1β2-expressing Rorgt+ ILC3s, together with B cells, control the splenic cDC niche size and the terminal differentiation of Sirpα+CD4+Esam+ cDC2s, independently of the microbiota and of bone marrow pre-cDC output. Whereas the size of the splenic cDC niche depended on lymphotoxin signaling only during a restricted time frame, the homeostasis of Sirpα+CD4+Esam+ cDC2s required continuous lymphotoxin input. This latter property made Sirpα+CD4+Esam+ cDC2s uniquely susceptible to pharmacological interventions with LTβR agonists and antagonists and to ILC reconstitution strategies. Together, our findings demonstrate that LTα1β2-expressing Rorgt+ ILC3s drive splenic cDC differentiation and highlight the critical role of ILC3s as perpetual regulators of lymphoid tissue homeostasis.

Tissue-resident innate lymphoid cells (ILCs) regulate tissue homeostasis and protect against pathogens at mucosal surfaces and are key players at the interface of innate and adaptive immunity. How ILCs adapt their phenotype and function to environmental cues in their tissue of residence remains to be fully understood. Here we show that Mycobacterium tuberculosis infection alters the biology of lung ILCs and, in particular, induces the emergence of a non-classical, protective, interferon-γ-producing ILC1-like population. Adoptive transfer, fate-mapping and in vitro differentiation experiments revealed that ILC1-like cells originate from immature ILC2 rather than from mature ILC2. This plasticity is controlled by type 1 cytokines and a glycolytic program involving the transcription factor HIF1α. Collectively, our data reveal how tissue-resident ILCs adapt to their inflammatory and metabolic environment to undergo phenotypic and functional changes toward a pathogen-adapted immune response.