Sean P. Spencer

Compartmentalized Control of Skin Immunity by Resident Commensals

Skin Specifics Much of the recent attention paid to the trillions of bacteria that colonize our bodies has been given to the bacteria that reside in the gut. Naik et al. (p. 1115, published online 26 July) report that colonization of the skin with commensal bacteria is important for tuning effector T cell responses in the skin and for protective immunity against cutaneous infection with the parasite Leishmania major in mice. In contrast, selective depletion of the gut microbiota, which plays an important role in modulating immune responses in the gut, had no impact on T cell responses in the skin. The skin microbiota play a selective role in modulating immunity in the skin of mice. Intestinal commensal bacteria induce protective and regulatory responses that maintain host-microbial mutualism. However, the contribution of tissue-resident commensals to immunity and inflammation at other barrier sites has not been addressed. We found that in mice, the skin microbiota have an autonomous role in controlling the local inflammatory milieu and tuning resident T lymphocyte function. Protective immunity to a cutaneous pathogen was found to be critically dependent on the skin microbiota but not the gut microbiota. Furthermore, skin commensals tuned the function of local T cells in a manner dependent on signaling downstream of the interleukin-1 receptor. These findings underscore the importance of the microbiota as a distinctive feature of tissue compartmentalization, and provide insight into mechanisms of immune system regulation by resident commensal niches in health and disease.

IL25 elicits a multipotent progenitor cell population that promotes TH2 cytokine responses

CD4+ T helper 2 (TH2) cells secrete interleukin (IL)4, IL5 and IL13, and are required for immunity to gastrointestinal helminth infections. However, TH2 cells also promote chronic inflammation associated with asthma and allergic disorders. The non-haematopoietic-cell-derived cytokines thymic stromal lymphopoietin, IL33 and IL25 (also known as IL17E) have been implicated in inducing TH2 cell-dependent inflammation at mucosal sites, but how these cytokines influence innate immune responses remains poorly defined. Here we show that IL25, a member of the IL17 cytokine family, promotes the accumulation of a lineage-negative (Lin-) multipotent progenitor (MPP) cell population in the gut-associated lymphoid tissue that promotes TH2 cytokine responses. The IL25-elicited cell population, termed MPPtype2 cells, was defined by the expression of Sca-1 (also known as Ly6a) and intermediate expression of c-Kit (c-Kitint), and exhibited multipotent capacity, giving rise to cells of monocyte/macrophage and granulocyte lineages both in vitro and in vivo. Progeny of MPPtype2 cells were competent antigen presenting cells, and adoptive transfer of MPPtype2 cells could promote TH2 cytokine responses and confer protective immunity to helminth infection in normally susceptible Il25-/- mice. The ability of IL25 to induce the emergence of an MPPtype2 cell population identifies a link between the IL17 cytokine family and extramedullary haematopoiesis, and suggests a previously unrecognized innate immune pathway that promotes TH2 cytokine responses at mucosal sites.

Microbiota-Dependent Crosstalk Between Macrophages and ILC3 Promotes Intestinal Homeostasis

Introduction The gastrointestinal tract is colonized by an extraordinarily large number of commensal microbes and is constantly exposed to ingested antigens and potential pathogens. Regulation of intestinal tolerance thus represents the main task of the immune system of the gut mucosa. Accumulated evidence suggests that gut commensals contribute to the maintenance of intestinal homeostasis, partly through their ability to control the differentiation of effector T lymphocytes in the mucosa and to modulate inflammatory responses through the induction of regulatory T cells (Tregs) and interleukin-10 (IL-10) production. Tissue-resident mononuclear phagocytes (MNPs), including macrophages (MPs) and dendritic cells (DCs), are specifically equipped to detect a wide range of microbial signals and to capture, process, and present extracellular antigenic material to T lymphocytes. MNPs have been shown to contribute to the maintenance of intestinal immune tolerance through the induction or expansion of Tregs in the intestine. Despite their key role in microbial sensing and immune tolerance, the cellular and molecular cues that translate microbial signals into immunoregulatory MNPs in the intestine are not completely understood. ILC3 translate microbial cues into immunoregulatory signals in the intestine. Microbial cues sensed by intestinal MPs lead to IL-1β release. IL-1β engages IL-1R on ILC3, promoting Csf2 release. ILC3-derived Csf2 triggers DC and MP production of regulatory molecules (i.e., RA and IL-10), which, in turn, promotes the induction and expansion of regulatory T cells. Csf2-primed DCs and MPs promote Treg homeostasis locally and in mesenteric lymph nodes. ILC3 translate microbial cues into immunoregulatory signals in the intestine. Microbial cues sensed by intestinal MPs lead to IL-1β release. IL-1β engages IL-1R on ILC3, promoting Csf2 release. ILC3-derived Csf2 triggers DC and MP production of regulatory molecules (i.e., RA and IL-10), which, in turn, promotes the induction and expansion of regulatory T cells. Csf2-primed DCs and MPs promote Treg homeostasis locally and in mesenteric lymph nodes. Rationale The cytokine granulocyte-macrophage colony-stimulating factor (GM-CSF), recently renamed Csf2, is a key determinant of myeloid lineage differentiation and is required for the optimal function of tissue MNPs. Recent results from our laboratory revealed that although Csf2-deficient mice have normal numbers of lymphoid tissue-resident DCs, they display significantly reduced numbers of steady-state nonlymphoid tissue-resident DCs in the small intestine, including the lamina propria CD103+CD11b+ DC subset implicated in the induction of lamina propria Tregs. These results prompted us to further explore the contribution of Csf2 to intestinal immune homeostasis in vivo. We used detailed profiling studies and functional immune assays of the MNP and lymphocyte compartment in the gut, as well as genetically engineered mice that lack Csf2 or the transducer Myd88 specifically in MNPs or lymphocytes, to explore the role of MNPs in the maintenance of immune homeostasis in the gut. Results Our results revealed a crosstalk between IL-1β–secreting MPs and Csf2-producing RORγt+ type 3 innate lymphoid cells (ILC3) in the intestinal mucosa. Microbiota-driven IL-1β production by MPs promoted the release of Csf2 by ILC3, which in turn controlled DCs and MPs to maintain colonic Treg homeostasis. Ablation of Csf2 reduced DC and MP numbers and impaired their ability to produce regulatory factors such as retinoic acid (RA) and IL-10, leading to disrupted Treg homeostasis in the large intestine. Conversely, administration of Csf2 cytokine increased Treg frequency in the gut. Most notably, cell type–specific ablation of IL-1 receptor (IL-1R)–dependent signaling in RORγt+ ILC3 abrogated oral tolerance to dietary antigens and compromised intestinal immune homeostasis in vivo. Although the reduction in Treg numbers was mostly observed in the large intestine, adoptive transfer studies in Csf2–/– mice revealed impaired Treg differentiation both in the small and large intestine, suggesting that Csf2-dependent MNP immunoregulatory functions control Treg induction in both tissues. Conclusion This study established the commensal-driven MNP-ILC-Csf2 axis as a key regulator of intestinal T cell homeostasis in the mouse intestine. Disturbance of this axis radically altered MNP effector function, resulting in impaired oral tolerance to dietary antigens. These results represent an important advance in our understanding of how commensal microbes can regulate host intestinal immunity and may inform the design of novel immunotherapies for patients with inflammatory intestinal diseases with impaired GM-CSF function. Gut Immune Tolerance With the constant assault of food antigens and its billions of resident microbes, the gut is an important site of immune tolerance. By studying specific intestinal immune cell populations in genetically modified mice, Mortha et al. (10.1126/science.1249288, published online 13 March; see the Perspective by Aychek and Jung) found that gut macrophages produce the cytokine interleukin-1 (IL-1) in response to signals derived from the microbiota. IL-1 acts on type 3 innate lymphoid cells in the intestine, which then produce the cytokine, colony-stimulating factor 2 (Csf2). Csf-2, in turn, induces myeloid cells (including dendritic cells and macrophages) to produce regulatory factors like retinoic acid and interleukin-10, which support the conversion and expansion of regulatory T cells, a population of cells known to be critical for maintaining immune tolerance in the gut. Myeloid cells, innate lymphoid cells, and the cytokines they secrete cooperate to maintain immune tolerance in the gut. [Also see Perspective by Aychek and Jung] The intestinal microbiota and tissue-resident myeloid cells promote immune responses that maintain intestinal homeostasis in the host. However, the cellular cues that translate microbial signals into intestinal homeostasis remain unclear. Here, we show that deficient granulocyte-macrophage colony-stimulating factor (GM-CSF) production altered mononuclear phagocyte effector functions and led to reduced regulatory T cell (Treg) numbers and impaired oral tolerance. We observed that RORγt+ innate lymphoid cells (ILCs) are the primary source of GM-CSF in the gut and that ILC-driven GM-CSF production was dependent on the ability of macrophages to sense microbial signals and produce interleukin-1β. Our findings reveal that commensal microbes promote a crosstalk between innate myeloid and lymphoid cells that leads to immune homeostasis in the intestine.

The Role of Retinoic Acid in Tolerance and Immunity

Vitamin A elicits a broad array of immune responses through its metabolite, retinoic acid (RA). Recent evidence indicates that loss of RA leads to impaired immunity, whereas excess RA can potentially promote inflammatory disorders. In this review, we discuss recent advances showcasing the crucial contributions of RA to both immunological tolerance and the elicitation of adaptive immune responses. Further, we provide a comprehensive overview of the cell types and factors that control the production of RA and discuss how host perturbations may affect the ability of this metabolite to control tolerance and immunity or to instigate pathology.

Adaptation of Innate Lymphoid Cells to a Micronutrient Deficiency Promotes Type 2 Barrier Immunity

How the immune system adapts to malnutrition to sustain immunity at barrier surfaces, such as the intestine, remains unclear. Vitamin A deficiency is one of the most common micronutrient deficiencies and is associated with profound defects in adaptive immunity. Here, we found that type 3 innate lymphoid cells (ILC3s) are severely diminished in vitamin A–deficient settings, which results in compromised immunity to acute bacterial infection. However, vitamin A deprivation paradoxically resulted in dramatic expansion of interleukin-13 (IL-13)–producing ILC2s and resistance to nematode infection in mice, which revealed that ILCs are primary sensors of dietary stress. Further, these data indicate that, during malnutrition, a switch to innate type 2 immunity may represent a powerful adaptation of the immune system to promote host survival in the face of ongoing barrier challenges. Vitamin A deficiency alters the balance of innate immune cells in the gut, promoting resistance to nematode infection. An Immune Response to Malnutrition Mucosal surfaces, such as those lining the intestine, are in constant contact with potentially pathogenic microbes, including bacteria and parasitic worms. This necessitates so-called barrier immunity, which is mediated in part by innate lymphoid cells, subsets of which combat specific types of infection. Although malnutrition has been associated with immunosuppression, Spencer et al. (p. 432) now show that vitamin A deficiency selectively activates one branch of barrier immunity. Vitamin A deficiency in mice enhanced immunity to chronic worm infections by increasing the levels of one subset of innate lymphoid cells lacking the corresponding retinoic acid receptor. In contrast, another innate lymphoid cell subset that carries the vitamin A receptor and is important for bacterial immunity was depleted. Thus, the immune system can adapt its response to dietary stress, thereby promoting host survival.

The Transcription Factor GATA3 Is Critical for the Development of All IL-7Rα-Expressing Innate Lymphoid Cells

Innate lymphoid cells (ILCs) are critical in innate immune responses to pathogens and lymphoid organ development. Similar to CD4(+) T helper (Th) cell subsets, ILC subsets positive for interleukin-7 receptor α (IL-7Rα) produce distinct sets of effector cytokines. However, the molecular control of IL-7Rα(+) ILC development and maintenance is unclear. Here, we report that GATA3 was indispensable for the development of all IL-7Rα(+) ILC subsets and T cells but was not required for the development of classical natural killer cells. Conditionally Gata3-deficient mice had no lymph nodes and were susceptible to Citrobactor rodentium infection. After the ILCs had fully developed, GATA3 remained important for the maintenance and functions of ILC2s. Genome-wide gene expression analyses indicated that GATA3 regulated a similar set of cytokines and receptors in Th2 cells and ILC2s, but not in ILC3s. Thus, GATA3 plays parallel roles in regulating the development and functions of CD4(+) T cells and IL-7Rα(+) ILCs.

Distinct requirements for T-bet in gut innate lymphoid cells

The transcription factor T-bet drives the differentiation of NKp46-expressing IL-22–producing innate lymphoid cells

Retinoic acid controls the homeostasis of pre-cDC–derived splenic and intestinal dendritic cells

Retinoic acid is required to maintain pre-DC–derived CD11b+CD8α−Esamhigh dendritic cells (DCs) in the spleen and CD11b+CD103+ DCs in the gut.

The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan

Neutrophils, eosinophils and ‘classical’ monocytes collectively account for about 70% of human blood leukocytes and are among the shortest-lived cells in the body. Precise regulation of the lifespan of these myeloid cells is critical to maintain protective immune responses and minimize the deleterious consequences of prolonged inflammation. However, how the lifespan of these cells is strictly controlled remains largely unknown. Here we identify a long non-coding RNA that we termed Morrbid, which tightly controls the survival of neutrophils, eosinophils and classical monocytes in response to pro-survival cytokines in mice. To control the lifespan of these cells, Morrbid regulates the transcription of the neighbouring pro-apoptotic gene, Bcl2l11 (also known as Bim), by promoting the enrichment of the PRC2 complex at the Bcl2l11 promoter to maintain this gene in a poised state. Notably, Morrbid regulates this process in cis, enabling allele-specific control of Bcl2l11 transcription. Thus, in these highly inflammatory cells, changes in Morrbid levels provide a locus-specific regulatory mechanism that allows rapid control of apoptosis in response to extracellular pro-survival signals. As MORRBID is present in humans and dysregulated in individuals with hypereosinophilic syndrome, this long non-coding RNA may represent a potential therapeutic target for inflammatory disorders characterized by aberrant short-lived myeloid cell lifespan.

Dietary and commensal derived nutrients: shaping mucosal and systemic immunity

The intestine serves as the primary site of nutrient absorption in the body while also harboring the highest burden of commensal microflora and representing a major portal of pathogen exposure. As such, the immune network of the intestine relies on both dietary and commensal derived signals to guide appropriate function. Recent advances highlight the role of dietary derived nutrients and commensal derived metabolites in shaping gastrointestinal immunity. In particular, vitamin A has been shown to have dominant and pleiotropic effects in the intestine. In addition, dietary derived AHR ligands and commensal derived metabolites are now emerging as important players in mucosal immunity. Thus nutrition, commensal microflora and the mucosal immune system are all intimately connected.