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Type I (IFN-α/β) and type III (IFN-λ) interferons (IFNs) exert shared antiviral activities through distinct receptors. However, their relative importance for antiviral protection of different organ systems against specific viruses remains to be fully explored. We used mouse strains deficient in type-specific IFN signaling, STAT1 and Rag2 to dissect distinct and overlapping contributions of type I and type III IFNs to protection against homologous murine (EW-RV strain) and heterologous (non-murine) simian (RRV strain) rotavirus infections in suckling mice. Experiments demonstrated that murine EW-RV is insensitive to the action of both types of IFNs, and that timely viral clearance depends upon adaptive immune responses. In contrast, both type I and type III IFNs can control replication of the heterologous simian RRV in the gastrointestinal (GI) tract, and they cooperate to limit extra-intestinal simian RRV replication. Surprisingly, intestinal epithelial cells were sensitive to both IFN types in neonatal mice, although their responsiveness to type I, but not type III IFNs, diminished in adult mice, revealing an unexpected age-dependent change in specific contribution of type I versus type III IFNs to antiviral defenses in the GI tract. Transcriptional analysis revealed that intestinal antiviral responses to RV are triggered through either type of IFN receptor, and are greatly diminished when receptors for both IFN types are lacking. These results also demonstrate a murine host-specific resistance to IFN-mediated antiviral effects by murine EW-RV, but the retention of host efficacy through the cooperative action by type I and type III IFNs in restricting heterologous simian RRV growth and systemic replication in suckling mice. Collectively, our findings revealed a well-orchestrated spatial and temporal tuning of innate antiviral responses in the intestinal tract where two types of IFNs through distinct patterns of their expression and distinct but overlapping sets of target cells coordinately regulate antiviral defenses against heterologous or homologous rotaviruses with substantially different effectiveness.

Whether activated inflammatory macrophages can adopt features of tissue resident macrophages and what mechanisms mediate this phenotypic conversion remain unclear. Here we show that vitamin A was required for phenotypic conversion of interleukin 4 (IL-4)-activated monocyte-derived F4/80intCD206+PD-L2+MHCII+ macrophages into macrophages with a tissue-resident F4/80hiCD206−PD-L2−MHCII−UCP1+ phenotype in the peritoneal cavity of mice and during liver granuloma formation in mice infected with Schistosoma mansoni. Phenotypic conversion of F4/80intCD206+ macrophages into F4/80hiCD206− macrophages was associated with almost complete remodeling of the chromatin landscape, as well as alteration of the transcriptional profiles. Vitamin A deficient mice infected with S. mansoni had disrupted liver granuloma architecture and increased mortality, indicating that failure to convert from F4/80intCD206+ macrophages to F4/80hiCD206− macrophages may lead to dysregulated inflammation during helminth infection.

32The immune systems of free-living mammals such as humans and wild mice display a 33 heightened degree of activation compared with laboratory mice maintained under artificial 34 conditions. Here, we demonstrate that releasing inbred laboratory mice into an outdoor enclosure 35to mimic life in a natural environment alters the state of immunity. In addition to enhancing the 36 differentiation of T cell populations previously associated with pathogen exposure, we found that 37 outdoor release of mice led to an increase in circulating granulocytes. However, rewilded mice 38 were not infected by pathogens previously implicated in immune activation. Rather, changes to 39 the immune system were associated with an altered composition of the microbiota, and fungi 40 isolated from rewilded mice were sufficient to increase circulating granulocytes. These findings 41 establish an experimental procedure to investigate the impact of the natural environment on 42 immune development and identify a role for sustained fungal exposure in determining 43 granulocyte numbers. 44 45 46 48 research and has enabled fundamental advances in basic immunology. Yet, this ubiquitous model 49 fails to recreate certain aspects of human immunity. Inbred laboratory mice and adult humans 50 differ in the proportion of leukocyte subsets, transcriptional responses to microbial challenges, 51 and other immune parameters (Masopust et al., 2017; Tao and Reese, 2017). Such differences 52 may limit the predictive value of experiments with mice when studying complex inflammatory 53 and infectious diseases, resulting in significant shortcomings in translating laboratory 54 observations to humans. 55Recent findings suggest that this shortcoming of the rodent model may be due to the 56 specific pathogen free (SPF) environment in which they are maintained. Wild mice and pet store 57 mice, both of which are exposed to a litany of pathogens that are typically excluded from SPF 58 facilities, display an abundance of differentiated memory T cells that more closely resembles the 59 state of immunity in adult humans (Abolins et al., 2017; Beura et al., 2016; Choi et al., 2019). 60Similarly, transferring embryos from lab mice into wild mice generates commensal-and 61 pathogen-exposed offspring (wildlings) that more faithfully recreate human immunity than 62 standard SPF mice, including the unresponsiveness to immunotherapies that failed in clinical 63 trials (Rosshart et al., 2019). Sequentially infecting SPF mice with 3 viruses and a helminth shifts 64 the gene expression profile of peripheral blood mononuclear cells (PBMCs) towards that of pet 65 store mice and adult humans (Reese et al., 2016), further highlighting the role for pathogen 66 experience in normalizing the immune system. SPF mice are also distinguished from free-living 67 mammals by the lack of exposure to potentially immuno-stimulatory members of the microbiota 68 that are absent in a laboratory animal facility. For example, the offspring of germ-free mice 69 inoculated with ileocecal contents from ...

The etiology of ulcerative colitis is poorly understood and is likely to involve perturbation of the complex interactions between the mucosal immune system and the commensal bacteria of the gut, with cytokines acting as important cross-regulators. Here we use IFN receptor-deficient mice in a dextran sulfate sodium (DSS) model of acute intestinal injury to study the contributions of type I and III interferons (IFN) to the initiation, progression and resolution of acute colitis. We find that mice lacking both types of IFN receptors exhibit enhanced barrier destruction, extensive loss of goblet cells and diminished proliferation of epithelial cells in the colon following DSS-induced damage. Impaired mucosal healing in double IFN receptor-deficient mice is driven by decreased amphiregulin expression, which IFN signaling can up-regulate in either the epithelial or hematopoietic compartment. Together, these data underscore the pleiotropic functions of IFNs and demonstrate that these critical antiviral cytokines also support epithelial regeneration following acute colonic injury.

How the human intestinal immune system is distinctly organized to respond to inflammation is still poorly understood. Here, we used single-cell RNA-sequencing to examine lamina propria CD45+ hematopoietic cells from patients with inflammatory bowel disease that have undergone ileal pouch-anal anastomosis, or the colon mucosa of ulcerative colitis patients. We identified a population of IL1B+ antimicrobial macrophages and FOXP3/+BATF+ T cells that are associated and expanded in inflamed tissues, which we further validated in other scRNA-seq datasets from IBD patients. CD8+ T cells were unexpectedly more abundant in the pouch than colon. Cell type specific markers obtained from single-cell RNA-sequencing was used to infer representation from bulk RNA sequencing datasets, which further implicated antimicrobial macrophages expressing IL1B with S100A8/A9 calprotectin as being associated with inflammation, as well as Bacteroides and Escherichia bacterial species. Finally, we find that non-responsiveness to anti-integrin biologic therapies in UC patients is associated with the signature of this antimicrobial macrophage population in a subset of patients. This study identified conserved and distinct features of intestinal inflammation between parts of the small and large intestine undergoing similar inflammation conditions..

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