SUMMARY Intestinal microbial metabolites are conjectured to affect mucosal integrity through an incompletely characterized mechanism. Here we showed microbial-specific indoles regulated intestinal barrier function through the xenobiotic sensor, pregnane X receptor (PXR). Indole 3-propionic acid (IPA), in the context of indole, is as a ligand for PXR in vivo, and IPA down-regulated enterocyte TNF–α while up-regulated junctional protein-coding mRNAs. PXR-deficient (Nr1i2−/−) mice showed a distinctly “leaky” gut physiology coupled with up-regulation of the Toll-like receptor (TLR) signaling pathway. These defects in the epithelial barrier were corrected in Nr1i2−/−Tlr4−/− mice. Our results demonstrate that a direct chemical communication between the intestinal symbionts and PXR regulates mucosal integrity through a pathway which involves luminal sensing and signaling by TLR4.

Previous studies have shown that some respiratory virus infections leave local populations of tissue TRM cells in the lungs which disappear as heterosubtypic immunity declines. The location of these TRM cells and their contribution to the protective CTL response have not been clearly defined. Here, fluorescence microscopy is used to show that some CD103(+) TRM cells remain embedded in the walls of the large airways long after pulmonary immunization but are absent from systemically primed mice. Viral clearance from the lungs of the locally immunized mice precedes the development of a robust Teff response in the lungs. Whereas large numbers of virus-specific CTLs collect around the bronchial tree during viral clearance, there is little involvement of the remaining lung tissue. Much larger numbers of TEM cells enter the lungs of the systemically immunized animals but do not prevent extensive viral replication or damage to the alveoli. Together, these experiments show that virus-specific antibodies and TRM cells are both required for optimal heterosubtypic immunity, whereas circulating memory CD8 T cells do not substantially alter the course of disease.

Through genetic recombination, the adaptive immune system generates a diverse T cell repertoire allowing recognition of a vast spectrum of foreign antigens. Any given CD8+ T cell specificity is thought to be rare, but none have been directly quantified. Here, major histocompatibility complex tetramer and magnetic-bead technology were coupled to quantitate naive antigen-specific CD8+ T cells and the early response to infection. Among six specificities measured, the number of naive antigen-specific precursors ranged from approximately 80 to 1200 cells/mouse. After vesicular stomatitis virus infection, the antigen-specific CD8+ T cell response occurred in discrete phases: prolonged activation of a subset of cells over the first 72 hr followed by a rapid proliferative burst. Naive precursor frequency altered response kinetics and regulated immunodominance, as well as the time required for the responding population to shift toward CD62L(hi) memory cells. Thus, initial endogenous precursor frequencies were surprisingly diverse and not only regulated initial immune response characteristics but also controlled memory CD8+ T cell lineage decisions.

Reactivation of herpes simplex virus type 1 from neuronal latency is a common and potentially devastating cause of disease worldwide. CD8 + T cells can completely inhibit HSV reactivation in mice, with IFN-γ affording a portion of this protection. Here, we found that CD8 + T cell lytic granules are also required for the maintenance of neuronal latency both in vivo and in ex vivo ganglia cultures, and that their directed release to the junction with neurons in latently infected ganglia did not induce neuronal apoptosis. We describe a non-lethal mechanism of viral inactivation in which the lytic granule component, granzyme B, degrades the herpes simplex virus type 1 immediate early protein, ICP4, which is essential for further viral gene expression.Several lines of evidence support a role for CD8 + T cells in controlling herpes simplex virus type 1 (HSV-1) latency. CD8 + T cells, many expressing granzyme B (GrB), are found juxtaposed to HSV-1 latently infected sensory neurons of both humans (1-4) and mice (5-8). In C57BL/6 mice, CD8 + T cells specific for the immunodominant HSV-1 glycoprotein B 498-505 epitope (gB-CD8) polarize their T cell receptor (TCR) to junctions with neurons in situ forming apparent immunologic synapses (9). Murine gB-CD8 can block HSV-1 reactivation from latency in vivo and in ex vivo ganglia cultures in an MHC-dependent manner (9-11). Because HSV-1 establishes latency solely within ganglionic neurons (12,13), we hypothesize that some latently infected neurons directly present viral antigens to HSV-specific * This manuscript has been accepted for publication in Science. This version has not undergone final editing. Please refer to the complete version of record at http://www.sciencemag.org/. The manuscript may not be reproduced or used in any manner that does not fall within the fair use provisions of the Copyright Act without the prior, written permission of AAAS. Published version available at

This study challenges the concept that herpes simplex virus type 1 (HSV-1) latency represents a silent infection that is ignored by the host immune system, and suggests antigen-directed retention of memory CD8(+) T cells. CD8(+) T cells specific for the immunodominant gB(498-505) HSV-1 epitope are selectively retained in the ophthalmic branch of the latently infected trigeminal ganglion, where they acquire and maintain an activation phenotype and the capacity to produce IFN-gamma. Some CD8(+) T cells showed TCR polarization to junctions with neurons. A gB(498-505) peptide-specific CD8(+) T cell clone can block HSV-1 reactivation from latency in ex vivo trigeminal ganglion cultures. We conclude that CD8(+) T cells provide active surveillance of HSV-1 gene expression in latently infected sensory neurons.

Recurrent herpes simplex virus type 1 (HSV-1) disease usually results from reactivation of latent virus in sensory neurons and transmission to peripheral sites. Therefore, defining the mechanisms that maintain HSV-1 in a latent state in sensory neurons may provide new approaches to reducing susceptibility to recurrent herpetic disease. After primary HSV-1 corneal infection, CD8+ T cells infiltrate the trigeminal ganglia (TGs) of mice, and are retained in latently infected ganglia. Here we demonstrate that CD8+ T cells that are present in the TGs at the time of excision can maintain HSV-1 in a latent state in sensory neurons in ex vivo TG cultures. Latently infected neurons expressed viral genome and some expressed HSV-1 immediate early and early proteins, but did not produce HSV-1 late proteins or infectious virions. Addition of anti-CD8α monoclonal antibody 5 d after culture initiation induced HSV-1 reactivation, as demonstrated by production of viral late proteins and infectious virions. Thus, CD8+ T cells can prevent HSV-1 reactivation without destroying the infected neurons. We propose that when the intrinsic capacity of neurons to inhibit HSV-1 reactivation from latency is compromised, production of HSV-1 immediate early and early proteins might activate CD8+ T cells aborting virion production.

Tissue-resident macrophages are a diverse population of cells that perform specialized functions including sustaining tissue homeostasis and tissue surveillance. Here, we report an interstitial subset of CD169+ lung-resident macrophages that are transcriptionally and developmentally distinct from alveolar macrophages (AMs). They are primarily localized around the airways and are found in close proximity to the sympathetic nerves in the bronchovascular bundle. These nerve- and airway-associated macrophages (NAMs) are tissue resident, yolk sac derived, self-renewing, and do not require CCR2+ monocytes for development or maintenance. Unlike AMs, the development of NAMs requires CSF1 but not GM-CSF. Bulk population and single-cell transcriptome analysis indicated that NAMs are distinct from other lung-resident macrophage subsets and highly express immunoregulatory genes under steady-state and inflammatory conditions. NAMs proliferated robustly after influenza infection and activation with the TLR3 ligand poly(I:C), and in their absence, the inflammatory response was augmented, resulting in excessive production of inflammatory cytokines and innate immune cell infiltration. Overall, our study provides insights into a distinct subset of airway-associated pulmonary macrophages that function to maintain immune and tissue homeostasis.

We recently demonstrated that CD8؉ T cells could block herpes simplex virus type 1 (HSV-1) reactivation from latency in ex vivo trigeminal ganglion (TG) cultures without destroying the infected neurons. Here we establish that CD8؉ T-cell prevention of HSV-1 reactivation from latency is mediated at least in part by gamma interferon (IFN-␥). We demonstrate that IFN-␥ was produced in ex vivo cultures of dissociated latently infected TG by CD8 ؉ T cells that were present in the TG at the time of excision. Depletion of CD8 ؉ T cells or neutralization of IFN-␥ significantly enhanced the rate of HSV-1 reactivation from latency in TG cultures. When TG cultures were treated with acyclovir for 4 days to insure uniform latency, supplementation with recombinant IFN-␥ blocked HSV-1 reactivation in 80% of cultures when endogenous CD8 ؉ T cells were present and significantly reduced and delayed HSV-1 reactivation when CD8 ؉ T cells or CD45 ؉ cells were depleted from the TG cultures. The effectiveness of recombinant IFN-␥ in blocking HSV-1 reactivation was lost when its addition to TG cultures was delayed by more than 24 h after acyclovir removal. We propose that when the intrinsic ability of neurons to inhibit HSV-1 gene expression is compromised, HSV-specific CD8 ؉ T cells are rapidly mobilized to produce IFN-␥ and perhaps other antiviral cytokines that block the viral replication cycle and maintain the viral genome in a latent state.Following primary infection of epithelial surfaces, herpes simplex virus type 1 (HSV-1) gains access to the termini of sensory neurons, is transported in a retrograde direction to the neuron cell bodies in sensory ganglia, replicates, spreads to other neurons, and establishes a lifelong latent infection in a portion of the neurons. Recurrent HSV-1 disease results from reactivation of latent HSV-1 in sensory neurons followed by anterograde axonal transport to epithelial or epidermal surfaces. Therefore, treatments that block reactivation of HSV-1 from latency could effectively prevent recurrent disease in the face of latent infection. The long-term retention of CD8 ϩ T cells and production of the cytokine gamma interferon (IFN-␥) in the latently infected trigeminal ganglion (TG) suggest a possible role for the immune system in controlling HSV-1 reactivation from latency (4,10,16,20).Ganglionic latency is classically defined as retention of HSV-1 genomes in neurons in the absence of virion production. The definition of latency at the molecular level is currently evolving. Clearly, a family of transcripts called latencyassociated transcripts is produced in abundance in at least a portion of latently infected neurons (6, 7). In addition, transcripts for the HSV-1 ␣ (immediate-early) gene, infected cell protein 4 (ICP4), and ␤ (early) gene thymidine kinase were detected in low abundance in latently infected murine sensory ganglia (13). Most studies have failed to detect latency-associated transcript translation products, and the production of any viral proteins in latently infected neurons is currentl...