SUMMARY Tissue-resident memory T cells (TRM) in mice mediate optimal protective immunity to infection and vaccination, while in humans, the existence and properties of TRM remain unclear. Here, we use a unique human tissue resource to determine whether human tissue memory T cells comprise a distinct subset in diverse mucosal and lymphoid tissues. We identify a core transcriptional profile within the CD69+ subset of memory CD4+ and CD8+ T cells in lung and spleen that is distinct from that of CD69−TEM cells in tissues and circulation, and defines human TRM based on homology to the transcriptional profile of mouse CD8+TRM. Human TRM in diverse sites exhibit increased expression of adhesion and inhibitory molecules, produce both pro-inflammatory and regulatory cytokines, and have reduced proliferation compared with circulating TEM, suggesting unique adaptations for in situ immunity. Together our results provide a unifying signature for human TRM and a blueprint for designing tissue-targeted immunotherapies.

Recapitulation of lung development from human pluripotent stem cells (hPSCs) in three dimensions (3D) would allow deeper insight into human development, as well as the development of innovative strategies for disease modeling, drug discovery and regenerative medicine1. We report here the generation from hPSCs of lung bud organoids (LBOs) that contain mesoderm and pulmonary endoderm and develop into branching airway and early alveolar structures after xenotransplantation and in Matrigel 3D culture. Expression analysis and structural features indicated that the branching structures reached the second trimester of human gestation. Infection in vitro with respiratory syncytial virus, which causes small airway obstruction and bronchiolitis in infants2, led to swelling, detachment and shedding of infected cells into the organoid lumens, similar to what has been observed in human lungs3. Introduction of mutation in HPS1, which causes an early-onset form of intractable pulmonary fibrosis4,5, led to accumulation of extracellular matrix and mesenchymal cells, suggesting the potential use of this model to recapitulate fibrotic lung disease in vitro. LBOs therefore recapitulate lung development and may provide a useful tool to model lung disease.

SUMMARY Maturation and migration to lymph nodes (LNs) constitutes a central paradigm in conventional dendritic cell (cDC) biology, but remains poorly defined in humans. Using our organ donor tissue resource, we analyzed cDC subset distribution, maturation and migration in mucosal tissues (lungs, intestines), associated lymph nodes (LNs), and other lymphoid sites from 78 individuals aged <1–93years. The distribution of cDC1 (CD141hiCD13hi) and cDC2 (Sirp-α+CD1c+) subsets was a function of tissue site and conserved between donors. We identified cDC2 as the major mature (HLA-DRhi) subset in LNs with the highest frequency in lung-draining LNs. Mature cDC2 in mucosal-draining LNs expressed tissue-specific markers derived from the paired mucosal site, reflecting their tissue-migratory origin. These distribution and maturation patterns were largely maintained throughout life, with site-specific variations. Our findings provide evidence for localized DC tissue surveillance and reveal a lifelong division of labor between DC subsets, with cDC2 functioning as guardians of the mucosa.

SUMMARYTissue-resident memory T cells (TRM) in mice mediate optimal protective immunity to infection and vaccination, while in humans, the existence and properties of TRM remain unclear. Here, we use a unique human tissue resource to determine whether human tissue memory T cells comprise a distinct subset in diverse mucosal and lymphoid tissues. We identify a core transcriptional profile within the CD69 + subset of memory CD4 + and CD8 + T cells in lung and spleen that is distinct from that of CD69 − TEM cells in tissues and circulation, and defines human TRM based on homology to the transcriptional profile of mouse CD8 + TRM. Human TRM in diverse sites exhibit increased expression of adhesion and inhibitory molecules, produce both pro-inflammatory and regulatory cytokines, and have reduced proliferation compared with circulating TEM, suggesting * Correspondence and lead contact: df2396@cumc.columbia.edu. 6 These authors contributed equally. 7 Senior author Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. AUTHOR CONTRIBUTIONS ACCESSION NUMBERSThe accession number for the RNA-Seq data reported in this paper is GEO: GSE94964. HHS Public Access eTOC BlurbKumar et al. identify a core transcriptional and phenotypic signature which defines human TRM for both CD4 + and CD8 + T cells that is preserved across diverse individuals and in mucosal and lymphoid sites.

The basis for the switch from CCR5 to CXCR4 coreceptor usage seen in ϳ50% of human immunodeficiency virus type 1 (HIV-1) subtype B-infected individuals as disease advances is not well understood. Among the reasons proposed are target cell limitation and better immune recognition of the CXCR4 (X4)-tropic compared to the CCR5 (R5)-tropic virus. We document here X4 virus emergence in a rhesus macaque (RM) infected with R5-tropic simian/human immunodeficiency virus, demonstrating that coreceptor switch can happen in a nonhuman primate model of HIV/AIDS. The switch to CXCR4 usage in RM requires envelope sequence changes in the V3 loop that are similar to those found in humans, suggesting that the R5-to-X4 evolution pathways in the two hosts overlap. Interestingly, compared to the inoculating R5 virus, the emerging CXCR4-using virus is highly neutralization sensitive. This finding, coupled with the observation of X4 evolution and appearance in an animal with undetectable circulating virus-specific antibody and low cellular immune responses, lends further support to an inhibitory role of antiviral immunity in HIV-1 coreceptor switch.The human immunodeficiency virus (HIV) enters target cells via interaction of the viral glycoprotein with the cellular receptor CD4 and two principal coreceptors, CCR5 (R5 viruses) and CXCR4 (X4 viruses) (2). Most HIV type 1 (HIV-1) transmission results in a predominantly R5 virus infection. With time, X4 variants arise and coexist with R5 virus variants in ϳ50% of subtype B-infected individuals, and this event is associated with rapid CD4 ϩ T-cell loss and disease progression (22, 37). The determinant(s) of phenotypic change from R5 to X4 maps largely to the V3 loop of the envelope gp120 (6, 18, 39) and can be inferred by analysis of the amino acid sequence of this region (11). Although the underlying basis for virus coreceptor switch late in infection remains ill defined, several hypotheses that include changes in target cell populations during the course of infection and/or differential immune recognition of X4 and R5 viruses have been proposed (31,34). Furthermore, it is unclear whether X4 viruses evolve during the course of infection or are transmitted but selected against early in infection.We have used infection of rhesus macaques (RM) with simian/human immunodeficiency viruses (SHIV) expressing the envelopes of X4 and R5 HIV-1 isolates to study the impact of coreceptor usage in virus transmission and pathogenesis. We previously reported that both X4 and R5 SHIVs can be transmitted intravenously or intravaginally but showed that the basis for the immunodeficiencies caused by these viruses is different. Whereas primary infection with X4 SHIV caused severe and sustained peripheral blood and secondary lymphoid tissue CD4ϩ T-cell loss, infection with R5 SHIV resulted in transient loss of CD4 ϩ T cells at these sites (15, 17). Thus, infection with SHIVs of different coreceptor usage recapitulates the different stages of HIV infection in humans: R5 SHIV provides a model of early infection ...