Allergic inflammatory memory in human respiratory epithelial progenitor cells

Barrier tissue dysfunction is a fundamental feature of chronic human inflammatory diseases [superscript 1]. Specialized subsets of epithelial cells—including secretory and ciliated cells—differentiate from basal stem cells to collectively protect the upper airway [superscript 2–4]. Allergic inflammation can develop from persistent activation [superscript 5] of type 2 immunity [superscript 6] in the upper airway, resulting in chronic rhinosinusitis, which ranges in severity from rhinitis to severe nasal polyps [superscript 7]. Basal cell hyperplasia is a hallmark of severe disease [superscript 7–9], but it is not known how these progenitor cells [superscript 2,10,11] contribute to clinical presentation and barrier tissue dysfunction in humans. Here we profile primary human surgical chronic rhinosinusitis samples (18,036 cells, n = 12) that span the disease spectrum using Seq-Well for massively parallel single-cell RNA sequencing [superscript 12], report transcriptomes for human respiratory epithelial, immune and stromal cell types and subsets from a type 2 inflammatory disease, and map key mediators. By comparison with nasal scrapings (18,704 cells, n = 9), we define signatures of core, healthy, inflamed and polyp secretory cells. We reveal marked differences between the epithelial compartments of the non-polyp and polyp cellular ecosystems, identifying and validating a global reduction in cellular diversity of polyps characterized by basal cell hyperplasia, concomitant decreases in glandular cells, and phenotypic shifts in secretory cell antimicrobial expression. We detect an aberrant basal progenitor differentiation trajectory in polyps, and propose cell-intrinsic [superscript 13], epigenetic [superscript 14,15] and extrinsic factors [superscript 11,16,17] that lock polyp basal cells into this uncommitted state. Finally, we functionally demonstrate that ex vivo cultured basal cells retain intrinsic memory of IL-4/IL-13 exposure, and test the potential for clinical blockade of the IL-4 receptor α-subunit to modify basal and secretory cell states in vivo. Overall, we find that reduced epithelial diversity stemming from functional shifts in basal cells is a key characteristic of type 2 immune-mediated barrier tissue dysfunction. Our results demonstrate that epithelial stem cells may contribute to the persistence of human disease by serving as repositories for allergic memories. KNational Institutes of Health (U.S.) (Grant 1DP2OD020839)National Institutes of Health (U.S.) (Grant 2U19AI089992)National Institutes of Health (U.S.) (Grant 1U54CA217377)National Institutes of Health (U.S.) (Grant P01AI039671)National Institutes of Health (U.S.) (Grant 5U24AI118672)National Institutes of Health (U.S.) (Grant 2RM1HG006193)National Institutes of Health (U.S.) (Grant 1R33CA202820)National Institutes of Health (U.S.) (Grant 2R01HL095791)National Institutes of Health (U.S.) (Grant 1R01AI138546)National Institutes of Health (U.S.) (Grant 1R01HL126554)National Institutes of Health (U.S.) (Grant 1R01DA046277)National Institutes of Health (U.S.) (Grant 2R01HL095791)Bill & Melinda Gates Foundation (Grant OPP1139972)Bill & Melinda Gates Foundation (Grant OPP1116944)National Institutes of Health (U.S.) (Grant 2R01GM081871–09 )National Cancer Institute (U.S.) (Grant P30-CA14051)National Institutes of Health (U.S.). Center for AIDS Research (Award P30 AI060354

Prevention of tuberculosis in macaques after intravenous BCG immunization

Mycobacterium tuberculosis (Mtb) is the leading cause of death from infection worldwide1. The only available vaccine, BCG (Bacillus Calmette–Guérin), is given intradermally and has variable efficacy against pulmonary tuberculosis, the major cause of mortality and disease transmission1,2. Here we show that intravenous administration of BCG profoundly alters the protective outcome of Mtb challenge in non-human primates (Macaca mulatta). Compared with intradermal or aerosol delivery, intravenous immunization induced substantially more antigen-responsive CD4 and CD8 T cell responses in blood, spleen, bronchoalveolar lavage and lung lymph nodes. Moreover, intravenous immunization induced a high frequency of antigen-responsive T cells across all lung parenchymal tissues. Six months after BCG vaccination, macaques were challenged with virulent Mtb. Notably, nine out of ten macaques that received intravenous BCG vaccination were highly protected, with six macaques showing no detectable levels of infection, as determined by positron emission tomography–computed tomography imaging, mycobacterial growth, pathology and granuloma formation. The finding that intravenous BCG prevents or substantially limits Mtb infection in highly susceptible rhesus macaques has important implications for vaccine delivery and clinical development, and provides a model for defining immune correlates and mechanisms of vaccine-elicited protection against tuberculosis

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

To explore the distinct genotypic and phenotypic states of melanoma tumors, we applied single-cell RNA sequencing (RNA-seq) to 4645 single cells isolated from 19 patients, profiling malignant, immune, stromal, and endothelial cells. Malignant cells within the same tumor displayed transcriptional heterogeneity associated with the cell cycle, spatial context, and a drug-resistance program. In particular, all tumors harbored malignant cells from two distinct transcriptional cell states, such that tumors characterized by high levels of the MITF transcription factor also contained cells with low MITF and elevated levels of the AXL kinase. Single-cell analyses suggested distinct tumor microenvironmental patterns, including cell-to-cell interactions. Analysis of tumor-infiltrating T cells revealed exhaustion programs, their connection to T cell activation and clonal expansion, and their variability across patients. Overall, we begin to unravel the cellular ecosystem of tumors and how single-cell genomics offers insights with implications for both targeted and immune therapies.National Cancer Institute (U.S.) (1U24CA180922)National Cancer Institute (U.S.) (P30-CA14051