Allergic inflammatory memory in human respiratory epithelial progenitor cells

Abstract

Barrier tissue dysfunction is a fundamental feature of chronic human inflammatory diseases. Specialized subsets of epithelial cells-including secretory and ciliated cells-differentiate from basal stem cells to collectively protect the upper airway. Allergic inflammation can develop from persistent activation of type 2 immunity in the upper airway, resulting in chronic rhinosinusitis, which ranges in severity from rhinitis to severe nasal polyps. Basal cell hyperplasia is a hallmark of severe disease, but it is not known how these progenitor cells 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, 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, epigenetic and extrinsic factors 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.

Two to Tango: Dialog between Immunity and Stem Cells in Health and Disease

“…Given their burgeoning role in controlling stem cells, conversations between stem cells and tissue resident immune cells seem likely to become unhinged in disease states. This hypothesis is consistent with a number of pathological conditions are associated with loss of immune regulation, inflammation, and tissue hyperplasia (Gersemann et al, 2011; Lowes et al, 2007; Naik et al, 2017; Ordovas-Montanes et al, 2018a). …”

“…Ordovas-Montanes and colleagues recently extended the findings of non-hematopoietic stem cell memory to respiratory epithelial progenitors in human allergic inflammatory disease (Ordovas-Montanes et al, 2018b). Airway epithelia from chronic rhinitis polyps displayed an enrichment for basal progenitor programs.…”

Single cell transcriptomics of human epidermis reveals basal stem cell transition states

“…The advent of single cell RNA-sequencing (scRNA-seq) technologies has enabled the study of cellular heterogeneity, reconstruction of lineage hierarchies, inference of signaling networks, and has partially enabled the dissemination of functional SC roles in complex tissues. scRNA-seq has been successfully applied to normal human tissues including skin epidermis (Cheng et al, 2018) and dermis (Philippeos et al, 2018;Tabib et al, 2018); skin-related pathologies such as nasal polyps (Ordovas-Montanes et al, 2018), acne, alopecia, leprosy, psoriasis and granuloma annulare (Hughes et al, 2019); and various human cancers including melanoma (Tirosh et al, 2016), breast (Karaayvaz et al, 2018;Nguyen et al, 2018), and head and neck (Puram et al, 2017). In mice, scRNA-seq has revealed extensive functional heterogeneity in skin (Dong et al, 2018;Gupta et al, 2019;Mok et al, 2019;Salzer et al, 2018), hair follicles (Joost et al, 2016;Yang et al, 2017), and regenerative and non-regenerative wounds (Guerrero-Juarez et al, 2019; 5 and CDH3 ( Figure 1C, D).…”

IL-5Rα marks nasal polyp IgG4 and IgE-secreting cells in aspirin-exacerbated respiratory disease

“…Ethmoid scRNA-seq data was obtained from a previously published study, 26 available from the dbGaP database under dbGaP accession 30434. The UMI-collapsed cells-by-genes matrix was input into Seurat, 27 and clustering was conducted as previously described.…”

“…The UMI-collapsed cells-by-genes matrix was input into Seurat, 27 and clustering was conducted as previously described. 26 Iterative clustering was conducted on the previously-defined Plasma cell cluster, consisting of 2,520 cells across 12 patient samples. Briefly, a list of the 1,902 most variable genes among these cells was generated by including genes with an average normalized and scaled expression value greater than 0.22 and with a dispersion (variance/mean) of between 0.22 and 7.…”