scRNA-seq (10x) from pediatric human terminal ileum show ACE2 and TMPRSS2 are most enriched within GSTA1+MGST3+ absorptive enterocytes. We collected single-cell RNA-seq data from biopsies of the human terminal ileum (epithelial and lamina propria) across 13 children diagnosed with functional gastrointestinal disease (without inflammation) and ranging in age 6-18 years old. Ileal absorptive epithelial cells appear significantly enriched for ACE2 and TMPRSS2 expression. Furthermore, we identify a subset (888 cells, ~6.5% of epithelial cells) which co-express both genes. By identifying rare co-expressing cells, we are able to perform differential expression testing and GO-term enrichment to highlight putative biological functions enriched within these cells such as... (continued)

Barrier tissue dysfunction is a fundamental feature of chronic human inflammatory diseases1. 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)... (continued)

In previously-unpublished NHP (Macaca mulatta) study, lung and ileal tissue was collected following necropsy of healthy adult animals, and analyzed using Seq-Well v1. From lung samples, we recovered at least 17 distinct major cell types, including various lymphoid, myeloid, and stromal populations. ACE2 and TMPRSS2 were primarily expressed in epithelial cells, with 6.7% of type II pneumocytes expressing ACE2, and 3.8% co-expressing ACE2 and TMPRSS2. Notably, the only double positive cells observed were classified within the type II pneumocyte population. We compared ACE2+ with ACE2- type II pneumocytes to explore broader gene programs that differentiate putative SARS-CoV-2-target cells from cells... (continued)

In this study, samples from adult human duodenum and ileum were collected and split for primary tissue single-cell RNA-seq and organoid culture. Human donor tissue was non-inflammed, with terminal ileum samples collected via pinch biopsy during the course of routine colonoscopy, and duodenal samples taken from excess tissue collected during bulk surgical resection. Organoids were cultured and passaged every 6-8 days in Matrigel domes with established media conditions meant to recapitulate the broad diversity of in vivo epithelial cell types (Fujii, M., et al., Cell Stem Cell. 2018). Organoid culture media contained recombinant Noggin, Rspondin-3, FGF2, IGF1, afamin-Wnt3A, in addition... (continued)

Epithelial cells were computationally identified from scRNA-Seq from samples of tissue consisting of granuloma and adjacent, uninvolved lung samples from 10 Mtb-infected NHPs were collected with Seq-Well S^3. Here we show Type 1 Pneumocytes, Type 2 Pneumocytes, Secretory, and Multiciliated subsets of these single cells to facilitate inquiry into the susceptibility of these cells to respiratory viruses, specifically COVID-19. We find that Type 2 Pneumocytes are enriched for cells that co-express the COVID-19 receptor (ACE2) and associated protease (TMPRSS2) and these cells are more frequently found in samples from granulomatous regions of the lung. Note that since this is a pre-publication... (continued)