Single-cell analysis of human lung epithelia reveals concomitant expression of the SARS-CoV-2 receptor ACE2 with multiple virus receptors and scavengers in alveolar type II cells

Guangchun Han; Ansam Sinjab; Warapen Treekitkarnmongkol; Patrick Brennan; Kieko Hara; Kyle Chang; Elena Bogatenkova; Beatriz Sanchez-Espiridion; Carmen Behrens; Boning Gao; Luc Girard; Jianjun Zhang; Boris Sepesi; Tina Cascone; Lauren Byers; Don L. Gibbons; Jichao Chen; Seyed Javad Moghaddam; Edwin J. Ostrin; Junya Fujimoto; Jerry Shay; John V. Heymach; John D. Minna; Steven Dubinett; Paul A. Scheet; Ignacio I. Wistuba; Edward Hill; Shannon Telesco; Christopher Stevenson; Avrum E. Spira; Linghua Wang; Humam Kadara

We performed single-cell analysis of normal lung tissues and matched treatment-naïve early-stage lung adenocarcinomas (LUADs) from five patients using droplet based scRNA-seq. We first processed two normal lung tissues and a LUAD from patient 1 which resulted in 15,370 cells that were retained for analysis. In line with studies of other organs 21 , we noted that the fraction of epithelial (EPCAM+) cells attained by unbiased analysis of lung tissues was limited (~4%, n = 624 cells) ( Table 2) . To better capture lung epithelial cells, including their heterogeneity, we performed single-cell analysis of fluorescent-activated cell sorting (FACS) enriched EPCAM+ cells from three normal lung tissues (per patient) and LUADs from four additional patients. Using this strategy, we were able to capture on average 20-fold more lung epithelial cells ( Table 2 ). Following quality control and filtering, we retained 70,085 lung epithelial cells from the 19 samples (5 tumor samples, n = 13,134 cells; 14 normal lung tissues, n = 56,951 cells) (Fig. 1a) . We achieved on average 146,574 reads, 9,202 unique molecular identifiers and 2,407 genes per cell ( Table 2) . Unsupervised clustering analysis identified a diverse repertoire of airway lineages which were divided into 10 cell clusters with distinct transcriptomic features (e.g., expression of lineage-specific markers) (Fig. 1a) . These cell Fig. 1c and Fig. S1 ). One cluster included bronchioalveolar cells that were enriched for markers of both AT2 and club lineages (Fig. 1b) . We also identified alveolar transitory or progenitor cells which expressed both AT2 and AT1 markers including HOPX as well as KRT7 (Fig. 1c) in line with previous reports 22, 23 .