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

The ongoing COVID-19 pandemic caused by infection with the novel coronavirus SARS-CoV-2 prompted us to leverage our lung scRNA-seq dataset and interrogate expression patterns of the SARS-Cov-2 receptor ACE2 in lung epithelial cells. We found that the fraction of ACE2-expressing cells among all lung epithelial cells was low (n= 1,208, 1.7%) (Fig. 2a) . The highest fractions of ACE2expressing cells were found in the malignant (3.5%), AT2 (2.2%) and club/secretory (2.4%) cell clusters (Fig. 2a) . Among those clusters with > 1% ACE2-positive cells, AT2 cells expressed the highest expression of ACE2 (Fig. 2b) . We then explored expression patterns of other members of the RAS 27 (Fig. 2c) . Of note, RAS genes were expressed at low levels in AT2 cells compared to other epithelial cell subsets and AT1 cells exhibited relatively higher expression of various RAS members such as adrenergic 2 beta receptor (ADRB2) (Fig. 2c) . We then examined ACE2 expression in subclusters of AT2 and malignant cells, the two populations with relatively highest fraction of cells positive for the SARS-CoV-2 receptor (Fig. S2) . The AT2 subcluster (AT2_c2) with relatively highest expression of ACE2 ( Fig. S2a and Fig. S2b ) exhibited similar levels of RAS genes compared to other AT2 subclusters except for elevated expression of amyloid precursor protein (APP) and the carboxypeptidase CPM (Fig. S2c) . Similarly, we did not find similar patterns of expression between The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.16.045617 doi: bioRxiv preprint significantly higher in losartan treated patients (P < 10 -16 ; Fig. S3 ). We also examined the expression and abundance patterns of TMPRS22, a serine protease recently shown to be crucial for SARS-CoV-2 spike protein priming upon host cell entry 6 , as well as ADAM17, a sheddase that was shown to cleave (shed) ACE2 30 . TMPRSS2 expression level and frequency were highest in AT2 cells among all lung subsets, whereas ADAM17 expression levels were highest in malignant cells (Fig. S4) . Also, among AT2 cells, expression levels of TMPRSS2 and ADAM17 were highest in the same AT2 subcluster as ACE2 (Figs. S2b and S4b) .