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

In addition to the bioinformatics approaches described above, all other statistical analysis was performed using R v3.6.0. Analysis of differences in genes between groups (e.g., between ACE2postive vs. ACE2-negative; smoker vs. non/light smoker) were calculated using the FindMarkers function in R. Pseudo-bulk gene expression values for defined cell clusters were calculated by taking mean expression of each gene across all cells in a specific cluster. Deconvolution of AT2 cell abundance was performed on the TCGA lung adenocarcinoma cohort by incorporating AT2 signature genes defined by our study into MCP-counter, an R package that permits the quantification of the absolute abundance of immune and stromal cell populations in heterogeneous tissues from transcriptome data 20 . All statistical significance testing was two-sided, and results were considered statistically significant at p-value < 0.05. The Benjamini-Hochberg method was applied to control the . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the .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 false discovery rate (FDR) in multiple comparisons (e.g. DEG analysis), and calculate adjusted pvalues (q-values).