Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Christoph Muus; Malte D Luecken; Gokcen Eraslan; Avinash Waghray; Graham Heimberg; Lisa Sikkema; Yoshihiko Kobayashi; Eeshit Dhaval Vaishnav; Ayshwarya Subramanian; Christopher Smillie; Karthik Jagadeesh; Elizabeth Thu Duong; Evgenij Fiskin; Elena Torlai Triglia; Christophe Becavin; Meshal Ansari; Peiwen Cai; Brian Lin; Justin Buchanan; Sijia Chen; Jian Shu; Adam L Haber; Hattie Chung; Daniel T Montoro; Taylor Adams; Hananeh Aliee; Samuel J Allon; Zaneta Andrusivova; Ilias Angelidis; Orr Ashenberg; Kevin Bassler; Christophe Becavin; Inbal Benhar; Joseph Bergenstrahle; Ludvig Bergenstrahle; Liam Bolt; Emelie Braun; Linh T Bui; Mark Chaffin; Evgeny Chichelnitskiy; Joshua Chiou; Thomas M Conlon; Michael S Cuoco; Marie Deprez; David S Fischer; Astrid Gillich; Joshua Gould; Minzhe Guo; Austin J Gutierrez; Arun C Habermann; Tyler Harvey; Peng He; Xiaomeng Hou; Lijuan Hu; Alok Jaiswal; Peiyong Jiang; Theodoros Kapellos; Christin S Kuo; Ludvig Larsson; Michael A Leney-Greene; Kyungtae Lim; Monika Litvinukova; Ji Lu; Leif S Ludwig; Wendy Luo; Henrike Maatz; Elo Maddissoon; Lira Mamanova; Kasidet Manakongtreecheep; Charles-Hugo Marquette; Ian Mbano; Alexi M McAdams; Ross J Metzger; Ahmad N Nabhan; Sarah K Nyquist; Jose Ordovas-Montanes; Lolita Penland; Olivier B Poirion; Segio Poli; CanCan Qi; Daniel Reichart; Ivan Rosas; Jonas Schupp; Rahul Sinha; Rene V Sit; Kamil Slowikowski; Michal Slyper; Neal Smith; Alex Sountoulidis; Maximilian Strunz; Dawei Sun; Carlos Talavera-Lopez; Peng Tan; Jessica Tantivit; Kyle J Travaglini; Nathan R Tucker; Katherine Vernon; Marc H Wadsworth; Julia Waldman; Xiuting Wang; Wenjun Yan; Ali Onder Yildirim; William Zhao; Carly G K Ziegler; Aviv Regev

In human smokers, statistical modeling uncovered a robust trend of increased ACE2 expression in airway epithelial cells, while expression in AT2 cells was reduced (Fig. 3d, Extended Data Fig. 6 ). To experimentally confirm these findings, we examined cell profiles from mice exposed daily to cigarette smoke for two months, followed by scRNA-seq of whole lungs (Fig. 5c) . Epithelial specific expression patterns of mouse Ace2 and the Ace2 + Tmprss2 + and Ace2 + Ctsl + dual-positive cells were largely consistent with the human data (Fig. 5d) . Upon smoke exposure, there was a significant increase in Ace2 + airway secretory cell numbers, while the fraction of Ace2 + AT2 cells was unaltered (Fig. 5e) . Moreover, the expression levels of Ace2 were significantly increased in airway secretory cells (Fig. 5f ), but not in AT2 cells (Fig. 5g) . This was in agreement with bulk RNA-seq of mouse lungs exposed to different doses of cigarette smoke 101 , in which Ace2 levels increased in a dose-dependent manner by daily cigarette smoke over 5 months (Fig. 5h) . Notably, the COVID-19 relevant proteases Tmprss2 and Ctsl were also significantly increased by smoke exposure in mice (Fig. 5i,j) . Thus, mouse smoking data shows similar trends as observed in humans and experimentally confirms the association of ACE2 levels with smoking.