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

We next asked whether human cell types of interest were present in animal models. While such analyses cannot address molecular compatibility (due to sequence variation in ACE2 across species, as shown for lower compatibility of SARS-CoV and mouse ACE2 98 ), they can help determine if dual-positive cells are present in commonly employed models, and if their characteristics, proportions, and programs are similar to those of their human counterparts. In a separate study 46 , our lung network showed strong similarities to the human data in a macaque model. Here, we focused on the more distant, but commonly used, mouse model. Ace2 + Tmprss2 + and Ace2 + Ctsl + dual-positive cells were present primarily in club and multiciliated cells in the airway epithelia of healthy mice 99 (Ace2 + Tmprss2 + club 5.1% [4.7%, 5.4%] and multiciliated 2.8% [2.3%, 3.5%], Ace2 + Ctsl + club 11.1% [10.6%, 11.6%] and multiciliated 3.5% [2.9%, 4.3%]), consistent with the expression patterns found in human airways (Fig. 5a) . Furthermore, Ace2 expression increased over a 2-month time-course of healthy mouse aging in both club (p=1.16e-06) and goblet (p=0.01911) cells (Fig. 5a) . The proportion of Ace2 + Tmprss2 + dual-positive cells did not significantly increase with age during this time course (data not shown), but the proportion of Ace2 + Ctsl + dual-positive cells significantly increased in club cells during this time-course (Fig. 5b) . Interestingly, the mice were aged between 2-4 months, a 2-month period that is reported to reflect the maturation period from early to mature adults 100 . Examining bulk RNA-Seq profiles of sorted populations of alveolar AT2 cells (SFTPC + ), airway basal cells (KRT5 + ), alveolar endothelial cells (CD45-CD31 + ), alveolar epithelial cells (Epcam + ), whole lung and whole trachea from a KRT5-CreER/LSL-TdTomato/SFTPC-eGFP transgenic mouse model, and across tissues from ENCODE, showed that Ace2, Tmprss2 and Ctsl are expressed in sorted AT2 cells, whole trachea and whole lung, as well as in stomach, intestine, kidney and bladder.