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

Our meta--analysis of scRNA-seq across studies provided the required statistical power to uncover population-level signals at a molecular level and at single-cell resolution. We found that the SARS-CoV-2 receptor and associated proteases were up-regulated in airway epithelial and AT2 cells with age and in males, an association that may shed light on the marked increase in mortality with age. Furthermore, ACE2 was up-regulated in airway epithelial cells (basal and multiciliated cells) in past or present smokers, but down-regulated in their AT2 cells; we have also confirmed this in an experimental system in a mouse model. These contrasting smoking associations show the importance of the single-cell resolution, as the down-regulation in AT2 cells will be masked by . CC-BY-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/10.1101/2020.04.19.049254 doi: bioRxiv preprint the airway epithelial signal, leading to loss of association or misinterpretation of seemingly consistent ACE2 signals in bulk RNA-Seq 147 . Importantly, ACE2 is particularly lowly expressed in young pediatric samples, also mirrored by lack of chromatin accessibility in the ACE2 locus. ACE2 expression is known to be regulated in complex ways across different tissues and may be affected by both common therapies (ACEi/ARB) (Tucker et al., companion manuscript 58 ), and during infection 46 . Moreover, both higher ACE2 expression per cell and a higher fraction of ACE2 + cells can in principle have implications for infection, but may have conflicting effects on pathogenesis, as ACE2 knockout mice show more severe ARDS upon lung injury because of its role in the renin-angiotensin pathway, which seems to protect from consequences of lung injury and inflammation 148 (for potential roles of this pathway on CoV infection (pre-COVID) see the review in 149 ). As SARS-CoV2 binding will lead to internalization and therefore downregulation of ACE2 on the cell surface, the protective function of ACE2 via its proteolytic processing of Angiotensin-II may be lost. Thus, the smoking mediated downregulation of ACE2 in AT2 cells may not protect cells from being infected but rather may increase ARDS due to more severe loss of ACE2 from the cell surface upon infection. Other confounders, including ACEi which are not available to our meta-analysis may further impact our results.