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

Finally, to explore therapeutic hypotheses related to disruption of viral processing via protease inhibition, we explored the expression of other proteases across our integrated atlases. Although a multitude of different SARS-CoV-2 features likely account for its high pathogenicity and transmissivity, it has been speculated that the PRRAR loop might contribute to increased COVID-19 severity. Introduction of similar polybasic cleavage sites into avian influenza viruses and human coronaviruses was shown to render them more pathogenic, increasing mortality and viral spread 158, 159 . One hypothesis is that acquisition of a PCSK cleavage site would expand the number of cell types that can be directly infected by SARS-CoV-2. A recent report has started to address expression of FURIN in cells expressing SARS-CoV-2 host factors ACE2 or TMPRSS2 47 , and FURIN activity is inhibited by Guanylate-binding proteins (GBPs), a group of interferonstimulated genes, in order to restrict viral envelope processing 160 . However, the highly overlapping recognition sequence of PCSK family members (Extended Data Fig. 14d) suggests that multiple PCSKs in addition to FURIN could mediate cleavage at the S1/S2 PRRAR motif (Extended Data Fig. 14e) . Our expression analysis confirms that PCSK family members, in particular FURIN, PCSK5 and PCSK7, are more broadly expressed than TMPRSS2 across lung cell types (Fig. 6d) , as well as across tissues (Extended Data Fig. 14i) . In the lung, we note the higher proportion of ACE2 + PCSK7 + basal cells and ACE2 + PCSK7/5 + fibroblasts (Fig. 6e, Extended Data Fig. 14h) . Interestingly, the host interactome of SARS-CoV-2 further suggests interaction of viral proteins with PCSK6 89 , which also showed significant ACE2 co-expression in AT2 cells (Fig. 6b, Extended Data Fig. 14b) . Moreover, because PCSK localization is detected in different membrane compartments along the secretory and endocytic pathways 107 , it is conceivable that PCSKs could process SARS-CoV-2 S-proteins at different stages of the viral life cycle. Moreover, further analysis is required to assess the extent to which SARS-CoV-2 relies on proteolytic activity provided in trans either by neighboring cells or extracellularly localized proteases 111 . Altogether, this could provide SARS-CoV-2 with an immense flexibility in different entry and egress pathways.