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
Authors: Muus Christoph , Luecken Malte D. , Eraslan Gokcen , Waghray Avinash , Heimberg Graham , Sikkema Lisa , Kobayashi Yoshihiko , Vaishnav Eeshit Dhaval , Subramanian Ayshwarya , Smilie Christopher , Jagadeesh Karthik , Duong Elizabeth Thu , Fiskin Evgenij , Triglia Elena Torlai , Ansari Meshal , Cai Peiwen , Lin Brian , Buchanan Justin , Chen Sijia , Shu Jian , Haber Adam L , Chung Hattie , Montoro Daniel T , Adams Taylor , Aliee Hananeh , Samuel J. , Andrusivova Allon Zaneta , Angelidis Ilias , Ashenberg Orr , Bassler Kevin , Bécavin Christophe , Benhar Inbal , Bergenstråhle Joseph , Bergenstråhle Ludvig , Bolt Liam , Braun Emelie , Bui Linh T , Chaffin Mark , Chichelnitskiy Evgeny , Chiou Joshua , Conlon Thomas M , Cuoco Michael S , Deprez Marie , Fischer David S , Gillich Astrid , Gould Joshua , Guo Minzhe , Gutierrez Austin J , Habermann Arun C , Harvey Tyler , He Peng , Hou Xiaomeng , Hu Lijuan , Jaiswal Alok , Jiang Peiyong , Kapellos Theodoros , Kuo Christin S , Larsson Ludvig , Leney-Greene Michael A. , Lim Kyungtae , Litviňuková Monika , Lu Ji , Ludwig Leif S , Luo Wendy , Maatz Henrike , Madissoon Elo , Mamanova Lira , Manakongtreecheep Kasidet , Marquette Charles-Hugo , Mbano Ian , McAdams Alexi Marie , Metzger Ross J , Nabhan Ahmad N , Nyquist Sarah K. , Penland Lolita , Poirion Olivier B , Poli Sergio , Qi CanCan , Queen Rachel , Reichart Daniel , Rosas Ivan , Schupp Jonas , Sinha Rahul , Sit Rene V , Slowikowski Kamil , Slyper Michal , Smith Neal , Sountoulidis Alex , Strunz Maximilian , Sun Dawei , Talavera-López Carlos , Tan Peng , Tantivit Jessica , Travaglini Kyle J , Tucker Nathan R. , Vernon Katherine , Wadsworth Marc H. , Waldman Julia , Wang Xiuting , Yan Wenjun , Zhao William , Ziegler Carly G. K. ,   The NHLBI LungMAP Consortium,   The Human Cell Atlas Lung Biological Network
Published: April 2020

The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression ofACE2,TMPRSS2, andCTSLthrough an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Joint expression ofACE2and the accessory proteases identifies specific subsets of respiratory epithelial cells as putative targets of viral infection in the nasal passages, airways, and alveoli. Cells that co-express ACE2 and proteases are also identified in cells from other organs, some of which have been associated with COVID-19 transmission or pathology, including gut enterocytes, corneal epithelial cells, cardiomyocytes, heart pericytes, olfactory sustentacular cells, and renal epithelial cells. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels ofACE2,TMPRSS2, andCTSLin specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. Notably, there was a particularly low expression of ACE2 in the few young pediatric samples in the analysis. Further analysis reveals a gene expression program shared byACE2+TMPRSS2+cells in nasal, lung and gut tissues, including genes that may mediate viral entry, subtend key immune functions, and mediate epithelial-macrophage cross-talk. Amongst these are IL6, its receptor and co-receptor,IL1R, TNF response pathways, and complement genes. Cell type specificity in the lung and airways and smoking effects were conserved in mice. Our analyses suggest that differences in the cell type-specific expression of mediators of SARS-CoV-2 viral entry may be responsible for aspects of COVID-19 epidemiology and clinical course, and point to putative molecular pathways involved in disease susceptibility and pathogenesis.