Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection

Allen Wang; Joshua A Chiou; Olivier B Poirion; Justin Buchanan; Michael J Valdez; Jamie M Verheyden; Xiaomeng Hou; Minzhe Guo; Jacklyn M Newsome; Parul Kudtarkar; Dina A Faddah; Kai Zhang; Randee E Young; Justinn Barr; Ravi Misra; Heidie Huyck; Lisa Rogers; Cory Poole; Jeffery A Whitsett; Gloria Pryhuber; Yan Xu; Kyle J Gaulton; Sebastian Preissl; Xin Sun

We next asked if there were genes enriched in ACE2 + AT2 cells as compared to ACE2 -223 AT2 cells to identify potentially co-expressed genes. Among genes that showed a trend 224 for higher expression in ACE2 + compared to ACE2cells was IFNGR1 (log2 (fold change) 225 = 0.4, -log10(p-value)=5.0; FDR corrected p=0.257, Supplementary Table 3) , raising the 226 possibility that ACE2 may be co-regulated with interferon pathway genes, in line with 227 conclusions of a recent study (Ziegler, 2020) . In our data generated from normal lungs 228 this correlation was modest, suggesting there is low baseline co-expression of ACE2 and 229 IFNGR1. Among genes with increased expression in TMPRSS2 + versus TMPRSS2 -AT2 230 cells was ICAM1 (log2 (fold change)=0.27, -log10(FDR corrected p)=12.2, Supplementary 231 Table 3 ), which encodes a receptor for Rhinovirus (Zhou et al., 2017) . The potential co-232 expression of TMPRSS2 and ICAM1 may contribute to the often-observed co-infection 233 by more than one respiratory virus. Indeed, co-infection of SARS-CoV-2 and other viruses 234 including Rhinovirus has been observed, promoting urgent calls to halt the clinical 235 The leading cause of death for COVID-19 is Acute Respiratory Distress Syndrome 251 (ARDS) which is characterized by failure of gas-exchange due to destruction of the 252 alveolar region of the lung (Du et al., 2020) . AT2 is an abundant epithelial cell type in the 253 alveolar region and expresses all of the SARS-CoV-2 viral entry genes assayed here and 254 likely bears the brunt of infection. Consequently, we focused on AT2 cells for follow up 255 analysis. We found that the percentage of AT2 cells expressing ACE2 had an increasing 256 trend in 30yo adult samples compared to 3yo samples ( Figure 1D ). In addition, we found 257 a strong trend of increase in the percentage of AT2 cells expressing TMPRSS2 in adult 258 samples compared to 3yo samples (41.2 ± 6.6% for 3yo and 57.4 ± 7.7% for 30yo, p = 259 0.05 (t-test), Figure 1E ). While very few ACE2 + /TMPRSS2 + double positive AT2 nuclei 260 were detected, the fraction of these nuclei in all AT2s increased with age (0.2 % (6 nuclei) 261 in 30wk GA , 0.3% (5 nuclei) in 3yo and 0.5% (10 nuclei) in 30yo, Supplementary Table 2) . 262