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

Abstract

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 of ACE2, TMPRSS2, and CTSL through 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integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs.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 of ACE2 and 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 of ACE2, TMPRSS2, and CTSL in 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 by ACE2 + 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.

Robust ACE2 protein expression localizes to the motile cilia of the respiratory tract epithelia and is not increased by ACE inhibitors or angiotensin receptor blockers

“…5a). These results differ from some, but not all, recent gene expression studies comparing ACE2 expression in patients with varying demographics and smoking status [35][36][37] . Our results suggest that host factors outside of ACE2 expression may determine why males, patients of older age, and smokers are epidemiologically linked to COVID-19 susceptibility.We next examined whether ACE2 expression in the upper respiratory cilia differs between healthy donors versus patients with chronic rhinosinusitis (CRS), a non-malignant chronic .…”

Anosmia as a presenting symptom of SARS-CoV-2 infection in healthcare workers – A systematic review of the literature, case series, and recommendations for clinical assessment and management

“…However, the presence of nasal obstructive symptoms (albeit subjectively reported) in patients with anosmia varied widely in the included studies. The reports of ACE2 receptor expression in non-neuronal cells and supporting olfactory sustentacular cells may support this finding (26)(27)(28)(29) .…”

Age-determined expression of priming protease TMPRSS2 and localization of SARS-CoV-2 infection in the lung epithelium

“…In a recently published study from China, 90% of children infected with SARS-CoV-2 exhibited mild symptoms or were asymptomatic 2 . The Human Cell Atlas Lung Biological Network recently reported an integrated analysis of single-cell transcriptomic data from multiple organs and datasets which demonstrated age, sex and smoking-associations of SARS-CoV-2 entry-related genes in several cell types, although this dataset was weighted heavily toward adult samples 11 . This led us to hypothesize that factors determining SARS-CoV-2 cellular infectivity in the respiratory epithelium may be developmentally regulated.…”