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Innate Immune Genes and Two Nasal Epithelial Cell Types: Expression of SARS-CoV-2 Entry Factors – COVID19 Cell Atlas

Reporter: Aviva Lev-Ari, PhD, RN

• Brief Communication
• Published: 23 April 2020

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

• Waradon Sungnak,
• Ni Huang,
• Christophe Bécavin,
• Marijn Berg,
• Rachel Queen,
• Monika Litvinukova,
• Carlos Talavera-López,
• Henrike Maatz,
• Daniel Reichart,
• Fotios Sampaziotis,
• Kaylee B. Worlock,
• Masahiro Yoshida,
• Josephine L. Barnes &
• HCA Lung Biological Network

Nature Medicine (2020)Cite this article

Abstract

We investigated SARS-CoV-2 potential tropism by surveying expression of viral entry-associated genes in single-cell RNA-sequencing data from multiple tissues from healthy human donors. We co-detected these transcripts in specific respiratory, corneal and intestinal epithelial cells, potentially explaining the high efficiency of SARS-CoV-2 transmission. These genes are co-expressed in nasal epithelial cells with genes involved in innate immunity, highlighting the cells’ potential role in initial viral infection, spread and clearance. The study offers a useful resource for further lines of inquiry with valuable clinical samples from COVID-19 patients and we provide our data in a comprehensive, open and user-friendly fashion at www.covid19cellatlas.org.

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To further characterize specific epithelial cell types expressing ACE2, we evaluated ACE2 expression within the lung and airway epithelium. We found that, despite a low level of expression overall, ACE2 was expressed in multiple epithelial cell types across the airway, as well as in alveolar epithelial type II cells in the parenchyma, consistently with previous studies^9,10,11. Notably, nasal epithelial cells, including two previously described clusters of goblet cells and one cluster of ciliated cells, show the highest expression among all investigated cells in the respiratory tree (Fig. 1b). We confirmed enriched ACE2 expression in nasal epithelial cells in an independent scRNA-seq study that includes nasal brushings and biopsies. The results were consistent; we found the highest expression of ACE2 in nasal secretory cells (equivalent to the two goblet cell clusters in the previous dataset) and ciliated cells (Fig. 1b).

In addition, scRNA-seq data from an in vitro epithelial regeneration system from nasal epithelial cells corroborated the expression of ACE2 in goblet/secretory cells and ciliated cells in air–liquid interface cultures (Extended Data Fig. 1). Notably, the differentiating cells in the air–liquid interface acquire progressively more ACE2 (Extended Data Fig. 1). The results also suggest that this in vitro culture system may be biologically relevant for the study of SARS-CoV-2 pathogenesis.

Coronavirus Entry Genes Highly Expressed in Two Nasal Epithelial Cell Types

Apr 23, 2020

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TEM of SARS-CoV-2 particles; Credit: NIAID-RML

This story has been updated to include information on a related study appearing in Cell.

NEW YORK – Two types of cells inside the nose express high levels of the genes encoding proteins the SARS-CoV-2 uses to enter cells, suggesting they are the likely entry points for the virus.

SARS-CoV-2, the virus that causes COVID-19, uses its spike protein to bind to cellular receptors in the human body. The virus relies on the ACE2 receptor protein and the TMPRSS2 protease to enter cells, but which cells are initially infected has been unclear.

An international team of researchers used single-cell RNA sequencing datasets put together by the Human Cell Atlas consortium to search for cell types that express both the ACE2 and TMPRSS2 genes. As they reported in Nature Medicine Thursday, they found a number of cells in different organs express the genes encoding these proteins, but they homed in on cells of the respiratory system, especially goblet cells and ciliated cells in the nose.

“Mucus-producing goblet cells and ciliated cells in the nose had the highest levels of both these [genes], of all cells in the airways,” first author Waradon Sungnak from the Wellcome Sanger Institute said in a statement. “This makes these cells the most likely initial infection route for the virus.”

Using the Human Cell Atlas dataset, Sungnak and his colleagues analyzed ACE2 and TMPRSS2 expression in a range of tissues, including not only respiratory tissue — previous analyses using immunohistochemistry had detected both ACE2 and TMPRSS2 in the nasal and bronchial epithelium — but also tissue from the eyes, digestive tract, muscle, and more.

ACE2 gene expression was generally low across the datasets analyzed, while TMPRSS2 was more broadly expressed, the researchers found. This suggested that ACE2 expression might be the limiting factor for viral entry in initial infections.

However, ACE2 was expressed in a number of epithelial cell types of respiratory tissues, and its expression was particularly high among goblet cells and ciliated cells of the nose. The researchers confirmed this finding using data from two other scRNA-seq studies.

Other genes often co-expressed alongside ACE2 in the respiratory system included ones involved in carbohydrate metabolism — possibly due to their role in goblet cell mucin synthesis — and those involved in innate and antiviral immune functions.

The ACE2 and TMPRSS2 genes were also expressed outside of the respiratory system, including by cells of the cornea and the lining of the intestine, which the researchers noted is in line with some clinical reports suggesting fecal shedding of the virus.

Where these viral entry receptor genes are expressed in the respiratory system could influence how transmissible a virus is. The researchers compared the tissue expression patterns of these viral receptor genes to those of receptor genes used by other coronaviruses and influenza viruses. The receptors used by highly infectious viruses like influenza were expressed more in the upper airway, while receptors for less infectious viruses like MERSCoV were expressed in the lower airway. This indicated to the researchers that the spatial distribution of the viral receptors may influence how transmissible a virus is.

“This is the first time these particular cells in the nose have been associated with COVID-19,” study co-author Martijn Nawijn from the University Medical Center Groningen and the HCA Lung Biological Network said in a statement. “The location of these cells on the surface of the inside of the nose make them highly accessible to the virus, and also may assist with transmission to other people.”

Another study that appeared as a preprint at Cell also used single-cell RNA-sequencing datasets from humans, nonhuman primates, and mice to examine where cells expressing both the ACE2 and TMPRSS2 genes are located. Those researchers, led by the Broad Institute’s Jose Ordovas-Montanes, found both genes were expressed among type II pneumocytes and ileal absorptive enterocytes as well as among nasal goblet secretory cells.

SOURCE

https://www.genomeweb.com/infectious-disease/coronavirus-entry-genes-highly-expressed-two-nasal-epithelial-cell-types?utm_source=Sailthru&utm_medium=email&utm_campaign=GWDN%20Thurs%20PM%202020-04-23&utm_term=GW%20Daily%20News%20Bulletin#.XqIbG1NKgdU

SOURCE for Original Research Study 

Sungnak, W., Huang, N., Bécavin, C. et al. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes. Nat Med (2020). https://doi.org/10.1038/s41591-020-0868-6

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• Received10 March 2020
• Accepted31 March 2020
• Published23 April 2020
• DOI https://doi.org/10.1038/s41591-020-0868-6