COVID-19: Researchers identified dozens of genes that enable/block the viruses to replicate in cells

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Researchers at Yale University and the Broad Institute of MIT and Harvard screened hundreds of millions of cells exposed to the COVID-19 and MERS viruses and identified dozens of genes that both enable the viruses to replicate in cells and also those that seem to slam the door on the virus.

The pro-viral and anti-viral role of these genes will help guide scientists in development of new therapies to combat COVID-19, the researchers say.

The findings were reported Oct. 26 in the journal Cell.

Scientists have previously identified how the SARS-CoV-2 coronovirus, which causes COVID-19, attaches to and invades cells, but less is known about why some cells are more susceptible to infection. Understanding the genetics behind the host cells’ susceptibility to infection may help explain why some people exposed to the virus experience few or no symptoms and others become extremely ill or die.

For the study, researchers performed a genome-wide screen of a line of green monkey cells, which are more likely to die after exposure to SARS-CoV-2 than commonly used human cell lines.

The screens for the first time allowed researchers to simultaneously track interactions of virus and cells. The screens confirmed earlier findings that the ACE-2 gene, which encodes a receptor on the cell surface, promotes infection by SARS-CoV-2.

However, the screens also identified two new pro-viral protein complexes and a third, which seems to assist in preventing infection.

They found that SWI/SNF complex, which turns genes on and off, and HMGB1, which has a myriad of functions including regulation of inflammation, were linked to increased cell death after infection.

The researchers then introduced small molecule drugs that inhibit function of two of the identified gene products and found they could increase survival of cells after infection in a dish.

By contrast, the histone H3 complex, which helps regulate expression of genes within the cell nucleus, seemed to provide a protective effect, inhibiting ability of SARS-CoV-2 to infect and kill cells.

“It is very important to understand wide variation of responses to COVID-19, for instance why advanced age makes it much more likely that people will die,” said Yale’s Craig Wilen, assistant professor in laboratory medicine and immunobiology and corresponding author of the paper. “We have identified both proviral and antiviral genes that may help us predict who is likely to get severely ill and what kind of drugs would be helpful or detrimental in treating patients.”

Wilen noted the information may not only be helpful in current pandemic, but also help prepare for outbreaks of future emerging coronaviruses.


SARS-CoV-2 causes pneumonia-associated respiratory syndrome, like coronavirus SARS-CoV and MERS-CoV [1]. An ongoing outbreak of SARS-CoV-2 started from the Huanan Seafood Wholesale Market in Wuhan, China since December of 2019.

The genome sequence of SARS-CoV-2 is 89.1% identical to bat SARS-like-CoVZXC45 and 96% identical to bat CoV RaTG13, suggesting that bat is the origin of SARS-CoV-2 [[2], [3], [4]].

A familial cluster of pneumonia associated with the SARS-CoV-2 and a retrospective study indicated person-to-person transmission [5]. Moreover, people seem to be generally susceptible to this strongly infectious disease. WHO has listed the novel coronavirus-infected pneumonia as Public Health Emergency of International Concern (PHEIC). Cases have already been diagnosed in dozens of countries.

The genome sequence of SARS-CoV-2 is 82% identical to SARS-CoV [4]. Angiotensin converting enzyme II (ACE2) was identified as the cell entry receptor of SARS-CoV-2 to infect human, similar to SARS-CoV [6]. ACE2 belongs to the angiotensin-converting enzyme family and catalyzes the cleavage of angiotensin II into the vasodilator angiotensin 1-7.

ACE2 is enriched in the epithelia of lung [7], while single-cell RNA-seq data analysis of ACE2 expression reveals potential risks of more human organs vulnerable to SARS-CoV-2 infection [8]. In reproductive system, single-cell transcriptomes of adult human testis showed high expression of ACE2 in spermatogonia, Leydig and Sertoli cells [9].

Coronaviruses are prone to mutation and recombination due to their error-prone RNA-dependent RNA polymerase (RdRP) [10], and virus variation may allow some subtypes of the virus to better bind to the receptor ACE2. Therefore, it is very important to reveal how ACE2 expression is regulated for both prevention and treatment of the infectious diseases caused by these coronaviruses in the future.

The major epigenetic markers in mammals include covalent modifications of DNA and post-translational modifications of histones. Since the N-terminal of histone is exposed to the surface of nucleosome, histone can undergo dynamic chemical modifications including methylation, acetylation, phosphorylation and ubiquitination [11].

Methylation of H3 lysine residues such as K4, K9, K27 and K36 are intensively studied because of their high correlationship with transcriptional activity.

K-to-M mutants of histone H3.3 play a dominant-negative role to suppress specific histone H3 methylation and are valuable tools for screening regulatory pattern of gene expression.

During mammalian embryonic development, H3K27me3 is associated with transcriptional silencing and is involved in repressing key developmental genes during embryonic stem cell (ESC) differentiation. H3K27me3 is catalyzed by the polycomb group (PcG), a group of conserved transcriptional gene repressors. EZH2 (enhancer of zeste homologue 2) is a human homologue of enhancer of zeste in drosophila and the key member of PcG [12,13], which is composed of PRC1 and PRC2 complexes [14].

EZH2 encodes the catalytic subunit of PRC2 and functions as a histone methyltransferase of H3K27 dimethylation and trimethylation [15] for silencing at specific genomic loci [16]. In ESCs, EZH2-mediated H3K27me3 is necessary for cell identity and cell differentiation [17].

To study the epigenetic regulation of ACE2 expression, we detected the level of Ace2 expression by overexpression of K-to-M H3.3 mutants in mouse germ cell line GC-2 (GC-2 spd, transformation of freshly isolated mouse spermatocytes).

Then we compared the levels of ACE2 expression and its epigenetic status at promoter region before and after EZH2 knockout in human ESCs. Generally, we found that EZH2-mediated H3K27me3 inhibits ACE2 expression, and this pattern may be conserved among mammalian cells. Our study provides clues for prevention and targeted therapy of coronavirus disease 2019 (COVID-19).

reference link : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7144854/


More information: Jin Wei et al, Genome-wide CRISPR screens reveal host factors critical for SARS-CoV-2 infection, Cell (2020). DOI: 10.1016/j.cell.2020.10.028

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