Genome-wide CRISPR screening used to identify factors essential for SARS-CoV-2 infection in humans

In a trailblazing methodological paper published in the journal The genetics of nature, a team of Belgian scientists discovered a collection of coronavirus host factors that could be used to develop drugs against acute respiratory coronavirus syndrome 2 (SARS-CoV-2), but also coronaviruses zoonotic to come.

The 2019 pandemic of coronavirus infection (COVID-19), caused by SARS-CoV-2, has led to a global health and economic crisis; however, although vaccines are now being used worldwide, only a few effective drugs are currently available to treat patients with the disease.

Although remdesivir was initially seen as a promising candidate for very severe cases of COVID-19, tests conducted by the World Health Organization (WHO) have shown that it has no significant effect on mortality. Dexamethasone, on the other hand, has been shown to reduce mortality by a third in the critically ill, primarily by suppressing the depressive immune response.

However, dexamethasone only wins real cases with relatively limited effects. There is therefore an urgent need for new, safe and effective treatment options. In that regard, the development of broad-spectrum drugs against coronaviruses would not only help in the treatment of the common pandemic disease but could also be used to prevent possible zoonotic events. future existence.

But to develop such drugs, a complete understanding of host factors used by coronaviruses to capture a cell is crucial, as each step of the viral reproduction cycle may be a target of intervention. Although the entry stage of coronaviruses has been explained in detail, the details of host virus interactions in later parts of the viral life cycle are not yet accessible.

As a result, a Belgian research group (led by Dr. Jim Baggen of the Rega Institute in Leuven) used genome-wide CRISPR (regular reproduction of short palindromic recycling) to produce established genetic scales. find to determine which host properties are essential for SARS -CoV-2 and human coronavirus 229E (HCoV-229E).

Genome-based knockout screen across CRISPR

In this study, the CRISPR-based genome-wide broadcaster screening was performed in a human Huh7 cell line (derived from male hepatoma material) without the involvement of an exogenous receptor from the SARS-CoV strain stimulus -2 used in the study to develop a pronounced cytopathic effect in these cells.

In addition, screens were made with both SARS-CoV-2 and much less pathogenic HCoV-229E that is endemic and causes the common cold. This, in turn, allowed to identify not only specific host factors for SARS-CoV-2 and HCoV-229E, but also for HCoV-OC43 and coronaviruses.

To validate the results obtained, the researchers have developed a single RNA guide targeting the named genes and the known receptor genes in Huh7 cells. As a result, they were able to see whether the maturation of these genes affected the sensitivity of the cells to a cytopathic effect induced by SARS-CoV-2 or HCoV-229E.

Common host factors for human coronaviruses

This study has revealed type 3 phosphoinositide 3-kinase (PI3K) as a common host factor for SARS-CoV-2, HCoV-229E and HCoV-OC43, which means that small molecules targeting the These proteins are generally relevant as anti-coronavirus protectors.

In addition, the screens have confirmed that TMEM106B lysosomal protein does indeed serve as a key host feature that enables SARS-CoV-2 infection in primary lung cells and liver-derived human cell lines . In patients with COVID-19, single-cell RNA-sequence of airway cells has been shown to express the expression TMEM106B associated with SARS-CoV-2 infection.

The researchers have also shown that TMEM41B – a novel regulator of autophagy (intracellular contaminant system) and lipid transport – is required for HCoV-229E infection, and to a lesser extent for SARS-CoV-2 infection.

Informing future research efforts

In a short time, this robust research study revealed the mechanism of action of several coronavirus host factors that may be used in the development of drugs against SARS-CoV-2 infection, but also a breakthrough. out zoonotic coronavirus that may occur in the future.

“The set of essential coronavirus host factors identified in our genome-wide scales will serve as the basis for studies to unravel the cellular pathways that these viruses overlap,” study authors say. “Furthermore, these factors may be targets for pharmacological chemistry efforts to counteract the prevalent or future COVID-19 pancreatic infections of pathogenic coronaviruses”, they conclude. add.

It is now clear that pathogenic coronaviruses tend to occur from time to time, which means that they will remain a global public health hazard longer than the existing COVID-19 pandemic. right now. As a result, conducting basic research studies (similar to this one) aimed at developing broad-spectrum anti-coronavirus inhibitors will be an essential step forward.