U of T Researchers to Identify Host Factors Essential for SARS-CoV-2

By identifying cellular factors that contribute to COVID-19, U of T researchers seek to find new targets for drug repurposing.

SARS-CoV-2 has shut down the world by spreading furiously from one host to another. Now scientists want to trace its steps within cells to stop it.

Supported by the Toronto COVID-19 Action Fund, Donnelly Centre investigators have joined forces with colleagues from across the university and affiliated hospitals, as well as McMaster University, to identify all components of the human cellular machinery involved in the life cycle of SARS-CoV-2.

Led by Jason Moffat, a professor of molecular genetics in the Donnelly Centre for Cellular and Biomolecular Research, the team will apply the CRISPR genome editing tool to pinpoint all gene-encoded protein factors in human cells exploited by the virus to to get inside and multiply. The hope is that there are already clinically approved drugs that target some of these factors which could be quickly repurposed for COVID-19.

“We want to understand the host factors required for the life cycle of the virus on a very deep molecular level,“ says Moffat. “Our goal is to see if we can repurpose any drugs in a rational way after we understand more what the host factors are doing.”

But he added that it is important also to understand the biology of the virus.

“Funding basic science is critical for understanding how to manage new biological threats like COVID-19”, says Moffat, “Had there been more opportunities for researchers to break down what the SARS virus was doing following the outbreak in 2003, we probably would have been in a much better position to manage the current pandemic.”

Like all viruses, SARS-CoV-2 hijacks host molecular machinery for its own ends. It is now established that the virus gains entry by binding the ACE2 receptor with help from another human enzyme known as TMPRSS2. But there are certainly many more factors involved at various stages of its life cycle.

“We often think of viruses as simple – they introduce their genome into the host cell and replicate themselves to release more virus,” says Moffat’s co-investigator Scott Gray-Owen, a professor of molecular genetics at U of T who studies infection and the body’s response to it.

“But for any pathogen to cause infection in a host, it has to overcome many different aspects of the immune response. Our aim is therefore to find creative ways to intervene in how the virus replicates or evades immunity so as to stop its spread and halt the progression of disease,” Gray-Owen says.

The researchers are casting a wide net to find all host factors involved. With CRISPR, they will switch off every gene in human cells infected with SARS-CoV-2. If a gene is essential for the virus, then turning it off will allow those cells to resist the infection while the rest will perish.

These experiments will be done in the Faculty of Medicine’s Containment Level 3 (CL3) lab, which is directed by Gray-Owen and supports research with all but the highest risk level pathogens, and is required for work with the risk group 3-rated SARS-CoV-2.

The research is being spearheaded by Katie Chan and Furkan Guvenc, a senior research associate and a graduate student in Moffat and Gray-Owen’s labs, respectively. To stay safe while handling the virus, they have to wear full body protection suit equipped with air purification system.

“Once you put on the suit, you don’t want to come out,” says Guvenc, who previously studied HIV, also a risk group 3 pathogen, and is accustomed to going without food, drink or bathroom breaks for an entire day. “It’s a very ascetic exercise. You perform the experiments until they are done, however long that may be,” he says.

Also on the team are Dr. Samira Mubareka, of the SunnyBrook Health Centre, and Karen Mossman, a professor of pathology and molecular medicine at McMaster University, who were among the first in Canada to isolate SARS-CoV-2 from patient samples and are providing the live virus for the experiments.

Furthermore, University Professor Jack Greenblatt and Professor Benjamin Blencowe, both in the Donnelly Centre, will study how gene expression changes in response to infection for more clues about how COVID-19 develops at the cellular level.

And Mikko Taipale, an assistant professor of molecular genetics in the Donnelly Centre, and Shana Kelley, University Professor at the Leslie Dan Faculty of Pharmacy, will identify the factors required for the production and maintenance of the ACE2 receptor on the cell surface.

Moffat expects that by July they will have a list of key host factors.

“If we could find a molecular pathway that is essential for the virus and there is a clinically viable drug, then this could have a rapid impact on intervention,” says Moffat.

“But the overall knowledge we’ll gain might also help us confront other coronaviruses in the future.”