Innovative method opens myriad new avenues for understanding the biology behind COVID-19

A highly innovative method using the latest technology has generated a comprehensive list of SARS-CoV-2 viral and human proteins that interact with each other, with one such interaction showing the virus directly influencing proteins that regulate the human immune system.

The technique, described in the study, "A Comprehensive SARS-CoV-2–Human Protein–Protein Interactome Reveals COVID-19 Pathobiology and Potential Host Therapeutic Targets," published Oct. 10 in Nature Biotechnology, opens myriad new avenues for research and for understanding the biology behind COVID-19, and for identifying new treatments that target protein binding sites.

In the study, the researchers identified 23 candidate drugs, each with potential to disrupt a virus-to-host binding site. In preliminary experiments, one of these drugs, an FDA-approved beta-blocker called carvedilol used to treat blood pressure, had low toxicity and was highly effective at inhibiting viral infection in a human lung cell line infected with SARS-CoV-2. Also, analysis of records of those infected with SARS-CoV-2 revealed that patients taking carvedilol for blood pressure had a 17% lower risk of SARS-CoV-2 infection, suggesting it inadvertently offered some protection.

We have a new and much fuller view of the SARS-CoV-2 viral-to-human protein interaction network, which shows how viral proteins are hijacking human proteins and [reveals] the pathways that are required for viral infection, replication and transmission."

Haiyuan Yu, Professor, Department of Computational Biology and the Weill Institute for Cell and Molecular Biology in the College of Agriculture and Life Sciences (CALS)

Yu is senior author of the paper, along with Cleveland Clinic associate professor Feixiong Cheng.

The methods described can also be applied to any virus or pathogen, Yu said. The researchers have already begun using these techniques to better understand protein interactions and investigate therapies for mosquito-transmitted Zika virus.

In the study, the researchers combined two complementary state-of-the-art approaches to get a complete picture of interactions between SARS-CoV-2 viral proteins and human host proteins. The first uses a quantitative proteomics technology where each viral protein found in SARS-CoV-2 is artificially expressed in human cells to see which host proteins and complexes are recruited by the virus. In the second approach, called Y2H, the researchers used their libraries of virus and human proteins. Individual proteins from each set were then paired together. The technique allowed researchers to observe which pairs had an affinity for each other and touched; when they did interact, such pairings were often brief.

"Some of the most important regulatory interactions are transient," Yu said. "A protein finds what it needs to bind only under the right condition and then it comes apart."

The techniques revealed 739 high-confidence protein-protein interactions among 579 human proteins and 28 SARS-CoV-2 proteins, validating 218 known human proteins that interact with SARS-CoV-2 and revealing 361 novel ones. The researchers also identified an interaction between a viral protein and a human transcription factor, which is directly involved in turning immune response genes on and off. The finding could provide clues to how the virus evades host immunity.

While the most relevant cells for use in research come from the lungs, they are hard to grow in culture. Previous SARS-CoV-2 research has therefore used kidney T cells. In this study, for the first time, the researchers used colon cell lines. "There is evidence that these cell lines express the two key marker proteins on the surface that are necessary for the infection," Yu said, adding that the kidney T cells don't express these markers.

In next steps, Yu and colleagues will investigate how SARS-CoV-2 regulates human gene expression, particularly with regard to evading immunity; and they are following up on other drug candidates, some of which appear effective, in collaboration with John Lis, professor of molecular biology and genetics (CALS),Cedric Feschotte, professor of molecular biology and genetics (CALS), Luis Schang, professor of chemical virology (College of Veterinary Medicine), and several other Cornell groups.

The research was primarily supported by the National Institute on Aging, the National Institute of General Medical Sciences and a Cornell Rapid Response to SARS-CoV-2 Seed Grant. The latter was instrumental in collecting preliminary data to launch this study, along with supporting sustained collaborations during the pandemic, Yu said.