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Studies Unravel SARS-CoV-2 Protein Interactions With Human Proteins

NEW YORK – Studies by two independent research teams have spelled out interactions between SARS-CoV-2 viral proteins and proteins from human host cells during COVID-19 infections, revealing protein-protein interaction networks with clues to disease biology and potential treatment strategies.

For the first of these studies, published in Nature Biotechnology on Monday, an international team led by investigators at the Pasteur Institute, Dana-Farber Cancer Institute, the University of Toronto, and the German Research Center for Environmental Health turned to yeast-two-hybrid experiments and other assays to examine interactions between more than two dozen viral open reading frames (ORFs) and almost 17,500 human ORFs.

"We anticipate that these findings and the contactome resource will stimulate important research toward characterizing new viral strains, understanding the mechanism of COVID-19 symptoms, and developing therapies for current and future pandemics," the authors of the study reported.

The team's analyses highlighted a host of interactions between SARS-CoV-2-encoded and human proteins, dubbed the SARS-CoV-2 interactome (HuSCI), prompting more detailed analyses and genetic knockdown experiments with gene-edited viruses and ACE2 receptor-expressing lung cell lines.

Among the specific contacts examined was an interaction between the viral protein NSP14 and a human transcription network under the control of NF-kappa-B, along with other interactions that impact human immune activity.

The team's results suggested that proteins encoded by SARS-CoV-2 may be particularly prone to interacting with human proteins that contain genetic alterations previously implicated in individuals' risk of severe COVID-19 or "long COVID" cases that persist over long periods of time.

"Our results connect viral proteins to human genetic architecture for COVID-19 severity and offer potential therapeutic targets," the study's authors wrote, noting that genetic or small molecule inhibitor-based knockdown of interacting host proteins, such as the ubiquitin-specific peptidase 25 enzyme, seemed to dial down SARS-CoV-2 replication in cell line experiments.

Even so, the authors noted, their results suggest that alterations affecting protein-coding portions of the SARS-CoV-2 genome — including changes linked to known SARS-CoV-2 variants — can lead to changes in interactions and network patterns associated with the viral proteins.

"Although it is currently unknown whether the respective interactions promote viral replication or facilitate immune recognition," they explained, "the observed changes demonstrate the plasticity of the contactome and, together with recent reports of increased replication of the Delta strain, strongly suggest that this dimension of viral evolution should also be monitored to assess the risk posed by emerging variants."

For another paper appearing in Nature Biotechnology, researchers at the Cleveland Clinic, Cornell University, and elsewhere reported on findings from their own yeast-two-hybrid- and mass spectrometry-based interactome analyses, which unearthed more than 700 apparent ties between SARS-CoV-2 proteins and human host proteins.

By setting these interactions against those described in prior interactome analyses, the team verified 218 previously described protein-protein interactions while revealing 361 new ones.

When they overlaid drug screening profiles for nearly 3,000 existing or proposed drugs, meanwhile, the investigators tracked down nearly two dozen compounds near host network sites that appear to be impacted by SARS-CoV-2 proteins.

"These top 23 drugs offer candidate treatment for SARS-CoV-2 infections across diverse mechanism-of-actions identified from our human-SARS-CoV-2 interactome," the authors reported, noting that the drugs found in the screen spanned anti-inflammatory, anti-infective, anti-hypertensive, and anti-neoplastic categories.

Based on lower-than-usual COVID-19 cases documented in electronic health records for patients on one of these drugs, for example, the researchers went on to perform a series of lung cell line experiments that pointed to antiviral activity in response to SARS-CoV-2 exposure.

Members of that team emphasized the apparent transcriptional consequences of SARS-CoV-2 proteins that make their way into human cells — in particular, those stemming from a co-immunoprecipitation-confirmed protein-protein interaction between SARS-CoV-2's ORF3a and the proposed human transcription factor ZNF579.

In subsequent chromatin immunoprecipitation sequencing and quantitative PCR experiments in a human cell line, the investigators saw signs that ZNF579 targets some of the same genes altered in SARS-CoV-2-infected cells.

"Our study demonstrates the value of network systems biology to understand human-virus interactions and provides hits for further research on COVID-19 therapeutics," they wrote.