Study identifies potential target for treatment of COVID-19
April 29, 2020
By Karina Toledo | Agência FAPESP – In Brazil, as in other countries around the world, the most severe cases of COVID-19 have been reported mainly among men over 60. In a study supported by FAPESP, researchers at São Paulo State University (UNESP) in Botucatu, Brazil, show that expression of the gene TRIB3 in the epithelial cells of the lungs, the preferred targets of the novel coronavirus SARS-CoV-2, is reduced in this group of patients.
The results of the study are published in a preprint (not yet peer-reviewed) paper on the platform bioRixv. The research group is coordinated by Robson Carvalho, a professor in UNESP’s Bioscience Institute (IBB).
The paper reviews data from previous research pointing to the potential capacity of the protein encoded by TRIB3 to inhibit infection and replication by viruses similar to SARS-CoV-2. “Thus, drugs that stimulate TRIB3 expression should be evaluated as a potential therapy for COVID-19,” the authors write.
“A drug with this action mechanism is being tested for use against endometrial cancer by a Spanish pharmaceutical company. We’re establishing partnerships to conduct in vitro testing of compounds that stimulate expression of TRIB3 in cells infected by the coronavirus,” Carvalho told Agência FAPESP.
Human-virus protein interaction
The researchers were initially interested in finding out why lung cancer is more prevalent among older people. To this end they investigated how gene expression in the lungs changes with aging. They used bioinformatics tools to analyze transcriptome data available in the Genotype-Tissue Expression Project (GTEx), an open-access repository funded by the US National Institutes of Health (NIH). It contains molecular data for over 17,000 samples of 54 different tissue types, including lung tissue. The transcriptome is the set of all RNA molecules in one cell or a population of cells.
“We started with data from 427 individuals. The samples were stratified into decadal age groups from 30-39 through 70-79,” Carvalho explained.
This first analysis showed that expression of the gene TRIB3 diminished steadily as aging progressed. According to Carvalho, data from the scientific literature suggests lower production of the protein TRIB3 may favor infection and replication by some viruses, including HCV, which causes hepatitis C. The protein is also known to play a role in two cellular signaling pathways – the unfolded protein response (UPR) and the autophagy pathway, both of which are important to the biological cycles of several coronaviruses.
The group then decided to find out how this finding about lung aging correlated with the contents of another database, called P-HIPSTer, an acronym for Pathogen-Host Interactome Prediction using STructurE similaRity.
Referred to as a “human-virus interactome atlas”, the database offers a catalogue of predicted interactions between viral and human proteins. It is based on an algorithm that exploits sequence- and structure-based information to infer these protein-protein interactions (PPIs), and can be used by scientists to identify potential therapeutic targets.
“The ‘atlas’ has nothing on the interactions between human proteins and those of the novel coronavirus, but it does cover SARS-CoV, the coronavirus that caused the 2002 severe acute respiratory syndrome outbreak and a close relative of SARS-CoV-2,” Carvalho said.
“We found a high probability of interaction between TRIB3 and the SARS-CoV nucleocapsid protein, and a comparison of SARS-CoV with SARS-CoV-2 showed 94% similarity between their respective nucleocapsid protein sequences.”
They next returned to GTEx and analyzed TRIB3 expression in a larger number of lung tissue samples, this time separating samples from men and women. “Curiously enough we found no change in TRIB3 expression in women over the years. This may help explain why older men are more likely to develop pneumonia and respiratory insufficiency when they’re infected by SARS-CoV-2,” Carvalho said.
The group then set out to discover which lung cells express the gene TRIB3, using the open-access databases Single Cell Portal and UCSC Cell Browser, which contain single-cell RNA sequences enabling data to be analyzed to obtain the transcriptome of each cell in a tissue sample (instead of analyzing the sample as a whole).
“We found that TRIB3 is expressed mainly in the epithelial cells of the alveoli, which also express ACE-2 [the gene that encodes angiotensin-converting enzyme 2]. The coronavirus binds to the protein ACE-2 in order to invade human cells. This finding reinforces the probability that the protein TRIB3 downregulates infection by SARS-CoV-2, protecting the cell against the virus,” Carvalho said.
According to Diogo de Moraes, first author of the article, alveolar epithelial cells produce pulmonary surfactant, without which the tissue surrounding the alveoli sticks together after exhalation, causing the lung to collapse.
“We observed a reduction in the expression of genes involved in the surfactant metabolism of lungs from older patients,” he said. “Other studies have shown that surfactant deficiency increases vulnerability to other viral infections, and in recent weeks some researchers have discussed the advisability of replenishing surfactant as part of the treatment of COVID-19.”
The UNESP team also included Brunno Paiva, Sarah Santiloni Cury and João Pessoa Araújo Jr.
Marcelo Mori, a researcher at the University if Campinas (UNICAMP) collaborated. In FAPESP’s recent call for research proposals entitled “Fast track supplements for projects against COVID-19”, Mori won a grant to investigate how aging contributes to infection by SARS-CoV-2.
The article “Prediction of SARS-CoV interaction with host proteins during lung aging reveals a potential role for TRIB3 in COVID-19” can be read at: www.biorxiv.org/content/10.1101/2020.04.07.030767v1.
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