Gwangju Institute of Science and Technology Researchers Develop a Tool for Studying Inflammatory Diseases Related to COVID-19

 Gwangju Institute of Science and Technology Researchers Develop a Tool for Studying Inflammatory Diseases Related to COVID-19


A new pipeline in bioinformatics will help investigate the mechanism underlying the progression of autoimmune diseases following SARS-CoV-2 infection.

GWANGJU, South Korea, May 17, 2022 / PRNewswire/-SARS-CoV-2, or the novel coronavirus, has affected more than 500 million people worldwide. In addition to the symptoms associated with COVID-19 infection, it was recently reported that the virus also leads to the subsequent progression of autoimmune diseases in patients.

Autoimmune diseases such as rheumatoid arthritis, lupus, or multi-inflammatory syndromes arise when the immune system confuses healthy cells with pathogens and begins to attack them. But the exact mechanism behind this “violation of self-determination” is unknown. One of the possible mechanisms proposed to be involved is so-called “molecular mimicry,” in which an autoimmune reaction is triggered when a T-cell receptor or an antibody is made from a B-cell. aimed against a specific antigen (foreign body) binding. with autoantigen, which is an antigen made from our own body. This occurs due to a molecular or structural similarity between the “epitopes” (the part of the antigen attached to the antibody) of the antigens. However, a comprehensive investigation of the role of molecular mimicry in the development of such autoimmune diseases has not yet been performed due to the complexity of epitope detection and lack of standard tools.

For this, a team of researchers from Gwangju Institute of Science and Technology (GIST) led by Prof. Jihwan Park created a new bioinformatics pipeline. Their new tool, called cross-reactive-epitope-search-using-structural-properties-of-proteins (CRESSP), was recently reported in the journal Bioinformatics Briefings. Previous studies of molecular mimicry have used bioinformatics pipelines that are different from each other that often involve complex algorithms and are not measured on proteome scales. As a result, we have created a pipeline that is easily accessible and measurable, ” explained by Prof. Park.It uses the structural properties of proteins to determine the epitope similarity between two proteins of interest, such as human proteins and SARS-CoV-2.

Using CRESSP, the team screened 4,911,245 proteins from 196,352 SARS-CoV-2 genomes obtained from an open-access database. The pipeline reduced 133 cross-reactive B-cells and 648 CD8+ T-cell epitopes that may be responsible for COVID-related autoimmune diseases. It even identified a target protein, PARP14, to be a potential promoter of the epitope spread between the COVID-19 virus and human lung proteins.

The pipeline also predicted cross-reactive epitopes of different coronavirus spike proteins. In addition, the team developed an interactive web application to enable an interactive view of the molecular mimicry map of SARS-CoV-2. The pipeline can also be used as an open-source package.

The team hopes their new tool will speed up comparisons between studies, providing a robust framework for further investigation of molecular replication and autoimmune diseases. “Even if autoimmune diseases affect less than 10% of the population, their study is important because they severely affect quality of life.. Our new tool can be used to study the possible involvement of molecular mimicry in the development of other autoimmune conditions in a systematic and scalable manner.“concluded Prof Park.

Hopefully, the new invention will help us deal with SARS-CoV-2 and other viral infections better.

references

Title of original paper: CRESSP: a comprehensive pipeline for the prediction of immunopathogenic SARS-CoV-2 epitopes using the structural properties of proteins

Journal: Bioinformatics Briefings

DOI: https://doi.org/10.1093/bib/bbac056

About Gwangju Institute of Science and Technology (GIST)
please visit: http://www.gist.ac.kr/.

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SOURCE Gwangju Institute of Science and Technology (GIST)



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