Gwangju Institute of Science and Technology


image: A new bioinformatics pipeline helps study the mechanism underlying the development of autoimmune diseases following SARS-CoV-2 infection
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Credit: Gwangju Institute of Science and Technology (GIST)

SARS-CoV-2, or the new coronavirus, has affected more than 500 million people worldwide. Apart from the symptoms associated with COVID-19 infection, it has recently been reported that the virus also leads to further development of autoimmune diseases in patients.

Autoimmune diseases such as rheumatoid arthritis, lupus or multi-inflammatory syndromes occur when the immune system mistakes healthy cells for pathogens and begins to attack them. But the precise mechanism underlying this violation of self-tolerance” is unknown. One of the possible mechanisms suggested to be involved is what is called molecular mimicry”, in which an autoimmune reaction is triggered when a T cell receptor or an antibody produced from a B cell directed against a specific antigen (foreign body) binds to a self antigen, which is an antigen produced from our own body. This occurs due to a molecular or structural resemblance between the epitopes” (the part of the antigen attached to the antibody) of the antigens. However, a thorough investigation of the role of molecular mimicry in the development of such autoimmune diseases has not yet been carried out due to the complexity of epitope finding and the lack of standardized tools.

To this end, a team of researchers from the Gwangju Institute of Science and Technology (GIST) led by Professor Jihwan Park has developed a novel bioinformatics pipeline. Their new tool, called cross-reactive-epitope-search-using-structural-properties-of-proteins (CRESSP), was recently published in the journal Bioinformatics Briefings. Previous studies on molecular mimicry used different bioinformatics pipelines that often involved complex algorithms and were not scalable at the proteome scale. In light of this, we have developed an easily accessible and scalable pipeline,” explains Professor Park.It uses the structural properties of proteins to identify epitope similarities 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 cell epitopes and 648 CD8+ T cell epitopes that may be responsible for COVID-related autoimmune diseases. He further identified a protein target, PARP14, as a potential initiator of epitope propagation between the COVID-19 virus and human lung proteins.

The pipeline also predicted the cross-reacting epitopes of different coronavirus spike proteins. Additionally, the team developed an interactive web application to enable interactive visualization of the molecular mimicry map of SARS-CoV-2. The pipeline is also available as an open source package.

The team hopes their new tool will make it easier to compare studies, providing a solid framework for further investigation into molecular mimicry and autoimmune diseases. Although autoimmune diseases affect less than 10% of the population, studying them is important because they severely impact quality of life.. Our new tool can be used to study the possible involvement of molecular mimicry in the development of other autoimmune diseases in a systemic and evolutionary way“, concludes Professor Park.

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




Authors: Hyunsu An, Minho Eun, Jawoon Yi, Jihwan Park

Affiliations: School of Life Sciences, Gwangju Institute of Science and Technology (GIST)

About Gwangju Institute of Science and Technology (GIST)

The Gwangju Institute of Science and Technology (GIST) was founded in 1993 by the Korean government as a research-oriented graduate school to help ensure Korea’s continued economic growth and prosperity by developing science and advanced technologies with an emphasis on collaboration with the international community. Since then, GIST pioneered a highly regarded undergraduate science program in 2010, which has become a model for other science universities in Korea. To learn more about GIST and its exciting opportunities for researchers and students, please visit:

About the Author

Jihwan Park is an associate professor at the School of Life Sciences at GIST Korea. He obtained a doctorate. in epigenomics from POSTECH in Korea. He continued his studies of genetics and epigenetics of human diseases using multi-omics analysis and single-cell analysis at the University of Pennsylvania in the United States under the supervision of Dr. Katalin Susztak. Currently, his group is exploring the molecular mechanisms of diseases such as cancer and chronic disease using single cell analyses. His lab also focuses on the development of single-cell sequencing techniques for full-length mRNA sequencing and cell lineage tracing in cancer progression and organogenesis.

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