Researchers use mass spectrometry to study immunogenic SARS-CoV-2 epitopes

The rapid development and rollout of effective vaccines to the global population are key measures to help arrest the ongoing coronavirus disease 2019 (COVID-19) pandemic. The current pandemic has been caused by a highly transmissible respiratory virus, namely, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

At present, several vaccines have received emergency use authorization (EUA) from global regulatory bodies, that could provide protection to the host against the SARS-CoV-2 virus by eliciting humoral (antibody) and cellular (T cell) responses.

In silico prediction algorithms

Various studies have used in silico prediction algorithms to determine Class I and Class II-restricted epitopes to investigate SARS-CoV-2 specific T cell responses and overlapping long peptide (OLP) pools. These peptides have various uses. For example, they help track responses in infected and convalescent individuals, develop multi-epitope vaccines, and also help determine the severity of the SARS-CoV-2 infection. To date, researchers have been successful in identifying around 1,500 predicted Class I epitopes for the SARS-CoV-2 virus using in silico prediction methods.

An immunogenic epitope is a peptide that is presented by self-MHC. Typically, immunogenic peptides can elicit an immune response. Researchers stated an immunogenic epitope of SARS-CoV-2 needs both empiric validations of T cell immunogenicity and direct sequencing of peptides presented by MHC. Even though many of these studies have determined the T cell response of these epitopes, they failed to consider their immunogenic properties. Hence, there is a gap in the research, i.e., no reports are available regarding the empirical validation of SARS-CoV-2 epitopes for immunogenicity.

A new study

A new study has been published on the bioRxiv* preprint server, which has used MS to identify T cell epitopes of SARS-CoV-2 conserved protein, i.e., the membrane glycol protein (MGP) and the non-structure protein-13 (NSP13). In this study, researchers isolated peptides from the MHC complexes of SARS-CoV-2-expressing cells. This is the first report on the use of MS to determine T cell epitopes of the virus’s protein. Additionally, empirical validation of immunogenicity by in vitro synthesis of SARS-CoV-2-specific cytotoxic T lymphocyte (CTL) has also been addressed for the first time.

For this study, the authors have used technology from their previous study, which involved the isolation of rare tumor-reactive T cells from peripheral blood. The researchers of this study have hypothesized that immunogenic epitopes for SARS-CoV-2 can be defined empirically by analyzing the peptides isolated from MHC. Subsequently, each peptide was analyzed for its ability to induce T cells against SARS-CoV-2 antigen-expressing targets.

Identification of antigenic epitopes using Mass Spectrometry (MS)

MS is a popular analytical tool used for the identification of naturally expressed antigenic epitopes. It helps to understand the complexity of the varied expression and processing of antigenic proteins in infected cells. The current research has identified and profiled SARS-CoV-2 immunopeptidome by studying the immunoaffinity of the MHC-antigenic peptide complex from the cells engineered to express SARS-CoV-2 genes.

The present study has identified and validated five Class I-restricted immunogenic epitopes of a highly conserved region of MGP and the NSP13 region of the SARS-CoV-2 genome. In this study, the researchers have used recombinant vectors encoding specific alleles and had engineered the expression of highly conserved regions of SARS-CoV-2 MGP and NSP13 genes.

Thereby, they recovered MHC and eluted peptides. The data-dependent analysis liquid chromatography-tandem mass spectrometry (DDA MS/MS) was used to analyze these peptides, which yielded over 12,000 spectra. These were deconvoluted and filtered, and five peptide epitopes were determined. The authors have empirically validated the SARS-CoV-2-infected cells and the presence of these peptides (endogenous) by triggering T cell responses against these candidate epitopes.

A recent study has also reported vaccine-induced T cell responses against SARS-CoV-2, which had been linked with the elimination of the virus and its components from the host. The scientists further determined MGP65- and NSP13-specific CTL that can identify and eliminate target cells with SARS-CoV-2 antigen.

Significance of the study

In the current scenario, concern has mounted among the scientific community about the effectiveness of the available vaccines against emergent SARS-CoV-2 variants. This is because all of these vaccines have been designed based on the SARS-CoV-2’s S protein, and a significant mutation in this area might lead to immunity evasion. To date, none of the mutations have been found in the epitopes of the SARS-CoV-2 variants.

Hence, developing vaccines targeting these epitopes could be extremely effective as it will provide a long-term viral immunoprotection via T cell synthesis. Additionally, the strategy for identifying the epitope is versatile, i.e., the technology can identify epitopes present in any region of the SARS-CoV2 gene.

*Important notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

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