Sequence-based prediction of SARS-CoV-2 vaccine targets using a mass spectrometry-basedbioinformatics predictor identifies immunogenic T-cellepitopes
Authors: A. Poran, D. Harjanto, M. Malloy, C. M. Arieta, D. A. Rothenberg, D. Lenkala, M. M. Van Buuren, T. A. Addona, M. S. Rooney, L. Srinivasan, R. B. Gaynor
Journal: Clinical Cancer Research (2020)

The ongoing COVID-19 pandemic has created an urgency to identify novel vaccine targets for protective immunityagainst SARS-CoV-2  Consistent with observations for the closely related SARS-CoV, early reports identify aprotective role for both humoral and cell-mediated immunity for SARS-CoV-2  In this study, we leveraged ourbioinformatics binding prediction tools for human leukocyte antigen (HLA)-I and HLA-II alleles that cover nearly theentire population and were developed using mass spectrometry-based profiling of 74 individual HLA-I and 83individual HLA-II alleles  We applied these binding predictors, initially developed to predict tumor neoantigenpresentation, to identify T-cell epitopes from SARS-CoV-2 proteins  To determine the ability of our tools to identifyviral T-cell epitopes, we validated HLA-I and HLA-II predictions on Coronaviridae family epitopes deposited in theVirus Pathogen Database and Analysis Resource (ViPR) database  We then applied our HLA-I and HLA-IIpredictors to 13 open reading frames (ORFs) of SARS-CoV-2 and identified 11,897 HLA-I and 8,046 HLA-IIcandidate peptides that were highly ranked for binding  From our SARS-CoV-2 predicted peptide-HLA-I allele pairs,374 pairs identically matched previously reported pairs in the ViPR database, originating from other coronaviruses with homologous sequences  Of these pairs, 333 (89 %) had a positive HLA-binding assay result, reinforcing thevalidity of our predictions  Furthermore, we assayed a subset of epitopes with highly predicted binding scores fortheir ability to be recognized by specific CD8+ T cell in human donor PBMCs  These epitopes were chosen fromfour structural proteins (S, N, M, E) and one nonstructural protein (ORF1ab) from SARS-CoV-2, and epitopes fromall five proteins were found to be immunogenic  Finally, it was important to address the expression of SARS-CoV-2proteins within cells since their subsequent processing is necessary for MHC presentation and the generation ofspecific epitopes  We utilized publicly available proteomic data to infer the relative expression of SARS-CoV-2proteins from infected cell lines and determined that the different proteins vary significantly in their expression levels, with the nucleocapsid being the most highly expressed viral protein across these studies  Our predictions identifyfew epitopes from each SARS-CoV-2 protein, which are predicted to bind multiple HLA-I or HLA-II alleles, potentiallycovering over 99% of the USA, European, and Asian populations  Finally, using our bioinformatic platform, weidentify multiple putative epitopes that are potential targets for CD4+ and CD8+ T cells whose predicted HLA bindingproperties cover nearly the entire population  We further propose that when considering the protein expressionlevels of these epitopes and their ability to elicit a T-cell response, these epitopes may be effective when included invaccines against SARS-CoV-2 to induce broad cellular immunity