Poster Presentation Asia-Pacific Vaccine and Immunotherapy Congress 2023

Immunoinformatic prediction of SARS-CoV-2 T-cell epitopes and ELISPOT assays on the PBMC samples from Indonesian people as the first step for vaccine design (#106)

Marsia Gustiananda 1 , Michael Jonathan 1 , Jyothsna Girish 1 , Vivi Julietta 1 , Sita Andarini 2 , Yacine Maringer 3 4 5 , Annika Nelde 3 4 5 , Jaturong Sewatanon 6 , Juliane Walz 3 4 5 7
  1. Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
  2. Department of Pulmonology and Respiratory Medicine, Faculty of Medicine University of Indonesia -Persahabatan Hospital, Jakarta, DKI Jakarta, Indonesia
  3. Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, Tübingen, Germany
  4. Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
  5. Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
  6. Department of Pulmonology and Respiratory Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkoknoi, Bangkok, Thailand
  7. Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tuebingen , Germany

The presence of memory T-cells recognizing peptide epitopes from SARS-CoV-2 might protect us from severe diseases due to infection caused by the new variants of coronavirus.  CD8+ and CD4+ T-cells recognize peptide epitopes that are presented by HLA Class-I and II, respectively.  CD8+ T-cells kill the infected cells and CD4+ T-cells orchestrate and help other immune cells such as B-cells to produce antibodies.  Immunoinformatic analysis of the entire SARS-CoV-2 proteome of Wuhan Hu-1 was conducted using netMHCpan(1) and netMHCIIpan(2) to predict T-cell epitopes presented by HLA Class-I and Class-II alleles, respectively.  As the aim is to study T-cell responses to SARS-CoV-2 in Indonesian population, the HLA alleles which have at least 5% frequency in the population were chosen(3).  Peptides that fulfil 2% rank threshold as binder were checked for sequence conservancy in Delta and Omicron variants using IEDB conservancy analysis tool(4), and conserved peptides were chosen for synthesis.  Several other criteria were applied such as cysteine containing peptides were not selected for synthesis and ORF1ab peptides that span the cleavage site of the 2 consecutive non-structural proteins were also not selected.  The immunoinformatic analysis generated 111 peptides presented by HLA Class-I and 34 peptides presented by HLA Class-II.  Initial ELISPOT assay was conducted to test the immunogenicity of 10 HLA Class-II peptides.  PBMC samples were collected from 5 study participants: 4 with history of SARS-CoV-2 infection and COVID-19 vaccination and 1 without prior infection nor vaccination.  Prior to the ELISPOT assay, the PBMC samples were stimulated with peptides for 12 days to expand the number of T-cells that recognize the peptides.  IL-2 were added at day 2, 5, and 7. Six peptides, 3 of them are listed already in IEDB and 3 others are new, were positive in IFNγ-ELISPOT assay, indicating the presence of T-cell memory among the study participants.

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  2. Reynisson B, Barra C, Kaabinejadian S, Hildebrand WH, Peters B, Nielsen M. Improved Prediction of MHC II Antigen Presentation through Integration and Motif Deconvolution of Mass Spectrometry MHC Eluted Ligand Data. J Proteome Res. 2020;19(6):2304-2315. doi:10.1021/acs.jproteome.9b00874
  3. Gonzalez-Galarza, F.F.; McCabe, A.; Santos, E.J.; Jones, J.; Takeshita, L.Y.; Ortega-Rivera, N.D.; del Cid-Pavon, G.M.; Ramsbottom, K.; Ghattaoraya, G.S.; Alfirevic, A.; et al. Allele Frequency Net Database (AFND) 2020 Update: Gold-Standard Data Classification, Open Access Genotype Data and New Query Tools. . Nucleic Acid Research 2020, 48, D783–D788.
  4. Bui HH, Sidney J, Li W, Fusseder N, Sette A. Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics. 2007;8:361. Published 2007 Sep 26. doi:10.1186/1471-2105-8-361