Iterative Vaccine Design in an Era of Emerging Infectious Diseases - healthy donors’ dataset

Description

This work demonstrates a rapid and responsive pipeline for T-cell-specific multi-target vaccine development that leverages epitope identification, protein folding, and docking to render a collection of viral proteomes into a ranked list of peptide candidates scored for immunogenicity, allele coverage, solubility, and epitope stability in cleavage and processing. After epitope reactiveness was evaluated by microarrays, molecular dynamics simulations were used to assess the epitope's correct binding to the target host MHC. Finally, flow cytometry evaluated T-cell antigen-specific immunogenicity on mice and human peripheral blood mononuclear cells (PBMCs). Most final epitopes could elicit strong T-cell activation with the secretion of IFN-ɣ, TNF-α, or IL-2 – varying by host species and HLA allele. Final candidates were selected by overall scores in a string-of-beads design. This furthers the specific aim of developing vaccines for alphaviruses and the general aim of establishing efficient and tunable processes for vaccine development in a global setting. Data here was organized by the figure panel on the original manuscript to allow straightforward interpretation. Each folder contains the raw data for each independent experiment and the analysis datasheet for the human PBMC experiments presented in the manuscript, including the original workspace on the statistical software used for data plot. Each folder also contains a plate map or sample ID to allow interpretation of the raw data.

Steps to reproduce

PBMCs were thawed and expanded as previously described [Bozkus et al., 2021. doi: 10.1016/j.xpro.2021.100758]. At least 250,000 singlet events (PBMCs) were acquired, with 50,000 events on the CD3+ gate, on a FACS Symphony™ A5 (BD Biosciences, USA) and BD LSRFortessa™ Cell Analyzer (BD Biosciences, USA) analyzed using FlowJo Software, V10 (Treestar Inc., Ashland, USA). For all samples, gating was established using a combination of isotype and fluorescence-minus-one controls.

Institutions

• Faculdade de Medicina de Sao Jose do Rio Preto

  SP, Sao Jose do Rio Preto
• Centro Nacional de Pesquisa em Energia e Materiais

  SP, Campinas
• Instituto Conmemorativo Gorgas de Estudios de la Salud

  Panamá, Panama
• University of Texas Medical Branch at Galveston

  TX, Galveston

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