Fighting Fire with Fire: Immunogenicity of Viral Vectored Vaccines against COVID-19

Identification of genes related to immune enhancement caused by heterologous ChAdOx1-BNT162b2 vaccines in lymphocytes at single-cell resolution with machine learning methods

The widely used ChAdOx1 nCoV-19 (ChAd) vector and BNT162b2 (BNT) mRNA vaccines have been shown to induce robust immune responses. Recent studies demonstrated that the immune responses of people who received one dose of ChAdOx1 and one dose of BNT were better than those of people who received vaccines with two homologous ChAdOx1 or two BNT doses. However, how heterologous vaccines function has not been extensively investigated. In this study, single-cell RNA sequencing data from three classes of samples: volunteers vaccinated with heterologous ChAdOx1-BNT and volunteers vaccinated with homologous ChAd-ChAd and BNT-BNT vaccinations after 7 days were divided into three types of immune cells (3654 B, 8212 CD4+ T, and 5608 CD8+ T cells). To identify differences in gene expression in various cell types induced by vaccines administered through different vaccination strategies, multiple advanced feature selection methods (max-relevance and min-redundancy, Monte Carlo feature selection, least absolute shrinkage and selection operator, light gradient boosting machine, and permutation feature importance) and classification algorithms (decision tree and random forest) were integrated into a computational framework. Feature selection methods were in charge of analyzing the importance of gene features, yielding multiple gene lists. These lists were fed into incremental feature selection, incorporating decision tree and random forest, to extract essential genes, classification rules and build efficient classifiers. Highly ranked genes include PLCG2, whose differential expression is important to the B cell immune pathway and is positively correlated with immune cells, such as CD8+ T cells, and B2M, which is associated with thymic T cell differentiation. This study gave an important contribution to the mechanistic explanation of results showing the stronger immune response of a heterologous ChAdOx1-BNT vaccination schedule than two doses of either BNT or ChAdOx1, offering a theoretical foundation for vaccine modification.

Nanovaccines to combat virus-related diseases

The invention and application of vaccines have made tremendous contributions to fight against pandemics for human beings. However, current vaccines still have shortcomings such as insufficient cellular immunity, the lack of cross-protection, and the risk of antibody-dependent enhancement (ADE). Thus, the prevention and control of pandemic viruses including Ebola Virus, human immunodeficiency virus (HIV), Influenza A viruses, Zika, and current SARS-CoV-2 are still extremely challenging. Nanoparticles with unique physical, chemical, and biological properties, hold promising potentials for the development of ideal vaccines against these viral infections. Moreover, the approval of the first nanoparticle-based mRNA vaccine BNT162b has established historic milestones that greatly inspired the clinical translation of nanovaccines. Given the safety and extensive application of subunit vaccines, and the rapid rise of mRNA vaccines, this review mainly focuses on these two vaccine strategies and provides an overview of the nanoparticle-based vaccine delivery platforms to tackle the current and next global health challenges. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Therapeutic Approaches and Drug Discovery > Emerging Technologies.