Project description:Next-generation T-cell-directed vaccines for COVID-19 aim to induce durable T-cell immunity against circulating and future hypermutated SARS-CoV-2 variants. Mass Spectrometry (MS)based immunopeptidomics holds promise for guiding vaccine design, but computational challenges impede the precise and unbiased identification of conserved T-cell epitopes crucial for vaccines against rapidly mutating viruses. We introduce a computational framework and analysis platform integrating a novel machine learning algorithm, immunopeptidomics, intra-host data, epitope immunogenicity, and geo-temporal CD8+ T-cell epitope conservation analyses. Central to our approach is MHCvalidator, a novel artificial neural network algorithm enhancing MS-based immunopeptidomics sensitivity by modeling antigen presentation and sequence features. MHCvalidator identified a novel nonconventional SARS-CoV-2 T-cell epitope presented by B7 supertype molecules, originating from a +1-frameshift in a truncated Spike (S) antigen, supported by ribo-seq data. Intra-host analysis of SARS-CoV-2 proteomes from ~100,000 COVID-19 patients revealed a prevalent S antigen truncation in ~51% of cases, exposing a rich source of frameshifted viral antigens. Our framework includes EpiTrack, a new computational pipeline tracking global mutational dynamics of MHCvalidator-identified SARS-CoV-2 CD8+ epitopes from vaccine BNT162b4. While most vaccine-encoded CD8+ epitopes exhibit global conservation from January 2020 to October 2023, a highly immunodominant A*01-associated epitope, especially in hospitalized patients, undergoes substantial mutations in Delta and Omicron variants. Our approach unveils unprecedented SARS-CoV-2 T-cell epitopes, elucidates novel antigenic features, and underscores mutational dynamics of vaccine-relevant epitopes. The analysis platform is applicable to any viruses, and underscores the need for continual vigilance in T-cell vaccine development against the evolving landscape of hypermutating SARS-CoV-2 variants.

Project description:Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of COVID-19 kidney to normal controls Methods/Results: Kidney mRNA profile of human COVID-19 tissue was generated by deep sequencing using Illumina Novaseq6000 Paired-end 150. After filtering reads mapped to contamination database, the reads that were uniquely aligned to the exon and splicing-junction segments with a maximal 2 mismatches for each transcript were then counted as expression level for corresponding transcript. Next, RNA-seq reads count data were downloaded from public resource GTEx project (https://www.gtexportal.org/home/datasets) and 12 normal kidney tissue samples were extracted as controls. The differential analysis by fold change difference was carried out to identify dysregulated genes at 1.5 fold change. The differential expressed genes were then subjected to Gene Ontology function and Pathway (KEGG, Ingenuity IPA, BIOCARTA, NABA, Panther, PID, REACTOME, Wiki-pathway) enrichment analysis by Fisher-exact test. Conclusions: RNA sequencing data revealed that biological processes from upregulated genes were enriched for cell cycle, chromosome segregation, response to wounding, humoral immune response, and blood coagulation, suggesting that cell injury/regeneration, inflammatory response, and endothelial injury were the major disease processes involved. The biological processes from downregulated genes were enriched for ion transport, metabolic processes, and oxidation, likely secondary to severe tubular cell injury. Pathway analysis from both up- and downregulated genes showed enrichment of transmembrane transport, oxidation, and blood coagulation consistent with the GO terms analysis. Upregulated genes were enriched only for the FOXM1 pathway, which was recently reported to promote tubular cell proliferation during injury repair. Additionally, genes related to the renin-angiotensin system were downregulated, but ACE2 expression did not differ from normal controls.

Project description:Bluetongue (BT) is a haemorrhagic disease of wild and domestic ruminants with a huge economic worldwide impact on livestock. The disease is caused by BT-virus transmitted by Culicoides biting midges and disease control without vaccination is hardly possible. Vaccination is the most feasible and cost-effective way to minimize economic losses. Marketed BT vaccines are successfully used in different parts of the world. Inactivated BT vaccines are efficacious and safe but relatively expensive, whereas live-attenuated vaccines are efficacious and cheap but are unsafe because of under-attenuation, onward spread, reversion to virulence, and reassortment events. Both manufactured BT vaccines do not enable differentiating infected from vaccinated animals (DIVA) and protection is limited to the respective serotype. The ideal BT vaccine is a licensed, affordable, completely safe DIVA vaccine, that induces quick, lifelong, broad protection in all susceptible ruminant species. Promising vaccine candidates show improvement for one or more of these main vaccine standards. BTV protein vaccines and viral vector vaccines have DIVA potential depending on the selected BTV antigens, but are less effective and likely more costly per protected animal than current vaccines. Several vaccine platforms based on replicating BTV are applied for many serotypes by exchange of serotype dominant outer shell proteins. These platforms based on one BTV backbone result in attenuation or abortive virus replication and prevent disease by and spread of vaccine virus as well as reversion to virulence. These replicating BT vaccines induce humoral and T-cell mediated immune responses to all viral proteins except to one, which could enable DIVA tests. Most of these replicating vaccines can be produced similarly as currently marketed BT vaccines. All replicating vaccine platforms developed by reverse genetics are classified as genetic modified organisms. This implies extensive and expensive safety trails in target ruminant species, and acceptance by the community could be hindered. Nonetheless, several experimental BT vaccines show very promising improvements and could compete with marketed vaccines regarding their vaccine profile, but none of these next generation BT vaccines have been licensed yet.

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Next-generation COVID-19 vaccines: here come the proteins.

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