In a study published in Scientific Reports, researchers from Spain developed a method to design vaccines for highly variable viruses like the hepatitis C virus (HCV) using combinatorial optimization.
They found that the method could create safe and immunogenic dendritic cell (DC) vaccines for HCV peptides, namely STG and DYP, inducing significant antiviral responses and suggesting broader applicability.
Study: Testing a vaccine candidate against Hepatitis C virus designed by combinatorial optimization. Image Credit: GroundPicture/Shutterstock.com
Background
Hepatitis C poses a significant global health burden, with 58 million people affected and 290,000 deaths recorded in 2019. Transmitted mostly by injection drug use, chronic HCV may lead to severe liver diseases, including cirrhosis and hepatocellular carcinoma.
Despite the recent success of direct-acting antivirals, there remain challenges, such as HCV re-infection. The World Health Organization targets a 90% reduction in hepatitis C by 2030, emphasizing the need for an effective HCV vaccine to accelerate this goal and address the diverse challenges associated with the virus.
HCV is a single-stranded ribonucleic acid (RNA) virus of size 60 nm, belonging to the Flaviviridae family and known for its high mutation rate.
Vaccine development against HCV has been hindered by several challenges, such as the virus's genetic variability, the unclear role of T-cell protection, the lack of a culture system and appropriate animal models, and the lack of understanding of the envelope protein structure.
Furthermore, the only phase II clinical trial conducted with an HCV vaccine candidate proved its inefficacy against chronic infection. Prevalence studies based on RNA and anti-HCV antibodies may not fully capture vaccine effectiveness, highlighting the need for computational strategies proposing designs that stimulate both humoral and cellular immune responses to HCV epitopes.
Addressing this need, researchers in the present study developed and validated a new vaccine design procedure aiming to offer protection against all the variants.
About the study
At first, the structure of human HCV was evaluated to identify vaccine candidates that include B- and T-cell epitopes. The researchers selected the E2 envelope glycoprotein as the target for vaccine candidates, as it is most targeted in HCV infections, instead of the nucleocapsid C protein.
A total of 1,803 variants were obtained from the European HCV database, and 439 relevant epitopes were selected from the Immune Epitope Database and Analysis Resource (IEDB).
Weights were assigned to each epitope based on the outcomes of T-cell assays, B-cell assays, and major histocompatibility complex (MHC) ligand assays, which were categorized as high-positive, intermediate-positive, low-positive, and negative.
A λ-superstring criterion was applied on the integer programming algorithm to optimize the vaccine candidates. The final vaccine candidate was chosen length of 39 amino acids and λ=1.889, as a union of 13 epitopes.
It was developed by disjunctively joining two peptide strings abbreviated as STG (the longer peptide) and DYP (the shorter peptide), which were synthesized separately and used in the assays. Mouse bone marrow-derived DCs without any peptide were used as controls in the assays.
Further, proof-of-concept experiments were conducted in mice to evaluate the safety and immunogenicity of the vaccine candidate.
The safety was assessed in vitro by studying the apoptosis of cells and toxicity and in vivo by measuring the levels of interleukin 1 (IL-1) in mice sera. Vaccines were prepared by loading the HCV-derived peptides into macrophages or DCs.
Local immune responses were evaluated through the induction of delayed-type hypersensitivity (DTH) reactions. T-cell responses were measured by flow cytometry, cytokines in mice sera were measured using multiparametric kits, and antibody levels were measured using enzyme-linked immunosorbent assay (ELISA).
The statistical analysis included the use of the Shapiro-Wilk test and Student’s t-test. Experiments were conducted in triplicates.
Results and discussion
The purity of the synthesized strings was found to be 98.5%. The chosen vaccine candidate showed positive results for all three types of assays. DC vaccines carrying HCV peptides were found to be safe both in vitro (cell viability up to 98.5%, apoptosis <4.5%) and in vivo (IL-1 level <1.3 pg/ml).
DTH analysis showed that DCs loaded with HCV peptides displayed 5.6–12-fold higher local immune responses than the responses elicited by controls.
As per the findings, DC vaccines containing the STG peptide showed greater efficacy than those containing the DYP peptide.
This was indicated by an increased antiviral cytokine response to STG. Additionally, an increase was observed in STG-specific T-cells (CD4 + and CD8 +) and antibodies (immunoglobulin G) that not only reacted with STG but also cross-reacted with envelope protein E1 and DYP, suggesting their potential universal application against HCV.
Conclusion
In conclusion, the present study unveils a novel vaccine design approach, demonstrating its efficacy in developing a vaccine against hepatitis C. The vaccine developed with this approach was safe and immunogenic in mice.
The method could be adapted to combat other high-mutation-rate viruses that currently lack effective vaccines. In the future, overcoming the method’s high computational cost limitation could open a promising avenue for advancing vaccine development in challenging areas.
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