Neoantigen-based multi-epitope vaccine designing against glioblastoma using reverse vaccinology and immunoinformatic...

One of the primary factors in the development of cancer is the accumulation of genetic mutations. Some of these genetic mutations result in the emergence of unique antigens called neoantigens. These neoantigens are perceived as non-self by T cells, making them prime targets for cancer vaccines. These neoantigen-based vaccines can elicit a promising immune response against the malignant cells. In the current research work, a computational approach was employed to design a multi-epitope vaccine for glioblastoma. A set of 126 neoantigens was retrieved from the CEDAR cancer epitopes database which yielded 446 epitopes. The epitopes were screened and 10 potential epitopes were selected to design a multi-epitope vaccine. GPGPG linkers were used for combining these epitopes, while adjuvants were connected to the vaccine via EAAAK and RVRR linkers to build the final construct of the vaccine. The physicochemical properties of the vaccine indicated that the designed vaccine is highly antigenic (0.7841 antigenicity score), non-allergenic, non-toxic, and also water soluble. Molecular docking assessed the interaction of the vaccine with MHC-I, MHC-II, and TLR-4, demonstrating strong binding affinities (-886.5 kcal/Mol, -1050.2 kcal/Mol, and - 1018.3 kcal/Mol, respectively). The docking results were further supported by the normal mode analysis and molecular dynamics simulation showing average RMSD values of 4.21 Å, 6.80 Å, and 5.68 Å for the three complexes, respectively. The in silico cloning of the vaccine into the bacterial plasmid (pET28a+) was carried out to enhance its expression achieving a GC content of 57.43 and a codon adaptation index of 1. The in silico immune simulation revealed that peak antigen levels (∼7.5 × 10⁵ counts/mL at approximately day 50) elicited strong humoral and cellular immune responses, characterized by elevated IgM + IgG titers (∼2.8 × 10⁵) and increased cytokine production, including IFN-γ (∼4.5 × 10⁵), IL-2 (∼6.0 × 10⁵), and TNF-α (∼1.2 × 10⁵ ng/mL), indicating robust immune activation. These findings indicated that our designed vaccine could be a potential therapeutic candidate against glioblastoma. Further experimental research is required to validate the potential, efficacy, and safety of the designed vaccine.