In silico design of the multi-epitope vaccine for lung adenocarcinoma based on hub gene-derived neoantigens.

[BACKGROUND] Lung adenocarcinoma (LUAD) is the most prevalent and lethal subtype of non-small cell lung cancer (NSCLC), characterized by an unfavorable 5-year survival rate ranging from 10% to 20%. Neoantigen-based vaccine platforms show encouraging benefits for NSCLC patients. However, the vaccine efficacy may be limited, partially due to low immunogenicity and an immunosuppressive tumor microenvironment. This study aims to design a multiple epitopes vaccine targeting neoantigens derived from hub genes in LUAD, using immunoinformatics based strategies to explore a potential immunotherapeutic approach for LUAD.

[METHOD] Multiple GEO datasets were ultilized to identify the up-regulated genes in LUAD. Protein-protein interaction networks were analyzed and hub gene were identified based on overlapping top-ranked nodes across five topological algorithms in cytoscape. Hub gene derived neoantigens were identified using TSNAdb v2.0 and futher screened for LUAD in the cBioportal database. Neoantigen-derived CTL epitopes were predicted across all 12 MHC class I supertypes and subsequently screened for antigenicity, allergenicity, and toxicity. Linear B-cell epitopes were predicted from the extracellular region of PD-L1 using established B-cell epitope prediction methods. The multi-epitope vaccine (MEV) was constructed by rationally conjugating selected CTL and B cell epitopes using appropriate peptide linker.

[RESULTS] 114 differential express genes were identified from GEO dataset in LUAD. Subsequently, ten hub genes were identified and validated and their expression was associated with poorer overall survival in patients with LUAD. Tumor specific neoantigens were screened from these hub genes, and eight neoantigen epitopes with antigencity, non-allergenicity and non-toxicity were selected as cytotoxic T lymphocyte (CTL) epitopes for multi-epitopes vaccine construction. The vaccine was further incorporated predicted PD-L1 derived linear B-cell epitopes, pan HLA DR-binding epitope (PADRE), a universal helper T-cell epitope and β-defensin to augment protective efficacy. The designed and optimized vaccine possessed properties of solubility, antigenicity, non-allergenicity, and non-toxicity. Molecular docking demonstrated stable and favorable binding interactions between MEV and TLR2, TLR3 and TLR4 complex, as validated by molecular dynamics simulations. Immune simulation analysis revealed that MEV had the potential to elicit a series of T cell and B cell specific immune responses. Finally, the optimized MEV was cloned in silico and successfully expressed in eukaryotic cells.

[CONCLUSIONS] Our findings suggest that hub genes may serve as a promising source of neoantigens in lung adenocarcinoma. The multiple epitopes vaccine engineered from these hub genes shows potential for stimulating immune responses which highlights the potential of hub genes as prioritized candidates for advancing neoantigen-based vaccine development against LUAD.

[SUPPLEMENTARY INFORMATION] The online version contains supplementary material available at 10.1186/s12885-026-15765-1.