biostudies-literatureYuan LBeijing Natural Science Foundation ProjectGuangdong Basic and Applied Basic Research FoundationSanming Project of Medicine in Shenzhen NanshanCAMS Innovation Fund for Medical SciencesScience and Technology Projects in GuangzhouShenzhen Science and Technology Program357https://www.ebi.ac.uk/biostudies/studies/S-EPMC12937623biostudies-literatureUnknown15(4)Influenza's pandemic threat is driven by antigenic drift, which limits the efficacy of conventional vaccines. To address this challenge, we established a clinical serum-anchored computational design pipeline for a broad-spectrum multi-epitope mRNA vaccine (MEMV), bridging the gap between pure in silico design and clinical applicability. Using 36 longitudinal sera (d0/d28/d365) from 12 well-characterized human cohorts (6 vaccine recipients and 6 influenza patients) and high-density antibody-peptide microarrays, we empirically identified 12 immunodominant B-cell linear epitopes from the nucleoprotein (NP) of influenza A (H1N1/H3N2) and B viruses. These experimentally validated epitopes were combined with in silico-predicted conserved helper T-lymphocyte (HTL)/cytotoxic T-lymphocyte (CTL) epiBiologyClinical Serum-Anchored Computational Design Pipeline for a Broad-Spectrum Influenza Multi-Epitope mRNA Vaccine.PMC12937623L2540232022-I2M-1-021;2023-I2M-2-0012024A04J4015SZSM202103008No. L242036KCXFZ20211020172545006; KQTD20200820145822023; ZDSYS202306260912030072023A1515011767Yan MBi RYuan LWen SLuo HZhao YSong JLi WLi XBai TLi YChen YOuyang ZShu YWu YfalseClinical Serum-Anchored Computational Design Pipeline for a Broad-Spectrum Influenza Multi-Epitope mRNA Vaccine.Influenza's pandemic threat is driven by antigenic drift, which limits the efficacy of conventional vaccines. To address this challenge, we established a clinical serum-anchored computational design pipeline for a broad-spectrum multi-epitope mRNA vaccine (MEMV), bridging the gap between pure in silico design and clinical applicability. Using 36 longitudinal sera (d0/d28/d365) from 12 well-characterized human cohorts (6 vaccine recipients and 6 influenza patients) and high-density antibody-peptide microarrays, we empirically identified 12 immunodominant B-cell linear epitopes from the nucleoprotein (NP) of influenza A (H1N1/H3N2) and B viruses. These experimentally validated epitopes were combined with in silico-predicted conserved helper T-lymphocyte (HTL)/cytotoxic T-lymphocyte (CTL) epi2026-01-01T00:00:00Z2026 Feb2026-07-11T03:16:26.018Z2026-07-11T03:11:44.167ZS-EPMC129376234174466610.3390/biology15040357