Objective This study aimed to identify and predict bioactive small molecules and immunogenic antigen epitopes targeting proteins with point mutations in colitis-associated colorectal cancer (CAC), using integrative bioinformatics approaches. Methods Genes associated with colorectal cancer (CRC), ulcerative colitis (UC), diabetes mellitus (DM), hyperlipidemia (HL), gout, and functional dyspepsia (FD) were obtained from disease databases and GEO. Overlapping genes were identified using jvenn. CIBERSORT was used for immune infiltration analysis. Prognostic significance was evaluated using KM Plotter, and gene co-expression correlations in CRC were assessed via TIMER. cBioPortal was employed to analyze mutation profiles, tumor mutational burden (TMB), and microsatellite instability (MSI). Allosteric sites were predicted using AlloDriver. Molecular docking (AutoDock Vina v1.2.3) and 100-ns molecular dynamics simulations (GROMACS v2022.03) assessed protein-ligand interactions. Neoantigen and B-cell epitope immunogenicity were predicted using NetMHCpan-4.1 and IEDB, respectively. Results SERPINE1, SELE, SPP1, PLAU, COL1A1, PTGES, IL6, KDR, and ICAM1 were significantly upregulated in CAC. Lower expression correlated with improved relapse-free and overall survival (log-rank P < 0.05) and was associated with CRC molecular subtypes and biomarkers (P < 0.05). Mutations PLAUY151H, SERPINE1V166A, and KDRP359H were located in allosteric sites. Anacetrapib and LY2090314—metabolism-related compounds—showed high affinity for wild-type KDR, PLAU, and SERPINE1.The KDRP359H and PLAUY151H significantly weakened LY2090314 binding, and SERPINE1V166A mutation significantly reduced Anacetrapib binding, whereas SERPINE1V166A significantly enhanced LY2090314 binding. Although HLA-I affinity of mutation-derived antigens was low, four mutated B-cell epitopes (COL1A1R493H, KDRP551S, ICAM1T1259M, KDRT1260M) exhibited higher immunogenicity than wild-type, suggesting potential for antibody-based therapy. Conclusion Based on bioinformatics analysis, this study identified nine genes significantly upregulated in CAC and associated with prognosis. Allosteric-site mutations in PLAU, SERPINE1, and KDR affect the binding stability of small-molecule drugs (Anacetrapib, LY2090314), suggesting their role in drug response. Four mutation-specific B-cell epitopes (COL1A1R493H, KDRP551S, ICAM1T1259M, KDRT1260M) exhibit enhanced immunogenicity, indicating potential for antibody-based therapy. Graphical Abstract

Bioinformatics-based screening and prediction of compounds and antigen epitopes for immune targets with point mutations in colitis-associated colorectal cancer

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2025年12月29日

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Xinyi Peng,
Quan Sun,
Dongli Zhao,
Changxin Huang,
Ying Zhu

摘要

Objective

This study aimed to identify and predict bioactive small molecules and immunogenic antigen epitopes targeting proteins with point mutations in colitis-associated colorectal cancer (CAC), using integrative bioinformatics approaches.

Methods

Genes associated with colorectal cancer (CRC), ulcerative colitis (UC), diabetes mellitus (DM), hyperlipidemia (HL), gout, and functional dyspepsia (FD) were obtained from disease databases and GEO. Overlapping genes were identified using jvenn. CIBERSORT was used for immune infiltration analysis. Prognostic significance was evaluated using KM Plotter, and gene co-expression correlations in CRC were assessed via TIMER. cBioPortal was employed to analyze mutation profiles, tumor mutational burden (TMB), and microsatellite instability (MSI). Allosteric sites were predicted using AlloDriver. Molecular docking (AutoDock Vina v1.2.3) and 100-ns molecular dynamics simulations (GROMACS v2022.03) assessed protein-ligand interactions. Neoantigen and B-cell epitope immunogenicity were predicted using NetMHCpan-4.1 and IEDB, respectively.

Results

SERPINE1, SELE, SPP1, PLAU, COL1A1, PTGES, IL6, KDR, and ICAM1 were significantly upregulated in CAC. Lower expression correlated with improved relapse-free and overall survival (log-rank P < 0.05) and was associated with CRC molecular subtypes and biomarkers (P < 0.05). Mutations PLAU^Y151H, SERPINE1^V166A, and KDR^P359H were located in allosteric sites. Anacetrapib and LY2090314—metabolism-related compounds—showed high affinity for wild-type KDR, PLAU, and SERPINE1.The KDR^P359H and PLAU^Y151H significantly weakened LY2090314 binding, and SERPINE1^V166A mutation significantly reduced Anacetrapib binding, whereas SERPINE1^V166A significantly enhanced LY2090314 binding. Although HLA-I affinity of mutation-derived antigens was low, four mutated B-cell epitopes (COL1A1^R493H, KDR^P551S, ICAM1^T1259M, KDR^T1260M) exhibited higher immunogenicity than wild-type, suggesting potential for antibody-based therapy.

Conclusion

Based on bioinformatics analysis, this study identified nine genes significantly upregulated in CAC and associated with prognosis. Allosteric-site mutations in PLAU, SERPINE1, and KDR affect the binding stability of small-molecule drugs (Anacetrapib, LY2090314), suggesting their role in drug response. Four mutation-specific B-cell epitopes (COL1A1^R493H, KDR^P551S, ICAM1^T1259M, KDR^T1260M) exhibit enhanced immunogenicity, indicating potential for antibody-based therapy.

Graphical Abstract