Multi-omics and network pharmacology identify IGFBP1 as an m6A-Epigenetic target of pueraria in NSCLC therapy

The dysregulation of N6-methyladenosine (m6A) modification drives progression in non-small cell lung cancer (NSCLC), yet its interplay with traditional medicine-derived therapeutics remains largely unexplored. We propose a novel strategy that integrates m6A-based prognostic subtypes with Pueraria pharmacology to identify prognostic markers and therapeutic targets related to m6A regulators for NSCLC treatment. Multi-omics clustering of 1,661 NSCLC samples identified three distinct m6A modification patterns. Based on these, a robust 19-gene prognostic signature was constructed via Cox regression and validated in the GSE31210 dataset. This risk model significantly correlated with immune infiltration and patient survival. Furthermore, the expression patterns of these genes were validated via single-cell RNA-sequencing (scRNA-seq) and RT-qPCR in NSCLC cell lines. To identify pharmacological interventions, we intersected the m6A prognostic signature with 7,333 NSCLC-related genes and 366 Pueraria targets, revealing IGFBP1 as the core therapeutic nexus. Immunohistochemistry confirmed the expression of IGFBP1 in NSCLC tissues. Molecular docking and 100-ns molecular dynamics (MD) simulations confirmed stable binding of Pueraria compounds to IGFBP1, specifically 7,8,4’-trihydroxyisoflavone (binding energy = -8.3 kcal/mol) and genistein (-7.4 kcal/mol). This study establishes IGFBP1 as a therapeutic nexus connecting m6A-driven NSCLC progression and the anti-tumor effects of Pueraria. Our RNA-modification-guided pharmacology approach advances the integration of traditional medicines into precision oncology.Author summary: We investigated how N6-methyladenosine (m6A), a prevalent RNA chemical modification, influences non-small cell lung cancer (NSCLC) progression and explored whether natural compounds from the medicinal plant Pueraria could target these pathways. Through the analysis of clinical multi-omics datasets and single-cell RNA sequencing (scRNA-seq), we identified a 19-gene signature linking m6A regulation to immune activity and treatment outcomes. By integrating these findings with network pharmacology, we established IGFBP1 as a critical therapeutic nexus bridging m6A-related tumor biology and Pueraria pharmacology. Experimental validation confirmed IGFBP1 protein expression in tumor tissues, and molecular docking combined with 100-nanosecond molecular dynamics simulations revealed the stable binding of two Pueraria isoflavonoids—7,8,4’-trihydroxyisoflavone and genistein—to IGFBP1. Collectively, our results highlight a viable strategy for repurposing plant-derived compounds to modulate RNA-modification networks in lung cancer. This study paves the way for preclinical testing of IGFBP1-targeting agents and the development of biomarkers to enhance therapeutic efficacy, including immunotherapy, for NSCLC patients.