Machine learning, molecular docking, and experimental validation identify shared molecular signatures between idiopathic pulmonary arterial hypertension and malignant pleural mesothelioma: a retrospective study.

Abstract

Background: Idiopathic pulmonary arterial hypertension (IPAH) exhibits cancer-like features, yet its pathogenesis remains unclear. Given molecular similarities between IPAH and malignant pleural mesothelioma (MPM), this study aimed to uncover shared transcriptomic patterns.

Methods: GEO datasets for IPAH and MPM were analyzed. Overlapping DEGs and WGCNA modules were identified. PPI network analysis combined with LASSO, random forest, and SVM-RFE was used to identify candidate biomarker genes. A classification model was constructed and evaluated using leave-one-out cross-validation and bootstrap optimism correction. Immune infiltration was evaluated by ssGSEA. Molecular docking and MD simulations assessed drug binding to candidate target proteins. qRT-PCR validated candidate biomarker gene expression.

Results: Six concordantly upregulated and eleven concordantly downregulated DEGs were shared between IPAH and MPM. Upregulated genes were enriched in cell cycle regulation, while downregulated genes were enriched in neutrophil chemotaxis. WGCNA identified 58 overlapping genes. CXCR2, S100A9, and LCN2 were identified as candidate biomarker genes. A ROTS sensitivity analysis confirmed that all 1710 MPM DEGs were reproducible and directionally concordant at the matching FDR <0.05 threshold despite the imbalanced case-control ratio. The classification model achieved AUCs of 0.909 and 0.875 in training and external validation sets, with a LOOCV AUC of 0.879 and an optimism-corrected AUC of 0.896. Immune infiltration revealed increased Th17 cells but decreased neutrophils in IPAH. CXCR2 and S100A9 expression correlated with neutrophil infiltration; LCN2 expression correlated with metabolic reprogramming. Navarixin showed the strongest binding affinity to CXCR2 (-10.1 kcal/mol). MD simulations confirmed stable binding of the CXCR2-Navarixin complex. qRT-PCR confirmed significant downregulation of all three genes in IPAH patients.

Conclusion: This hypothesis-generating study identifies shared transcriptomic signatures between IPAH and MPM, highlighting CXCR2, S100A9, and LCN2 as candidate biomarkers linked to immune dysregulation and metabolic reprogramming. The computational and correlative nature of these findings, together with the limited size of the external validation cohort, requires confirmation through functional experiments and validation in larger, independent, and multicentre cohorts before clinical translation can be considered.