An endothelial-centered regulatory framework reveals context-dependent roles of MYLK in lung adenocarcinoma

Background Lung adenocarcinoma (LUAD) is shaped by the tumor microenvironment, yet endothelial cell (EC) regulatory programs and their biological roles remain insufficiently defined. Methods We analyzed scRNA-seq data to map EC-associated programs and applied hdWGCNA to identify EC modules and communication patterns. Network pharmacology integrated EC-module genes with LUAD-related targets to prioritize MYLK. MYLK expression and function were evaluated by RT-qPCR, immunohistochemistry, and gain-/loss-of-function assays in endothelial and LUAD cell models. We then performed network-based in silico knockout in LUAD tumors (GSE164789) and exploratory immune-cell eQTL analysis. Results EC modules were enriched for junction organization, angiogenesis, and immune-related pathways, with extensive epithelial-stromal-endothelial interactions. Network pharmacology nominated MYLK as an EC-linked LUAD candidate. MYLK expression was reduced in LUAD and associated with unfavorable clinical outcomes. In endothelial cells, MYLK perturbation altered junction integrity and trans-endothelial tumor cell migration; in LUAD cells, MYLK gain/loss affected migration, invasion, and proliferation. In silico knockout of MYLK produced regulatory shifts enriched for tight junction organization, endothelial apoptosis, angiogenesis, vascular permeability, and vascular/cancer-related pathways. Immune-cell eQTL analysis identified an association between increased MYLK expression in dendritic cells and elevated LUAD risk. Conclusions These findings define an endothelial-centered regulatory framework in LUAD and highlight the context-dependent, cell-type–specific roles of MYLK at the tumor–endothelial–immune interface.