MYO6+Epithelial Subpopulation as a Prognostic Hub in Lung Adenocarcinoma Identified by Multi-Omics Integration

Background Lung adenocarcinoma (LUAD) exhibits profound cellular heterogeneity, with epithelial subpopulations playing pivotal yet incompletely characterized roles in tumor progression. Here, we sought to delineate the key heterogeneous epithelial subpopulations and to uncover the molecular determinants that govern their influence on LUAD prognosis. Methods We integrated two publicly available single-cell RNA-seq datasets derived from normal lung and LUAD tissues. Epithelial cells were extracted and subpopulations annotated via Seurat-based clustering. Transcriptional dynamics during malignant transformation were quantified using Monocle3 trajectory inference and ternary plots. A machine-learning framework comprising 101 algorithmic combinations screened signature genes from poorly differentiated clusters (11/26). Prognostic models were constructed and validated in TCGA cohorts. MYO6⁺ epithelial cells were functionally characterized through differential-expression analysis and GO/KEGG pathway enrichment.Verification of MYO6 mRNA levels and protein expression levels by quantitative real-time PCR (qRT-PCR) and Western blot. Results Single-cell profiling demonstrated that LUAD epithelial cells transition from lineage-specific identities (AT1, AT2, airway) to a dedifferentiated state. Cluster 11/26 displayed low lineage-specific gene scores and selective enrichment in LUAD. Machine learning identified MYO6, ASPH, and KRT8 as core prognostic genes among 140 intersecting markers. The StepCox[forward]+Ridge model reliably stratified patients into high- and low-risk groups (HR = 2.48, p < 0.001; 3-year AUC = 0.82). MYO6⁺ epithelial cells were spatially distinct, exhibited MAPK-pathway activation, and correlated with proliferative signatures and adverse outcomes. Compared with 16HBE, MYO6 mRNA was significantly elevated in A549 and H1299 cells; LUAD tissue MYO6 protein levels were also significantly higher than those in adjacent non-cancerous tissue. Conclusion We identify a low-lineage-score epithelial subpopulation (Cluster 11/26) in LUAD whose attenuated lineage-specific gene expression is linked to malignant progression. A StepCox+Ridge prognostic model, built upon core genes derived from this subpopulation, delivers significant clinical stratification. MYO6⁺ cells, a central constituent of this subpopulation, propel tumor progression via MAPK signaling and represent a promising target for precision therapy.