Longitudinal transcriptomic profiling of paired early and metastatic EGFR-mutant lung adenocarcinomas reveals molecular programs associated with disease progression.

BACKGROUND: The molecular mechanisms driving the progression of EGFR-mutated lung adenocarcinoma (LUAD) from localized to metastatic disease remain incompletely understood. We aimed to characterize transcriptomic alterations associated with disease progression by analyzing longitudinally paired tumor samples from patients with early-stage and subsequent metastatic EGFR-mutated LUAD. METHODS: Whole-transcriptome sequencing was performed on eight paired tumor samples obtained at resectable disease (stage IB-IIIA) and after progression to stage IV disease. Differential gene expression, pathway enrichment, and tumor microenvironment analyses were conducted. Progression-associated genes were further evaluated for prognostic relevance in The Cancer Genome Atlas lung adenocarcinoma (TCGA-LUAD) cohort using elastic net-regularized Cox regression, and subsequently validated in an independent transcriptomic cohort (GSE50081) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC)-LUAD proteomic dataset. RESULTS: Comparative transcriptomic analysis identified 445 differentially expressed genes between early-stage and metastatic tumors. Early-stage tumors were enriched for developmental, tissue remodeling, hypoxia response, and surfactant metabolism programs, whereas metastatic tumors showed enrichment of pathways related to metabolic adaptation, transmembrane transport, extracellular matrix remodeling, complement and coagulation signaling, platelet activation, and xenobiotic metabolism. No significant differences in inferred immune cell composition were observed between disease stages. A 19-gene signature derived from progression-associated genes stratified overall survival in TCGA-LUAD (HR 2.53, 95% CI 1.86-3.44, p < 0.0001) and remained independently prognostic after adjustment for clinicopathological variables. The prognostic value of the signature was confirmed in GSE50081 (HR 2.12, 95% CI 1.20-3.74, p = 0.0083) and was recapitulated at the protein level in CPTAC-LUAD. CONCLUSION: Longitudinal transcriptomic profiling of paired early-stage and metastatic EGFR-mutated LUAD revealed significant molecular reprogramming associated with disease progression. Metabolic adaptation, transport-related pathways, extracellular matrix remodeling, and coagulation-associated signaling were identified as key features of advanced disease. These progression-associated molecular programs showed prognostic relevance across independent transcriptomic and proteomic cohorts.