Integrative clinico-molecular analysis reveals actionable subtypes and biomarkers in lung adenocarcinoma

Deeper insights into omics in the clinical and tumor microenvironments of lung adenocarcinoma (LUAD) could reveal therapy-sensitive subtypes and novel treatments. From a cohort of 1008 samples from Chinese patients with LUAD with whole-genome and transcriptome sequencing data along with comprehensive longitudinal clinical and therapeutic information, we identified four prognostically distinct subtypes, namely, low proliferation and invasion (LPI), immune-desert (IMD), immune-enriched (IME), and high proliferation and invasion (HPI), based on the transcriptomic features linked to the radiological, pathological, and microenvironmental dimensions. Compared with chemotherapy, tyrosine kinase inhibitor (TKI) therapy demonstrated significantly superior efficacy for LPI and IMD, whereas no such difference was observed for HPI. VOPP1 and RRM2B amplification were closely associated with TKI resistance and sensitivity, respectively. VOPP1 knockdown restored sensitivity to TKI treatment, while RRM2B knockdown induced TKI resistance, and its overexpression restored sensitivity. Patients with RRM2B amplification had a 5-year survival rate of nearly 100%. Additionally, the IME subtype exhibited higher immune checkpoint activity and a higher frequency of DYNC2H1 mutation, with patients benefiting from immunotherapy. These findings provide critical insights into LUAD treatment optimization.