Integrating multi-omics to unveil PSMD12 as a critical gene in promoting brain metastases of lung adenocarcinoma

BACKGROUND: Brain metastases (BM) remain the leading cause of death in patients with lung adenocarcinoma (LUAD) despite the availability of comprehensive therapeutics. This study aimed to systematically identify crucial genes associated with BM in patients with LUAD, and develop a heuristic search algorithm combining information filtering and multiple stepwise regression to construct a multi-layered transcription factor regulatory network. METHODS: We used the mRNA expression profiles of primary tumours derived from LUAD patients with different organ metastasis and adjacent normal tissue samples to identify differentially expressed genes specific to BM, and validated it in bulk, spatial and single-cell RNA-sequencing data. Furthermore, we collected 110 stage I-III LUAD specimens to validate the correlation of high PSMD12 (proteasome 26 S subunit, non-ATPase 12) protein expression with BM incidence and patient prognosis. We also developed an in vitro blood-brain barrier (BBB) model to investigate the disruption of PSMD12 on the barrier. Mechanistically, we developed an algorithm to construct an upstream regulator network of PSMD12 overexpression. RESULTS: Through integrated bioinformatics analyses, we identified PSMD12 as a critical gene associated with BM. The associations of PSMD12 with BM and poor survival were validated in multiple public datasets comprising 706 patients. Immunohistochemical results confirmed that patients exhibiting high PSMD12 protein expression had a significantly higher incidence of BM within 5 years and shorter progression-free survival. Functional experiments revealed that PSMD12 overexpression in A549 cells disrupted BBB integrity and enhanced tumor cell invasiveness, whereas PSMD12 knockdown attenuated these effects. Furthermore, upstream regulator network and knockdown experiments indicated that downregulated EOMES expression would contribute to PSMD12 overexpression. CONCLUSIONS: PSMD12 emerges as a crucial gene in promoting BM, potentially serving as an early warning indicator of BM in early-stage LUAD. The upstream regulatory network of PSMD12 overexpression provides potential mechanisms for BM in LUAD patients.