Comprehensive Profiling of Serum Exosomes by a Multi-Omics Approach Reveals Potential Diagnostic Markers for Brain Metastasis in Lung Cancer

Background: Brain metastasis occurs in 40–50% of lung cancer patients and is associated with poor prognosis. This study aimed to identify potential exosomal biomarkers for the early detection of brain metastasis in lung cancer using a comprehensive multi-omics approach. Methods: Using a lung cancer mouse model, which develops brain metastasis, we collected serum samples at different stages (control, 6 weeks for lung cancer, and 10 weeks for brain metastasis). We profiled the contents of serum-derived exosomes using small RNA sequencing and LC-MS/MS proteomic analysis, and assessed the clinical relevance of candidate biomarkers using publicly available patient datasets. Results: RNA sequencing identified 11 differentially expressed miRNAs across disease progression, with miR-206-3p showing significant upregulation during brain metastasis. Pathway analysis of miR-206-3p targets revealed enrichment in cancer-related pathways, including Hippo, MAPK, Ras, and PI3K-Akt signaling. Proteomic analysis revealed 77 proteins specifically upregulated in the brain metastasis stage, with vinculin (VCL) emerging as a promising marker. While VCL expression decreased in lung tissues and showed no significant changes in brain tissues, its levels were significantly elevated in serum-derived exosomes during brain metastasis. Clinical database analysis revealed that higher VCL expression correlated with poor patient survival. Conclusions: Our study identified exosomal miR-206-3p and VCL as promising non-invasive biomarkers for brain metastasis in lung cancer using the mouse model. These findings provide new opportunities for early detection and monitoring of brain metastasis, potentially enabling timely therapeutic intervention.