Multi‑omics liquid biopsy approach for sensitive detection of lung cancer via cfDNA and extracellular vesicles‑RNA

Background: Early detection of lung cancer remains challenging due to tumor heterogeneity and the limitations of single-analyte assays. Circulating cell-free DNA (cfDNA) captures genomic alterations, including mutations, copy number variations, and methylation patterns, but does not reflect gene activity. Circulating extracellular vesicles (EVs) carry varieties of small non-coding RNAs reflecting dynamic tumor processes, especially miRNAs that are implicated in regulating the expressions of oncogenes and tumor suppressors in cancer progression. Methods: Under IRB approval, plasma from 5 normal subjects and 10 pathology-confirmed lung cancer patients, collected with informed consent from BioChain Institute's repository, was analyzed. cfDNA was isolated using BioChain's bead-based automatable cfPure® MAX Cell-Free DNA Extraction Kit and profiled with a targeted lung cancer gene panel. EV-RNA was extracted using SBI's SmartSEC EV isolation kit and EVery EV RNA Isolation Kit, followed by RNA-sequencing. Human normal Cell-Free DNA Control from 5 pooled normal donors from BioChain Institute was used as a control. Integration of cfDNA and EV-RNA readouts was performed to assess complementary genomic and transcriptomic signals. Results and Conclusions: Combined cfDNA targeted NGS and EV-RNA sequencing from a single plasma sample is feasible and provides complementary insights into tumor biology. This multi-omics liquid biopsy approach reduces false negatives compared with single-analyte tests and enables identification of biomarkers that may be overlooked when assessing DNA or RNA alone. Together, cfDNA and EV-RNA profiling offer a more comprehensive, non-invasive strategy for early detection, monitoring disease progression, and informing treatment decisions in lung cancer.