Plasma Exosomal DNA Methylation Profiles and Therapeutic Response in Non-Small Cell Lung Cancer

Objective To investigate the differential methylation profiles of plasma exosomal DNA in non-small cell lung cancer (NSCLC) patients, their association with treatment and clinical outcomes, and the epigenetic regulatory mechanisms mediating NSCLC therapeutic response. Methods 20 NSCLC patients were enrolled, and plasma exosomes were isolated and identified pre- and post-treatment. Bioinformatics analyses were performed to analyze differentially methylated loci (DMLs) and regions (DMRs) of plasma exosomal DNA between pre- and post-treatment samples, and between partial response (PR) and stable disease (SD) groups. Subsequent analyses included DMR genomic features and GO/KEGG enrichment of corresponding differentially methylated genes (DMGs). Results Isolated exosomes displayed typical characteristics. Post- vs. pre-treatment comparison identified 3896 DMLs and 43 DMRs (mainly enriched in proximal promoter region), corresponding to key DMGs including KCNJ9, RYR2, INHBB, SOX2, H3C3, H2BC11, RBPJL and MAFA. PR vs. SD comparison found 176 DMLs and 17 DMRs; PR group showed overall hypomethylation, with DMRs enriched in distal intergenic region (clustered on chr16, chr21 and chr22) and only GP1BB as the associated DMG. Treatment-related methylation targeted proximal promoters and distal cis-elements, while efficacy-related epigenetic reprogramming relied on distal regulatory elements. Treatment-associated DMGs mediated cellular stress and signal regulation, and efficacy-associated DMGs were enriched in immune-hematopoietic processes. Conclusion Plasma exosomal DNA methylation profiles in NSCLC patients change significantly post-treatment, with PR patients showing characteristic hypomethylation. This epigenetic feature modulates therapeutic response via immune-hematopoietic pathways, and plasma exosomal DNA methylation may serve as a promising epigenetic marker for evaluating NSCLC treatment efficacy.