Exosomal-derived DNA with quantitative differences as a biomarker for the early prediction of nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is a common head and neck malignancy in southern China, and there is a need for better early prediction and prognostic monitoring methods due to its high invasiveness, recurrence tendency, and biopsy difficulties. Exosome-derived DNA (exoDNA) has been studied in various cancers. This research aimed to find NPC early prediction biomarkers in exoDNA from NPC patients' blood.Methods involved extracting exosomes from blood samples of 20 healthy volunteers and 20 newly diagnosed NPC patients via ultracentrifugation, characterized by electron microscopy, particle size measurement, and Western Blot. ExoDNA was extracted, and a DNA library was built, with gene information obtained through NGS and bioinformatics analysis. Then, with 45 NPC patients and 55 healthy volunteers, qPCR and ddPCR were used to verify NGS results.Results showed that the extracted exosomes had a double-membrane structure, an average size of 100.72 nm, and marker proteins CD9 and TSG101 were detected. Three gene fragments specific to NPC patients from KAZN, NRXN3, and CAMTA1 were found, and F-NRXN3 from exoDNA had a significant quantity difference between patients and healthy people (P < 0.0001).In conclusion, unlike previous studies on exoDNA SNPs, this study found the F-NRXN3 gene fragment with significant quantity difference in NPC patients' exoDNA, which may serve as an early NPC prediction biomarker. The proposed exoDNA target with quantity differences offers a new perspective for future tumor marker discovery.