Noninvasive detection of early nasopharyngeal carcinoma based on three gene methylation analysis in bilateral nasal swab samples processed automatically

Background Efforts have been made to improve the performance of nasopharyngeal carcinoma screening strategies, including EBV related biomarkers. However, the advances achieved still remain imperfect. DNA methylation occurs early in cancer development and can be used as potential diagnostic biomarker. This study aimed to investigate the diagnostic performance of three methylated genes in patients with nasopharyngeal carcinoma (NPC). Methods 255 nasopharyngeal swabs and 35 plasma samples were collected from patients with newly diagnosed or treated NPC and healthy controls. Methylation-specific PCR (MSP) was carried out to evaluate the methylation status of three genes ( SEPTIN9 , RASSF1A , and H4C6 ) in the swabs and plasma samples. Methylation rates, sensitivity, and specificity of the candidate genes were calculated. Furthermore, the detectability of methylated genes in paired swabs and plasma was compared. Results In the nasopharyngeal swabs of patients with newly diagnosed NPC, the detection rate of methylated SEPTIN9 , RASSF1A , and H4C6 was 88.2%, 92.9% and 71.8%, while the rate decreased to 54.3%, 42.9% and 45.7% by blood plasma, respectively. The sensitivity of detecting methylated SEPTIN9 , RASSF1A , and H4C6 to differentiate between untreated NPC, and treated NPC plus healthy controls was 88%, 93%, and 72%. Methylated RASSF1A showed the best classification accuracy (AUC = 0.956). The detection rate of the target methylated genes was significantly lower in the paired plasma samples. Conclusion The detection of RASSF1A methylation through non-invasive nasopharyngeal cavity swab sampling demonstrates significant potential in NPC diagnosis.