Saliva biopsy: Detecting the difference of EBV DNA methylation in the diagnosis of nasopharyngeal carcinoma
Xiao-Hui Zheng
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorChang-Mi Deng
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorTing Zhou
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorXi-Zhao Li
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorCao-Li Tang
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorCheng-Tao Jiang
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorYing Liao
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorTong-Min Wang
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorYong-Qiao He
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorCorresponding Author
Wei-Hua Jia
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Correspondence
Wei-Hua Jia, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong 510060, China.
Email: [email protected]
Search for more papers by this authorXiao-Hui Zheng
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorChang-Mi Deng
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorTing Zhou
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorXi-Zhao Li
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorCao-Li Tang
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorCheng-Tao Jiang
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorYing Liao
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorTong-Min Wang
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorYong-Qiao He
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Search for more papers by this authorCorresponding Author
Wei-Hua Jia
State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
Correspondence
Wei-Hua Jia, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong 510060, China.
Email: [email protected]
Search for more papers by this authorXiao-Hui Zheng and Chang-Mi Deng have contributed equally to this study.
Abstract
Saliva sampling is a non-invasive method, and could be performed by donors themselves. However, there are few studies reporting biomarkers in saliva in the diagnosis of NPC. A total of 987 salivary samples were used in this study. First, EBV DNA methylation was profiled by capture sequencing in the discovery cohort (n = 36). Second, a q-PCR based method was developed and five representative EBV DNA CpG sites (11 029 bp, 45 849 bp, 57 945 bp, 66 226 bp and 128 102 bp) were selected and quantified to obtain the methylated density in the validation cohort1 (n = 801). Third, a validation cohort2 (n = 108) was used to further verify the differences of EBV methylation in saliva. A significant increase of EBV methylation was found in NPC patients compared with controls. The methylated score of EBV genome obtained by capture sequencing could distinguish NPC from controls (sensitivity 90%, specificity 100%). Further, the methylated density of EBV DNA CpG sites revealed by q-PCR showed a good diagnostic performance. The sensitivity and specificity of detecting a single CpG site (11 029 bp) could reach 75.4% and 99.7% in the validation cohort1, and 78.2% and 100% in the validation cohort2. Besides, the methylated density of the CpG site was found to decrease below the COV in NPC patients after therapy, and increase above the COV after recurrence. Our study provides an appealing alternative for the non-invasive detection of NPC without clinical setting. It paves the way for conducting a home-based large-scale screening in the future.
Graphical Abstract
What's new?
While various Epstein-Barr virus (EBV)-related biomarkers have been established as potential screening biomarkers for nasopharyngeal carcinoma, most of them rely on blood or nasopharyngeal swab samples. Using saliva samples, this study found a significant increase in EBV DNA methylation in nasopharyngeal carcinoma patients compared to controls. Detection at a single CpG site could reach a sensitivity of 75.8% and specificity of 99.7%. The methylated density of the CpG site was found to decrease below the cut-off value after therapy and increase above the cut-off value after recurrence. This study potentially provides a non-invasive alternative for the detection of nasopharyngeal carcinoma.
CONFLICT OF INTEREST STATEMENT
The authors declare that they have no competing interests.
Open Research
DATA AVAILABILITY STATEMENT
The datasets used and analyzed during the current study are available from the corresponding author on reasonable request.
Supporting Information
| Filename | Description |
|---|---|
| ijc34561-sup-0001-Supinfo.pdfPDF document, 615.2 KB | DATA S1. Supporting Information. |
| ijc34561-sup-0002-Tables.xlsExcel spreadsheet, 9.8 MB | TABLE S4. The methylated density of all CpG sites detected in the capture sequencing was listed. TABLE S5. The methylated region divided by 200 bp length and the methylated score was listed TABLE S6. The methylated density of EBV genes divided into four infection phase was listed. TABLE S7. The methylated density of 17 CpG sites located in the EBV DNA was listed. A model containing these 17 CpG sites was used. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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