Methylation analysis of plasma DNA informs etiologies of Epstein-Barr virus-associated diseases

Abstract

Epstein-Barr virus (EBV) is associated with a number of diseases, including malignancies. Currently, it is not known whether patients with different EBV-associated diseases have different methylation profiles of circulating EBV DNA. Through whole-genome methylation analysis of plasma samples from patients with nasopharyngeal carcinoma (NPC), EBV-associated lymphoma and infectious mononucleosis, we demonstrate that EBV DNA methylation profiles exhibit a disease-associated pattern. This observation implies a significant potential for the development of methylation analysis of plasma EBV DNA for NPC diagnostics. We further analyse the plasma EBV DNA methylome of NPC and non-NPC subjects from a prospective screening cohort. Plasma EBV DNA fragments demonstrate differential methylation patterns between NPC and non-NPC subjects. Combining such differential methylation patterns with the fractional concentration (count) and size of plasma EBV DNA, population screening of NPC is performed with an improved positive predictive value of 35.1%, compared to a count- and size-based only protocol.

Environmental Influencers, MicroRNA, and Multiple Sclerosis

“…107 Although EBVinduced DNA methylation is not documented in MS patients, it has been recognized in several other diseases, such as nasopharyngeal carcinoma, Hodgkin lymphoma, Burkitt lymphoma, and gastric carcinoma. [267][268][269][270][271][272] miRNAs signatures in MS patients may be defined by the environment and genetics. However, data from diverse groups, ethnicities, and countries need to be consolidated and reproduced to be accepted as robust.…”

Comparison of methylation patterns generated from genomic and cell-line derived DNA using the Illumina Infinium MethylationEPIC BeadChip array

“…Through this analysis, we have established that approximately 6% of the CpG sites covered by the Methylatio-nEPIC array provided significantly different p-values between gDNA and clDNA based on their methylation beta values. We have not addressed potential causes of the observed differences in methylation [20]. This may be due to the method through which the cell-line transformation occurs [21][22][23].…”

Clinical utility of Epstein‐Barr virus DNA and other liquid biopsy markers in nasopharyngeal carcinoma

“…Hypermethylation of the CpG island of promoter region results in the silence of tumor suppressor genes, and this feature is a characteristic abnormality seen in EBVassociated cancers [58][59][60]. Using a viral-wide genome approach, Lam et al [61] found distinct EBV DNA methy-lation profiles among different EBV-associated diseases; and by analyzing methylated DNA sequences allowed differentiation between NPC and non-NPC subjects. Aberrant methylation of tumor suppressor genes such as cadherin 4 (CDH4), cyclin-dependent kinase inhibitor 2A (CDKN2A/p16), and RAS association domain family protein 1A (RASSF1A) are early events in NPC tumorigenesis [62][63][64].…”

“…Mechanistically, epigenetic changes occur early in NPC and are readily detectable by hypermethylation panels; in locally advanced cases, the increased tumor burden is better detected via plasma EBV DNA assays. Furthermore, through whole-genome methylation analysis, Lam et al [61] demonstrated that methylation profiles exhibit a disease-associated pattern which differs for NPC, lymphoma, and infectious mononucleosis. By combining the differential methylation patterns with EBV DNA size and quantity, the study demonstrated an increased PPV of 35.1% in population screening of NPC, as compared to a PPV of 11.2% using only the conventional count-based plasma EBV DNA detection method [61].…”