NEW YORK – Building on past research linking the presence of Epstein-Barr virus (EBV) DNA in blood plasma to nasopharyngeal carcinoma (NPC), a new study suggests additional NPC risk prediction clues can obtained by measuring the quantity of circulating EBV DNA fragments as well as their size, motif, and methylation features.
"The discovery of the NPC-associated fragmentomics profile of plasma EBV DNA was translated into an enhanced performance of plasma EBV DNA analysis for NPC risk prediction in the context of screening," senior and corresponding author Dennis Lo and his colleagues wrote in Cancer Cell on Thursday. Lo is founding scientific director with the Hong Kong Science Park's Centre for Novostics and vice-chancellor and president of the Chinese University of Hong Kong.
For their prospective study of this fragmentomics-based prediction approach, Lo and colleagues began by using a real-time PCR assay to search for the presence of cell-free EBV DNA in blood plasma samples from 20,174 symptom-free male participants between the ages of 40 and 62 years old, who were recruited into the study from 2013 to 2016.
From there, the team turned to targeted EBV sequencing and "fragmentomics-based methylation analysis" (FRAGMA) to profile EBV DNA fragment features and methylation profiles, respectively, in cell-free DNA blood plasma samples from 309 individuals who continued to test positive for EBV DNA after a second round of PCR testing within a month of the initial PCR screening test.
Together, the investigators' results suggested that individuals who went on to develop NPC tended to have sequences marked by lower-than-usual levels of a so-called C-C end motif in EBV DNA detected in blood samples. NPC risk was also informed by EBV DNA levels in the blood, along with EBV DNA fragment sizes and methylation patterns.
"Subjects with these aberrant fragmentomics features and higher quantity of EBV DNA had a relative risk of 87.1 times greater for developing NPC in the second round compared to subjects tested negative for EBV DNA on PCR," the authors reported, adding that the findings "demonstrate plasma DNA fragmentomics could predict future cancer risk."
Within the group of 309 individuals with two positive PCR-based screening tests for EBV DNA, for example, researchers initially found 34 NPC cases with PCR screening alone. Four more NPC cases turned up when they used targeted sequencing to profile EBV DNA fragment features found in blood samples from 237 members classified as "persistently positive" in the PCR screening stage of the study.
Likewise, EBV DNA fragment features found through sequencing revealed three additional NPC cases in a group of 677 individuals who screened positive for EBV DNA on one of the two PCR tests. The team identified 17 more NPC cases by using targeted sequencing to profile samples from nearly 17,000 participants who tested negative for EBV DNA on both PCR screening tests.
The authors conceded that targeted next-generation sequencing costs more than PCR-based screening for circulating EBV DNA. On the other hand, they suggested that the "enhanced specificity would substantially reduce the number of endoscopies and MRI examinations needed to confirm or exclude the diagnosis."
"Our current study finding suggests that the NGS-based molecular profiling of plasma EBV DNA could provide an additional layer of clinical information regarding NPC screening," they wrote, adding that the "proposed molecular analysis enabled better risk stratification of screened subjects."