DNA Methylation Analysis Of Plasma Circulating Cell-Free DNA By Targeted-Deep Sequencing Reveals Potential Epigenetic Biomarkers For High-Risk Monitoring And Detection Of Liver Cancer

Athena SKLIAS, International Agency for Research on Cancer, France
DEGLI ESPOSTI D. 1 , MULLER D. 2 , GUILLOREAU P. 3 , MCKAY J. 4 , SANGRAJRANG S. 5 , SRIVATANAKUL P. 5 , HAINAUT P. 6 , MERLE P. 3,7 , NOGUEIRA DA COSTA A. 8 , HOLMILA R. 1,9 , HERCEG Z. 1,9

1 Epigenetics group, IARC, Lyon, France
2 Genetic Epidemiology group, IARC, Lyon, France
3 Croix-Rousse Hospital, Lyon, France
4 Genetic Cancer Susceptibility group, IARC, Lyon, France
5 National Cancer Institute, Bangkok, Thailand
6 INSERM Unité 823, Institut Albert Bonniot, La Tronche, France
7 UMR INSERM 1052, CRCL, Lyon, France
8 UCB BioPharma SPRL, Braine L'Alleud, Belgium
9 (Equal Contribution)

Purpose: Tumor-derived cell-free circulating DNA (cfDNA) isolated from the plasma and serum of individuals with cancer has been shown to contain cancer-associated genetic and epigenetic alterations. Epigenetic changes (such as DNA methylation) are tumour specific and appear early in tumor development, thus they can provide particularly attractive markers with broad application in diagnostics and risk assessment. However, reliable detection of DNA methylation changes in body fluids has proven to be technically challenging. With the recent development of high-throughput sequencing technologies there has been a growing interest in cfDNA that has the potential to be used in the context of developing of non-invasive biomarkers.
Methods: Here, we applied massively parallel semiconductor sequencing to assess the methylation of a panel of genes in plasma circulating cell-free DNA (cfDNA), also to evaluate the potential of these genes as novel biomarkers for hepatocellular carcinoma (HCC) in two different case-control studies, in France and in Thailand (HCC cases, chronic liver disease cases and controls). We also analysed a set of HCC and adjacent tissue samples as well as different liver cell lines to further compare with ‘The Cancer Genome Atlas’ (TCGA) data.
Results: Methylation in cfDNA was detected for FBLN1, PSMA7, PXDN and VIM, with substantial differences in methylation patterns between cases and controls. Further, the average methylation level across analysed CpG-sites was associated with higher odds of HCC for VIM for French cases and for Thai cases, and lower odds of HCC for FBLN1.
Conclusions: Together, our study provides evidence that deep sequencing is a suitable method for analysing methylation profiles in cfDNA, and that changes in methylation levels of specific genes in cfDNA are associated with HCC which may represent useful plasma-based biomarkers for improved diagnosis accuracy and patient surveillance.
Funding source: Ligue Nationale Contre le Cancer (Comité du Rhône)