Methylome sequencing for fibrolamellar hepatocellular carcinoma depicts distinctive features

<b>Objective</b>: To study epigenetic alterations in fibrolamellar hepatocellular carcinoma (FLC) and establish an associated DNA methylation signature. <b>Design</b>: We analyzed <i>LINE-1</i> methylation in a cohort of FLC and performed next-generation sequencing of DNA methylation in a training set of pure-FLCs and non-cirrhotic hepatocellular carcinomas (nc-HCC). DNA methylation was correlated with gene expression. Furthermore, we established and validated an epigenetic signature differentiating pure-FLC from other HCCs. <b>Results</b>: <i>LINE-1</i> methylation correlates with shorter recurrence-free survival and overall survival in resected pure-FLC patients. Unsupervised clustering using CG sites located in islands distinguishes pure-FLC from nc-HCC. Major DNA methylation changes occurred outside promoters, mainly in gene bodies and intergenic regions located in the vicinity of liver developmental genes (ie, <i>SMARCA4, RXRA</i>). Partially methylated domains were the regions found to be more prone to DNA methylation changes. Furthermore, we identified several putative tumor suppressor genes (i.e. <i>DLEU7</i>) and oncogenes (i.e. <i>DUSP4</i>). While ˜70% of identified gene promoters gaining methylation were marked by bivalent histone marks (H3K4me3/H3K27me3) in embryonic stem cells, ˜70% of those losing methylation were marked by H3K4me3. Finally, we established a pure FLC DNA methylation signature and validate it in an independent dataset. <b>Conclusions</b>: Our analysis reveals distinct epigenetic signature of pure FLC as compared to nc-HCC, with DNA methylation changes occurring in the vicinity of liver developmental genes. These data suggest new options for targeting FLC based on cancer epigenome aberrations.