DNA Methylation Profiling of Human Hepatocarcinogenesis

Abstract

BaCKgRoUND aND aIMS: Mutations in TERT (telomerase reverse transcriptase) promoter are established gatekeepers in early hepatocarcinogenesis, but little is known about other molecular alterations driving this process. Epigenetic deregulation is a critical event in early malignancies. Thus, we aimed to (1) analyze DNA methylation changes during the transition from preneoplastic lesions to early HCC (eHCC) and identify candidate epigenetic gatekeepers, and to (2) assess the prognostic potential of methylation changes in cirrhotic tissue. appRoaCH aND ReSUltS: Methylome profiling was performed using Illumina HumanMethylation450 (485,000 cytosine-phosphateguanine, 96% of known cytosinephosphateguanine islands), with data available for a total of 390 samples: 16 healthy liver, 139 cirrhotic tissue, 8 dysplastic nodules, and 227 HCC samples, including 40 eHCC below 2cm. A phylo-epigenetic tree derived from the Euclidean distances between differentially DNA-methylated sites (n = 421,997) revealed a gradient of methylation changes spanning healthy liver, cirrhotic tissue, dysplastic nodules, and HCC with closest proximity of dysplasia to HCC. Focusing on promoter regions, we identified epigenetic gatekeeper candidates with an increasing proportion of hypermethylated samples (beta value > 0.5) from cirrhotic tissue (<1%), to dysplastic nodules (≥25%), to eHCC (≥50%), and confirmed inverse correlation between DNA methylation and gene expression for TSPYL5 (testis-specific Y-encoded-like protein 5), KCNA3 (potassium voltage-gated channel, shaker-related subfamily, member 3), LDHB (lactate dehydrogenase B), and SPINT2 (serine peptidase inhibitor, Kunitz type 2) (all P < 0.001). Unsupervised clustering of genome-wide methylation profiles of cirrhotic tissue identified two clusters, M1 and M2, with 42% and 58% of patients, respectively, which correlates with survival (P < 0.05), independent of etiology.CoNClUSIoNS: Genome-wide DNA-methylation profiles accurately discriminate the different histological stages of human hepatocarcinogenesis. We report on epigenetic gatekeepers in the transition between dysplastic nodules and eHCC. DNA-methylation changes in cirrhotic tissue correlate with clinical outcomes. (Hepatology 2021;74:183-199).H CC, the most common form of primary liver cancer, typically occurs in patients with chronic liver disease, primarily cirrhosis. HBV and HCV virus infection, alcohol use disorder, and NAFLD are the major etiologies. (1) In the USA, the liver cancer death rate increased 43% between 2000 and 2016. (2) There is a limited understanding of the molecular events leading to malignant transformation in the context of cirrhosis. (3) Specifically, little is known about the molecular mechanisms that govern the transition from cirrhosis to dysplasia and early HCC (eHCC). TERT (telomerase reverse transcriptase) promoter mutations are the only bone fide early molecular events in hepatocarcinogenesis.

Epigenetic priming in chronic liver disease impacts the transcriptional and genetic landscapes of hepatocellular carcinoma

“…2A, Fig. A), reflecting a recent study showing a gradient of methylation changes spanning the progression from health liver to HCC [48]. We identified 54 888 differential methylated (DM, |log2FC| > 1.5, q < 0.05) CpG sites in the HCC samples compared with normal tissue, the majority of which (46 669, 85%) were hypomethylated (Fig.…”

Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications

“…These mechanisms involve various structures (e.g., intercellular desmosome, gap, tight, and adherens junctions; extracellular matrix hemidesmosomes and focal contact), interacting protein families (e.g., integrins, actins, connexins, claudins, occludin, catenins, cadherins, fibronectin), and signaling pathways (TGFβ-SMAD3, WNT-β CATENIN, and NOTCH) inducing the expression of transcription factors (e.g., ZEB1, ZEB2, SNAIL, SLUG, TWIST) to downregulate or upregulate the expression of epithelial (e.g., E-CADHERIN, CLAUDINS, OCCLUDIN), and mesenchymal markers (e.g., N-CADHERIN, VIMENTIN, FIBRONECTIN). There is an increasing number of studies on different cancers highlighting epigenetic modifications and changes in gene expression that have already occurred by the stage of dysplasia [558][559][560][561][562], and later during EMT [557]. Therefore, monitoring epigenetic deregulation may assist in better predicting the potential adversity of cellular transformation processes.…”

Systematic Investigation of DNA Methylation Associated With Platinum Chemotherapy Resistance Across 13 Cancer Types

“…In recent years, the importance of pharmacological epigenetics has received increasing attention from medical researchers and clinicians. DMRs and DMPs are worthwhile indicators to determine the molecular characteristics ( Choudhury et al, 2020 ; Hernandez-Meza et al, 2020 ). In this study, we attempted to analyze the methylation profiles at various levels from the overall methylation status to the value of a single probe by integrating 618 platinum-treated patients across 13 TCGA cancer types.…”