Premium
DNA Methylation Profiling of Human Hepatocarcinogenesis
Author(s) -
HernandezMeza Gabriela,
Felden Johann,
GonzalezKozlova Edgar E.,
GarciaLezana Teresa,
Peix Judit,
Portela Anna,
Craig Amanda J.,
Sayols Sergi,
Schwartz Myron,
Losic Bojan,
Mazzaferro Vincenzo,
Esteller Manel,
Llovet Josep M.,
Villanueva Augusto
Publication year - 2021
Publication title -
hepatology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.488
H-Index - 361
eISSN - 1527-3350
pISSN - 0270-9139
DOI - 10.1002/hep.31659
Subject(s) - dna methylation , epigenetics , biology , methylation , microbiology and biotechnology , cpg site , cancer research , differentially methylated regions , gene expression , genetics , gene
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 cytosine‐phosphateguanine 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.