A pre-neoplastic epigenetic field defect in HCV-infected liver at transcription factor binding sites and polycomb targets.

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Published in Oncogene on October 10, 2016

Authors

N A Wijetunga1, M Pascual1,2, J Tozour1, F Delahaye3, M Alani4,5, M Adeyeye1, A W Wolkoff4,5, A Verma6, J M Greally1

Author Affiliations

1: Department of Genetics and Center for Epigenomics, Bronx, NY, USA.
2: Centro de Investigación Médica Aplicada (CIMA), IDISNA, Oncohematology Department, Pamplona, Spain.
3: Department of Obstetrics, Gynecology and Women's Health, Bronx, NY, USA.
4: Department of Medicine (Division of Gastroenterology and Liver Diseases), Bronx, NY, USA.
5: Marion Bessin Liver Research Center, Bronx, NY, USA.
6: Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx, NY, USA.

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Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46

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Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63

Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int J Cancer (2014) 40.30

The epigenomics of cancer. Cell (2007) 30.91

The fundamental role of epigenetic events in cancer. Nat Rev Genet (2002) 30.05

CpG-rich islands and the function of DNA methylation. Nature (1986) 24.90

CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet (2009) 18.90

Epigenetics in cancer. N Engl J Med (2008) 17.36

The accessible chromatin landscape of the human genome. Nature (2012) 16.86

Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet (2012) 15.21

A unique chromatin signature uncovers early developmental enhancers in humans. Nature (2010) 14.02

The Polycomb group protein EZH2 directly controls DNA methylation. Nature (2005) 13.67

CpG island methylator phenotype in colorectal cancer. Proc Natl Acad Sci U S A (1999) 13.02

Cancer epigenetics comes of age. Nat Genet (1999) 12.63

The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet (2013) 11.29

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17

Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet (2006) 10.47

Epigenetic stem cell signature in cancer. Nat Genet (2006) 9.62

A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat Genet (2007) 9.47

Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N Engl J Med (2008) 9.20

DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature (2011) 8.75

Aberrant CpG-island methylation has non-random and tumour-type-specific patterns. Nat Genet (2000) 8.58

Classification and prediction of survival in hepatocellular carcinoma by gene expression profiling. Hepatology (2004) 6.98

Gene expression patterns in human liver cancers. Mol Biol Cell (2002) 6.93

Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat Genet (2012) 6.65

DNA hypermethylation in tumorigenesis: epigenetics joins genetics. Trends Genet (2000) 6.57

A novel prognostic subtype of human hepatocellular carcinoma derived from hepatic progenitor cells. Nat Med (2006) 6.31

Global epigenomic reconfiguration during mammalian brain development. Science (2013) 6.14

Charting a dynamic DNA methylation landscape of the human genome. Nature (2013) 5.80

DNA methylation and gene silencing in cancer. Nat Clin Pract Oncol (2005) 5.02

Transcriptome classification of HCC is related to gene alterations and to new therapeutic targets. Hepatology (2007) 4.73

Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat Genet (2011) 4.38

Focal gains of VEGFA and molecular classification of hepatocellular carcinoma. Cancer Res (2008) 4.35

Prediction of venous metastases, recurrence, and prognosis in hepatocellular carcinoma based on a unique immune response signature of the liver microenvironment. Cancer Cell (2006) 4.33

EpCAM and alpha-fetoprotein expression defines novel prognostic subtypes of hepatocellular carcinoma. Cancer Res (2008) 4.17

Pivotal role of mTOR signaling in hepatocellular carcinoma. Gastroenterology (2008) 4.03

Met-regulated expression signature defines a subset of human hepatocellular carcinomas with poor prognosis and aggressive phenotype. J Clin Invest (2006) 3.95

The initiation of liver development is dependent on Foxa transcription factors. Nature (2005) 3.88

Genome-wide molecular profiles of HCV-induced dysplasia and hepatocellular carcinoma. Hepatology (2007) 3.85

Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data. Proc Natl Acad Sci U S A (2011) 3.80

Integrative transcriptome analysis reveals common molecular subclasses of human hepatocellular carcinoma. Cancer Res (2009) 3.77

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res (2011) 3.57

RXR alpha mutant mice establish a genetic basis for vitamin A signaling in heart morphogenesis. Genes Dev (1994) 3.54

On the use of the word 'epigenetic'. Curr Biol (2007) 3.21

Epigenetics and colorectal cancer. Nat Rev Gastroenterol Hepatol (2011) 3.15

Exome sequencing of hepatitis B virus-associated hepatocellular carcinoma. Nat Genet (2012) 3.14

Function and information content of DNA methylation. Nature (2015) 3.09

Steatosis and liver cancer in transgenic mice expressing the structural and nonstructural proteins of hepatitis C virus. Gastroenterology (2002) 3.02

Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell (2011) 2.77

Fields of aberrant CpG island hypermethylation in Barrett's esophagus and associated adenocarcinoma. Cancer Res (2000) 2.73

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res (2012) 2.49

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet (2013) 2.41

Gene-expression signature of vascular invasion in hepatocellular carcinoma. J Hepatol (2011) 2.39

A molecular signature to discriminate dysplastic nodules from early hepatocellular carcinoma in HCV cirrhosis. Gastroenterology (2006) 2.32

Hepatitis C virus induces a mutator phenotype: enhanced mutations of immunoglobulin and protooncogenes. Proc Natl Acad Sci U S A (2004) 2.30

Utility of methylation markers in cervical cancer early detection: appraisal of the state-of-the-science. Gynecol Oncol (2008) 2.08

Identification of Potent, Selective, Cell-Active Inhibitors of the Histone Lysine Methyltransferase EZH2. ACS Med Chem Lett (2012) 2.04

Predicting hepatocellular carcinoma by detection of aberrant promoter methylation in serum DNA. Clin Cancer Res (2007) 2.02

Aberrant methylation of multiple tumor suppressor genes in aging liver, chronic hepatitis, and hepatocellular carcinoma. Hepatology (2008) 1.97

Oxidative stress in the absence of inflammation in a mouse model for hepatitis C virus-associated hepatocarcinogenesis. Cancer Res (2001) 1.91

Convergence of Wnt signaling on the HNF4alpha-driven transcription in controlling liver zonation. Gastroenterology (2009) 1.85

Differential expression of three C/EBP isoforms in multiple tissues during the acute phase response. J Biol Chem (1992) 1.85

Hepatocellular carcinoma displays distinct DNA methylation signatures with potential as clinical predictors. PLoS One (2010) 1.84

Genome-wide DNA methylation profiles in hepatocellular carcinoma. Hepatology (2012) 1.81

Expression of hepatic transcription factors during liver development and oval cell differentiation. J Cell Biol (1994) 1.80

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res (2012) 1.78

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol (2013) 1.71

Hepatic stem-like phenotype and interplay of Wnt/beta-catenin and Myc signaling in aggressive childhood liver cancer. Cancer Cell (2008) 1.70

Loss of FOXA1/2 is essential for the epithelial-to-mesenchymal transition in pancreatic cancer. Cancer Res (2010) 1.69

Genetic evidence that small maf proteins are essential for the activation of antioxidant response element-dependent genes. Mol Cell Biol (2005) 1.66

General transcription factor binding at CpG islands in normal cells correlates with resistance to de novo DNA methylation in cancer cells. Cancer Res (2010) 1.64

Hepatocellular carcinoma: ESMO Clinical Practice Guidelines for diagnosis, treatment and follow-up. Ann Oncol (2010) 1.63

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res (2014) 1.63

Definition of the landscape of promoter DNA hypomethylation in liver cancer. Cancer Res (2011) 1.58

Hepatocyte-specific ablation of Foxa2 alters bile acid homeostasis and results in endoplasmic reticulum stress. Nat Med (2008) 1.57

Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions. PLoS Genet (2013) 1.51

HNF4A is essential for specification of hepatic progenitors from human pluripotent stem cells. Development (2011) 1.50

Widespread hypomethylation occurs early and synergizes with gene amplification during esophageal carcinogenesis. PLoS Genet (2011) 1.47

A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. Bioinformatics (2009) 1.42

Cancer-associated molecular signature in the tissue samples of patients with cirrhosis. Hepatology (2004) 1.41

Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips. Epigenetics (2012) 1.39

Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites. Genome Res (2012) 1.37

Hepatitis C virus infection activates the immunologic (type II) isoform of nitric oxide synthase and thereby enhances DNA damage and mutations of cellular genes. J Virol (2004) 1.30

The lymphoid system in hepatitis C virus infection: autoimmunity, mixed cryoglobulinemia, and Overt B-cell malignancy. Semin Liver Dis (2000) 1.28

High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma. Mol Genet Genomics (2010) 1.27

Optimized design and data analysis of tag-based cytosine methylation assays. Genome Biol (2010) 1.23

Targeting of EZH2 to a defined genomic site is sufficient for recruitment of Dnmt3a but not de novo DNA methylation. Epigenetics (2009) 1.22

Nuclear export of retinoid X receptor alpha in response to interleukin-1beta-mediated cell signaling: roles for JNK and SER260. J Biol Chem (2006) 1.21

Hepatitis C virus inhibits DNA damage repair through reactive oxygen and nitrogen species and by interfering with the ATM-NBS1/Mre11/Rad50 DNA repair pathway in monocytes and hepatocytes. J Immunol (2010) 1.16

Elucidating the landscape of aberrant DNA methylation in hepatocellular carcinoma. PLoS One (2013) 1.15

Competition between DNA methylation and transcription factors determines binding of NRF1. Nature (2015) 1.14

An overview of the crosstalk between inflammatory processes and metabolic dysregulation during diabetic cardiomyopathy. Int J Cardiol (2013) 1.13

CpG island shore methylation regulates caveolin-1 expression in breast cancer. Oncogene (2012) 1.12

DNA methylation of transcriptional enhancers and cancer predisposition. Cell (2013) 1.12

Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated. BMC Genomics (2010) 1.10

Kidney cancer is characterized by aberrant methylation of tissue-specific enhancers that are prognostic for overall survival. Clin Cancer Res (2014) 1.09

Intermediate methylation epigenotype and its correlation to KRAS mutation in conventional colorectal adenoma. Am J Pathol (2011) 1.07

Myeloma is characterized by stage-specific alterations in DNA methylation that occur early during myelomagenesis. J Immunol (2013) 1.07