Chronic liver inflammation modifies DNA methylation at the precancerous stage of murine hepatocarcinogenesis

Chronic liver inflammation precedes the majority of hepatocellular carcinomas (HCC). Here, we explore the connection between chronic inflammation and DNA methylation in the liver at the late precancerous stages of HCC development in Mdr2−/− (Mdr2/Abcb4-knockout) mice, a model of inflammation-mediated HCC. Using methylated DNA immunoprecipitation followed by hybridization with “CpG islands” (CGIs) microarrays, we found specific CGIs in 76 genes which were hypermethylated in the Mdr2−/− liver compared to age-matched healthy controls. The observed hypermethylation resulted mainly from an age-dependent decrease of methylation of the specific CGIs in control livers with no decrease in mutant mice. Chronic inflammation did not change global levels of DNA methylation in Mdr2−/− liver, but caused a 2-fold decrease of the global 5-hydroxymethylcytosine level in mutants compared to controls. Liver cell fractionation revealed, that the relative hypermethylation of specific CGIs in Mdr2−/− livers affected either hepatocyte, or non-hepatocyte, or both fractions without a correlation between changes of gene methylation and expression. Our findings demonstrate that chronic liver inflammation causes hypermethylation of specific CGIs, which may affect both hepatocytes and non-hepatocyte liver cells. These changes may serve as useful markers of an increased regenerative activity and of a late precancerous stage in the chronically inflamed liver.

[1]  C. Lian,et al.  Decrease of 5‐hydroxymethylcytosine in rat liver with subchronic exposure to genotoxic carcinogens riddelliine and aristolochic acid , 2015, Molecular carcinogenesis.

[2]  K. Rithidech,et al.  Induction of chronic oxidative stress, chronic inflammation and aberrant patterns of DNA methylation in the liver of titanium-exposed CBA/CaJ mice , 2015, International journal of radiation biology.

[3]  Stephanie A. Tammen,et al.  Aging Alters Hepatic DNA Hydroxymethylation, as Measured by Liquid Chromatography/Mass Spectrometry , 2014, Journal of cancer prevention.

[4]  I. Steinfeld,et al.  Specific genomic and transcriptomic aberrations in tumors induced by partial hepatectomy of a chronically inflamed murine liver , 2014, Oncotarget.

[5]  Kevin Y. Yip,et al.  Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation , 2014, Genome Biology.

[6]  O. Yanuka,et al.  Aberrant DNA Methylation in ES Cells , 2014, PloS one.

[7]  Richard J. Thompson,et al.  Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency , 2014, Nature Communications.

[8]  Jia Fan,et al.  High expression of 5-hydroxymethylcytosine and isocitrate dehydrogenase 2 is associated with favorable prognosis after curative resection of hepatocellular carcinoma , 2014, Journal of experimental & clinical cancer research : CR.

[9]  Israel Steinfeld,et al.  Molecular and Cellular Pathobiology Molecular Rules Governing De Novo Methylation in Cancer , 2022 .

[10]  Yi Zhang,et al.  TET enzymes, TDG and the dynamics of DNA demethylation , 2013, Nature.

[11]  Zizhen Yao,et al.  Fundamental differences in promoter CpG island DNA hypermethylation between human cancer and genetically engineered mouse models of cancer , 2013, Epigenetics.

[12]  S. Horvath.  DNA methylation age of human tissues and cell types , 2013, Genome Biology.

[13]  Ido D. Weiss,et al.  Inflammation‐induced hepatocellular carcinoma is dependent on CCR5 in mice , 2013, Hepatology.

[14]  M. Kals,et al.  Ontogeny, distribution and potential roles of 5-hydroxymethylcytosine in human liver function , 2013, Genome Biology.

[15]  N. Shimoda,et al.  Transient reduction of 5-methylcytosine and 5-hydroxymethylcytosine is associated with active DNA demethylation during regeneration of zebrafish fin , 2013, Epigenetics.

[16]  Evgeniy Stoyanov,et al.  Interstrain differences in chronic hepatitis and tumor development in a murine model of inflammation‐mediated hepatocarcinogenesis , 2013, Hepatology.

[17]  A. Miyajima,et al.  To divide or not to divide: revisiting liver regeneration , 2013, Cell Division.

[18]  Limei Liu,et al.  Decrease of 5-Hydroxymethylcytosine Is Associated with Progression of Hepatocellular Carcinoma through Downregulation of TET1 , 2013, PloS one.

[19]  A. Andriulli,et al.  Associations between Genetic Polymorphisms in IL-33, IL1R1 and Risk for Inflammatory Bowel Disease , 2013, PloS one.

[20]  P. Meltzer,et al.  Succinate dehydrogenase mutation underlies global epigenomic divergence in gastrointestinal stromal tumor. , 2013, Cancer discovery.

[21]  Howard Cedar,et al.  DNA methylation dynamics in health and disease , 2013, Nature Structural &Molecular Biology.

[22]  Gordon Okimoto,et al.  Elucidating the Landscape of Aberrant DNA Methylation in Hepatocellular Carcinoma , 2013, PloS one.

[23]  Frank Lyko,et al.  Combined deficiency of Tet1 and Tet2 causes epigenetic abnormalities but is compatible with postnatal development. , 2013, Developmental cell.

[24]  Z. Ling,et al.  Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation , 2013, Oncogene.

[25]  J. Cherfils,et al.  Fam65b Is a New Transcriptional Target of FOXO1 That Regulates RhoA Signaling for T Lymphocyte Migration , 2013, The Journal of Immunology.

[26]  Olaf Neumann,et al.  Methylome analysis and integrative profiling of human HCCs identify novel protumorigenic factors , 2012, Hepatology.

[27]  Colm E. Nestor,et al.  Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns , 2012, Genome Biology.

[28]  J. Stauffer,et al.  Chronic inflammation, immune escape, and oncogenesis in the liver: A unique neighborhood for novel intersections , 2012, Hepatology.

[29]  M. Kudo,et al.  Characteristic patterns of altered DNA methylation predict emergence of human hepatocellular carcinoma , 2012, Hepatology.

[30]  R. Siebert,et al.  Distinct DNA methylation patterns in cirrhotic liver and hepatocellular carcinoma , 2012, International journal of cancer.

[31]  Z. Herceg,et al.  From hepatitis to hepatocellular carcinoma: a proposed model for cross-talk between inflammation and epigenetic mechanisms , 2012, Genome Medicine.

[32]  G. Schackert,et al.  5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations. , 2011, Cancer research.

[33]  Y. Kanai,et al.  Carcinogenetic risk estimation based on quantification of DNA methylation levels in liver tissue at the precancerous stage , 2011, International journal of cancer.

[34]  M. Szyf,et al.  Definition of the landscape of promoter DNA hypomethylation in liver cancer. , 2011, Cancer research.

[35]  Weiwei Li,et al.  Distribution of 5-Hydroxymethylcytosine in Different Human Tissues , 2011, Journal of nucleic acids.

[36]  Z. Herceg,et al.  Epigenetic mechanisms in hepatocellular carcinoma: how environmental factors influence the epigenome. , 2011, Mutation research.

[37]  M. Takasugi.  Progressive age-dependent DNA methylation changes start before adulthood in mouse tissues , 2011, Mechanisms of Ageing and Development.

[38]  N. Iizuka,et al.  Efficient detection of hepatocellular carcinoma by a hybrid blood test of epigenetic and classical protein markers. , 2011, Clinica chimica acta; international journal of clinical chemistry.

[39]  Sean V. Tavtigian,et al.  Hepatocellular Carcinoma Displays Distinct DNA Methylation Signatures with Potential as Clinical Predictors , 2010, PloS one.

[40]  Yae Kanai,et al.  Genome‐wide DNA methylation profiles in precancerous conditions and cancers , 2010, Cancer science.

[41]  N. Iizuka,et al.  The assessment of methylated BASP1 and SRD5A2 levels in the detection of early hepatocellular carcinoma. , 2009, International journal of oncology.

[42]  M. T. McCabe,et al.  Cancer DNA Methylation: Molecular Mechanisms and Clinical Implications , 2009, Clinical Cancer Research.

[43]  K. Wallace,et al.  Interleukin-1 participates in the progression from liver injury to fibrosis. , 2009, American journal of physiology. Gastrointestinal and liver physiology.

[44]  Israel Steinfeld,et al.  Developmental programming of CpG island methylation profiles in the human genome , 2009, Nature Structural &Molecular Biology.

[45]  G. Tiegs,et al.  Down-regulation of the De-ubiquitinating Enzyme Ubiquitin-specific Protease 2 Contributes to Tumor Necrosis Factor-α-induced Hepatocyte Survival* , 2009, Journal of Biological Chemistry.

[46]  A. Riggs,et al.  Methylation of polycomb target genes in intestinal cancer is mediated by inflammation. , 2008, Cancer research.

[47]  C. Boland,et al.  Aberrant methylation of multiple tumor suppressor genes in aging liver, chronic hepatitis, and hepatocellular carcinoma , 2008, Hepatology.

[48]  Eytan Domany,et al.  Molecular Mechanisms of Liver Carcinogenesis in the Mdr2-Knockout Mice , 2007, Molecular Cancer Research.

[49]  S. Thorgeirsson,et al.  Mechanistic and prognostic significance of aberrant methylation in the molecular pathogenesis of human hepatocellular carcinoma. , 2007, The Journal of clinical investigation.

[50]  Eytan Domany,et al.  Multiple adaptive mechanisms to chronic liver disease revealed at early stages of liver carcinogenesis in the Mdr2-knockout mice. , 2006, Cancer research.

[51]  I. Simon,et al.  Evidence for an instructive mechanism of de novo methylation in cancer cells , 2006, Nature Genetics.

[52]  Suman Lee,et al.  Estimating the total mouse DNA methylation according to the B1 repetitive elements. , 2005, Biochemical and biophysical research communications.

[53]  R. Jaenisch,et al.  Opposing effects of DNA hypomethylation on intestinal and liver carcinogenesis. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Y. Ben-Neriah,et al.  NF-κB functions as a tumour promoter in inflammation-associated cancer , 2004, Nature.

[55]  H. Tilg,et al.  Regurgitation of bile acids from leaky bile ducts causes sclerosing cholangitis in Mdr2 (Abcb4) knockout mice. , 2004, Gastroenterology.

[56]  Yau-Huei Wei,et al.  Somatic mutations in the D-loop and decrease in the copy number of mitochondrial DNA in human hepatocellular carcinoma. , 2004, Mutation research.

[57]  Hyeon Joo Lee,et al.  Aberrant CpG island hypermethylation along multistep hepatocarcinogenesis. , 2003, The American journal of pathology.

[58]  Long-Cheng Li,et al.  MethPrimer: designing primers for methylation PCRs , 2002, Bioinform..

[59]  A. Nakao,et al.  Human livers with cirrhosis and hepatocellular carcinoma have less mitochondrial DNA deletion than normal human livers. , 1999, Life sciences.

[60]  S. Baylin.  Tying It All Together: Epigenetics, Genetics, Cell Cycle, and Cancer , 1997, Science.

[61]  A. Tanaka,et al.  The frequency of 4977 base pair deletion of mitochondrial DNA in various types of liver disease and in normal liver , 1995, Hepatology.

[62]  A. Groen,et al.  Mice with homozygous disruption of the mdr2 P-glycoprotein gene. A novel animal model for studies of nonsuppurative inflammatory cholangitis and hepatocarcinogenesis. , 1994, The American journal of pathology.

[63]  Stephan Beck,et al.  Inflammatory signalling as mediator of epigenetic modulation in tissue-specific chronic inflammation. , 2009, The international journal of biochemistry & cell biology.

[64]  Dirk Schübeler,et al.  Methylated DNA immunoprecipitation (MeDIP). , 2009, Methods in molecular biology.

[65]  Rinat Abramovitch,et al.  NF-kappaB functions as a tumour promoter in inflammation-associated cancer. , 2004, Nature.

[66]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.