1 5717 160 SIRTUIN-6-DEPENDENT GENETIC AND EPIGENETIC ALTERATIONS ARE ASSOCIATED WITH POOR CLINICAL OUTCOME IN HEPATOCELLULAR CARCINOMA PATIENTS. SIRTUIN 6 (SIRT6) IS A MEMBER OF THE SIRTUIN FAMILY OF NAD+-DEPENDENT DEACETYLASES. GENETIC DELETION OF SIRT6 IN MICE RESULTS IN A SEVERE DEGENERATIVE PHENOTYPE WITH IMPAIRED LIVER FUNCTION AND PREMATURE DEATH. THE ROLE OF SIRT6 IN DEVELOPMENT AND PROGRESSION OF HEPATOCELLULAR CARCINOMA IS CURRENTLY UNKNOWN. WE FIRST INVESTIGATED SIRT6 EXPRESSION IN 153 PRIMARY HUMAN LIVER CANCERS AND IN NORMAL AND CIRRHOTIC LIVERS USING MICROARRAY ANALYSIS. SIRT6 WAS SIGNIFICANTLY DOWN-REGULATED IN BOTH CIRRHOTIC LIVERS AND CANCER. A SIRT6 KNOCKOUT (KO) GENE EXPRESSION SIGNATURE WAS GENERATED FROM PRIMARY HEPATOCTYES ISOLATED FROM 3-WEEK-OLD SIRT6-DEFICIENT ANIMALS. SIRT6-DEFICIENT HEPATOCYTES SHOWED UP-REGULATION OF ESTABLISHED HEPATOCELLULAR CARCINOMA (HCC) BIOMARKERS ALPHA-FETOPROTEIN (AFP), INSULIN-LIKE GROWTH FACTOR 2 (IGF2), H19, AND GLYPICAN-3. FURTHERMORE, DECREASED SIRT6 EXPRESSION WAS OBSERVED IN HEPATOMA CELL LINES THAT ARE KNOWN TO BE APOPTOSIS-INSENSITIVE. RE-EXPRESSION OF SIRT6 IN HEPG2 CELLS INCREASED APOPTOSIS SENSITIVITY TO CD95-STIMULATION OR CHEMOTHERAPY TREATMENT. LOSS OF SIRT6 WAS CHARACTERIZED BY ONCOGENIC CHANGES, SUCH AS GLOBAL HYPOMETHYLATION, AS WELL AS METABOLIC CHANGES, SUCH AS HYPOGLYCEMIA AND INCREASED FAT DEPOSITION. THE HEPATOCYTE-SPECIFIC SIRT6-KO SIGNATURE HAD A PROGNOSTIC IMPACT AND WAS ENRICHED IN PATIENTS WITH POORLY DIFFERENTIATED TUMORS WITH HIGH AFP LEVELS AS WELL AS RECURRENT DISEASE. FINALLY, WE DEMONSTRATED THAT THE SIRT6-KO SIGNATURE POSSESSED A PREDICTIVE VALUE FOR TUMORS OTHER THAN HCC (E.G., BREAST AND LUNG CANCER). CONCLUSION: LOSS OF SIRT6 INDUCES EPIGENETIC CHANGES THAT MAY BE RELEVANT TO CHRONIC LIVER DISEASE AND HCC DEVELOPMENT. DOWN-REGULATION OF SIRT6 AND GENES DYSREGULATED BY LOSS OF SIRT6 POSSESS ONCOGENIC EFFECTS IN HEPATOCARCINOGENESIS. OUR DATA DEMONSTRATE THAT DEFICIENCY IN ONE EPIGENETIC REGULATOR PREDISPOSES A TUMORIGENIC PHENOTYPE THAT ULTIMATELY HAS RELEVANCE FOR OUTCOME OF HCC AND OTHER CANCER PATIENTS.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
2 1615  37 DNA METHYLTRANSFERASE 3B PLAYS A PROTECTIVE ROLE AGAINST HEPATOCARCINOGENESIS CAUSED BY CHRONIC INFLAMMATION VIA MAINTAINING MITOCHONDRIAL HOMEOSTASIS. MOST HEPATOCELLULAR CARCINOMAS (HCCS) DEVELOP ON THE BASIS OF CHRONIC HEPATITIS, BUT THE MECHANISM OF EPIGENETIC REGULATION IN INFLAMMATORY HEPATOCARCINOGENESIS HAS YET TO BE ELUCIDATED. AMONG DE NOVO DNA METHYLTRANSFERASES (DNMTS), DNMT3B HAS LATELY BEEN REPORTED TO ACT SPECIFICALLY ON ACTIVELY TRANSCRIBED GENES, SUGGESTING THE POSSIBILITY THAT IT PLAYS A ROLE IN THE PATHOGENESIS OF CANCER. WE CONFIRMED THAT DNMT3B ISOFORMS LACKING ITS CATALYTIC DOMAIN WERE HIGHLY EXPRESSED IN HCCS COMPARED WITH NON-TUMOROUS LIVER TISSUE. TO ELUCIDATE THE ROLE OF DNMT3B IN HEPATOCARCINOGENESIS, WE GENERATED A GENETICALLY ENGINEERED MOUSE MODEL WITH HEPATOCYTE-SPECIFIC DNMT3B DELETION. THE LIVER OF THE DNMT3B-DEFICIENT MICE EXHIBITED AN EXACERBATION OF THIOACETAMIDE-INDUCED HEPATITIS, PROGRESSION OF LIVER FIBROSIS AND A HIGHER INCIDENCE OF HCC COMPARED WITH THE LIVER OF THE CONTROL MICE. WHOLE-GENOME BISULFITE SEQUENCING VERIFIED A LOWER CG METHYLATION LEVEL IN THE DNMT3B-DEFICIENT LIVER, DEMONSTRATING DIFFERENTIALLY METHYLATED REGIONS THROUGHOUT THE GENOME. TRANSCRIPTOME ANALYSIS REVEALED DECREASED EXPRESSION OF GENES RELATED TO OXIDATIVE PHOSPHORYLATION IN THE DNMT3B-DEFICIENT LIVER. MOREOVER, PRIMARY HEPATOCYTES ISOLATED FROM THE DNMT3B-DEFICIENT MICE SHOWED REDUCED MITOCHONDRIAL RESPIRATORY CAPACITY, LEADING TO THE ENHANCEMENT OF OXIDATIVE STRESS IN THE LIVER TISSUE. OUR FINDINGS SUGGEST THE PROTECTIVE ROLE OF DNMT3B AGAINST CHRONIC INFLAMMATION AND HCC DEVELOPMENT VIA MAINTAINING MITOCHONDRIAL HOMEOSTASIS.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
3 3795  39 INTERLEUKIN-6 CONTRIBUTES TO GROWTH IN CHOLANGIOCARCINOMA CELLS BY ABERRANT PROMOTER METHYLATION AND GENE EXPRESSION. THE ASSOCIATION BETWEEN CHRONIC INFLAMMATION AND THE DEVELOPMENT AND PROGRESSION OF MALIGNANCY IS EXEMPLIFIED IN THE BILIARY TRACT WHERE PERSISTENT INFLAMMATION STRONGLY PREDISPOSES TO CHOLANGIOCARCINOMA. THE INFLAMMATORY CYTOKINE INTERLEUKIN-6 (IL-6) ENHANCES TUMOR GROWTH IN CHOLANGIOCARCINOMA BY ALTERED GENE EXPRESSION VIA AUTOCRINE MECHANISMS. IL-6 CAN REGULATE THE ACTIVITY OF DNA METHYLTRANSFERASES, AND MOREOVER, ABERRANT DNA METHYLATION CAN CONTRIBUTE TO CARCINOGENESIS. WE THEREFORE INVESTIGATED THE EFFECT OF CHRONIC EXPOSURE TO IL-6 ON METHYLATION-DEPENDENT GENE EXPRESSION AND TRANSFORMED CELL GROWTH IN HUMAN CHOLANGIOCARCINOMA. THE RELATIONSHIP BETWEEN AUTOCRINE IL-6 PATHWAYS, DNA METHYLATION, AND TRANSFORMED CELL GROWTH WAS ASSESSED USING MALIGNANT CHOLANGIOCYTES STABLY TRANSFECTED TO OVEREXPRESS IL-6. TREATMENT WITH THE DNA METHYLATION INHIBITOR 5-AZA-2'-DEOXYCYTIDINE DECREASED CELL PROLIFERATION, GROWTH IN SOFT AGAR, AND METHYLCYTOSINE CONTENT OF MALIGNANT CHOLANGIOCYTES. HOWEVER, THIS EFFECT WAS NOT OBSERVED IN IL-6-OVEREXPRESSING CELLS. IL-6 OVEREXPRESSION RESULTED IN THE ALTERED EXPRESSION AND PROMOTER METHYLATION OF SEVERAL GENES, INCLUDING THE EPIDERMAL GROWTH FACTOR RECEPTOR (EGFR). EGFR PROMOTER METHYLATION WAS DECREASED AND GENE AND PROTEIN EXPRESSION WAS INCREASED BY IL-6. THUS, EPIGENETIC REGULATION OF GENE EXPRESSION BY IL-6 CAN CONTRIBUTE TO TUMOR PROGRESSION BY ALTERING PROMOTER METHYLATION AND GENE EXPRESSION OF GROWTH-REGULATORY PATHWAYS, SUCH AS THOSE INVOLVING EGFR. MOREOVER, ENHANCED IL-6 EXPRESSION MAY DECREASE THE SENSITIVITY OF TUMOR CELLS TO THERAPEUTIC TREATMENTS USING METHYLATION INHIBITORS. THESE OBSERVATIONS HAVE IMPORTANT IMPLICATIONS FOR CANCER TREATMENT AND PROVIDE A MECHANISM BY WHICH PERSISTENT CYTOKINE STIMULATION CAN PROMOTE TUMOR GROWTH.	2006	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
4  332  42 ALTERATION OF EPIGENETIC PROFILE IN HUMAN HEPATOCELLULAR CARCINOMA AND ITS CLINICAL IMPLICATIONS. HEPATOCELLULAR CARCINOMA (HCC) IS A COMMON CANCER WORLDWIDE AND DEVELOPS AGAINST A BACKGROUND OF CHRONIC LIVER DAMAGE. A VARIETY OF HCC-RELATED GENES ARE KNOWN TO BE ALTERED BY GENETIC AND EPIGENETIC MECHANISMS. THEREFORE, INFORMATION REGARDING ALTERATION OF THE GENETIC AND EPIGENETIC PROFILES IN HCC IS ESSENTIAL FOR UNDERSTANDING THE BIOLOGY OF THIS TYPE OF TUMOR. METHYLATION AT CPG SITES IN GENE PROMOTERS IS KNOWN TO AFFECT THE TRANSCRIPTION OF THE CORRESPONDING GENES. ABNORMAL REGIONAL HYPERMETHYLATION IS OBSERVED IN THE 5' REGION OF SEVERAL TUMOR SUPPRESSOR GENES (TSGS) IN HCC, AND THIS HYPERMETHYLATION MAY PROMOTE CARCINOGENESIS THROUGH THE TRANSCRIPTIONAL INACTIVATION OF DOWNSTREAM TSGS. THE DNA DAMAGE INDUCED BY OXIDATION IS A TRIGGER OF ABNORMAL DNA METHYLATION AND INACTIVATION OF TSGS THROUGH RECRUITMENT OF THE POLYCOMB REPRESSIVE COMPLEX TO THE PROMOTER SEQUENCE. THUS, OXIDATIVE STRESS MAY BE RESPONSIBLE FOR THE EMERGENCE OF HCC FROM CHRONIC HEPATITIS AND LIVER CIRRHOSIS THROUGH THE EPIGENETIC ALTERATION OF TSGS. THERE HAVE BEEN SEVERAL ATTEMPTS TO APPLY EPIGENETIC INFORMATION TO THE DIAGNOSIS AND TREATMENT OF HCC. THE PREDICTIVE VALUE OF SELECTED METHYLATION EVENTS ON SURVIVAL IN HCC PATIENTS HAS BEEN REPORTED, AND THE METHYLATION PROFILE OF BACKGROUND LIVER COULD BE ASSOCIATED WITH RECURRENCE-FREE SURVIVAL OF HCC PATIENTS WHO HAVE UNDERGONE HEPATECTOMY. ANOTHER STUDY DETECTED METHYLATED DNA FROM HCC CELLS IN SERUM, AND THE CIRCULATING TUMOR DNA WAS REGARDED AS A POTENTIAL TUMOR MARKER. IN ADDITION, SEVERAL TRIALS OF HCC THERAPY HAVE TARGETED THE EPIGENETIC MACHINERY AND WERE BASED UPON COMPREHENSIVE ANALYSES OF DNA METHYLATION OF THIS TYPE OF TUMOR. HERE, WE PRESENT AN OVERVIEW OF RESEARCH REGARDING DNA METHYLATION STATUS IN HUMAN HCC AND DESCRIBE THE CLINICAL APPLICATION OF EPIGENETIC INFORMATION TO HCC.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
5 6723  46 VITAMIN D RECEPTOR GENE METHYLATION IN HEPATOCELLULAR CARCINOMA. WORLDWIDE, HEPATOCELLULAR CARCINOMA (HCC) IS THE MAJOR SUBTYPE OF PRIMARY LIVER CANCERS. HCC IS TYPICALLY DIAGNOSED LATE IN ITS COURSE. WITH RESPECT TO CANCER, THE GENOMIC ACTIONS OF VITAMIN D ARE MEDIATED THROUGH BINDING TO THE VITAMIN D RECEPTOR (VDR), WHICH ALLOWS IT TO MODULATE THE EXPRESSION OF GENES IN A CELL-AND TISSUE-SPECIFIC MANNER. EPIGENETICS IS A RAPIDLY EVOLVING FIELD OF GENETIC STUDY APPLICABLE TO HCC. CHANGES IN DNA METHYLATION PATTERNS ARE THOUGHT TO BE EARLY EVENTS IN HEPATOCARCINOGENESIS. CURCUMIN HAS GREAT POTENTIAL AS AN EPIGENETIC AGENT. ACCORDINGLY, THE CURRENT STUDY HAS BEEN DESIGNED TO STUDY THE METHYLATION STATUS OF VDR GENE PROMOTER FOR THE FIRST TIME IN HCC AIMING TO FIND ITS CLINICAL SIGNIFICANCE AND POTENTIAL SCREENING ROLE IN CHRONIC LIVER DISEASE (CLD). ADDITIONALLY, WE AIMED TO INVESTIGATE, THE EFFECT OF CURCUMIN ON HCC CELL LINE, AIMING TO DISCOVER NEW THERAPEUTIC TARGETS THROUGH EPIGENETICS. THIS STUDY WAS CONDUCTED ON 45 FORMALIN-FIXED, PARAFFIN-EMBEDDED LIVER TISSUE BLOCKS INCLUDING 15 HCC SAMPLES (GROUP A), 15 CLD SAMPLES (GROUP B) AND 15 APPARENTLY NORMAL TISSUE TAKEN FROM AROUND BENIGN LESIONS (GROUP C). METHYLATION SPECIFIC RESTRICTION DIGESTION AND QPCR WERE DONE ON ALL SAMPLES AFTER DNA EXTRACTION. THE PERCENTAGE OF VDR GENE PROMOTER METHYLATION WAS SIGNIFICANTLY HIGHER IN THE HCC GROUP COMPARED TO BOTH CLD AND CONTROL GROUPS (P < 0.01). VDR PROMOTER METHYLATION BY (MS-QPCR) WAS DECREASED AND THE RELATIVE EXPRESSION OF VDR BY (QRT-PCR) WAS MARKEDLY INCREASED IN A DOSE-DEPENDENT FASHION IN CELLS GROWN IN CURCUMIN-ADEQUATE MEDIUM. IN CONCLUSION, THIS STUDY MAY OPEN A NEW GATE FOR THE USE OF VDR PROMOTER METHYLATION AS A POTENTIAL BIOMARKER IN HCC.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
6 4677  50 NEW LNCRNAS IN CHRONIC HEPATITIS C PROGRESSION: FROM FIBROSIS TO HEPATOCELLULAR CARCINOMA. HEPATOCELLULAR CARCINOMA (HCC) IS THE THIRD LEADING CAUSE OF CANCER-RELATED DEATH IN THE WORLD, AND ABOUT 80% OF THE CASES ARE ASSOCIATED WITH HEPATITIS B OR C. GENETIC AND EPIGENETIC ALTERATIONS ARE ACCUMULATED OVER DECADES OF CHRONIC INJURY AND MAY AFFECT THE FUNCTIONING OF TUMOR SUPPRESSOR GENES AND PROTOONCOGENES. STUDIES HAVE EVIDENCED THE ROLE OF LONG NON-CODING RNAS (LNCRNA) WITH ONCOGENIC OR TUMOR SUPPRESSOR ACTIVITIES, SUGGESTING A GREAT POTENTIAL IN THE TREATMENT, DIAGNOSIS OR INDICATOR OF PROGNOSIS IN CANCER. IN THIS CONTEXT, THE AIM OF THIS STUDY WAS TO EVALUATE THE GLOBAL EXPRESSION PROFILE LNCRNA IN HEPATIC TISSUE SAMPLES WITH DIFFERENT STAGES OF FIBROSIS ASSOCIATED WITH CHRONIC HEPATITIS C, HCC AND NORMAL LIVER, IN ORDER TO IDENTIFY NEW LNCRNAS THAT COULD CONTRIBUTE TO STUDY THE PROGRESSION OF HEPATIC FIBROSIS TO HCC ASSOCIATED WITH CHRONIC HEPATITIS C. RNA-SEQ WAS PERFORMED ON ILLUMINA NEXTSEQ PLATFORM TO IDENTIFY LNCRNAS EXPRESSED DIFFERENTLY IN 15 PATIENTS WITH CHRONIC HEPATITIS C, THREE PATIENTS WITH HCC AND THREE NORMAL LIVER SPECIMENS. WHEN THE PATHOLOGICAL TISSUES (FIBROSIS AND CARCINOMA) WERE COMPARED TO NORMAL HEPATIC TISSUE, WERE IDENTIFIED 2, 6 E 34 DIFFERENTIALLY EXPRESSED LNCRNAS IN MODERATE FIBROSIS, ADVANCED FIBROSIS AND HCC, RESPECTIVELY. THE CARCINOMA GROUP HAD THE HIGHEST PROPORTION OF DIFFERENTIALLY EXPRESSED LNCRNA (34) AND OF THESE, 29 WERE EXCLUSIVE IN THIS TYPE OF TISSUE. A HEAT MAP OF THE DEREGULATED LNCRNA REVEALED DIFFERENT EXPRESSION PATTERNS ALONG THE PROGRESSION OF FIBROSIS TO HCC. THE RESULTS SHOWED THE DEREGULATION OF SOME LNCRNA ALREADY CLASSIFIED AS TUMOR SUPPRESSORS IN HCC AND OTHER CANCERS, AS WELL AS SOME UNPUBLISHED LNCRNA WHOSE FUNCTION IS UNKNOWN. SOME OF THESE LNCRNAS ARE DYSREGULATED SINCE THE EARLY STAGES OF LIVER INJURY IN PATIENTS WITH HEPATITIS C, OTHERS OVEREXPRESSED ONLY IN TUMOR TISSUE, INDICATING THEMSELVES AS CANDIDATES OF MARKERS OF FIBROSIS PROGRESSION OR TUMOR, WITH POTENTIAL CLINICAL APPLICATIONS IN PROGNOSIS AS WELL AS A THERAPEUTIC TARGET. ALTHOUGH THERE ARE ALREADY STUDIES ON LNCRNA IN HEPATOCELLULAR CARCINOMA, THIS IS THE FIRST STUDY CONDUCTED IN SAMPLES EXCLUSIVELY OF HCV-RELATED LIVER AND HCV HCC.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
7 2234  43 EPIGENETIC MODIFICATIONS PRECEDE MOLECULAR ALTERATIONS AND DRIVE HUMAN HEPATOCARCINOGENESIS. DEVELOPMENT OF PRIMARY LIVER CANCER IS A MULTISTAGE PROCESS. DETAILED UNDERSTANDING OF SEQUENTIAL EPIGENETIC ALTERATIONS IS LARGELY MISSING. HERE, WE PERFORMED INFINIUM HUMAN METHYLATION 450K BEADCHIPS AND RNA-SEQ ANALYSES FOR GENOME-WIDE METHYLOME AND TRANSCRIPTOME PROFILING OF CIRRHOTIC LIVER (N = 7), LOW- (N = 4) AND HIGH-GRADE (N = 9) DYSPLASTIC LESIONS, AND EARLY (N = 5) AND PROGRESSED (N = 3) HEPATOCELLULAR CARCINOMAS (HCC) SYNCHRONOUSLY DETECTED IN 8 PATIENTS WITH HCC WITH CHRONIC HEPATITIS B INFECTION. INTEGRATIVE ANALYSES OF EPIGENETICALLY DRIVEN MOLECULAR CHANGES WERE IDENTIFIED AND VALIDATED IN 2 INDEPENDENT COHORTS COMPRISING 887 HCCS. MITOCHONDRIAL DNA SEQUENCING WAS FURTHER EMPLOYED FOR CLONALITY ANALYSES, INDICATING MULTICLONAL ORIGIN IN THE MAJORITY OF INVESTIGATED HCCS. ALTERATIONS IN DNA METHYLATION PROGRESSIVELY INCREASED FROM LIVER CIRRHOSIS (CL) TO DYSPLASTIC LESIONS AND REACHED A MAXIMUM IN EARLY HCCS. ASSOCIATED EARLY ALTERATIONS IDENTIFIED BY INGENUITY PATHWAY ANALYSIS (IPA) INVOLVED APOPTOSIS, IMMUNE REGULATION, AND STEMNESS PATHWAYS, WHILE LATE CHANGES CENTERED ON CELL SURVIVAL, PROLIFERATION, AND INVASION. WE FURTHER VALIDATED 23 PUTATIVE EPIDRIVERS WITH CONCOMITANT EXPRESSION CHANGES AND ASSOCIATED WITH OVERALL SURVIVAL. FUNCTIONALLY, STRIATIN 4 (STRN4) WAS DEMONSTRATED TO BE EPIGENETICALLY REGULATED, AND INHIBITION OF STRN4 SIGNIFICANTLY SUPPRESSED TUMORIGENICITY OF HCC CELL LINES. OVERALL, APPLICATION OF INTEGRATIVE GENOMIC ANALYSES DEFINES EPIGENETIC DRIVER ALTERATIONS AND PROVIDES PROMISING TARGETS FOR POTENTIALLY NOVEL THERAPEUTIC APPROACHES.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
8 3567  32 IMPACT OF HEPATITIS VIRUS AND AGING ON DNA METHYLATION IN HUMAN HEPATOCARCINOGENESIS. HEPATOCELLULAR CARCINOMA (HCC) USUALLY DEVELOPS ON THE BASIS OF CHRONIC HEPATITIS AND LIVER CIRRHOSIS, WHERE INACTIVATION OF SEVERAL TUMOR SUPPRESSOR GENES (TSGS) TAKES PLACE VIA METHYLATION OF THE PROMOTER. INTERESTINGLY, THESE METHYLATION EVENTS ARE MORE PREVALENT IN A BACKGROUND LIVER AT HIGH RISK OF HCC THAN ONE AT LOW RISK. ABNORMAL METHYLATION IS ALSO OBSERVED IN PRECANCEROUS NODULES SUCH AS DYSPLASTIC NODULES AND ADENOMAS, SUGGESTING THAT EPIGENETIC ALTERATION IS AN EARLY EVENT FOR HCC CARCINOGENESIS. IT IS POSSIBLE THAT INFECTION WITH THE HEPATITIS VIRUS INDUCES ALTERATION OF METHYLATION AT PROMOTERS OF TSGS. SOME STUDIES SUGGESTED THAT VIRAL PROTEINS INTERFERE WITH DNA METHYLTRANSFERASE IN CHRONIC HEPATITIS B. INDUCTION OF EPIGENETIC ALTERATION IN CHRONIC HEPATITIS C MIGHT, HOWEVER, MIGHT BE A CONSEQUENCE OF OXIDATIVE STRESS. IN ADDITION, WE PROPOSED AGE SHOULD BE TAKEN INTO CONSIDERATION FOR HCC DEVELOPMENT VIA EPIGENETIC PATHWAYS. FURTHER INVESTIGATIONS ARE REQUIRED TO UNDERSTAND THE MECHANISM OF INDUCING EPIGENETIC INSTABILITY DURING HEPATOCARCINOGENESIS.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
9 4056  42 MAPPING THE HETEROGENEITY OF HISTONE MODIFICATIONS ON HEPATITIS B VIRUS DNA USING LIVER NEEDLE BIOPSIES OBTAINED FROM CHRONICALLY INFECTED PATIENTS. COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) FORMS THE BASIS FOR REPLICATION AND PERSISTENCE OF HEPATITIS B VIRUS (HBV) IN THE CHRONICALLY INFECTED LIVER. WE HAVE PREVIOUSLY SHOWN THAT VIRAL TRANSCRIPTION IS SUBJECT TO REGULATION BY POSTTRANSLATIONAL MODIFICATIONS (PTMS) OF HISTONE PROTEINS BOUND TO CCCDNA THROUGH ANALYSIS OF DE NOVO HBV-INFECTED CELL LINES. WE NOW REPORT THE SUCCESSFUL ADAPTATION OF THIS CHROMATIN IMMUNOPRECIPITATION SEQUENCING (CHIPSEQ) APPROACH FOR ANALYSIS OF FINE-NEEDLE PATIENT LIVER BIOPSY SPECIMENS TO INVESTIGATE THE ROLE OF HISTONE PTMS IN CHRONICALLY HBV-INFECTED PATIENTS. USING 18 SPECIMENS FROM PATIENTS IN DIFFERENT STAGES OF CHRONIC HBV INFECTION, OUR WORK SHOWS THAT THE PROFILE OF HISTONE PTMS IN CHRONIC INFECTION IS MORE NUANCED THAN PREVIOUSLY OBSERVED IN IN VITRO MODELS OF ACUTE INFECTION. IN LINE WITH OUR PREVIOUS FINDINGS, WE FIND THAT THE MAJORITY OF HBV-DERIVED SEQUENCES ARE ASSOCIATED WITH THE ACTIVATING HISTONE PTM H3K4ME3. HOWEVER, WE SHOW A STRIKING INTERPATIENT VARIABILITY OF ITS DEPOSITION IN THIS PATIENT COHORT CORRELATED WITH VIRAL TRANSCRIPTION AND PATIENT HBV EARLY ANTIGEN (HBEAG) STATUS. UNEXPECTEDLY, WE DETECTED DEPOSITION OF THE CLASSICAL INHIBITORY HISTONE PTM H3K9ME3 ON HBV-DNA IN AROUND HALF OF THE PATIENT BIOPSY SPECIMENS, WHICH COULD NOT BE LINKED TO REDUCED LEVELS OF VIRAL TRANSCRIPTS. OUR RESULTS SHOW THAT CURRENT IN VITRO MODELS ARE UNABLE TO FULLY RECAPITULATE THE COMPLEX EPIGENETIC LANDSCAPE OF CHRONIC HBV INFECTION OBSERVED IN VIVO AND DEMONSTRATE THAT FINE-NEEDLE LIVER BIOPSY SPECIMENS CAN PROVIDE SUFFICIENT MATERIAL TO FURTHER INVESTIGATE THE INTERACTION OF VIRAL AND HOST PROTEINS ON HBV-DNA.IMPORTANCE HEPATITIS B VIRUS (HBV) IS A MAJOR GLOBAL HEALTH CONCERN, CHRONICALLY INFECTING MILLIONS OF PATIENTS AND CONTRIBUTING TO A RISING BURDEN OF LIVER DISEASE. THE VIRAL GENOME FORMS THE BASIS FOR CHRONIC INFECTION AND HAS BEEN SHOWN TO BE SUBJECT TO REGULATION BY EPIGENETIC MECHANISMS, SUCH AS POSTTRANSLATIONAL MODIFICATION OF HISTONE PROTEINS. HERE, WE CONFIRM AND EXPAND ON PREVIOUS RESULTS BY ADAPTING A HIGH-RESOLUTION TECHNIQUE FOR ANALYSIS OF HISTONE MODIFICATIONS FOR USE WITH PATIENT-DERIVED FINE-NEEDLE LIVER BIOPSY SPECIMENS. OUR WORK HIGHLIGHTS THAT THE SITUATION IN VIVO IS MORE COMPLEX THAN PREDICTED BY CURRENT IN VITRO MODELS, FOR EXAMPLE, BY SUGGESTING A NOVEL, NONCANONICAL ROLE OF THE HISTONE MODIFICATION H3K9ME3 IN THE HBV LIFE CYCLE. IMPORTANTLY, ENABLING THE USE OF FINE-NEEDLE LIVER BIOPSY SPECIMENS FOR SUCH HIGH-RESOLUTION ANALYSES MAY FACILITATE FURTHER RESEARCH INTO THE EPIGENETIC REGULATION OF THE HBV GENOME.	2019	

10 3527  27 IL-6 ENHANCES THE NUCLEAR TRANSLOCATION OF DNA CYTOSINE-5-METHYLTRANSFERASE 1 (DNMT1) VIA PHOSPHORYLATION OF THE NUCLEAR LOCALIZATION SEQUENCE BY THE AKT KINASE. THE EPIGENETIC PROGRAMMING OF GENOMIC DNA IS ACCOMPLISHED, IN PART, BY SEVERAL DNA CYTOSINE-5-METHYLTRANSFERASES THAT ACT BY COVALENTLY MODIFYING CYTOSINES WITH THE ADDITION OF A METHYL GROUP. THIS COVALENT MODIFICATION IS MAINTAINED BY THE DNA CYTOSINE-5-METHYLTRANSFERASE-1 ENZYME (DNMT1), WHICH IS CAPABLE OF ACTING IN CONCERT WITH OTHER SIMILAR ENZYMES TO SILENCE IMPORTANT TUMOR SUPPRESSOR GENES. IL-6 IS A MULTIFUNCTIONAL MEDIATOR OF INFLAMMATION, ACTING THROUGH SEVERAL MAJOR SIGNALING CASCADES, INCLUDING THE PHOSPHATIDYLINOSITOL-3-KINASE PATHWAY (PI-3-K), WHICH ACTIVATES PROTEIN KINASE B (AKT/PKB) DOWNSTREAM. HERE, WE SHOW THAT THE SUBCELLULAR LOCALIZATION OF DNMT1 CAN BE ALTERED BY THE ADDITION OF IL-6, INCREASING THE RATE OF NUCLEAR TRANSLOCATION OF THE ENZYME FROM THE CYTOSOLIC COMPARTMENT. THE MECHANISM OF NUCLEAR TRANSLOCATION OF DNMT1 IS GREATLY ENHANCED BY PHOSPHORYLATION OF THE DNMT1 NUCLEAR LOCALIZATION SIGNAL (NLS) BY PKB/AKT KINASE. MUTAGENIC ALTERATION OF THE TWO AKT TARGET AMINO ACIDS WITHIN THE NLS RESULTS IN A MAJOR LOSS OF DNMT1 NUCLEAR TRANSLOCATION, WHILE THE CREATION OF A "PHOSPHO-MIMIC" AMINO ACID (MUTATION TO ACIDIC RESIDUES) RESTORES THIS COMPARTMENTATION ABILITY. THESE OBSERVATIONS SUGGEST AN INTERESTING HYPOTHESIS REGARDING HOW MEDIATORS OF CHRONIC INFLAMMATION MAY DISTURB THE DELICATE BALANCE OF CELLULAR COMPARTMENTALIZATION OF IMPORTANT PROTEINS, AND REVEALS A POTENTIAL MECHANISM FOR THE INDUCTION OR ENHANCEMENT OF TUMOR GROWTH VIA ALTERATION OF THE COMPONENTS INVOLVED IN THE EPIGENETIC PROGRAMMING OF A CELL.	2007	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
11 3646  42 INCREASED PROTEIN EXPRESSION OF DNA METHYLTRANSFERASE (DNMT) 1 IS SIGNIFICANTLY CORRELATED WITH THE MALIGNANT POTENTIAL AND POOR PROGNOSIS OF HUMAN HEPATOCELLULAR CARCINOMAS. ALTERATION OF DNA METHYLATION IS ONE OF THE MOST CONSISTENT EPIGENETIC CHANGES IN HUMAN CANCERS. DNA METHYLTRANSFERASE (DNMT) 1 IS A MAJOR ENZYME INVOLVED IN ESTABLISHING GENOMIC METHYLATION PATTERNS. MOST OF THE STUDIES CONCERNING DNMT1 EXPRESSION IN HUMAN CANCERS HAVE BEEN PERFORMED ONLY AT THE MRNA LEVEL. TO DIRECTLY EXAMINE DNMT1 PROTEIN EXPRESSION LEVELS DURING HUMAN HEPATOCARCINOGENESIS, 16 HISTOLOGICALLY NORMAL LIVER TISSUES, 51 NONCANCEROUS LIVER TISSUES EXHIBITING CHRONIC HEPATITIS OR CIRRHOSIS, WHICH ARE CONSIDERED TO BE PRECANCEROUS CONDITIONS, AND 53 HEPATOCELLULAR CARCINOMAS (HCCS) WERE SUBJECTED TO IMMUNOHISTOCHEMIC EXAMINATION. IF MORE THAN 20% OF THE CELLS EXHIBITED NUCLEAR DNMT1 STAINING, THE TISSUE SAMPLE WAS CONSIDERED TO BE DNMT1-POSITIVE. DNMT1 IMMUNOREACTIVITY WAS OBSERVED IN 23 (43%) OF THE HCCS, BUT IN NONE (0%) OF THE HISTOLOGICALLY NORMAL LIVER OR NONCANCEROUS LIVER TISSUES EXHIBITING CHRONIC HEPATITIS OR CIRRHOSIS. THE INCIDENCE OF INCREASED DNMT1 PROTEIN EXPRESSION IN HCCS CORRELATED SIGNIFICANTLY WITH POOR TUMOR DIFFERENTIATION (P = 0.0006) AND PORTAL VEIN INVOLVEMENT (P = 0.0002). MOREOVER, THE RECURRENCE-FREE (P = 0.0001) AND OVERALL (P < 0.0001) SURVIVAL RATES OF PATIENTS WITH HCCS EXHIBITING INCREASED DNMT1 PROTEIN EXPRESSION WERE SIGNIFICANTLY LOWER THAN THOSE OF PATIENTS WITH HCCS THAT DID NOT EXHIBIT INCREASED EXPRESSION. INCREASED DNMT1 PROTEIN EXPRESSION MAY PLAY A CRITICAL ROLE IN THE MALIGNANT PROGRESSION OF HCCS AND BE A BIOLOGIC PREDICTOR OF BOTH HCC RECURRENCE AND A POOR PROGNOSIS IN HCC PATIENTS.	2003	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
12 2926  33 GENERATION OF AN EPIGENETIC SIGNATURE BY CHRONIC HYPOXIA IN PROSTATE CELLS. INCREASING LEVELS OF TISSUE HYPOXIA HAVE BEEN REPORTED AS A NATURAL FEATURE OF THE AGING PROSTATE GLAND AND MAY BE A RISK FACTOR FOR THE DEVELOPMENT OF PROSTATE CANCER. IN THIS STUDY, WE HAVE USED PWR-1E BENIGN PROSTATE EPITHELIAL CELLS AND AN EQUIVALENTLY AGED HYPOXIA-ADAPTED PWR-1E SUB-LINE TO IDENTIFY PHENOTYPIC AND EPIGENETIC CONSEQUENCES OF CHRONIC HYPOXIA IN PROSTATE CELLS. WE HAVE IDENTIFIED A SIGNIFICANTLY ALTERED CELLULAR PHENOTYPE IN RESPONSE TO CHRONIC HYPOXIA AS CHARACTERIZED BY INCREASED RECEPTOR-MEDIATED APOPTOTIC RESISTANCE, THE INDUCTION OF CELLULAR SENESCENCE, INCREASED INVASION AND THE INCREASED SECRETION OF IL-1 BETA, IL6, IL8 AND TNFALPHA CYTOKINES. IN ASSOCIATION WITH THESE PHENOTYPIC CHANGES AND THE ABSENCE OF HIF-1 ALPHA PROTEIN EXPRESSION, WE HAVE DEMONSTRATED SIGNIFICANT INCREASES IN GLOBAL LEVELS OF DNA METHYLATION AND H3K9 HISTONE ACETYLATION IN THESE CELLS, CONCOMITANT WITH THE INCREASED EXPRESSION OF DNA METHYLTRANSFERASE DMNT3B AND GENE-SPECIFIC CHANGES IN DNA METHYLATION AT KEY IMPRINTING LOCI. IN CONCLUSION, WE HAVE DEMONSTRATED A GENOME-WIDE ADJUSTMENT OF DNA METHYLATION AND HISTONE ACETYLATION UNDER CHRONIC HYPOXIC CONDITIONS IN THE PROSTATE. THESE EPIGENETIC SIGNATURES MAY REPRESENT AN ADDITIONAL MECHANISM TO PROMOTE AND MAINTAIN A HYPOXIC-ADAPTED CELLULAR PHENOTYPE WITH A POTENTIAL ROLE IN TUMOUR DEVELOPMENT.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
13 6707  38 VIRAL HEPATITIS AND HEPATOCELLULAR CARCINOMA: STATE OF THE ART. VIRAL HEPATITIS IS ONE OF THE MAIN CAUSES LEADING TO HEPATOCELLULAR CARCINOMA (HCC). THE CONTINUED RISE IN INCIDENCE OF HCC SUGGESTS ADDITIONAL FACTORS FOLLOWING INFECTION MAY BE INVOLVED. THIS REVIEW EXAMINES RECENT STUDIES INVESTIGATING THE MOLECULAR MECHANISMS OF CHRONIC HEPATITIS AND ITS ASSOCIATION WITH HEPATOCARCINOGENESIS. HEPATITIS B VIRUS PATIENTS WITH GENOTYPE C DISPLAY AN AGGRESSIVE DISEASE COURSE LEADING TO HCC MORE THAN OTHER GENOTYPES. FURTHERMORE, HEPATITIS B EXCRETORY ANTIGEN (HBEAG) SEEMS TO BE A MORE SENSITIVE PREDICTIVE TUMOR MARKER EXHIBITING A SIX-FOLD HIGHER RELATIVE RISK IN PATIENTS WITH POSITIVE HBSAG AND HBEAG THAN THOSE WITH HBSAG ONLY. SINGLE OR COMBINED MUTATIONS OF VIRAL GENOME CAN PREDICT HCC DEVELOPMENT IN UP TO 80% OF PATIENTS. SEVERAL MUTATIONS IN HBX-GENE ARE RELATED WITH HIGHER HCC INCIDENCE. OVEREXPRESSION OF THE CORE PROTEIN IN HCV LEADS TO HEPATOCELLULAR LIPID ACCUMULATION ASSOCIATED WITH ONCOGENESIS. REDUCED NUMBER AND DECREASED FUNCTIONALITY OF NATURAL KILLER CELLS IN CHRONIC HCV INDIVIDUALS DYSREGULATE THEIR SURVEILLANCE FUNCTION IN TUMOR AND VIRAL CELLS RESULTING IN HCC. FURTHERMORE, HIGH T-CELL IMMUNOGLOBULIN AND MUCIN 3 LEVELS SUPRESS CD8+ T-CELLS, WHICH LEAD TO IMMUNOLOGICAL DYSREGULATION. HEPATITIS D PROMOTES HCC DEVELOPMENT INDIRECTLY VIA MODIFICATIONS TO INNATE IMMUNITY, EPIGENETIC ALTERATIONS AND PRODUCTION OF REACTIVE OXYGEN SPECIES WITH THE LHDAG BEING THE MOST HIGHLY ASSOCIATED WITH HCC DEVELOPMENT. SUMMARIZING THE RESULTS, HBV AND HCV INFECTION REPRESENT THE MOST ASSOCIATED FORMS OF VIRAL HEPATITIS CAUSING HCC. FURTHER STUDIES ARE WARRANTED TO FURTHER IMPROVE THE PREDICTION OF HIGH-RISK PATIENTS AND DEVELOPMENT OF TARGETED THERAPEUTICS PREVENTING THE TRANSITION FROM HEPATIC INFLAMMATION-FIBROSIS TO CANCER.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
14 3658  40 INDUCTION OF ABERRANT TRIMETHYLATION OF HISTONE H3 LYSINE 27 BY INFLAMMATION IN MOUSE COLONIC EPITHELIAL CELLS. A FIELD FOR CANCERIZATION (FIELD DEFECT), WHERE GENETIC AND EPIGENETIC ALTERATIONS ARE ACCUMULATED IN NORMAL-APPEARING TISSUES, IS INVOLVED IN HUMAN CARCINOGENESIS, ESPECIALLY CANCERS ASSOCIATED WITH CHRONIC INFLAMMATION. ALTHOUGH ABERRANT DNA METHYLATION IS INVOLVED IN THE FIELD DEFECT AND INDUCED BY CHRONIC INFLAMMATION, IT IS STILL UNCLEAR FOR TRIMETHYLATION OF HISTONE H3 LYSINE 27 (H3K27ME3), WHICH IS INVOLVED IN GENE REPRESSION INDEPENDENT OF DNA METHYLATION AND FUNCTIONS AS A PRE-MARK FOR ABERRANT DNA METHYLATION. IN THIS STUDY, USING A MOUSE COLITIS MODEL INDUCED BY DEXTRAN SULFATE SODIUM (DSS), WE AIMED TO CLARIFY WHETHER ABERRANT H3K27ME3 IS INDUCED BY INFLAMMATION AND INVOLVED IN A FIELD DEFECT. CHIP-ON-CHIP ANALYSIS OF COLONIC EPITHELIAL CELLS REVEALED THAT H3K27ME3 LEVELS WERE INCREASED OR DECREASED FOR 266 GENOMIC REGIONS BY AGING, AND MORE EXTENSIVELY (23 INCREASED AND 3574 DECREASED REGIONS) BY COLITIS. SUCH INCREASE OR DECREASE OF H3K27ME3 WAS INDUCED AS EARLY AS 2 WEEKS AFTER THE INITIATION OF DSS TREATMENT, AND PERSISTED AT LEAST FOR 16 WEEKS EVEN AFTER THE INFLAMMATION DISAPPEARED. SOME OF THE ABERRANT H3K27ME3 IN COLONIC EPITHELIAL CELLS WAS CARRIED OVER INTO COLON TUMORS. FURTHERMORE, H3K27ME3 ACQUIRED AT DAPK1 BY COLITIS WAS FOLLOWED BY INCREASED DNA METHYLATION, SUPPORTING ITS FUNCTION AS A PRE-MARK FOR ABERRANT DNA METHYLATION. THESE RESULTS DEMONSTRATED THAT ABERRANT H3K27ME3 CAN BE INDUCED BY EXPOSURE TO A SPECIFIC ENVIRONMENT, SUCH AS COLITIS, AND SUGGESTED THAT ABERRANT HISTONE MODIFICATION, IN ADDITION TO ABERRANT DNA METHYLATION, IS INVOLVED IN THE FORMATION OF A FIELD DEFECT.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
15 3791  44 INTERLEUKIN 6 SUPPORTS THE MAINTENANCE OF P53 TUMOR SUPPRESSOR GENE PROMOTER METHYLATION. A STRONG ASSOCIATION EXISTS BETWEEN STATES OF CHRONIC INFLAMMATION AND CANCER, AND IT IS BELIEVED THAT MEDIATORS OF INFLAMMATION MAY BE RESPONSIBLE FOR THIS PHENOMENON. INTERLEUKIN 6 (IL-6) IS AN INFLAMMATORY CYTOKINE KNOWN TO PLAY A ROLE IN THE GROWTH AND SURVIVAL OF MANY TYPES OF TUMORS, YET THE MECHANISMS EMPLOYED BY THIS PLEOMORPHIC CYTOKINE TO ACCOMPLISH THIS FEAT ARE STILL POORLY UNDERSTOOD. ANOTHER IMPORTANT FACTOR IN TUMOR DEVELOPMENT SEEMS TO BE THE HYPERMETHYLATION OF CPG ISLANDS LOCATED WITHIN THE PROMOTER REGIONS OF TUMOR SUPPRESSOR GENES. THIS COMMON EPIGENETIC ALTERATION ENABLES TUMOR CELLS TO REDUCE OR INACTIVATE THE EXPRESSION OF IMPORTANT TUMOR SUPPRESSOR AND CELL CYCLE REGULATORY GENES. HERE WE SHOW THAT IN THE IL-6-RESPONSIVE HUMAN MULTIPLE MYELOMA CELL LINE KAS 6/1, THE PROMOTER REGION OF P53 IS EPIGENETICALLY MODIFIED BY METHYLTRANSFERASES, RESULTING IN DECREASED LEVELS OF EXPRESSION. FURTHERMORE, CELLS TREATED WITH IL-6 EXHIBIT AN INCREASE IN THE EXPRESSION OF THE DNA MAINTENANCE METHYLATION ENZYME, DNMT-1. THE DNA METHYLTRANSFERASE INHIBITOR ZEBULARINE REVERSES THE METHYLATION OF THE P53 PROMOTER, ALLOWING THE RESUMPTION OF ITS EXPRESSION. HOWEVER, WHEN ZEBULARINE IS WITHDRAWN FROM THE CELLS, THE REESTABLISHMENT OF THE ORIGINAL CPG ISLAND METHYLATION WITHIN THE P53 PROMOTER DOES NOT OCCUR IN THE ABSENCE OF IL-6, AND CELLS WHICH DO NOT RECEIVE IL-6 EVENTUALLY DIE, AS P53 EXPRESSION CONTINUES UNCHECKED BY REMETHYLATION. INTERESTINGLY, THIS LOSS OF VIABILITY SEEMS TO INVOLVE NOT THE WITHDRAWAL OF CYTOKINE, BUT THE INABILITY OF THE CELL TO RESILENCE THE PROMOTER. CONSISTENT WITH THIS MODEL, WHEN CELLS THAT EXPRESS IL-6 IN AN AUTOCRINE FASHION ARE SUBJECTED TO IDENTICAL TREATMENT, P53 EXPRESSION IS REDUCED SHORTLY AFTER WITHDRAWAL OF ZEBULARINE. THEREFORE, IT SEEMS IL-6 IS CAPABLE OF MAINTAINING PROMOTER METHYLATION THUS REPRESENTING ONE OF THE POSSIBLE MECHANISMS USED BY INFLAMMATORY MEDIATORS IN THE GROWTH AND SURVIVAL OF TUMORS.	2005	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
16 5921  42 TARGETING CLINICAL EPIGENETIC REPROGRAMMING FOR CHEMOPREVENTION OF METABOLIC AND VIRAL HEPATOCELLULAR CARCINOMA. OBJECTIVE: HEPATOCELLULAR CARCINOMA (HCC) IS THE FASTEST-GROWING CAUSE OF CANCER-RELATED MORTALITY WITH CHRONIC VIRAL HEPATITIS AND NON-ALCOHOLIC STEATOHEPATITIS (NASH) AS MAJOR AETIOLOGIES. TREATMENT OPTIONS FOR HCC ARE UNSATISFACTORY AND CHEMOPREVENTIVE APPROACHES ARE ABSENT. CHRONIC HEPATITIS C (CHC) RESULTS IN EPIGENETIC ALTERATIONS DRIVING HCC RISK AND PERSISTING FOLLOWING CURE. HERE, WE AIMED TO INVESTIGATE EPIGENETIC MODIFICATIONS AS TARGETS FOR LIVER CANCER CHEMOPREVENTION. DESIGN: LIVER TISSUES FROM PATIENTS WITH NASH AND CHC WERE ANALYSED BY CHIP-SEQ (H3K27AC) AND RNA-SEQ. THE LIVER DISEASE-SPECIFIC EPIGENETIC AND TRANSCRIPTIONAL REPROGRAMMING IN PATIENTS WAS MODELLED IN A LIVER CELL CULTURE SYSTEM. PERTURBATION STUDIES COMBINED WITH A TARGETED SMALL MOLECULE SCREEN FOLLOWED BY IN VIVO AND EX VIVO VALIDATION WERE USED TO IDENTIFY CHROMATIN MODIFIERS AND READERS FOR HCC CHEMOPREVENTION. RESULTS: IN PATIENTS, CHC AND NASH SHARE SIMILAR EPIGENETIC AND TRANSCRIPTOMIC MODIFICATIONS DRIVING CANCER RISK. USING A CELL-BASED SYSTEM MODELLING EPIGENETIC MODIFICATIONS IN PATIENTS, WE IDENTIFIED CHROMATIN READERS AS TARGETS TO REVERT LIVER GENE TRANSCRIPTION DRIVING CLINICAL HCC RISK. PROOF-OF-CONCEPT STUDIES IN A NASH-HCC MOUSE MODEL SHOWED THAT THE PHARMACOLOGICAL INHIBITION OF CHROMATIN READER BROMODOMAIN 4 INHIBITED LIVER DISEASE PROGRESSION AND HEPATOCARCINOGENESIS BY RESTORING TRANSCRIPTIONAL REPROGRAMMING OF THE GENES THAT WERE EPIGENETICALLY ALTERED IN PATIENTS. CONCLUSION: OUR RESULTS UNRAVEL THE FUNCTIONAL RELEVANCE OF METABOLIC AND VIRUS-INDUCED EPIGENETIC ALTERATIONS FOR PATHOGENESIS OF HCC DEVELOPMENT AND IDENTIFY CHROMATIN READERS AS TARGETS FOR CHEMOPREVENTION IN PATIENTS WITH CHRONIC LIVER DISEASES.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
17 5972  27 TET REPRESSION AND INCREASED DNMT ACTIVITY SYNERGISTICALLY INDUCE ABERRANT DNA METHYLATION. CHRONIC INFLAMMATION IS DEEPLY INVOLVED IN VARIOUS HUMAN DISORDERS, SUCH AS CANCER, NEURODEGENERATIVE DISORDERS, AND METABOLIC DISORDERS. INDUCTION OF EPIGENETIC ALTERATIONS, ESPECIALLY ABERRANT DNA METHYLATION, IS ONE OF THE MAJOR MECHANISMS, BUT HOW IT IS INDUCED IS STILL UNCLEAR. HERE, WE FOUND THAT EXPRESSION OF TET GENES, METHYLATION ERASERS, WAS DOWNREGULATED IN INFLAMED MOUSE AND HUMAN TISSUES, AND THAT THIS WAS CAUSED BY UPREGULATION OF TET-TARGETING MIRNAS SUCH AS MIR20A, MIR26B, AND MIR29C, LIKELY DUE TO ACTIVATION OF NF-KAPPAB SIGNALING DOWNSTREAM OF IL-1BETA AND TNF-ALPHA. HOWEVER, TET KNOCKDOWN INDUCED ONLY MILD ABERRANT METHYLATION. NITRIC OXIDE (NO), PRODUCED BY NOS2, ENHANCED ENZYMATIC ACTIVITY OF DNA METHYLTRANSFERASES (DNMTS), METHYLATION WRITERS, AND NO EXPOSURE INDUCED MINIMAL ABERRANT METHYLATION. IN CONTRAST, A COMBINATION OF TET KNOCKDOWN AND NO EXPOSURE SYNERGISTICALLY INDUCED ABERRANT METHYLATION, INVOLVING GENOMIC REGIONS NOT METHYLATED BY EITHER ALONE. THE RESULTS SHOWED THAT A VICIOUS COMBINATION OF TET REPRESSION, DUE TO NF-KAPPAB ACTIVATION, AND DNMT ACTIVATION, DUE TO NO PRODUCTION, IS RESPONSIBLE FOR ABERRANT METHYLATION INDUCTION IN HUMAN TISSUES.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
18 2435  48 EPIGENETIC SILENCING OF SFRP1 ACTIVATES THE CANONICAL WNT PATHWAY AND CONTRIBUTES TO INCREASED CELL GROWTH AND PROLIFERATION IN HEPATOCELLULAR CARCINOMA. THE WNT PATHWAY IS A KEY REGULATOR OF EMBRYONIC DEVELOPMENT AND STEM CELLS, AND ITS ABERRANT ACTIVATION IS ASSOCIATED WITH HUMAN MALIGNANCIES, MOST NOTABLY HEPATOCELLULAR CARCINOMA (HCC). EPIGENETIC DEREGULATION OF THE GENES ENCODING THE SECRETED FRIZZLED-RELATED PROTEINS (SFRPS), THE WNT SIGNALLING ANTAGONISTS, HAS BEEN LINKED WITH ABERRANT HYPERACTIVATION OF THE WNT SIGNALLING IN HCC CELLS; HOWEVER, THE PRECISE UNDERLYING MECHANISM REMAINS ELUSIVE. WE INVESTIGATED THE METHYLATION PROFILES OF WNT ANTAGONISTS IN LIVER SAMPLES OF DIFFERENT STAGES OF HCC DEVELOPMENT AND LIVER CANCER CELL LINES AND STUDIED THE FUNCTIONAL IMPACT OF ABERRANT EPIGENETIC SILENCING OF SFRPS ON THE CANONICAL WNT PATHWAY AND CELL VIABILITY. WE FOUND THAT THE SFRP1 GENE ENCODING THE SUBUNIT IS A FREQUENT TARGET OF ABERRANT DNA HYPERMETHYLATION AND SILENCING IN HCC TUMOURS, WHEREAS OTHER EXTRACELLULAR WNT ANTAGONISTS, WIF1 AND DKK3, EXHIBITED NO METHYLATION IN TUMOUR CELLS, CONSISTENT WITH THE NOTION THAT ABERRANT METHYLATION EVENTS IN CANCER CELLS ARE NON-RANDOMLY DISTRIBUTED AMONG THE GENES AND THAT THERE IS A STRONG PREFERENCE FOR HYPERMETHYLATION OF SPECIFIC GENES IN HCC. IN ADDITION, BY COMPARING SFRP1 METHYLATION STATUS IN HCC TUMOURS WITH NORMAL, CIRRHOTIC AND CHRONIC HEPATITIS LIVER TISSUES, WE IDENTIFIED SFRP1 GENE AS A POTENTIAL EARLY MARKER OF HCC. THE RESTORATION OF SFRP1 EXPRESSION IN CANCER CELLS BY ECTOPIC EXPRESSION INHIBITED WNT ACTIVITY ACCOMPANIED WITH DESTABILIZATION OF BETA-CATENIN AND DOWNREGULATION OF C-MYC AND CYCLIN D1, THE KNOWN DOWNSTREAM TARGETS OF WNT PATHWAY. IMPORTANTLY, RESTORING SFRP1 LEVELS IN CANCER CELLS INHIBITED CELL GROWTH AND INDUCED APOPTOTIC CELL DEATH. THIS STUDY SUPPORTS THE CRITICAL ROLE FOR SFRP1 SILENCING IN HEPATOCELLULAR CARCINOMA AND REINFORCES THE IMPORTANCE OF THE WNT ANTAGONISTS IN PREVENTING ONCOGENIC STABILIZATION OF BETA-CATENIN AND CHRONIC ACTIVATION OF THE CANONICAL WNT PATHWAY, SUGGESTING THAT SFRP1 MAY BE AN ATTRACTIVE TARGET FOR EARLY CANCER DETECTION AND THERAPEUTIC INTERVENTION.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
19 2682  40 EVALUATION OF SERUM LINE-1 HYPOMETHYLATION AS A PROGNOSTIC MARKER FOR HEPATOCELLULAR CARCINOMA. BACKGROUND AND STUDY AIMS: GLOBAL HYPOMETHYLATION IS ONE OF THE MOST CONSISTENT EPIGENETIC CHANGES IN CANCER. DEVELOPMENT OF HEPATOCELLULAR CARCINOMA (HCC) MUST BE UNDERSTOOD AS A MULTISTEP PROCESS WITH ACCUMULATION OF GENETIC AND EPIGENETIC ALTERATIONS. IN THE LAST DECADES, IN ADDITION TO GENETIC ALTERATIONS, EPIGENETIC CHANGES HAVE BEEN RECOGNIZED AS AN IMPORTANT AND ALTERNATIVE MECHANISM IN TUMOURIGENESIS. WE INVESTIGATED THE CLINICAL IMPLICATIONS OF GLOBAL HYPOMETHYLATION IN THE SERA OF PATIENTS WITH HEPATOCELLULAR CARCINOMA (HCC). PATIENTS AND METHODS: PCR WAS USED TO ASSESS THE METHYLATION STATUS OF LONG INTERSPERSED NUCLEAR ELEMENT TYPE 1 (LINE-1) REPETITIVE SEQUENCES IN GENOMIC DNA DERIVED FROM SERA OF 50 PATIENTS WITH HCC, 20 PATIENTS WITH CIRRHOSIS, 20 PATIENTS WITH CHRONIC HEPATITIS C AND 10 HEALTHY SUBJECTS. RESULTS: SERUM GENOME HYPOMETHYLATION WAS SIGNIFICANTLY INCREASED IN PATIENTS WITH HCC (P<0.001). THE LEVELS OF SERUM LINE-1 HYPOMETHYLATION AT INITIAL PRESENTATION CORRELATED SIGNIFICANTLY WITH TUMOUR SIZE, TUMOUR NUMBER AND ALPHA-FOETOPROTEIN LEVEL. MOREOVER HIGH SERUM LINE-1 HYPOMETHYLATION CORRELATES SIGNIFICANTLY WITH POOR SURVIVAL. CONCLUSION: SERUM LINE-1 HYPOMETHYLATION MAY SERVE AS A PROGNOSTIC MARKER FOR PATIENTS WITH HCC.	2011	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
20 6488  55 TP53 R72P POLYMORPHISM MODULATES DNA METHYLATION IN HEPATOCELLULAR CARCINOMA. BACKGROUND: HEPATOCELLULAR CARCINOMA (HCC) IS CHARACTERIZED BY WIDESPREAD EPIDEMIOLOGICAL AND MOLECULAR HETEROGENEITY. PREVIOUS WORK SHOWED THAT IN THE WESTERN PART OF NORTH AFRICA, A REGION OF LOW INCIDENCE OF HCC, MUTATIONS ARE SCARCE FOR THIS TUMOR TYPE. AS EPIGENETIC CHANGES ARE CONSIDERED POSSIBLE SURROGATES TO MUTATIONS IN HUMAN CANCERS, WE DECIDED, THUS, TO CHARACTERIZE DNA METHYLATION IN HCC FROM NORTH-AFRICAN PATIENTS. METHODS: A SET OF 11 LOCI WAS INVESTIGATED IN A SERIES OF 45 TUMOR SPECIMENS USING METHYLATION-SPECIFIC AND COMBINED-BISULFITE RESTRICTION ASSAY PCR. RESULTS OBTAINED ON CLINICAL SAMPLES WERE SUBSEQUENTLY VALIDATED IN LIVER CANCER CELL LINES. RESULTS: DNA METHYLATION AT TUMOR SUPPRESSOR LOCI IS SIGNIFICANTLY HIGHER IN SAMPLES DISPLAYING CHROMOSOME INSTABILITY. MORE IMPORTANTLY, DNA METHYLATION WAS SIGNIFICANTLY HIGHER IN ARG/ARG WHEN COMPARED TO PRO/PRO GENOTYPE CARRIERS AT CODON 72 RS1042522 OF TP53 (65% VS 20% METHYLATED LOCI, P = 0.0006), A POLYMORPHISM ALREADY KNOWN TO AFFECT SOMATIC MUTATION RATE IN HUMAN CARCINOMAS. IN VITRO EXPERIMENTS IN CELL LINES INDICATED THAT ENZYMES CONTROLLING DNA METHYLATION WERE DIFFERENTIALLY REGULATED BY CODON 72 ARG OR PRO ISOFORMS OF P53. FURTHERMORE, THE ARG72-CARRYING VERSION OF P53 WAS SHOWN TO RE-METHYLATE DNA MORE RAPIDLY THAN THE PRO-HARBORING ISOFORM. FINALLY, PRO-CARRYING CELL LINES WERE SHOWN TO BE SIGNIFICANTLY MORE RESISTANT TO DECITABINE TREATMENT (TWO-FOLD, P = 0.005). CONCLUSIONS: OUR DATA SUGGEST THAT ARG72PRO POLYMORPHISM IN A WT P53 CONTEXT MAY ACT AS A PRIMARY DRIVER OF EPIGENETIC CHANGES IN HCC. IT SUGGESTS, IN ADDITION, THAT RS1042522 GENOTYPE MAY PREDICT SENSITIVITY TO EPIGENETIC-TARGETED THERAPY. THIS MODEL OF LIVER TUMORIGENESIS THAT ASSOCIATES LOW PENETRANCE GENETIC PREDISPOSITION TO EPIGENETIC CHANGES EMERGES FROM A REGION OF LOW HCC INCIDENCE AND IT MAY, THEREFORE, APPLY ESSENTIALLY TO POPULATION LIVING IN SIMILAR AREAS. SURVEYS ON POPULATIONS SUBMITTED TO HIGHLY MUTAGENIC CONDITIONS AS PERINATALLY-ACQUIRED CHRONIC HEPATITIS B OR AFLATOXIN B1 EXPOSURE REMAINED TO BE CONDUCTED TO VALIDATE OUR OBSERVATIONS AS A GENERAL MODEL.	2015