1 5844 136 STUDY OF PROMOTER HYPOMETHYLATION PROFILES OF RAS ONCOGENES IN HEPATOCELLULAR CARCINOMA DERIVED FROM HEPATITIS C VIRUS GENOTYPE 3A IN PAKISTANI POPULATION. EPIGENETIC MODIFICATIONS SUCH AS DNA METHYLATION CONTRIBUTE TO PROGRESSION OF HEPATITIS C VIRUS (HCV) INFECTION TO LIFE-THREATENING HEPATOCELLULAR CARCINOMA (HCC) BY PROMOTING THE SILENCING OF TUMOR SUPPRESSOR GENES THROUGH DNA HYPERMETHYLATION AND BY CAUSING GENOMIC INSTABILITY THROUGH GLOBAL HYPOMETHYLATION. HOWEVER FEW STUDIES HAVE ADDRESSED THE PROMOTER REGION HYPOMETHYLATION STATUS OF THE ONCOGENES INVOLVED IN HCV DERIVED HCC. IN THIS STUDY, WE ANALYZED THE PROMOTER REGION METHYLATION PATTERN OF RAS ONCOGENES (HRAS, KRAS, AND NRAS) USING METHYLATION-SPECIFIC PCR FOR 50 CHRONIC HCV PATIENTS INFECTED WITH GENOTYPE 3A (27 HCC PATIENTS AND 23 CONTROL NON-HCC PATIENTS). METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION ANALYSIS REVEALED THAT THE NRAS ONCOGENE PROMOTER (P = .0025) WAS SIGNIFICANTLY HYPOMETHYLATED IN HCC PATIENTS COMPARED TO THE NON-HCC PATIENTS SUGGESTING ITS CONTRIBUTION TO THE PROGRESSION OF HCV TOWARDS HCC. TO IDENTIFY THE AGENT FOR ALTERATION IN THE RAS ONCOGENE EXPRESSION, 7 HCV GENES WERE EXPRESSED IN THE HUH-7 CELL LINE FOLLOWED BY MEASUREMENT OF THE NRAS EXPRESSION LEVEL IN HUH-7 BY A QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION. AN INCREASE IN THE MESSENGER RNA LEVEL OF THE NRAS GENE WAS DETECTED WHEN HUH-7 WERE TRANSFECTED WITH CORE, NS5A, AND NS2 GENES. OUR FINDINGS SUGGEST THE INVOLVEMENT OF NRAS ONCOGENE IN THE PATHOGENESIS OF HCV3A DERIVED HCC IN PAKISTANI POPULATION AND ALSO IDENTIFIES THE HCV GENES RESPONSIBLE FOR ITS ENHANCED EXPRESSION. OUR STUDY RAISES THE HYPOTHESIS THAT A SINGLE HCV GENE MAY INCREASE THE CHANCES OF MALIGNANCY. THEREFORE, OUR STUDY MAY HAVE IDENTIFIED A USEFUL EPIGENETIC BIOMARKER OF HCC PROGRESSION IN HCV PATIENTS AND MAY HELP TO DEVELOP NOVEL DIAGNOSTIC TOOLS.	2018	
                                                                                                                                                                                                                                                                                                                                    
2 6488  43 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	

3 6645  39 UP-REGULATION OF DBPA MRNA IN HEPATOCELLULAR CARCINOMA ASSOCIATED WITH METABOLIC SYNDROME. PURPOSE: METABOLIC SYNDROME (MS) IS A GROUP OF RECOGNIZED RISK FACTORS FOR THE DEVELOPMENT OF HEPATOCELLULAR CARCINOMA (HCC) IN PATIENTS WITH CHRONIC LIVER DISEASE. THE AIM OF THIS STUDY WAS TO ANALYZE THE CLINICOPATHOLOGICAL CHARACTERISTICS OF HCC PATIENTS WITH MS AND THE RISK FACTORS FOR RECURRENCE. ALSO, THE AIM WAS TO INVESTIGATE THE COLD SHOCK PROTEIN: DNA-BINDING PROTEIN A (DBPA) EXPRESSION IN HCC PATIENTS WITH MS. METHODS: A TOTAL OF 243 PATIENTS WHO UNDERWENT CURATIVE RESECTIONS FOR HCC WERE CLASSIFIED INTO TWO GROUPS. DBPA EXPRESSION WAS INVESTIGATED IN 66 HCC PATIENTS WITH MS AND IN 30 PATIENTS WITHOUT MS BY USING REAL-TIME RT-PCR. PROMOTER METHYLATION STATUS WAS EXAMINED BY USING MS-PCR. RESULTS: THE INCIDENCE OF METABOLIC FACTORS AFFECT THE HCC SIGNIFICANTLY HIGHER IN NON-B NON-C PATIENTS THAN IN HEPATITIS B VIRUS (HBV) OR HEPATITIS C VIRUS (HCV) PATIENTS (P < 0.001). UNIVARIATE ANALYSIS OF HCC PATIENTS WITH MS RECURRENCE REVEALED ASPARTATE AMINO TRANSFERASE (AST), MULTIPLE TUMORS, LIVER DAMAGE, HEPATIC VEIN INVASION, ADVANCED CANCER STAGES (P < 0.01), ALPHA-FETOPROTEIN (AFP) AND DIABETES MELLITUS TYPE II (P < 0.05) AS RISK FACTORS. MULTIVARIATE ANALYSIS, AST, MULTIPLE TUMORS, AND HEPATIC VEIN INVASION (P < 0.01) WERE IDENTIFIED AS INDEPENDENT FACTORS FOR THE RECURRENCE. DBPA MRNA WAS HIGHER IN PATIENTS WITH MS THAN IN THOSE WITHOUT MS (P = 0.016), AND IT WAS MOSTLY UPREGULATED IN NON-B NON-C HCC PATIENTS WITH MS THAN IN NON-B NON-C HCC PATIENTS WITHOUT HBV OR HCV. ESPECIALLY, IN HCC PATIENTS WITH DIABETES MELLITUS TYPE II, THE MRNA AND PROTEIN LEVELS WERE HIGHLY UPREGULATED. THE DBPA EXPRESSION WAS REGULATED BY PROMOTER METHYLATION STATUS (P < 0.05). CONCLUSIONS: THIS STUDY IDENTIFIES THAT DBPA MAY ACCELERATE THE HEPATOCARCINOGENESIS IN HCC PATIENTS WITH MS VIA INFLAMMATION-INDUCED AND OXIDATIVE STRESS PATHWAYS. THE DEMETHYLATION-RELATED EPIGENETIC ACTIVATION MAY BE ONE OF THE REGULATING FACTORS FOR HCC PATIENTS WITH MS.	2013	
                                                                                                                                                                      
4 2234  38 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
5 3248  36 HEPATITIS B VIRUS GENOME ASYMMETRY IN HEPATOCELLULAR CARCINOMA. BACKGROUND: THE ASSOCIATION BETWEEN HEPATITIS B VIRUS (HBV) MUTATIONS AND HEPATOCARCINOGENESIS WERE REPORTED IN THE LITERATURE. PREFERENCE FOR G OVER C IN THE LEADING DNA STRAND HAS BEEN REPORTED TO ACCOUNT FOR THE ASYMMETRY IN NUCLEOTIDE (NT) COMPOSITION. THE AIM OF THIS STUDY WAS TO ANALYZE THE COMPLETE GENOME SEQUENCE AND COMPOSITIONAL ASYMMETRY OF HBV IN DIFFERENT STAGES OF HEPATITIS B. METHODS: FULL GENOME SEQUENCING OF 24 PATIENTS WITH CHRONIC HEPATITIS B, SOME OF WHOM ALSO HAD CIRRHOSIS AND HEPATOCELLULAR CARCINOMA (HCC) WAS PERFORMED. MUTATIONS ANALYSIS WAS IMPLEMENTED IN A COMPARISON WITH A HBV GENOTYPE D REFERENCE FROM AN INTERNATIONAL DNA DATABASE. CPGPROD, A WEB-BASED APPLICATION, WAS USED TO EVALUATE CG CONTENT AND PREDICT CPG ISLANDS. RESULTS: ALL STRAINS WERE 3182 BASE PAIRS (BP) IN LENGTH, EXCEPT FOR TWO CASES OF HCC IN WHICH 9 AND 21 NT, RESPECTIVELY, WERE DELETED IN PRES2. THE GENETIC RELATEDNESS OF THESE ISOLATES WAS 97%-100%. THERE WERE COMMON CPG-RICH REGIONS IN ALL 24 ISOLATED FULL GENOME SEQUENCES, HOWEVER A STRONG NEGATIVE GC SKEW FOR FORMING A CPG ISLAND IN THE MINUS STRAND WERE EXHIBITED IN OVERLAP WITH ENHANCER I IN THREE HCC PATIENTS, A CIRRHOTIC PATIENT AND THREE WITH CHRONIC HEPATITIS. CONCLUSION: THE HIGH PERCENTAGE OF SEQUENCE IDENTITY BETWEEN HBV ISOLATES IN OUR PATIENTS DEMONSTRATES THAT GENOMIC FACTORS, EXCEPT FOR GENOTYPE, ARE INVOLVED IN HEPATOCARCINOGENESIS. VARIATIONS IN GC CONTENT WHICH WERE CAUSED BY A DIFFERENT SPECTRUM OF MUTATIONS MAY AFFECT DNA COMPOSITIONAL ASYMMETRY AND EPIGENETIC MODIFICATION OF HBV DNA IN HCC.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
6 3307  35 HIGH-RESOLUTION GENOMIC PROFILING OF LIVER CANCER LINKS ETIOLOGY WITH MUTATION AND EPIGENETIC SIGNATURES. BACKGROUND & AIMS: HEPATOCELLULAR CARCINOMA (HCC) IS A MODEL OF A DIVERSE SPECTRUM OF CANCERS BECAUSE IT IS INDUCED BY WELL-KNOWN ETIOLOGIES, MAINLY HEPATITIS C VIRUS (HCV) AND HEPATITIS B VIRUS. HERE, WE AIMED TO IDENTIFY HCV-SPECIFIC MUTATIONAL SIGNATURES AND EXPLORED THE LINK BETWEEN THE HCV-RELATED REGIONAL VARIATION IN MUTATIONS RATES AND HCV-INDUCED ALTERATIONS IN GENOME-WIDE CHROMATIN ORGANIZATION. METHODS: TO IDENTIFY AN HCV-SPECIFIC MUTATIONAL SIGNATURE IN HCC, WE PERFORMED HIGH-RESOLUTION TARGETED SEQUENCING TO DETECT PASSENGER MUTATIONS ON 64 HCC SAMPLES FROM 3 ETIOLOGY GROUPS: HEPATITIS B VIRUS, HCV, OR OTHER. TO EXPLORE THE LINK BETWEEN THE GENOMIC SIGNATURE AND GENOME-WIDE CHROMATIN ORGANIZATION WE PERFORMED CHROMATIN IMMUNOPRECIPITATION SEQUENCING FOR THE TRANSCRIPTIONALLY PERMISSIVE H3K4ME3, H3K9AC, AND SUPPRESSIVE H3K9ME3 MODIFICATIONS AFTER HCV INFECTION. RESULTS: REGIONAL VARIATION IN MUTATION RATE ANALYSIS SHOWED SIGNIFICANT ETIOLOGY-DEPENDENT REGIONAL MUTATION RATES IN 12 GENES: LRP2, KRT84, TMEM132B, DOCK2, DMD, INADL, JAK2, DNAH6, MTMR9, ATM, SLX4, AND ARSD. WE FOUND AN ENRICHMENT OF C->T TRANSVERSION MUTATIONS IN THE HCV-ASSOCIATED HCC CASES. FURTHERMORE, THESE CASES SHOWED REGIONAL VARIATION IN MUTATION RATES ASSOCIATED WITH GENOMIC INTERVALS IN WHICH HCV INFECTION DICTATED EPIGENETIC ALTERATIONS. THIS SIGNATURE MAY BE RELATED TO THE HCV-INDUCED DECREASED EXPRESSION OF GENES ENCODING KEY ENZYMES IN THE BASE EXCISION REPAIR PATHWAY. CONCLUSIONS: WE IDENTIFIED NOVEL DISTINCT HCV ETIOLOGY-DEPENDENT MUTATION SIGNATURES IN HCC ASSOCIATED WITH HCV-INDUCED ALTERATIONS IN HISTONE MODIFICATION. THIS STUDY PRESENTS A LINK BETWEEN CANCER-CAUSING MUTAGENESIS AND THE INCREASED PREDISPOSITION TO LIVER CANCER IN CHRONIC HCV-INFECTED INDIVIDUALS, AND UNVEILS NOVEL ETIOLOGY-SPECIFIC MECHANISMS LEADING TO HCC AND CANCER IN GENERAL.	2023	
                                                                                                                                                                                                                                                        
7 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
8 2258  32 EPIGENETIC PRIMING IN CHRONIC LIVER DISEASE IMPACTS THE TRANSCRIPTIONAL AND GENETIC LANDSCAPES OF HEPATOCELLULAR CARCINOMA. HEPATOCELLULAR CARCINOMAS (HCCS) USUALLY ARISE FROM CHRONIC LIVER DISEASE (CLD). PRECANCEROUS CELLS IN CHRONICALLY INFLAMED ENVIRONMENTS MAY BE 'EPIGENETICALLY PRIMED', SENSITISING THEM TO ONCOGENIC TRANSFORMATION. WE INVESTIGATED WHETHER EPIGENETIC PRIMING IN CLD MAY AFFECT HCC OUTCOMES BY INFLUENCING THE GENOMIC AND TRANSCRIPTOMIC LANDSCAPES OF HCC. ANALYSIS OF DNA METHYLATION ARRAYS FROM 10 PAIRED CLD-HCC IDENTIFIED 339 SHARED DYSREGULATED CPG SITES AND 18 SHARED DIFFERENTIALLY METHYLATED REGIONS COMPARED WITH HEALTHY LIVERS. THESE REGIONS WERE ASSOCIATED WITH DYSREGULATED EXPRESSION OF GENES WITH RELEVANCE IN HCC, INCLUDING UBIQUITIN D (UBD), CYTOCHROME P450 FAMILY 2 SUBFAMILY C MEMBER 19 (CYP2C19) AND O-6-METHYLGUANINE-DNA METHYLTRANSFERASE (MGMT). METHYLATION CHANGES WERE RECAPITULATED IN AN INDEPENDENT COHORT OF NINE PAIRED CLD-HCC. HIGH CLD METHYLATION SCORE, DEFINED USING THE 124 DYSREGULATED CPGS IN CLD AND HCC IN BOTH COHORTS, WAS ASSOCIATED WITH POOR SURVIVAL, INCREASED SOMATIC GENETIC ALTERATIONS AND TP53 MUTATIONS IN TWO INDEPENDENT HCC COHORTS. ONCOGENIC TRANSCRIPTIONAL AND METHYLATION DYSREGULATION IS EVIDENT IN CLD AND COMPOUNDED IN HCC. EPIGENETIC PRIMING IN CLD SCULPTS THE TRANSCRIPTIONAL LANDSCAPE OF HCC AND CREATES AN ENVIRONMENT FAVOURING THE ACQUISITION OF GENETIC ALTERATIONS, SUGGESTING THAT THE EXTENT OF EPIGENETIC PRIMING IN CLD COULD INFLUENCE DISEASE OUTCOME.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
9 1587  36 DNA METHYLATION PROFILING IDENTIFIES NOVEL MARKERS OF PROGRESSION IN HEPATITIS B-RELATED CHRONIC LIVER DISEASE. BACKGROUND: CHRONIC HEPATITIS B INFECTION IS CHARACTERIZED BY HEPATIC IMMUNE AND INFLAMMATORY RESPONSE WITH CONSIDERABLE VARIATION IN THE RATES OF PROGRESSION TO CIRRHOSIS. GENETIC VARIANTS AND ENVIRONMENTAL CUES INFLUENCE PREDISPOSITION TO THE DEVELOPMENT OF CHRONIC LIVER DISEASE; HOWEVER, IT REMAINS UNKNOWN IF ABERRANT DNA METHYLATION IS ASSOCIATED WITH FIBROSIS PROGRESSION IN CHRONIC HEPATITIS B. RESULTS: TO IDENTIFY EPIGENETIC MARKS ASSOCIATED WITH INFLAMMATORY AND FIBROTIC PROCESSES OF THE HEPATITIS B-INDUCED CHRONIC LIVER DISEASE, WE CARRIED OUT HEPATIC GENOME-WIDE METHYLATION PROFILING USING ILLUMINA INFINIUM BEADARRAYS COMPARING MILD AND SEVERE FIBROTIC DISEASE IN A DISCOVERY COHORT OF 29 PATIENTS. WE OBTAINED 310 DIFFERENTIALLY METHYLATED REGIONS AND SELECTED FOUR LOCI COMPRISING THREE GENES FROM THE TOP DIFFERENTIALLY METHYLATED REGIONS: HYPERMETHYLATION OF HOXA2 AND HDAC4 ALONG WITH HYPOMETHYLATION OF PPP1R18 WERE SIGNIFICANTLY LINKED TO SEVERE FIBROSIS. WE REPLICATED THE PROMINENT METHYLATION MARKS IN AN INDEPENDENT COHORT OF 102 PATIENTS BY BISULFITE MODIFICATION AND PYROSEQUENCING. THE TIMING AND CAUSAL RELATIONSHIP OF EPIGENETIC MODIFICATIONS WITH DISEASE SEVERITY WAS FURTHER INVESTIGATED USING A COHORT OF PATIENTS WITH SERIAL BIOPSIES. CONCLUSIONS: OUR FINDINGS SUGGEST A LINKAGE OF WIDESPREAD EPIGENETIC DYSREGULATION WITH DISEASE PROGRESSION IN CHRONIC HEPATITIS B INFECTION. CPG METHYLATION AT NOVEL GENES SHEDS LIGHT ON NEW MOLECULAR PATHWAYS, WHICH CAN BE POTENTIALLY EXPLOITED AS A BIOMARKER OR TARGETED TO ATTENUATE INFLAMMATION AND FIBROSIS.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
10 3897  40 LARGE-SCALE ANALYSIS OF THE GENETIC AND EPIGENETIC ALTERATIONS IN HEPATOCELLULAR CARCINOMA FROM SOUTHEAST CHINA. OUR KNOWLEDGE ABOUT MOLECULAR ALTERATIONS DURING HEPATOCARCINOGENESIS IS STILL FRAGMENTARY, DUE TO LACK OF COMPREHENSIVE GENETIC AND EPIGENETIC ANALYSES IN THE SAME SET OF HEPATOCELLULAR CARCINOMAS (HCCS). IN THIS STUDY, WE CONDUCTED A LARGE-SCALE ANALYSIS, INCLUDING MUTATION SCREENING IN 50 GENES AND METHYLATION ASSAYS IN THREE GENES IN 54 PAIRS OF HCCS AND THEIR NEIGHBORING NON-CANCEROUS TISSUES. ALL SAMPLES WERE COLLECTED FROM THE RESIDENTS IN SOUTHEAST CHINA. WE FOUND HBV INFECTION AND CHRONIC HEPATITIS/CIRRHOSIS IN 83.3% AND 98.1% OF THE CASES, RESPECTIVELY. MUTATIONS WERE IDENTIFIED IN 18 OUT OF 54 (33.3%) SAMPLES, WITH P53 ALTERATIONS IN 14 CASES AND BETA-CATENIN MUTATIONS IN FOUR TUMORS. NO MUTATIONS WERE IDENTIFIED IN THE NEIGHBORING TISSUES. INTERESTINGLY, 9 OUT OF 14 (64.3%) TUMORS CARRYING P53 MUTATIONS DISPLAYED SUBSTITUTION OF SERINE BY ARGININE AT CODON 249, A CHARACTERISTIC CHANGE BELIEVED TO BE INDUCED BY AFLATOXIN-B1. FURTHERMORE, P53 MUTATION WAS SIGNIFICANTLY ASSOCIATED WITH SHORTER RECURRENCE-FREE SURVIVAL (P=0.004). THE RESULTS ALSO REVEALED ABERRANT METHYLATION IN TWO OR MORE GENES IN AS HIGH AS 90% OF TUMORS AND 40% OF ADJACENT TISSUES. THE FREQUENCY OF RASSF1A HYPERMETHYLATION WAS MUCH HIGHER THAN THAT OF P16INK4A AND HAI2 IN BOTH HCC AND NEIGHBORING TISSUES, INDICATING THAT DEREGULATION OF RASSF1A MAY PRECEDE THE OTHER TWO GENES. THESE DATA SUGGEST THAT ABERRANT METHYLATION OCCURS BEFORE MUTATION AND IS AN EARLY EVENT IN THE DEVELOPMENT OF THIS SET OF HCC. OUR FINDINGS HIGHLIGHT P53 AS A PROGNOSTIC FACTOR OF HCC AND RASSF1A AS A POTENTIAL TARGET IN PREVENTING MALIGNANT TRANSFORMATION OF HEPATOCYTES.	2008	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
11 1342  48 DETECTING ABNORMAL METHYLATION OF TUMOR SUPPRESSOR GENES GSTP1, P16, RIZ1, AND RASSF1A IN HEPATOCELLULAR CARCINOMA AND ITS CLINICAL SIGNIFICANCE. HEPATOCELLULAR CARCINOMA (HCC) HAS A HIGH RATE OF MORTALITY. FURTHER STUDIES INTO EPIGENETIC CHANGES IN HCC, PARTICULARLY THE ABNORMAL METHYLATION OF TUMOR SUPPRESSOR GENES (TSGS), ARE REQUIRED, SINCE THESE CHANGES MAY PROVIDE NOVEL BIOMARKERS FOR EARLY SCREENING AND DIAGNOSIS OF HCC. BY USING METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (MSP), THE PRESENT STUDY DETECTED THE METHYLATION STATUS IN THE PROMOTER REGION OF 4 CANDIDATE TSGS, GSTP1, P16, RIZ1, AND RASSF1A, RESPECTIVELY, IN 35 PAIRED HCC AND TUMOR-ADJACENT LIVER TISSUES IN ADDITION TO 20 NORMAL LIVER TISSUES. THEIR EFFECT ON THE INITIATION AND PROGRESSION OF HCC WAS ALSO INVESTIGATED BY ANALYZING THE CLINICOPATHOLOGICAL DATA. THE RESULTS OF THE PRESENT STUDY REVEALED THAT THE METHYLATION LEVEL OF RIZ1 AND GSTP1 GENES IN HCC WAS SIGNIFICANTLY INCREASED COMPARED WITH THAT IN THE ADJACENT TISSUES (P<0.01) AND THE NORMAL LIVER TISSUES (P<0.01). THE METHYLATION FREQUENCY OF P16 AND RASSF1A GENES WAS NOT SIGNIFICANTLY INCREASED COMPARED WITH THAT OBSERVED IN THE ADJACENT TISSUES (P>0.05) BUT WAS SIGNIFICANTLY INCREASED COMPARED WITH THE NORMAL TISSUES (P<0.01). IN HCC TISSUES, THE METHYLATION FREQUENCY OF THE GSTP1 GENE IN TUMORS WITH CAPSULAR INVASION WAS SIGNIFICANTLY INCREASED COMPARED WITH THAT IN TUMORS WITHOUT CAPSULAR INVASION (P<0.05). THE METHYLATION FREQUENCY OF P16 GENE IN HEPATITIS B SURFACE ANTIGEN (HBSAG)-POSITIVE HCC PATIENTS WAS SIGNIFICANTLY INCREASED COMPARED WITH THAT IN HBSAG-NEGATIVE PATIENTS (P<0.05). THE METHYLATION STATUS OF RIZ1 AND RASSF1A GENES WAS NOT SIGNIFICANTLY CORRELATED WITH THE CLINICOPATHOLOGICAL DATA (P>0.05). PREVIOUS STUDIES HAVE DEMONSTRATED THAT THE METHYLATION STATUS OF RIZ1 AND GSTP1 GENES IS HCC-SPECIFIC, AND THUS MAY BE USED AS A BIOMARKER TO ASSIST THE CLINICAL DIAGNOSIS OF HCC. WHILE THE METHYLATION OF GSTP1 GENE PROMOTER MAY ASSOCIATE WITH THE INVASIVENESS OF HCC, CHRONIC HEPATITIS B VIRUS INFECTION MAY BE THE CAUSE OF METHYLATION-INDUCED P16 INACTIVATION.	2015	
                                                                                    
12 3392  36 HOST AND VIRAL GENETIC VARIATION IN HBV-RELATED HEPATOCELLULAR CARCINOMA. HEPATOCELLULAR CARCINOMA (HCC) IS THE FIFTH MOST COMMON CANCER IN MEN AND THE SECOND LEADING CAUSE OF CANCER DEATHS GLOBALLY. THE HIGH PREVALENCE OF HCC IS DUE IN PART TO THE HIGH PREVALENCE OF CHRONIC HBV INFECTION AND THE HIGH MORTALITY RATE IS DUE TO THE LACK OF BIOMARKERS FOR EARLY DETECTION AND LIMITED TREATMENT OPTIONS FOR LATE STAGE HCC. THE OBSERVED INDIVIDUAL VARIANCE IN DEVELOPMENT OF HCC IS ATTRIBUTABLE TO DIFFERENCES IN HBV GENOTYPE AND MUTATIONS, HOST PREDISPOSING GERMLINE GENETIC VARIATIONS, THE ACQUISITION OF TUMOR-SPECIFIC SOMATIC MUTATIONS, AS WELL AS ENVIRONMENTAL FACTORS. HBV GENOTYPE C AND MUTATIONS IN THE PRES, BASIC CORE PROMOTER (BCP) OR HBX REGIONS ARE ASSOCIATED WITH AN INCREASED RISK OF HCC. GENOME-WIDE ASSOCIATION STUDIES HAVE IDENTIFIED COMMON POLYMORPHISMS IN KIF1B, HLA-DQ, STAT4, AND GRIK1 WITH ALTERED RISK OF HBV-RELATED HCC. HBV INTEGRATION INTO GROWTH CONTROL GENES (SUCH AS TERT), PRO-ONCOGENIC GENES, OR TUMOR SUPPRESSOR GENES AND THE ONCOGENIC ACTIVITY OF TRUNCATED HBX PROMOTE HEPATOCARCINOGENESIS. SOMATIC MUTATIONS IN THE TERT PROMOTER AND CLASSIC CANCER SIGNALING PATHWAYS, INCLUDING WNT (CTNNB1), CELL CYCLE REGULATION (TP53), AND EPIGENETIC MODIFICATION (ARID2 AND MLL4) ARE FREQUENTLY DETECTED IN HEPATIC TUMOR TISSUES. THE IDENTIFICATION OF HBV AND HOST VARIATION ASSOCIATED WITH TUMOR INITIATION AND PROGRESSION HAS CLINICAL UTILITY FOR IMPROVING EARLY DIAGNOSIS AND PROGNOSIS; WHEREAS THE IDENTIFICATION OF SOMATIC MUTATIONS DRIVING TUMORIGENESIS HOLD PROMISE TO INFORM PRECISION TREATMENT FOR HCC PATIENTS.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
13 5349  41 RASSF1A AND DOK1 PROMOTER METHYLATION LEVELS IN HEPATOCELLULAR CARCINOMA, CIRRHOTIC AND NON-CIRRHOTIC LIVER, AND CORRELATION WITH LIVER CANCER IN BRAZILIAN PATIENTS. HEPATOCELLULAR CARCINOMA (HCC) IS THE SECOND MOST COMMON CAUSE OF CANCER MORTALITY WORLDWIDE. MOST CASES OF HCC ARE ASSOCIATED WITH CIRRHOSIS RELATED TO CHRONIC HEPATITIS B VIRUS OR HEPATITIS C VIRUS INFECTIONS. HYPERMETHYLATION OF PROMOTER REGIONS IS THE MAIN EPIGENETIC MECHANISM OF GENE SILENCING AND HAS BEEN INVOLVED IN HCC DEVELOPMENT. THE AIM OF THIS STUDY WAS TO DETERMINE WHETHER ABERRANT METHYLATION OF RASSF1A AND DOK1 GENE PROMOTERS IS ASSOCIATED WITH THE PROGRESSION OF LIVER DISEASE IN BRAZILIAN PATIENTS. METHYLATION LEVELS WERE MEASURED BY PYROSEQUENCING IN 41 (20 HCC, 9 CIRRHOTIC, AND 12 NON-CIRRHOTIC) LIVER TISSUE SAMPLES. MEAN RATES OF METHYLATION IN RASSF1A AND DOK1 WERE 16.2% AND 12.0% IN NON-CIRRHOTIC, 26.1% AND 19.6% IN CIRRHOTIC, AND 59.1% AND 56.0% IN HCC TISSUES, RESPECTIVELY, SHOWING A GRADUAL INCREASE ACCORDING TO THE PROGRESSION OF THE DISEASE, WITH SIGNIFICANTLY HIGHER LEVELS IN TUMOR TISSUES. IN ADDITION, HYPERMETHYLATION OF RASSF1A AND DOK1 WAS FOUND IN THE VAST MAJORITY (88%) OF THE HCC CASES. INTERESTINGLY, DOK1 METHYLATION LEVELS IN HCC SAMPLES WERE SIGNIFICANTLY HIGHER IN THE GROUP OF YOUNGER (<40 YEARS) PATIENTS, AND HIGHER IN MODERATELY DIFFERENTIATED THAN IN POORLY DIFFERENTIATED TUMORS (P < 0.05). OUR RESULTS REINFORCE THE HYPOTHESIS THAT HYPERMETHYLATION OF RASSF1A AND DOK1 CONTRIBUTES TO HEPATOCARCINOGENESIS AND IS ASSOCIATED TO CLINICOPATHOLOGICAL CHARACTERISTICS. RASSF1A AND DOK1 PROMOTER HYPERMETHYLATION MAY BE A VALUABLE BIOMARKER FOR EARLY DIAGNOSIS OF HCC AND A POTENTIAL MOLECULAR TARGET FOR EPIGENETIC-BASED THERAPY.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
14  155  31 ABERRANT METHYLATION OF POLO-LIKE KINASE CPG ISLANDS IN PLK4 HETEROZYGOUS MICE. BACKGROUND: HEPATOCELLULAR CARCINOMA (HCC), ONE OF THE MOST COMMON CANCERS WORLD-WIDE OCCURS TWICE AS OFTEN IN MEN COMPARED TO WOMEN. PREDISPOSING CONDITIONS SUCH AS ALCOHOLISM, CHRONIC VIRAL HEPATITIS, AFLATOXIN B1 INGESTION, AND CIRRHOSIS ALL CONTRIBUTE TO THE DEVELOPMENT OF HCC. METHODS: WE USED A COMBINATION OF METHYLATION SPECIFIC PCR AND BISULFITE SEQUENCING, QREAL-TIME PCR (QPCR), AND WESTERN BLOT ANALYSIS TO EXAMINE EPIGENETIC CHANGES FOR THE POLO-LIKE KINASES (PLKS) DURING THE DEVELOPMENT OF HEPATOCELLULAR CARCINOMA (HCC) IN PLK4 HETEROZYGOUS MICE AND MURINE EMBRYONIC FIBROBLASTS (MEFS). RESULTS: HERE WE REPORT THAT THE PROMOTER METHYLATION OF PLK4 CPG ISLANDS INCREASES WITH AGE, WAS MORE PREVALENT IN MALES AND THAT PLK4 EPIGENETIC MODIFICATION AND SUBSEQUENT DOWNREGULATION OF EXPRESSION WAS ASSOCIATED WITH THE DEVELOPMENT OF HCC IN PLK4 MUTANT MICE. INTERESTINGLY, THE OPPOSITE OCCURS WITH ANOTHER PLK FAMILY MEMBER, PLK1 WHICH WAS TYPICALLY HYPERMETHYLATED IN NORMAL LIVER TISSUE BUT BECAME HYPOMETHYLATED AND UPREGULATED IN LIVER TUMOURS. FURTHERMORE, UPON ALCOHOL EXPOSURE MURINE EMBRYONIC FIBROBLASTS EXHIBITED INCREASED PLK4 HYPERMETHYLATION AND DOWNREGULATION ALONG WITH INCREASED CENTROSOME NUMBERS AND MULTINUCLEATION. CONCLUSIONS: THESE RESULTS SUGGEST THAT ABERRANT PLK METHYLATION IS CORRELATED WITH THE DEVELOPMENT OF HCC IN MICE.	2011	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
15 1545  44 DNA METHYLATION IN LIVER TUMORIGENESIS IN FISH FROM THE ENVIRONMENT. THE LINK BETWEEN ENVIRONMENT, ALTERATION IN DNA METHYLATION AND CANCER HAS BEEN WELL ESTABLISHED IN HUMANS; YET, IT IS UNDER-STUDIED IN UNSEQUENCED NON-MODEL ORGANISMS. THE OCCURRENCE OF LIVER TUMORS IN THE FLATFISH DAB COLLECTED AT CERTAIN UK SAMPLING SITES EXCEEDS 20%, YET THE CAUSATIVE AGENTS AND THE MOLECULAR MECHANISMS OF TUMOR FORMATION ARE NOT KNOWN, ESPECIALLY REGARDING THE BALANCE BETWEEN EPIGENETIC AND GENETIC FACTORS. METHYLATED DNA IMMUNOPRECIPITATION (MEDIP) COMBINED WITH DE NOVO HIGH-THROUGHPUT DNA SEQUENCING WERE USED TO INVESTIGATE DNA METHYLATION CHANGES IN DAB HEPATOCELLULAR ADENOMA TUMORS FOR THE FIRST TIME IN AN UNSEQUENCED SPECIES. NOVEL CUSTOM-MADE DAB GENE EXPRESSION ARRAYS WERE DESIGNED AND USED TO DETERMINE THE RELATIONSHIP BETWEEN DNA METHYLATION AND GENE EXPRESSION. IN ADDITION, THE CONFIRMATORY TECHNIQUES OF BISULFITE SEQUENCING PCR (BSP) AND RT-PCR WERE APPLIED. GENES INVOLVED IN PATHWAYS RELATED TO CANCER, INCLUDING APOPTOSIS, WNT/BETA-CATENIN SIGNALING AND GENOMIC AND NON-GENOMIC ESTROGEN RESPONSES, WERE ALTERED BOTH IN METHYLATION AND TRANSCRIPTION. GLOBAL METHYLATION WAS STATISTICALLY SIGNIFICANTLY 1.8-FOLD REDUCED IN HEPATOCELLULAR ADENOMA AND NON-CANCEROUS SURROUNDING TISSUES COMPARED WITH LIVER FROM NON-CANCER BEARING DAB. BASED ON THE IDENTIFIED CHANGES AND CHEMICAL EXPOSURE DATA, OUR STUDY SUPPORTS THE EPIGENETIC MODEL OF CANCER. WE HYPOTHESIZE THAT CHRONIC EXPOSURE TO A MIXTURE OF ENVIRONMENTAL CONTAMINANTS CONTRIBUTES TO A GLOBAL HYPOMETHYLATION FOLLOWED BY FURTHER EPIGENETIC AND GENOMIC CHANGES. THE FINDINGS SUGGEST A LINK BETWEEN ENVIRONMENT, EPIGENETICS AND CANCER IN FISH TUMORS IN THE WILD AND SHOW THE UTILITY OF THIS METHODOLOGY FOR STUDIES IN NON-MODEL ORGANISMS.	2011	
                                                                                                                                                                                                                                                                                                                                                                                                                                 
16 1617  42 DNA METHYLTRANSFERASE EXPRESSION AND DNA METHYLATION IN HUMAN HEPATOCELLULAR CARCINOMA AND THEIR CLINICOPATHOLOGICAL CORRELATION. ABERRANT DNA METHYLATION ON CPG ISLANDS IS ONE OF THE MOST CONSISTENT EPIGENETIC CHANGES IN HUMAN CANCERS, AND THE METHYLATION PROCESS IS CATALYZED BY DNA METHYLTRANSFERASE (DNMT). WE EVALUATED I) THE MRNA LEVELS OF THREE DNMTS; DNMT1, DNMT3A AND DNMT3B, IN 25 HEPATOCELLULAR CARCINOMAS (HCCS), IN THEIR CORRESPONDING NON-CANCEROUS LIVER TISSUES AND IN 7 NORMAL LIVERS BY USING REAL-TIME REVERSE TRANSCRIPTASE-POLYMERASE CHAIN REACTION; II) NUCLEAR EXPRESSION OF DNMT1 AND DNMT3A PROTEINS IN THE HCCS BY IMMUNOHISTOCHEMISTRY, III) THE METHYLATION STATUS OF 5 GENES; P16, P15, E-CADHERIN, HIC-1 AND RASSF1A IN THE SAME TISSUES, AND IV) THE RELATIONSHIPS BETWEEN THE ABOVE RESULTS AND THE CLINICOPATHOLOGICAL CHARACTERISTICS, INCLUDING PROGNOSIS. THE DIFFERENCES IN MRNA EXPRESSION LEVELS FOR DNMT1, DNMT3A AND DNMT3B WERE STATISTICALLY SIGNIFICANT BETWEEN HCC AND NORMAL LIVERS (P<0.001), HCC AND CHRONIC HEPATITIS (P<0.001) AND HCC AND CIRRHOSIS (P<0.001). AN INCREASE IN MRNA EXPRESSION LEVELS OF >4-FOLD FOR DNMT3B IN HCCS WAS SIGNIFICANTLY ASSOCIATED WITH A POORER OVERALL SURVIVAL (P=0.027) AND SHORTER METASTASIS-FREE SURVIVAL (P=0.0299). A POORER RECURRENCE-FREE SURVIVAL WAS NOTED IN HCCS WITH A >4-FOLD INCREASE IN DNMT3A MRNA (P=0.0120). THE AVERAGE NUMBERS OF METHYLATED GENES WERE 0, 1.27, 1.38 AND 2.72 FOR NORMAL LIVERS, CHRONIC HEPATITIS, CIRRHOSIS AND HCCS, RESPECTIVELY, AND THIS PROGRESSIVE INCREASE FROM NORMAL LIVERS TO CHRONIC HEPATITIS/CIRRHOSIS THROUGH HCC MAY SUGGEST THAT TUMOR SUPPRESSOR GENE METHYLATION IS AN EARLY EVENT IN HEPATOCARCINOGENESIS. THESE RESULTS FIRST SUGGEST THAT HEPATOCARCINOGENESIS INVOLVES AN INCREASED EXPRESSION OF DNMT1, DNMT3A AND DNMT3B MRNA AND A PROGRESSIVE INCREASE IN THE NUMBER OF METHYLATED GENES FROM NORMAL LIVER, CHRONIC HEPATITIS/CIRRHOSIS TO HCC AND SECONDLY THAT AN INCREASE IN THE DNMT3A AND DNMT3B MRNA LEVELS IN HCCS RELATIVE TO THEIR NON-CANCEROUS TISSUES MAY BE A PREDICTOR OF POOR SURVIVAL.	2007	
                                                                                                                                      
17   59  34 A GENOME-WIDE SCREEN IDENTIFIES FREQUENTLY METHYLATED GENES IN HAEMATOLOGICAL AND EPITHELIAL CANCERS. BACKGROUND: GENETIC AS WELL AS EPIGENETIC ALTERATIONS ARE A HALLMARK OF BOTH EPITHELIAL AND HAEMATOLOGICAL MALIGNANCIES. HIGH THROUGHPUT SCREENS ARE REQUIRED TO IDENTIFY EPIGENETIC MARKERS THAT CAN BE USEFUL FOR DIAGNOSTIC AND PROGNOSTIC PURPOSES ACROSS MALIGNANCIES. RESULTS: HERE WE REPORT FOR THE FIRST TIME THE USE OF THE MIRA ASSAY (METHYLATED CPG ISLAND RECOVERY ASSAY) IN COMBINATION WITH GENOME-WIDE CPG ISLAND ARRAYS TO IDENTIFY EPIGENETIC MOLECULAR MARKERS IN CHILDHOOD ACUTE LYMPHOBLASTIC LEUKEMIA (ALL) ON A GENOME-WIDE SCALE. WE IDENTIFIED 30 GENES DEMONSTRATING METHYLATION FREQUENCIES OF > OR =25% IN CHILDHOOD ALL, NINE GENES SHOWED SIGNIFICANTLY DIFFERENT METHYLATION FREQUENCIES IN B VS T-ALL. FOR MAJORITY OF THE GENES EXPRESSION COULD BE RESTORED IN METHYLATED LEUKEMIA LINES AFTER TREATMENT WITH 5-AZADC. FORTY-FOUR PERCENT OF THE GENES REPRESENT TARGETS OF THE POLYCOMB COMPLEX. IN CHRONIC MYELOID LEUKEMIA (CML) TWO OF THE GENES, (TFAP2A AND EBF2), DEMONSTRATED INCREASED METHYLATION IN BLAST CRISIS COMPARED TO CHRONIC PHASE (P < 0.05). FURTHERMORE HYPERMETHYLATION OF AN AUTOPHAGY RELATED GENE ATG16L2 WAS ASSOCIATED WITH POORER PROGNOSIS IN TERMS OF MOLECULAR RESPONSE TO IMATINIB TREATMENT. LASTLY WE DEMONSTRATED THAT TEN OF THESE GENES WERE ALSO FREQUENTLY METHYLATED IN COMMON EPITHELIAL CANCERS. CONCLUSION: IN SUMMARY WE HAVE IDENTIFIED A LARGE NUMBER OF GENES SHOWING FREQUENT METHYLATION IN CHILDHOOD ALL, METHYLATION STATUS OF TWO OF THESE GENES IS ASSOCIATED WITH ADVANCED DISEASE IN CML AND METHYLATION STATUS OF ANOTHER GENE IS ASSOCIATED WITH PROGNOSIS. IN ADDITION A SUBSET OF THESE GENES MAY ACT AS EPIGENETIC MARKERS ACROSS HEMATOLOGICAL MALIGNANCIES AS WELL AS COMMON EPITHELIAL CANCERS.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                       
18 6707  35 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	
                                                                                                                                                                                                                                                                                                                                                                                   
19 6692  40 VARIABLE DNA METHYLATION PATTERNS ASSOCIATED WITH PROGRESSION OF DISEASE IN HEPATOCELLULAR CARCINOMAS. HEPATOCELLULAR CARCINOMA (HCC) MOST COMMONLY ARISES FROM CHRONIC INFLAMMATION DUE TO VIRAL INFECTION, AS A RESULT OF GENETIC AND EPIGENETIC ABNORMALITIES. A GLOBAL PICTURE OF EPIGENETIC CHANGES IN HCC IS LACKING. WE USED METHYLATED CPG ISLAND AMPLIFICATION MICROARRAYS (MCAMS) TO STUDY 6458 CPG ISLANDS IN HCC AND ADJACENT PRENEOPLASTIC TISSUES [CHRONIC HEPATITIS (CH) OR LIVER CIRRHOSIS (LC)] IN COMPARISON WITH NORMAL LIVER TISSUES WHERE NEITHER VIRAL INFECTION NOR HEPATITIS HAS EXISTED. MCAM IDENTIFIED 719 (11%) PROMINENT GENES OF HYPERMETHYLATION IN HCCS. HCCS ARISING FROM LC HAD SIGNIFICANTLY MORE METHYLATION THAN THOSE ARISING FROM CH (1249 GENES OR 19% VERSUS 444 GENES OR 7%, P < 0.05). THERE WERE FOUR PATTERNS OF ABERRANT METHYLATION: TYPE I (4%, E.G. MATRIX METALLOPROTEINASE 14) SHOWS A SUBSTANTIALLY HIGH METHYLATION LEVEL IN ADJACENT TISSUE AND DOES NOT INCREASE FURTHER IN CANCER. TYPE II (55%, E.G. RASSF1A) SHOWS PROGRESSIVELY INCREASING METHYLATION FROM ADJACENT TISSUE TO HCC. TYPE III (4%, E.G. GNA14) SHOWS DECREASED METHYLATION IN ADJACENT TISSUE BUT EITHER SIMILAR OR INCREASED METHYLATION IN HCC. TYPE IV (37%, E.G. CDKN2A) SHOWS LOW LEVELS OF METHYLATION IN NORMAL TISSUE AND ADJACENT TISSUE BUT HIGH LEVELS IN HCC. THESE DNA METHYLATION CHANGES WERE CONFIRMED BY QUANTITATIVE PYROSEQUENCING METHYLATION ANALYSIS IN REPRESENTATIVE 24 GENES AND WERE ANALYZED FOR CORRELATION WITH CLINICOPATHOLOGICAL PARAMETERS IN 38 PATIENTS. INTRIGUINGLY, METHYLATION IN THE TYPE IV GENES IS CHARACTERISTIC OF MODERATELY/POORLY DIFFERENTIATED CANCER. OUR GLOBAL EPIGENOME ANALYSIS REVEALS DISTINCT PATTERNS OF METHYLATION THAT ARE PROBABLY TO REPRESENT DIFFERENT PATHOPHYSIOLOGIC PROCESSES IN HCCS.	2008	
                                                                                                                                                                                                                                                                                                                                                                                                                         
20  412  41 ANALYSIS OF LONG NON-CODING RNA (LNCRNA) EXPRESSION IN HEPATITIS B PATIENTS. LONG NON-CODING RNAS (LNCRNAS) HAVE BEEN IMPLICATED IN NUMEROUS BIOLOGICAL PROCESSES, INCLUDING EPIGENETIC REGULATION, CELL-CYCLE CONTROL, AND TRANSCRIPTIONAL/TRANSLATIONAL REGULATION OF GENE EXPRESSION. DIFFERENTIAL EXPRESSION OF LNCRNAS AND DISRUPTION OF THE REGULATORY PROCESSES ARE RECOGNIZED AS CRITICAL STEPS IN CANCER DEVELOPMENT. THE ROLE OF LNCRNAS IN HEPATITIS B VIRUS (HBV) INFECTION IS NOT WELL UNDERSTOOD. HERE WE ANALYZED THE EXPRESSION OF 135 LNCRNAS IN PLASMA SAMPLES OF 82 HBV PATIENTS (CLASSIFIED AS CHRONIC PATIENTS, INACTIVE CARRIERS, OR RESOLVED PATIENTS) AT DIAGNOSIS AND AT 12 MONTHS OF TREATMENT IN RELATION TO CONTROL GROUP (81 HEALTHY VOLUNTEERS). WE ALSO INVESTIGATED THE EFFECT OF SMALL INTERFERING RNA (SIRNA)-MEDIATED SILENCING OF LINCRNA-SFMBT2 ON HBV-POSITIVE HUMAN LIVER CANCER CELL LINE. LNCRNA EXPRESSION WAS ANALYZED BY QUANTITATIVE REVERSE TRANSCRIPTION-POLYMERASE CHAIN REACTION (QRT-PCR). CHEMICALLY SYNTHESIZED SIRNAS WERE TRANSFECTED INTO THE CELL LINES USING LIPOFECTAMINE 2000 REAGENT (THERMO FISHER SCIENTIFIC). HBV DNA AND HBSAG AND HBEAG WERE DETECTED IN TRANSFECTED CULTURES BY REAL-TIME PCR AND ELISA, RESPECTIVELY, USING COMMERCIAL KITS. WE OBSERVED CHANGES IN LNCRNA EXPRESSION IN ALL THREE HBV GROUPS, COMPARED TO CONTROL GROUP. MOST NOTABLY, THE EXPRESSION OF ANTI-NOS2A, LINCRNA-SFMBT2, AND ZFHX2AS WAS SIGNIFICANTLY INCREASED AND EXPRESSION OF Y5 LNCRNA WAS DECREASED IN CHRONIC HBV PATIENTS. A DECREASED Y5 EXPRESSION AND INCREASED LINCRNA-SFMBT2 EXPRESSION WERE OBSERVED IN INACTIVE HBSAG CARRIERS. THE EXPRESSION OF HOTTIP, MEG9, AND PCAT-32 WAS INCREASED IN RESOLVED HBV PATIENTS, AND NO SIGNIFICANT CHANGE IN THE EXPRESSION OF Y5 WAS OBSERVED, COMPARED TO CONTROL GROUP. SIRNA-MEDIATED INHIBITION OF LINCRNA-SFMBT2 DECREASED THE LEVEL OF HBV DNA IN HUMAN LIVER CANCER CELLS. FURTHER RESEARCH IS NEEDED TO CONFIRM THE PROGNOSTIC AS WELL AS THERAPEUTIC ROLE OF THESE LNCRNAS IN HBV PATIENTS.	2018