1 1022 135 CIRCULAR RNA HSA_CIRC_0098181 INHIBITS METASTASIS IN HEPATOCELLULAR CARCINOMA BY ACTIVATING THE HIPPO SIGNALING PATHWAY VIA INTERACTION WITH EEF2. INTRODUCTION AND OBJECTIVES: THE DEVELOPMENT OF HEPATOCELLULAR CARCINOMA (HCC) IS A MULTI-STEP PROCESS THAT ACCUMULATES GENETIC AND EPIGENETIC ALTERATIONS, INCLUDING CHANGES IN CIRCULAR RNA (CIRCRNA). THIS STUDY AIMED TO UNDERSTAND THE ALTERATIONS IN CIRCRNA EXPRESSION IN HCC DEVELOPMENT AND METASTASIS AND TO EXPLORE THE BIOLOGICAL FUNCTIONS OF CIRCRNA. MATERIALS AND METHODS: TEN PAIRS OF ADJACENT CHRONIC HEPATITIS TISSUES AND HCC TISSUES FROM PATIENTS WITHOUT VENOUS METASTASES, AND TEN HCC TISSUES FROM PATIENTS WITH VENOUS METASTASES WERE ANALYZED USING HUMAN CIRCRNA MICROARRAYS. DIFFERENTIALLY EXPRESSED CIRCRNAS WERE THEN VALIDATED BY QUANTITATIVE REAL-TIME PCR. IN VITRO AND IN VIVO ASSAYS WERE PERFORMED TO ASSESS THE ROLES OF THE CIRCRNA IN HCC PROGRESSION. RNA PULL-DOWN ASSAY, MASS SPECTROMETRY ANALYSIS, AND RNA-BINDING PROTEIN IMMUNOPRECIPITATION WERE CONDUCTED TO EXPLORE THE PROTEIN PARTNERS OF THE CIRCRNA. RESULTS: CIRCRNA MICROARRAYS REVEALED THAT THE EXPRESSION PATTERNS OF CIRCRNAS ACROSS THE THREE GROUPS WERE SIGNIFICANTLY DIFFERENT. AMONG THESE, HSA_CIRC_0098181 WAS VALIDATED TO BE LOWLY EXPRESSED AND ASSOCIATED WITH POOR PROGNOSIS IN HCC PATIENTS. ECTOPIC EXPRESSION OF HSA_CIRC_0098181 DELAYED HCC METASTASIS IN VITRO AND IN VIVO. MECHANISTICALLY, HSA_CIRC_0098181 SEQUESTERED EUKARYOTIC TRANSLATION ELONGATION FACTOR 2 (EEF2) AND DISSOCIATED EEF2 FROM FILAMENTOUS ACTIN (F-ACTIN) TO PREVENT F-ACTIN FORMATION, WHICH BLOCKED ACTIVATION OF THE HIPPO SIGNALING PATHWAY. IN ADDITION, THE RNA BINDING PROTEIN QUAKING-5 BOUND DIRECTLY TO HSA_CIRC_0098181 AND INDUCED ITS BIOGENESIS. CONCLUSIONS: OUR STUDY REVEALS CHANGES IN CIRCRNA EXPRESSION FROM CHRONIC HEPATITIS, PRIMARY HCC, TO METASTATIC HCC. FURTHER, THE QKI5-HSA_CIRC_0098181-EEF2-HIPPO SIGNALING PATHWAY EXERTS A REGULATORY ROLE IN HCC.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
2 3752  42 INTEGRATED ANALYSIS OF CIRCRNAS AND MRNAS EXPRESSION PROFILE REVEALED THE INVOLVEMENT OF HSA_CIRC_0007919 IN THE PATHOGENESIS OF ULCERATIVE COLITIS. BACKGROUND: ULCERATIVE COLITIS (UC) IS CHARACTERIZED BY CHRONIC INFLAMMATION IN THE COLON AND EPIGENETIC FACTORS UNDERLYING THE OCCURRENCE. CIRCULAR RNAS (CIRCRNAS) HAVE BEEN UNDER INTENSIVE FOCUS DUE TO THE CIRCULAR CONSTRUCT AND GENE-REGULATING FUNCTIONS. HOWEVER, THE CHANGES AND ROLES OF CIRCRNAS IN UC REMAIN UNKNOWN. METHODS: MICROARRAYS WERE USED TO DETECT THE DIFFERENTIALLY EXPRESSED GENES, AND QUANTITATIVE REAL-TIME PCR WAS USED TO IDENTIFY THE CHANGES IN UC. IN SILICO ANALYSES WERE PERFORMED TO PREDICT THE FUNCTIONS OF CIRCRNAS AND MRNAS. IN VITRO, EPITHELIAL CELL LINES WERE STIMULATED BY PRO-INFLAMMATION EFFECTORS TO TEST THE ALTERATIONS IN CIRCRNAS. CIRCRNAS-MICRORNAS-MRNAS NETWORK CLARIFIED THE POTENTIAL MECHANISMS UNDERLYING CIRCRNAS IN UC. THE BINDING SITE BETWEEN HSA_CIRC_0007919 AND MIR-138 OR LET-7A WAS VERIFIED USING DUAL-LUCIFERASE ASSAY. RESULTS: A TOTAL OF 264 SIGNIFICANTLY DYSREGULATED CIRCRNAS AND 1869 DIFFERENTIALLY EXPRESSED MRNAS IN INFLAMED MUCOSA WERE COMPARED WITH THE NON-INFLAMED MUCOSA IN UC. HSA_CIRC_0004662 AND HSA_CIRC_0007919 WERE ALTERED LARGELY IN UC TISSUES. HSA_CIRC_0007919 WAS REDUCED PERSISTENTLY AFTER INFLAMMATORY TREATMENTS, AND IT WAS RELEVANT TO MAYO ENDOSCOPIC SUBSCORES AND THE EXPRESSION OF TIGHT JUNCTION MOLECULES. FINALLY, HSA_CIRC_0007919 COULD HARBOR MIR-138, AND LET-7A TO REGULATE THE TARGETED MRNAS EPC1 AND VIPR1. CONCLUSIONS: SEVERAL CIRCRNAS WERE DIFFERENTIALLY EXPRESSED IN UC. HSA_CIRC_0007919 IS RELATED TO CLINICAL CHARACTERISTICS AND EPITHELIAL INTEGRITY BY BINDING TO HSA-LET-7A, HSA-MIR-138 TO REGULATE THE TARGET GENES. CIRCRNAS, ESPECIALLY HSA_CIRC_0007919, ARE ASSOCIATED WITH THE PATHOGENESIS AND DEVELOPMENT OF UC, WITH POTENTIAL DIAGNOSTIC AND THERAPEUTIC IMPLICATIONS.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
3 1615  32 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
4 3504  45 IDENTIFICATION OF POTENTIALLY FUNCTIONAL CIRCRNAS AND PREDICTION OF CIRCRNA-MIRNA-MRNA REGULATORY NETWORK IN PERIODONTITIS: BRIDGING THE GAP BETWEEN BIOINFORMATICS AND CLINICAL NEEDS. BACKGROUND AND OBJECTIVE: PERIODONTITIS IS A MULTIFACTORIAL CHRONIC INFLAMMATORY DISEASE THAT CAN LEAD TO THE IRREVERSIBLE DESTRUCTION OF DENTAL SUPPORT TISSUES. AS AN EPIGENETIC FACTOR, THE EXPRESSION OF CIRCRNA IS TISSUE-DEPENDENT AND DISEASE-DEPENDENT. THIS STUDY AIMED TO IDENTIFY NOVEL PERIODONTITIS-ASSOCIATED CIRCRNAS AND PREDICT RELEVANT CIRCRNA-PERIODONTITIS REGULATORY NETWORK BY USING RECENTLY DEVELOPED BIOINFORMATIC TOOLS AND INTEGRATING SEQUENCING PROFILING WITH CLINICAL INFORMATION FOR GETTING A BETTER AND MORE THOROUGH IMAGE OF PERIODONTITIS PATHOGENESIS, FROM GENE TO CLINIC. MATERIAL AND METHODS: HIGH-THROUGHPUT SEQUENCING AND RT-QPCR WERE CONDUCTED TO IDENTIFY DIFFERENTIALLY EXPRESSED CIRCRNAS IN GINGIVAL TISSUES FROM PERIODONTITIS PATIENTS. THE RELATIONSHIP BETWEEN UPREGULATED CIRCRNAS EXPRESSION AND PROBING DEPTH (PD) WAS PERFORMED USING SPEARMAN'S CORRELATION ANALYSIS. BIOINFORMATIC ANALYSES INCLUDING GO ANALYSIS, CIRCRNA-DISEASE ASSOCIATION PREDICTION, AND CIRCRNA-MIRNA-MRNA NETWORK PREDICTION WERE PERFORMED TO CLARIFY POTENTIAL REGULATORY FUNCTIONS OF IDENTIFIED CIRCRNAS IN PERIODONTITIS. A RECEIVER-OPERATING CHARACTERISTIC (ROC) CURVE WAS ESTABLISHED TO ASSESS THE DIAGNOSTIC SIGNIFICANCE OF IDENTIFIED CIRCRNAS. RESULTS: HIGH-THROUGHPUT SEQUENCING IDENTIFIED 70 DIFFERENTIALLY EXPRESSED CIRCRNAS (68 UPREGULATED AND 2 DOWNREGULATED CIRCRNAS) IN HUMAN PERIODONTITIS (FOLD CHANGE >2.0 AND P < .05). THE TOP FIVE UPREGULATED CIRCRNAS WERE VALIDATED BY RT-QPCR THAT HAD STRONG ASSOCIATIONS WITH MULTIPLE HUMAN DISEASES, INCLUDING PERIODONTITIS. THE UPREGULATION OF CIRCRNAS WERE POSITIVELY CORRELATED WITH PD (R = .40-.69, P < .05, MODERATE). A CIRCRNA-MIRNA-MRNA NETWORK WITH THE TOP FIVE UPREGULATED CIRCRNAS, DIFFERENTIALLY EXPRESSED MRNAS, AND OVERLAPPED PREDICTED MIRNAS INDICATED POTENTIAL ROLES OF CIRCRNAS IN IMMUNE RESPONSE, CELL APOPTOSIS, MIGRATION, ADHESION, AND REACTION TO OXIDATIVE STRESS. THE ROC CURVE SHOWED THAT CIRCRNAS HAD POTENTIAL VALUE IN PERIODONTITIS DIAGNOSIS (AUC = 0.7321-0.8667, P < .05). CONCLUSION: CIRCRNA-DISEASE ASSOCIATIONS WERE PREDICTED BY ONLINE BIOINFORMATIC TOOLS. POSITIVE CORRELATION BETWEEN UPREGULATED CIRCRNAS, CIRCPTP4A2, CHR22:23101560-23135351+, CIRCARHGEF28, CIRCBARD1 AND CIRCRASA2, AND PD SUGGESTED FUNCTION OF CIRCRNAS IN PERIODONTITIS. NETWORK PREDICTION FURTHER FOCUSED ON DOWNSTREAM TARGETS REGULATED BY CIRCRNAS DURING PERIODONTITIS PATHOGENESIS.	2022	

5 2234  39 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
6 1131  39 COMPREHENSIVE CIRCULAR RNA EXPRESSION PROFILING WITH ASSOCIATED CERNA NETWORK REVEALS THEIR THERAPEUTIC POTENTIAL IN CHOLESTEATOMA. CHOLESTEATOMA IS A CHRONIC DISEASE THAT PATHOLOGICALLY DISPLAYS A BENIGN TUMOR WITH EXCESSIVE SQUAMOUS EPITHELIAL CELL PROLIFERATION IN THE MIDDLE EAR. CLINICALLY, HOWEVER, IT CAN MANIFEST MALIGNANT BEHAVIOR BY DESTROYING ADJACENT TISSUES AND ORGANS. ALTHOUGH PREVIOUS STUDIES HAVE DEMONSTRATED THAT THE PATHOGENESIS OF CHOLESTEATOMA IS CORRELATED WITH EPIGENETIC DYSREGULATION, THE EXACT MECHANISM REMAINS UNCLEAR. CIRCULAR RNAS (CIRCRNAS) HAVE BEEN REVEALED AS BEING ABUNDANTLY EXPRESSED IN VARIOUS ORGANISMS AND HAVE BEEN FOUND TO CONTRIBUTE TO THE REGULATION OF MANY DISEASES. TO DATE, NO REPORTS HAVE ELUCIDATED THEIR EXPRESSION PROFILES AND FUNCTIONS IN CHOLESTEATOMA. IN THE PRESENT STUDY, THE CIRCRNA EXPRESSION PROFILE IN CHOLESTEATOMA WAS EXPLORED FOR THE FIRST TIME BY USING MICROARRAY ANALYSIS. WE OBTAINED A TOTAL OF 355 SIGNIFICANTLY DIFFERENTIALLY EXPRESSED CIRCRNAS IN CHOLESTEATOMA, AMONG WHICH 101 WERE IDENTIFIED TO BE UPREGULATED AND 254 DOWNREGULATED. BY CONSTRUCTING CIRCRNA?LNCRNA?MIRNA?MRNA COMPETING ENDOGENOUS RNA (CERNA) NETWORK, IT WAS DISCOVERED THAT CIRCRNAS MAY FUNCTION AS CERNAS AND CONTRIBUTE TO THE FORMATION OF CHOLESTEATOMA. THESE RESULTS PROVIDE NOVEL INSIGHT INTO THE PATHOGENESIS OF CHOLESTEATOMA AND SUGGEST CIRCRNAS AS POTENTIAL PROMISING THERAPEUTIC TARGETS FOR CHOLESTEATOMA.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
7 5844  36 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
8 2679  40 EVALUATION OF CIRCULATORY RNA-BASED BIOMARKER PANEL IN HEPATOCELLULAR CARCINOMA. BACKGROUND: THE CIRCULATING TRANSCRIPTOME (CODING AND NON-CODING) PLAYS A CRITICAL ROLE IN CANCER. NOVEL ACCURATE STRATEGIES FOR EARLY DETECTION OF HEPATOCELLULAR CARCINOMA (HCC) ARE STRONGLY NEEDED. PATIENTS AND METHODS: WE CHOSE AN HCC-SPECIFIC RNA-BASED BIOMARKER PANEL BASED ON THE INTEGRATION OF DIFFERENTIAL LYSOSOMAL-ASSOCIATED MEMBRANE PROTEIN 2 (LAMP2) GENE EXPRESSION WITH ITS SELECTED EPIGENETIC REGULATORS USING BIOINFORMATIC METHODS. THIS WAS FOLLOWED BY RT-QPCR VALIDATION IN SERUM OF 78 PATIENTS WITH HCC, 36 PATIENTS WITH CHRONIC HEPATITIS C (CHC) INFECTION AND 44 HEALTHY VOLUNTEERS. WE USED RISK-SCORE ANALYSIS TO EVALUATE THE DIAGNOSTIC EFFICACY OF THE SERUM PROFILING SYSTEM. MOREOVER, IN TWENTY OF THE 78 HCC CASES INVOLVED IN THE STUDY WE EXAMINED THE EXPRESSION OF RNA-BASED BIOMARKER PANEL IN BOTH HCC AND ADJACENT NON-TUMOR TISSUES AND ASSESSED THEIR CORRELATION WITH THE SERUM LEVEL OF THIS PANEL. RESULTS: THE FOUR RIBONUCLEIC ACID (RNA)-BASED BIOMARKER PANEL [LONG NON-CODING RNA-C TERMINAL BINDING PROTEIN, ANDROGEN RESPONSIVE (LNCRNA-CTBP), MICRORNA-16-2 (MIR-16-2), MICRORNA-21-5-P (MIR-21-5P) AND LAMP2], HAD HIGH SENSITIVITY AND SPECIFICITY FOR DISCRIMINATING HCC FROM HEALTHY CONTROLS AND ALSO FROM CHC PATIENTS. AMONG THESE FOUR RNAS, SERUM MIR-16-2 AND MIR-21-5P WERE INDEPENDENT PROGNOSTIC FACTORS. CONCLUSION: THE CIRCULATORY RNA-BASED BIOMARKER PANEL CAN SERVE AS A POTENTIAL BIOMARKER FOR HCC DIAGNOSIS AND PROGNOSIS.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
9 4677  40 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	
                                                                                                                                                                                                                                                                                                                                  
10 5120  35 POSSIBLE EPIGENETIC REGULATORY EFFECT OF DYSREGULATED CIRCULAR RNAS IN EPILEPSY. CIRCULAR RNAS (CIRCRNAS) INVOLVE IN THE EPIGENETIC REGULATION AND ITS MAJOR MECHANISM IS THE SEQUESTRATION OF THE TARGET MICRO RNAS (MIRNAS). WE HYPOTHESIZED THAT CIRCRNAS MIGHT BE RELATED WITH THE PATHOPHYSIOLOGY OF CHRONIC EPILEPSY AND EVALUATED THE ALTERED CIRCRNA EXPRESSIONS AND THEIR POSSIBLE REGULATORY EFFECTS ON THEIR TARGET MIRNAS AND MRNAS IN A MOUSE EPILEPSY MODEL. THE CIRCRNA EXPRESSION PROFILE IN THE HIPPOCAMPUS OF THE PILOCARPINE MICE WAS ANALYZED AND COMPARED WITH CONTROL. THE CORRELATION BETWEEN THE EXPRESSION OF MIRNA BINDING SITES (MIRNA RESPONSE ELEMENTS, MRE) IN THE DYSREGULATED CIRCRNAS AND THE EXPRESSION OF THEIR TARGET MIRNAS WAS EVALUATED. AS MIRNAS ALSO INHIBIT THEIR TARGET MRNAS, CIRCRNA-MIRNA-MRNA REGULATORY NETWORK, COMPRISED OF DYSREGULATED RNAS THAT TARGETS ONE ANOTHER WERE SEARCHED. FOR THE IDENTIFIED NETWORKS, BIOINFORMATICS ANALYSES WERE PERFORMED. AS THE RESULT, FORTY-THREE CIRCRNAS WERE DYSREGULATED IN THE HIPPOCAMPUS (UP-REGULATED, 26; DOWN-REGULATED, 17). THE CHANGE IN THE EXPRESSION OF MRE IN THOSE CIRCRNAS NEGATIVELY CORRELATED WITH THE CHANGE IN THE RELEVANT TARGET MIRNA EXPRESSION (R = -0.461, P<0.001), SUPPORTING THAT CIRCRNAS INHIBIT THEIR TARGET MIRNA. 333 DYSREGULATED CIRCRNA-MIRNA-MRNA NETWORKS WERE IDENTIFIED. GENE ONTOLOGY AND PATHWAY ANALYSES DEMONSTRATED THAT THE UP-REGULATED MRNAS IN THOSE NETWORKS WERE CLOSELY RELATED TO THE MAJOR PROCESSES IN EPILEPSY. AMONG THEM, STRING ANALYSIS IDENTIFIED 37 KEY MRNAS WITH ABUNDANT (>/=4) INTERACTIONS WITH OTHER DYSREGULATED TARGET MRNAS. THE DYSREGULATION OF THE CIRCRNAS WHICH HAD MULTIPLE INTERACTIONS WITH KEY MRNAS WERE VALIDATED BY PCR. WE CONCLUDED THAT DYSREGULATED CIRCRNAS MIGHT HAVE A PATHOPHYSIOLOGIC ROLE IN CHRONIC EPILEPSY BY REGULATING MULTIPLE DISEASE RELEVANT MRNAS VIA CIRCRNA-MIRNA-MRNA INTERACTIONS.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
11 6684  28 VALIDATION OF AN LC-MS BASED APPROACH FOR PROFILING HISTONES IN CHRONIC LYMPHOCYTIC LEUKEMIA. THE IN VITRO EVALUATION OF HISTONES AND THEIR PTMS HAS DRAWN SUBSTANTIAL INTEREST IN THE DEVELOPMENT OF EPIGENETIC THERAPIES. THE DIFFERENTIAL EXPRESSION OF HISTONE ISOFORMS MAY SERVE AS A POTENTIAL MARKER IN THE CLASSIFICATION OF DISEASES AFFECTED BY CHROMATIN ABNORMALITIES. IN THIS STUDY, PROTEIN PROFILING BY LC AND MS WAS USED TO EXPLORE DIFFERENCES IN HISTONE COMPOSITION IN PRIMARY CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) CELLS. EXTENSIVE METHOD VALIDATIONS WERE PERFORMED TO DETERMINE THE EXPERIMENTAL VARIANCES THAT WOULD IMPACT HISTONE RELATIVE ABUNDANCE. THE RESULTING DATA DEMONSTRATED THAT THE PROPOSED METHODOLOGY WAS SUITABLE FOR THE ANALYSIS OF HISTONE PROFILES. IN 4 NORMAL INDIVIDUALS AND 40 CLL PATIENTS, A SIGNIFICANT DECREASE IN THE RELATIVE ABUNDANCE OF HISTONE H2A VARIANTS (H2AFL AND H2AFA/M*) WAS OBSERVED IN PRIMARY CLL CELLS AS COMPARED TO NORMAL B CELLS. PROTEIN IDENTITIES WERE DETERMINED USING HIGH MASS ACCURACY MS AND SHOTGUN PROTEOMICS.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
12 1587  30 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
13 6431  35 THE USE OF TARGETED NEXT GENERATION SEQUENCING TO EXPLORE CANDIDATE REGULATORS OF TGF-BETA1'S IMPACT ON KIDNEY CELLS. AIMS/HYPOTHESIS: TRANSFORMING GROWTH FACTOR-BETA (TGF-BETA1) PLAYS AN IMPORTANT REGULATORY ROLE IN THE PROGRESSION OF CHRONIC KIDNEY FAILURE. FURTHER, DAMAGE TO KIDNEY GLOMERULAR MESANGIAL CELLS IS CENTRAL TO THE PROGRESSION OF DIABETIC NEPHROPATHY. THE AIM OF THIS STUDY WAS TO EXPLORE THE GENETIC ASSOCIATIONS BETWEEN MRNA, MICRORNA, AND EPIGENETICS IN MESANGIAL CELLS IN RESPONSE TO TGF-BETA1. METHODS: THE REGULATORY EFFECTS OF TGF-BETA1 ON MESANGIAL CELLS WERE INVESTIGATED AT DIFFERENT MOLECULAR LEVELS BY TREATING MESANGIAL CELLS WITH TGF-BETA1 FOR 3 DAYS FOLLOWED BY GENOME-WIDE MIRNA, RNA, DNA METHYLATION, AND H3K27ME3 EXPRESSION PROFILING USING NEXT GENERATION SEQUENCING (NGS). RESULTS: OUR RESULTS PROVIDE THE FIRST COMPREHENSIVE, COMPUTATIONALLY INTEGRATED REPORT OF RNA-SEQ, MIRNA-SEQ, AND EPIGENOMIC ANALYSES ACROSS ALL GENETIC VARIATIONS, CONFIRMING THE OCCURRENCE OF DNA METHYLATION AND H3K27ME3 IN RESPONSE TO TGF-BETA1. OUR FINDINGS SHOW THAT THE EXPRESSION OF KLF7 AND GJA4 ARE INVOLVED IN TGF-BETA1 REGULATED DNA METHYLATION. OUR DATA ALSO PROVIDE EVIDENCE OF THE ASSOCIATION BETWEEN EPIGENETIC CHANGES AND THE EXPRESSION OF GENES CLOSELY RELATED TO TGF-BETA1 REGULATION. CONCLUSION: THIS STUDY HAS ADVANCED OUR CURRENT KNOWLEDGE OF MECHANISMS THAT CONTRIBUTE TO THE EXPRESSION OF TGF-BETA1-REGULATED GENES INVOLVED IN THE PATHOGENESIS OF KIDNEY DISEASE. THE MOLECULAR UNDERPINNINGS OF TGF-BETA1 STIMULATION OF KIDNEY CELLS WAS DETERMINED, THEREBY PROVIDING A ROBUST PLATFORM FOR FURTHER TARGET EXPLORATION.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
14  412  38 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
15 3248  34 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
16 4286  46 MICRORNA EXPRESSION ANALYSIS IN HIGH FAT DIET-INDUCED NAFLD-NASH-HCC PROGRESSION: STUDY ON C57BL/6J MICE. BACKGROUND: HEPATOCELLULAR CARCINOMA (HCC) IS THE MOST COMMON MALIGNANT TUMOR OF THE LIVER. NON-ALCOHOLIC FATTY LIVER DISEASE (NAFLD) IS A FREQUENT CHRONIC LIVER DISORDER IN DEVELOPED COUNTRIES. NAFLD CAN PROGRESS THROUGH THE MORE SEVERE NON ALCOHOLIC STEATOHEPATITIS (NASH), CIRRHOSIS AND, LASTLY, HCC. GENETIC AND EPIGENETIC ALTERATIONS OF CODING GENES AS WELL AS DEREGULATION OF MICRORNAS (MIRNAS) ACTIVITY PLAY A ROLE IN HCC DEVELOPMENT. IN THIS STUDY, THE C57BL/6J MOUSE MODEL WAS LONG TERM HIGH-FAT (HF) OR LOW-FAT (LF) DIET FED, IN ORDER TO ANALYZE MOLECULAR MECHANISMS RESPONSIBLE FOR THE HEPATIC DAMAGE PROGRESSION. METHODS: MICE WERE HF OR LF DIET FED FOR DIFFERENT TIME POINTS, THEN PLASMA AND HEPATIC TISSUES WERE COLLECTED. HISTOLOGICAL AND CLINICAL CHEMISTRY ASSAYS WERE PERFORMED TO ASSESS THE PROGRESSION OF LIVER DISEASE. MICRORNAS' DIFFERENTIAL EXPRESSION WAS EVALUATED ON POOLED RNAS FROM TISSUES, AND SOME MIRNAS SHOWING DYSREGULATION WERE FURTHER ANALYZED AT THE INDIVIDUAL LEVEL. RESULTS: CHOLESTEROL, LOW AND HIGH DENSITY LIPOPROTEINS, TRIGLYCERIDES AND ALANINE AMINOTRANSFERASE INCREASE WAS DETECTED IN HF MICE. GROSS ANATOMICAL EXAMINATION REVEALED HEPATOMEGALY IN HF LIVERS, AND HISTOLOGICAL ANALYSIS HIGHLIGHTED DIFFERENT DEGREES AND LEVELS OF STEATOSIS, INFLAMMATORY INFILTRATE AND FIBROSIS IN HF AND LF ANIMALS, DEMONSTRATING THE PROGRESSION FROM NAFLD THROUGH NASH. MACROSCOPIC NODULES, SHOWING TYPICAL NEOPLASTIC FEATURES, WERE OBSERVED IN 20% OF HF DIET FED MICE. FIFTEEN MIRNAS DIFFERENTIALLY EXPRESSED IN HF WITH RESPECT TO LF HEPATIC TISSUES DURING THE PROGRESSION OF LIVER DAMAGE, AND IN TUMORS WITH RESPECT TO HF NON TUMOR LIVER SPECIMENS WERE IDENTIFIED. AMONG THEM, MIR-340-5P, MIR-484, MIR-574-3P, MIR-720, WHOSE EXPRESSION WAS NEVER DESCRIBED IN NAFLD, NASH AND HCC TISSUES, AND MIR-125A-5P AND MIR-182, WHICH SHOWED EARLY AND SIGNIFICANT DYSREGULATION IN THE SEQUENTIAL HEPATIC DAMAGE PROCESS. CONCLUSIONS: IN THIS STUDY, FIFTEEN MICRORNAS WHICH WERE MODULATED IN HEPATIC TISSUES AND IN TUMORS DURING THE TRANSITION NAFLD-NASH-HCC ARE REPORTED. BESIDES SOME ALREADY DESCRIBED, NEW AND EARLY DYSREGULATED MIRNAS WERE IDENTIFIED. FUNCTIONAL ANALYSES ARE NEEDED TO VALIDATE THE RESULTS HERE OBTAINED, AND TO BETTER DEFINE THE ROLE OF THESE MOLECULES IN THE PROGRESSION OF THE HEPATIC DISEASE.	2016	
                                                                                                                                                                                        
17 1568  20 DNA METHYLATION OF TUMOR-SUPPRESSOR MIRNA GENES IN CHRONIC LYMPHOCYTIC LEUKEMIA. DNA METHYLATION IS ONE OF THE MOST IMPORTANT EPIGENETIC MODIFICATIONS OF THE GENOME INVOLVED IN THE REGULATION OF NUMEROUS CELLULAR PROCESSES THROUGH GENE SILENCING WITHOUT ALTERING DNA SEQUENCES. MIRNAS, A CLASS OF SINGLE-STRANDED NONCODING RNAS OF 19-25 NUCLEOTIDES IN LENGTH, FUNCTION AS POST-TRANSCRIPTIONAL REGULATORS OF GENE EXPRESSION LEADING TO MRNA CLEAVAGE OR TRANSLATIONAL REPRESSION OF THEIR CORRESPONDING TARGET PROTEIN-CODING GENES. RECENTLY, DYSREGULATION OF TUMOR SUPPRESSOR MIRNAS MEDIATED BY PROMOTER DNA HYPERMETHYLATION IS IMPLICATED IN HUMAN CANCERS, INCLUDING B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). MOREOVER, IT APPEARS THAT METHYLATED MIRNA GENES COULD BE POTENTIAL BIOMARKERS FOR CLL DIAGNOSIS OR THERAPY. THIS REVIEW WILL HIGHLIGHT THE ROLE OF ABERRANT METHYLATION OF MIRNA GENES IN THE PATHOGENESIS OF CLL.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
18 6488  40 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	
                                                                                                                                                                                                                                                                                                                                                                                                             
19  332  34 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
20 6723  37 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