1  2723 143 EXOSOMES: NOMENCLATURE, ISOLATION, AND BIOLOGICAL ROLES IN LIVER DISEASES. THE BIOGENESIS AND BIOLOGICAL ROLES OF EXTRACELLULAR VESICLES (EVS) IN THE PROGRESSION OF LIVER DISEASES HAVE ATTRACTED CONSIDERABLE ATTENTION IN RECENT YEARS. EVS ARE MEMBRANE-BOUND NANOSIZED VESICLES FOUND IN DIFFERENT TYPES OF BODY FLUIDS AND CONTAIN VARIOUS BIOACTIVE MATERIALS, INCLUDING PROTEINS, LIPIDS, NUCLEIC ACIDS, AND MITOCHONDRIAL DNA. BASED ON THEIR ORIGIN AND BIOGENESIS, EVS CAN BE CLASSIFIED AS APOPTOTIC BODIES, MICROVESICLES, AND EXOSOMES. AMONG THESE, EXOSOMES ARE THE SMALLEST EVS (30-150 NM IN DIAMETER), WHICH PLAY A SIGNIFICANT ROLE IN CELL-TO-CELL COMMUNICATION AND EPIGENETIC REGULATION. MOREOVER, EXOSOMAL CONTENT ANALYSIS CAN REVEAL THE FUNCTIONAL STATE OF THE PARENTAL CELL. THEREFORE, EXOSOMES CAN BE APPLIED TO VARIOUS PURPOSES, INCLUDING DISEASE DIAGNOSIS AND TREATMENT, DRUG DELIVERY, CELL-FREE VACCINES, AND REGENERATIVE MEDICINE. HOWEVER, EXOSOME-RELATED RESEARCH FACES TWO MAJOR LIMITATIONS: ISOLATION OF EXOSOMES WITH HIGH YIELD AND PURITY AND DISTINCTION OF EXOSOMES FROM OTHER EVS (ESPECIALLY MICROVESICLES). NO STANDARDIZED EXOSOME ISOLATION METHOD HAS BEEN ESTABLISHED TO DATE; HOWEVER, VARIOUS EXOSOME ISOLATION STRATEGIES HAVE BEEN PROPOSED TO INVESTIGATE THEIR BIOLOGICAL ROLES. EXOSOME-MEDIATED INTERCELLULAR COMMUNICATIONS ARE KNOWN TO BE INVOLVED IN ALCOHOLIC LIVER DISEASE AND NONALCOHOLIC FATTY LIVER DISEASE DEVELOPMENT. DAMAGED HEPATOCYTES OR NONPARENCHYMAL CELLS RELEASE LARGE NUMBERS OF EXOSOMES THAT PROMOTE THE PROGRESSION OF INFLAMMATION AND FIBROGENESIS THROUGH INTERACTIONS WITH NEIGHBORING CELLS. EXOSOMES ARE EXPECTED TO PROVIDE INSIGHT ON THE PROGRESSION OF LIVER DISEASE. HERE, WE REVIEW THE BIOGENESIS OF EXOSOMES, EXOSOME ISOLATION TECHNIQUES, AND BIOLOGICAL ROLES OF EXOSOMES IN ALCOHOLIC LIVER DISEASE AND NONALCOHOLIC FATTY LIVER DISEASE.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
2  1138  26 COMPUTATIONAL METHODS FOR DETECTION OF DIFFERENTIALLY METHYLATED REGIONS USING KERNEL DISTANCE AND SCAN STATISTICS. MOTIVATION: RESEARCHERS IN GENOMICS ARE INCREASINGLY INTERESTED IN EPIGENETIC FACTORS SUCH AS DNA METHYLATION BECAUSE THEY PLAY AN IMPORTANT ROLE IN REGULATING GENE EXPRESSION WITHOUT CHANGES IN THE SEQUENCE OF DNA. ABNORMAL DNA METHYLATION IS ASSOCIATED WITH MANY HUMAN DISEASES. RESULTS: WE PROPOSE TWO DIFFERENT APPROACHES TO TEST FOR DIFFERENTIALLY METHYLATED REGIONS (DMRS) ASSOCIATED WITH COMPLEX TRAITS, WHILE ACCOUNTING FOR CORRELATIONS AMONG CPG SITES IN THE DMRS. THE FIRST APPROACH IS A NONPARAMETRIC METHOD USING A KERNEL DISTANCE STATISTIC AND THE SECOND ONE IS A LIKELIHOOD-BASED METHOD USING A BINOMIAL SPATIAL SCAN STATISTIC. THE KERNEL DISTANCE METHOD USES THE KERNEL FUNCTION, WHILE THE BINOMIAL SCAN STATISTIC APPROACH USES A MIXED-EFFECTS MODEL TO INCORPORATE CORRELATIONS AMONG CPG SITES. EXTENSIVE SIMULATIONS SHOW THAT BOTH APPROACHES HAVE EXCELLENT CONTROL OF TYPE I ERROR, AND BOTH HAVE REASONABLE STATISTICAL POWER. THE BINOMIAL SCAN STATISTIC APPROACH APPEARS TO HAVE HIGHER POWER, WHILE THE KERNEL DISTANCE METHOD IS COMPUTATIONALLY FASTER. THE PROPOSED METHODS ARE DEMONSTRATED USING DATA FROM A CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) STUDY.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
3   507  30 ASSOCIATION OF INCREASED DNA METHYLTRANSFERASE EXPRESSION WITH CARCINOGENESIS AND POOR PROGNOSIS IN PANCREATIC DUCTAL ADENOCARCINOMA. INTRODUCTION: EPIGENETIC MODIFICATIONS PLAY AN IMPORTANT ROLE IN MULTISTAGE CARCINOGENESIS. THE ROLE OF THE THREE FUNCTIONAL DNA METHYLTRANSFERASES (DNMTS) IN PANCREATIC CARCINOGENESIS HAS NOT BEEN FULLY UNDERSTOOD. THE MAIN GOAL OF THIS STUDY WAS TO EXAMINE DNMT EXPRESSION IN DIFFERENT STAGES OF PANCREATIC DUCTAL ADENOCARCINOMA (PDAC), AND EVALUATE THEIR PROGNOSTIC SIGNIFICANCE IN PDAC. MATERIALS AND METHODS: A LARGE NUMBER OF PREMALIGNANT AND MALIGNANT PANCREATIC LESIONS WERE OBTAINED BY MANUAL MICRODISSECTION. QUANTITATIVE REAL-TIME RT-PCR WAS USED TO DETECT DNMTS MRNA EXPRESSION. NONPARAMETRIC TEST, LOGRANK TEST AND COX REGRESSION ANALYSIS WERE USED TO EVALUATE THE CLINICAL SIGNIFICANCE OF DNMT EXPRESSION. RESULTS: THE MRNA EXPRESSION OF THE THREE DNMTS INCREASED WITH THE DEVELOPMENT OF PANCREATIC CANCER FROM NORMAL DUCT TO PANCREATIC INTRADUCTAL NEOPLASIA AND FURTHER TO PDAC, AND WERE STATISTICALLY CORRELATED WITH EACH OTHER. EXPRESSION OF THE THREE DNMTS WAS STATISTICALLY CORRELATED WITH TNM STAGING AND HISTORY OF CHRONIC PANCREATITIS. DNMT3A AND DNMT3B, BUT NOT DNMT1 EXPRESSION, WAS STATISTICALLY CORRELATED WITH TUMOUR SIZE. PATIENTS WITH HIGHER LEVELS OF DNMT1, DNMT3A AND/OR DNMT3B EXPRESSION HAD AN OVERALL LOWER SURVIVAL THAN THOSE WITH LOWER LEVELS OF EXPRESSION. UNIVARIATE ANALYSIS SHOWED THAT HIGH EXPRESSION LEVELS OF DNMTS, ALCOHOL CONSUMPTION, TUMOUR DIFFERENTIATION AND TNM STAGING WERE STATISTICALLY SIGNIFICANT RISK FACTORS. MULTIVARIATE ANALYSIS SHOWED THAT HIGH LEVEL OF DNMT3B EXPRESSION AND TUMOUR DIFFERENTIATION WERE STATISTICALLY SIGNIFICANT INDEPENDENT POOR PROGNOSTIC FACTORS. CONCLUSIONS: THESE RESULTS SUGGESTED THAT PANCREATIC CARCINOGENESIS INVOLVES AN INCREASED MRNA EXPRESSION OF THREE DNMTS, AND THEY MAY BECOME VALUABLE DIAGNOSTIC AND PROGNOSTIC MARKERS AS WELL AS POTENTIAL THERAPEUTIC TARGETS FOR PANCREATIC CANCER.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
4  4334  18 MICRORNAS: NOVEL DIAGNOSTIC AND THERAPEUTIC TOOLS FOR PANCREATIC DUCTAL ADENOCARCINOMA? PANCREATIC DUCTAL ADENOCARCINOMA (PDAC) IS KNOWN FOR ITS VERY POOR OVERALL PROGNOSIS, MAKING TOOLS FOR EARLY DIAGNOSIS AND NEW THERAPEUTIC MODALITIES URGENTLY NEEDED. MICRORNAS (MIRNAS), ENDOGENOUS NONCODING RNA MOLECULES OF APPROXIMATELY 22 NT, HAVE GAINED ATTENTION AS AN EPIGENETIC COMPONENT INVOLVED IN THE DEVELOPMENT OF MANY CANCERS, INCLUDING PDAC. MIRNA EXPRESSION PROFILES OF VARYING PANCREATIC TISSUES HAVE IDENTIFIED A NUMBER OF DIFFERENTIALLY EXPRESSED MIRNAS AND SEEM TO BE ABLE TO DIFFERENTIATE BETWEEN THREE TISSUES OF CLINICAL IMPORTANCE: NORMAL PANCREAS, CHRONIC PANCREATITIS, AND PDAC. THIS ARTICLE GATHERS OUR CURRENT KNOWLEDGE OF DIFFERENTIALLY EXPRESSED MIRNAS IN PANCREATIC TISSUES WITH RELEVANCE TO PDAC AND PRESENTS POTENTIAL DIAGNOSTIC AND THERAPEUTIC OPPORTUNITIES.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
5   779  17 CELL-FREE DNA PROMOTER HYPERMETHYLATION AS A DIAGNOSTIC MARKER FOR PANCREATIC DUCTAL ADENOCARCINOMA - AN EXTERNAL VALIDATION STUDY. BACKGROUND: WE RECENTLY IDENTIFIED A DIAGNOSTIC PREDICTION MODEL BASED ON PROMOTER HYPERMETHYLATION OF EIGHT SELECTED GENES IN PLASMA CELL-FREE (CF) DNA, WHICH SHOWED PROMISING RESULTS AS A DIAGNOSTIC BIOMARKER FOR PANCREATIC DUCTAL ADENOCARCINOMA (PDAC). THE AIM OF THE PRESENT STUDY WAS TO VALIDATE THIS BIOMARKER PROFILE IN AN EXTERNAL PATIENT COHORT AND EXAMINE ANY ADDITIONAL EFFECT OF SERUM CA 19-9. METHODS: PATIENTS WITH PDAC (N = 346, STAGE I-IV) AND CHRONIC PANCREATITIS (N = 25) WERE INCLUDED. METHYLATION-SPECIFIC PCR OF A 28-GENE PANEL WAS PERFORMED ON SERUM CFDNA SAMPLES. THE PREVIOUSLY DEVELOPED DIAGNOSTIC PREDICTION MODEL (AGE>65 YEARS, BMP3, RASSF1A, BNC1, MESTV2, TFPI2, APC, SFRP1 AND SFRP2) WAS VALIDATED ALONE AND IN COMBINATION WITH SERUM CA 19-9 IN THIS EXTERNAL PATIENT COHORT. RESULTS: PATIENTS WITH PDAC HAD A HIGHER NUMBER OF HYPERMETHYLATED GENES (MEAN 8.11, 95% CI 7.70-8.52) THAN PATIENTS WITH CHRONIC PANCREATITIS (MEAN 5.60, 95% CI 4.42-6.78, P = 0.011). VALIDATION OF THE DIAGNOSTIC PREDICTION MODEL YIELDED AN AUC OF 0.77 (95% CI 0.69-0.84). THE COMBINATION OF SERUM CA 19-9 AND OUR TEST HAD AN AUC OF 0.93 (95% CI 0.89-0.96) IN THE PRIMARY STUDY AND 0.85 (95% CI 0.79-0.91) IN THE VALIDATION STUDY. CONCLUSION: IN THIS VALIDATION STUDY, PDAC WAS ASSOCIATED WITH A HIGHER NUMBER OF HYPERMETHYLATED GENES IN SERUM CFDNA THAN CHRONIC PANCREATITIS. OUR DIAGNOSTIC TEST WAS SUPERIOR TO THE PREDICTIVE VALUE OF SERUM CA 19-9 ALONE IN BOTH THE PRIMARY AND THE VALIDATION STUDY. THE COMBINATION OF OUR TEST WITH CA 19-9 MAY SERVE AS A CLINICALLY USEFUL DIAGNOSTIC BIOMARKER FOR PDAC.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
6  6596  26 TUMOR-SUPPRESSIVE MIR-192-5P HAS PROGNOSTIC VALUE IN PANCREATIC DUCTAL ADENOCARCINOMA. PANCREATIC DUCTAL ADENOCARCINOMA (PDAC) IS CHARACTERIZED BY FAST TUMOR PROGRESSION AND DIAGNOSIS AT ADVANCED, INOPERABLE STAGES. PREVIOUS STUDIES COULD DEMONSTRATE AN INVOLVEMENT OF MIR-192-5P IN EPIGENETIC REGULATION OF VISCERAL CARCINOMAS. DUE TO CONTRADICTORY RESULTS, HOWEVER, THE CLINICAL UTILITY OF MIR-192-5P IN PDAC HAS YET TO BE DETERMINED. MIR-192-5P EXPRESSION WAS ANALYZED BY RT-QRT-PCR IN HUMAN PDAC AND BENIGN TISSUE (N = 78), BLOOD SERUM (N = 81) AND SERUM EXOSOMES (N = 74), AS WELL AS IN PDAC CELL LINES (N = 5), CHEMORESISTANT CELL CLONES (N = 2), AND PANCREATIC DUCT CELL LINE H6C7. ANALYSIS OF EMT-ASSOCIATED (EPITHELIAL-TO-MESENCHYMAL TRANSITION) PROTEINS WAS PERFORMED BY IMMUNOHISTOCHEMISTRY AND WESTERN BLOT. MIR-192-5P WAS DEREGULATED IN PDAC AS COMPARED TO HEALTHY CONTROLS (HCS), WITH DOWNREGULATION IN MACRODISSECTED TISSUE (P < 0.001) AND UPREGULATION IN BLOOD SERUM OF PDAC UICC (UNION FOR INTERNATIONAL CANCER CONTROL) STAGE IV (P = 0.016) AND SERUM EXOSOMES OF PDAC UICC STAGES II TO IV (P < 0.001). MIR-192-5P EXPRESSION IN TUMOR TISSUE WAS SIGNIFICANTLY LOWER AS COMPARED TO CORRESPONDING PERITUMORAL TISSUE (PDAC UICC STAGE II: P < 0.001; PDAC UICC STAGE III: P = 0.024), WHILE EMT MARKERS ZEB1 AND ZEB2 WERE MORE FREQUENTLY EXPRESSED IN TUMOR TISSUE AS COMPARED TO PERITUMORAL TISSUE, HCS, AND CHRONIC PANCREATITIS. TISSUE-DERIVED (AUC OF 0.86; P < 0.0001) AND EXOSOMAL (AUC OF 0.83; P = 0.0004) MIR-192-5P COULD DIFFERENTIATE BETWEEN PDAC AND HCS WITH GOOD ACCURACY. FURTHERMORE, HIGH EXPRESSION OF MIR-192-5P IN PDAC TISSUE OF CURATIVELY RESECTED PDAC PATIENTS CORRELATED WITH PROLONGED OVERALL AND RECURRENCE-FREE SURVIVAL IN MULTIVARIATE ANALYSIS. IN VITRO, MIR-192-5P WAS DOWNREGULATED IN GEMCITABINE-RESISTANT CELL CLONES OF ASPC-1 (P = 0.029). TRANSIENT TRANSFECTION OF MIA PACA-2 CELLS WITH MIR-192-5P MIMIC RESULTED IN DOWNREGULATION OF ZEB2. MIR-192-5P SEEMS TO POSSESS A TUMOR-SUPPRESSIVE ROLE AND HIGH POTENTIAL AS A DIAGNOSTIC AND PROGNOSTIC MARKER IN PDAC.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
7   778  31 CELL-FREE DNA METHYLATION: THE NEW FRONTIERS OF PANCREATIC CANCER BIOMARKERS' DISCOVERY. PANCREATIC DUCTAL ADENOCARCINOMA (PDAC) IS AMONG THE MOST LETHAL CANCER TYPES WORLD-WIDE. ITS HIGH MORTALITY IS RELATED TO THE DIFFICULTY IN THE DIAGNOSIS, WHICH OFTEN OCCURS WHEN THE DISEASE IS ALREADY ADVANCED. AS OF TODAY, NO EARLY DIAGNOSTIC TESTS ARE AVAILABLE, WHILE ONLY A LIMITED NUMBER OF PROGNOSTIC TESTS HAVE REACHED CLINICAL PRACTICE. THE MAIN REASON IS THE LACK OF RELIABLE BIOMARKERS THAT ARE ABLE TO CAPTURE THE EARLY DEVELOPMENT OR THE PROGRESSION OF THE DISEASE. HENCE, THE DISCOVERY OF BIOMARKERS FOR EARLY DIAGNOSIS OR PROGNOSIS OF PDAC REMAINS, DE FACTO, AN UNMET NEED. AN INCREASING NUMBER OF STUDIES HAS SHOWN THAT CELL-FREE DNA (CFDNA) METHYLATION ANALYSIS REPRESENTS A PROMISING NON-INVASIVE APPROACH FOR THE DISCOVERY OF BIOMARKERS WITH DIAGNOSTIC OR PROGNOSTIC POTENTIAL. IN PARTICULAR, CFDNA METHYLATION COULD BE UTILIZED FOR THE IDENTIFICATION OF DISEASE-SPECIFIC SIGNATURES IN PRE-NEOPLASTIC LESIONS OR CHRONIC PANCREATITIS (CP), REPRESENTING A SENSITIVE AND NON-INVASIVE METHOD OF EARLY DIAGNOSIS OF PDAC. IN THIS REVIEW, WE WILL DISCUSS THE ADVANTAGES AND PITFALLS OF CFDNA METHYLATION STUDIES. FURTHER, WE WILL PRESENT THE CURRENT ADVANCES IN THE DISCOVERY OF PANCREATIC CANCER BIOMARKERS WITH EARLY DIAGNOSTIC OR PROGNOSTIC POTENTIAL, FOCUSING ON PANCREAS-SPECIFIC (E.G., CUX2 OR REG1A) OR ABNORMAL (E.G., ADAMTS1 OR BNC1) CFDNA METHYLATION SIGNATURES IN HIGH RISK PRE-NEOPLASTIC CONDITIONS AND PDAC.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
8  1485  22 DMRFUSION: A DIFFERENTIALLY METHYLATED REGION DETECTION TOOL BASED ON THE RANKED FUSION METHOD. DNA METHYLATION IS AN IMPORTANT EPIGENETIC MODIFICATION INVOLVED IN MANY BIOLOGICAL PROCESSES AND DISEASES. COMPUTATIONAL ANALYSIS OF DIFFERENTIALLY METHYLATED REGIONS (DMRS) COULD EXPLORE THE UNDERLYING REASONS OF METHYLATION. DMRFUSION IS PRESENTED AS A USEFUL TOOL FOR COMPREHENSIVE DNA METHYLATION ANALYSIS OF DMRS ON METHYLATION SEQUENCING DATA. THIS TOOL IS DESIGNED BASE ON THE INTEGRATION OF SEVERAL RANKING METHODS; INFORMATION GAIN, BETWEEN VERSUS WITHIN CLASS SCATTER RATIO, FISHER RATIO, Z-SCORE AND WELCH'S T-TEST. IN THIS STUDY, DMRFUSION ON REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS) DATA IN CHRONIC LYMPHOCYTIC LEUKEMIA CANCER DISPLAYED 30 NOMINATED REGIONS AND CPG SITES WITH A MAXIMUM METHYLATION DIFFERENCE DETECTED IN THE HYPERMETHYLATION DMRS. WE REALIZED THAT DMRFUSION IS ABLE TO PROCESS METHYLATION SEQUENCING DATA IN AN EFFICIENT AND ACCURATE MANNER AND TO PROVIDE ANNOTATION AND VISUALIZATION FOR DMRS WITH HIGH FOLD DIFFERENCE SCORE (P-VALUE AND FDR<0.05 AND TYPE I ERROR: 0.04).	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
9  1435  38 DIFFERENTIAL METHYLATION LANDSCAPE OF PANCREATIC DUCTAL ADENOCARCINOMA AND ITS PRECANCEROUS LESIONS. BACKGROUND: PANCREATIC CANCER IS ONE OF THE MOST LETHAL DISEASES WITH AN INCIDENCE ALMOST EQUAL TO THE MORTALITY. IN ADDITION TO HAVING GENETIC CAUSES, CANCER CAN ALSO BE CONSIDERED AN EPIGENETIC DISEASE. DNA METHYLATION IS THE PREMIER EPIGENETIC MODIFICATION AND PATTERNS OF ABERRANT DNA METHYLATION ARE RECOGNIZED TO BE A COMMON HALLMARK OF HUMAN TUMOR. IN THE MULTISTAGE CARCINOGENESIS OF PANCREAS STARTING FROM PRECANCEROUS LESIONS TO PANCREATIC DUCTAL ADENOCARCINOMA (PDAC), THE EPIGENETIC CHANGES PLAY A SIGNIFICANT ROLE. DATA SOURCES: RELEVANT STUDIES FOR THIS REVIEW WERE DERIVED VIA AN EXTENSIVE LITERATURE SEARCH IN PUBMED VIA USING VARIOUS KEYWORDS SUCH AS PANCREATIC DUCTAL ADENOCARCINOMA, PRECANCEROUS LESIONS, METHYLATION PROFILE, EPIGENETIC BIOMARKERS THAT ARE RELEVANT DIRECTLY OR CLOSELY ASSOCIATED WITH THE CONCERNED AREA OF OUR INTEREST. THE LITERATURE SEARCH WAS INTENSIVELY DONE CONSIDERING A TIME FRAME OF 20 YEARS (1998-2018). RESULT: IN THIS REVIEW WE HAVE HIGHLIGHTED THE HYPERMETHYLATION AND HYPOMETHYLATION OF THE PRECANCEROUS PDAC LESIONS (PANCREATIC INTRA-EPITHELIAL NEOPLASIA, INTRADUCTAL PAPILLARY MUCINOUS NEOPLASM, MUCINOUS CYSTIC NEOPLASM AND CHRONIC PANCREATITIS) AND PDAC ALONG WITH THE POTENTIAL BIOMARKERS. WE HAVE ALSO ACHIEVED THE EARLY EPIGENETIC DRIVER THAT LEADS TO PROGRESSION FROM PRECANCEROUS LESIONS TO PDAC. A BUNCH OF EPIGENETIC DRIVER GENES LEADS TO PROGRESSION OF PRECANCEROUS LESIONS TO PDAC (PPENK, APC, P14/5/16/17, HMLH1 AND MGMT) ARE ALSO DOCUMENTED. WE SUMMARIZED THE IMPORTANCE OF THESE OBSERVATIONS IN THERAPEUTICS AND DIAGNOSIS OF PDAC HENCE IDENTIFYING THE POTENTIAL USE OF EPIGENETIC BIOMARKERS IN EPIGENETIC TARGETED THERAPY. EPIGENETIC INACTIVATION OCCURS BY HYPERMETHYLATION OF CPG ISLANDS IN THE PROMOTER REGIONS OF TUMOR SUPPRESSOR GENES. WE LISTED ALL HYPER- AND HYPOMETHYLATION OF CPG ISLANDS OF SEVERAL GENES IN PDAC INCLUDING ITS PRECANCEROUS LESIONS. CONCLUSIONS: THE CONCEPT OF THE REVIEW WOULD HELP TO UNDERSTAND THEIR BIOLOGICAL EFFECTS, AND TO DETERMINE WHETHER THEY MAY BE SUCCESSFULLY COMBINED WITH OTHER EPIGENETIC DRUGS. HOWEVER, WE NEED TO CONTINUE OUR RESEARCH TO DEVELOP MORE SPECIFIC DNA-DEMETHYLATING AGENTS, WHICH ARE THE TARGETS FOR HYPERMETHYLATED CPG METHYLATION SITES.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
10  1345  32 DETECTION OF DIFFERENTIALLY METHYLATED REGIONS USING BAYES FACTOR FOR ORDINAL GROUP RESPONSES. RESEARCHERS IN GENOMICS ARE INCREASINGLY INTERESTED IN EPIGENETIC FACTORS SUCH AS DNA METHYLATION, BECAUSE THEY PLAY AN IMPORTANT ROLE IN REGULATING GENE EXPRESSION WITHOUT CHANGES IN THE DNA SEQUENCE. THERE HAVE BEEN SIGNIFICANT ADVANCES IN DEVELOPING STATISTICAL METHODS TO DETECT DIFFERENTIALLY METHYLATED REGIONS (DMRS) ASSOCIATED WITH BINARY DISEASE STATUS. MOST OF THESE METHODS ARE BEING DEVELOPED FOR DETECTING DIFFERENTIAL METHYLATION RATES BETWEEN CASES AND CONTROLS. WE CONSIDER MULTIPLE SEVERITY LEVELS OF DISEASE, AND DEVELOP A BAYESIAN STATISTICAL METHOD TO DETECT THE REGION WITH INCREASING (OR DECREASING) METHYLATION RATES AS THE DISEASE SEVERITY INCREASES. PATIENTS ARE CLASSIFIED INTO MORE THAN TWO GROUPS, BASED ON THE DISEASE SEVERITY (E.G., STAGES OF CANCER), AND DMRS ARE DETECTED BY USING MOVING WINDOWS ALONG THE GENOME. WITHIN EACH WINDOW, THE BAYES FACTOR IS CALCULATED TO TEST THE HYPOTHESIS OF MONOTONIC INCREASE IN METHYLATION RATES CORRESPONDING TO SEVERITY OF THE DISEASE VERSUS NO DIFFERENCE. A MIXED-EFFECT MODEL IS USED TO INCORPORATE THE CORRELATION OF METHYLATION RATES OF NEARBY CPG SITES IN THE REGION. RESULTS FROM EXTENSIVE SIMULATION INDICATE THAT OUR PROPOSED METHOD IS STATISTICALLY VALID AND REASONABLY POWERFUL. WE DEMONSTRATE OUR APPROACH ON A BISULFITE SEQUENCING DATASET FROM A CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) STUDY.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
11   780  30 CELL-FREE DNA PROMOTER HYPERMETHYLATION IN PLASMA AS A DIAGNOSTIC MARKER FOR PANCREATIC ADENOCARCINOMA. BACKGROUND: PANCREATIC CANCER HAS A 5-YEAR SURVIVAL RATE OF ONLY 5-7%. DIFFICULTIES IN DETECTING PANCREATIC CANCER AT EARLY STAGES RESULTS IN THE HIGH MORTALITY AND SUBSTANTIATES THE NEED FOR ADDITIONAL DIAGNOSTIC TOOLS. SURGERY IS THE ONLY CURATIVE TREATMENT AND UNFORTUNATELY ONLY POSSIBLE IN LOCALIZED TUMOURS. A DIAGNOSTIC BIOMARKER FOR PANCREATIC CANCER WILL HAVE A MAJOR IMPACT ON PATIENT SURVIVAL BY FACILITATING EARLY DETECTION AND THE POSSIBILITY FOR CURATIVE TREATMENT. DNA PROMOTER HYPERMETHYLATION IS A MECHANISM OF EARLY CARCINOGENESIS, WHICH CAN CAUSE INACTIVATION OF TUMOUR SUPPRESSOR GENES. THE AIM OF THIS STUDY WAS TO EXAMINE PROMOTER HYPERMETHYLATION IN A PANEL OF SELECTED GENES FROM CELL-FREE DNA, AS A DIAGNOSTIC MARKER FOR PANCREATIC ADENOCARCINOMA. METHODS: PATIENTS WITH SUSPECTED OR BIOPSY-VERIFIED PANCREATIC CANCER WERE INCLUDED PROSPECTIVELY AND CONSECUTIVELY. PATIENTS WITH CHRONIC/ACUTE PANCREATITIS WERE INCLUDED AS ADDITIONAL BENIGN CONTROL GROUPS. BASED ON AN OPTIMIZED ACCELERATED BISULFITE TREATMENT PROTOCOL, METHYLATION-SPECIFIC PCR OF A 28 GENE PANEL WAS PERFORMED ON PLASMA SAMPLES. A DIAGNOSTIC PREDICTION MODEL WAS DEVELOPED BY MULTIVARIABLE LOGISTIC REGRESSION ANALYSIS USING BACKWARD STEPWISE ELIMINATION. RESULTS: PATIENTS WITH PANCREATIC ADENOCARCINOMA (N = 95), CHRONIC PANCREATITIS (N = 97) AND ACUTE PANCREATITIS (N = 59) AND PATIENTS SCREENED, BUT NEGATIVE FOR PANCREATIC ADENOCARCINOMA (N = 27), WERE INCLUDED. THE DIFFERENCE IN MEAN NUMBER OF METHYLATED GENES IN THE CANCER GROUP (8.41 (95% CI 7.62-9.20)) VS THE TOTAL CONTROL GROUP (4.74 (95% CI 4.40-5.08)) WAS HIGHLY SIGNIFICANT (P < 0.001). A DIAGNOSTIC PREDICTION MODEL (AGE >65, BMP3, RASSF1A, BNC1, MESTV2, TFPI2, APC, SFRP1 AND SFRP2) HAD AN AREA UNDER THE CURVE OF 0.86 (SENSITIVITY 76%, SPECIFICITY 83%). THE MODEL PERFORMANCE WAS INDEPENDENT OF CANCER STAGE. CONCLUSIONS: CELL-FREE DNA PROMOTER HYPERMETHYLATION HAS THE POTENTIAL TO BE A DIAGNOSTIC MARKER FOR PANCREATIC ADENOCARCINOMA AND DIFFERENTIATE BETWEEN MALIGNANT AND BENIGN PANCREATIC DISEASE. THIS STUDY BRINGS US CLOSER TO A CLINICAL USEFUL DIAGNOSTIC MARKER FOR PANCREATIC CANCER, WHICH IS URGENTLY NEEDED. EXTERNAL VALIDATION IS, HOWEVER, REQUIRED BEFORE THE TEST CAN BE APPLIED IN THE CLINIC. TRIAL REGISTRATION: CLINICALTRIALS.GOV, NCT02079363.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
12  2679  29 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
13  6539  26 TRANSCRIPTIONAL VARIATIONS IN THE WIDER PERITUMORAL TISSUE ENVIRONMENT OF PANCREATIC CANCER. TRANSCRIPTIONAL PROFILING WAS PERFORMED ON 452 RNA PREPARATIONS ISOLATED FROM VARIOUS TYPES OF PANCREATIC TISSUE FROM TUMOUR PATIENTS AND HEALTHY DONORS, WITH A PARTICULAR FOCUS ON PERITUMORAL SAMPLES. PANCREATIC DUCTAL ADENOCARCINOMAS (PDAC) AND CYSTIC TUMOURS WERE MOST DIFFERENT IN THESE NON-TUMOROUS TISSUES SURROUNDING THEM, WHEREAS THE ACTUAL TUMOURS EXHIBITED RATHER SIMILAR TRANSCRIPT PATTERNS. THE ENVIRONMENT OF CYSTIC TUMOURS WAS TRANSCRIPTIONALLY NEARLY IDENTICAL TO NORMAL PANCREAS TISSUE. IN CONTRAST, THE TISSUE AROUND PDAC BEHAVED A LOT LIKE THE TUMOUR, INDICATING SOME KIND OF FIELD DEFECT, WHILE SHOWING FAR LESS MOLECULAR RESEMBLANCE TO BOTH CHRONIC PANCREATITIS AND HEALTHY TISSUE. THIS SUGGESTS THAT THE MAJOR PATHOGENIC DIFFERENCE BETWEEN CYSTIC AND DUCTAL TUMOURS MAY BE DUE TO THEIR CELLULAR ENVIRONMENT RATHER THAN THE FEW VARIATIONS BETWEEN THE TUMOURS. LACK OF CORRELATION BETWEEN DNA METHYLATION AND TRANSCRIPT LEVELS MAKES IT UNLIKELY THAT THE OBSERVED FIELD DEFECT IN THE PERITUMORAL TISSUE OF PDAC IS CONTROLLED TO A LARGE EXTENT BY SUCH EPIGENETIC REGULATION. FUNCTIONALLY, A STRIKINGLY LARGE NUMBER OF AUTOPHAGY-RELATED TRANSCRIPTS WAS CHANGED IN BOTH PDAC AND ITS PERITUMORAL TISSUE, BUT NOT IN OTHER PANCREATIC TUMOURS. A TRANSCRIPTION SIGNATURE OF 15 AUTOPHAGY-RELATED GENES WAS ESTABLISHED THAT PERMITS A PROGNOSIS OF SURVIVAL WITH HIGH ACCURACY AND INDICATES THE ROLE OF AUTOPHAGY IN TUMOUR BIOLOGY.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
14  1064  32 CLINICAL SIGNIFICANCE OF PROMOTER METHYLATION STATUS OF TUMOR SUPPRESSOR GENES IN CIRCULATING DNA OF PANCREATIC CANCER PATIENTS. INTRODUCTION: PANCREATIC DUCTAL ADENOCARCINOMA (PDAC) IS A VERY AGGRESSIVE CANCER. THERE ARE VARIOUS SUB-CELLULAR EVENTS (BOTH GENETIC AND EPIGENETIC) THAT GET DYSREGULATED LEADING TO TUMORIGENESIS. METHYLATION IN PROMOTERS OF TUMOR SUPPRESSOR GENES IS ONE OF THESE EPIGENETIC PHENOMENA CONTRIBUTING TO THE PATHOGENESIS OF CANCER. GENES ANALYZED FOR PROMOTER METHYLATION STATUS IN THIS STUDY NAMELY SPARC (SECRETED PROTEIN ACIDIC AND RICH IN CYSTEINE, UCHL1 (UBIQUITIN CARBOXY-TERMINAL HYDROLASE L1), NPTX2 (NEURONAL PENTRAXIN 2), PENK (PROENKEPHALIN) HAD BEEN STUDIED IN PANCREATIC CANCER, BUT THERE IS A NEED TO CHECK METHYLATION IN THESE GENES AS CIRCULATORY NON-INVASIVE MARKERS. THIS STUDY ANALYZED THE ABSOLUTE QUANTIFICATION OF METHYLATION LEVELS OF SPARC, UCHL1, PENK, AND NPTX2 GENES PROMOTERS IN PDAC PATIENTS AS WELL AS IN CHRONIC PANCREATITIS (CP) PATIENTS AND HEALTHY SUBJECTS (HC) AND EVALUATED ITS CLINICAL SIGNIFICANCE IN PDAC. MATERIALS AND METHODS: THE STUDY INCLUDED 65 PDAC PATIENTS, 25 CP PATIENTS, AND 25 HEALTHY CONTROLS. DNA WAS EXTRACTED FROM THEIR PLASMA SAMPLES AND SUBSEQUENTLY GIVEN BISULFITE TREATMENT. ABSOLUTE QUANTIZATION OF METHYLATED AND UNMETHYLATED COPIES OF GENE PROMOTERS OF ALL THE FOUR GENES WAS PERFORMED USING REAL-TIME PCR (SYBR GREEN) BY THE STANDARD CURVE METHOD. METHYLATION LEVELS WERE EXPRESSED AS METHYLATION INDEX (MI) FOR EACH GENE IN EACH PATIENT. MI WAS CALCULATED FROM ABSOLUTE COPY NUMBERS AS FOLLOWS: MI-METHYLATED COPY NUMBER/METHYLATED COPY NUMBER + UNMETHYLATED COPY NUMBER). THESE INDICES WERE USED TO COMPARE GENE METHYLATION LEVELS WITHIN DIFFERENT GROUPS AND TO CORRELATE WITH CLINICOPATHOLOGICAL FEATURES AND SURVIVAL OF PANCREATIC CANCER PATIENTS. AN APPROPRIATE STATISTICAL ANALYSIS WAS APPLIED. RESULTS: METHYLATION INDICES FOR ALL THE FOUR GENES IN PDAC CASES WERE FOUND TO BE SIGNIFICANTLY HIGHER AS COMPARED TO THAT IN HEALTHY INDIVIDUALS. SPARC MI VALUES WERE FOUND TO DIFFERENTIATE EARLY-STAGE PDAC PATIENTS FROM CP PATIENTS. PDAC PATIENTS WITH THE METASTASIZED DISEASE AND STAGE IV DISEASE WERE FOUND TO HAVE HIGH MI FOR THE SPARC GENE AS WELL AS FOR THE NPTX2 GENE, WHILE A HIGHER UCHL1 METHYLATION INDEX WAS FOUND TO CORRELATE WITH AN ADVANCED STAGE OF THE DISEASE. HIGHER MI VALUES FOR SPARC AND NPTX2 GENES WERE FOUND TO ASSOCIATE WITH POOR SURVIVAL IN PATIENTS WITH PDAC. CONCLUSION: METHYLATION LOAD IN THE FORM OF MI FOR EACH OF THE FOUR GENES ASSESSED IN PLASMA MAY EMERGE AS A NON-INVASIVE BIOMARKER TO DIFFERENTIATE PANCREATIC CANCER FROM HEALTHY INDIVIDUALS. BUT ONLY SPARC AND NPTX2 HYPERMETHYLATION WERE ABLE TO DISTINGUISH PANCREATIC CANCER FROM CHRONIC PANCREATITIS. ASSOCIATION OF ABERRANT METHYLATION IN SPARC AND NPTX2 GENE WITH METASTASIS AND POOR SURVIVAL OF PATIENTS SUGGEST THE ROLE OF METHYLATION IN THESE GENES AS PROGNOSTIC MARKERS.	2020	

15  5144  25 POTENTIAL ROLE OF LNCRNA-TSIX, MIR-548-A-3P, AND SOGA1 MRNA IN THE DIAGNOSIS OF HEPATOCELLULAR CARCINOMA. RECENT TRENDS ARE MOVING TOWARDS THE USE OF THE CIRCULATING TRANSCRIPTOME AS A POTENTIAL DIAGNOSTIC AND THERAPEUTIC TOOL FOR HEPATOCELLULAR CARCINOMA (HCC). THE AIM OF THIS STUDY IS TO IDENTIFY CIRCULATORY RNA BASED BIOMARKER PANEL, IN ADDITION TO THEIR RELATIONSHIP TO THE OUTCOME IN HCC. FIRST, UTILIZING BIOINFORMATICS TOOLS, WE SELECTED AN HCC-SPECIFIC RNA-BASED BIOMARKER PANEL THAT DEPENDED ON THE INTEGRATION OF SUPPRESSOR OF GLUCOSE AUTOPHAGY-ASSOCIATED (SOGA1) GENE EXPRESSION WITH THE CHOSEN PANEL OF EPIGENETIC REGULATORS OF THIS GENE [LONG NON-CODING RNA ANTISENSE FOR X-INACTIVE-SPECIFIC TRANSCRIPT (LNCRNA-TSIX) AND MICRORNA-548-A-3P (MIR-548-A-3P)]. SECOND, WE ATTEMPTED TO VALIDATE THESE BIOMARKERS USING THE SERA OF 65 PATIENTS WITH HCC, 34 PATIENTS WITH CHRONIC HEPATITIS C VIRUS (CHC) INFECTION AND 32 HEALTHY VOLUNTEERS. FINALLY, THE EXPRESSION LEVELS OF THE CHOSEN RNA-BASED BIOMARKER PANEL WERE ASSESSED IN THE SERUM SAMPLES USING QRT-PCR ASSAYS. THE PANEL OF 3 RNA-BASED BIOMARKERS (LNCRNA-TSIX, MIR-548-A-3P, AND SOGA1) EXHIBITED HIGH SENSITIVITY AND SPECIFICITY IN DIFFERENTIATING HCC PATIENTS FROM CHC PATIENTS AND HEALTHY CONTROLS. AMONG THESE 3 RNAS, SERUM LNCRNA-TSIX AND SOGA1 WERE INDEPENDENT PROGNOSTIC FACTOR. THE CHOSEN CIRCULATORY RNA-BASED BIOMARKER PANEL MAY SERVE AS A DIAGNOSTIC AND PROGNOSTIC BIOMARKER FOR HCC.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
16  5237  34 PROFILING OF CELL-FREE DNA METHYLATION AND HISTONE SIGNATURES IN PEDIATRIC NAFLD: A PILOT STUDY. NONALCOHOLIC FATTY LIVER DISEASE (NAFLD) HAS BECOME THE MOST COMMON CHRONIC LIVER DISEASE IN CHILDREN AND ADOLESCENTS, INCREASING THE RISK OF ITS PROGRESSION TOWARD NONALCOHOLIC STEATOHEPATITIS (NASH), CIRRHOSIS, AND CANCER. THERE IS AN URGENT NEED FOR NONINVASIVE EARLY DIAGNOSTIC AND PROGNOSTIC TOOLS SUCH AS EPIGENETIC MARKS (EPIMARKS), WHICH WOULD REPLACE LIVER BIOPSY IN THE FUTURE. WE USED PLASMA SAMPLES FROM 67 CHILDREN WITH BIOPSY-PROVEN NAFLD, AND AS CONTROLS WE USED SAMPLES FROM 20 CHILDREN NEGATIVE FOR STEATOSIS BY ULTRASOUND. ALL PATIENTS WERE GENOTYPED FOR PATATIN-LIKE PHOSPHOLIPASE DOMAIN CONTAINING 3 (PNPLA3), TRANSMEMBRANE 6 SUPERFAMILY MEMBER 2 (TM6SF2), MEMBRANE BOUND O-ACYLTRANSFERASE DOMAIN CONTAINING 7 (MBOAT7), AND KLOTHO-BETA (KLB) GENE VARIANTS, AND DATA ON ANTHROPOMETRIC AND BIOCHEMICAL PARAMETERS WERE COLLECTED. FURTHERMORE, PLASMA CELL-FREE DNA (CFDNA) METHYLATION WAS QUANTIFIED USING A COMMERCIALLY AVAILABLE KIT, AND IMAGESTREAM(X) WAS USED FOR THE DETECTION OF FREE CIRCULATING HISTONE COMPLEXES AND VARIANTS. WE FOUND A SIGNIFICANT ENRICHMENT OF THE LEVELS OF HISTONE MACROH2A1.2 IN THE PLASMA OF CHILDREN WITH NAFLD COMPARED TO CONTROLS, AND A STRONG CORRELATION BETWEEN CFDNA METHYLATION LEVELS AND NASH. RECEIVER OPERATING CHARACTERISTIC CURVE ANALYSIS DEMONSTRATED THAT COMBINATION OF CFDNA METHYLATION, PNPLA3 RS738409 VARIANT, COUPLED WITH EITHER HIGH-DENSITY LIPOPROTEIN CHOLESTEROL OR ALANINE AMINOTRANSFERASE LEVELS CAN STRONGLY PREDICT THE PROGRESSION OF PEDIATRIC NAFLD TO NASH WITH AREA UNDER THE CURVE >0.87. CONCLUSION: OUR PILOT STUDY COMBINED EPIMARKS AND GENETIC AND METABOLIC MARKERS FOR A ROBUST RISK ASSESSMENT OF NAFLD DEVELOPMENT AND PROGRESSION IN CHILDREN, OFFERING A PROMISING NONINVASIVE TOOL FOR THE CONSISTENT DIAGNOSIS AND PROGNOSIS OF PEDIATRIC NAFLD. FURTHER STUDIES ARE NECESSARY TO IDENTIFY THEIR PATHOGENIC ORIGIN AND FUNCTION.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
17    27  24 A B-CELL EPIGENETIC SIGNATURE DEFINES THREE BIOLOGIC SUBGROUPS OF CHRONIC LYMPHOCYTIC LEUKEMIA WITH CLINICAL IMPACT. PROSPECTIVE IDENTIFICATION OF PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) DESTINED TO PROGRESS WOULD GREATLY FACILITATE THEIR CLINICAL MANAGEMENT. RECENTLY, WHOLE-GENOME DNA METHYLATION ANALYSES IDENTIFIED THREE CLINICOBIOLOGIC CLL SUBGROUPS WITH AN EPIGENETIC SIGNATURE RELATED TO DIFFERENT NORMAL B-CELL COUNTERPARTS. HERE, WE DEVELOPED A CLINICALLY APPLICABLE METHOD TO IDENTIFY THESE SUBGROUPS AND TO STUDY THEIR CLINICAL RELEVANCE. USING A SUPPORT VECTOR MACHINE APPROACH, WE BUILT A PREDICTION MODEL USING FIVE EPIGENETIC BIOMARKERS THAT WAS ABLE TO CLASSIFY CLL PATIENTS ACCURATELY INTO THE THREE SUBGROUPS, NAMELY NAIVE B-CELL-LIKE, INTERMEDIATE AND MEMORY B-CELL-LIKE CLL. DNA METHYLATION WAS QUANTIFIED BY HIGHLY REPRODUCIBLE BISULFITE PYROSEQUENCING ASSAYS IN TWO INDEPENDENT CLL SERIES. IN THE INITIAL SERIES (N=211), THE THREE SUBGROUPS SHOWED DIFFERENTIAL LEVELS OF IGHV (IMMUNOGLOBULIN HEAVY-CHAIN LOCUS) MUTATION (P<0.001) AND VH USAGE (P<0.03), AS WELL AS DIFFERENT CLINICAL FEATURES AND OUTCOME IN TERMS OF TIME TO FIRST TREATMENT (TTT) AND OVERALL SURVIVAL (P<0.001). A MULTIVARIATE COX MODEL SHOWED THAT EPIGENETIC CLASSIFICATION WAS THE STRONGEST PREDICTOR OF TTT (P<0.001) ALONG WITH BINET STAGE (P<0.001). THESE FINDINGS WERE CORROBORATED IN A VALIDATION SERIES (N=97). IN THIS STUDY, WE DEVELOPED A SIMPLE AND ROBUST METHOD USING EPIGENETIC BIOMARKERS TO CATEGORIZE CLLS INTO THREE SUBGROUPS WITH DIFFERENT CLINICOBIOLOGIC FEATURES AND OUTCOME.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
18  1065  26 CLINICAL SIGNIFICANCE OF SERUM DRAM1 MRNA, ARSA MRNA, HSA-MIR-2053 AND LNCRNA-RP1-86D1.3 AXIS EXPRESSION IN MALIGNANT PLEURAL MESOTHELIOMA. AIM AND BACKGROUND: MALIGNANT PLEURAL MESOTHELIOMA (MPM) IS A LETHAL CANCER MAINLY CAUSED BY CHRONIC EXPOSURE OF ASBESTOS. IN THIS PILOT STUDY, WE AIMED TO ASSESS THE EXPRESSION OF SERUM RNA-BASED BIOMARKER PANEL EXPLORING THEIR CLINICAL UTILITY AS DIAGNOSTIC AND PROGNOSTIC BIOMARKERS FOR MPM. METHODS: WE HAVE SELECTED AN MPM-SPECIFIC RNA-BASED BIOMARKER PANEL THROUGH BIOINFORMATICS ANALYSIS BASED ON THE INTEGRATION OF DNA DAMAGE REGULATED AUTOPHAGY MODULATOR 1 (DRAM1) AND ARYLSULFATASE A ( ARSA) GENE EXPRESSION WITH THEIR EPIGENETIC REGULATORS MICRORNA ( MIR-2053) AND LONG NONCODING RNA ( LNCRNA-RP1-86D1.3). THEN, QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION (QPCR) VALIDATION IN SERA OF 60 MPM PATIENTS, 20 CHRONIC ASBESTOS EXPOSURE PATIENTS, AND 20 HEALTHY VOLUNTEERS WAS DONE. LASTLY, THE PROGNOSTIC POWER OF THE SELECTED PANEL WAS ASSESSED. RESULTS: THE EXPRESSION OF SERUM DRAM1 MESSENGER RNA (MRNA), ARSA MRNA, HSA-MIR-2053 AND LNCRNA-RP1-86D1.3 WERE POSITIVE IN 78.3%, 90%, 85%, AND 83.3% OF MPM PATIENTS, RESPECTIVELY. THE RNA-BASED BIOMARKER PANEL WAS ABLE TO DISCRIMINATE BETWEEN MPM PATIENTS AND CONTROLS WITH HIGH ACCURACY AND THEIR COMBINED SENSITIVITY REACHED 100% FOR THE DIAGNOSIS OF MPM. KAPLAN-MEIER ANALYSIS SHOWED THAT HSA-MIR-2053 IS AN INDEPENDENT PROGNOSTIC FACTOR OF MPM. CONCLUSION: OUR PRELIMINARY DATA REVEALED THAT THE CHOSEN RNAS PLAY AN IMPORTANT ROLE IN DRIVING MPM DEVELOPMENT AND PROGRESSION.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
19   408  27 ANALYSIS OF GENE EXPRESSION AND METHYLATION DATASETS IDENTIFIED ADAMTS9, FKBP5, AND PFKBF3 AS BIOMARKERS FOR OSTEOARTHRITIS. BACKGROUND: OSTEOARTHRITIS (OA) IS A KIND OF CHRONIC OSTEOARTHROPATHY AND DEGENERATIVE JOINT DISEASE. EPIGENETIC REGULATION IN THE GENE EXPRESSION DYNAMICS HAS BECOME INCREASINGLY IMPORTANT IN OA. WE PERFORMED A COMBINED ANALYSIS OF TWO TYPES OF MICROARRAY DATASETS (GENE EXPRESSION AND DNA METHYLATION) TO IDENTIFY METHYLATION-BASED KEY BIOMARKERS TO PROVIDE A BETTER UNDERSTANDING OF MOLECULAR BIOLOGICAL MECHANISMS OF OA. METHODS: WE OBTAINED TWO EXPRESSION PROFILING DATASETS (GSE55235, GSE55457) AND ONE DNA METHYLATION PROFILING DATA SET (GSE63695) FROM THE GENE EXPRESSION OMNIBUS. FIRST, DIFFERENTIALLY EXPRESSED GENES (DEGS) BETWEEN PATIENTS WITH OA AND CONTROLS WERE IDENTIFIED USING THE LIMMA PACKAGE IN R(V3.4.4). THEN, FUNCTION ENRICHMENT ANALYSIS OF DEGS WAS PERFORMED USING A DAVID DATABASE. FOR DNA METHYLATION DATASETS, CHAMP METHYLATION ANALYSIS PACKAGE WAS USED TO IDENTIFY DIFFERENTIAL METHYLATION GENES (DMGS). FINALLY, A COMPREHENSIVE ANALYSIS OF DEGS AND DMGS WAS CONDUCTED TO IDENTIFY GENES THAT EXHIBITED DIFFERENTIAL EXPRESSION AND METHYLATION SIMULTANEOUSLY. RESULTS: WE IDENTIFIED 112 DEGS AND 2,896 DMGS IN PATIENTS WITH OA COMPARED WITH CONTROLS. FUNCTIONAL ANALYSIS OF DEGS OBTAINED THAT INFLAMMATORY RESPONSES, IMMUNE RESPONSES, AND POSITIVE REGULATION OF APOPTOSIS, TUMOR NECROSIS FACTOR (TNF) SIGNALING PATHWAY, AND OSTEOCLAST DIFFERENTIATION MAY BE INVOLVED IN THE PATHOGENESIS OF OA. CROSS-ANALYSIS REVEALED 26 GENES THAT EXHIBITED DIFFERENTIAL EXPRESSION AND METHYLATION IN OA. AMONG THEM, ADAMTS9, FKBP5, AND PFKBF3 WERE IDENTIFIED AS VALUABLE METHYLATION-BASED BIOMARKERS FOR OA. CONCLUSION: IN SUMMARY, OUR STUDY IDENTIFIED DIFFERENT MOLECULAR FEATURES BETWEEN PATIENTS WITH OA AND CONTROLS. THIS MAY PROVIDE NEW CLUES FOR CLARIFYING THE PATHOGENETIC MECHANISMS OF OA.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
20  3925  29 LIQUID BIOPSIES BASED ON DNA METHYLATION AS BIOMARKERS FOR THE DETECTION AND PROGNOSIS OF LUNG CANCER. LUNG CANCER (LC) IS THE MAIN CAUSE OF CANCER-RELATED MORTALITY. MOST LC PATIENTS ARE DIAGNOSED IN AN ADVANCED STAGE WHEN THE SYMPTOMS ARE OBVIOUS, AND THE PROGNOSIS IS QUITE POOR. ALTHOUGH LOW-DOSE COMPUTED TOMOGRAPHY (LDCT) IS A ROUTINE CLINICAL EXAMINATION FOR EARLY DETECTION OF LC, THE FALSE-POSITIVE RATE IS OVER 90%. AS ONE OF THE INTENSELY STUDIED EPIGENETIC MODIFICATIONS, DNA METHYLATION PLAYS A KEY ROLE IN VARIOUS DISEASES, INCLUDING CANCER AND OTHER DISEASES. HYPERMETHYLATION IN TUMOR SUPPRESSOR GENES OR HYPOMETHYLATION IN ONCOGENES IS AN IMPORTANT EVENT IN TUMORIGENESIS. REMARKABLY, DNA METHYLATION USUALLY OCCURS IN THE VERY EARLY STAGE OF MALIGNANT TUMORS. THUS, DNA METHYLATION ANALYSIS MAY PROVIDE SOME USEFUL INFORMATION ABOUT THE EARLY DETECTION OF LC. IN RECENT YEARS, LIQUID BIOPSY HAS DEVELOPED RAPIDLY. LIQUID BIOPSY CAN DETECT AND MONITOR BOTH PRIMARY AND METASTATIC MALIGNANT TUMORS AND CAN REFLECT TUMOR HETEROGENEITY. MOREOVER, IT IS A MINIMALLY INVASIVE PROCEDURE, AND IT CAUSES LESS PAIN FOR PATIENTS. THIS REVIEW SUMMARIZED VARIOUS LIQUID BIOPSIES BASED ON DNA METHYLATION FOR LC. AT FIRST, WE BRIEFLY DISCUSSED SOME EMERGING TECHNOLOGIES FOR DNA METHYLATION ANALYSIS. SUBSEQUENTLY, WE OUTLINED CELL-FREE DNA (CFDNA), SPUTUM, BRONCHOALVEOLAR LAVAGE FLUID, BRONCHIAL ASPIRATES, AND BRONCHIAL WASHINGS DNA METHYLATION-BASED LIQUID BIOPSY FOR THE EARLY DETECTION OF LC. FINALLY, THE PROGNOSTIC VALUE OF DNA METHYLATION IN CFDNA AND SPUTUM AND THE DIAGNOSTIC VALUE OF OTHER DNA METHYLATION-BASED LIQUID BIOPSIES FOR LC WERE ALSO ANALYZED.	2022