1 5237 170 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                               
2  413  47 ANALYSIS OF MIRNAS PROFILES IN SERUM OF PATIENTS WITH STEATOSIS AND STEATOHEPATITIS. NON-ALCOHOLIC FATTY LIVER DISEASE (NAFLD) IS EMERGING AS ONE OF THE MOST COMMON CHRONIC LIVER DISEASES WORLDWIDE, AFFECTING 25% OF THE WORLD POPULATION. IN RECENT YEARS, THERE HAS BEEN INCREASING EVIDENCE FOR THE INVOLVEMENT OF MICRORNAS IN THE EPIGENETIC REGULATION OF GENES TAKING PART IN THE DEVELOPMENT OF STEATOSIS AND STEATOHEPATITIS-TWO MAIN STAGES OF NAFLD PATHOGENESIS. IN THE PRESENT STUDY, MIRNA PROFILES WERE STUDIED IN GROUPS OF PATIENTS WITH STEATOSIS AND STEATOHEPATITIS TO COMPARE THE CHARACTERISTICS OF RNA-DEPENDENT EPIGENETIC REGULATION OF THE STAGES OF NAFLD DEVELOPMENT. ACCORDING TO THE RESULTS OF MIRNA SCREENING, 23 MIRNAS WERE DIFFERENTIALLY EXPRESSED SERUM IN A GROUP OF PATIENTS WITH STEATOHEPATITIS AND 2 IN A GROUP OF PATIENTS WITH STEATOSIS. MIR-195-5P AND MIR-16-5P ARE COMMON DIFFERENTIALLY EXPRESSED MIRNAS FOR BOTH STEATOSIS AND STEATOHEPATITIS. WE ANALYZED THE OBTAINED RESULTS: THE SEARCH FOR TARGET GENES FOR THE DIFFERENTIALLY EXPRESSED MIRNAS IN OUR STUDY AND THE SUBSEQUENT GENE SET ENRICHMENT ANALYSIS PERFORMED ON KEGG AND REACTOME DATABASES REVEALED WHICH METABOLIC PATHWAYS UNDERGO CHANGES IN RNA-DEPENDENT EPIGENETIC REGULATION IN STEATOSIS AND STEATOHEPATITIS. NEW FINDINGS WITHIN THE FRAMEWORK OF THIS STUDY ARE THE DYSREGULATION OF NEUROHUMORAL PATHWAYS IN THE PATHOGENESIS OF NAFLD AS AN OBJECT OF CHANGES IN RNA-DEPENDENT EPIGENETIC REGULATION. THE MIRNAS DIFFERENTIALLY EXPRESSED IN OUR STUDY WERE FOUND TO TARGET 7% OF GENES IN THE CLASSIC PATHOGENESIS OF NAFLD IN THE GROUP OF PATIENTS WITH STEATOSIS AND 50% IN THE GROUP OF PATIENTS WITH STEATOHEPATITIS. THE EFFECTS OF THESE MICRORNAS ON GENES FOR THE PATHOGENESIS OF NAFLD WERE ANALYZED IN DETAIL. MIR-374A-5P, MIR-1-3P AND MIR-23A-3P DO NOT TARGET GENES DIRECTLY INVOLVED IN THE PATHOGENESIS OF NAFLD. THE DIFFERENTIALLY EXPRESSED MIRNAS FOUND IN THIS STUDY TARGET GENES LARGELY RESPONSIBLE FOR MITOCHONDRIAL FUNCTION. THE ROLE OF MIR-423-5P, MIR-143-5P AND MIR-200C-3 IN REGULATING APOPTOTIC PROCESSES IN THE LIVER AND HEPATOCARCINOGENESIS IS OF INTEREST FOR FUTURE EXPERIMENTAL STUDIES. THESE MIR-374A, MIR-143, MIR-1, MIR-23A, AND MIR-423 HAVE POTENTIAL FOR STEATOHEPATITIS DIAGNOSIS AND ARE POORLY STUDIED IN THE CONTEXT OF NAFLD. THUS, THIS WORK OPENS UP PROSPECTS FOR FURTHER STUDIES OF MICRORNAS AS DIAGNOSTIC AND THERAPEUTIC BIOMARKERS FOR NAFLD.	2021	

3 1519  35 DNA METHYLATION AT ATP11A CG11702988 IS A BIOMARKER OF LUNG DISEASE SEVERITY IN CYSTIC FIBROSIS: A LONGITUDINAL STUDY. CYSTIC FIBROSIS (CF) IS A CHRONIC GENETIC DISEASE THAT MAINLY AFFECTS THE RESPIRATORY AND GASTROINTESTINAL SYSTEMS. NO CURATIVE TREATMENTS ARE AVAILABLE, BUT THE FOLLOW-UP IN SPECIALIZED CENTERS HAS GREATLY IMPROVED THE PATIENT LIFE EXPECTANCY. ROBUST BIOMARKERS ARE REQUIRED TO MONITOR THE DISEASE, GUIDE TREATMENTS, STRATIFY PATIENTS, AND PROVIDE OUTCOME MEASURES IN CLINICAL TRIALS. IN THE PRESENT STUDY, WE OUTLINE A STRATEGY TO SELECT PUTATIVE DNA METHYLATION BIOMARKERS OF LUNG DISEASE SEVERITY IN CYSTIC FIBROSIS PATIENTS. IN THE DISCOVERY STEP, WE SELECTED SEVEN POTENTIAL BIOMARKERS USING A GENOME-WIDE DNA METHYLATION DATASET THAT WE GENERATED IN NASAL EPITHELIAL SAMPLES FROM THE METHYLCF COHORT. IN THE REPLICATION STEP, WE ASSESSED THE SAME BIOMARKERS USING SPUTUM CELL SAMPLES FROM THE METHYLBIOMARK COHORT. OF INTEREST, DNA METHYLATION AT THE CG11702988 SITE (ATP11A GENE) POSITIVELY CORRELATED WITH LUNG FUNCTION AND BMI, AND NEGATIVELY CORRELATED WITH LUNG DISEASE SEVERITY, P. AERUGINOSA CHRONIC INFECTION, AND THE NUMBER OF EXACERBATIONS. THESE RESULTS WERE REPLICATED IN PROSPECTIVE SPUTUM SAMPLES COLLECTED AT FOUR TIME POINTS WITHIN AN 18-MONTH PERIOD AND LONGITUDINALLY. TO CONCLUDE, (I) WE IDENTIFIED A DNA METHYLATION BIOMARKER THAT CORRELATES WITH CF SEVERITY, (II) WE PROVIDED A METHOD TO EASILY ASSESS THIS BIOMARKER, AND (III) WE CARRIED OUT THE FIRST LONGITUDINAL ANALYSIS OF DNA METHYLATION IN CF PATIENTS. THIS NEW EPIGENETIC BIOMARKER COULD BE USED TO STRATIFY CF PATIENTS IN CLINICAL TRIALS.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
4 4286  51 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	
         
5 1587  41 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
6 5638  41 SERUM METABOLOMICS REVEALS PATHWAYS AND BIOMARKERS ASSOCIATED WITH ASTHMA PATHOGENESIS. BACKGROUND: ASTHMA IS A CHRONIC INFLAMMATORY DISEASE CAUSED BY COMPLEX INTERACTIONS OF GENETIC, EPIGENETIC, AND ENVIRONMENTAL FACTORS. FOR THIS REASON, NEW APPROACHES ARE REQUIRED TO CLARIFY THE PATHOGENESIS OF ASTHMA BY SYSTEMIC REVIEW. OBJECTIVE: WE APPLIED A (1)H-NMR METABOLOMICS APPROACH TO INVESTIGATE THE ALTERED METABOLIC PATTERN IN SERA FROM PATIENTS WITH ASTHMA AND SOUGHT TO IDENTIFY THE MECHANISM UNDERLYING ASTHMA AND POTENTIAL BIOMARKERS. METHOD: A GLOBAL PROFILE OF SERA FROM PATIENTS WITH ASTHMA (N = 39) AND CONTROLS (N = 26) WAS GENERATED USING (1)H-NMR SPECTROSCOPY COUPLED WITH MULTIVARIATE STATISTICAL ANALYSIS. ENDOGENOUS METABOLITES IN SERUM WERE RAPIDLY MEASURED USING THE TARGET-PROFILING PROCEDURE. RESULTS: MULTIVARIATE STATISTICAL ANALYSIS SHOWED A CLEAR DISTINCTION BETWEEN PATIENTS WITH ASTHMA AND HEALTHY SUBJECTS. SERA OF ASTHMA PATIENTS WERE CHARACTERIZED BY INCREASED LEVELS OF METHIONINE, GLUTAMINE, AND HISTIDINE AND BY DECREASED LEVELS OF FORMATE, METHANOL, ACETATE, CHOLINE, O-PHOSPHOCHOLINE, ARGININE, AND GLUCOSE. THE METABOLITES DETECTED IN THE SERA OF PATIENTS WITH ASTHMA ARE INVOLVED IN HYPERMETHYLATION, RESPONSE TO HYPOXIA, AND IMMUNE REACTION. FURTHERMORE, THE LEVELS OF SERUM METABOLITES FROM PATIENTS WITH ASTHMA CORRELATED WITH ASTHMA SEVERITY; IN PARTICULAR, LIPID METABOLISM WAS ALTERED IN PATIENTS WITH LOWER FORCED EXPIRATORY VOLUME IN 1 S PERCENTAGE (FEV(1)%) PREDICTED VALUES. IN ADDITION, POTENTIAL BIOMARKERS SHOWED STRONG PREDICTIVE POWER IN ROC ANALYSIS, AND THE PRESENCE OF ASTHMA IN EXTERNAL VALIDATION MODELS WAS PREDICTED WITH HIGH ACCURACY (90.9% FOR ASTHMA AND 100% FOR CONTROL SUBJECTS). CONCLUSION & CLINICAL RELEVANCE: THESE DATA SHOWED THAT (1)H-NMR-BASED METABOLITE PROFILING OF SERUM MAY BE USEFUL FOR THE EFFECTIVE DIAGNOSIS OF ASTHMA AND A FURTHER UNDERSTANDING OF ITS PATHOGENESIS.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
7 1444  48 DIFFERENTIALLY HYPOMETHYLATED CELL-FREE DNA AND CORONARY COLLATERAL CIRCULATION. BACKGROUND: THE FACTORS AFFECTING CARDIOPROTECTIVE COLLATERAL CIRCULATION ARE STILL INCOMPLETELY UNDERSTOOD. RECENTLY, CHARACTERISTICS, SUCH AS CPG METHYLATION OF CELL-FREE DNA (CFDNA), HAVE BEEN REPORTED AS MARKERS WITH CLINICAL UTILITY. THE AIM OF THIS STUDY WAS TO EVALUATE WHETHER CFDNA METHYLATION PATTERNS ARE ASSOCIATED WITH THE GRADE OF CORONARY COLLATERAL CIRCULATION (CCC). RESULT: IN THIS CASE-CONTROL STUDY, CLINICAL AND ANGIOGRAPHIC DATA WERE OBTAINED FROM 143 PATIENTS (MEAN AGE, 58 YEARS, MALE 71%) WITH CHRONIC TOTAL CORONARY OCCLUSION. ENZYMATIC METHYL-SEQUENCING (EM-SEQ) LIBRARIES WERE PREPARED USING THE CFDNA EXTRACTED FROM THE PLASMA. DATA WERE PROCESSED TO OBTAIN THE AVERAGE METHYLATION FRACTION (AMF) TABLES OF GENOMIC REGIONS FROM WHICH BLACKLISTED REGIONS WERE REMOVED. UNSUPERVISED ANALYSIS OF THE OBTAINED AMF VALUES SHOWED THAT SOME OF THE CHANGES IN METHYLATION WERE DUE TO CCC. THROUGH RANDOM FOREST PREPARATION PROCESS, 256 DIFFERENTIALLY METHYLATED REGION (DMR) CANDIDATES SHOWING STRONG ASSOCIATION WITH CCC WERE SELECTED. A RANDOM FOREST CLASSIFIER WAS THEN CONSTRUCTED, AND THE AREA UNDER THE CURVE OF THE RECEIVER OPERATING CHARACTERISTIC CURVE INDICATED AN APPROPRIATE PREDICTIVE FUNCTION FOR CCC. FINALLY, 20 DMRS WERE IDENTIFIED TO HAVE SIGNIFICANTLY DIFFERENT AMF VALUES BETWEEN THE GOOD AND POOR CCC GROUPS. PARTICULARLY, THE GOOD CCC GROUP EXHIBITED HYPOMETHYLATED DMRS. PATHWAY ANALYSIS REVEALED FIVE PATHWAYS, INCLUDING TGF-BETA SIGNALING, TO BE ASSOCIATED WITH GOOD CCC. CONCLUSION: THESE DATA HAVE DEMONSTRATED THAT DIFFERENTIAL HYPOMETHYLATION WAS IDENTIFIED IN DOZENS OF CFDNA REGIONS IN PATIENTS WITH GOOD CCC. OUR RESULTS SUPPORT THE CLINICAL UTILITY OF NONINVASIVELY OBTAINED EPIGENETIC SIGNATURES FOR PREDICTING COLLATERAL CIRCULATION IN PATIENTS WITH VASCULAR DISEASES.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
8 1345  42 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
9 2653  37 EPIGENOTYPING IN PERIPHERAL BLOOD CELL DNA AND BREAST CANCER RISK: A PROOF OF PRINCIPLE STUDY. BACKGROUND: EPIGENETIC CHANGES ARE EMERGING AS ONE OF THE MOST IMPORTANT EVENTS IN CARCINOGENESIS. TWO ALTERATIONS IN THE PATTERN OF DNA METHYLATION IN BREAST CANCER (BC) HAVE BEEN PREVIOUSLY REPORTED; ACTIVE ESTROGEN RECEPTOR-ALPHA (ER-ALPHA) IS ASSOCIATED WITH DECREASED METHYLATION OF ER-ALPHA TARGET (ERT) GENES, AND POLYCOMB GROUP TARGET (PCGT) GENES ARE MORE LIKELY THAN OTHER GENES TO HAVE PROMOTER DNA HYPERMETHYLATION IN CANCER. HOWEVER, WHETHER DNA METHYLATION IN NORMAL UNRELATED CELLS IS ASSOCIATED WITH BC RISK AND WHETHER THESE IMPRINTS CAN BE RELATED TO FACTORS WHICH CAN BE MODIFIED BY THE ENVIRONMENT, IS UNCLEAR. METHODOLOGY/PRINCIPAL FINDINGS: USING QUANTITATIVE METHYLATION ANALYSIS IN A CASE-CONTROL STUDY (N = 1,083) WE FOUND THAT DNA METHYLATION OF PERIPHERAL BLOOD CELL DNA PROVIDES GOOD PREDICTION OF BC RISK. WE ALSO REPORT THAT INVASIVE DUCTAL AND INVASIVE LOBULAR BC IS CHARACTERIZED BY TWO DIFFERENT SETS OF GENES, THE LATTER PARTICULAR BY GENES INVOLVED IN THE DIFFERENTIATION OF THE MESENCHYME (PITX2, TITF1, GDNF AND MYOD1). FINALLY WE DEMONSTRATE THAT ONLY ERT GENES PREDICT ER POSITIVE BC; LACK OF PERIPHERAL BLOOD CELL DNA METHYLATION OF ZNF217 PREDICTED BC INDEPENDENT OF AGE AND FAMILY HISTORY (ODDS RATIO 1.49; 95% CONFIDENCE INTERVAL 1.12-1.97; P = 0.006) AND WAS ASSOCIATED WITH ER-ALPHA BIOACTIVITY IN THE CORRESPONDING SERUM. CONCLUSION/SIGNIFICANCE: THIS FIRST LARGE-SCALE EPIGENOTYPING STUDY DEMONSTRATES THAT DNA METHYLATION MAY SERVE AS A LINK BETWEEN THE ENVIRONMENT AND THE GENOME. FACTORS THAT CAN BE MODULATED BY THE ENVIRONMENT (LIKE ESTROGENS) LEAVE AN IMPRINT IN THE DNA OF CELLS THAT ARE UNRELATED TO THE TARGET ORGAN AND INDICATE THE PREDISPOSITION TO DEVELOP A CANCER. FURTHER RESEARCH WILL NEED TO DEMONSTRATE WHETHER DNA METHYLATION PROFILES WILL BE ABLE TO SERVE AS A NEW TOOL TO PREDICT THE RISK OF DEVELOPING CHRONIC DISEASES WITH SUFFICIENT ACCURACY TO GUIDE PREVENTIVE MEASURES.	2008	
                                                                                                                                                                                                                                                                                                                                                                                                                          
10 3925  31 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
11 1607  35 DNA METHYLATION, COLON CANCER AND MEDITERRANEAN DIET: RESULTS FROM THE EPIC-ITALY COHORT. THE BIOLOGICAL MECHANISMS THROUGH WHICH ADHERENCE TO MEDITERRANEAN DIET (MD) PROTECTS AGAINST COLON CANCER (CC) ARE POORLY UNDERSTOOD. EVIDENCE SUGGESTS THAT CHRONIC INFLAMMATION MAY BE IMPLICATED IN THE PATHWAY. BOTH DIET AND CC ARE RELATED TO EPIGENETIC REGULATION. WE PERFORMED A NESTED CASE-CONTROL STUDY ON 161 PAIRS FROM THE ITALIAN COMPONENT OF THE EUROPEAN PROSPECTIVE INVESTIGATION INTO CANCER AND NUTRITION (EPIC) COHORT, IN WHICH WE LOOKED FOR THE METHYLATION SIGNALS IN DNA EXTRACTED FROM LEUCOCYTES ASSOCIATED WITH BOTH CC AND MD IN 995 CPGS LOCATED IN 48 INFLAMMATION GENES. THE DNA METHYLATION SIGNALS DETECTED IN THIS ANALYSIS WERE VALIDATED IN A SUBGROUP OF 47 CASE-CONTROL PAIRS AND FURTHER REPLICATED (WHERE VALIDATED) IN 95 NEW PAIRS BY MEANS OF PYROSEQUENCING. AMONG THE CPG SITES SELECTED A-PRIORI IN INFLAMMATION-RELATED GENES, SEVEN CPG SITES WERE FOUND TO BE ASSOCIATED WITH CC STATUS AND WITH MD, IN LINE WITH ITS PROTECTIVE EFFECT. ONLY TWO CPG SITES (CG17968347-SERPINE1 AND CG20674490-RUNX3) WERE VALIDATED USING BISULPHITE PYROSEQUENCING AND, AFTER REPLICATION, WE FOUND THAT DNA METHYLATION OF CG20674490-RUNX3 MAY BE A POTENTIAL MOLECULAR MEDIATOR EXPLAINING THE PROTECTIVE EFFECT OF MD ON CC ONSET. THE USE OF A 'MEET-IN-THE-MIDDLE' APPROACH TO IDENTIFY THE OVERLAP BETWEEN EXPOSURE AND PREDICTIVE MARKERS OF DISEASE IS INNOVATIVE IN STUDIES ON THE RELATIONSHIP BETWEEN DIET AND CANCER, IN WHICH EXPOSURE ASSESSMENT IS DIFFICULT AND THE MECHANISMS THROUGH WHICH THE NUTRIENTS EXERT THEIR PROTECTIVE EFFECT IS LARGELY UNKNOWN.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
12 5304  39 PROTEOMIC ANALYSIS OF INFLAMMATORY BIOMARKERS ASSOCIATED WITH BREAST CANCER RECURRENCE. INTRODUCTION: BREAST CANCER IS THE MOST FREQUENT CANCER DETECTED FOR WOMEN, AND WHILE OUR ABILITY TO TREAT BREAST CANCER HAS IMPROVED SUBSTANTIALLY OVER THE YEARS, RECURRENCE REMAINS A MAJOR OBSTACLE. STANDARD SCREENING FOR NEW AND RECURRENT BREAST CANCER INVOLVES CLINICAL BREAST IMAGING. HOWEVER, THERE IS NO CLINICALLY APPROVED NONINVASIVE BODY FLUID TEST FOR THE EARLY DETECTION OF RECURRENT BREAST CANCER. MATERIALS AND METHOD: IN THIS STUDY, WE ANALYZED SERUM SAMPLES FROM BOTH RECURRENT AND NONRECURRENT BREAST CANCER PATIENTS BY DIFFERENT PROTEOMICS METHODS TO IDENTIFY BIOMARKERS IN PATIENTS WITH RECURRENCE OF DISEASE. RESULTS: COMPARATIVE DATA ANALYSIS IDENTIFIED SEVERAL HISTONE DEACETYLASE (HDAC) PROTEINS, WHICH WERE FOUND AT SIGNIFICANTLY HIGHER LEVELS IN THE SERUM OF RECURRENT BREAST CANCER PATIENTS: HDAC9 (C-TERM) (P = 0.0035), HDAC5 (C-TERM) (P = 0.013), SMALL UBIQUITIN-LIKE MODIFIER 1 (N-TERM) (P = 0.017), EMBRYONIC STEM CELL-EXPRESSED RAS (INTER) (P = 0.018), AND HDAC7 (C-TERM) (P = 0.020). CHRONIC INFLAMMATION PLAYS A CRITICAL ROLE IN THE DEVELOPMENT OF THE BREAST CANCER RECURRENCE, AND WE IDENTIFIED SEVERAL PROINFLAMMATORY CYTOKINES THAT WERE PRESENT AT ELEVATED LEVELS ONLY IN RECURRENT BREAST CANCER PATIENT SERUM. CONCLUSIONS: OUR DATA INDICATED THAT THE EPIGENETIC REGULATION OF INFLAMMATORY PROCESSES PLAYS A CRITICAL ROLE IN BREAST CANCER RECURRENCE. THE IDENTIFIED PROTEINS COULD LAY THE GROUNDWORK FOR THE DEVELOPMENT OF A SERUM-BASED BREAST CANCER RECURRENCE ASSAY.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
13 2820  32 FINE-MAPPING INFLAMMATORY BOWEL DISEASE LOCI TO SINGLE-VARIANT RESOLUTION. INFLAMMATORY BOWEL DISEASES ARE CHRONIC GASTROINTESTINAL INFLAMMATORY DISORDERS THAT AFFECT MILLIONS OF PEOPLE WORLDWIDE. GENOME-WIDE ASSOCIATION STUDIES HAVE IDENTIFIED 200 INFLAMMATORY BOWEL DISEASE-ASSOCIATED LOCI, BUT FEW HAVE BEEN CONCLUSIVELY RESOLVED TO SPECIFIC FUNCTIONAL VARIANTS. HERE WE REPORT FINE-MAPPING OF 94 INFLAMMATORY BOWEL DISEASE LOCI USING HIGH-DENSITY GENOTYPING IN 67,852 INDIVIDUALS. WE PINPOINT 18 ASSOCIATIONS TO A SINGLE CAUSAL VARIANT WITH GREATER THAN 95% CERTAINTY, AND AN ADDITIONAL 27 ASSOCIATIONS TO A SINGLE VARIANT WITH GREATER THAN 50% CERTAINTY. THESE 45 VARIANTS ARE SIGNIFICANTLY ENRICHED FOR PROTEIN-CODING CHANGES (N = 13), DIRECT DISRUPTION OF TRANSCRIPTION-FACTOR BINDING SITES (N = 3), AND TISSUE-SPECIFIC EPIGENETIC MARKS (N = 10), WITH THE LAST CATEGORY SHOWING ENRICHMENT IN SPECIFIC IMMUNE CELLS AMONG ASSOCIATIONS STRONGER IN CROHN'S DISEASE AND IN GUT MUCOSA AMONG ASSOCIATIONS STRONGER IN ULCERATIVE COLITIS. THE RESULTS OF THIS STUDY SUGGEST THAT HIGH-RESOLUTION FINE-MAPPING IN LARGE SAMPLES CAN CONVERT MANY DISCOVERIES FROM GENOME-WIDE ASSOCIATION STUDIES INTO STATISTICALLY CONVINCING CAUSAL VARIANTS, PROVIDING A POWERFUL SUBSTRATE FOR EXPERIMENTAL ELUCIDATION OF DISEASE MECHANISMS.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
14 3248  36 HEPATITIS B VIRUS GENOME ASYMMETRY IN HEPATOCELLULAR CARCINOMA. BACKGROUND: THE ASSOCIATION BETWEEN HEPATITIS B VIRUS (HBV) MUTATIONS AND HEPATOCARCINOGENESIS WERE REPORTED IN THE LITERATURE. PREFERENCE FOR G OVER C IN THE LEADING DNA STRAND HAS BEEN REPORTED TO ACCOUNT FOR THE ASYMMETRY IN NUCLEOTIDE (NT) COMPOSITION. THE AIM OF THIS STUDY WAS TO ANALYZE THE COMPLETE GENOME SEQUENCE AND COMPOSITIONAL ASYMMETRY OF HBV IN DIFFERENT STAGES OF HEPATITIS B. METHODS: FULL GENOME SEQUENCING OF 24 PATIENTS WITH CHRONIC HEPATITIS B, SOME OF WHOM ALSO HAD CIRRHOSIS AND HEPATOCELLULAR CARCINOMA (HCC) WAS PERFORMED. MUTATIONS ANALYSIS WAS IMPLEMENTED IN A COMPARISON WITH A HBV GENOTYPE D REFERENCE FROM AN INTERNATIONAL DNA DATABASE. CPGPROD, A WEB-BASED APPLICATION, WAS USED TO EVALUATE CG CONTENT AND PREDICT CPG ISLANDS. RESULTS: ALL STRAINS WERE 3182 BASE PAIRS (BP) IN LENGTH, EXCEPT FOR TWO CASES OF HCC IN WHICH 9 AND 21 NT, RESPECTIVELY, WERE DELETED IN PRES2. THE GENETIC RELATEDNESS OF THESE ISOLATES WAS 97%-100%. THERE WERE COMMON CPG-RICH REGIONS IN ALL 24 ISOLATED FULL GENOME SEQUENCES, HOWEVER A STRONG NEGATIVE GC SKEW FOR FORMING A CPG ISLAND IN THE MINUS STRAND WERE EXHIBITED IN OVERLAP WITH ENHANCER I IN THREE HCC PATIENTS, A CIRRHOTIC PATIENT AND THREE WITH CHRONIC HEPATITIS. CONCLUSION: THE HIGH PERCENTAGE OF SEQUENCE IDENTITY BETWEEN HBV ISOLATES IN OUR PATIENTS DEMONSTRATES THAT GENOMIC FACTORS, EXCEPT FOR GENOTYPE, ARE INVOLVED IN HEPATOCARCINOGENESIS. VARIATIONS IN GC CONTENT WHICH WERE CAUSED BY A DIFFERENT SPECTRUM OF MUTATIONS MAY AFFECT DNA COMPOSITIONAL ASYMMETRY AND EPIGENETIC MODIFICATION OF HBV DNA IN HCC.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
15 1024  42 CIRCULATING MICRORNAS 34A, 122, AND 192 ARE LINKED TO OBESITY-ASSOCIATED INFLAMMATION AND METABOLIC DISEASE IN PEDIATRIC PATIENTS. BACKGROUND: OBESITY-ASSOCIATED CHRONIC LOW-GRADE INFLAMMATION LEADS TO DYSREGULATION OF CENTRAL LIPID AND GLUCOSE METABOLISM PATHWAYS LEADING TO METABOLIC DISORDERS. MICRORNAS (MIRNAS) ARE KNOWN TO CONTROL REGULATORS OF METABOLIC HOMEOSTASIS. WE AIMED TO ASSESS THE RELATIONSHIP OF CIRCULATING MIRNAS WITH INFLAMMATORY MODULATORS AND METABOLIC DISORDERS IN PEDIATRIC OBESITY. METHODS: FROM A PEDIATRIC COHORT WITH SEVERE OBESITY (N = 109), CLINICALLY THOROUGHLY CHARACTERIZED INCLUDING DIVERSE ROUTINE BLOOD PARAMETERS, ORAL GLUCOSE TOLERANCE TEST, AND LIVER MRI, A PANEL OF 16 CIRCULATING MIRNAS WAS QUANTIFIED USING QRT-PCR. ADDITIONALLY, MARKERS OF INFLAMMATION TNFALPHA, IL1 RECEPTOR ANTAGONIST, PROCALCITONIN, CRP, AND IL-6 WERE MEASURED. RESULTS: MARKERS OF OBESITY-ASSOCIATED INFLAMMATION, TNFALPHA, IL-1RA, AND PROCALCITONIN, ALL SIGNIFICANTLY CORRELATED WITH CONCENTRATIONS OF MIRNAS 122 AND 192. CONCENTRATIONS OF THESE MIRNAS NEGATIVELY CORRELATED WITH SERUM ADIPONECTIN AND WERE AMONG THOSE STRONGLY LINKED TO PARAMETERS OF DYSLIPIDEMIA AND LIVER FUNCTION. MOREOVER, MIRNA122 CONCENTRATIONS CORRELATED WITH HOMA-IR. SEVERAL MIRNA LEVELS INCLUDING MIRNAS 34A, 93, 122, AND 192 WERE STATISTICALLY SIGNIFICANTLY DIFFERING BETWEEN INDIVIDUALS WITH PREDIABETES, IMPAIRED GLUCOSE TOLERANCE, METABOLIC SYNDROME, OR NONALCOHOLIC FATTY LIVER DISEASE COMPARED TO THE RESPECTIVE CONTROLS. ADDITIONALLY, MIRNA 192 WAS SIGNIFICANTLY ELEVATED IN METABOLICALLY UNHEALTHY OBESITY. CONCLUSIONS: A MIRNA PATTERN ASSOCIATED WITH OBESITY-ASSOCIATED INFLAMMATION AND COMORBIDITIES MAY BE USED TO DISTINGUISH METABOLICALLY HEALTHY FROM UNHEALTHY PEDIATRIC PATIENTS WITH OBESITY. MOREOVER, THESE CHANGES IN EPIGENETIC REGULATION COULD POTENTIALLY BE INVOLVED IN THE ETIOLOGY OF OBESITY-LINKED METABOLIC DISEASE IN CHILDREN AND ADOLESCENTS.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
16  782  42 CELL-FREE MICRORNA-148A IS ASSOCIATED WITH RENAL ALLOGRAFT DYSFUNCTION: IMPLICATION FOR BIOMARKER DISCOVERY. BACKGROUND: CHRONIC ALLOGRAFT DYSFUNCTION (CAD), THE FOREMOST CAUSE OF RENAL GRAFT LOSS WORLDWIDE, IS A SERIOUS CHALLENGE FOR MOST OF THE RECIPIENTS. AS THE EPIGENETIC ERA IS EMERGING, EPIGENETIC BIOMARKERS ESPECIALLY MICRORNAS (MIRNAS) MAY REFLECT THE CURRENT STAGE OF THE DISEASE AND PATIENT'S THERAPY RESPONSE. THE CURRENT STUDY INVESTIGATED THE POTENTIAL SIGNIFICANCE OF CIRCULATING MIRNA-148A IN PREDICTING THE RENAL GRAFT FUNCTION. DESIGN AND METHODS: CIRCULATING MIRNAS WERE ISOLATED FROM 53 PLASMA SAMPLES OF RECIPIENTS WITH HISTOLOGICALLY VALIDATED INTERSTITIAL FIBROSIS AND TUBULAR ATROPHY (IFTA, N = 26), AND RECIPIENTS WITH STABLE GRAFT FUNCTION (SGF, N = 27), AND ALSO HEALTHY INDIVIDUALS ( N = 15). THE LEVEL OF MIRNA-148A WAS EVALUATED BY THE QUANTITATIVE POLYMERASE CHAIN REACTION (QPCR) AND CORRELATED WITH CLINICAL AND HISTOLOGICAL PARAMETERS. RESULTS: SIGNIFICANTLY, MIRNA-148A DECREASED IN IFTA COMPARED WITH SGF SUBJECTS (P < 0.001). MIRNA-148A LEVELS INDICATED A SIGNIFICANT ASSOCIATION WITH SERUM CREATININE LEVELS ( R = 0.451, P = 0.021) AND GLOMERULAR FILTRATION RATE ( R = -0.520, P = 0.006). MIRNA-148A EXPRESSION LEVELS COULD DISCRIMINATE IFTA CASES FROM SGF INDIVIDUALS WITH AN AREA UNDER THE CURVE OF 0.89 ( P < 0.001), 97% SENSITIVITY, AND 72% SPECIFICITY. A NUMBER OF PREDICTED TARGETS THAT MIGHT BE INVOLVED IN CAD BY MIRNA-148A WERE PREDICTED. CONCLUSION: PLASMA CELL-FREE MIRNA-148A CORRELATED WITH RENAL FUNCTION AND HISTOLOGICAL GRADES; THEREFORE, IT MAY BE FURTHER INVESTIGATED AS A NOVEL NONINVASIVE MOLECULAR MARKER OF THE PROGRESSION TO IFTA IN RENAL TRANSPLANT RECIPIENTS; MOREOVER, THE EMERGING BIOMARKER MAY BECOME A THERAPEUTIC TARGET IN THE FUTURE CLINIC.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
17 4884  43 OVERVIEW OF THE PATHOGENESIS, GENETIC, AND NON-INVASIVE CLINICAL, BIOCHEMICAL, AND SCORING METHODS IN THE ASSESSMENT OF NAFLD. NONALCOHOLIC FATTY LIVER DISEASE (NAFLD) IS THE MOST PREVALENT CHRONIC LIVER DISEASE WORLDWIDE. IT REPRESENTS A RANGE OF DISORDERS, INCLUDING SIMPLE STEATOSIS, NONALCOHOLIC STEATOHEPATITIS (NASH), AND LIVER CIRRHOSIS, AND ITS PREVALENCE CONTINUES TO RISE. IN SOME CASES, HEPATOCELLULAR CARCINOMA (HCC) MAY DEVELOP. THE DEVELOP;MENT OF NON-INVASIVE DIAGNOSTIC AND SCREENING TOOLS IS NEEDED, IN ORDER TO REDUCE THE FREQUENCY OF LIVER BIOPSIES. THE MOST PROMISING METHODS ARE THOSE ABLE TO EXCLUDE ADVANCED FIBROSIS AND QUANTIFY STEATOSIS. IN THIS STUDY, NEW PERSPECTIVE MARKERS FOR INFLAMMATION, OXIDATIVE STRESS, APOPTOSIS, AND FIBROGENESIS; EMERGING SCORING MODELS FOR DETECTING HEPATIC STEATOSIS AND FIBROSIS; AND NEW GENETIC, EPIGENETIC, AND MULTIOMIC STUDIES ARE DISCUSSED. AS ISOLATED BIOCHEMICAL PARAMETERS ARE NOT SPECIFIC OR SENSITIVE ENOUGH TO PREDICT THE PRESENCE OF NASH AND FIBROSIS, THERE IS A TENDENCY TO USE VARIOUS MARKERS AND COMBINE THEM INTO MATHEMATICAL ALGORITHMS. SEVERAL PREDICTIVE MODELS AND SCORING SYSTEMS HAVE BEEN DEVELOPED. CURRENT DATA SUGGESTS THAT PANELS OF MARKERS (NAFLD FIBROSIS SCORE, FIB-4 SCORE, BARD SCORE, AND OTHERS) ARE USEFUL DIAGNOSTIC MODALITIES TO MINIMIZE THE NUMBER OF LIVER BIOPSIES. THE REVIEW UNVEILS PATHOPHYSIOLOGICAL ASPECTS RELATED TO NEW TRENDS IN CURRENT NON-INVASIVE BIOCHEMICAL, GENETIC, AND SCORING METHODS, AND PROVIDES INSIGHT INTO THEIR DIAGNOSTIC ACCURACIES AND SUITABILITY IN CLINICAL PRACTICE.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
18  177  39 ACCELERATED EPIGENETIC AGING AND INFLAMMATORY/IMMUNOLOGICAL PROFILE (IPAGE) IN PATIENTS WITH CHRONIC KIDNEY DISEASE. CHRONIC KIDNEY DISEASE (CKD) IS DEFINED BY A REDUCED ESTIMATED GLOMERULAR FILTRATION RATE (EGFR). THIS FAILURE CAN BE RELATED TO A PHENOTYPE OF ACCELERATED AGING. IN THIS WORK, WE CONSIDERED 76 PATIENTS WITH END-STAGE RENAL DISEASE (ESRD) AND 83 HEALTHY CONTROLS. WE CONCOMITANTLY EVALUATED FOR THE FIRST TIME TWO MEASURES THAT CAN BE INFORMATIVE OF THE RATE OF AGING, I.E., WHOLE BLOOD DNA METHYLATION USING THE ILLUMINA INFINIUM EPIC ARRAY AND PLASMA LEVELS OF A SELECTION OF INFLAMMATORY/IMMUNOLOGICAL PROTEINS USING MULTIPLEX IMMUNOASSAYS. FIRST OF ALL, WE DEMONSTRATED ACCELERATED AGING IN TERMS OF THE MOST COMMON EPIGENETIC AGE ESTIMATORS IN CKD PATIENTS. MOREOVER, WE DEVELOPED A NEW CLOCK/PREDICTOR OF AGE BASED ON THE INFLAMMATORY/IMMUNOLOGICAL PROFILE (IPAGE) AND IDENTIFIED THE INFLAMMATORY/IMMUNOLOGICAL BIOMARKERS DIFFERENTIALLY EXPRESSED BETWEEN CASES AND CONTROLS. IPAGE APPEARED TO BE MORE SENSITIVE THAN EPIGENETIC CLOCKS IN QUANTIFYING THE ACCELERATED AGING PHENOTYPE OF ESRD PATIENTS. INTERESTINGLY, WE DID NOT FIND ANY CORRELATION BETWEEN THE AGE ACCELERATION EVALUATED ACCORDING TO THE EPIGENETIC CLOCKS AND IPAGE IN EITHER THE ESRD GROUP OR THE CONTROL GROUP. ON THE WHOLE, OUR DATA SHOW A CONSISTENT ACCELERATED AGING PHENOTYPE IN ESRD PATIENTS, WHICH IS BETTER APPRECIATED BY QUANTIFYING THE UNDERLYING INFLAMMATORY PROCESSES (INFLAMMAGING) BY IPAGE THAN BY USING EPIGENETIC CLOCKS.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
19 6488  38 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	
                                                                                                                                                                                                                             
20 2420  46 EPIGENETIC SIGNATURE OF IMPAIRED FASTING GLUCOSE IN THE OLD ORDER AMISH. INTRODUCTION: TYPE 2 DIABETES (T2D) IS A COMMON CHRONIC DISEASE WITH SUBSTANTIAL DISEASE BURDEN AND ECONOMIC IMPACT. LIFESTYLE CHANGES CAN SIGNIFICANTLY ALTER THE COURSE OF THE DISEASE, IF DETECTED AT AN EARLY STAGE. DNA METHYLATION SIGNATURE MAY SERVE AS A BIOMARKER FOR EARLY DETECTION OF INCREASED T2D RISK. DESIGN: DNA METHYLATION PROFILING WAS PERFORMED USING THE ILLUMINA INFINIUM HUMAN METHYLATION 450K BEAD CHIP ARRAY IN 24 NORMOGLYCEMIC OLD ORDER AMISH (OOA) INDIVIDUALS WHO LATER DEVELOPED IMPAIRED FASTING GLUCOSE (IFG) (CASES), AND 24 OOA INDIVIDUALS WHO REMAINED NORMOGLYCEMIC AFTER AN AVERAGE FOLLOW UP OF 10 YEARS (CONTROLS). CASES AND CONTROLS WERE MATCHED ON AGE, SEX, BMI, BASELINE FASTING GLUCOSE, AND GLUCOSE LEVEL AFTER 2 H FROM 75 G ORAL GLUCOSE TOLERANCE TEST (OGTT). RESULTS: ASSOCIATION ANALYSIS FOUND NO SIGNIFICANT DIFFERENCE IN EITHER GLOBAL METHYLATION OR INDIVIDUAL PROBE METHYLATION BETWEEN CASES AND CONTROLS, HOWEVER, THE TOP 34 SUGGESTIVE SIGNIFICANT SITES WERE LOCATED IN GENES WITH INTERESTING BIOLOGICAL LINKS TO T2D AND GLYCEMIC TRAITS. THESE GENES INCLUDE BTC THAT PLAYS A ROLE IN PANCREATIC CELL PROLIFERATION AND INSULIN SECRETION, ITGA1 A KNOWN BONE MINERAL DENSITY GENE THAT WAS RECENTLY FOUND TO BE ASSOCIATED ALSO WITH T2D AND GLYCEMIC TRAITS, AND MAY EXPLAIN THE LINK BETWEEN T2D AND BMD, AND RPTOR AND TSC2 BOTH OF WHICH ARE PART OF INSULIN SIGNALING PATHWAY. CONCLUSIONS: THESE RESULTS MAY SHED LIGHT ON THE INITIATION AND DEVELOPMENT OF HYPERGLYCEMIA AND T2D AND HELP TO IDENTIFY HIGH RISK INDIVIDUALS FOR EARLY INTERVENTION; HOWEVER, FURTHER STUDIES ARE REQUIRED FOR VALIDATION.	2017