1   512 137 ASSOCIATION OF SAT-A AND ALU METHYLATION STATUS WITH HCV-INDUCED CHRONIC LIVER DISEASE AND HEPATOCELLULAR CARCINOMA. BACKGROUND: THE COMBINATION OF EPIGENETIC AND GENETIC ABNORMALITIES CONTRIBUTES TOGETHER TO THE DEVELOPMENT OF LIVER CANCER. THE METHYLATION STATUS OF THE REPETITIVE ELEMENTS (RES) IN DNA HAS BEEN INVESTIGATED IN A VARIETY OF HUMAN ILLNESSES. HOWEVER, THE METHYLATION PATTERNS OF SAT-ALPHA AND ALU RES IN CHRONIC LIVER DISEASE (CLD) AND HEPATOCELLULAR CARCINOMA (HCC) CAUSED BY HEPATITIS C VIRUS (HCV) HAVE NEVER BEEN STUDIED BEFORE. METHODOLOGY: IN THIS STUDY, 3 GROUPS OF PARTICIPANTS INCLUDING 50 PATIENTS HAVING HCV-INDUCED CLD, 50 PATIENTS HAVING HCV-INDUCED HCC, AND 46 HEALTHY SUBJECTS WERE SUBJECTED TO MEASUREMENT OF SAT-ALPHA AND ALU METHYLATION USING THE QUANTITATIVE METHYLIGHT ASSAY. RESULTS: SAT-ALPHA AND ALU METHYLATION PERCENTAGES DECREASED SIGNIFICANTLY IN BOTH CLD AND HCC, COMPARED TO CONTROL. ALSO, A SIGNIFICANT SAT-ALPHA HYPOMETHYLATION WAS DETECTED IN HCC, COMPARED TO CLD. IN ADDITION, SAT-ALPHA AND ALU METHYLATION SHOWED A SIGNIFICANT DECLINE AS LESION SIZE GREW. HOWEVER, ONLY SAT-ALPHA HYPOMETHYLATION WAS SIGNIFICANTLY INCREASED IN ASSOCIATION WITH PORTAL VEIN THROMBOSIS AND THE MELD SCORE. SAT-ALPHA METHYLATION PERCENTAGE HAD THE HIGHEST SENSITIVITY AND SPECIFICITY FOR DIAGNOSING HCC (100% AND 84.4%) FOLLOWED BY ALPHA-FETOPROTEIN (80% AND 84.4%) AND ALU METHYLATION (66% AND 61.5%). FURTHERMORE, THERE WAS A STRONG POSITIVE CORRELATION BETWEEN SAT-ALPHA AND ALU METHYLATION. CONCLUSIONS: MEASURING SAT-ALPHA AND ALU METHYLATION PROVIDES US WITH A NEW TOOL FOR EARLY DETECTING HCV-INDUCED CLD AND HEPATOCARCINOGENESIS. SAT-ALPHA HAS THE POTENTIAL TO BE UTILIZED AS AN INDEPENDENT PREDICTIVE PARAMETER FOR HCC DEVELOPMENT AND PROGRESSION BECAUSE OF ITS ABILITY TO DISTINGUISH BETWEEN CLD AND HCC WITH THEIR DIFFERENT MELD SCORES.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
2  6492  39 TRAFFIC-RELATED AIR POLLUTION AND GROUND-LEVEL OZONE ASSOCIATED GLOBAL DNA HYPOMETHYLATION AND BULKY DNA ADDUCT FORMATION. STUDIES HAVE INDICATED THAT AIR POLLUTION, INCLUDING SURFACE-LEVEL OZONE (O(3)), CAN SIGNIFICANTLY INFLUENCE THE RISK OF CHRONIC DISEASES. TO BETTER UNDERSTAND THE CARCINOGENIC MECHANISMS OF AIR POLLUTANTS AND IDENTIFY PREDICTIVE DISEASE BIOMARKERS, WE EXAMINED THE ASSOCIATION BETWEEN TRAFFIC-RELATED POLLUTANTS WITH DNA METHYLATION ALTERATIONS AND BULKY DNA ADDUCTS, TWO BIOMARKERS OF CARCINOGEN EXPOSURE AND CANCER RISK, IN THE PERIPHERAL BLOOD OF 140 VOLUNTEERS-95 TRAFFIC POLICE OFFICERS, AND 45 UNEXPOSED SUBJECTS. THE DNA METHYLATION AND ADDUCT MEASUREMENTS WERE PERFORMED BY BISULFITE-PCR AND PYROSEQUENCING AND (32)P-POSTLABELING ASSAY. AIRBORNE LEVELS OF BENZO(A)PYRENE [B(A)P], CARBON MONOXIDE, AND TROPOSPHERIC O(3) WERE DETERMINED BY PERSONAL EXPOSURE BIOMONITORING OR BY FIXED MONITORING STATIONS. OVERALL, AIR POLLUTION EXPOSURE WAS ASSOCIATED WITH A SIGNIFICANT REDUCTION (1.41 UNITS) IN GLOBAL DNA METHYLATION (95% C.I. -2.65-0.04, P = 0.026). THE DECREMENT IN ALU REPETITIVE ELEMENTS WAS GREATEST IN THE POLICEMEN WORKING DOWNTOWN (95% C.I. -3.23--0.49, P = 0.008). THE DNA ADDUCTS WERE FOUND TO BE SIGNIFICANTLY INCREASED (0.45 UNITS) IN THE MUNICIPAL OFFICERS WITH RESPECT TO UNEXPOSED SUBJECTS (95% C.I. 0.02-0.88, P = 0.039), MAINLY IN THOSE WHO WERE CONTROLLING TRAFFIC IN DOWNTOWN AREAS (95% C.I. 0.39-1.29, P < 0.001). REGRESSION MODELS INDICATED AN INCREMENT OF ALU METHYLATION AT HIGHER B(A)P CONCENTRATIONS (95% C.I. 0.03-0.60, P = 0.032). MOREOVER, STATISTICAL MODELS SHOWED A DECREMENT IN ALU METHYLATION AND AN INCREMENT OF DNA DAMAGE ONLY ABOVE THE CUT-OFF VALUE OF 30 MICROG/M(3) O(3). A SIGNIFICANT INCREMENT OF 0.73 UNITS OF IL-6 GENE METHYLATION WAS ALSO FOUND IN SMOKERS WITH RESPECT TO NON-SMOKERS. OUR RESULTS HIGHLIGHTED THE ROLE OF AIR POLLUTION ON EPIGENETIC ALTERATIONS AND GENOTOXIC EFFECTS, ESPECIALLY ABOVE THE TARGET VALUE OF 30 MICROG/M(3) SURFACE-LEVEL O(3), SUPPORTING THE NECESSITY FOR DEVELOPING PUBLIC HEALTH STRATEGIES AIMED TO REDUCE TRAFFIC-RELATED AIR POLLUTION MOLECULAR ALTERATIONS.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
3  5683  35 SHORTER TELOMERE LENGTH IN PERIPHERAL BLOOD LYMPHOCYTES OF WORKERS EXPOSED TO POLYCYCLIC AROMATIC HYDROCARBONS. SHORTER TELOMERE LENGTH (TL) IN PERIPHERAL BLOOD LYMPHOCYTES (PBLS) IS PREDICTIVE OF LUNG CANCER RISK. POLYCYCLIC AROMATIC HYDROCARBONS (PAHS) ARE ESTABLISHED LUNG CARCINOGENS THAT CAUSE CHROMOSOME INSTABILITY. WHETHER PAH EXPOSURE AND ITS MOLECULAR EFFECTS ARE LINKED WITH SHORTER TL HAS NEVER BEEN EVALUATED. IN THE PRESENT STUDY, WE INVESTIGATED THE EFFECT OF CHRONIC EXPOSURE TO PAHS ON TL MEASURED IN PBLS OF POLISH MALE NON-CURRENT SMOKING COKEOVEN WORKERS AND MATCHED CONTROLS. PAH EXPOSURE AND MOLECULAR EFFECTS WERE CHARACTERIZED USING MEASURES OF INTERNAL DOSE (URINARY 1-PYRENOL), EFFECTIVE DOSE [ANTI-BENZO[A]PYRENE DIOLEPOXIDE (ANTI-BPDE)-DNA ADDUCT], GENETIC INSTABILITY (MICRONUCLEI, MN) AND DNA METHYLATION [P53 PROMOTER AND ALU AND LONG INTERSPERSED NUCLEAR ELEMENT-1 (LINE-1) REPETITIVE ELEMENTS, AS SURROGATE MEASURES OF GLOBAL METHYLATION] IN PBLS. TL WAS MEASURED BY REAL-TIME POLYMERASE CHAIN REACTION. COKEOVEN WORKERS WERE HEAVILY EXPOSED TO PAHS (79% EXCEEDED THE URINARY 1-PYRENOL BIOLOGICAL EXPOSURE INDEX) AND EXHIBITED LOWER TL (P = 0.038) THAN CONTROLS, AS WELL AS HIGHER LEVELS OF GENETIC AND CHROMOSOMAL ALTERATIONS [I.E. ANTI-BPDE-DNA ADDUCT AND MN (P < 0.0001)] AND EPIGENETIC CHANGES [I.E. P53 GENE-SPECIFIC PROMOTER AND GLOBAL METHYLATION (P <OR= 0.001)]. TL DECREASED WITH LONGER DURATION OF WORK AS COKEOVEN WORKER (P = 0.039) AND IN ALL SUBJECTS WITH HIGHER LEVELS OF ANTI-BPDE-DNA ADDUCT (P = 0.042), P53 HYPOMETHYLATION (P = 0.005) AND MN (P = 0.009). IN MULTIVARIATE ANALYSIS, YEARS OF WORK IN COKERY (P = 0.008) AND P53 HYPOMETHYLATION (P = 0.001) WERE THE PRINCIPAL DETERMINANTS OF SHORTER TL. OUR RESULTS INDICATE THAT SHORTER TL IS ASSOCIATED WITH CHRONIC PAH EXPOSURE. THE INTERRELATIONS WITH OTHER GENETIC AND EPIGENETIC MECHANISMS IN OUR DATA SUGGEST THAT SHORTER TL COULD BE A CENTRAL EVENT IN PAH CARCINOGENESIS.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
4  4378  36 MITOCHONDRIAL DNA COPY NUMBER AND EXPOSURE TO POLYCYCLIC AROMATIC HYDROCARBONS. BACKGROUND: INCREASED MITOCHONDRIAL DNA COPY NUMBER (MTDNACN) IS A BIOLOGIC RESPONSE TO MTDNA DAMAGE AND DYSFUNCTION, PREDICTIVE OF LUNG CANCER RISK. POLYCYCLIC AROMATIC HYDROCARBONS (PAHS) ARE ESTABLISHED LUNG CARCINOGENS AND MAY CAUSE MITOCHONDRIAL TOXICITY. WHETHER PAH EXPOSURE AND PAH-RELATED NUCLEAR DNA (NDNA) GENOTOXIC EFFECTS ARE LINKED WITH INCREASED MTDNACN HAS NEVER BEEN EVALUATED. METHODS: WE INVESTIGATED THE EFFECT OF CHRONIC EXPOSURE TO PAHS ON MTDNACN IN PERIPHERAL BLOOD LYMPHOCYTES (PBLS) OF 46 POLISH MALE NONCURRENT SMOKING COKE-OVEN WORKERS AND 44 MATCHED CONTROLS, WHO WERE PART OF A GROUP OF 94 STUDY INDIVIDUALS EXAMINED IN OUR PREVIOUS WORK. SUBJECTS' PAH EXPOSURE AND GENETIC ALTERATIONS WERE CHARACTERIZED THROUGH MEASURES OF INTERNAL DOSE (URINARY 1-PYRENOL), TARGET DOSE [ANTI-BENZO[A]PYRENE DIOLEPOXIDE (ANTI-BPDE)-DNA ADDUCT], GENETIC INSTABILITY (MICRONUCLEI AND TELOMERE LENGTH), AND DNA METHYLATION (P53 PROMOTER) IN PBLS. MTDNACN (MT/S) WAS MEASURED USING A VALIDATED REAL-TIME PCR METHOD. RESULTS: WORKERS WITH PAH EXPOSURE ABOVE THE MEDIAN VALUE (>3 MUMOL 1-PYRENOL/MOL CREATININE) SHOWED HIGHER MTDNACN [GEOMETRIC MEANS (GM) OF 1.06 (UNADJUSTED) AND 1.07 (AGE-ADJUSTED)] COMPARED WITH CONTROLS [GM 0.89 (UNADJUSTED); 0.89 (AGE-ADJUSTED); (P = 0.029 AND 0.016)], AS WELL AS HIGHER LEVELS OF GENETIC AND CHROMOSOMAL [I.E., ANTI-BPDE-DNA ADDUCTS (P < 0.001), MICRONUCLEI (P < 0.001), AND TELOMERE LENGTH (P = 0.053)] AND EPIGENETIC [I.E., P53 GENE-SPECIFIC PROMOTER METHYLATION (P < 0.001)] ALTERATIONS IN THE NDNA. IN THE WHOLE STUDY POPULATION, UNADJUSTED AND AGE-ADJUSTED MTDNACN WAS POSITIVELY CORRELATED WITH 1-PYRENOL (P = 0.043 AND 0.032) AND ANTI-BPDE-DNA ADDUCTS (P = 0.046 AND 0.049). CONCLUSIONS: PAH EXPOSURE AND PAH-RELATED NDNA GENOTOXICITY ARE ASSOCIATED WITH INCREASED MTDNACN. IMPACT: THE PRESENT STUDY IS SUGGESTIVE OF POTENTIAL ROLES OF MTDNACN IN PAH-INDUCED CARCINOGENESIS.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
5  4242  36 METHYLATION STATUS OF ALU AND LINE-1 INTERSPERSED REPETITIVE SEQUENCES IN BEHCET'S DISEASE PATIENTS. BEHCET'S DISEASE (BD) IS A MULTISYSTEM CHRONIC INFLAMMATORY DISEASE. THE PATHOLOGY IS BELIEVED TO INVOLVE BOTH GENETIC SUSCEPTIBILITY AND ENVIRONMENTAL FACTORS. HYPOMETHYLATION LEADING TO ACTIVATION OF INTERSPERSED REPETITIVE SEQUENCES (IRSS) SUCH AS LINE-1 AND ALU CONTRIBUTES TO THE PATHOLOGIES OF AUTOIMMUNE DISEASES AND CANCER. HEREIN, THE EPIGENETIC CHANGES OF IRSS IN BD WERE EVALUATED USING COMBINED BISULFITE RESTRICTION ANALYSIS-INTERSPERSED REPETITIVE SEQUENCES (COBRA-IRS). DNA FROM NEUTROPHILS AND PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) OF BD PATIENTS WITH OCULAR INVOLVEMENT THAT WERE IN ACTIVE OR INACTIVE STATES AND HEALTHY CONTROLS WERE USED TO ANALYZE LINE-1 AND ALU METHYLATION LEVELS. FOR ALU SEQUENCES, SIGNIFICANT DIFFERENCES WERE OBSERVED IN THE FREQUENCY OF (U)C(U)C ALLELES BETWEEN PBMCS OF PATIENTS AND CONTROLS (P = 0.03), AND BETWEEN INACTIVE PATIENTS AND CONTROLS (P = 0.03). FOR NEUTROPHILS, THE FREQUENCY OF (U)C(U)C WAS SIGNIFICANTLY HIGHER BETWEEN PATIENTS AND CONTROLS (P = 0.006) AND BETWEEN INACTIVE PATIENTS AND CONTROLS (P = 0.002). THE PARTIAL METHYLATION ((U)C(M)C + (M)C(U)C) FREQUENCIES OF ALU BETWEEN INACTIVE PATIENTS AND CONTROL SAMPLES ALSO DIFFERED (P = 0.02). NO STATISTICALLY SIGNIFICANT DIFFERENCES FOR LINE-1 WERE DETECTED. THUS, CHANGES IN THE METHYLATION LEVEL OF IRS ELEMENTS MIGHT CONTRIBUTE TO THE PATHOGENESIS OF BD. THE ROLE OF ALU TRANSCRIPTS IN BD SHOULD BE INVESTIGATED FURTHER.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
6   811  29 CHANGES IN DNA METHYLATION OF TANDEM DNA REPEATS ARE DIFFERENT FROM INTERSPERSED REPEATS IN CANCER. HYPOMETHYLATION OF DNA REPETITIVE ELEMENTS IS A COMMON FINDING IN CANCER, BUT VERY LITTLE IS KNOWN ABOUT THE DNA METHYLATION CHANGES OF DIFFERENT TYPES OF DNA REPETITIVE ELEMENTS, SUCH AS INTERSPERSED REPEATS (LINE1 AND ALU YB8) AND TANDEM REPEATS (SAT-ALPHA, NBL-2 AND D4Z4). WE USED BISULFITE-PCR PYROSEQUENCING TO QUANTITATIVELY MEASURE THE DNA METHYLATION OF FIVE DIFFERENT DNA REPETITIVE ELEMENTS IN NORMAL TISSUE AND CANCER. IN ALL WE STUDIED 10 DIFFERENT TISSUES FROM FOUR INDIVIDUALS UNDERGOING AUTOPSY, 34 PAIRED NORMAL AND TUMOR TISSUES FROM PATIENTS WITH BLADDER CANCER, 58 PATIENTS WITH CHRONIC MYELOGENOUS LEUKEMIA AND 23 PATIENTS WITH ACUTE PROMYELOCYTIC LEUKEMIA. WE FOUND THAT THE DNA METHYLATION OF INTERSPERSED REPEATS (LINE1 AND ALU YB8) WAS VERY CONSISTENT FROM PERSON TO PERSON AND TISSUE TO TISSUE WHILE TANDEM DNA REPEATS APPEARED MORE VARIABLE IN NORMAL TISSUES. IN BLADDER CANCER WE FOUND CLEAR HYPOMETHYLATION OF LINE1, ALU YB8, SAT-ALPHA AND NBL-2. CONVERSELY, WE FOUND AN INCREASE IN THE DNA METHYLATION LEVELS OF D4Z4 FROM NORMAL TO CANCER. IN CONTRAST LEUKEMIA SHOWED NO SIGNIFICANT CHANGES IN THE DNA METHYLATION OF LINE1 AND ALU YB8, BUT DNA METHYLATION INCREASES IN NBL-2 AND D4Z4 TANDEM REPEATS. OUR FINDINGS SHOW THAT THE CHANGES IN DNA METHYLATION LEVELS OF INDIVIDUAL DNA REPETITIVE ELEMENTS ARE UNIQUE FOR EACH REPETITIVE ELEMENT, WHICH MAY REFLECT DISTINCT EPIGENETIC FACTORS AND MAY HAVE IMPORTANT IMPLICATIONS IN THE USE OF DNA METHYLATION OF REPETITIVE ELEMENTS AS GLOBAL DNA METHYLATION BIOMARKERS.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
7  1550  30 DNA METHYLATION IS ASSOCIATED WITH AIRFLOW OBSTRUCTION IN PATIENTS LIVING WITH HIV. INTRODUCTION: PEOPLE LIVING WITH HIV (PLWH) SUFFER FROM AGE-RELATED COMORBIDITIES SUCH AS COPD. THE PROCESSES RESPONSIBLE FOR REDUCED LUNG FUNCTION IN PLWH ARE LARGELY UNKNOWN. WE PERFORMED AN EPIGENOME-WIDE ASSOCIATION STUDY TO INVESTIGATE WHETHER BLOOD DNA METHYLATION IS ASSOCIATED WITH IMPAIRED LUNG FUNCTION IN PLWH. METHODS: USING BLOOD DNA METHYLATION PROFILES FROM 161 PLWH, WE TESTED THE EFFECT OF METHYLATION ON FEV(1), FEV(1)/FVC RATIO AND FEV(1) DECLINE OVER A MEDIAN OF 5 YEARS. WE EVALUATED THE GLOBAL METHYLATION OF PLWH WITH AIRFLOW OBSTRUCTION BY TESTING THE DIFFERENTIAL METHYLATION OF TRANSPOSABLE ELEMENTS ALU AND LINE-1, A WELL-DESCRIBED MARKER OF EPIGENETIC AGEING. RESULTS: AIRFLOW OBSTRUCTION AS DEFINED BY A FEV(1)/FVC<0.70 WAS ASSOCIATED WITH 1393 DIFFERENTIALLY METHYLATED POSITIONS (DMPS), WHILE 4676 WERE ASSOCIATED WITH AIRFLOW OBSTRUCTION BASED ON THE FEV(1)/FVC<LOWER LIMIT OF NORMAL. THESE DMPS WERE ENRICHED FOR BIOLOGICAL PATHWAYS ASSOCIATED WITH CHRONIC VIRAL INFECTIONS. THE AIRFLOW OBSTRUCTION GROUP WAS GLOBALLY HYPOMETHYLATED COMPARED WITH THOSE WITHOUT AIRFLOW OBSTRUCTION. 103 AND 7112 DMPS WERE ASSOCIATED WITH FEV(1) AND FEV(1)/FVC, RESPECTIVELY. NO POSITIONS WERE ASSOCIATED WITH FEV(1) DECLINE. CONCLUSION: A LARGE NUMBER OF DMPS WERE ASSOCIATED WITH AIRFLOW OBSTRUCTION AND LUNG FUNCTION IN A UNIQUE COHORT OF PLWH. AIRFLOW OBSTRUCTION IN EVEN RELATIVELY YOUNG PLWH IS ASSOCIATED WITH GLOBAL HYPOMETHYLATION, SUGGESTING ADVANCED EPIGENETIC AGEING COMPARED WITH THOSE WITH NORMAL LUNG FUNCTION. THE DISTURBANCE OF THE EPIGENETIC REGULATION OF KEY GENES NOT PREVIOUSLY IDENTIFIED IN NON-HIV COPD COHORTS COULD EXPLAIN THE UNIQUE RISK OF COPD IN PLWH.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
8   304  37 AIRWAY AGING AND METHYLATION DISRUPTIONS IN HIV-ASSOCIATED CHRONIC OBSTRUCTIVE PULMONARY DISEASE. RATIONALE: AGE-RELATED DISEASES LIKE CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) OCCUR AT HIGHER RATES IN PEOPLE LIVING WITH HUMAN IMMUNODEFICIENCY VIRUS (PLWH) THAN IN UNINFECTED POPULATIONS. OBJECTIVES: TO IDENTIFY WHETHER ACCELERATED AGING CAN BE OBSERVED IN THE AIRWAYS OF PLWH WITH COPD, MANIFEST BY A UNIQUE DNA METHYLATION SIGNATURE. METHODS: BRONCHIAL EPITHELIAL BRUSHINGS FROM PLWH WITH AND WITHOUT COPD AND HIV-UNINFECTED ADULTS WITH AND WITHOUT COPD (N = 76) WERE PROFILED FOR DNA METHYLATION AND GENE EXPRESSION. WE EVALUATED GLOBAL ALU AND LINE-1 METHYLATION AND CALCULATED THE EPIGENETIC AGE USING THE HORVATH CLOCK AND THE METHYLATION TELOMERE LENGTH ESTIMATOR. TO IDENTIFY GENOME-WIDE DIFFERENTIAL DNA METHYLATION AND GENE EXPRESSION ASSOCIATED WITH HIV AND COPD, ROBUST LINEAR MODELS WERE USED FOLLOWED BY AN EXPRESSION QUANTITATIVE TRAIT METHYLATION (EQTM) ANALYSIS. MEASUREMENTS AND MAIN RESULTS: EPIGENETIC AGE ACCELERATION AND SHORTER METHYLATION ESTIMATES OF TELOMERE LENGTH WERE FOUND IN PLWH WITH COPD COMPARED WITH PLWH WITHOUT COPD AND UNINFECTED PATIENTS WITH AND WITHOUT COPD. GLOBAL HYPOMETHYLATION WAS IDENTIFIED IN PLWH. WE IDENTIFIED 7,970 CYTOSINE BASES LOCATED NEXT TO A GUANINE BASE (CPG SITES), 293 GENES, AND 9 EXPRESSION QUANTITATIVE TRAIT METHYLATION-GENE PAIRS ASSOCIATED WITH THE INTERACTION BETWEEN HIV AND COPD. ACTIN BINDING LIM PROTEIN FAMILY MEMBER 3 (ABLIM3) WAS ONE OF THE NOVEL CANDIDATE GENES FOR HIV-ASSOCIATED COPD HIGHLIGHTED BY OUR ANALYSIS. CONCLUSIONS: METHYLATION AGE ACCELERATION IS OBSERVED IN THE AIRWAY EPITHELIUM OF PLWH WITH COPD, A PROCESS THAT MAY BE RESPONSIBLE FOR THE HEIGHTENED RISK OF COPD IN THIS POPULATION. THEIR DISTINCT METHYLATION PROFILE, DIFFERING FROM THAT OBSERVED IN PATIENTS WITH COPD ALONE, SUGGESTS A UNIQUE PATHOGENESIS TO HIV-ASSOCIATED COPD. THE ASSOCIATIONS WARRANT FURTHER INVESTIGATION TO ESTABLISH CAUSALITY.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
9  4249  34 METHYLATION-BASED BIOLOGICAL AGE AND BREAST CANCER RISK. BACKGROUND: AGE IS ONE OF THE STRONGEST PREDICTORS OF CANCER, CHRONIC DISEASE, AND MORTALITY, BUT BIOLOGICAL RESPONSES TO AGING DIFFER AMONG PEOPLE. EPIGENETIC DNA MODIFICATIONS HAVE BEEN USED TO ESTIMATE "BIOLOGICAL AGE," WHICH MAY BE A USEFUL PREDICTOR OF DISEASE RISK. WE TESTED THIS HYPOTHESIS FOR BREAST CANCER. METHODS: USING A CASE-COHORT APPROACH, WE MEASURED BASELINE BLOOD DNA METHYLATION OF 2764 WOMEN ENROLLED IN THE SISTER STUDY, 1566 OF WHOM SUBSEQUENTLY DEVELOPED BREAST CANCER AFTER AN AVERAGE OF 6 YEARS. USING THREE PREVIOUSLY ESTABLISHED METHYLATION-BASED "CLOCKS" (HANNUM, HORVATH, AND LEVINE), WE DEFINED BIOLOGICAL AGE ACCELERATION FOR EACH WOMAN BY COMPARING HER ESTIMATED BIOLOGICAL AGE WITH HER CHRONOLOGICAL AGE. HAZARD RATIOS AND 95% CONFIDENCE INTERVALS FOR BREAST CANCER RISK WERE ESTIMATED USING COX REGRESSION MODELS. ALL STATISTICAL TESTS WERE TWO-SIDED. RESULTS: EACH OF THE THREE CLOCKS SHOWED THAT BIOLOGICAL AGE ACCELERATION WAS STATISTICALLY SIGNIFICANTLY ASSOCIATED WITH INCREASED RISK OF DEVELOPING BREAST CANCER (5-YEAR AGE ACCELERATION, HANNUM'S CLOCK: HAZARD RATIO [HR] = 1.10, 95% CONFIDENCE INTERVAL [CI] = 1.00 TO 1.21, P = .04; HORVATH'S CLOCK: HR = 1.08, 95% CI = 1.00 TO 1.17, P = .04; LEVINE'S CLOCK: HR = 1.15, 95% CI = 1.07 TO 1.23, P < .001). FOR LEVINE'S CLOCK, EACH 5-YEAR ACCELERATION IN BIOLOGICAL AGE CORRESPONDED WITH A 15% INCREASE IN BREAST CANCER RISK. ALTHOUGH BIOLOGICAL AGE MAY ACCELERATE WITH MENOPAUSAL TRANSITION, AGE ACCELERATION IN PREMENOPAUSAL WOMEN INDEPENDENTLY PREDICTED BREAST CANCER. CASE-ONLY ANALYSIS SUGGESTED THAT, AMONG WOMEN WHO DEVELOP BREAST CANCER, INCREASED AGE ACCELERATION IS ASSOCIATED WITH INVASIVE CANCER (ODDS RATIO FOR INVASIVE = 1.09, 95% CI = 0.98 TO 1.22, P = .10). CONCLUSIONS: DNA METHYLATION-BASED MEASURES OF BIOLOGICAL AGE MAY BE IMPORTANT PREDICTORS OF BREAST CANCER RISK.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
10  6314  31 THE RELATIONSHIP BETWEEN THE EPIGENETIC AGING BIOMARKER "GRIMAGE" AND LUNG FUNCTION IN BOTH THE AIRWAY AND BLOOD OF PEOPLE LIVING WITH HIV: AN OBSERVATIONAL COHORT STUDY. BACKGROUND: AGE-RELATED COMORBIDITIES SUCH AS CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) ARE COMMON IN PEOPLE LIVING WITH HUMAN IMMUNODEFICIENCY VIRUS (PLWH). WE INVESTIGATED THE RELATIONSHIP BETWEEN COPD AND THE EPIGENETIC AGE OF THE AIRWAY EPITHELIUM AND PERIPHERAL BLOOD OF PLWH. METHODS: AIRWAY EPITHELIAL BRUSHINGS FROM 34 PLWH ENROLLED IN THE ST. PAUL'S HOSPITAL HIV BRONCHOSCOPY COHORT AND PERIPHERAL BLOOD FROM 378 PLWH ENROLLED IN THE STRATEGIC TIMING OF ANTIRETROVIRAL TREATMENT (START) STUDY WERE PROFILED FOR DNA METHYLATION. THE DNA METHYLATION BIOMARKER OF AGE AND HEALTHSPAN, GRIMAGE, WAS CALCULATED IN BOTH TISSUE COMPARTMENTS. WE TESTED THE ASSOCIATION OF GRIMAGE WITH COPD IN THE AIRWAY EPITHELIUM AND AIRFLOW OBSTRUCTION AS DEFINED BY AN FEV(1)/FVC<0.70, AND FEV(1) DECLINE OVER 6 YEARS IN BLOOD. FINDINGS: THE AIRWAY EPITHELIUM OF PLWH WITH COPD WAS ASSOCIATED WITH GREATER GRIMAGE RESIDUALS COMPARED TO PLWH WITHOUT COPD (BETA=3.18, 95%CI=1.06-5.31, P=0.005). IN BLOOD, FEV(1)/FVC<LLN WAS ASSOCIATED WITH GREATER GRIMAGE RESIDUALS (BETA=1.74, 95%CI=0.37-3.24, P=0.019). FEV(1) DECLINE WAS INVERSELY CORRELATED WITH GRIMAGE RESIDUALS IN BLOOD (R=-0.13, P=0.012). PLWH WHO HAD NORMAL LUNG FUNCTION BUT WHO SUBSEQUENTLY DEVELOPED AN FEV(1)/FVC<0.70 OVER THE COURSE OF 6 YEARS HAD HIGHER GRIMAGE RESIDUALS AT BASELINE (BETA=2.33, 95%CI=0.23-4.44, P=0.031). INTERPRETATION: GRIMAGE MAY REFLECT LUNG AND SYSTEMIC EPIGENETIC CHANGES THAT OCCUR WITH ADVANCED AIRFLOW OBSTRUCTION AND MAY HELP TO IDENTIFY PLWH WITH A HIGHER RISK OF DEVELOPING COPD. FUNDING: CANADIAN INSTITUTES OF HEALTH RESEARCH AND THE BRITISH COLUMBIA LUNG ASSOCIATION. THE START SUBSTUDY WAS FUNDED BY NIH GRANTS: UM1-AI068641, UM1-AI120197, AND RO1HL096453.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
11   974  40 CHRONIC OCCUPATIONAL EXPOSURE ENDURED BY TOBACCO FARMERS FROM BRAZIL AND ASSOCIATION WITH DNA DAMAGE. TOBACCO FARMING IS AN IMPORTANT ECONOMIC INCOME IN BRAZIL, ALTHOUGH IT HAS BEEN CHALLENGED AS REGARD THE OCCUPATIONAL EXPOSURE TO BOTH PESTICIDES AND NICOTINE ENDURED BY FARMERS. CHRONIC OCCUPATIONAL EXPOSURE TO COMPLEX MIXTURES CAN LEAD TO HEALTH HAZARDOUS. WE EXAMINED GENOMIC INSTABILITY AND EPIGENETIC CHANGES IN TOBACCO FARMERS OCCUPATIONALLY EXPOSED TO PESTICIDE MIXTURES AND NICOTINE AT TOBACCO FIELDS. DNA DAMAGE WAS ASSESSED BY ALKALINE COMET ASSAY IN BLOOD CELLS. GENOMIC DNA WAS ISOLATED, AND TELOMERE LENGTH WAS MEASURED USING QUANTITATIVE POLYMERASE CHAIN REACTION ASSAY. WE MEASURED 5-METHYL-2'-DEOXYCYTIDINE, A MARKER OF GLOBAL DNA METHYLATION, AND P16 PROMOTER METHYLATION. THE OXIDATIVE PROFILE WAS EVALUATED BY TROLOX EQUIVALENT ANTIOXIDANT CAPACITY AND LIPID PEROXIDATION (THIOBARBITURIC ACID REACTIVE SUBSTANCES) IN SERUM. EXPOSURE PARAMETERS, PLASMA COTININE AND INORGANIC ELEMENT LEVELS, WERE ALSO MEASURED. DNA DAMAGE WAS SIGNIFICANTLY ELEVATED FOR FARMERS IN RELATION TO UNEXPOSED GROUP (P < 0.001; MANN-WHITNEY TEST) AND POSITIVELY ASSOCIATED WITH YEARS OF EXPOSURE. INVERSE RELATIONSHIP BETWEEN DNA DAMAGE AND TOTAL EQUIVALENT ANTIOXIDANT ACTIVITY WAS DEMONSTRATED FOR EXPOSED AND UNEXPOSED GROUPS. EXPOSED GROUP SHOWED SIGNIFICANTLY SHORTER TELOMERES (P < 0.001; UNPAIRED T-TEST) AND DNA HYPOMETHYLATION (P < 0.001; UNPAIRED T-TEST), AS WELL AS P16 HYPERMETHYLATION (P = 0.003; MANN-WHITNEY TEST). LIPID PEROXIDATION WAS INCREASED FOR EXPOSED GROUP IN RELATION TO UNEXPOSED ONE (P = 0.02; MANN-WHITNEY TEST) AND PRESENTED A POSITIVE CORRELATION WITH GLOBAL DNA METHYLATION (P = 0.0264). FARMERS HAVE INCREASED PLASMA COTININE LEVELS (P < 0.001) AND INORGANIC ELEMENTS (PHOSPHORUS, SULPHUR AND CHLORINE) IN RELATION TO UNEXPOSED GROUP. ELEVATED OXIDATIVE STRESS LEVELS DUE TO CHRONIC OCCUPATIONAL PESTICIDE MIXTURES AND NICOTINE EXPOSURE IN TOBACCO FARMERS WERE ASSOCIATED WITH HIGHER DNA DAMAGE, SHORTER TELOMERES AND ALTERED DNA METHYLATION. TELOMERE-ACCELERATED ATTRITION DUE TO EXPOSURE MAY BE POTENTIAL INTERMEDIATE STEP BEFORE A DISEASE STATE.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
12   415  38 ANALYSIS OF RETROTRANSPOSON SUBFAMILY DNA METHYLATION REVEALS NOVEL EARLY EPIGENETIC CHANGES IN CHRONIC LYMPHOCYTIC LEUKEMIA. RETROTRANSPOSONS SUCH AS LINE-1 AND ALU COMPRISE >25% OF THE HUMAN GENOME. WHILE GLOBAL HYPOMETHYLATION OF THESE ELEMENTS HAS BEEN WIDELY REPORTED IN SOLID TUMOURS, THEIR EPIGENETIC DYSREGULATION IS YET TO BE CHARACTERISED IN CHRONIC LYMPHOCYTIC LEUKAEMIA, AND THERE HAS BEEN SCANT CONSIDERATION OF THEIR EVOLUTIONARY HISTORY THAT MEDIATES SENSITIVITY TO HYPOMETHYLATION. HERE, WE DEVELOPED AN APPROACH FOR LOCUS- AND EVOLUTIONARY SUBFAMILY-SPECIFIC ANALYSIS OF RETROTRANSPOSONS USING THE ILLUMINA INFINIUM HUMAN METHYLATION 450K MICROARRAY PLATFORM, WHICH WE APPLIED TO PUBLICLY-AVAILABLE DATASETS FROM CHRONIC LYMPHOCYTIC LEUKAEMIA AND OTHER HAEMATOLOGICAL MALIGNANCIES. WE IDENTIFIED 9,797 MICROARRAY PROBES MAPPING TO 117 LINE-1 SUBFAMILIES AND 13,130 MAPPING TO 37 ALU SUBFAMILIES. OF THESE, 10,782 WERE DIFFERENTIALLY METHYLATED (PFDR<0.05) IN CHRONIC LYMPHOCYTIC LEUKAEMIA PATIENTS (N=139) COMPARED WITH HEALTHY INDIVIDUALS (N=14), WITH ENRICHMENT AT ENHANCERS (P=0.002). DIFFERENTIAL METHYLATION WAS ASSOCIATED WITH EVOLUTIONARY AGE OF LINE-1 (R2=0.31, P=0.003) AND ALU (R2=0.74, P=0.002) ELEMENTS, WITH GREATER HYPOMETHYLATION OF OLDER SUBFAMILIES (L1M, ALUJ). LOCUS-SPECIFIC HYPOMETHYLATION WAS ASSOCIATED WITH DIFFERENTIAL EXPRESSION OF PROXIMAL GENES, INCLUDING DCLK2, HK1, ILRUN, TANK, TBCD, TNFRSF1B AND TXNRD2, WITH HIGHER EXPRESSION OF DCLK2 AND TNFRSF1B ASSOCIATED WITH REDUCED PATIENT SURVIVAL. HYPOMETHYLATION AT NINE LOCI WAS HIGHLY FREQUENT IN CHRONIC LYMPHOCYTIC LEUKAEMIA (>90% PATIENTS) BUT NOT OBSERVED IN HEALTHY INDIVIDUALS OR OTHER LEUKAEMIAS, AND WAS DETECTABLE IN BLOOD SAMPLES TAKEN PRIOR TO CHRONIC LYMPHOCYTIC LEUKAEMIA DIAGNOSIS IN 9 OF 82 INDIVIDUALS FROM THE MELBOURNE COLLABORATIVE COHORT STUDY. OUR RESULTS DEMONSTRATE DIFFERENTIAL METHYLATION OF RETROTRANSPOSONS IN CHRONIC LYMPHOCYTIC LEUKAEMIA BY THEIR EVOLUTIONARY HERITAGE THAT MODULATES EXPRESSION OF PROXIMAL GENES.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
13   659  38 BLOOD GLOBAL DNA METHYLATION IS DECREASED IN NON-SEVERE CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) PATIENTS. BACKGROUND: ALTERATIONS IN GLOBAL DNA METHYLATION HAVE BEEN ASSOCIATED WITH OXIDATIVE STRESS (OS). SINCE CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS CHARACTERIZED BY INCREASED OXIDATIVE STRESS WE AIMED TO EVALUATE THE LEVELS OF GLOBAL DNA METHYLATION IN THIS PATIENT GROUP. METHODS: WE ASSESSED METHYLCYTOSINE (MCYT) LEVELS IN DNA FROM BLOOD COLLECTED IN 43 COPD PATIENTS (29 WITH MILD AND 14 WITH MODERATE DISEASE) AND 43 AGE- AND SEX-MATCHED HEALTHY CONTROLS. RESULTS: DNA METHYLATION WAS SIGNIFICANTLY LOWER IN COPD PATIENTS VS. CONTROLS (4.20 +/- 0.18% MCYT VS. 4.29 +/- 0.18% MCYT, P = 0.02). FURTHERMORE, DNA METHYLATION IN COPD PATIENTS WITH MODERATE DISEASE WAS SIGNIFICANTLY LOWER THAN THAT IN PATIENTS WITH MILD DISEASE (4.14 +/- 0.15% MCYT VS. 4.23 +/- 0.19% MCYT, P < 0.05). UNIVARIATE LOGISTIC REGRESSION ANALYSIS SHOWED THAT LOWER DNA METHYLATION LEVELS WERE ASSOCIATED WITH PRESENCE OF COPD (CRUDE OR = 0.06, 95% CI 0.00 TO 0.67, P = 0.023). THIS RELATIONSHIP REMAINED SIGNIFICANT AFTER ADJUSTING FOR SEVERAL CONFOUNDERS (OR 0.03, 95% CI 0.00 TO 0.67; P = 0.028). RECEIVER OPERATING CHARACTERISTICS (ROC) CURVE ANALYSIS DEMONSTRATED THE AREA UNDER THE CURVE OF MCYT WAS 0.646, WITH 46.6% SENSITIVITY AND 79.1% SPECIFICITY FOR PRESENCE OF COPD. CONCLUSIONS: THERE WERE NO SIGNIFICANT CORRELATIONS BETWEEN METHYLATION AND OS INDICES. THE PRESENCE AND SEVERITY OF COPD IS ASSOCIATED WITH PROGRESSIVELY LOWER DNA METHYLATION IN BLOOD. HOWEVER, THIS EPIGENETIC ALTERATION SEEMS INDEPENDENT OF OXIDATIVE STRESS.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
14  1189  39 CORRELATION BETWEEN GLOBAL METHYLATION LEVEL OF PERIPHERAL BLOOD LEUKOCYTES AND SERUM C REACTIVE PROTEIN LEVEL MODIFIED BY MTHFR POLYMORPHISM: A CROSS-SECTIONAL STUDY. BACKGROUND: CHRONIC INFLAMMATORY CONDITIONS ARE ASSOCIATED WITH HIGHER TUMOR INCIDENCE THROUGH EPIGENETIC AND GENETIC ALTERATIONS. HERE, WE FOCUSED ON AN ASSOCIATION BETWEEN AN INFLAMMATION MARKER, C-REACTIVE-PROTEIN (CRP), AND GLOBAL DNA METHYLATION LEVELS OF PERIPHERAL BLOOD LEUKOCYTES. METHODS: THE SUBJECTS WERE 384 HEALTHY JAPANESE WOMEN ENROLLED AS THE CONTROL GROUP OF A CASE-CONTROL STUDY FOR BREAST CANCER CONDUCTED FROM 2001 TO 2005. GLOBAL DNA METHYLATION WAS QUANTIFIED BY LUMINOMETRIC METHYLATION ASSAY (LUMA). RESULTS: WITH ADJUSTMENT FOR LIFESTYLE-RELATED FACTORS, INCLUDING FOLATE INTAKE, THE GLOBAL DNA METHYLATION LEVEL OF PERIPHERAL BLOOD LEUKOCYTES WAS SIGNIFICANTLY BUT WEAKLY INCREASED BY 0.43% PER QUARTILE CATEGORY FOR CRP (P FOR TREND = 0.010). ESTIMATED METHYLATION LEVELS STRATIFIED BY CRP QUARTILE WERE 70.0%, 70.8%, 71.4%, AND 71.3%, RESPECTIVELY. IN ADDITION, INTERACTION BETWEEN POLYMORPHISM OF MTHFR (RS1801133, KNOWN AS C677T) AND CRP WAS SIGNIFICANT (P FOR INTERACTION = 0.046); THE GLOBAL METHYLATION LEVEL WAS SIGNIFICANTLY INCREASED BY 0.61% PER QUARTILE CATEGORY FOR CRP IN THE CT/TT GROUP (THOSE WITH THE MINOR ALLELE T, P FOR TREND = 0.001), WHEREAS NO ASSOCIATION WAS OBSERVED IN THE CC GROUP (WILD TYPE). CONCLUSIONS: OUR STUDY SUGGESTS THAT CRP CONCENTRATION IS WEAKLY ASSOCIATED WITH GLOBAL DNA METHYLATION LEVEL. HOWEVER, THIS ASSOCIATION WAS OBSERVED MORE CLEARLY IN INDIVIDUALS WITH THE MINOR ALLELE OF THE MTHFR MISSENSE SNP RS1801133. BY ELUCIDATING THE COMPLEX MECHANISM OF THE REGULATION OF DNA METHYLATION BY BOTH ACQUIRED AND GENETIC FACTORS, OUR RESULTS MAY BE IMPORTANT FOR CANCER PREVENTION.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
15  4818  30 OCCURRENCE OF ACCELERATED EPIGENETIC AGING AND METHYLATION DISRUPTIONS IN HUMAN IMMUNODEFICIENCY VIRUS INFECTION BEFORE ANTIRETROVIRAL THERAPY. BACKGROUND: WHETHER ACCELERATED AGING DEVELOPS OVER THE COURSE OF CHRONIC HUMAN IMMUNODEFICIENCY VIRUS (HIV) INFECTION OR CAN BE OBSERVED BEFORE SIGNIFICANT IMMUNOSUPPRESSION ON IS UNKNOWN. WE STUDIED DNA METHYLATION IN BLOOD TO ESTIMATE CELLULAR AGING IN PERSONS LIVING WITH HIV (PLWH) BEFORE THE INITIATION OF ANTIRETROVIRAL THERAPY (ART). METHODS: A TOTAL OF 378 ART-NAIVE PLWH WHO HAD CD4 T-CELL COUNTS >500/MICROL AND WERE ENROLLED IN THE STRATEGIC TIMING OF ANTIRETROVIRAL THERAPY TRIAL (PULMONARY SUBSTUDY) WERE COMPARED WITH 34 HIV-NEGATIVE CONTROLS. DNA METHYLATION WAS PERFORMED USING THE ILLUMINA METHYLATIONEPIC BEADCHIP. DIFFERENTIALLY METHYLATED POSITIONS (DMPS) AND DIFFERENTIALLY METHYLATED REGIONS (DMRS) IN PLWH COMPARED WITH CONTROLS WERE IDENTIFIED USING A ROBUST LINEAR MODEL. METHYLATION AGE WAS CALCULATED USING A PREVIOUSLY DESCRIBED EPIGENETIC CLOCK. RESULTS: THERE WERE A TOTAL OF 56 639 DMPS AND 6103 DMRS AT A FALSE DISCOVERY RATE OF <0.1. THE TOP 5 DMPS CORRESPONDED TO GENES NLRC5, VRK2, B2M, AND GPR6 AND WERE HIGHLY ENRICHED FOR CANCER-RELATED PATHWAYS. PLWH HAD SIGNIFICANTLY HIGHER METHYLATION AGE THAN HIV-NEGATIVE CONTROLS (P = .001), WITH BLACK RACE, LOW CD4 AND HIGH CD8 T-CELL COUNTS, AND DURATION OF HIV BEING RISK FACTORS FOR AGE ACCELERATION. CONCLUSIONS: PLWH BEFORE THE INITIATION OF ART AND WITH PRESERVED IMMUNE STATUS SHOW EVIDENCE OF ADVANCED METHYLATION AGING.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
16   779  30 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
17  6460  27 TIME TO RELAPSE IN CHRONIC LYMPHOCYTIC LEUKEMIA AND DNA-METHYLATION-BASED BIOLOGICAL AGE. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS A MATURE B CELL NEOPLASM WITH A PREDILECTION FOR OLDER INDIVIDUALS. WHILE PREVIOUS STUDIES HAVE IDENTIFIED EPIGENETIC SIGNATURES ASSOCIATED WITH CLL, WHETHER AGE-RELATED DNA METHYLATION CHANGES MODULATE CLL RELAPSE REMAINS ELUSIVE. IN THIS STUDY, WE EXAMINED THE ASSOCIATION BETWEEN EPIGENETIC AGE ACCELERATION AND TIME TO CLL RELAPSE IN A PUBLICLY AVAILABLE DATASET. DNA METHYLATION PROFILING OF 35 CLL PATIENTS PRIOR TO INITIATING CHEMOIMMUNOTHERAPY WAS PERFORMED USING THE INFINIUM HUMANMETHYLATION450 BEADCHIP. FOUR EPIGENETIC AGE ACCELERATION METRICS (INTRINSIC EPIGENETIC AGE ACCELERATION [IEAA], EXTRINSIC EPIGENETIC AGE ACCELERATION [EEAA], PHENOAGE ACCELERATION [PHENOAA], AND GRIMAGE ACCELERATION [GRIMAA]) WERE ESTIMATED FROM BLOOD DNA METHYLATION LEVELS. LINEAR, QUANTILE, AND LOGISTIC REGRESSION AND RECEIVER OPERATING CHARACTERISTIC CURVE ANALYSES WERE CONDUCTED TO ASSESS THE ASSOCIATION BETWEEN EACH EPIGENETIC AGE METRIC AND TIME TO CLL RELAPSE. EEAA (P = 0.011) AND PHENOAA (P = 0.046) WERE NEGATIVELY AND GRIMAA (P = 0.040) WAS POSITIVELY ASSOCIATED WITH TIME TO CLL RELAPSE. SIMULTANEOUS ASSESSMENT OF EEAA AND GRIMAA IN MALE PATIENTS DISTINGUISHED PATIENTS WHO RELAPSED EARLY FROM PATIENTS WHO RELAPSED LATER (P = 0.039). NO ASSOCIATIONS WERE OBSERVED WITH IEAA. THESE FINDINGS SUGGEST EPIGENETIC AGE ACCELERATION PRIOR TO CHEMOIMMUNOTHERAPY INITIATION IS ASSOCIATED WITH TIME TO CLL RELAPSE. OUR RESULTS PROVIDE NOVEL INSIGHT INTO THE ASSOCIATION BETWEEN AGE-RELATED DNA METHYLATION CHANGES AND CLL RELAPSE AND MAY SERVE HAS BIOMARKERS FOR TREATMENT RELAPSE, AND POTENTIALLY, TREATMENT SELECTION.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
18  3995  34 LONGITUDINAL STUDY OF DNA METHYLATION OF INFLAMMATORY GENES AND CANCER RISK. BACKGROUND: CHRONIC INFLAMMATION PLAYS A KEY ROLE IN CANCER ETIOLOGY. DNA METHYLATION MODIFICATION, ONE OF THE EPIGENETIC MECHANISMS REGULATING GENE EXPRESSION, IS CONSIDERED A HALLMARK OF CANCER. HUMAN AND ANIMAL MODELS HAVE IDENTIFIED NUMEROUS LINKS BETWEEN DNA METHYLATION AND INFLAMMATORY BIOMARKERS. OUR OBJECTIVE WAS TO PROSPECTIVELY AND LONGITUDINALLY EXAMINE ASSOCIATIONS BETWEEN METHYLATION OF FOUR INFLAMMATORY GENES AND CANCER RISK. METHODS: WE INCLUDED 795 NORMATIVE AGING STUDY PARTICIPANTS WITH BLOOD DRAWN ONE TO FOUR TIMES FROM 1999 TO 2012 (MEDIAN FOLLOW-UP, 10.6 YEARS). PROMOTER DNA METHYLATION OF IL6, ICAM-1, IFN, AND TLR2 IN BLOOD LEUKOCYTES WAS MEASURED USING PYROSEQUENCING AT MULTIPLE CPG SITES AND AVERAGED BY GENE FOR DATA ANALYSIS. WE USED COX REGRESSION MODELS TO EXAMINE PROSPECTIVE ASSOCIATIONS OF BASELINE AND TIME-DEPENDENT METHYLATION WITH CANCER RISK AND COMPARED MEAN METHYLATION DIFFERENCES OVER TIME BETWEEN CANCER CASES AND CANCER-FREE PARTICIPANTS. RESULTS: BASELINE IFN HYPERMETHYLATION WAS ASSOCIATED WITH ALL-CANCER (HR, 1.49; P = 0.04) AND PROSTATE CANCER INCIDENCE (HR, 1.69; P = 0.02). BASELINE ICAM-1 AND IL6 HYPERMETHYLATION WERE ASSOCIATED WITH PROSTATE CANCER INCIDENCE (HR, 1.43; P = 0.02; HR, 0.70; P = 0.03, RESPECTIVELY). IN OUR TIME-DEPENDENT ANALYSES, IFN HYPERMETHYLATION WAS ASSOCIATED WITH ALL-CANCER (HR, 1.79; P = 0.007) AND PROSTATE CANCER (HR, 1.57; P = 0.03) INCIDENCE; AND ICAM-1 AND IL6 HYPERMETHYLATION WERE ASSOCIATED WITH PROSTATE CANCER INCIDENCE (HR, 1.39; P = 0.02; HR, 0.69; P = 0.03, RESPECTIVELY). WE DETECTED SIGNIFICANT ICAM-1 HYPERMETHYLATION IN CANCER CASES (P = 0.0003) 10 TO 13 YEARS PREDIAGNOSIS. CONCLUSION: HYPERMETHYLATION OF IFN AND ICAM-1 MAY PLAY IMPORTANT ROLES IN EARLY CARCINOGENESIS, PARTICULARLY THAT OF PROSTATE CANCER. IMPACT: THESE METHYLATION CHANGES COULD INFORM THE DEVELOPMENT OF EARLY DETECTION BIOMARKERS AND POTENTIAL TREATMENTS OF INFLAMMATION-RELATED CARCINOGENESIS.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
19  1953  26 EPIGENETIC AGE ACCELERATION AND CHRONIC HEALTH CONDITIONS AMONG ADULT SURVIVORS OF CHILDHOOD CANCER. BACKGROUND: MOUNTING EVIDENCE SUPPORTS THE OCCURRENCE OF ACCELERATING AGING AMONG LONG-TERM SURVIVORS OF CHILDHOOD CANCER. WE AIMED TO INVESTIGATE EPIGENETIC AGE ACCELERATION (EAA) IN SURVIVORS AND EVALUATE ASSOCIATIONS BETWEEN EAA, TREATMENT EXPOSURES, HEALTH BEHAVIORS, AND CHRONIC HEALTH CONDITIONS (CHCS). METHODS: GENOME-WIDE METHYLATION DATA WERE GENERATED WITH INFINIUM EPIC BEADCHIP ON BLOOD-DERIVED DNA FROM 2139 SURVIVORS AND 282 FREQUENCY MATCHED CONTROLS FROM THE ST JUDE LIFETIME COHORT STUDY. EAAS WERE ESTIMATED AS RESIDUALS FROM A LINEAR REGRESSION OF EPIGENETIC AGE (LEVINE'S CLOCK) AGAINST CHRONOLOGICAL AGE. ADJUSTED LEAST SQUARE MEAN (ALSM) OF EAA WAS CALCULATED AND COMPARED BETWEEN SURVIVORS AND CONTROLS, ACROSS TREATMENT EXPOSURES AND HEALTH BEHAVIORS. ASSOCIATIONS OF EAA WITH 20 CLINICALLY ASSESSED CHCS WERE EVALUATED WITH MULTIVARIABLE PIECEWISE-EXPONENTIAL MODELS. ALL STATISTICAL TESTS FOR P VALUES BELOW WERE 2-SIDED. RESULTS: EAA WAS STATISTICALLY SIGNIFICANTLY HIGHER IN SURVIVORS THAN CONTROLS (ALSM = 0.63, 95% CONFIDENCE INTERVAL [CI] = 0.26 TO 1.01 VS -3.61, 95% CI = -4.43 TO 2.80). IN A MULTIVARIABLE MODEL AMONG SURVIVORS, STATISTICALLY SIGNIFICANTLY HIGHER EAA (P < .05) WAS OBSERVED IN THOSE EXPOSED TO CHEST RADIOTHERAPY, ABDOMEN OR PELVIC RADIOTHERAPY, ALKYLATING AGENTS, GLUCOCORTICOIDS, OR EPIPODOPHYLLOTOXINS. COMPARED WITH SURVIVORS WITH FAVORABLE HEALTH BEHAVIORS (ALSM = 0.26, 95% CI=-0.36 TO 0.87), EAA WAS STATISTICALLY SIGNIFICANTLY HIGHER AMONG SURVIVORS WITH INTERMEDIATE (ALSM = 1.07, 95% CI = 0.59 TO 1.54) OR UNFAVORABLE HEALTH BEHAVIORS (ALSM = 1.45, 95% CI = 0.60 TO 2.30). IN TIME-TO-EVENT ANALYSES, STATISTICALLY SIGNIFICANT ASSOCIATIONS WERE IDENTIFIED BETWEEN EAA TERTILES AND INCIDENCE OF 7 CHCS: HYPERTENSION (3RD VS 1ST TERTILE, RELATIVE RATE [RR] = 1.83, 95% CI = 1.17 TO 2.83), MYOCARDIAL INFARCTION (RR = 2.91, 95% CI = 1.27 TO 7.21), OBESITY (RR = 1.39, 95% CI = 1.17 TO 1.66), OBSTRUCTIVE PULMONARY DEFICIT (RR = 1.86, 95% CI = 0.95 TO 3.77), PERIPHERAL MOTOR NEUROPATHY (RR = 2.89, 95% CI = 1.24 TO 6.97), PERIPHERAL SENSORY NEUROPATHY (RR = 2.04, 95% CI = 0.99 TO 4.26), AND PULMONARY DIFFUSION DEFICITS (RR = 2.75, 95% CI = 0.95 TO 7.63). CONCLUSIONS: EAA IS STATISTICALLY SIGNIFICANTLY HIGHER IN SURVIVORS OF CHILDHOOD CANCER THAN IN NONCANCER CONTROLS AND IS ASSOCIATED WITH SPECIFIC TREATMENT EXPOSURES, UNFAVORABLE HEALTH BEHAVIORS, AND PRESENCE OF SPECIFIC CHCS.	2021	
                                                                                                                                                                                                                                                                                                                                                     
20  3458  34 HYPOMETHYLATION OF LINE-1 REPEAT ELEMENTS AND GLOBAL LOSS OF DNA HYDROXYMETHYLATION IN VAPERS AND SMOKERS. THE OUTBREAK OF VAPING-RELATED SEVERE LUNG INJURIES AND DEATHS AND THE EPIDEMIC OF TEEN VAPING IN THE U.S. UNDERSCORE THE URGENT NEED FOR DETERMINING THE BIOLOGICAL CONSEQUENCES OF ELECTRONIC CIGARETTE (E-CIG) USE. WE HAVE INVESTIGATED THE ASSOCIATION BETWEEN VAPING AND EPIGENETIC CHANGES BY QUANTIFYING DNA METHYLATION LEVELS IN LONG INTERSPERSED NUCLEOTIDE ELEMENT 1 (LINE-1) AND GLOBAL DNA HYDROXYMETHYLATION (5-HMC) LEVELS AND MEASURING THE EXPRESSION LEVEL OF ENZYMES CATALYSING THE RESPECTIVE PROCESSES IN PERIPHERAL BLOOD OF EXCLUSIVE VAPERS, SMOKERS, AND CONTROLS, MATCHED FOR AGE, GENDER, AND RACE (N = 45). BOTH VAPERS AND SMOKERS SHOWED SIGNIFICANT LOSS OF METHYLATION IN LINE-1 REPEAT ELEMENTS IN COMPARISON TO CONTROLS (P = 0.00854 AND P = 0.03078, RESPECTIVELY). SIMILARLY, VAPERS AND SMOKERS HAD SIGNIFICANT REDUCTIONS IN 5-HMC LEVELS RELATIVE TO CONTROLS (P = 0.04884 AND P = 0.0035, RESPECTIVELY). NEITHER THE LINE-1 METHYLATION LEVELS NOR THE GLOBAL 5-HMC LEVELS WERE DIFFERENT BETWEEN VAPERS AND SMOKERS. THERE WAS A DIRECT CORRELATION BETWEEN METHYLATION LEVELS IN THE LINE-1 ELEMENTS AND GLOBAL 5-HMC LEVELS IN THE STUDY SUBJECTS (R = 0.31696, P = 0.03389). INVERSE AND STATISTICALLY SIGNIFICANT CORRELATIONS WERE FOUND BETWEEN BOTH THE LINE-1 METHYLATION LEVELS AND THE GLOBAL 5-HMC LEVELS AND VARIOUS VAPING/SMOKING METRICS IN THE STUDY SUBJECTS. THERE WERE MODEST BUT NOT STATISTICALLY SIGNIFICANT CHANGES IN TRANSCRIPTION OF DNA METHYLTRANSFERASES AND TEN-ELEVEN TRANSLOCATION ENZYMES IN BOTH VAPERS AND SMOKERS RELATIVE TO CONTROLS. OUR FINDINGS SUPPORT FOLLOW-UP GENOME-WIDE INVESTIGATIONS INTO THE EPIGENETIC EFFECTS OF VAPING, WHICH MAY FURTHER CLARIFY THE HEALTH CONSEQUENCES OF E-CIG USE. ABBREVIATIONS: 5-MC: 5-METHYLCYTOSINE; 5-HMC: 5-HYDROXYMETHYLCYTOSINE; 8-OHDG: 8-HYDROXY-2'-DEOXYGUANOSINE; ACTIN: ACTIN BETA; ANOVA: ANALYSIS OF VARIANCE; BER: BASE EXCISION REPAIR; BMI: BODY MASS INDEX; CO: CARBON MONOXIDE; COHB: CARBOXYHAEMOGLOBIN; COBRA: COMBINED BISULPHITE RESTRICTION ANALYSIS; COPD: CHRONIC OBSTRUCTIVE PULMONARY DISEASE; DNMT1: DNA METHYLTRANSFERASE 1; DNMT3A: DNA METHYLTRANSFERASE 3A; DNMT3B: DNA METHYLTRANSFERASE 3B; E-CIGS: ELECTRONIC CIGARETTES; ELISA: ENZYME-LINKED IMMUNOSORBENT ASSAY; ENDS: ELECTRONIC NICOTINE DELIVERY SYSTEMS; FDA: FOOD AND DRUG ADMINISTRATION; GAPDH; GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE; HPLC: HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY; LINE-1: LONG INTERSPERSED NUCLEOTIDE ELEMENT 1; PBS: PHOSPHATE-BUFFERED SALINE; RFU: RELATIVE FLUORESCENCE UNITS; RT-QPCR: QUANTITATIVE REVERSE-TRANSCRIPTION POLYMERASE CHAIN REACTION; ROS: REACTIVE OXYGEN SPECIES; SAM, S-ADENOSYLMETHIONINE; SE: STANDARD ERROR; TET1: TEN-ELEVEN TRANSLOCATION 1; TET2: TEN-ELEVEN TRANSLOCATION 2; TET3: TEN-ELEVEN TRANSLOCATION 3.	2020