1  3557 141 IMPACT OF BMI AND WAIST CIRCUMFERENCE ON EPIGENOME-WIDE DNA METHYLATION AND IDENTIFICATION OF EPIGENETIC BIOMARKERS IN BLOOD: AN EWAS IN MULTI-ETHNIC ASIAN INDIVIDUALS. BACKGROUND: THE PREVALENCE OF OBESITY AND ITS RELATED CHRONIC DISEASES HAVE BEEN INCREASING ESPECIALLY IN ASIAN COUNTRIES. OBESITY-RELATED GENETIC VARIANTS HAVE BEEN IDENTIFIED, BUT THESE EXPLAIN LITTLE OF THE VARIATION IN BMI. RECENT STUDIES REPORTED ASSOCIATIONS BETWEEN DNA METHYLATION AND OBESITY, MOSTLY IN NON-ASIAN POPULATIONS. METHODS: WE PERFORMED AN EPIGENOME-WIDE ASSOCIATION STUDY (EWAS) ON GENERAL ADIPOSITY (BODY MASS INDEX, BMI) AND ABDOMINAL ADIPOSITY (WAIST CIRCUMFERENCE, WC) IN 409 MULTI-ETHNIC ASIAN INDIVIDUALS AND REPLICATED BMI AND WAIST-ASSOCIATED DNA METHYLATION CPGS IDENTIFIED IN OTHER POPULATIONS. THE CROSS-LAGGED PANEL MODEL AND MENDELIAN RANDOMIZATION WERE USED TO ASSESS THE TEMPORAL RELATIONSHIP BETWEEN METHYLATION AND BMI. THE TEMPORAL RELATIONSHIP BETWEEN THE IDENTIFIED CPGS AND INFLAMMATION AND METABOLIC MARKERS WAS ALSO EXAMINED. RESULTS: EWAS IDENTIFIED 116 DNA METHYLATION CPGS INDEPENDENTLY ASSOCIATED WITH BMI AND EIGHT INDEPENDENTLY ASSOCIATED WITH WC AT FALSE DISCOVERY RATE P(FDR) < 0.05 IN 409 ASIAN SAMPLES. WE REPLICATED 110 BMI-ASSOCIATED CPGS PREVIOUSLY REPORTED IN EUROPEANS AND IDENTIFIED SIX NOVEL BMI-ASSOCIATED CPGS AND TWO NOVEL WC-ASSOCIATED CPGS. WE OBSERVED HIGH CONSISTENCY IN ASSOCIATION DIRECTION OF EFFECT COMPARED TO STUDIES IN OTHER POPULATIONS. CAUSAL RELATIONSHIP ANALYSES INDICATED THAT BMI WAS MORE LIKELY TO BE THE CAUSE OF DNA METHYLATION ALTERATION, RATHER THAN THE CONSEQUENCE. THE CAUSAL ANALYSES USING BMI-ASSOCIATED METHYLATION RISK SCORE ALSO SUGGESTED THAT HIGHER LEVELS OF THE INFLAMMATION MARKER IL-6 WERE LIKELY THE CONSEQUENCE OF METHYLATION CHANGE. CONCLUSION: OUR STUDY PROVIDES EVIDENCE OF AN ASSOCIATION BETWEEN OBESITY AND DNA METHYLATION IN MULTI-ETHNIC ASIANS AND SUGGESTS THAT OBESITY CAN DRIVE METHYLATION CHANGE. THE RESULTS ALSO SUGGESTED POSSIBLE CAUSAL INFLUENCE THAT OBESITY-RELATED METHYLATION CHANGES MIGHT HAVE ON INFLAMMATION AND LIPOPROTEIN LEVELS.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
2   490  55 ASSESSING THE IMPACT OF ARSENIC METABOLISM EFFICIENCY ON DNA METHYLATION USING MENDELIAN RANDOMIZATION. BACKGROUND: ARSENIC EXPOSURE AFFECTS >100 MILLION PEOPLE GLOBALLY AND INCREASES RISK FOR CHRONIC DISEASES. ONE POSSIBLE TOXICITY MECHANISM IS EPIGENETIC MODIFICATION. PREVIOUS EPIGENOME-WIDE ASSOCIATION STUDIES (EWAS) HAVE IDENTIFIED ASSOCIATIONS BETWEEN ARSENIC EXPOSURE AND CPG-SPECIFIC DNA METHYLATION. TO PROVIDE ADDITIONAL EVIDENCE THAT OBSERVED ASSOCIATIONS REPRESENT CAUSAL RELATIONSHIPS, WE EXAMINE THE ASSOCIATION BETWEEN GENETIC DETERMINANTS OF ARSENIC METABOLISM EFFICIENCY (PERCENT DIMETHYLARSINIC ACID, DMA%, IN URINE) AND DNA METHYLATION AMONG INDIVIDUALS FROM THE HEALTH EFFECTS OF ARSENIC LONGITUDINAL STUDY (N = 379) AND BANGLADESH VITAMIN E AND SELENIUM TRIAL (N = 393). METHODS: WE USED MULTIVARIATE LINEAR MODELS TO ASSESS THE ASSOCIATION OF METHYLATION AT 221 ARSENIC-ASSOCIATED CPGS WITH DMA% AND MEASURES OF GENETICALLY PREDICTED DMA% DERIVED FROM THREE SNPS (RS9527, RS11191527, AND RS61735836). WE ALSO CONDUCTED TWO-SAMPLE MENDELIAN RANDOMIZATION ANALYSES TO ESTIMATE THE ASSOCIATION BETWEEN ARSENIC METABOLISM EFFICIENCY AND CPG METHYLATION. RESULTS: AMONG THE ASSOCIATIONS BETWEEN DMA% AND METHYLATION AT EACH OF 221 CPGS, 64% WERE DIRECTIONALLY CONSISTENT WITH ASSOCIATIONS OBSERVED BETWEEN ARSENIC EXPOSURE AND THE 221 CPGS FROM A PRIOR EWAS. SIMILARLY, AMONG THE ASSOCIATIONS BETWEEN GENETICALLY PREDICTED DMA% AND EACH CPG, 62% WERE DIRECTIONALLY CONSISTENT WITH THE PRIOR EWAS RESULTS. TWO-SAMPLE MENDELIAN RANDOMIZATION ANALYSES PRODUCED SIMILAR CONCLUSIONS. CONCLUSION: OUR FINDINGS SUPPORT THE HYPOTHESIS THAT ARSENIC EXPOSURE EFFECTS DNA METHYLATION AT SPECIFIC CPGS IN WHOLE BLOOD. OUR NOVEL APPROACH FOR ASSESSING THE IMPACT OF ARSENIC EXPOSURE ON DNA METHYLATION REQUIRES LARGER SAMPLES IN ORDER TO DRAW MORE ROBUST CONCLUSIONS FOR SPECIFIC CPG SITES.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
3  1672  42 DRD4 METHYLATION AS A POTENTIAL BIOMARKER FOR PHYSICAL AGGRESSION: AN EPIGENOME-WIDE, CROSS-TISSUE INVESTIGATION. EPIGENETIC PROCESSES THAT REGULATE GENE EXPRESSION, SUCH AS DNA METHYLATION (DNAM), HAVE BEEN LINKED TO INDIVIDUAL DIFFERENCES IN PHYSICAL AGGRESSION. YET, IT IS CURRENTLY UNCLEAR WHETHER: (A) DNAM PATTERNS IN HUMANS ASSOCIATE WITH PHYSICAL AGGRESSION INDEPENDENTLY OF OTHER CO-OCCURRING PSYCHIATRIC AND BEHAVIORAL SYMPTOMS; (B) WHETHER THESE PATTERNS ARE OBSERVABLE ACROSS MULTIPLE TISSUES; AND (C) WHETHER THEY MAY FUNCTION AS A CAUSAL VERSUS NONCAUSAL BIOMARKER OF PHYSICAL AGGRESSION. HERE, WE USED A MULTISAMPLE, CROSS-TISSUE DESIGN TO ADDRESS THESE QUESTIONS. FIRST, WE EXAMINED GENOME-WIDE DNAM PATTERNS (BUCCAL SWABS; ILLUMINA 450K) ASSOCIATED WITH ENGAGEMENT IN PHYSICAL FIGHTS IN A SAMPLE OF HIGH-RISK YOUTH (N = 119; AGE = 16-24 YEARS; 53% FEMALE). WE IDENTIFIED ONE DIFFERENTIALLY METHYLATED REGION IN DRD4, WHICH SURVIVED GENOME-WIDE CORRECTION, ASSOCIATED WITH PHYSICAL AGGRESSION ABOVE AND BEYOND CO-OCCURRING SYMPTOMATOLOGY (E.G., ADHD, SUBSTANCE USE), AND SHOWED STRONG CROSS-TISSUE CONCORDANCE WITH BOTH BLOOD AND BRAIN. SECOND, WE FOUND THAT DNAM SITES WITHIN THIS REGION WERE ALSO DIFFERENTIALLY METHYLATED IN AN INDEPENDENT SAMPLE OF YOUNG ADULTS, BETWEEN INDIVIDUALS WITH A HISTORY OF CHRONIC-HIGH VERSUS LOW PHYSICAL AGGRESSION (PERIPHERAL T CELLS; AGES 26-28). FINALLY, WE RAN A MENDELIAN RANDOMIZATION ANALYSIS USING GWAS DATA FROM THE EAGLE CONSORTIUM TO TEST FOR A CAUSAL ASSOCIATION OF DRD4 METHYLATION WITH PHYSICAL AGGRESSION. ONLY ONE GENETIC INSTRUMENT WAS ELIGIBLE FOR THE ANALYSIS, AND RESULTS PROVIDED NO EVIDENCE FOR A CAUSAL ASSOCIATION. OVERALL, OUR FINDINGS LEND SUPPORT FOR PERIPHERAL DRD4 METHYLATION AS A POTENTIAL BIOMARKER OF PHYSICALLY AGGRESSIVE BEHAVIOR, WITH NO EVIDENCE YET OF A CAUSAL RELATIONSHIP.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
4  2643  45 EPIGENOMIC ASSOCIATION ANALYSIS IDENTIFIES SMOKING-RELATED DNA METHYLATION SITES IN AFRICAN AMERICANS. CIGARETTE SMOKING IS AN ENVIRONMENTAL RISK FACTOR FOR MANY CHRONIC DISEASES, AND DISEASE RISK CAN OFTEN BE MANAGED BY SMOKING CONTROL. SMOKING CAN INDUCE CELLULAR AND MOLECULAR CHANGES, INCLUDING EPIGENETIC MODIFICATION, BUT THE SHORT- AND LONG-TERM EPIGENETIC MODIFICATIONS CAUSED BY CIGARETTE SMOKING AT THE GENE LEVEL HAVE NOT BEEN WELL UNDERSTOOD. RECENT STUDIES HAVE IDENTIFIED SMOKING-RELATED DNA METHYLATION (DNAM) SITES IN CAUCASIANS. TO DETERMINE WHETHER THE SAME DNAM SITES ASSOCIATE WITH SMOKING IN AFRICAN AMERICANS, AND TO IDENTIFY NOVEL SMOKING-RELATED DNAM SITES, WE CONDUCTED A METHYLOME-WIDE ASSOCIATION STUDY OF CIGARETTE SMOKING USING A DISCOVERY SAMPLE OF 972 AFRICAN AMERICANS, AND A REPLICATION SAMPLE OF 239 AFRICAN AMERICANS WITH TWO ARRAY-BASED METHODS. AMONG 15 DNAM SITES SIGNIFICANTLY ASSOCIATED WITH SMOKING AFTER CORRECTION FOR MULTIPLE TESTING IN OUR DISCOVERY SAMPLE, 5 DNAM SITES ARE REPLICATED IN AN INDEPENDENT COHORT, AND 14 SITES IN THE REPLICATION SAMPLE HAVE EFFECTS IN THE SAME DIRECTION AS IN THE DISCOVERY SAMPLE. THE TOP TWO SMOKING-RELATED DNAM SITES IN F2RL3 (FACTOR II RECEPTOR-LIKE 3) AND GPR15 (G-PROTEIN-COUPLED RECEPTOR 15) OBSERVED IN AFRICAN AMERICANS ARE CONSISTENT WITH PREVIOUS FINDINGS IN CAUCASIANS. THE ASSOCIATIONS BETWEEN THE REPLICATED DNAM SITES AND SMOKING REMAIN SIGNIFICANT AFTER ADJUSTING FOR GENETIC BACKGROUND. DESPITE THE DISTINCT GENETIC BACKGROUND BETWEEN AFRICAN AMERICANS AND CAUCASIANS, THE DNAM FROM THE TWO ETHNIC GROUPS SHARES COMMON ASSOCIATIONS WITH CIGARETTE SMOKING, WHICH SUGGESTS A COMMON MOLECULAR MECHANISM OF EPIGENETIC MODIFICATION INFLUENCED BY ENVIRONMENTAL EXPOSURE.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
5   521  37 ASSOCIATIONS BETWEEN MATERNAL PSYCHOSOCIAL STRESS, DNA METHYLATION, AND NEWBORN BIRTH WEIGHT IDENTIFIED BY INVESTIGATING METHYLATION AT INDIVIDUAL, REGIONAL, AND GENOME LEVELS. STRESS IS KNOWN TO AFFECT HEALTH THROUGHOUT LIFE AND INTO FUTURE GENERATIONS, BUT THE UNDERLYING MOLECULAR MECHANISMS ARE UNKNOWN. WE TESTED THE HYPOTHESIS THAT MATERNAL PSYCHOSOCIAL STRESS INFLUENCES DNA METHYLATION (DNAM), WHICH IN TURN IMPACTS NEWBORN HEALTH OUTCOMES. SPECIFICALLY, WE ANALYZED DNAM AT INDIVIDUAL, REGIONAL, AND GENOME-WIDE LEVELS TO TEST FOR ASSOCIATIONS WITH MATERNAL STRESS AND NEWBORN BIRTH WEIGHT. MATERNAL VENOUS BLOOD AND NEWBORN CORD BLOOD (N = 24 AND 22, RESPECTIVELY) WERE ASSAYED FOR METHYLATION AT APPROXIMATELY 450,000 CPG SITES. METHYLATION WAS ANALYZED BY EXAMINING CPG SITES INDIVIDUALLY IN AN EPIGENOME-WIDE ASSOCIATION STUDY (EWAS), AS REGIONAL GROUPS USING VARIABLY METHYLATED REGION (VMR) ANALYSIS IN MATERNAL BLOOD ONLY, AND THROUGH THE EPIGENOME-WIDE MEASURES USING GENOME-WIDE MEAN METHYLATION (GMM), HORVATH'S EPIGENETIC CLOCK, AND MITOTIC AGE. THESE METHYLATION MEASURES WERE TESTED FOR ASSOCIATION WITH THREE MEASURES OF MATERNAL STRESS (MATERNAL WAR TRAUMA, CHRONIC STRESS, AND EXPERIENCE OF SEXUAL VIOLENCE) AND ONE HEALTH OUTCOME (NEWBORN BIRTH WEIGHT). WE OBSERVED THAT MATERNAL EXPERIENCES OF WAR TRAUMA, CHRONIC STRESS, AND SEXUAL ASSAULT WERE EACH ASSOCIATED WITH DECREASED NEWBORN BIRTH WEIGHT (P < 1.95 X 10(-7) IN ALL CASES). TESTING INDIVIDUAL CPG SITES USING EWAS, WE OBSERVED NO ASSOCIATIONS BETWEEN DNAM AND ANY MEASURE OF MATERNAL STRESS OR NEWBORN BIRTH WEIGHT IN EITHER MATERNAL OR CORD BLOOD, AFTER BONFERRONI MULTIPLE TESTING CORRECTION. HOWEVER, THE TOP-RANKED CPG SITE IN MATERNAL BLOOD THAT ASSOCIATED WITH MATERNAL CHRONIC STRESS AND SEXUAL VIOLENCE BEFORE MULTIPLE TESTING CORRECTION IS LOCATED NEAR THE SPON1 GENE. TESTING AT A REGIONAL LEVEL, WE FOUND INCREASED METHYLATION OF A VMR IN MATERNAL BLOOD NEAR SPON1 THAT WAS ASSOCIATED WITH CHRONIC STRESS AND SEXUAL VIOLENCE AFTER BONFERRONI MULTIPLE TESTING CORRECTION (P = 1.95 X 10(-7) AND 8.3 X 10(-6), RESPECTIVELY). AT THE EPIGENOMIC LEVEL, CORD BLOOD GMM WAS ASSOCIATED WITH SIGNIFICANTLY HIGHER LEVELS OF WAR TRAUMA (P = 0.025) AND WAS SUGGESTIVELY ASSOCIATED WITH SEXUAL VIOLENCE (P = 0.053). THE OTHER TWO EPIGENOME-WIDE MEASURES WERE NOT ASSOCIATED WITH MATERNAL STRESS OR NEWBORN BIRTH WEIGHT IN EITHER TISSUE TYPE. DESPITE OUR SMALL SAMPLE SIZE, WE IDENTIFIED ASSOCIATIONS EVEN AFTER CONSERVATIVE MULTIPLE TESTING CORRECTION. SPECIFICALLY, WE FOUND ASSOCIATIONS BETWEEN DNAM AND THE THREE MEASURES OF MATERNAL STRESS ACROSS BOTH TISSUES; SPECIFICALLY, A VMR IN MATERNAL BLOOD AND GMM IN CORD BLOOD WERE BOTH ASSOCIATED WITH DIFFERENT MEASURES OF MATERNAL STRESS. THE ASSOCIATION OF CORD BLOOD GMM, BUT NOT MATERNAL BLOOD GMM, WITH MATERNAL STRESS MAY SUGGEST DIFFERENT RESPONSES TO STRESS IN MOTHER AND NEWBORN. IT IS NOTEWORTHY THAT WE FOUND ASSOCIATIONS ONLY WHEN CPG SITES WERE ANALYZED IN AGGREGATE, EITHER AS VMRS OR AS A BROAD SUMMARY MEASURE OF GMM.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
6   504  30 ASSOCIATION OF CIGARETTE SMOKING AND CRP LEVELS WITH DNA METHYLATION IN ALPHA-1 ANTITRYPSIN DEFICIENCY. ALPHA-1 ANTITRYPSIN (AAT) DEFICIENCY AND TOBACCO SMOKING ARE CONFIRMED RISK FACTORS FOR CHRONIC OBSTRUCTIVE PULMONARY DISEASE. WE HYPOTHESIZED THAT VARIABLE DNA METHYLATION WOULD BE ASSOCIATED WITH SMOKING AND INFLAMMATION, AS REFLECTED BY THE LEVEL OF C-REACTIVE PROTEIN (CRP) IN AAT-DEFICIENT SUBJECTS. METHYLATION LEVELS OF 1,411 AUTOSOMAL CPG SITES FROM THE ILLUMINA GOLDENGATE METHYLATION CANCER PANEL I WERE ANALYZED IN 316 SUBJECTS. ASSOCIATIONS OF FIVE SMOKING BEHAVIORS AND CRP LEVELS WITH INDIVIDUAL CPG SITES AND AVERAGE METHYLATION LEVELS WERE ASSESSED USING NON-PARAMETRIC TESTING, LINEAR REGRESSION AND LINEAR MIXED EFFECT MODELS, WITH AND WITHOUT ADJUSTMENT FOR AGE AND GENDER. UNIVARIATE LINEAR REGRESSION ANALYSIS REVEALED THAT METHYLATION LEVELS OF 16 CPG SITES SIGNIFICANTLY ASSOCIATED WITH EVER-SMOKING STATUS. A CPG SITE IN THE TGFBI GENE WAS THE ONLY SITE ASSOCIATED WITH EVER-SMOKING AFTER ADJUSTMENT FOR AGE AND GENDER. NO HIGHLY SIGNIFICANT ASSOCIATIONS EXISTED BETWEEN AGE AT SMOKING INITIATION, PACK-YEARS SMOKED, DURATION OF SMOKING, AND TIME SINCE QUITTING SMOKING AS PREDICTORS OF INDIVIDUAL CPG SITE METHYLATION LEVELS. HOWEVER, EVER-SMOKING AND YOUNGER AGE AT SMOKING INITIATION ASSOCIATED WITH LOWER METHYLATION LEVEL AVERAGED ACROSS ALL SITES. DNA METHYLATION AT CPG SITES IN THE RUNX3, JAK3 AND KRT1 GENES ASSOCIATED WITH CRP LEVELS. THE MOST SIGNIFICANTLY ASSOCIATED CPG SITES WITH GENDER AND AGE MAPPED TO THE CASP6 AND FZD9 GENES, RESPECTIVELY. IN SUMMARY, THIS STUDY IDENTIFIED MULTIPLE POTENTIAL CANDIDATE CPG SITES ASSOCIATED WITH EVER-SMOKING AND CRP LEVEL IN AAT-DEFICIENT SUBJECTS. PHENOTYPIC VARIABILITY IN MENDELIAN DISEASES MAY BE DUE TO EPIGENETIC FACTORS.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
7  1780  32 EDUCATION AND LIFESTYLE FACTORS ARE ASSOCIATED WITH DNA METHYLATION CLOCKS IN OLDER AFRICAN AMERICANS. DNA METHYLATION (DNAM) CLOCKS ARE IMPORTANT BIOMARKERS OF CELLULAR AGING AND ARE ASSOCIATED WITH A VARIETY OF AGE-RELATED CHRONIC DISEASES AND ALL-CAUSE MORTALITY. EXAMINING THE RELATIONSHIP BETWEEN EDUCATION AND LIFESTYLE RISK FACTORS FOR AGE-RELATED DISEASES AND MULTIPLE DNAM CLOCKS CAN INCREASE THE UNDERSTANDING OF HOW RISK FACTORS CONTRIBUTE TO AGING AT THE CELLULAR LEVEL. THIS STUDY EXPLORED THE ASSOCIATION BETWEEN EDUCATION OR LIFESTYLE RISK FACTORS FOR AGE-RELATED DISEASES AND THE ACCELERATION OF FOUR DNAM CLOCKS, INCLUDING INTRINSIC (IEAA) AND EXTRINSIC EPIGENETIC AGE ACCELERATION (EEAA), PHENOAGE ACCELERATION (PHENOAA), AND GRIMAGE ACCELERATION (GRIMAA) IN THE AFRICAN AMERICAN PARTICIPANTS OF THE GENETIC EPIDEMIOLOGY NETWORK OF ARTERIOPATHY. WE PERFORMED BOTH CROSS-SECTIONAL AND LONGITUDINAL ANALYSES. IN CROSS-SECTIONAL ANALYSES, GENDER, EDUCATION, BMI, SMOKING, AND ALCOHOL CONSUMPTION WERE ALL INDEPENDENTLY ASSOCIATED WITH GRIMAA, WHEREAS ONLY SOME OF THEM WERE ASSOCIATED WITH OTHER CLOCKS. THE EFFECT OF SMOKING AND EDUCATION ON GRIMAA VARIED BY GENDER. LONGITUDINAL ANALYSES SUGGEST THAT AGE AND BMI CONTINUED TO INCREASE GRIMAA, AND THAT AGE AND CURRENT SMOKING CONTINUED TO INCREASE PHENOAA AFTER CONTROLLING DNAM CLOCKS AT BASELINE. IN CONCLUSION, EDUCATION AND COMMON LIFESTYLE RISK FACTORS WERE ASSOCIATED WITH MULTIPLE DNAM CLOCKS. HOWEVER, THE ASSOCIATION WITH EACH RISK FACTOR VARIED BY CLOCK, WHICH SUGGESTS THAT DIFFERENT CLOCKS MAY CAPTURE ADVERSE EFFECTS FROM DIFFERENT ENVIRONMENTAL STIMULI.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
8  6761  43 X CHROMOSOME-WIDE ANALYSIS IDENTIFIES DNA METHYLATION SITES INFLUENCED BY CIGARETTE SMOKING. BACKGROUND: TOBACCO SMOKING IS A MAJOR CAUSE OF CHRONIC DISEASE WORLDWIDE. SMOKING MAY INDUCE CELLULAR AND MOLECULAR CHANGES INCLUDING EPIGENETIC MODIFICATION, WITH BOTH SHORT-TERM AND LONG-TERM MODIFICATION PATTERNS THAT MAY CONTRIBUTE TO PHENOTYPIC EXPRESSION OF DISEASES. RECENT EPIGENOME-WIDE ASSOCIATION STUDIES (EWAS) HAVE IDENTIFIED DOZENS OF SMOKING-RELATED DNA METHYLATION (DNAM) SITES. HOWEVER, THE X CHROMOSOMAL DNAM SITES HAVE BEEN LARGELY OVERLOOKED DUE TO A LACK OF AN ANALYTICAL FRAMEWORK FOR DEALING WITH THE SEX-DIMORPHIC DISTRIBUTION. TO IDENTIFY NOVEL SMOKING-RELATED DNAM SITES ON THE X CHROMOSOME, WE EXAMINED THE MODALITY OF EACH X CHROMOSOMAL DNAM SITE AND CONDUCTED A SEX-SPECIFIC ASSOCIATION STUDY OF CIGARETTE SMOKING. RESULTS: WE USED A DISCOVERY SAMPLE OF 139 MIDDLE-AGE TWINS, AND THREE REPLICATION SAMPLES OF 78 TWINS, 464 AND 333 UNRELATED INDIVIDUALS INCLUDING 47, 17, 22, AND 89 CURRENT SMOKERS, RESPECTIVELY. AFTER CORRECTION FOR MULTIPLE TESTING, THE TOP SMOKING-RELATED DNAM SITES IN BCOR AND TSC22D3 WERE SIGNIFICANTLY HYPERMETHYLATED AND HYPOMETHYLATED, RESPECTIVELY, AMONG CURRENT SMOKERS. THESE SMOKING-ASSOCIATED SITES WERE REPLICATED WITH META-ANALYSIS P-VALUES OF 9.17 X 10(-12) AND 1.61 X 10(-9). FOR BOTH SITES, THE SMOKING EFFECTS ON METHYLATION LEVELS WERE LARGER IN MALES THAN THAT IN FEMALES. CONCLUSIONS: OUR FINDINGS HIGHLIGHT THE IMPORTANCE OF INVESTIGATING X CHROMOSOME METHYLATION PATTERNS AND THEIR ASSOCIATIONS WITH ENVIRONMENTAL EXPOSURES AND DISEASE PHENOTYPES AND DEMONSTRATE A ROBUST STATISTICAL METHODOLOGY FOR SUCH STUDY. EXISTING EWAS OF HUMAN DISEASES SHOULD INCORPORATE THE X CHROMOSOMAL SITES TO COMPLETE A COMPREHENSIVE EPIGENOME-WIDE SCAN.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
9  2150  36 EPIGENETIC MEASURES OF AGEING PREDICT THE PREVALENCE AND INCIDENCE OF LEADING CAUSES OF DEATH AND DISEASE BURDEN. BACKGROUND: INDIVIDUALS OF THE SAME CHRONOLOGICAL AGE DISPLAY DIFFERENT RATES OF BIOLOGICAL AGEING. A NUMBER OF MEASURES OF BIOLOGICAL AGE HAVE BEEN PROPOSED WHICH HARNESS AGE-RELATED CHANGES IN DNA METHYLATION PROFILES. THESE MEASURES INCLUDE FIVE 'EPIGENETIC CLOCKS' WHICH PROVIDE AN INDEX OF HOW MUCH AN INDIVIDUAL'S BIOLOGICAL AGE DIFFERS FROM THEIR CHRONOLOGICAL AGE AT THE TIME OF MEASUREMENT. THE FIVE CLOCKS ENCOMPASS METHYLATION-BASED PREDICTORS OF CHRONOLOGICAL AGE (HORVATHAGE, HANNUMAGE), ALL-CAUSE MORTALITY (DNAM PHENOAGE, DNAM GRIMAGE) AND TELOMERE LENGTH (DNAM TELOMERE LENGTH). A SIXTH EPIGENETIC MEASURE OF AGEING DIFFERS FROM THESE CLOCKS IN THAT IT ACTS AS A SPEEDOMETER PROVIDING A SINGLE TIME-POINT MEASUREMENT OF THE PACE OF AN INDIVIDUAL'S BIOLOGICAL AGEING. THIS MEASURE OF AGEING IS TERMED DUNEDINPOAM. IN THIS STUDY, WE TEST THE ASSOCIATION BETWEEN THESE SIX EPIGENETIC MEASURES OF AGEING AND THE PREVALENCE AND INCIDENCE OF THE LEADING CAUSES OF DISEASE BURDEN AND MORTALITY IN HIGH-INCOME COUNTRIES (N </= 9537, GENERATION SCOTLAND: SCOTTISH FAMILY HEALTH STUDY). RESULTS: DNAM GRIMAGE PREDICTED INCIDENCE OF CLINICALLY DIAGNOSED CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD), TYPE 2 DIABETES AND ISCHEMIC HEART DISEASE AFTER 13 YEARS OF FOLLOW-UP (HAZARD RATIOS = 2.22, 1.52 AND 1.41, RESPECTIVELY). DUNEDINPOAM PREDICTED THE INCIDENCE OF COPD AND LUNG CANCER (HAZARD RATIOS = 2.02 AND 1.45, RESPECTIVELY). DNAM PHENOAGE PREDICTED INCIDENCE OF TYPE 2 DIABETES (HAZARD RATIO = 1.54). DNAM TELOMERE LENGTH ASSOCIATED WITH THE INCIDENCE OF ISCHEMIC HEART DISEASE (HAZARD RATIO = 0.80). DNAM GRIMAGE ASSOCIATED WITH ALL-CAUSE MORTALITY, THE PREVALENCE OF COPD AND SPIROMETRY MEASURES AT THE STUDY BASELINE. THESE ASSOCIATIONS WERE PRESENT AFTER ADJUSTING FOR POSSIBLE CONFOUNDING RISK FACTORS INCLUDING ALCOHOL CONSUMPTION, BODY MASS INDEX, DEPRIVATION, EDUCATION AND TOBACCO SMOKING AND SURPASSED STRINGENT BONFERRONI-CORRECTED SIGNIFICANCE THRESHOLDS. CONCLUSIONS: OUR DATA SUGGEST THAT EPIGENETIC MEASURES OF AGEING MAY HAVE UTILITY IN CLINICAL SETTINGS TO COMPLEMENT GOLD-STANDARD METHODS FOR DISEASE ASSESSMENT AND MANAGEMENT.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
10  4609  37 NEONATAL DNA METHYLATION AND CHILDHOOD LOW PROSOCIAL BEHAVIOR: AN EPIGENOME-WIDE ASSOCIATION META-ANALYSIS. LOW PROSOCIAL BEHAVIOR IN CHILDHOOD HAS BEEN CONSISTENTLY LINKED TO LATER PSYCHOPATHOLOGY, WITH EVIDENCE SUPPORTING THE INFLUENCE OF BOTH GENETIC AND ENVIRONMENTAL FACTORS ON ITS DEVELOPMENT. ALTHOUGH NEONATAL DNA METHYLATION (DNAM) HAS BEEN FOUND TO PROSPECTIVELY ASSOCIATE WITH A RANGE OF PSYCHOLOGICAL TRAITS IN CHILDHOOD, ITS POTENTIAL ROLE IN PROSOCIAL DEVELOPMENT HAS YET TO BE INVESTIGATED. THIS STUDY INVESTIGATED PROSPECTIVE ASSOCIATIONS BETWEEN CORD BLOOD DNAM AT BIRTH AND LOW PROSOCIAL BEHAVIOR WITHIN AND ACROSS FOUR LONGITUDINAL BIRTH COHORTS FROM THE PREGNANCY AND CHILDHOOD EPIGENETICS (PACE) CONSORTIUM. WE EXAMINED (A) DEVELOPMENTAL TRAJECTORIES OF "CHRONIC-LOW" VERSUS "TYPICAL" PROSOCIAL BEHAVIOR ACROSS CHILDHOOD IN A CASE-CONTROL DESIGN (N = 2,095), AND (B) CONTINUOUS "LOW PROSOCIAL" SCORES AT COMPARABLE CROSS-COHORT TIME-POINTS (N = 2,121). META-ANALYSES WERE PERFORMED TO EXAMINE DIFFERENTIALLY METHYLATED POSITIONS AND REGIONS. AT THE COHORT-SPECIFIC LEVEL, THREE CPGS WERE FOUND TO ASSOCIATE WITH CHRONIC LOW PROSOCIAL BEHAVIOR; HOWEVER, NONE OF THESE ASSOCIATIONS WAS REPLICATED IN ANOTHER COHORT. META-ANALYSIS REVEALED NO EPIGENOME-WIDE SIGNIFICANT CPGS OR REGIONS. OVERALL, WE FOUND NO EVIDENCE FOR ASSOCIATIONS BETWEEN DNAM PATTERNS AT BIRTH AND LOW PROSOCIAL BEHAVIOR ACROSS CHILDHOOD. FINDINGS HIGHLIGHT THE IMPORTANCE OF EMPLOYING MULTI-COHORT APPROACHES TO REPLICATE EPIGENETIC ASSOCIATIONS AND REDUCE THE RISK OF FALSE POSITIVE DISCOVERIES.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
11  3063  47 GENOME-WIDE DNA METHYLATION AND LONG-TERM AMBIENT AIR POLLUTION EXPOSURE IN KOREAN ADULTS. BACKGROUND: AMBIENT AIR POLLUTION IS ASSOCIATED WITH NUMEROUS ADVERSE HEALTH OUTCOMES, BUT THE UNDERLYING MECHANISMS ARE NOT WELL UNDERSTOOD; EPIGENETIC EFFECTS INCLUDING ALTERED DNA METHYLATION COULD PLAY A ROLE. TO EVALUATE ASSOCIATIONS OF LONG-TERM AIR POLLUTION EXPOSURE WITH DNA METHYLATION IN BLOOD, WE CONDUCTED AN EPIGENOME-WIDE ASSOCIATION STUDY IN A KOREAN CHRONIC OBSTRUCTIVE PULMONARY DISEASE COHORT (N = 100 INCLUDING 60 CASES) USING ILLUMINA'S INFINIUM HUMANMETHYLATION450K BEADCHIP. ANNUAL AVERAGE CONCENTRATIONS OF PARTICULATE MATTER </= 10 MUM IN DIAMETER (PM(10)) AND NITROGEN DIOXIDE (NO(2)) WERE ESTIMATED AT PARTICIPANTS' RESIDENTIAL ADDRESSES USING EXPOSURE PREDICTION MODELS. WE USED ROBUST LINEAR REGRESSION TO IDENTIFY DIFFERENTIALLY METHYLATED PROBES (DMPS) AND TWO DIFFERENT APPROACHES, DMRCATE AND COMB-P, TO IDENTIFY DIFFERENTIALLY METHYLATED REGIONS (DMRS). RESULTS: AFTER MULTIPLE TESTING CORRECTION (FALSE DISCOVERY RATE < 0.05), THERE WERE 12 DMPS AND 27 DMRS ASSOCIATED WITH PM(10) AND 45 DMPS AND 57 DMRS RELATED TO NO(2). DMP CG06992688 (OTUB2) AND SEVERAL DMRS WERE ASSOCIATED WITH BOTH EXPOSURES. ELEVEN DMPS IN RELATION TO NO(2) CONFIRMED PREVIOUS FINDINGS IN EUROPEANS; THE REMAINDER WERE NOVEL. METHYLATION LEVELS OF 39 DMPS WERE ASSOCIATED WITH EXPRESSION LEVELS OF NEARBY GENES IN A SEPARATE DATASET OF 3075 INDIVIDUALS. ENRICHED NETWORKS WERE RELATED TO OUTCOMES ASSOCIATED WITH AIR POLLUTION INCLUDING CARDIOVASCULAR AND RESPIRATORY DISEASES AS WELL AS INFLAMMATORY AND IMMUNE RESPONSES. CONCLUSIONS: THIS STUDY PROVIDES EVIDENCE THAT LONG-TERM AMBIENT AIR POLLUTION EXPOSURE IMPACTS DNA METHYLATION. THE DIFFERENTIAL METHYLATION SIGNALS CAN SERVE AS POTENTIAL AIR POLLUTION BIOMARKERS. THESE RESULTS MAY HELP BETTER UNDERSTAND THE INFLUENCES OF AMBIENT AIR POLLUTION ON HUMAN HEALTH.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
12  2631  52 EPIGENOME-WIDE ASSOCIATION STUDY OF WHOLE BLOOD GENE EXPRESSION IN FRAMINGHAM HEART STUDY PARTICIPANTS PROVIDES MOLECULAR INSIGHT INTO THE POTENTIAL ROLE OF CHRNA5 IN CIGARETTE SMOKING-RELATED LUNG DISEASES. BACKGROUND: DNA METHYLATION IS A KEY EPIGENETIC MODIFICATION THAT CAN DIRECTLY AFFECT GENE REGULATION. DNA METHYLATION IS HIGHLY INFLUENCED BY ENVIRONMENTAL FACTORS SUCH AS CIGARETTE SMOKING, WHICH IS CAUSALLY RELATED TO CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) AND LUNG CANCER. TO DATE, THERE HAVE BEEN FEW LARGE-SCALE, COMBINED ANALYSES OF DNA METHYLATION AND GENE EXPRESSION AND THEIR INTERRELATIONS WITH LUNG DISEASES. RESULTS: WE PERFORMED AN EPIGENOME-WIDE ASSOCIATION STUDY OF WHOLE BLOOD GENE EXPRESSION IN ~ 6000 INDIVIDUALS FROM FOUR COHORTS. WE DISCOVERED AND REPLICATED NUMEROUS CPGS ASSOCIATED WITH THE EXPRESSION OF CIS GENES WITHIN 500 KB OF EACH CPG, WITH 148 TO 1,741 CIS CPG-TRANSCRIPT PAIRS IDENTIFIED ACROSS COHORTS. WE FOUND THAT THE CLOSER A CPG RESIDED TO A TRANSCRIPTION START SITE, THE LARGER ITS EFFECT SIZE, AND THAT 36% OF CIS CPG-TRANSCRIPT PAIRS SHARE THE SAME CAUSAL GENETIC VARIANT. MENDELIAN RANDOMIZATION ANALYSES REVEALED THAT HYPOMETHYLATION AND LOWER EXPRESSION OF CHRNA5, WHICH ENCODES A SMOKING-RELATED NICOTINIC RECEPTOR, ARE CAUSALLY LINKED TO INCREASED RISK OF COPD AND LUNG CANCER. THIS PUTATIVELY CAUSAL RELATIONSHIP WAS FURTHER VALIDATED IN LUNG TISSUE DATA. CONCLUSIONS: OUR RESULTS PROVIDE A LARGE AND COMPREHENSIVE ASSOCIATION STUDY OF WHOLE BLOOD DNA METHYLATION WITH GENE EXPRESSION. EXPRESSION PLATFORM DIFFERENCES RATHER THAN POPULATION DIFFERENCES ARE CRITICAL TO THE REPLICATION OF CIS CPG-TRANSCRIPT PAIRS. THE LOW REPRODUCIBILITY OF TRANS CPG-TRANSCRIPT PAIRS SUGGESTS THAT DNA METHYLATION REGULATES NEARBY RATHER THAN REMOTE GENE EXPRESSION. THE PUTATIVELY CAUSAL ROLES OF METHYLATION AND EXPRESSION OF CHRNA5 IN RELATION TO COPD AND LUNG CANCER PROVIDE EVIDENCE FOR A MECHANISTIC LINK BETWEEN PATTERNS OF SMOKING-RELATED EPIGENETIC VARIATION AND LUNG DISEASES, AND HIGHLIGHT POTENTIAL THERAPEUTIC TARGETS FOR LUNG DISEASES AND SMOKING CESSATION.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
13  4256  36 METHYLOMIC MARKERS OF PERSISTENT CHILDHOOD ASTHMA: A LONGITUDINAL STUDY OF ASTHMA-DISCORDANT MONOZYGOTIC TWINS. BACKGROUND: ASTHMA IS THE MOST COMMON CHRONIC INFLAMMATORY DISORDER IN CHILDREN. THE AETIOLOGY OF ASTHMA PATHOLOGY IS COMPLEX AND HIGHLY HETEROGENEOUS, INVOLVING THE INTERPLAY BETWEEN GENETIC AND ENVIRONMENTAL RISK FACTORS THAT IS HYPOTHESIZED TO INVOLVE EPIGENETIC PROCESSES. OUR AIM WAS TO EXPLORE WHETHER METHYLOMIC VARIATION IN EARLY CHILDHOOD IS ASSOCIATED WITH DISCORDANCE FOR ASTHMA SYMPTOMS WITHIN MONOZYGOTIC (MZ) TWIN PAIRS RECRUITED FROM THE ENVIRONMENTAL RISK (E-RISK) LONGITUDINAL TWIN STUDY. WE ALSO AIMED TO IDENTIFY DIFFERENCES IN DNA METHYLATION THAT ARE ASSOCIATED WITH ASTHMA THAT DEVELOPS IN CHILDHOOD AND PERSISTS INTO EARLY ADULTHOOD AS THESE MAY REPRESENT USEFUL PROGNOSTIC BIOMARKERS. RESULTS: WE EXAMINED GENOME-WIDE PATTERNS OF DNA METHYLATION IN BUCCAL CELL SAMPLES COLLECTED FROM 37 MZ TWIN PAIRS DISCORDANT FOR ASTHMA AT AGE 10. DNA METHYLATION AT INDIVIDUAL CPG SITES DEMONSTRATED SIGNIFICANT VARIABILITY WITHIN DISCORDANT MZ TWIN PAIRS WITH THE TOP-RANKED NOMINALLY SIGNIFICANT DIFFERENTIALLY METHYLATED POSITION (DMP) LOCATED IN THE HGSNAT GENE. WE STRATIFIED OUR ANALYSIS BY ASSESSING DNA METHYLATION DIFFERENCES IN A SUB-GROUP OF MZ TWIN PAIRS WHO REMAINED PERSISTENTLY DISCORDANT FOR ASTHMA AT AGE 18. THE TOP-RANKED NOMINALLY SIGNIFICANT DMP ASSOCIATED WITH PERSISTING ASTHMA IS LOCATED IN THE VICINITY OF THE HLX GENE, WHICH HAS BEEN PREVIOUSLY IMPLICATED IN CHILDHOOD ASTHMA. CONCLUSIONS: WE IDENTIFIED DNA METHYLATION DIFFERENCES ASSOCIATED WITH CHILDHOOD ASTHMA IN PERIPHERAL DNA SAMPLES FROM DISCORDANT MZ TWIN PAIRS. OUR DATA SUGGEST THAT DIFFERENCES IN DNA METHYLATION ASSOCIATED WITH CHILDHOOD ASTHMA WHICH PERSISTS INTO EARLY ADULTHOOD ARE DISTINCT FROM THOSE ASSOCIATED WITH ASTHMA WHICH REMITS.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
14  5395  41 REDUCED EPIGENETIC AGE IN OLDER ADULTS WITH HIGH SENSE OF PURPOSE IN LIFE. PSYCHOSOCIAL RISK FACTORS HAVE BEEN LINKED WITH ACCELERATED EPIGENETIC AGING, BUT LITTLE IS KNOWN ABOUT WHETHER PSYCHOSOCIAL RESILIENCE FACTORS (EG, SENSE OF PURPOSE IN LIFE) MIGHT REDUCE EPIGENETIC AGE ACCELERATION. IN THIS STUDY, WE TESTED IF OLDER ADULTS WHO EXPERIENCE HIGH LEVELS OF PURPOSE MIGHT SHOW REDUCED EPIGENETIC AGE ACCELERATION. WE EVALUATED THE RELATIONSHIP BETWEEN PURPOSE AND EPIGENETIC AGE ACCELERATION AS MEASURED BY 13 DNA METHYLATION (DNAM) "EPIGENETIC CLOCKS" ASSESSED IN 1 572 OLDER ADULTS FROM THE HEALTH AND RETIREMENT STUDY (MEAN AGE 70 YEARS). WE QUANTIFIED THE TOTAL ASSOCIATION BETWEEN PURPOSE AND DNAM AGE ACCELERATION AS WELL AS THE EXTENT TO WHICH THAT TOTAL ASSOCIATION MIGHT BE ATTRIBUTABLE TO DEMOGRAPHIC FACTORS, CHRONIC DISEASE, OTHER PSYCHOSOCIAL VARIABLES (EG, POSITIVE AFFECT), AND HEALTH-RELATED BEHAVIORS (HEAVY DRINKING, SMOKING, PHYSICAL ACTIVITY, AND BODY MASS INDEX [BMI]). PURPOSE IN LIFE WAS ASSOCIATED WITH REDUCED EPIGENETIC AGE ACCELERATION ACROSS 4 "SECOND-GENERATION" DNAM CLOCKS OPTIMIZED FOR PREDICTING HEALTH AND LONGEVITY (FALSE DISCOVERY RATE [FDR] Q < 0.0001: PHENOAGE, GRIMAGE, ZHANG EPIGENETIC MORTALITY INDEX; FDR Q < 0.05: DUNEDINPOAM). THESE ASSOCIATIONS WERE INDEPENDENT OF DEMOGRAPHIC AND PSYCHOSOCIAL FACTORS, BUT SUBSTANTIALLY ATTENUATED AFTER ADJUSTING FOR HEALTH-RELATED BEHAVIORS (DRINKING, SMOKING, PHYSICAL ACTIVITY, AND BMI). PURPOSE SHOWED NO SIGNIFICANT ASSOCIATION WITH 9 "FIRST-GENERATION" DNAM EPIGENETIC CLOCKS TRAINED ON CHRONOLOGICAL AGE. OLDER ADULTS WITH GREATER PURPOSE IN LIFE SHOW "YOUNGER" DNAM EPIGENETIC AGE ACCELERATION. THESE RESULTS MAY BE DUE IN PART TO ASSOCIATED DIFFERENCES IN HEALTH-RELATED BEHAVIORS. RESULTS SUGGEST NEW OPPORTUNITIES TO REDUCE BIOLOGICAL AGE ACCELERATION BY ENHANCING PURPOSE AND ITS BEHAVIORAL SEQUELAE IN LATE ADULTHOOD.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
15   667  47 BLOOD-BASED EPIGENOME-WIDE ANALYSES OF 19 COMMON DISEASE STATES: A LONGITUDINAL, POPULATION-BASED LINKED COHORT STUDY OF 18,413 SCOTTISH INDIVIDUALS. BACKGROUND: DNA METHYLATION IS A DYNAMIC EPIGENETIC MECHANISM THAT OCCURS AT CYTOSINE-PHOSPHATE-GUANINE DINUCLEOTIDE (CPG) SITES. EPIGENOME-WIDE ASSOCIATION STUDIES (EWAS) INVESTIGATE THE STRENGTH OF ASSOCIATION BETWEEN METHYLATION AT INDIVIDUAL CPG SITES AND HEALTH OUTCOMES. ALTHOUGH BLOOD METHYLATION MAY ACT AS A PERIPHERAL MARKER OF COMMON DISEASE STATES, PREVIOUS EWAS HAVE TYPICALLY FOCUSED ONLY ON INDIVIDUAL CONDITIONS AND HAVE HAD LIMITED POWER TO DISCOVER DISEASE-ASSOCIATED LOCI. THIS STUDY EXAMINED THE ASSOCIATION OF BLOOD DNA METHYLATION WITH THE PREVALENCE OF 14 DISEASE STATES AND THE INCIDENCE OF 19 DISEASE STATES IN A SINGLE POPULATION OF OVER 18,000 SCOTTISH INDIVIDUALS. METHODS AND FINDINGS: DNA METHYLATION WAS ASSAYED AT 752,722 CPG SITES IN WHOLE-BLOOD SAMPLES FROM 18,413 VOLUNTEERS IN THE FAMILY-STRUCTURED, POPULATION-BASED COHORT STUDY GENERATION SCOTLAND (AGE RANGE 18 TO 99 YEARS). EWAS TESTED FOR CROSS-SECTIONAL ASSOCIATIONS BETWEEN BASELINE CPG METHYLATION AND 14 PREVALENT DISEASE STATES, AND FOR LONGITUDINAL ASSOCIATIONS BETWEEN BASELINE CPG METHYLATION AND 19 INCIDENT DISEASE STATES. PREVALENT CASES WERE SELF-REPORTED ON HEALTH QUESTIONNAIRES AT THE BASELINE. INCIDENT CASES WERE IDENTIFIED USING LINKAGE TO SCOTTISH PRIMARY (READ 2) AND SECONDARY (ICD-10) CARE RECORDS, AND THE CENSORING DATE WAS SET TO OCTOBER 2020. THE MEAN TIME-TO-DIAGNOSIS RANGED FROM 5.0 YEARS (FOR CHRONIC PAIN) TO 11.7 YEARS (FOR CORONAVIRUS DISEASE 2019 (COVID-19) HOSPITALISATION). THE 19 DISEASE STATES CONSIDERED IN THIS STUDY WERE SELECTED IF THEY WERE PRESENT ON THE WORLD HEALTH ORGANISATION'S 10 LEADING CAUSES OF DEATH AND DISEASE BURDEN OR INCLUDED IN BASELINE SELF-REPORT QUESTIONNAIRES. EWAS MODELS WERE ADJUSTED FOR AGE AT METHYLATION TYPING, SEX, ESTIMATED WHITE BLOOD CELL COMPOSITION, POPULATION STRUCTURE, AND 5 COMMON LIFESTYLE RISK FACTORS. A STRUCTURED LITERATURE REVIEW WAS ALSO CONDUCTED TO IDENTIFY EXISTING EWAS FOR ALL 19 DISEASE STATES TESTED. THE MEDLINE, EMBASE, WEB OF SCIENCE, AND PREPRINT SERVERS WERE SEARCHED TO RETRIEVE RELEVANT ARTICLES INDEXED AS OF MARCH 27, 2023. FIFTY-FOUR OF APPROXIMATELY 2,000 INDEXED ARTICLES MET OUR INCLUSION CRITERIA: ASSAYED BLOOD-BASED DNA METHYLATION, HAD >20 INDIVIDUALS IN EACH COMPARISON GROUP, AND EXAMINED ONE OF THE 19 CONDITIONS CONSIDERED. FIRST, WE ASSESSED WHETHER THE ASSOCIATIONS IDENTIFIED IN OUR STUDY WERE REPORTED IN PREVIOUS STUDIES. WE IDENTIFIED 69 ASSOCIATIONS BETWEEN CPGS AND THE PREVALENCE OF 4 CONDITIONS, OF WHICH 58 WERE NEWLY DESCRIBED. THE CONDITIONS WERE BREAST CANCER, CHRONIC KIDNEY DISEASE, ISCHEMIC HEART DISEASE, AND TYPE 2 DIABETES MELLITUS. WE ALSO UNCOVERED 64 CPGS THAT ASSOCIATED WITH THE INCIDENCE OF 2 DISEASE STATES (COPD AND TYPE 2 DIABETES), OF WHICH 56 WERE NOT REPORTED IN THE SURVEYED LITERATURE. SECOND, WE ASSESSED REPLICATION ACROSS EXISTING STUDIES, WHICH WAS DEFINED AS THE REPORTING OF AT LEAST 1 COMMON SITE IN >2 STUDIES THAT EXAMINED THE SAME CONDITION. ONLY 6/19 DISEASE STATES HAD EVIDENCE OF SUCH REPLICATION. THE LIMITATIONS OF THIS STUDY INCLUDE THE NONCONSIDERATION OF MEDICATION DATA AND A POTENTIAL LACK OF GENERALIZABILITY TO INDIVIDUALS THAT ARE NOT OF SCOTTISH AND EUROPEAN ANCESTRY. CONCLUSIONS: WE DISCOVERED OVER 100 ASSOCIATIONS BETWEEN BLOOD METHYLATION SITES AND COMMON DISEASE STATES, INDEPENDENTLY OF MAJOR CONFOUNDING RISK FACTORS, AND A NEED FOR GREATER STANDARDISATION AMONG EWAS ON HUMAN DISEASE.	2023	

16  1746  29 EARLY LIFE ADVERSITY, PUBERTAL TIMING, AND EPIGENETIC AGE ACCELERATION IN ADULTHOOD. BACKGROUND: GIVEN ASSOCIATIONS LINKING EARLY LIFE ADVERSITY, PUBERTAL TIMING, AND BIOLOGICAL AGING, WE EXAMINED THE DIRECT AND INDIRECT EFFECTS OF EARLY LIFE TRAUMA ON ADULT BIOLOGICAL AGING (VIA AGE OF MENARCHE). METHODS: PARTICIPANTS WERE PREMENOPAUSAL WOMEN (N = 183). PATH MODELS EVALUATED WHETHER EARLY LIFE TRAUMA PREDICTED EARLY PUBERTAL TIMING AND THEREBY, ADULT EPIGENETIC AGE ACCELERATION (INDEXED VIA FOUR EPIGENETIC CLOCKS: HORVATH DNAM AGE, HANNUM DNAM AGE, DNAM PHENOAGE, AND DNAM GRIMAGE). SECONDARY ANALYSES EXPLORED THE EFFECTS OF TYPE OF TRAUMA (ABUSE AND NEGLECT) AND ADULT CHRONIC STRESS STATUS (CAREGIVER OF CHILD WITH AUTISM AND NON-CAREGIVER). RESULTS: EARLY LIFE TRAUMA AND EARLIER AGE AT MENARCHE INDEPENDENTLY PREDICTED ACCELERATED AGING BASED ON ONE OF THE FOUR EPIGENETIC CLOCKS, DNAM GRIMAGE, THOUGH EARLY LIFE TRAUMA WAS NOT ASSOCIATED WITH AGE OF MENARCHE. CHILDHOOD ABUSE, BUT NOT NEGLECT, PREDICTED FASTER EPIGENETIC AGING; RESULTS DID NOT DIFFER BY CHRONIC STRESS STATUS. CONCLUSIONS: EARLY TRAUMA AND EARLY MENARCHE APPEAR TO EXERT INDEPENDENT EFFECTS ON DNAM GRIMAGE, WHICH HAS BEEN SHOWN TO BE THE STRONGEST EPIGENETIC PREDICTOR OF MORTALITY RISK. THIS STUDY IDENTIFIES A POTENTIAL CORRELATE OR DETERMINANT OF ACCELERATED EPIGENETIC AGING-MENARCHEAL AGE. FUTURE RESEARCH SHOULD ADDRESS THE LIMITATIONS OF THIS STUDY BY USING RACIALLY DIVERSE SAMPLES.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
17   253  33 ADVANCES AND PERSPECTIVES FROM GENETIC RESEARCH: DEVELOPMENT OF BIOLOGICAL MARKERS IN ALZHEIMER'S DISEASE. DESPITE IMPORTANT RECENT ADVANCES, A FULL UNDERSTANDING OF THE (GENETIC) ETIOLOGY OF ALZHEIMER'S DISEASE (AD) IS STILL A LONG WAY OFF. LARGE COLLABORATIVE EFFORTS ARE ONGOING, AS WELL AS THE EXPLORATION OF VARIOUS SOURCES OF GENETIC VARIATION. EVIDENCE SUPPORTS THE VIEW THAT MENDELIAN EARLY-ONSET FAMILIAL FORMS OF AD ARE CAUSED BY RARE AND USUALLY HIGHLY PENETRANT MUTATIONS IN THREE GENES (APP, PSEN1 AND PSEN2). CONSIDERING SPORADIC LATE-ONSET AD (LOAD), THE APOE EPSILON4 ALLELE IS BY FAR THE BEST-ESTABLISHED RISK GENE. RECENTLY PUBLISHED LARGE-SCALE GENOME-WIDE ANALYSES POINT TO ADDITIONALLY RELEVANT GENETICALLY ASSOCIATED LOCI, PARTICULARLY CLU, PICALM AND CR1. THESE SUSCEPTIBILITY LOCI SUPPORT EXISTING HYPOTHESES ABOUT THE AMYLOID, LIPID, CHAPERONE AND CHRONIC INFLAMMATORY MECHANISMS IN AD PATHOGENESIS, AND ARE THEREFORE LIKELY TO PROVIDE THE BASIS FOR THE DEVELOPMENT OF HYPOTHESIS-DRIVEN NOVEL BIOMARKER CANDIDATES. ADDITIONAL GENES, LISTED ONLINE IN ALZGENE (E.G., GAB2 OR SORL1) HAVE REPEATEDLY SHOWN RISK EFFECTS IN LOAD, AND MAY BE TRUE RISK GENES, BUT THIS IS MUCH LESS CERTAIN. NEW EPIGENETIC RESEARCH PROVIDED SOME EVIDENCE THAT DNA MODIFICATIONS MAYBE INVOLVED IN LOAD (E.G., POST-MORTEM STUDIES DESCRIBED BOTH HYPO- AND HYPER-METHYLATION IN AD-RELATED SUSCEPTIBILITY GENES). WITH RESPECT TO BIOMARKERS, ELDERLY NONDEMENTED APOE EPSILON4 CARRIERS DEMONSTRATED DISTINCT CEREBROSPINAL FLUID BIOMARKER SIGNATURES AND ALTERATIONS OF BRAIN GLUCOSE METABOLISM SIMILAR TO THOSE OBSERVED IN AD. FUTURE RESEARCH SHOULD EVALUATE THE USEFULNESS OF NEWLY DETECTED AD RISK GENES AND EPIGENETIC CHANGES AS POTENTIAL BIOMARKERS TOWARDS GENETIC PROFILING OF AD OR FOR CORRELATION WITH ENDOPHENOTYPES AND THERAPEUTIC OUTCOME.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
18  2734  41 EXPLORING THE RELATIONSHIP BETWEEN DNA METHYLATION AGE MEASURES AND PSYCHONEUROLOGICAL SYMPTOMS IN WOMEN WITH EARLY-STAGE BREAST CANCER. PURPOSE: THE EPIGENETIC CLOCK HAS BEEN ACKNOWLEDGED AS AN INDICATOR FOR MOLECULAR AGING, BUT FEW STUDIES HAVE EXAMINED POSSIBLE ASSOCIATIONS OF DNA METHYLATION (DNAM) AGE OR AGE ACCELERATION (AA) WITH SYMPTOM BURDEN IN INDIVIDUALS WHO ARE TREATED FOR CANCER. THIS STUDY EXPLORED THE ASSOCIATION OF DNAM AGE OR AA WITH PSYCHONEUROLOGICAL (PN) SYMPTOMS, INCLUDING COGNITIVE IMPAIRMENT, FATIGUE, SLEEP DISTURBANCES, PAIN, AND DEPRESSIVE SYMPTOMS, IN BREAST CANCER SURVIVORS OVER A 2-YEAR PERIOD. METHODS: WE MEASURED PN SYMPTOMS USING RELIABLE INSTRUMENTS AND DNAM LEVELS BY INFINIUM HUMANMETHYLATION450K BEADCHIP (N = 72). DNAM AGE WAS CALCULATED BY THE HORVATH, GRIM, AND HANNUM-BASED INTRINSIC AND EXTRINSIC AGE ESTIMATIONS. AA WAS DEFINED BY THE RESIDUAL REGRESSING ESTIMATED EPIGENETIC AGE ON CHRONOLOGICAL AGE. MIXED REGRESSION MODELS WERE FITTED FOR AA AND CHANGES IN AA TO STUDY THE ASSOCIATION OVER TIME. SEPARATE LINEAR REGRESSION MODELS AND A MIXED-EFFECTS MODEL WERE FITTED FOR AA AT EACH TIME POINT. RESULTS: HORVATH-AA, GRIM-AA, AND EXTRINSIC EPIGENETIC AA WERE SIGNIFICANTLY CHANGED OVER TIME, WHILE INTRINSIC EPIGENETIC AA DID NOT EXHIBIT ANY TEMPORAL CHANGES. INCREASED AA WAS ASSOCIATED WITH GREATER ANXIETY AND FATIGUE, AS WELL AS WORSE COGNITIVE MEMORY, ADJUSTING FOR RACE, BMI, INCOME, CHEMOTHERAPY, RADIATION THERAPY, AND CHRONOLOGICAL AGE. INCREASED DNAM AGE WAS ASSOCIATED WITH GREATER ANXIETY OVER 2 YEARS. CONCLUSION: OUR FINDINGS SUGGEST DNAM AGE AND AA MAY BE ASSOCIATED WITH PN SYMPTOMS OVER THE COURSE OF CANCER TREATMENT AND SURVIVORSHIP. SOME PN SYMPTOMS MAY BE AMENABLE TO PREVENTIVE INTERVENTIONS TARGETED TO EPIGENETIC CLOCKS THAT INFLUENCE AGING-ASSOCIATED PROCESSES.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
19  2622  42 EPIGENOME-WIDE ASSOCIATION STUDIES IN ASTHMA: A SYSTEMATIC REVIEW. OBJECTIVE: ASTHMA IS A COMMON CHRONIC RESPIRATORY AIRWAY DISEASE INFLUENCED BY ENVIRONMENTAL FACTORS AND POSSIBLY THEIR INTERACTION WITH THE HUMAN GENOME CAUSING EPIGENETIC CHANGES. EPIGENOME-WIDE ASSOCIATION STUDIES (EWAS) HAVE MAINLY INVESTIGATED DNA METHYLATION AND ITS ASSOCIATION WITH DISEASE OR TRAITS, EXPOSURE FACTORS OR GENE EXPRESSION. THIS SYSTEMATIC REVIEW AIMED TO IDENTIFY ALL EWAS ASSESSING DIFFERENTIALLY METHYLATED SITES ASSOCIATED WITH ASTHMA IN HUMANS. DESIGN: STRUCTURED SYSTEMATIC LITERATURE SEARCH FOLLOWING PRISMA GUIDELINES, NEWCASTLE-OTTAWA SCALE (NOS) FOR COHORT STUDIES WAS USED FOR BIAS ASSESSMENT. DATA SOURCES: WE SEARCHED PUBMED AND EMBASE DATABASES FROM 2005 TO 2019. ELIGIBILITY CRITERIA: EPIGENOME-WIDE ASSOCIATION STUDIES TESTING ASSOCIATION BETWEEN DIFFERENTIAL METHYLATION AND ASTHMA IN HUMANS. RESULTS: OVERALL, WE IDENTIFIED 16 EWAS STUDIES COMPLYING WITH OUR SEARCH CRITERIA. TWELVE STUDIES WERE CONDUCTED ON CHILDREN, AND 10 WERE CONDUCTED ON SAMPLE SIZES <150 SUBJECTS. FOUR HUNDRED AND NINETEEN CPGS WERE REPORTED IN CHILDREN STUDIES AFTER CORRECTION FOR MULTIPLE TESTING. IN THE ADULT STUDIES, THOUSANDS OF DIFFERENTIALLY METHYLATED SITES WERE IDENTIFIED. DIFFERENTIAL METHYLATION IN INFLAMMATORY-RELATED GENES CORRELATED WITH HIGHER LEVELS OF GENE EXPRESSIONS OF INFLAMMATORY MODULATORS IN ASTHMA. DIFFERENTIALLY METHYLATED GENES ASSOCIATED WITH ASTHMA INCLUDED SMAD3, SERPINC1, PROK1, IL13, RUNX3 AND TIGIT. FORTY-ONE CPGS WERE REPLICATED AT LEAST ONCE IN BLOOD SAMPLES, AND 28 CPGS WERE REPLICATED IN NASAL SAMPLES. CONCLUSION: ALTHOUGH MANY DIFFERENTIALLY METHYLATED CPGS IN GENES KNOWN TO BE INVOLVED IN ASTHMA HAVE BEEN IDENTIFIED IN EWAS TO DATE, WE CONCLUDE THAT FURTHER STUDIES OF LARGER SAMPLE SIZES AND ANALYSES OF DIFFERENTIAL METHYLATION BETWEEN DIFFERENT PHENOTYPES ARE NEEDED IN ORDER TO COMPREHENSIVELY EVALUATE THE ROLE OF EPIGENETIC FACTORS IN THE PATHOPHYSIOLOGY AND HETEROGENEITY OF ASTHMA, AND THE POTENTIAL CLINICAL UTILITY TO PREDICT OR CLASSIFY PATIENTS WITH ASTHMA.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
20  2624  45 EPIGENOME-WIDE ASSOCIATION STUDY (EWAS) OF BMI, BMI CHANGE AND WAIST CIRCUMFERENCE IN AFRICAN AMERICAN ADULTS IDENTIFIES MULTIPLE REPLICATED LOCI. OBESITY IS AN IMPORTANT COMPONENT OF THE PATHOPHYSIOLOGY OF CHRONIC DISEASES. IDENTIFYING EPIGENETIC MODIFICATIONS ASSOCIATED WITH ELEVATED ADIPOSITY, INCLUDING DNA METHYLATION VARIATION, MAY POINT TO GENOMIC PATHWAYS THAT ARE DYSREGULATED IN NUMEROUS CONDITIONS. THE ILLUMINA 450K BEAD CHIP ARRAY WAS USED TO ASSAY DNA METHYLATION IN LEUKOCYTE DNA OBTAINED FROM 2097 AFRICAN AMERICAN ADULTS IN THE ATHEROSCLEROSIS RISK IN COMMUNITIES (ARIC) STUDY. MIXED-EFFECTS REGRESSION MODELS WERE USED TO TEST THE ASSOCIATION OF METHYLATION BETA VALUE WITH CONCURRENT BODY MASS INDEX (BMI) AND WAIST CIRCUMFERENCE (WC), AND BMI CHANGE, ADJUSTING FOR BATCH EFFECTS AND POTENTIAL CONFOUNDERS. REPLICATION USING WHOLE-BLOOD DNA FROM 2377 WHITE ADULTS IN THE FRAMINGHAM HEART STUDY AND CD4+ T CELL DNA FROM 991 WHITES IN THE GENETICS OF LIPID LOWERING DRUGS AND DIET NETWORK STUDY WAS FOLLOWED BY TESTING USING ADIPOSE TISSUE DNA FROM 648 WOMEN IN THE MULTIPLE TISSUE HUMAN EXPRESSION RESOURCE COHORT. SEVENTY-SIX BMI-RELATED PROBES, 164 WC-RELATED PROBES AND 8 BMI CHANGE-RELATED PROBES PASSED THE THRESHOLD FOR SIGNIFICANCE IN ARIC (P < 1 X 10(-7); BONFERRONI), INCLUDING PROBES IN THE RECENTLY REPORTED HIF3A, CPT1A AND ABCG1 REGIONS. REPLICATION USING BLOOD DNA WAS ACHIEVED FOR 37 BMI PROBES AND 1 ADDITIONAL WC PROBE. SIXTEEN OF THESE ALSO REPLICATED IN ADIPOSE TISSUE, INCLUDING 15 NOVEL METHYLATION FINDINGS NEAR GENES INVOLVED IN LIPID METABOLISM, IMMUNE RESPONSE/CYTOKINE SIGNALING AND OTHER DIVERSE PATHWAYS, INCLUDING LGALS3BP, KDM2B, PBX1 AND BBS2, AMONG OTHERS. ADIPOSITY TRAITS ARE ASSOCIATED WITH DNA METHYLATION AT NUMEROUS CPG SITES THAT REPLICATE ACROSS STUDIES DESPITE VARIATION IN TISSUE TYPE, ETHNICITY AND ANALYTIC APPROACHES.	2015