1 5498 140 REVIEW: DNA METHYLATION AND ALCOHOL USE DISORDERS: PROGRESS AND CHALLENGES. BACKGROUND AND OBJECTIVES: RISK FOR ALCOHOL USE DISORDERS (AUDS) IS INFLUENCED BY GENE-ENVIRONMENT INTERACTIONS. ENVIRONMENTAL FACTORS CAN AFFECT GENE EXPRESSION THROUGH EPIGENETIC MECHANISMS SUCH AS DNA METHYLATION. THIS REVIEW OUTLINES THE FINDINGS REGARDING THE ASSOCIATION OF DNA METHYLATION AND AUDS. METHODS: WE SEARCHED PUBMED (BY APRIL 2016) AND IDENTIFIED 29 STUDIES THAT EXAMINED THE ASSOCIATION OF DNA METHYLATION AND AUDS. WE ALSO EVALUATED THE METHODS USED IN THESE STUDIES. RESULTS: TWO STUDIES DEMONSTRATED ELEVATED GLOBAL (REPETITIVE ELEMENT) DNA METHYLATION LEVELS IN AUD SUBJECTS. FIFTEEN CANDIDATE GENE STUDIES SHOWED HYPERMETHYLATION OF PROMOTER REGIONS OF SIX GENES (AVP, DNMT3B, HERP, HTR3A, OPRM1, AND SNCA) OR HYPOMETHYLATION OF THE GDAP1 PROMOTER REGION IN AUD SUBJECTS. FIVE GENOME-WIDE DNA METHYLATION STUDIES DEMONSTRATED WIDESPREAD DNA METHYLATION CHANGES ACROSS THE GENOME IN AUD SUBJECTS. SIX STUDIES SHOWED SIGNIFICANT CORRELATIONS OF DNA METHYLATION WITH GENE EXPRESSION IN AUD SUBJECTS. THREE STUDIES REVEALED INTERACTIVE EFFECTS OF GENETIC VARIATION AND DNA METHYLATION ON SUSCEPTIBILITY TO AUDS. MOST STUDIES ANALYZED AUD-ASSOCIATED DNA METHYLATION CHANGES IN THE PERIPHERAL BLOOD; A FEW STUDIES EXAMINED DNA METHYLATION CHANGES IN POSTMORTEM BRAINS OF AUD SUBJECTS. DISCUSSION AND CONCLUSIONS: CHRONIC ALCOHOL CONSUMPTION MAY RESULT IN DNA METHYLATION CHANGES, LEADING TO NEUROADAPTATIONS THAT MAY UNDERLIE SOME OF THE MECHANISMS OF AUD RISK AND PERSISTENCE. FUTURE STUDIES ARE NEEDED TO CONFIRM THE FEW EXISTING RESULTS, AND THEN TO ELUCIDATE WHETHER DNA METHYLATION CHANGES ARE THE CAUSE OR CONSEQUENCE OF AUDS. SCIENTIFIC SIGNIFICANCE: DNA METHYLATION PROFILES MAY BE USED TO ASSESS AUD STATUS OR MONITOR AUD TREATMENT RESPONSE. (AM J ADDICT 2017;26:502-515). 2017 2 6685 38 VALIDATION OF DIFFERENTIAL GDAP1 DNA METHYLATION IN ALCOHOL DEPENDENCE AND ITS POTENTIAL FUNCTION AS A BIOMARKER FOR DISEASE SEVERITY AND THERAPY OUTCOME. ALCOHOL DEPENDENCE IS A SEVERE DISORDER CONTRIBUTING SUBSTANTIALLY TO THE GLOBAL BURDEN OF DISEASE. DESPITE THE DETRIMENTAL CONSEQUENCES OF CHRONIC ALCOHOL ABUSE AND DEPENDENCE, EFFECTIVE PREVENTION STRATEGIES AS WELL AS TREATMENT OPTIONS ARE LARGELY MISSING TO DATE. ACCUMULATING EVIDENCE SUGGESTS THAT GENE-ENVIRONMENT INTERACTIONS, INCLUDING EPIGENETIC MECHANISMS, PLAY A ROLE IN THE ETIOLOGY OF ALCOHOL DEPENDENCE. A RECENT EPIGENOME-WIDE STUDY REPORTED WIDESPREAD ALTERATIONS OF DNA METHYLATION PATTERNS IN ALCOHOL DEPENDENT PATIENTS COMPARED TO CONTROL INDIVIDUALS. IN THE PRESENT STUDY, WE VALIDATE AND REPLICATE ONE OF THE TOP FINDINGS FROM THIS PREVIOUS INVESTIGATION IN AN INDEPENDENT COHORT: THE HYPOMETHYLATION OF GDAP1 IN PATIENTS. TO OUR KNOWLEDGE, THIS IS THE FIRST INDEPENDENT REPLICATION OF AN EPIGENOME-WIDE FINDING IN ALCOHOL DEPENDENCE. FURTHERMORE, THE AUDIT AS WELL AS THE GSI SCORE WERE NEGATIVELY ASSOCIATED WITH GDAP1 METHYLATION AND WE FOUND A TREND TOWARD A NEGATIVE ASSOCIATION BETWEEN GDAP1 METHYLATION AND THE YEARS OF ALCOHOL DEPENDENCY, POINTING TOWARD A POTENTIAL ROLE OF GDAP1 HYPOMETHYLATION AS BIOMARKER FOR DISEASE SEVERITY. IN ADDITION, WE SHOW THAT THE HYPOMETHYLATION OF GDAP1 IN PATIENTS REVERSES DURING A SHORT-TERM ALCOHOL TREATMENT PROGRAM, SUGGESTING THAT GDAP1 DNA METHYLATION COULD ALSO SERVE AS A POTENTIAL BIOMARKER FOR TREATMENT OUTCOME. OUR DATA ADD TO THE GROWING BODY OF KNOWLEDGE ON EPIGENETIC EFFECTS IN ALCOHOL DEPENDENCE AND SUPPORT GDAP1 AS A NOVEL CANDIDATE GENE IMPLICATED IN THIS DISORDER. AS THE ROLE OF GDAP1 IN ALCOHOL DEPENDENCE IS UNKNOWN, THIS NOVEL CANDIDATE GENE SHOULD BE FOLLOWED UP IN FUTURE STUDIES. 2016 3 1967 45 EPIGENETIC ALTERATION OF THE DOPAMINE TRANSPORTER GENE IN ALCOHOL-DEPENDENT PATIENTS IS ASSOCIATED WITH AGE. CHRONIC ALCOHOL ABUSE AND DEPENDENCE ARE ASSOCIATED WITH DYSFUNCTIONAL DOPAMINERGIC NEUROTRANSMISSION IN MESOCORTICOLIMBIC CIRCUITS. GENETIC AND ENVIRONMENTAL FACTORS HAVE BEEN SHOWN TO MODULATE SUSCEPTIBILITY TO ALCOHOL DEPENDENCE, AND BOTH MAY ACT THROUGH EPIGENETIC MECHANISMS THAT CAN MODULATE GENE EXPRESSION, E.G. DNA METHYLATION AT CPG SITES. RECENT STUDIES HAVE SUGGESTED THAT DNA METHYLATION PATTERNS MAY CHANGE OVER TIME. HOWEVER, FEW DATA ARE AVAILABLE CONCERNING THE RATE OF THESE CHANGES IN SPECIFIC GENES. A RECENT STUDY FOUND THAT HYPERMETHYLATION OF THE PROMOTER OF THE DOPAMINE TRANSPORTER (DAT) GENE WAS POSITIVELY CORRELATED WITH ALCOHOL DEPENDENCE AND NEGATIVELY CORRELATED WITH ALCOHOL CRAVING. THE AIM OF THE PRESENT STUDY WAS TO REPLICATE THESE FINDINGS IN A LARGER SAMPLE OF ALCOHOL-DEPENDENT PATIENTS AND POPULATION-BASED CONTROLS MATCHED FOR AGE AND SEX. NO DIFFERENCE IN METHYLATION LEVEL WAS OBSERVED BETWEEN PATIENTS AND CONTROLS, AND NO DIFFERENCE IN METHYLATION LEVEL WAS OBSERVED BEFORE AND AFTER ALCOHOL WITHDRAWAL IN PATIENTS. HOWEVER, PATIENTS WITH MORE SEVERE CRAVING SHOWED A TREND TOWARDS LOWER DAT METHYLATION LEVELS (P = 0.07), WHICH IS CONSISTENT WITH PREVIOUS FINDINGS. FURTHERMORE, IN OUR OVERALL SAMPLE, DAT METHYLATION LEVELS INCREASED WITH AGE. INTERESTINGLY, A SEPARATE ANALYSIS OF PATIENTS SUGGESTED THAT THIS FINDING WAS MAINLY DRIVEN BY THE PATIENT GROUP. ALTHOUGH THE PRESENT DATA DO NOT CLARIFY WHETHER CHRONIC ALCOHOL ABUSE IS RESPONSIBLE FOR THIS PHENOMENON OR MERELY ENHANCES AN AGEING-SPECIFIC PROCESS, OUR FINDINGS SUGGEST THAT HYPERMETHYLATION IN ALCOHOL-DEPENDENT PATIENTS IS A CONSEQUENCE, RATHER THAN A CAUSE, OF THE DISORDER. 2014 4 311 48 ALCOHOL AND THE METHYLOME: DESIGN AND ANALYSIS CONSIDERATIONS FOR RESEARCH USING HUMAN SAMPLES. BACKGROUND: A GROWING NUMBER OF STUDIES IN HUMAN SAMPLES HAVE SOUGHT TO DETERMINE WHETHER CHRONIC ALCOHOL USE AND ALCOHOL USE DISORDERS (AUDS) MAY BE ASSOCIATED WITH EPIGENETIC FACTORS, SUCH AS DNA METHYLATION. WE REVIEW THE EXTANT LITERATURE IN LIGHT OF SOME OF THE CHALLENGES THAT CURRENTLY AFFECT THE DESIGN AND INTERPRETATION OF EPIGENETIC RESEARCH IN HUMAN SAMPLES. METHOD: A LITERATURE SEARCH WAS USED TO IDENTIFY STUDIES THAT HAVE EXAMINED DNA METHYLATION IN RELATION TO ALCOHOL USE OR AUDS IN HUMAN SAMPLES (THROUGH JULY 2013). A TOTAL OF 22 STUDIES WERE IDENTIFIED. RESULTS: ASSOCIATIONS WITH QUANTITATIVE OR DIAGNOSTIC PHENOTYPES OF ALCOHOL USE OR AUDS HAVE BEEN REPORTED FOR SEVERAL GENES. HOWEVER, ALL STUDIES TO DATE HAVE RELIED ON RELATIVELY SMALL SAMPLES AND CROSS-SECTIONAL STUDY DESIGNS. ADDITIONALLY, ATTEMPTS TO REPLICATE RESULTS HAVE BEEN RARE. MORE GENERALLY, RESEARCH PROGRESS IS HAMPERED BY SEVERAL ISSUES, INCLUDING LIMITATIONS OF THE TECHNOLOGIES USED TO ASSESS DNA METHYLATION, TISSUE- AND CELL-SPECIFICITY OF METHYLATION PATTERNS, THE DIFFICULTIES OF RELATING OBSERVED METHYLATION DIFFERENCES AT A GIVEN LOCUS TO A FUNCTIONAL EFFECT, AND LIMITED KNOWLEDGE ABOUT THE MOLECULAR MECHANISMS UNDERLYING THE EFFECTS OF ALCOHOL ON DNA METHYLATION. CONCLUSIONS: ALTHOUGH WE SHARE THE OPTIMISM THAT EPIGENETICS MAY LEAD TO NEW INSIGHTS INTO THE ETIOLOGY AND PATHOPHYSIOLOGY OF AUDS, THE METHODOLOGICAL AND SCIENTIFIC CHALLENGES ASSOCIATED WITH CONDUCTING METHYLOMIC RESEARCH IN HUMAN SAMPLES NEED TO BE CAREFULLY CONSIDERED WHEN DESIGNING AND EVALUATING SUCH STUDIES. 2013 5 2625 37 EPIGENOME-WIDE ASSOCIATION STUDY AND MULTI-TISSUE REPLICATION OF INDIVIDUALS WITH ALCOHOL USE DISORDER: EVIDENCE FOR ABNORMAL GLUCOCORTICOID SIGNALING PATHWAY GENE REGULATION. ALCOHOL USE DISORDER (AUD) IS A CHRONIC DEBILITATING DISORDER WITH LIMITED TREATMENT OPTIONS AND POORLY DEFINED PATHOPHYSIOLOGY. THERE ARE SUBSTANTIAL GENETIC AND EPIGENETIC COMPONENTS; HOWEVER, THE UNDERLYING MECHANISMS CONTRIBUTING TO AUD REMAIN LARGELY UNKNOWN. WE CONDUCTED THE LARGEST DNA METHYLATION EPIGENOME-WIDE ASSOCIATION STUDY (EWAS) ANALYSES CURRENTLY AVAILABLE FOR AUD (TOTAL N = 625) AND EMPLOYED A TOP HIT REPLICATION (N = 4798) USING A CROSS-TISSUE/CROSS-PHENOTYPIC APPROACH WITH THE GOAL OF IDENTIFYING NOVEL EPIGENETIC TARGETS RELEVANT TO AUD. RESULTS SHOW THAT A NETWORK OF DIFFERENTIALLY METHYLATED REGIONS IN GLUCOCORTICOID SIGNALING AND INFLAMMATION-RELATED GENES WERE ASSOCIATED WITH ALCOHOL USE BEHAVIORS. A TOP PROBE CONSISTENTLY ASSOCIATED ACROSS ALL COHORTS WAS LOCATED IN THE LONG NON-CODING RNA GROWTH ARREST SPECIFIC FIVE GENE (GAS5) (P < 10(-24)). GAS5 HAS BEEN IMPLICATED IN REGULATING TRANSCRIPTIONAL ACTIVITY OF THE GLUCOCORTICOID RECEPTOR AND HAS MULTIPLE FUNCTIONS RELATED TO APOPTOSIS, IMMUNE FUNCTION AND VARIOUS CANCERS. ENDOPHENOTYPIC ANALYSES USING PERIPHERAL CORTISOL LEVELS AND NEUROIMAGING PARADIGMS SHOWED THAT METHYLOMIC VARIATION IN GAS5 NETWORK-RELATED PROBES WERE ASSOCIATED WITH STRESS PHENOTYPES. POSTMORTEM BRAIN ANALYSES DOCUMENTED INCREASED GAS5 EXPRESSION IN THE AMYGDALA OF INDIVIDUALS WITH AUD. OUR DATA SUGGEST THAT ALCOHOL USE IS ASSOCIATED WITH DIFFERENTIAL METHYLATION IN THE GLUCOCORTICOID SYSTEM THAT MIGHT INFLUENCE STRESS AND INFLAMMATORY REACTIVITY AND SUBSEQUENTLY RISK FOR AUD. 2021 6 3080 46 GENOME-WIDE METHYLATION IN ALCOHOL USE DISORDER SUBJECTS: IMPLICATIONS FOR AN EPIGENETIC REGULATION OF THE CORTICO-LIMBIC GLUCOCORTICOID RECEPTORS (NR3C1). ENVIRONMENTAL FACTORS, INCLUDING SUBSTANCE ABUSE AND STRESS, CAUSE LONG-LASTING CHANGES IN THE REGULATION OF GENE EXPRESSION IN THE BRAIN VIA EPIGENETIC MECHANISMS, SUCH AS DNA METHYLATION. WE EXAMINED GENOME-WIDE DNA METHYLATION PATTERNS IN THE PREFRONTAL CORTEX (PFC, BA10) OF 25 PAIRS OF CONTROL AND INDIVIDUALS WITH ALCOHOL USE DISORDER (AUD), USING THE INFINIUM((R)) METHYLATIONEPIC BEADCHIP. WE IDENTIFIED 5254 DIFFERENTIALLY METHYLATED CPGS (P(NOMINAL) < 0.005). BIOINFORMATIC ANALYSES HIGHLIGHTED BIOLOGICAL PROCESSES CONTAINING GENES RELATED TO STRESS ADAPTATION, INCLUDING THE GLUCOCORTICOID RECEPTOR (ENCODED BY NR3C1). CONSIDERING THAT ALCOHOL IS A STRESSOR, WE FOCUSED OUR ATTENTION ON DIFFERENTIALLY METHYLATED REGIONS OF THE NR3C1 GENE AND VALIDATED THE DIFFERENTIAL METHYLATION OF SEVERAL GENES IN THE NR3C1 NETWORK. CHRONIC ALCOHOL DRINKING RESULTS IN A SIGNIFICANT INCREASED METHYLATION OF THE NR3C1 EXON VARIANT 1(H), WITH A PARTICULAR INCREASE IN THE LEVELS OF 5-HYDROXYMETHYLCYTOSINE OVER 5-METHYLCYTOSINE. THESE CHANGES IN DNA METHYLATION WERE ASSOCIATED WITH REDUCED NR3C1 MRNA AND PROTEIN EXPRESSION LEVELS IN PFC, AS WELL AS OTHER CORTICO-LIMBIC REGIONS OF AUD SUBJECTS WHEN COMPARED WITH CONTROLS. FURTHERMORE, WE SHOW THAT THE EXPRESSION OF SEVERAL STRESS-RESPONSIVE GENES (E.G., CRF, POMC, AND FKBP5) IS ALTERED IN THE PFC OF AUD SUBJECTS. THESE STRESS-RESPONSE GENES WERE ALSO CHANGED IN THE HIPPOCAMPUS, A REGION THAT IS HIGHLY SUSCEPTIBLE TO STRESS. THESE DATA SUGGEST THAT ALCOHOL-DEPENDENT ABERRANT DNA METHYLATION OF NR3C1 AND CONSEQUENT CHANGES IN OTHER STRESS-RELATED GENES MIGHT BE FUNDAMENTAL IN THE PATHOPHYSIOLOGY OF AUD AND LAY THE GROUNDWORK FOR TREATMENTS TARGETING THE EPIGENETIC MECHANISMS REGULATING NR3C1 IN AUD. 2021 7 990 36 CHRONIC SOCIAL STRESS INDUCES DNA METHYLATION CHANGES AT AN EVOLUTIONARY CONSERVED INTERGENIC REGION IN CHROMOSOME X. CHRONIC STRESS RESULTING FROM PROLONGED EXPOSURE TO NEGATIVE LIFE EVENTS INCREASES THE RISK OF MOOD AND ANXIETY DISORDERS. ALTHOUGH CHRONIC STRESS CAN CHANGE GENE EXPRESSION RELEVANT FOR BEHAVIOR, MOLECULAR REGULATORS OF THIS CHANGE HAVE NOT BEEN FULLY DETERMINED. ONE PROCESS THAT COULD PLAY A ROLE IS DNA METHYLATION, AN EPIGENETIC PROCESS WHEREBY A METHYL GROUP IS ADDED ONTO NUCLEOTIDES, PREDOMINANTLY CYTOSINE IN THE CPG CONTEXT, AND WHICH CAN BE INDUCED BY CHRONIC STRESS. IT IS UNKNOWN TO WHAT EXTENT CHRONIC SOCIAL DEFEAT, A MODEL OF HUMAN SOCIAL STRESS, INFLUENCES DNA METHYLATION PATTERNS ACROSS THE GENOME. OUR STUDY ADDRESSED THIS QUESTION BY USING A TARGETED-CAPTURE APPROACH CALLED METHYL-SEQ TO INVESTIGATE DNA METHYLATION PATTERNS OF THE DENTATE GYRUS AT PUTATIVE REGULATORY REGIONS ACROSS THE MOUSE GENOME FROM MICE EXPOSED TO 14 DAYS OF SOCIAL DEFEAT. FINDINGS WERE REPLICATED IN INDEPENDENT COHORTS BY BISULFITE-PYROSEQUENCING. TWO DIFFERENTIALLY METHYLATED REGIONS (DMRS) WERE IDENTIFIED. ONE DMR WAS LOCATED AT INTRON 9 OF DROSHA, AND IT SHOWED REDUCED METHYLATION IN STRESSED MICE. THIS OBSERVATION REPLICATED IN ONE OF TWO INDEPENDENT COHORTS. A SECOND DMR WAS IDENTIFIED AT AN INTERGENIC REGION OF CHROMOSOME X, AND METHYLATION IN THIS REGION WAS INCREASED IN STRESSED MICE. THIS METHYLATION DIFFERENCE REPLICATED IN TWO INDEPENDENT COHORTS AND IN MAJOR DEPRESSIVE DISORDER (MDD) POSTMORTEM BRAINS. THESE RESULTS HIGHLIGHT A REGION NOT PREVIOUSLY KNOWN TO BE DIFFERENTIALLY METHYLATED BY CHRONIC SOCIAL DEFEAT STRESS AND WHICH MAY BE INVOLVED IN MDD. 2018 8 1583 34 DNA METHYLATION PROFILES OF BLOOD CELLS ARE DISTINCT BETWEEN EARLY-ONSET OBESE AND CONTROL INDIVIDUALS. OBESITY IS A HIGHLY PREVALENT, CHRONIC DISORDER THAT HAS BEEN INCREASING IN INCIDENCE IN YOUNG PATIENTS. BOTH EPIGENETIC AND GENETIC ABERRATIONS MAY PLAY A ROLE IN THE PATHOGENESIS OF OBESITY. THEREFORE, IN-DEPTH EPIGENOMIC AND GENOMIC ANALYSES WILL ADVANCE OUR UNDERSTANDING OF THE DETAILED MOLECULAR MECHANISMS UNDERLYING OBESITY AND AID IN THE SELECTION OF POTENTIAL BIOMARKERS FOR OBESITY IN YOUTH. HERE, WE PERFORMED MICROARRAY-BASED DNA METHYLATION AND GENE EXPRESSION PROFILING OF PERIPHERAL WHITE BLOOD CELLS OBTAINED FROM SIX YOUNG, OBESE INDIVIDUALS AND SIX HEALTHY CONTROLS. WE OBSERVED THAT THE HIERARCHICAL CLUSTERING OF DNA METHYLATION, BUT NOT GENE EXPRESSION, CLEARLY SEGREGATES THE OBESE INDIVIDUALS FROM THE CONTROLS, SUGGESTING THAT THE METABOLIC DISTURBANCE THAT OCCURS AS A RESULT OF OBESITY AT A YOUNG AGE MAY AFFECT THE DNA METHYLATION OF PERIPHERAL BLOOD CELLS WITHOUT ACCOMPANYING TRANSCRIPTIONAL CHANGES. TO EXAMINE THE GENOME-WIDE DIFFERENCES IN THE DNA METHYLATION PROFILES OF YOUNG OBESE AND CONTROL INDIVIDUALS, WE IDENTIFIED DIFFERENTIALLY METHYLATED CPG SITES AND INVESTIGATED THEIR GENOMIC AND EPIGENOMIC CONTEXTS. THE ABERRANT DNA METHYLATION PATTERNS IN OBESE INDIVIDUALS CAN BE SUMMARIZED AS RELATIVE GAINS AND LOSSES OF DNA METHYLATION IN GENE PROMOTERS AND GENE BODIES, RESPECTIVELY. WE ALSO OBSERVED THAT THE CPG ISLANDS OF OBESE INDIVIDUALS ARE MORE SUSCEPTIBLE TO DNA METHYLATION COMPARED TO CONTROLS. OUR PILOT STUDY SUGGESTS THAT THE GENOME-WIDE ABERRANT DNA METHYLATION PATTERNS OF OBESE INDIVIDUALS MAY ADVANCE NOT ONLY OUR UNDERSTANDING OF THE EPIGENOMIC PATHOGENESIS BUT ALSO EARLY SCREENING OF OBESITY IN YOUTH. 2017 9 287 33 AGING AND CHRONIC SUN EXPOSURE CAUSE DISTINCT EPIGENETIC CHANGES IN HUMAN SKIN. EPIGENETIC CHANGES ARE WIDELY CONSIDERED TO PLAY AN IMPORTANT ROLE IN AGING, BUT EXPERIMENTAL EVIDENCE TO SUPPORT THIS HYPOTHESIS HAS BEEN SCARCE. WE HAVE USED ARRAY-BASED ANALYSIS TO DETERMINE GENOME-SCALE DNA METHYLATION PATTERNS FROM HUMAN SKIN SAMPLES AND TO INVESTIGATE THE EFFECTS OF AGING, CHRONIC SUN EXPOSURE, AND TISSUE VARIATION. OUR RESULTS REVEAL A HIGH DEGREE OF TISSUE SPECIFICITY IN THE METHYLATION PATTERNS AND ALSO SHOWED VERY LITTLE INTERINDIVIDUAL VARIATION WITHIN TISSUES. DATA STRATIFICATION BY AGE REVEALED THAT DNA FROM OLDER INDIVIDUALS WAS CHARACTERIZED BY A SPECIFIC HYPERMETHYLATION PATTERN AFFECTING LESS THAN 1% OF THE MARKERS ANALYZED. INTERESTINGLY, STRATIFICATION BY SUN EXPOSURE PRODUCED A FUNDAMENTALLY DIFFERENT PATTERN WITH A SIGNIFICANT TREND TOWARDS HYPOMETHYLATION. OUR RESULTS THUS IDENTIFY DEFINED AGE-RELATED DNA METHYLATION CHANGES AND SUGGEST THAT THESE ALTERATIONS MIGHT CONTRIBUTE TO THE PHENOTYPIC CHANGES ASSOCIATED WITH SKIN AGING. 2010 10 5682 36 SHORT-TERM CHANGES IN GLOBAL METHYLATION AND HYDROXYMETHYLATION DURING ALCOHOL DETOXIFICATION. ALCOHOL DEPENDENCE IS A COMMON PUBLIC HEALTH PROBLEM AND EPIGENETICS MAY OFFER NEW ASPECTS IN UNDERSTANDING THE BIOLOGICAL AND GENETIC UNDERPINNINGS AND IMPROVE TREATMENT OF THIS COMPLEX DISEASE. SUPPOSEDLY, METHYLATION AND HYDROXYMETHYLATION ARE ALTERED IN BRAIN TISSUES AND IN SYNAPSE-RELATED GENES DUE TO CHRONIC ALCOHOL INTAKE AND DURING WITHDRAWAL. TO ASSESS POTENTIAL EPIGENETIC CHANGES AFTER CESSATION OF CHRONIC ALCOHOL INTAKE, WE COMPARED 23 ALCOHOL-DEPENDENT INDIVIDUALS DURING INPATIENT ALCOHOL DETOXIFICATION WITH 13 CAREFULLY MATCHED CONTROLS. BLOOD SAMPLES WERE TAKEN ON THE DAY OF ADMISSION, AFTER ONE AND AFTER TWO WEEKS AT THE END OF INPATIENT TREATMENT. GENOME-WIDE GLOBAL METHYLATION AND GLOBAL DNA HYDROXYMETHYLATION WERE COMPARED ACROSS GROUPS. THERE WERE SIGNIFICANT DIFFERENCES IN GLOBAL METHYLATION ACROSS TIME FROM ADMISSION TO ONE AND TWO WEEKS OF INPATIENT WITHDRAWAL (P < 0.001). THESE FINDINGS WERE PARALLELED TO CHANGES IN GLOBAL DNA HYDROXYMETHYLATION ACROSS TIME WHEN AGE WAS EMPLOYED AS A COFACTOR (P < 0.001). SEVERAL POTENTIALLY INFLUENCING VARIABLES LIKE SEVERITY OF WITHDRAWAL, DOSE OF WITHDRAWAL MEDICATION AND ALCOHOL INTAKE BEFORE ADMISSION DID NOT YIELD SIGNIFICANT INFLUENCE ON EPIGENETIC CHANGES. THE RESULTS CONFIRM PREVIOUS FINDINGS OF SIGNIFICANT ALTERATIONS OF EPIGENETIC PATTERNS DURING ALCOHOL INTOXICATION AND PRESENT FOR THE FIRST TIME HYDROXYMETHYLATION CHANGES IN THESE INDIVIDUALS. 2019 11 1623 48 DNA MODIFICATIONS IN MODELS OF ALCOHOL USE DISORDERS. CHRONIC ALCOHOL USE AND ABUSE RESULT IN WIDESPREAD CHANGES TO GENE EXPRESSION, SOME OF WHICH CONTRIBUTE TO THE DEVELOPMENT OF ALCOHOL-USE DISORDERS (AUD). GENE EXPRESSION IS CONTROLLED, IN PART, BY A GROUP OF REGULATORY SYSTEMS OFTEN REFERRED TO AS EPIGENETIC FACTORS, WHICH INCLUDES, AMONG OTHER MECHANISMS, CHEMICAL MARKS MADE ON THE HISTONE PROTEINS AROUND WHICH GENOMIC DNA IS WOUND TO FORM CHROMATIN, AND ON NUCLEOTIDES OF THE DNA ITSELF. IN PARTICULAR, ALCOHOL HAS BEEN SHOWN TO PERTURB THE EPIGENETIC MACHINERY, LEADING TO CHANGES IN GENE EXPRESSION AND CELLULAR FUNCTIONS CHARACTERISTIC OF AUD AND, ULTIMATELY, TO ALTERED BEHAVIOR. DNA MODIFICATIONS IN PARTICULAR ARE SEEING INCREASING RESEARCH IN THE CONTEXT OF ALCOHOL USE AND ABUSE. TO DATE, STUDIES OF DNA MODIFICATIONS IN AUD HAVE PRIMARILY LOOKED AT GLOBAL METHYLATION PROFILES IN HUMAN BRAIN AND BLOOD, GENE-SPECIFIC METHYLATION PROFILES IN ANIMAL MODELS, METHYLATION CHANGES ASSOCIATED WITH PRENATAL ETHANOL EXPOSURE, AND THE POTENTIAL THERAPEUTIC ABILITIES OF DNA METHYLTRANSFERASE INHIBITORS. FUTURE STUDIES MAY BE AIMED AT IDENTIFYING CHANGES TO MORE RECENTLY DISCOVERED DNA MODIFICATIONS, UTILIZING NEW METHODS TO DISCRIMINATE METHYLATION PROFILES BETWEEN CELL TYPES, THUS CLARIFYING HOW ALCOHOL INFLUENCES THE METHYLOMES OF CELL-TYPE POPULATIONS AND HOW THIS MAY AFFECT DOWNSTREAM PROCESSES. THESE STUDIES AND MORE IN-DEPTH PROBING OF DNA METHYLATION WILL BE KEY TO DETERMINING WHETHER DNA-LEVEL EPIGENETIC REGULATION PLAYS A CAUSATIVE ROLE IN AUD AND CAN THUS BE TARGETED FOR TREATMENT OF THE DISORDER. 2017 12 344 39 ALTERED BDNF METHYLATION IN PATIENTS WITH CHRONIC MUSCULOSKELETAL PAIN AND HIGH BIOPSYCHOSOCIAL COMPLEXITY. PURPOSE: THE INTERMED INSTRUMENT, WHICH WAS DEVELOPED TO MEASURE PATIENT'S BIOPSYCHOSOCIAL (BPS) COMPLEXITY, REPRESENTS A POWERFUL DIAGNOSTIC AND THERAPEUTIC TOOL. EPIGENETIC CHANGES ARE THE INTERFACE BETWEEN SIGNALS FROM THE ENVIRONMENT AND GENETIC MODIFICATIONS, AFFECTING GENE EXPRESSION, IN PARTICULAR, BY DNA METHYLATION OF CPG DINUCLEOTIDES IN PROMOTOR REGIONS OF THE CORRESPONDING GENES. THE BRAIN-DERIVED NEUROTROPHIC FACTOR (BDNF) GENE PLAYS A CRUCIAL ROLE IN THE CENTRAL SENSITIZATION (CS) OF PAIN. IN THIS STUDY, WE HYPOTHESIZED THAT CHRONIC PAIN MODIFIES THE METHYLATION LEVELS OF THE BDNF GENE IN A MANNER THAT IS INTERCONNECTED WITH THE BPS STATUS. PATIENTS AND METHODS: FIFTY-EIGHT CHRONIC MUSCULOSKELETAL PAIN PATIENTS (CMSP) WERE ENROLLED IN THE STUDY. DNA WAS EXTRACTED FROM BLOOD SAMPLES, THE METHYLATION LEVELS OF 13 CPG SITES IN THE BDNF PROMOTER WERE MEASURED BY PYROSEQUENCING, AND ASSOCIATION STUDIES WITH VARIOUS PATIENT PARAMETERS AND THE INTERMED SCORES WERE PERFORMED. RESULTS: INTERESTINGLY, A NEGATIVE CORRELATION (-0.40) WAS FOUND BETWEEN THE TOTAL INTERMED SCORES AND THE AVERAGE CPG METHYLATION VALUES OF THE BDNF GENE, BUT NO CORRELATION WAS OBSERVED WITH THE SEVERITY OF PAIN, DEGREE OF ANXIETY, DEPRESSION, OR KINESIOPHOBIA AND CATASTROPHISM. MOREOVER, THE ASSOCIATION WAS INDEPENDENT OF AGE, SEX AND LEVEL OF COMORBIDITIES. CONCLUSION: THIS RESULT SHOWS THAT CMSP, IN ASSOCIATION WITH ITS BIOPSYCHOSOCIAL CONTEXT, EPIGENETICALLY DECREASES THE DEGREE OF METHYLATION OF THE BDNF PROMOTER AND SHOULD THEREFORE INCREASE THE LEVEL OF BDNF TRANSCRIPTION. IT ALSO SUGGESTS A ROLE OF THE INTERMED TOOL TO DETECT A RELATIONSHIP BETWEEN THE BPS COMPLEXITY AND THE EPIGENETIC CONTROL OF A TARGET GENE. THE POSSIBLE UPREGULATION OF BDNF EXPRESSION MIGHT BE, AT LEAST IN PART, THE SIGNAL FOR CHRONIC PAIN-INDUCED CENTRAL SENSITIZATION (CS). THIS COULD PARTLY EXPLAIN WHY PATIENTS WITH A HIGHER LEVEL OF COMPLEXITY FEEL MORE PAIN THAN THOSE WITH LOWER COMPLEXITY. 2020 13 1503 42 DNA METHYLATION AND GENE EXPRESSION DIFFERENCES IN CHILDREN CONCEIVED IN VITRO OR IN VIVO. EPIDEMIOLOGICAL DATA INDICATE THAT CHILDREN CONCEIVED IN VITRO HAVE A GREATER RELATIVE RISK OF LOW BIRTH-WEIGHT, MAJOR AND MINOR BIRTH DEFECTS, AND RARE DISORDERS INVOLVING IMPRINTED GENES, SUGGESTING THAT EPIGENETIC CHANGES MAY BE ASSOCIATED WITH ASSISTED REPRODUCTION. WE EXAMINED DNA METHYLATION AT MORE THAN 700 GENES (1536 CPG SITES) IN PLACENTA AND CORD BLOOD AND MEASURED GENE EXPRESSION LEVELS OF A SUBSET OF GENES THAT DIFFERED IN METHYLATION LEVELS BETWEEN CHILDREN CONCEIVED IN VITRO VERSUS IN VIVO. OUR RESULTS SUGGEST THAT IN VITRO CONCEPTION IS ASSOCIATED WITH LOWER MEAN METHYLATION AT CPG SITES IN PLACENTA AND HIGHER MEAN METHYLATION AT CPG SITES IN CORD BLOOD. WE ALSO FIND THAT IN VITRO CONCEPTION-ASSOCIATED DNA METHYLATION DIFFERENCES ARE ASSOCIATED WITH GENE EXPRESSION DIFFERENCES AT BOTH IMPRINTED AND NON-IMPRINTED GENES. THE RANGE OF INTER-INDIVIDUAL VARIATION IN GENE EXPRESSION OF THE IN VITRO AND IN VIVO GROUPS OVERLAPS SUBSTANTIALLY BUT SOME INDIVIDUALS FROM THE IN VITRO GROUP DIFFER FROM THE IN VIVO GROUP MEAN BY MORE THAN TWO STANDARD DEVIATIONS. SEVERAL OF THE GENES WHOSE EXPRESSION DIFFERS BETWEEN THE TWO GROUPS HAVE BEEN IMPLICATED IN CHRONIC METABOLIC DISORDERS, SUCH AS OBESITY AND TYPE II DIABETES. THESE FINDINGS SUGGEST THAT THERE MAY BE EPIGENETIC DIFFERENCES IN THE GAMETES OR EARLY EMBRYOS DERIVED FROM COUPLES UNDERGOING TREATMENT FOR INFERTILITY. ALTERNATIVELY, ASSISTED REPRODUCTION TECHNOLOGY MAY HAVE AN EFFECT ON GLOBAL PATTERNS OF DNA METHYLATION AND GENE EXPRESSION. IN EITHER CASE, THESE DIFFERENCES OR CHANGES MAY AFFECT LONG-TERM PATTERNS OF GENE EXPRESSION. 2009 14 1599 36 DNA METHYLATION SIGNATURE OF CHILDHOOD CHRONIC PHYSICAL AGGRESSION IN T CELLS OF BOTH MEN AND WOMEN. BACKGROUND: HIGH FREQUENCY OF PHYSICAL AGGRESSION IS THE CENTRAL FEATURE OF SEVERE CONDUCT DISORDER AND IS ASSOCIATED WITH A WIDE RANGE OF SOCIAL, MENTAL AND PHYSICAL HEALTH PROBLEMS. WE HAVE PREVIOUSLY TESTED THE HYPOTHESIS THAT DIFFERENTIAL DNA METHYLATION SIGNATURES IN PERIPHERAL T CELLS ARE ASSOCIATED WITH A CHRONIC AGGRESSION TRAJECTORY IN MALES. DESPITE THE FACT THAT SEX DIFFERENCES APPEAR TO PLAY A PIVOTAL ROLE IN DETERMINING THE DEVELOPMENT, MAGNITUDE AND FREQUENCY OF AGGRESSION, MOST OF PREVIOUS STUDIES FOCUSED ON MALES, SO LITTLE IS KNOWN ABOUT FEMALE CHRONIC PHYSICAL AGGRESSION. WE THEREFORE TESTED HERE WHETHER OR NOT THERE IS A SIGNATURE OF PHYSICAL AGGRESSION IN FEMALE DNA METHYLATION AND, IF THERE IS, HOW IT RELATES TO THE SIGNATURE OBSERVED IN MALES. METHODOLOGY/PRINCIPAL FINDINGS: METHYLATION PROFILES WERE CREATED USING THE METHOD OF METHYLATED DNA IMMUNOPRECIPITATION (MEDIP) FOLLOWED BY MICROARRAY HYBRIDIZATION AND STATISTICAL AND BIOINFORMATIC ANALYSES ON T CELL DNA OBTAINED FROM ADULT WOMEN WHO WERE FOUND TO BE ON A CHRONIC PHYSICAL AGGRESSION TRAJECTORY (CPA) BETWEEN 6 AND 12 YEARS OF AGE COMPARED TO WOMEN WHO FOLLOWED A NORMAL PHYSICAL AGGRESSION TRAJECTORY. WE CONFIRMED THE EXISTENCE OF A WELL-DEFINED, GENOME-WIDE SIGNATURE OF DNA METHYLATION ASSOCIATED WITH CHRONIC PHYSICAL AGGRESSION IN THE PERIPHERAL T CELLS OF ADULT FEMALES THAT INCLUDES MANY OF THE GENES SIMILARLY ASSOCIATED WITH PHYSICAL AGGRESSION IN THE SAME CELL TYPES OF ADULT MALES. CONCLUSIONS: THIS STUDY IN A SMALL NUMBER OF WOMEN PRESENTS PRELIMINARY EVIDENCE FOR A GENOME-WIDE VARIATION IN PROMOTER DNA METHYLATION THAT ASSOCIATES WITH CPA IN WOMEN THAT WARRANT LARGER STUDIES FOR FURTHER VERIFICATION. A SIGNIFICANT PROPORTION OF THESE ASSOCIATIONS WERE PREVIOUSLY OBSERVED IN MEN WITH CPA SUPPORTING THE HYPOTHESIS THAT THE EPIGENETIC SIGNATURE OF EARLY LIFE AGGRESSION IN FEMALES IS COMPOSED OF A COMPONENT SPECIFIC TO FEMALES AND ANOTHER COMMON TO BOTH MALES AND FEMALES. 2014 15 6790 35 [DNA METHYLATION ANALYSIS IN ENVIRONMENTAL AND OCCUPATIONAL CANCER RESEARCH]. THE PRESENT PAPER REVIEWS RECENT LABORATORY METHODS AND EXPERIMENTAL EVIDENCE CONCERNING EPIGENETIC BIOMARKERS INVOLVED IN CARCINOGENESIS MECHANISMS. WE INTRODUCE DNA METHYLATION AND ITS ROLE IN GENE EXPRESSION CONTROL. DNA METHYLATION ANALYSIS MAY ALLOW TO IDENTIFY EARLY CHANGES LEADING TO CANCER AND OTHER CHRONIC DISEASES. WE DESCRIBE HERE STRATEGIES FOR LABORATORY ANALYSES AND THEIR POSSIBLE APPLICATIONS. WE EXAMINE RESULTS FROM RECENT EXPERIMENTAL STUDIES SUGGESTING THAT THE EFFECTS OF CERTAIN OCCUPATIONAL AGENTS ARE MEDIATED BY ALTERATIONS IN DNA METHYLATION. PLANNING AND CONDUCTING INVESTIGATIONS ON EXPOSED HUMAN SUBJECTS WILL ALLOW TO VERIFY WHETHER DNA METHYLATION CHANGES IDENTIFIED IN ANIMAL AND IN-VITRO STUDIES MAY BE USED AS EARLY-EFFECT AND SUSCEPTIBILITY BIOMARKERS. DNA METHYLATION ANALYSIS HAS THE POTENTIAL FOR FUTURE APPLICATIONS IN RISK ASSESSMENT AND PREVENTION PROGRAMS CONDUCTED ON SUBJECTS EXPOSED TO HUMAN CARCINOGENS. 2005 16 2920 43 GENE-SET ANALYSIS IS SEVERELY BIASED WHEN APPLIED TO GENOME-WIDE METHYLATION DATA. MOTIVATION: DNA METHYLATION IS AN EPIGENETIC MARK THAT CAN STABLY REPRESS GENE EXPRESSION. BECAUSE OF ITS BIOLOGICAL AND CLINICAL SIGNIFICANCE, SEVERAL METHODS HAVE BEEN DEVELOPED TO COMPARE GENOME-WIDE PATTERNS OF METHYLATION BETWEEN GROUPS OF SAMPLES. THE APPLICATION OF GENE SET ANALYSIS TO IDENTIFY RELEVANT GROUPS OF GENES THAT ARE ENRICHED FOR DIFFERENTIALLY METHYLATED GENES IS OFTEN A MAJOR COMPONENT OF THE ANALYSIS OF THESE DATA. THIS CAN BE USED, FOR EXAMPLE, TO IDENTIFY PROCESSES OR PATHWAYS THAT ARE PERTURBED IN DISEASE DEVELOPMENT. WE SHOW THAT GENE-SET ANALYSIS, AS IT IS TYPICALLY APPLIED TO GENOME-WIDE METHYLATION ASSAYS, IS SEVERELY BIASED AS A RESULT OF DIFFERENCES IN THE NUMBERS OF CPG SITES ASSOCIATED WITH DIFFERENT CLASSES OF GENES AND GENE PROMOTERS. RESULTS: WE DEMONSTRATE THIS BIAS USING PUBLISHED DATA FROM A STUDY OF DIFFERENTIAL CPG ISLAND METHYLATION IN LUNG CANCER AND A DATASET WE GENERATED TO STUDY METHYLATION CHANGES IN PATIENTS WITH LONG-STANDING ULCERATIVE COLITIS. WE SHOW THAT SEVERAL OF THE GENE SETS THAT SEEM ENRICHED WOULD ALSO BE IDENTIFIED WITH RANDOMIZED DATA. WE SUGGEST TWO EXISTING APPROACHES THAT CAN BE ADAPTED TO CORRECT THE BIAS. ACCOUNTING FOR THE BIAS IN THE LUNG CANCER AND ULCERATIVE COLITIS DATASETS PROVIDES NOVEL BIOLOGICAL INSIGHTS INTO THE ROLE OF METHYLATION IN CANCER DEVELOPMENT AND CHRONIC INFLAMMATION, RESPECTIVELY. OUR RESULTS HAVE SIGNIFICANT IMPLICATIONS FOR MANY PREVIOUS GENOME-WIDE METHYLATION STUDIES THAT HAVE DRAWN CONCLUSIONS ON THE BASIS OF SUCH STRONGLY BIASED ANALYSIS. CONTACT: CATHAL.SEOIGHE@NUIGALWAY.IE SUPPLEMENTARY INFORMATION: SUPPLEMENTARY DATA ARE AVAILABLE AT BIOINFORMATICS ONLINE. 2013 17 5741 37 SMOKING INDUCES DNA METHYLATION CHANGES IN MULTIPLE SCLEROSIS PATIENTS WITH EXPOSURE-RESPONSE RELATIONSHIP. CIGARETTE SMOKING IS AN ESTABLISHED ENVIRONMENTAL RISK FACTOR FOR MULTIPLE SCLEROSIS (MS), A CHRONIC INFLAMMATORY AND NEURODEGENERATIVE DISEASE, ALTHOUGH A MECHANISTIC BASIS REMAINS LARGELY UNKNOWN. WE AIMED AT INVESTIGATING HOW SMOKING AFFECTS BLOOD DNA METHYLATION IN MS PATIENTS, BY ASSAYING GENOME-WIDE DNA METHYLATION AND COMPARING SMOKERS, FORMER SMOKERS AND NEVER SMOKERS IN TWO SWEDISH COHORTS, DIFFERING FOR KNOWN MS RISK FACTORS. SMOKING AFFECTS DNA METHYLATION GENOME-WIDE SIGNIFICANTLY, AN EXPOSURE-RESPONSE RELATIONSHIP EXISTS AND THE TIME SINCE SMOKING CESSATION AFFECTS METHYLATION LEVELS. THE RESULTS ALSO SHOW THAT THE CHANGES WERE LARGER IN THE COHORT BEARING THE MAJOR GENETIC RISK FACTORS FOR MS (FEMALE SEX AND HLA RISK HAPLOTYPES). FURTHERMORE, CPG SITES MAPPING TO GENES WITH KNOWN GENETIC OR FUNCTIONAL ROLE IN THE DISEASE ARE DIFFERENTIALLY METHYLATED BY SMOKING. MODELING OF THE METHYLATION LEVELS FOR A CPG SITE IN THE AHRR GENE INDICATES THAT MS MODIFIES THE EFFECT OF SMOKING ON METHYLATION CHANGES, BY SIGNIFICANTLY INTERACTING WITH THE EFFECT OF SMOKING LOAD. ALONGSIDE, WE REPORT THAT THE GENE EXPRESSION OF AHRR INCREASED IN MS PATIENTS AFTER SMOKING. OUR RESULTS SUGGEST THAT EPIGENETIC MODIFICATIONS MAY REVEAL THE LINK BETWEEN A MODIFIABLE RISK FACTOR AND THE PATHOGENETIC MECHANISMS. 2017 18 3652 29 INDIVIDUAL DNA METHYLATION PATTERN SHIFTS IN NANOPARTICLES-EXPOSED WORKERS ANALYZED IN FOUR CONSECUTIVE YEARS. A DNA METHYLATION PATTERN REPRESENTS AN ORIGINAL PLAN OF THE FUNCTION SETTINGS OF INDIVIDUAL CELLS AND TISSUES. THE BASIC STRATEGIES OF ITS DEVELOPMENT AND CHANGES DURING THE HUMAN LIFETIME ARE KNOWN, BUT THE DETAILS RELATED TO ITS MODIFICATION OVER THE YEARS ON AN INDIVIDUAL BASIS HAVE NOT YET BEEN STUDIED. MOREOVER, CURRENT EVIDENCE SHOWS THAT ENVIRONMENTAL EXPOSURE COULD GENERATE CHANGES IN DNA METHYLATION SETTINGS AND, SUBSEQUENTLY, THE FUNCTION OF GENES. IN THIS STUDY, WE ANALYZED THE EFFECT OF CHRONIC EXPOSURE TO NANOPARTICLES (NP) IN OCCUPATIONALLY EXPOSED WORKERS REPEATEDLY SAMPLED IN FOUR CONSECUTIVE YEARS (2016-2019). A DETAILED METHYLATION PATTERN ANALYSIS OF 14 PERSONS (10 EXPOSED AND 4 CONTROLS) WAS PERFORMED ON AN INDIVIDUAL BASIS. A MICROARRAY-BASED APPROACH USING CHIPS, ALLOWING THE ASSESSMENT OF MORE THAN 850 K CPG LOCI, WAS USED. INDIVIDUAL DNA METHYLATION PATTERNS WERE COMPARED BY PRINCIPAL COMPONENT ANALYSIS (PCA). THE RESULTS SHOW THE SHIFT IN DNA METHYLATION PATTERNS IN INDIVIDUAL YEARS IN ALL THE EXPOSED AND CONTROL SUBJECTS. THE OVERALL RANGE OF DIFFERENCES VARIED BETWEEN THE YEARS IN INDIVIDUAL PERSONS. THE DIFFERENCES BETWEEN THE FIRST AND LAST YEAR OF EXAMINATION (A THREE-YEAR TIME PERIOD) SEEM TO BE CONSISTENTLY GREATER IN THE NP-EXPOSED SUBJECTS IN COMPARISON WITH THE CONTROLS. THE SELECTED 14 MOST DIFFERENTLY METHYLATED CG LOCI WERE RELATIVELY STABLE IN THE CHRONICALLY EXPOSED SUBJECTS. IN SUMMARY, THE SPECIFIC TYPE OF LONG-TERM EXPOSURE CAN CONTRIBUTE TO THE FIXING OF RELEVANT EPIGENETIC CHANGES RELATED TO A SPECIFIC ENVIRONMENT AS, E.G., NP INHALATION. 2021 19 1705 38 DYNAMICS OF SMOKING-INDUCED GENOME-WIDE METHYLATION CHANGES WITH TIME SINCE SMOKING CESSATION. SEVERAL STUDIES HAVE RECENTLY IDENTIFIED STRONG EPIGENETIC SIGNALS RELATED TO TOBACCO SMOKING. HOWEVER, AN ASPECT THAT DID NOT RECEIVE MUCH ATTENTION IS THE EVOLUTION OF EPIGENETIC CHANGES WITH TIME SINCE SMOKING CESSATION. WE CONDUCTED A SERIES OF EPIGENOME-WIDE ASSOCIATION STUDIES TO CAPTURE THE DYNAMICS OF SMOKING-INDUCED EPIGENETIC CHANGES AFTER SMOKING CESSATION, USING GENOME-WIDE METHYLATION PROFILES OBTAINED FROM BLOOD SAMPLES IN 745 WOMEN FROM 2 EUROPEAN POPULATIONS. TWO DISTINCT CLASSES OF CPG SITES WERE IDENTIFIED: SITES WHOSE METHYLATION REVERTS TO LEVELS TYPICAL OF NEVER SMOKERS WITHIN DECADES AFTER SMOKING CESSATION, AND SITES REMAINING DIFFERENTIALLY METHYLATED, EVEN MORE THAN 35 YEARS AFTER SMOKING CESSATION. OUR RESULTS SUGGEST THAT THE DYNAMICS OF METHYLATION CHANGES FOLLOWING SMOKING CESSATION ARE DRIVEN BY A DIFFERENTIAL AND SITE-SPECIFIC MAGNITUDE OF THE SMOKING-INDUCED ALTERATIONS (WITH PERSISTENT SITES BEING MOST AFFECTED) IRRESPECTIVE OF THE INTENSITY AND DURATION OF SMOKING. ANALYSES OF THE LINK BETWEEN METHYLATION AND EXPRESSION LEVELS REVEALED THAT METHYLATION PREDOMINANTLY AND REMOTELY DOWN-REGULATES GENE EXPRESSION. AMONG GENES WHOSE EXPRESSION WAS ASSOCIATED WITH OUR CANDIDATE CPG SITES, LRRN3 APPEARED TO BE PARTICULARLY INTERESTING AS IT WAS ONE OF THE FEW GENES WHOSE METHYLATION AND EXPRESSION WERE DIRECTLY ASSOCIATED, AND THE ONLY GENE IN WHICH BOTH METHYLATION AND GENE EXPRESSION WERE FOUND ASSOCIATED WITH SMOKING. OUR STUDY HIGHLIGHTS PERSISTENT EPIGENETIC MARKERS OF SMOKING, WHICH CAN POTENTIALLY BE DETECTED DECADES AFTER CESSATION. SUCH HISTORICAL SIGNATURES ARE PROMISING BIOMARKERS TO REFINE INDIVIDUAL RISK PROFILING OF SMOKING-INDUCED CHRONIC DISEASE SUCH AS LUNG CANCER. 2015 20 5034 32 PHARMACOEPIGENETICS OF THE ROLE OF DNA METHYLATION IN MU-OPIOID RECEPTOR EXPRESSION IN DIFFERENT HUMAN BRAIN REGIONS. AIM: EXPOSURE TO OPIOIDS HAS BEEN ASSOCIATED WITH EPIGENETIC EFFECTS. STUDIES IN RODENTS SUGGESTED A ROLE OF VARYING DEGREES OF DNA METHYLATION IN THE DIFFERENTIAL REGULATION OF MU-OPIOID RECEPTOR EXPRESSION ACROSS THE BRAIN. METHODS: IN A TRANSLATIONAL INVESTIGATION, USING TISSUE ACQUIRED POSTMORTEM FROM 21 BRAIN REGIONS OF FORMER OPIATE ADDICTS, REPRESENTING A HUMAN COHORT WITH CHRONIC OPIOID EXPOSURE, MU-OPIOID RECEPTOR EXPRESSION WAS ANALYZED AT THE LEVEL OF DNA METHYLATION, MRNA AND PROTEIN. RESULTS & CONCLUSION: WHILE HIGH OR LOW MU-OPIOID RECEPTOR EXPRESSION SIGNIFICANTLY CORRELATED WITH LOCAL OPRM1 MRNA LEVELS, THERE WAS NO CORRESPONDING ASSOCIATION WITH OPRM1 METHYLATION STATUS. ADDITIONAL EXPERIMENTS IN HUMAN CELL LINES SHOWED THAT CHANGES IN DNA METHYLATION ASSOCIATED WITH CHANGES IN MU-OPIOID EXPRESSION WERE AN ORDER OF MAGNITUDE GREATER THAN DIFFERENCES IN BRAIN. HENCE, DIFFERENT DEGREES OF DNA METHYLATION ASSOCIATED WITH CHRONIC OPIOID EXPOSURE ARE UNLIKELY TO EXERT A MAJOR ROLE IN THE REGION-SPECIFICITY OF MU-OPIOID RECEPTOR EXPRESSION IN THE HUMAN BRAIN. 2016