1 1556 144 DNA METHYLATION MODIFICATIONS ASSOCIATED WITH CHRONIC FATIGUE SYNDROME. CHRONIC FATIGUE SYNDROME (CFS), ALSO KNOWN AS MYALGIC ENCEPHALOMYELITIS, IS A COMPLEX MULTIFACTORIAL DISEASE THAT IS CHARACTERIZED BY THE PERSISTENT PRESENCE OF FATIGUE AND OTHER PARTICULAR SYMPTOMS FOR A MINIMUM OF 6 MONTHS. SYMPTOMS FAIL TO DISSIPATE AFTER SUFFICIENT REST AND HAVE MAJOR EFFECTS ON THE DAILY FUNCTIONING OF CFS SUFFERERS. CFS IS A MULTI-SYSTEM DISEASE WITH A HETEROGENEOUS PATIENT POPULATION SHOWING A WIDE VARIETY OF FUNCTIONAL DISABILITIES AND ITS BIOLOGICAL BASIS REMAINS POORLY UNDERSTOOD. STABLE ALTERATIONS IN GENE FUNCTION IN THE IMMUNE SYSTEM HAVE BEEN REPORTED IN SEVERAL STUDIES OF CFS. EPIGENETIC MODIFICATIONS HAVE BEEN IMPLICATED IN LONG-TERM EFFECTS ON GENE FUNCTION, HOWEVER, TO OUR KNOWLEDGE, GENOME-WIDE EPIGENETIC MODIFICATIONS ASSOCIATED WITH CFS HAVE NOT BEEN EXPLORED. WE EXAMINED THE DNA METHYLOME IN PERIPHERAL BLOOD MONONUCLEAR CELLS ISOLATED FROM CFS PATIENTS AND HEALTHY CONTROLS USING THE ILLUMINA HUMANMETHYLATION450 BEADCHIP ARRAY, CONTROLLING FOR INVARIANT PROBES AND PROBES OVERLAPPING POLYMORPHIC SEQUENCES. GENE ONTOLOGY (GO) AND NETWORK ANALYSIS OF DIFFERENTIALLY METHYLATED GENES WAS PERFORMED TO DETERMINE POTENTIAL BIOLOGICAL PATHWAYS SHOWING CHANGES IN DNA METHYLATION IN CFS. WE FOUND AN INCREASED ABUNDANCE OF DIFFERENTIALLY METHYLATED GENES RELATED TO THE IMMUNE RESPONSE, CELLULAR METABOLISM, AND KINASE ACTIVITY. GENES ASSOCIATED WITH IMMUNE CELL REGULATION, THE LARGEST COORDINATED ENRICHMENT OF DIFFERENTIALLY METHYLATED PATHWAYS, SHOWED HYPOMETHYLATION WITHIN PROMOTERS AND OTHER GENE REGULATORY ELEMENTS IN CFS. THESE DATA ARE CONSISTENT WITH EVIDENCE OF MULTISYSTEM DYSREGULATION IN CFS AND IMPLICATE THE INVOLVEMENT OF DNA MODIFICATIONS IN CFS PATHOLOGY. 2014 2 1699 41 DYNAMIC EPIGENETIC CHANGES DURING A RELAPSE AND RECOVERY CYCLE IN MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME. MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A COMPLEX DISEASE WITH VARIABLE SEVERITY. PATIENTS EXPERIENCE FREQUENT RELAPSES WHERE SYMPTOMS INCREASE IN SEVERITY, LEAVING THEM WITH A MARKED REDUCTION IN QUALITY OF LIFE. PREVIOUS WORK HAS INVESTIGATED MOLECULAR DIFFERENCES BETWEEN ME/CFS PATIENTS AND HEALTHY CONTROLS, BUT NOT THE DYNAMIC CHANGES SPECIFIC TO EACH INDIVIDUAL PATIENT. WE APPLIED PRECISION MEDICINE HERE TO MAP GENOMIC CHANGES IN TWO SELECTED ME/CFS PATIENTS THROUGH A PERIOD THAT CONTAINED A RELAPSE RECOVERY CYCLE. DNA WAS ISOLATED FROM TWO PATIENTS AND A HEALTHY AGE/GENDER MATCHED CONTROL AT REGULAR INTERVALS AND CAPTURED THE PATIENT RELAPSE IN EACH CASE. REDUCED REPRESENTATION DNA METHYLATION SEQUENCING PROFILES WERE OBTAINED SPANNING THE RELAPSE RECOVERY CYCLE. BOTH PATIENTS SHOWED A SIGNIFICANTLY LARGER METHYLOME VARIABILITY (10-20-FOLD) THROUGH THE PERIOD OF SAMPLING COMPARED WITH THE CONTROL. DURING THE RELAPSE, CHANGES IN THE METHYLOME PROFILES OF THE TWO PATIENTS WERE DETECTED IN REGULATORY-ACTIVE REGIONS OF THE GENOME THAT WERE ASSOCIATED, RESPECTIVELY, WITH 157 AND 127 DOWNSTREAM GENES, INDICATING DISTURBED METABOLIC, IMMUNE AND INFLAMMATORY FUNCTIONS. SEVERE HEALTH RELAPSES IN THE ME/CFS PATIENTS RESULTED IN FUNCTIONALLY IMPORTANT CHANGES IN THEIR DNA METHYLOMES THAT, WHILE DIFFERING BETWEEN THE TWO PATIENTS, LED TO VERY SIMILAR COMPROMISED PHYSIOLOGY. DNA METHYLATION AS A SIGNATURE OF DISEASE VARIABILITY IN ONGOING ME/CFS MAY HAVE PRACTICAL APPLICATIONS FOR STRATEGIES TO DECREASE RELAPSE FREQUENCY. 2022 3 2920 45 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 4 5856 35 SUBSTRATE UTILISATION OF CULTURED SKELETAL MUSCLE CELLS IN PATIENTS WITH CFS. CHRONIC FATIGUE SYNDROME (CFS) PATIENTS OFTEN SUFFER FROM SEVERE MUSCLE PAIN AND AN INABILITY TO EXERCISE DUE TO MUSCLE FATIGUE. IT HAS PREVIOUSLY BEEN SHOWN THAT CFS SKELETAL MUSCLE CELLS HAVE LOWER LEVELS OF ATP AND HAVE AMP-ACTIVATED PROTEIN KINASE DYSFUNCTION. THIS STUDY OUTLINES EXPERIMENTS LOOKING AT THE UTILISATION OF DIFFERENT SUBSTRATES BY SKELETAL MUSCLE CELLS FROM CFS PATIENTS (N = 9) AND HEALTHY CONTROLS (N = 11) USING EXTRACELLULAR FLUX ANALYSIS. RESULTS SHOW THAT CFS SKELETAL MUSCLE CELLS ARE UNABLE TO UTILISE GLUCOSE TO THE SAME EXTENT AS HEALTHY CONTROL CELLS. CFS SKELETAL MUSCLE CELLS WERE SHOWN TO OXIDISE GALACTOSE AND FATTY ACIDS NORMALLY, INDICATING THAT THE BIOENERGETIC DYSFUNCTION LIES UPSTREAM OF THE TCA CYCLE. THE DYSFUNCTION IN GLUCOSE OXIDATION IS SIMILAR TO WHAT HAS PREVIOUSLY BEEN SHOWN IN BLOOD CELLS FROM CFS PATIENTS. THE CONSISTENCY OF CELLULAR BIOENERGETIC DYSFUNCTION IN DIFFERENT CELL TYPES SUPPORTS THE HYPOTHESIS THAT CFS IS A SYSTEMIC DISEASE. THE RETENTION OF BIOENERGETIC DEFECTS IN CULTURED CELLS INDICATES THAT THERE IS A GENETIC OR EPIGENETIC COMPONENT TO THE DISEASE. THIS IS THE FIRST STUDY TO USE CELLS DERIVED FROM SKELETAL MUSCLE BIOPSIES IN CFS PATIENTS AND HEALTHY CONTROLS TO LOOK AT CELLULAR BIOENERGETIC FUNCTION IN WHOLE CELLS. 2020 5 287 37 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 6 2207 74 EPIGENETIC MODIFICATIONS AND GLUCOCORTICOID SENSITIVITY IN MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS). BACKGROUND: MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A DEBILITATING IDIOPATHIC DISEASE CHARACTERIZED BY UNEXPLAINED FATIGUE THAT FAILS TO RESOLVE WITH SUFFICIENT REST. DIAGNOSIS IS BASED ON A LIST OF SYMPTOMS AND EXCLUSION OF OTHER FATIGUE-RELATED HEALTH CONDITIONS. DESPITE A HETEROGENEOUS PATIENT POPULATION, IMMUNE AND HYPOTHALAMIC-PITUITARY-ADRENAL (HPA) AXIS FUNCTION DIFFERENCES, SUCH AS ENHANCED NEGATIVE FEEDBACK TO GLUCOCORTICOIDS, ARE RECURRING FINDINGS IN ME/CFS STUDIES. EPIGENETIC MODIFICATIONS, SUCH AS CPG METHYLATION, ARE KNOWN TO REGULATE LONG-TERM PHENOTYPIC DIFFERENCES AND PREVIOUS WORK BY OUR GROUP FOUND DNA METHYLOME DIFFERENCES IN ME/CFS, HOWEVER THE RELATIONSHIP BETWEEN DNA METHYLOME MODIFICATIONS, CLINICAL AND FUNCTIONAL CHARACTERISTICS ASSOCIATED WITH ME/CFS HAS NOT BEEN EXAMINED. METHODS: WE EXAMINED THE DNA METHYLOME IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) OF A LARGER COHORT OF FEMALE ME/CFS PATIENTS USING THE ILLUMINA HUMANMETHYLATION450 BEADCHIP ARRAY. IN PARALLEL TO THE DNA METHYLOME ANALYSIS, WE INVESTIGATED IN VITRO GLUCOCORTICOID SENSITIVITY DIFFERENCES BY STIMULATING PBMCS WITH PHYTOHAEMAGGLUTININ AND SUPPRESSED GROWTH WITH DEXAMETHASONE. WE EXPLORED DNA METHYLATION DIFFERENCES USING BISULFITE PYROSEQUENCING AND STATISTICAL PERMUTATION. LINEAR REGRESSION WAS IMPLEMENTED TO DISCOVER EPIGENOMIC REGIONS ASSOCIATED WITH SELF-REPORTED QUALITY OF LIFE AND NETWORK ANALYSIS OF GENE ONTOLOGY TERMS TO BIOLOGICALLY CONTEXTUALIZE RESULTS. RESULTS: WE DETECTED 12,608 DIFFERENTIALLY METHYLATED SITES BETWEEN ME/CFS PATIENTS AND HEALTHY CONTROLS PREDOMINANTLY LOCALIZED TO CELLULAR METABOLISM GENES, SOME OF WHICH WERE ALSO RELATED TO SELF-REPORTED QUALITY OF LIFE HEALTH SCORES. AMONG ME/CFS PATIENTS, GLUCOCORTICOID SENSITIVITY WAS ASSOCIATED WITH DIFFERENTIAL METHYLATION AT 13 LOCI. CONCLUSIONS: OUR RESULTS INDICATE DNA METHYLATION MODIFICATIONS IN CELLULAR METABOLISM IN ME/CFS DESPITE A HETEROGENEOUS PATIENT POPULATION, IMPLICATING THESE PROCESSES IN IMMUNE AND HPA AXIS DYSFUNCTION IN ME/CFS. MODIFICATIONS TO EPIGENETIC LOCI ASSOCIATED WITH DIFFERENCES IN GLUCOCORTICOID SENSITIVITY MAY BE IMPORTANT AS BIOMARKERS FOR FUTURE CLINICAL TESTING. OVERALL, THESE FINDINGS ALIGN WITH RECENT ME/CFS WORK THAT POINT TOWARDS IMPAIRMENT IN CELLULAR ENERGY PRODUCTION IN THIS PATIENT POPULATION. 2017 7 1583 38 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 8 6159 48 THE GENETICS AND EPIGENETICS OF FATIGUE. FATIGUE IS A COMMON SYMPTOM AND INCLUDES BOTH PHYSICAL AND MENTAL COMPONENTS. IT CAN BE ASSOCIATED WITH A VARIETY OF DIFFERENT SYNDROMES AND DISEASES, BUT IN MANY CASES IS NOT ASSOCIATED WITH OTHER COMORBID CONDITIONS. MOST HUMANS HAVE EXPERIENCED ACUTE FATIGUE IN RELATION TO DIFFERENT STRESSORS. ACUTE FATIGUE TYPICALLY DECREASES AS THE EFFECT OF THE TRIGGERING FACTOR IS REDUCED AND A NORMAL HOMEOSTATIC BALANCE IS RESTORED. FATIGUE THAT PERSISTS FOR 6 MONTHS OR MORE IS TERMED CHRONIC FATIGUE. CHRONIC FATIGUE (CF) IN COMBINATION WITH A MINIMUM OF 4 OF 8 SYMPTOMS AND THE ABSENCE OF DISEASES THAT COULD EXPLAIN THESE SYMPTOMS, CONSTITUTE THE CASE DEFINITION FOR CHRONIC FATIGUE SYNDROME. IN SPITE OF ITS PREVALENCE, THE BIOLOGY OF FATIGUE IS RELATIVELY POORLY UNDERSTOOD AND BIOLOGICAL MARKERS HAVE NOT YET BEEN IDENTIFIED. THIS LITERATURE SEARCH WAS PERFORMED IN PUBMED TO IDENTIFY RESEARCH ON THE GENETICS AND EPIGENETICS OF FATIGUE. PUBLICATIONS WERE INCLUDED IF FATIGUE WAS A MAJOR TOPIC AND THE TOPIC WAS COMBINED WITH GENETIC AND/OR EPIGENETIC MEASUREMENTS IN ADULT HUMANS. A TOTAL OF 40 PUBLICATIONS WERE IDENTIFIED. ALTHOUGH ALTERED FUNCTIONING IN THE HYPOTHALAMIC-PITUITARY-ADRENAL AXIS, THE SEROTONERGIC SYSTEM, AND ASSOCIATIONS WITH INFECTIOUS AGENTS HAVE BEEN IDENTIFIED, THE SEARCH FOR GENETIC OR EPIGENETIC MARKERS OF FATIGUE, EITHER IN THE CONTEXT OF CF OR CHRONIC FATIGUE SYNDROME (CFS) HAS BEEN RELATIVELY UNPRODUCTIVE OR, IN THE CASE OF EPIGENETICS, NONEXISTENT. ALTHOUGH SEVERAL STUDIES, BOTH HYPOTHESIS-TESTING AND HYPOTHESIS-GENERATING, HAVE BEEN PERFORMED TO SEARCH FOR BIOMARKERS, THEY HAVE MOSTLY BEEN UNDERPOWERED, RESTRICTED BY THE HETEROGENEITY OF THE PHENOTYPE, OR LIMITED BY AN UNSYSTEMATIC STUDY DESIGN. TO BE ABLE TO CONFIRM THE HYPOTHESIS THAT RISK FOR, OR LEVELS OF, FATIGUE ARE INFLUENCED BY THE GENETIC OR EPIGENETIC BACKGROUND OF AN INDIVIDUAL, STUDIES NEED TO BE BASED ON LARGER SAMPLE SIZES WITH A MORE CLEARLY DEFINED PHENOTYPE. STUDIES NEED TO FOCUS NOT ONLY ON THE INFLUENCE OF A SINGLE ASPECT SUCH AS SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) OR DIFFERENTIAL GENE EXPRESSION ON DISEASE RISK OR STATE, BUT ALSO ON THE SYSTEMS BIOLOGY BEHIND THE DISEASE IN COMBINATION WITH INFORMATION ON ENVIRONMENTAL INFLUENCES AND VALIDATION OF FINDINGS IN FUNCTIONAL STUDIES. 2010 9 822 37 CHARACTERIZATION OF BLOOD SURROGATE IMMUNE-METHYLATION BIOMARKERS FOR IMMUNE CELL INFILTRATION IN CHRONIC INFLAMMAGING DISORDERS. ALZHEIMER'S DISEASE (AD) AND ATHEROSCLEROSIS ARE BOTH CHRONIC AGE- AND INFLAMMATION-DEPENDENT DISEASES. IN ADDITION, ATHEROSCLEROSIS IS FREQUENTLY OBSERVED IN AD PATIENTS INDICATING COMMON INVOLVEMENT OF VASCULAR COMPONENTS IN BOTH DISEASE ETIOLOGIES. RECENTLY, EPIGENOME-WIDE ASSOCIATION STUDIES HAVE IDENTIFIED EPIGENETIC ALTERATIONS, AND IN PARTICULARLY DNA METHYLATION CHANGES FOR BOTH DISORDERS. WE HYPOTHESIZED THE EXISTENCE OF A COMMON DNA METHYLATION PROFILE IN ATHEROSCLEROSIS AND AD WHICH MAY BE VALUABLE AS A BLOOD-BASED DNA METHYLATION INFLAMMAGING BIOMARKER. USING PUBLICLY AVAILABLE 450K ILLUMINA METHYLATION DATASETS, WE IDENTIFIED A CO-METHYLATION NETWORK ASSOCIATED WITH BOTH ATHEROSCLEROSIS AND AD IN WHOLE BLOOD SAMPLES. THIS METHYLATION PROFILE APPEARED TO INDICATE SHIFTS IN BLOOD IMMUNE CELL TYPE DISTRIBUTION. REMARKABLY, SIMILAR METHYLATION CHANGES WERE ALSO DETECTED IN DISEASE TISSUES, INCLUDING AD BRAIN TISSUES, ATHEROSCLEROTIC PLAQUES, AND TUMORS AND WERE FOUND TO CORRELATE WITH IMMUNE CELL INFILTRATION. IN ADDITION, THIS IMMUNE-RELATED METHYLATION PROFILE COULD ALSO BE DETECTED IN OTHER INFLAMMAGING DISEASES, INCLUDING PARKINSON'S DISEASE AND OBESITY, BUT NOT IN MULTIPLE SCLEROSIS, SCHIZOPHRENIA, AND OSTEOPOROSIS. IN CONCLUSION, WE IDENTIFIED A BLOOD-BASED IMMUNE-RELATED DNA METHYLATION SIGNATURE IN MULTIPLE INFLAMMAGING DISEASES ASSOCIATED WITH CHANGES IN BLOOD IMMUNE CELL COUNTS AND PREDICTIVE FOR IMMUNE CELL INFILTRATION IN DISEASED TISSUES. IN ADDITION TO EPIGENETIC CLOCK MEASUREMENTS, THIS IMMUNE-METHYLATION SIGNATURE MAY BECOME A VALUABLE BLOOD-BASED BIOMARKER TO PREVENT CHRONIC INFLAMMATORY DISEASE DEVELOPMENT OR MONITOR LIFESTYLE INTERVENTION STRATEGIES WHICH PROMOTE HEALTHY AGING. 2019 10 1599 38 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 11 3041 50 GENOME-EPIGENOME INTERACTIONS ASSOCIATED WITH MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME. MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A COMPLEX DISEASE OF UNKNOWN ETIOLOGY. MULTIPLE STUDIES POINT TO DISRUPTIONS IN IMMUNE FUNCTIONING IN ME/CFS PATIENTS AS WELL AS SPECIFIC GENETIC POLYMORPHISMS AND ALTERATIONS OF THE DNA METHYLOME IN LYMPHOCYTES. HOWEVER, POTENTIAL INTERACTIONS BETWEEN DNA METHYLATION AND GENETIC BACKGROUND IN RELATION TO ME/CFS HAVE NOT BEEN EXAMINED. IN THIS STUDY WE EXPLORED THIS ASSOCIATION BY CHARACTERIZING THE EPIGENETIC (~480 THOUSAND CPG LOCI) AND GENETIC (~4.3 MILLION SNPS) VARIATION BETWEEN COHORTS OF ME/CFS PATIENTS AND HEALTHY CONTROLS. WE FOUND SIGNIFICANT ASSOCIATIONS OF DNA METHYLATION STATES IN T-LYMPHOCYTES AT SEVERAL CPG LOCI AND REGIONS WITH ME/CFS PHENOTYPE. THESE METHYLATION ANOMALIES ARE IN CLOSE PROXIMITY TO GENES INVOLVED WITH IMMUNE FUNCTION AND CELLULAR METABOLISM. FINALLY, WE FOUND SIGNIFICANT CORRELATIONS OF GENOTYPES WITH METHYLATION MODIFICATIONS ASSOCIATED WITH ME/CFS. THE FINDINGS FROM THIS STUDY HIGHLIGHT THE ROLE OF EPIGENETIC AND GENETIC INTERACTIONS IN COMPLEX DISEASES, AND SUGGEST SEVERAL GENETIC AND EPIGENETIC ELEMENTS POTENTIALLY INVOLVED IN THE MECHANISMS OF DISEASE IN ME/CFS. 2018 12 1717 39 DYSREGULATED IMMUNE SYSTEM NETWORKS IN WAR VETERANS WITH PTSD IS AN OUTCOME OF ALTERED MIRNA EXPRESSION AND DNA METHYLATION. POST-TRAUMATIC STRESS DISORDER PATIENTS EXPERIENCE CHRONIC SYSTEMIC INFLAMMATION. HOWEVER, THE MOLECULAR PATHWAYS INVOLVED AND MECHANISMS REGULATING THE EXPRESSION OF GENES INVOLVED IN INFLAMMATORY PATHWAYS IN PTSD ARE REPORTED INADEQUATELY. THROUGH RNA SEQUENCING AND MIRNA MICROARRAY, WE IDENTIFIED 326 GENES AND 190 MIRNAS THAT WERE SIGNIFICANTLY DIFFERENT IN THEIR EXPRESSION LEVELS IN THE PBMCS OF PTSD PATIENTS. EXPRESSION PAIRING OF THE DIFFERENTIALLY EXPRESSED GENES AND MIRNAS INDICATED AN INVERSE RELATIONSHIP IN THEIR EXPRESSION. FUNCTIONAL ANALYSIS OF THE DIFFERENTIALLY EXPRESSED GENES INDICATED THEIR INVOLVEMENT IN THE CANONICAL PATHWAYS SPECIFIC TO IMMUNE SYSTEM BIOLOGY. DNA METHYLATION ANALYSIS OF DIFFERENTIALLY EXPRESSED GENES ALSO SHOWED A GRADUAL TREND TOWARDS DIFFERENCES BETWEEN CONTROL AND PTSD PATIENTS, AGAIN INDICATING A POSSIBLE ROLE OF THIS EPIGENETIC MECHANISM IN PTSD INFLAMMATION. OVERALL, COMBINING DATA FROM THE THREE TECHNIQUES PROVIDED A HOLISTIC VIEW OF SEVERAL PATHWAYS IN WHICH THE DIFFERENTIALLY EXPRESSED GENES WERE IMPACTED THROUGH EPIGENETIC MECHANISMS, IN PTSD. THUS, ANALYSIS COMBINING DATA FROM RNA-SEQ, MIRNA ARRAY AND DNA METHYLATION, CAN PROVIDE KEY EVIDENCE ABOUT DYSREGULATED PATHWAYS AND THE CONTROLLING MECHANISM IN PTSD. MOST IMPORTANTLY, THE PRESENT STUDY PROVIDES FURTHER EVIDENCE THAT INFLAMMATION IN PTSD COULD BE EPIGENETICALLY REGULATED. 2016 13 70 37 A METHOD TO DETECT DIFFERENTIALLY METHYLATED LOCI WITH NEXT-GENERATION SEQUENCING. EPIGENETIC CHANGES, ESPECIALLY DNA METHYLATION AT CPG LOCI HAVE IMPORTANT IMPLICATIONS IN CANCER AND OTHER COMPLEX DISEASES. WITH THE DEVELOPMENT OF NEXT-GENERATION SEQUENCING (NGS), IT IS FEASIBLE TO GENERATE DATA TO INTERROGATE THE DIFFERENCE IN METHYLATION STATUS FOR GENOME-WIDE LOCI USING CASE-CONTROL DESIGN. HOWEVER, A PROPER AND EFFICIENT STATISTICAL TEST IS LACKING. THERE ARE SEVERAL CHALLENGES. FIRST, UNLIKE METHYLATION EXPERIMENTS USING MICROARRAYS, WHERE THERE IS ONE MEASURE OF METHYLATION FOR ONE INDIVIDUAL AT A PARTICULAR CPG SITE, HERE WE HAVE THE COUNTS OF METHYLATION ALLELE AND UNMETHYLATION ALLELE FOR EACH INDIVIDUAL. SECOND, DUE TO THE NATURE OF SAMPLE PREPARATION, THE MEASURED METHYLATION REFLECTS THE METHYLATION STATUS OF A MIXTURE OF CELLS INVOLVED IN SAMPLE PREPARATION. THEREFORE, THE UNDERLYING DISTRIBUTION OF THE MEASURED METHYLATION LEVEL IS UNKNOWN, AND A ROBUST TEST IS MORE DESIRABLE THAN PARAMETRIC APPROACH. THIRD, CURRENTLY NGS MEASURES METHYLATION AT OVER 2 MILLION CPG SITES. ANY STATISTICAL TESTS HAVE TO BE COMPUTATIONALLY EFFICIENT IN ORDER TO BE APPLIED TO THE NGS DATA. TAKING THESE CHALLENGES INTO ACCOUNT, WE PROPOSE A TEST FOR DIFFERENTIAL METHYLATION BASED ON CLUSTERED DATA ANALYSIS BY MODELING THE METHYLATION COUNTS. WE PERFORMED SIMULATIONS TO SHOW THAT IT IS ROBUST UNDER SEVERAL DISTRIBUTIONS FOR THE MEASURED METHYLATION LEVELS. IT HAS GOOD POWER AND IS COMPUTATIONALLY EFFICIENT. FINALLY, WE APPLY THE TEST TO OUR NGS DATA ON CHRONIC LYMPHOCYTIC LEUKEMIA. THE RESULTS INDICATE THAT IT IS A PROMISING AND PRACTICAL TEST. 2013 14 1269 39 CYTOSINE METHYLATION CHANGES IN ENHANCER REGIONS OF CORE PRO-FIBROTIC GENES CHARACTERIZE KIDNEY FIBROSIS DEVELOPMENT. BACKGROUND: ONE IN ELEVEN PEOPLE IS AFFECTED BY CHRONIC KIDNEY DISEASE, A CONDITION CHARACTERIZED BY KIDNEY FIBROSIS AND PROGRESSIVE LOSS OF KIDNEY FUNCTION. EPIDEMIOLOGICAL STUDIES INDICATE THAT ADVERSE INTRAUTERINE AND POSTNATAL ENVIRONMENTS HAVE A LONG-LASTING ROLE IN CHRONIC KIDNEY DISEASE DEVELOPMENT. EPIGENETIC INFORMATION REPRESENTS A PLAUSIBLE CARRIER FOR MEDIATING THIS PROGRAMMING EFFECT. HERE WE DEMONSTRATE THAT GENOME-WIDE CYTOSINE METHYLATION PATTERNS OF HEALTHY AND CHRONIC KIDNEY DISEASE TUBULE SAMPLES OBTAINED FROM PATIENTS SHOW SIGNIFICANT DIFFERENCES. RESULTS: WE IDENTIFY DIFFERENTIALLY METHYLATED REGIONS AND VALIDATE THESE IN A LARGE REPLICATION DATASET. THE DIFFERENTIALLY METHYLATED REGIONS ARE RARELY OBSERVED ON PROMOTERS, BUT MOSTLY OVERLAP WITH PUTATIVE ENHANCER REGIONS, AND THEY ARE ENRICHED IN CONSENSUS BINDING SEQUENCES FOR IMPORTANT RENAL TRANSCRIPTION FACTORS. THIS INDICATES THEIR IMPORTANCE IN GENE EXPRESSION REGULATION. A CORE SET OF GENES THAT ARE KNOWN TO BE RELATED TO KIDNEY FIBROSIS, INCLUDING GENES ENCODING COLLAGENS, SHOW CYTOSINE METHYLATION CHANGES CORRELATING WITH DOWNSTREAM TRANSCRIPT LEVELS. CONCLUSIONS: OUR REPORT RAISES THE POSSIBILITY THAT EPIGENETIC DYSREGULATION PLAYS A ROLE IN CHRONIC KIDNEY DISEASE DEVELOPMENT VIA INFLUENCING CORE PRO-FIBROTIC PATHWAYS AND CAN AID THE DEVELOPMENT OF NOVEL BIOMARKERS AND FUTURE THERAPEUTICS. 2013 15 6405 48 THE SARS-COV-2 RECEPTOR ANGIOTENSIN-CONVERTING ENZYME 2 (ACE2) IN MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME: ANALYSIS OF HIGH-THROUGHPUT EPIGENETIC AND GENE EXPRESSION STUDIES. PATIENTS AFFECTED BY MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) SHOW SPECIFIC EPIGENETIC AND GENE EXPRESSION SIGNATURES OF THE DISEASE. HOWEVER, IT IS UNKNOWN WHETHER THESE SIGNATURES INCLUDE ABNORMAL LEVELS OF THE HUMAN ANGIOTENSIN-CONVERTING ENZYMES, ACE AND ACE2, THE LATTER BEING THE MAIN RECEPTOR DESCRIBED FOR THE HOST-CELL INVASION BY SARS-COV-2. TO INVESTIGATE THAT, WE FIRST RE-ANALYZED AVAILABLE CASE-CONTROL EPIGENOME-WIDE ASSOCIATION STUDIES BASED ON DNA METHYLATION DATA, AND CASE-CONTROL GENE EXPRESSION STUDIES BASED ON MICROARRAY DATA. FROM THESE PUBLISHED STUDIES, WE FOUND AN ASSOCIATION BETWEEN ME/CFS AND 4 POTENTIALLY HYPOMETHYLATED PROBES LOCATED IN THE ACE LOCUS. WE ALSO FOUND ANOTHER DISEASE ASSOCIATION WITH ONE HYPOMETHYLATED PROBE LOCATED IN THE TRANSCRIPTION START SITE OF ACE2. THE SAME DISEASE ASSOCIATIONS WERE OBTAINED FOR WOMEN BUT NOT FOR MEN AFTER PERFORMING SEX-SPECIFIC ANALYSES. IN CONTRAST, A META-ANALYSIS OF GENE EXPRESSION LEVELS COULD NOT PROVIDE EVIDENCE FOR A DIFFERENTIALLY EXPRESSION OF ACE AND ACE2 IN AFFECTED PATIENTS WHEN COMPARED TO HEALTHY CONTROLS. IN LINE WITH THIS NEGATIVE FINDING, THE ANALYSIS OF A NEW DATA SET ON THE GENE EXPRESSION OF ACE AND ACE2 IN PERIPHERAL BLOOD MONONUCLEAR CELLS DID NOT FIND ANY DIFFERENCES BETWEEN A FEMALE COHORT OF 37 PATIENTS AND 34 AGE-MATCHED HEALTHY CONTROLS. FUTURE STUDIES SHOULD BE CONDUCTED TO EXTEND THIS INVESTIGATION TO OTHER POTENTIAL RECEPTORS USED BY SARS-COV-2. THESE STUDIES WILL HELP RESEARCHERS AND CLINICIANS TO IMPROVE THE UNDERSTANDING OF THE HEALTH RISK IMPOSED BY THIS VIRUS WHEN INFECTING PATIENTS AFFECTED BY THIS DEBILITATING DISEASE. 2021 16 1307 49 DEFINING A METHYLATION SIGNATURE ASSOCIATED WITH OPERATIONAL TOLERANCE IN KIDNEY TRANSPLANT RECIPIENTS. OPERATIONAL TOLERANCE AFTER KIDNEY TRANSPLANTATION IS DEFINED AS STABLE GRAFT ACCEPTANCE WITHOUT THE NEED FOR IMMUNOSUPPRESSION THERAPY. HOWEVER, IT IS NOT CLEAR WHICH CELLULAR AND MOLECULAR PATHWAYS ARE DRIVING TOLERANCE IN THESE PATIENTS. WE PERFORMED GENOME-WIDE ANALYSIS OF DNA METHYLATION IN PERIPHERAL BLOOD MONONUCLEAR CELLS FROM KIDNEY TRANSPLANT RECIPIENTS WITH CHRONIC REJECTION AND OPERATIONAL TOLERANCE FROM THE GENETIC ANALYSIS OF MOLECULAR BIOMARKERS OF IMMUNOLOGICAL TOLERANCE (GAMBIT) STUDY. OUR RESULTS SHOWED THAT BOTH CLINICAL STAGES DIVERGE IN 2737 GENES, INDICATING THAT EACH ONE HAS A SPECIFIC METHYLATION SIGNATURE ASSOCIATED WITH TRANSPLANT OUTCOME. WE ALSO OBSERVED THAT TOLERANCE IS ASSOCIATED WITH DEMETHYLATION IN GENES INVOLVED IN IMMUNE FUNCTION, INCLUDING B AND T CELL ACTIVATION AND TH17 DIFFERENTIATION, WHILE IN CHRONIC REJECTION IT IS ASSOCIATED WITH INTRACELLULAR SIGNALING AND UBIQUITINATION PATHWAYS. USING CO-EXPRESSION NETWORK ANALYSIS, WE SELECTED 12 GENOMIC REGIONS THAT ARE SPECIFICALLY HYPOMETHYLATED OR HYPERMETHYLATED IN TOLERANT PATIENTS. ANALYSIS OF THESE GENES IN TRANSPLANTED PATIENTS WITH LOW DOSE OF STEROIDS SHOWED THAT THESE HAVE A SIMILAR METHYLATION SIGNATURE TO THAT OF TOLERANT RECIPIENTS. OVERALL, THESE RESULTS DEMONSTRATE THAT METHYLATION ANALYSIS CAN MIRROR THE IMMUNE STATUS ASSOCIATED WITH TRANSPLANT OUTCOME AND PROVIDES A STARTING POINT FOR UNDERSTANDING THE EPIGENETIC MECHANISMS ASSOCIATED WITH TOLERANCE. 2021 17 1967 43 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 18 3 45 "EPIGENOME-WIDE METHYLATION PROFILE OF CHRONIC KIDNEY DISEASE-DERIVED ARTERIAL DNA UNCOVERS NOVEL PATHWAYS IN DISEASE-ASSOCIATED CARDIOVASCULAR PATHOLOGY.". CHRONIC KIDNEY DISEASE (CKD) RELATED CARDIOVASCULAR DISEASE (CVD) IS CHARACTERIZED BY VASCULAR REMODELLING WITH WELL-ESTABLISHED STRUCTURAL AND FUNCTIONAL CHANGES IN THE VASCULAR WALL SUCH AS ARTERIAL STIFFNESS, MATRIX DEPOSITION, AND CALCIFICATION. THESE PHENOTYPIC CHANGES RESEMBLE PATHOLOGY SEEN IN AGEING, AND ARE LIKELY TO BE MEDIATED BY SUSTAINED ALTERATIONS IN GENE EXPRESSION, WHICH MAY BE CAUSED BY EPIGENETIC CHANGES SUCH AS TISSUE-SPECIFIC DNA METHYLATION. WE AIMED TO INVESTIGATE TISSUE SPECIFIC CHANGES IN DNA METHYLATION THAT OCCUR IN CKD-RELATED CVD. GENOME-WIDE DNA METHYLATION CHANGES WERE EXAMINED IN BISULPHITE CONVERTED GENOMIC DNA ISOLATED FROM THE VASCULAR MEDIA OF CKD AND HEALTHY ARTERIES. METHYLATION-SPECIFIC PCR WAS USED TO VALIDATE THE ARRAY DATA, AND THE ASSOCIATION BETWEEN DNA METHYLATION AND GENE AND PROTEIN EXPRESSION WAS EXAMINED. THE DNA METHYLATION AGE WAS COMPARED TO THE CHRONOLOGICAL AGE IN BOTH CASES AND CONTROLS. THREE HUNDRED AND NINETEEN DIFFERENTIALLY METHYLATED REGIONS (DMR) WERE IDENTIFIED SPREAD ACROSS THE GENOME. PATHWAY ANALYSIS REVEALED THAT DMRS ASSOCIATED WITH GENES WERE INVOLVED IN EMBRYONIC AND VASCULAR DEVELOPMENT, AND SIGNALLING PATHWAYS SUCH AS TGFBETA AND FGF. EXPRESSION OF TOP DIFFERENTIALLY METHYLATED GENE HOXA5 SHOWED A SIGNIFICANT NEGATIVE CORRELATION WITH DNA METHYLATION. INTERESTINGLY, DNA METHYLATION AGE AND CHRONOLOGICAL AGE WERE HIGHLY CORRELATED, BUT THERE WAS NO EVIDENCE OF ACCELERATED AGE-RELATED DNA METHYLATION IN THE ARTERIES OF CKD PATIENTS. IN CONCLUSION, WE DEMONSTRATED THAT DIFFERENTIAL DNA METHYLATION IN THE ARTERIAL TISSUE OF CKD PATIENTS REPRESENTS A POTENTIAL MEDIATOR OF ARTERIAL PATHOLOGY AND MAY BE USED TO UNCOVER NOVEL PATHWAYS IN THE GENESIS OF CKD-ASSOCIATED COMPLICATIONS. 2021 19 2400 50 EPIGENETIC REPROGRAMMING OF IMMUNE CELLS IN WOMEN WITH PCOS IMPACT GENES CONTROLLING REPRODUCTIVE FUNCTION. CONTEXT: POLYCYSTIC OVARY SYNDROME (PCOS) IS A CHRONIC DISEASE AFFECTING REPRODUCTIVE FUNCTION AND WHOLE-BODY METABOLISM. ALTHOUGH THE ETIOLOGY IS UNCLEAR, EMERGING EVIDENCE INDICATES THAT THE EPIGENETICS MAY BE A CONTRIBUTING FACTOR. OBJECTIVE: TO DETERMINE THE ROLE OF GLOBAL AND GENOME-WIDE EPIGENETIC MODIFICATIONS IN SPECIFIC IMMUNE CELLS IN PCOS COMPARED WITH CONTROLS AND WHETHER THESE COULD BE RELATED TO CLINICAL FEATURES OF PCOS. DESIGN: CROSS-SECTIONAL STUDY. PARTICIPANTS: WOMEN WITH (N = 17) OR WITHOUT PCOS (N = 17). SETTING: RECRUITED FROM THE GENERAL COMMUNITY. MAIN OUTCOME MEASURES: ISOLATED PERIPHERAL BLOOD MONONUCLEAR CELLS WERE ANALYZED USING MULTICOLOR FLOW CYTOMETRY METHODS TO DETERMINE GLOBAL DNA METHYLATION LEVELS IN A CELL-SPECIFIC FASHION. TRANSCRIPTOMIC AND GENOME-WIDE DNA METHYLATION ANALYSES WERE PERFORMED ON T HELPER CELLS USING RNA SEQUENCING AND REDUCED REPRESENTATION BISULFITE SEQUENCING. RESULTS: WOMEN WITH PCOS HAD LOWER GLOBAL DNA METHYLATION IN MONOCYTES (P = 0.006) AND IN T HELPER (P = 0.004), T CYTOTOXIC (P = 0.004), AND B CELLS (P = 0.03). SPECIFIC GENOME-WIDE DNA METHYLATION ANALYSIS OF T HELPER CELLS FROM WOMEN WITH PCOS IDENTIFIED 5581 DIFFERENTIALLY METHYLATED CPG SITES. FUNCTIONAL GENE ONTOLOGY ENRICHMENT ANALYSIS SHOWED THAT GENES LOCATED AT THE PROXIMITY OF DIFFERENTIALLY METHYLATED CPG SITES BELONG TO PATHWAYS RELATED TO REPRODUCTIVE FUNCTION AND IMMUNE CELL FUNCTION. HOWEVER, THESE GENES WERE NOT ALTERED AT THE TRANSCRIPTOMIC LEVEL. CONCLUSIONS: IT WAS SHOWN THAT PCOS IS ASSOCIATED WITH GLOBAL AND GENE-SPECIFIC DNA METHYLATION REMODELING IN A CELL TYPE-SPECIFIC MANNER. FURTHER INVESTIGATION IS WARRANTED TO DETERMINE WHETHER EPIGENETIC REPROGRAMMING OF IMMUNE CELLS IS IMPORTANT IN DETERMINING THE DIFFERENT PHENOTYPES OF PCOS. 2019 20 3994 45 LONGITUDINAL PROFILING IN PATIENTS UNDERGOING CARDIAC SURGERY REVEALS POSTOPERATIVE CHANGES IN DNA METHYLATION. BACKGROUND: CARDIAC SURGERY AND CARDIOPULMONARY BYPASS INDUCE A SUBSTANTIAL IMMUNE AND INFLAMMATORY RESPONSE, THE OVERACTIVATION OF WHICH IS ASSOCIATED WITH SIGNIFICANT PULMONARY, CARDIOVASCULAR, AND NEUROLOGIC COMPLICATIONS. COMMENSURATE WITH THE IMMUNE AND INFLAMMATORY RESPONSE ARE CHANGES IN THE HEART AND VASCULATURE ITSELF, WHICH TOGETHER DRIVE POSTOPERATIVE COMPLICATIONS THROUGH MECHANISMS THAT ARE POORLY UNDERSTOOD. LONGITUDINAL DNA METHYLATION PROFILING HAS THE POTENTIAL TO IDENTIFY CHANGES IN GENE REGULATORY MECHANISMS THAT ARE SECONDARY TO SURGERY AND TO IDENTIFY MOLECULAR PROCESSES THAT PREDICT AND/OR CAUSE POSTOPERATIVE COMPLICATIONS. IN THIS STUDY, WE MEASURE DNA METHYLATION IN PREOPERATIVE AND POSTOPERATIVE WHOLE BLOOD SAMPLES FROM 96 PATIENTS UNDERGOING CARDIAC SURGERY ON CARDIOPULMONARY BYPASS. RESULTS: WHILE THE VAST MAJORITY OF DNA METHYLATION IS UNCHANGED BY SURGERY AFTER ACCOUNTING FOR CHANGES IN CELL-TYPE COMPOSITION, WE IDENTIFY SEVERAL LOCI WITH STATISTICALLY SIGNIFICANT POSTOPERATIVE CHANGES IN METHYLATION. ADDITIONALLY, TWO OF THESE LOCI ARE ASSOCIATED WITH NEW-ONSET POSTOPERATIVE ATRIAL FIBRILLATION, A SIGNIFICANT COMPLICATION AFTER CARDIAC SURGERY. PAIRED STATISTICAL ANALYSIS, USE OF FACS DATA TO SUPPORT SUFFICIENT CONTROL OF CELL-TYPE HETEROGENEITY, AND MEASUREMENT OF IL6 LEVELS IN A SUBSET OF PATIENTS ADD RIGOR TO THIS ANALYSIS, ALLOWING US TO DISTINGUISH CELL-TYPE VARIABILITY FROM ACTUAL CHANGES IN METHYLATION. CONCLUSIONS: THIS STUDY IDENTIFIES SIGNIFICANT CHANGES IN DNA METHYLATION THAT OCCUR IMMEDIATELY AFTER CARDIAC SURGERY AND DEMONSTRATES THAT THESE ACUTE ALTERATIONS IN DNA METHYLATION HAVE THE GRANULARITY TO IDENTIFY PROCESSES ASSOCIATED WITH MAJOR POSTOPERATIVE COMPLICATIONS. THIS RESEARCH ALSO ESTABLISHES METHODS FOR CONTROLLING FOR CELL-TYPE VARIABILITY IN A LARGE HUMAN COHORT THAT MAY BE USEFUL TO DEPLOY IN OTHER LONGITUDINAL STUDIES OF EPIGENETIC MARKS IN THE SETTING OF ACUTE AND CHRONIC DISEASE. 2022