1  1574 186 DNA METHYLATION PATTERNS OF CHRONIC EXPLOSIVE BREACHING IN U.S. MILITARY WARFIGHTERS. BACKGROUND: INJURIES FROM EXPOSURE TO EXPLOSIONS ROSE DRAMATICALLY DURING THE IRAQ AND AFGHANISTAN WARS, WHICH MOTIVATED INVESTIGATION OF BLAST-RELATED NEUROTRAUMA. WE HAVE UNDERTAKEN HUMAN STUDIES INVOLVING MILITARY "BREACHERS" -EXPOSED TO CONTROLLED, LOW-LEVEL BLAST DURING A 3-DAYS EXPLOSIVE BREACHING COURSE. METHODS: WE SCREENED EPIGENETIC PROFILES IN PERIPHERAL BLOOD SAMPLES FROM 59 SUBJECTS (IN TWO SEPARATE U.S. MILITARY TRAINING SESSIONS) USING INFINIUM METHYLATIONEPIC BEADCHIPS. PARTICIPANTS HAD VARYING NUMBERS OF EXPOSURES TO BLAST OVER THEIR MILITARY CAREERS (EMPIRICALLY DEFINED AS HIGH >/= 40, AND CONVERSELY, LOW < 39 BREACHING EXPOSURES). DAILY SELF-REPORTED PHYSIOLOGICAL SYMPTOMS WERE RECORDED. TINNITUS, MEMORY PROBLEMS, HEADACHES, AND SLEEP DISTURBANCES ARE MOST FREQUENTLY REPORTED. RESULTS: WE IDENTIFIED 14 SIGNIFICANTLY DIFFERENTIALLY METHYLATED REGIONS (DMRS) WITHIN GENES ASSOCIATED WITH CUMULATIVE BLAST EXPOSURE IN PARTICIPANTS WITH HIGH RELATIVE TO LOW CUMULATIVE BLAST EXPOSURE. NOTABLY, NTSR1 AND SPON1 WERE SIGNIFICANTLY DIFFERENTIALLY METHYLATED IN HIGH RELATIVE TO LOW BLAST EXPOSED GROUPS, SUGGESTING THAT SLEEP DYSREGULATION MAY BE ALTERED IN RESPONSE TO CHRONIC CUMULATIVE BLAST EXPOSURE. IN COMPARING LIFETIME BLAST EXPOSURE AT BASELINE (PRIOR TO EXPOSURE IN CURRENT TRAINING), AND TOP ASSOCIATED SYMPTOMS, WE IDENTIFIED SIGNIFICANT DMRS ASSOCIATED WITH TINNITUS, SLEEP DIFFICULTIES, AND HEADACHE. NOTABLY, WE IDENTIFIED KCNN3, SOD3, MUC4, GALR1, AND WDR45B, WHICH ARE IMPLICATED IN AUDITORY FUNCTION, AS DIFFERENTIALLY METHYLATED ASSOCIATED WITH SELF-REPORTED TINNITUS. THESE FINDINGS SUGGEST NEUROBIOLOGICAL MECHANISMS BEHIND AUDITORY INJURIES IN OUR MILITARY WARFIGHTERS AND ARE PARTICULARLY RELEVANT GIVEN TINNITUS IS NOT ONLY A PRIMARY DISABILITY AMONG VETERANS, BUT HAS ALSO BEEN DEMONSTRATED IN ACTIVE DUTY MEDICAL RECORDS FOR POPULATIONS EXPOSED TO BLAST IN TRAINING. ADDITIONALLY, WE FOUND THAT DIFFERENTIALLY METHYLATED REGIONS ASSOCIATED WITH THE GENES CCDC68 AND COMT TRACK WITH SLEEP DIFFICULTIES, AND THOSE WITHIN FMOD AND TNXB TRACK WITH PAIN AND HEADACHE. CONCLUSION: SLEEP DISTURBANCES, AS WELL AS TINNITUS AND CHRONIC PAIN, ARE WIDELY REPORTED IN U.S. MILITARY SERVICE MEMBERS AND VETERANS. AS WE HAVE PREVIOUSLY DEMONSTRATED, DNA METHYLATION ENCAPSULATES LIFETIME EXPOSURE TO BLAST. THE CURRENT DATA SUPPORT PREVIOUS FINDINGS AND RECAPITULATE TRANSCRIPTIONAL REGULATORY ALTERATIONS IN GENES INVOLVED IN SLEEP, AUDITORY FUNCTION, AND PAIN. THESE DATA UNCOVERED NOVEL EPIGENETIC AND TRANSCRIPTIONAL REGULATORY MECHANISM UNDERLYING THE ETIOLOGICAL BASIS OF THESE SYMPTOMS.	2020	
                                                                                                                                                                                                                                                                                                                                                              
2   214  78 ACUTE AND CHRONIC MOLECULAR SIGNATURES AND ASSOCIATED SYMPTOMS OF BLAST EXPOSURE IN MILITARY BREACHERS. INJURIES FROM EXPOSURE TO EXPLOSIONS ROSE DRAMATICALLY DURING THE IRAQ AND AFGHANISTAN WARS, WHICH MOTIVATED INVESTIGATIONS OF BLAST-RELATED NEUROTRAUMA AND OPERATIONAL BREACHING. IN THIS STUDY, MILITARY "BREACHERS" WERE EXPOSED TO CONTROLLED, LOW-LEVEL BLAST DURING A 10-DAY EXPLOSIVE BREACHING COURSE. USING AN OMICS APPROACH, WE ASSESSED EPIGENETIC, TRANSCRIPTIONAL, AND INFLAMMATORY PROFILE CHANGES IN BLOOD FROM OPERATIONAL BREACHING TRAINEES, WITH VARYING LEVELS OF LIFETIME BLAST EXPOSURE, ALONG WITH DAILY SELF-REPORTED SYMPTOMS (WITH TINNITUS, HEADACHES, AND SLEEP DISTURBANCES AS THE MOST FREQUENTLY REPORTED). ALTHOUGH ACUTE EXPOSURE TO BLAST DID NOT CONFER EPIGENETIC CHANGES, SPECIFICALLY IN DNA METHYLATION, DIFFERENTIALLY METHYLATED REGIONS (DMRS) WITH COORDINATED GENE EXPRESSION CHANGES ASSOCIATED WITH LIFETIME CUMULATIVE BLAST EXPOSURES WERE IDENTIFIED. THE ACCUMULATIVE EFFECT OF BLAST SHOWED INCREASED METHYLATION OF PAX8 ANTISENSE TRANSCRIPT WITH COORDINATED REPRESSION OF GENE EXPRESSION, WHICH HAS BEEN ASSOCIATED WITH SLEEP DISTURBANCE. DNA METHYLATION ANALYSES CONDUCTED IN CONJUNCTION WITH REPORTED SYMPTOMS OF TINNITUS IN THE LOW VERSUS HIGH BLAST INCIDENTS GROUPS IDENTIFIED DMRS IN KCNE1 AND CYP2E1 GENES. KCNE1 AND CYP2E1 SHOWED THE EXPECTED INVERSE CORRELATION BETWEEN DNA METHYLATION AND GENE EXPRESSION, WHICH HAVE BEEN PREVIOUSLY IMPLICATED IN NOISE-RELATED HEARING LOSS. ALTHOUGH NO SIGNIFICANT TRANSCRIPTIONAL CHANGES WERE OBSERVED IN SAMPLES OBTAINED AT THE ONSET OF THE TRAINING COURSE RELATIVE TO CHRONIC CUMULATIVE BLAST, WE IDENTIFIED A LARGE NUMBER OF TRANSCRIPTIONAL PERTURBATIONS ACUTELY PRE- VERSUS POST-BLAST EXPOSURE. ACUTELY, 67 ROBUSTLY DIFFERENTIALLY EXPRESSED GENES (FOLD CHANGE >/=1.5), INCLUDING UFC1 AND YOD1 UBIQUITIN-RELATED PROTEINS, WERE IDENTIFIED. INFLAMMATORY ANALYSES OF CYTOKINES AND CHEMOKINES REVEALED DYSREGULATION OF MCP-1, GCSF, HGF, MCSF, AND RANTES ACUTELY AFTER BLAST EXPOSURE. THESE DATA SHOW THE IMPORTANCE OF AN OMICS APPROACH, REVEALING THAT TRANSCRIPTIONAL AND INFLAMMATORY BIOMARKERS CAPTURE ACUTE LOW-LEVEL BLAST OVERPRESSURE EXPOSURE, WHEREAS DNA METHYLATION MARKS ENCAPSULATE CHRONIC LONG-TERM SYMPTOMS.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
3  3032  31 GENETICS OF TINNITUS: AN EMERGING AREA FOR MOLECULAR DIAGNOSIS AND DRUG DEVELOPMENT. SUBJECTIVE TINNITUS IS THE PERCEPTION OF SOUND IN THE ABSENCE OF EXTERNAL OR BODILY-GENERATED SOUNDS. CHRONIC TINNITUS IS A HIGHLY PREVALENT CONDITION AFFECTING OVER 70 MILLION PEOPLE IN EUROPE. A WIDE VARIETY OF COMORBIDITIES, INCLUDING HEARING LOSS, PSYCHIATRIC DISORDERS, NEURODEGENERATIVE DISORDERS, AND TEMPOROMANDIBULAR JOINT (TMJ) DYSFUNCTION, HAVE BEEN SUGGESTED TO CONTRIBUTE TO THE ONSET OR PROGRESSION OF TINNITUS; HOWEVER, THE PRECISE MOLECULAR MECHANISMS OF TINNITUS ARE NOT WELL UNDERSTOOD AND THE CONTRIBUTION OF GENETIC AND EPIGENETIC FACTORS REMAINS UNKNOWN. HUMAN GENETIC STUDIES COULD ENABLE THE IDENTIFICATION OF NOVEL MOLECULAR THERAPEUTIC TARGETS, POSSIBLY LEADING TO THE DEVELOPMENT OF NOVEL PHARMACEUTICAL THERAPEUTICS. IN THIS ARTICLE, WE BRIEFLY DISCUSS THE AVAILABLE EVIDENCE FOR A ROLE OF GENETICS IN TINNITUS AND CONSIDER POTENTIAL HURDLES IN DESIGNING GENETIC STUDIES FOR TINNITUS. SINCE MULTIPLE DISEASES HAVE TINNITUS AS A SYMPTOM AND THE SUPPORTING GENETIC EVIDENCE IS SPARSE, WE PROPOSE VARIOUS STRATEGIES TO INVESTIGATE THE GENETIC UNDERPINNINGS OF TINNITUS, FIRST BY SHOWING EVIDENCE OF HERITABILITY USING CONCORDANCE STUDIES IN TWINS, AND SECOND BY IMPROVING PATIENT SELECTION ACCORDING TO PHENOTYPE AND/OR ETIOLOGY IN ORDER TO CONTROL POTENTIAL BIASES AND OPTIMIZE GENETIC DATA OUTPUT. THE INCREASED KNOWLEDGE RESULTING FROM THIS ENDEAVOR COULD ULTIMATELY IMPROVE THE DRUG DEVELOPMENT PROCESS AND LEAD TO THE PREVENTIVE OR CURATIVE TREATMENT OF TINNITUS.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
4   325  47 ALLELE-SPECIFIC DNA METHYLATION LEVEL OF FKBP5 IS ASSOCIATED WITH POST-TRAUMATIC STRESS DISORDER. BACKGROUND: FK506-BINDING PROTEIN 5 (FKBP5) BINDS TO GLUCOCORTICOID RECEPTORS AND MODULATES GLUCOCORTICOID SENSITIVITY. THE FKBP5 GENE HAS BEEN IMPLICATED IN THE DYSREGULATION OF HUMAN STRESS RESPONSES, CONTRIBUTING TO THE RISK AND TREATMENT RESPONSE OF STRESS-RELATED DISORDERS. THE PRESENT STUDY EXAMINED WHETHER EPIGENETIC CHANGES IN FKBP5 ARE ASSOCIATED WITH CHRONIC POST-TRAUMATIC STRESS DISORDER (PTSD) STATUS IN THE CONTEXT OF FKBP5 GENETIC VARIATION (RS1360780 POLYMORPHISM) AMONG MALE VETERANS EXPOSED TO COMBAT TRAUMA. METHODS: KOREAN MALE VETERANS WHO SERVED ON ACTIVE DUTY DURING THE VIETNAM WAR WERE CATEGORIZED INTO 2 GROUPS: WITH PTSD (N = 123) AND WITHOUT PTSD (N = 116). THE GENOTYPE OF FKBP5 RS1360780 AND DNA METHYLATION LEVELS OF TWO CPG SITES AT THE FKBP5 INTRON 7 REGION WERE ASSESSED IN PERIPHERAL BLOOD. ANALYSIS OF COVARIANCE WAS PERFORMED TO EXAMINE MAIN AND INTERACTION EFFECTS OF PTSD STATUS AND FKBP5 GENOTYPE ON FKBP5 DNA METHYLATION LEVEL, WITH AGE, TRAUMA LEVELS, AND ALCOHOL USE AS COVARIATES. RESULTS: A SIGNIFICANT MAIN EFFECT OF FKBP5 RS1360780 AND PTSD AND AN INTERACTION EFFECT BETWEEN GENOTYPE AND PTSD STATUS WERE FOUND ON MEAN FKBP5 DNA METHYLATION LEVEL. THE T ALLELE OF RS1360780 WAS ASSOCIATED WITH LOWER FKBP5 METHYLATION LEVEL. IN ADDITION, THE PTSD GROUP SHOWED SIGNIFICANTLY HIGHER METHYLATION THAN DID THE NON-PTSD GROUP AMONG VETERANS CARRYING THE RISK T ALLELE (N = 96), WHILE NO GROUP DIFFERENCE WAS OBSERVED ON METHYLATION LEVELS AMONG VETERANS WITH THE CC GENOTYPE (N = 143). AMONG VETERANS CARRYING THE T ALLELE, FKBP5 METHYLATION LEVELS WERE POSITIVELY CORRELATED WITH THE SEVERITY OF PTSD SYMPTOMS. CONCLUSIONS: THE PRESENT STUDY DEMONSTRATED DIFFERENT FKBP5 METHYLATION LEVELS IN PTSD DEPENDING ON FKBP5 GENETIC VARIATION AMONG VETERANS EXPOSED TO COMBAT TRAUMA. THE PRESENT FINDING SUGGESTS THAT THE GENETIC AND EPIGENETIC MODULATION OF FKBP5 IS INVOLVED IN THE PATHOPHYSIOLOGY OF PTSD. FURTHER LONGITUDINAL RESEARCH INVOLVING PEOPLE EXPOSED TO TRAUMA IS REQUIRED TO UNDERSTAND CAUSAL RELATIONSHIPS OF FKBP5 IN THE DEVELOPMENT AND RECOVERY OF PTSD.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
5  2630  48 EPIGENOME-WIDE ASSOCIATION STUDY OF POSTTRAUMATIC STRESS DISORDER IDENTIFIES NOVEL LOCI IN U.S. MILITARY VETERANS. POSTTRAUMATIC STRESS DISORDER (PTSD) IS A CHRONIC AND DISABLING PSYCHIATRIC DISORDER PREVALENT IN MILITARY VETERANS. EPIGENETIC MECHANISMS HAVE BEEN IMPLICATED IN THE ETIOLOGY OF PTSD, WITH DNA METHYLATION BEING THE MOST STUDIED TO IDENTIFY NOVEL MOLECULAR BIOMARKERS ASSOCIATED WITH THIS DISORDER. WE PERFORMED ONE OF THE LARGEST SINGLE-SAMPLE EPIGENOME-WIDE ASSOCIATION STUDIES (EWAS) OF PTSD TO DATE. OUR SAMPLE INCLUDED 1135 MALE EUROPEAN-AMERICAN U.S. VETERANS WHO PARTICIPATED IN THE NATIONAL HEALTH AND RESILIENCE IN VETERANS STUDY (NHRVS). DNA WAS COLLECTED FROM SALIVA SAMPLES AND THE ILLUMINA HUMANMETHYLATION EPIC BEADCHIP WAS USED FOR THE METHYLATION ANALYSIS. PTSD WAS ASSESSED USING THE PTSD CHECKLIST. AN EWAS WAS CONDUCTED USING LINEAR REGRESSION ADJUSTED FOR AGE, CELL-TYPE PROPORTIONS, FIRST 10 PRINCIPAL COMPONENTS, AND SMOKING STATUS. AFTER BONFERRONI CORRECTION, WE IDENTIFIED SIX GENOME-WIDE SIGNIFICANT (GWS) CPG SITES ASSOCIATED WITH PAST-MONTH PTSD AND THREE CPGS WITH LIFETIME PTSD (P(RANGE) = 10(-10)-10(-8)). THESE CPG SITES MAP TO GENES INVOLVED IN IMMUNE FUNCTION, TRANSCRIPTION REGULATION, AXONAL GUIDANCE, CELL SIGNALING, AND PROTEIN BINDING. AMONG THESE, SENP7, WHICH IS INVOLVED IN TRANSCRIPTION REGULATION AND HAS BEEN LINKED TO RISK-TAKING BEHAVIOR AND ALCOHOL CONSUMPTION IN GENOME-WIDE ASSOCIATION STUDIES, REPLICATED IN AN INDEPENDENT VETERAN COHORT AND WAS DOWNREGULATED IN MEDIAL ORBITOFRONTAL CORTEX OF PTSD POSTMORTEM BRAIN TISSUE. THESE FINDINGS SUGGEST POTENTIAL EPIGENETIC BIOMARKERS OF PTSD THAT MAY HELP INFORM THE PATHOPHYSIOLOGY OF THIS DISORDER IN VETERANS AND OTHER TRAUMA-AFFECTED POPULATIONS.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
6    63  31 A HIGH METHYLATION LEVEL OF A NOVEL -284 BP CPG ISLAND IN THE RAMP1 GENE PROMOTER IS POTENTIALLY ASSOCIATED WITH MIGRAINE IN WOMEN. MIGRAINE IS A COMPLEX NEUROVASCULAR DISORDER AFFECTING ONE BILLION PEOPLE WORLDWIDE, MAINLY FEMALES. IT IS CHARACTERIZED BY ATTACKS OF MODERATE TO SEVERE HEADACHE PAIN, WITH ASSOCIATED SYMPTOMS. RECEPTOR ACTIVITY MODIFYING PROTEIN (RAMP1) IS PART OF THE CALCITONIN GENE-RELATED PEPTIDE (CGRP) RECEPTOR, A PHARMACOLOGICAL TARGET FOR MIGRAINE. EPIGENETIC PROCESSES, SUCH AS DNA METHYLATION, PLAY A ROLE IN CLINICAL PRESENTATION OF VARIOUS DISEASES. DNA METHYLATION OCCURS MOSTLY IN THE GENE PROMOTER AND CAN CONTROL GENE EXPRESSION. WE INVESTIGATED THE METHYLATION STATE OF THE RAMP1 PROMOTER IN 104 FEMALE BLOOD DNA SAMPLES: 54 MIGRAINEURS AND 50 CONTROLS. WE TREATED DNA WITH SODIUM BISULFITE AND PERFORMED PCR, SANGER SEQUENCING, AND EPIGENETIC SEQUENCING METHYLATION (ESME) SOFTWARE ANALYSIS. WE IDENTIFIED 51 CPG DINUCLEOTIDES, AND 5 SHOWED METHYLATION VARIABILITY. MIGRAINEURS HAD A HIGHER NUMBER OF INDIVIDUALS WITH ALL FIVE CPG METHYLATED WHEN COMPARED TO CONTROLS (26% VS. 16%), ALTHOUGH NON-SIGNIFICANT (P = 0.216). WE ALSO FOUND THAT CPG -284 BP, RELATED TO THE TRANSCRIPTION START SITE (TSS), SHOWED HIGHER METHYLATION LEVELS IN CASES (P = 0.011). THIS CPG MAY POTENTIALLY PLAY A ROLE IN MIGRAINE, AFFECTING RAMP1 TRANSCRIPTION OR RECEPTOR MALFUNCTIONING AND/OR ALTERED CGRP BINDING. WE HOPE TO CONFIRM THIS FINDING IN A LARGER COHORT AND ESTABLISH AN EPIGENETIC BIOMARKER TO PREDICT FEMALE MIGRAINE RISK.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
7  3056  43 GENOME-WIDE DNA METHYLATION ANALYSIS IMPLICATES ENRICHMENT OF INTERFERON PATHWAY IN AFRICAN AMERICAN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS AND EUROPEAN AMERICANS WITH LUPUS NEPHRITIS. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC, MULTISYSTEM, INFLAMMATORY AUTOIMMUNE DISEASE THAT DISPROPORTIONATELY AFFECTS WOMEN. TRENDS IN SLE PREVALENCE AND CLINICAL COURSE DIFFER BY ANCESTRY, WITH THOSE OF AFRICAN AMERICAN ANCESTRY PRESENTING WITH MORE ACTIVE, SEVERE AND RAPIDLY PROGRESSIVE DISEASE THAN EUROPEAN AMERICANS. PREVIOUS RESEARCH ESTABLISHED ALTERED EPIGENETIC SIGNATURES IN SLE PATIENTS COMPARED TO CONTROLS. HOWEVER, THE CONTRIBUTION OF ABERRANT DNA METHYLATION (DNAM) TO THE RISK OF SLE BY ANCESTRY AND DIFFERENCES AMONG PATIENTS WITH SLE-ASSOCIATED LUPUS NEPHRITIS (LN) HAS NOT BEEN WELL DESCRIBED. WE EVALUATED THE DNA METHYLOMES OF 87 INDIVIDUALS INCLUDING 41 SLE PATIENTS, WITH AND WITHOUT LN, AND 46 CONTROLS ENROLLED IN AN ANCESTRY DIVERSE, WELL-CHARACTERIZED COHORT STUDY OF ESTABLISHED SLE (41 SLE PATIENTS [20 SLE-LN+, 21 SLE-LN-] AND 46 SEX-, RACE- AND AGE-MATCHED CONTROLS; 55% AFRICAN AMERICAN, 45% EUROPEAN AMERICAN). PARTICIPANTS WERE GENOTYPED USING THE INFINIUM GLOBAL DIVERSITY ARRAY (GDA), AND GENETIC ANCESTRY WAS ESTIMATED USING PRINCIPAL COMPONENTS. GENOME-WIDE DNA METHYLATION WAS INITIALLY MEASURED USING THE ILLUMINA METHYLATIONEPIC 850K BEADCHIP ARRAY FOLLOWED BY METHYLATION-SPECIFIC QPCR TO VALIDATE THE METHYLATION STATUS AT PUTATIVE LOCI. DIFFERENTIALLY METHYLATED POSITIONS (DMP) WERE IDENTIFIED USING A CASE-CONTROL APPROACH ADJUSTED FOR ANCESTRY. WE IDENTIFIED A TOTAL OF 51 DMPS IN CPGS AMONG SLE PATIENTS COMPARED TO CONTROLS. GENES PROXIMAL TO THESE CPGS WERE HIGHLY ENRICHED FOR INVOLVEMENT IN TYPE I INTERFERON SIGNALING. DMPS AMONG EUROPEAN AMERICAN SLE PATIENTS WITH LN WERE SIMILAR TO AFRICAN AMERICAN SLE PATIENTS WITH AND WITHOUT LN. OUR FINDINGS WERE VALIDATED USING AN ORTHOGONAL, METHYL-SPECIFIC PCR FOR THREE SLE-ASSOCIATED DMPS NEAR OR PROXIMAL TO MX1, USP18, AND IFITM1. OUR STUDY CONFIRMS PREVIOUS REPORTS THAT DMPS IN CPGS ASSOCIATED WITH SLE ARE ENRICHED IN TYPE I INTERFERON GENES. HOWEVER, WE SHOW THAT EUROPEAN AMERICAN SLE PATIENTS WITH LN HAVE SIMILAR DNAM PATTERNS TO AFRICAN AMERICAN SLE PATIENTS IRRESPECTIVE OF LN, SUGGESTING THAT ABERRANT DNAM ALTERS ACTIVITY OF TYPE I INTERFERON PATHWAY LEADING TO MORE SEVERE DISEASE INDEPENDENT OF ANCESTRY.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
8  2207  50 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
9   521  43 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	

10   812  54 CHANGES IN DNA METHYLATION PROFILES OF MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME PATIENTS REFLECT SYSTEMIC DYSFUNCTIONS. BACKGROUND: MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A LIFELONG DEBILITATING DISEASE WITH A COMPLEX PATHOLOGY NOT YET CLEARLY DEFINED. SUSCEPTIBILITY TO ME/CFS INVOLVES GENETIC PREDISPOSITION AND EXPOSURE TO ENVIRONMENTAL FACTORS, SUGGESTING AN EPIGENETIC ASSOCIATION. EPIGENETIC STUDIES WITH OTHER ME/CFS COHORTS HAVE USED ARRAY-BASED TECHNOLOGY TO IDENTIFY DIFFERENTIALLY METHYLATED INDIVIDUAL SITES. CHANGES IN RNA QUANTITIES AND PROTEIN ABUNDANCE HAVE BEEN DOCUMENTED IN OUR PREVIOUS INVESTIGATIONS WITH THE SAME ME/CFS COHORT USED FOR THIS STUDY. RESULTS: DNA FROM A WELL-CHARACTERISED NEW ZEALAND COHORT OF 10 ME/CFS PATIENTS AND 10 AGE-/SEX-MATCHED HEALTHY CONTROLS WAS ISOLATED FROM PERIPHERAL BLOOD MONONUCLEAR (PBMC) CELLS, AND USED TO GENERATE REDUCED GENOME-SCALE DNA METHYLATION MAPS USING REDUCED REPRESENTATION BISULPHITE SEQUENCING (RRBS). THE SEQUENCING DATA WERE ANALYSED UTILISING THE DMAP ANALYSIS PIPELINE TO IDENTIFY DIFFERENTIALLY METHYLATED FRAGMENTS, AND THE METHYLKIT PIPELINE WAS USED TO QUANTIFY METHYLATION DIFFERENCES AT INDIVIDUAL CPG SITES. DMAP IDENTIFIED 76 DIFFERENTIALLY METHYLATED FRAGMENTS AND METHYLKIT IDENTIFIED 394 DIFFERENTIALLY METHYLATED CYTOSINES THAT INCLUDED BOTH HYPER- AND HYPO-METHYLATION. FOUR CLUSTERS WERE IDENTIFIED WHERE DIFFERENTIALLY METHYLATED DNA FRAGMENTS OVERLAPPED WITH OR WERE WITHIN CLOSE PROXIMITY TO MULTIPLE DIFFERENTIALLY METHYLATED INDIVIDUAL CYTOSINES. THESE CLUSTERS IDENTIFIED REGULATORY REGIONS FOR 17 PROTEIN ENCODING GENES RELATED TO METABOLIC AND IMMUNE ACTIVITY. ANALYSIS OF DIFFERENTIALLY METHYLATED GENE BODIES (EXONS/INTRONS) IDENTIFIED 122 UNIQUE GENES. COMPARISON WITH OTHER STUDIES ON PBMCS FROM ME/CFS PATIENTS AND CONTROLS WITH ARRAY TECHNOLOGY SHOWED 59% OF THE GENES IDENTIFIED IN THIS STUDY WERE ALSO FOUND IN ONE OR MORE OF THESE STUDIES. FUNCTIONAL PATHWAY ENRICHMENT ANALYSIS IDENTIFIED 30 ASSOCIATED PATHWAYS. THESE INCLUDED IMMUNE, METABOLIC AND NEUROLOGICAL-RELATED FUNCTIONS DIFFERENTIALLY REGULATED IN ME/CFS PATIENTS COMPARED TO THE MATCHED HEALTHY CONTROLS. CONCLUSIONS: MAJOR DIFFERENCES WERE IDENTIFIED IN THE DNA METHYLATION PATTERNS OF ME/CFS PATIENTS THAT CLEARLY DISTINGUISHED THEM FROM THE HEALTHY CONTROLS. OVER HALF FOUND IN GENE BODIES WITH RRBS IN THIS STUDY HAD BEEN IDENTIFIED IN OTHER ME/CFS STUDIES USING THE SAME CELLS BUT WITH ARRAY TECHNOLOGY. WITHIN THE ENRICHED FUNCTIONAL IMMUNE, METABOLIC AND NEUROLOGICAL PATHWAYS, A NUMBER OF ENRICHED NEUROTRANSMITTER AND NEUROPEPTIDE REACTOME PATHWAYS HIGHLIGHTED A DISTURBED NEUROLOGICAL PATHOPHYSIOLOGY WITHIN THE PATIENT GROUP.	2020	
                                                                                                                                                                                                                                                                                                                                    
11  3063  48 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  5451  43 REPROGRAMMING CELLS FROM GULF WAR VETERANS INTO NEURONS TO STUDY GULF WAR ILLNESS. GULF WAR ILLNESS (GWI), WHICH AFFLICTS AT LEAST 25% OF VETERANS WHO SERVED IN THE 1990-1991 WAR IN THE PERSIAN GULF, IS THOUGHT TO BE CAUSED BY DEPLOYMENT EXPOSURES TO VARIOUS NEUROTOXICANTS, INCLUDING PESTICIDES, ANTI-NERVE GAS PILLS, AND LOW-LEVEL NERVE AGENTS INCLUDING SARIN/CYCLOSARIN. GWI IS A MULTISYMPTOM DISORDER CHARACTERIZED BY FATIGUE, JOINT PAIN, COGNITIVE PROBLEMS, AND GASTROINTESTINAL COMPLAINTS. THE MOST PROMINENT SYMPTOMS OF GWI (MEMORY PROBLEMS, POOR ATTENTION/CONCENTRATION, CHRONIC HEADACHES, MOOD ALTERATIONS, AND IMPAIRED SLEEP) SUGGEST THAT THE DISEASE PRIMARILY AFFECTS THE CNS. DEVELOPMENT OF URGENTLY NEEDED TREATMENTS DEPENDS ON EXPERIMENTAL MODELS APPROPRIATE FOR TESTING MECHANISTIC HYPOTHESES AND FOR SCREENING THERAPEUTIC COMPOUNDS. RODENT MODELS HAVE BEEN USEFUL THUS FAR, BUT ARE LIMITED BY THEIR INABILITY TO ASSESS THE CONTRIBUTION OF GENETIC OR EPIGENETIC BACKGROUND TO THE DISEASE, AND BECAUSE DISEASE-VULNERABLE PROTEINS AND PATHWAYS MAY BE DIFFERENT IN HUMANS RELATIVE TO RODENTS. AS OF YET, NO POSTMORTEM TISSUE FROM THE VETERANS HAS BECOME AVAILABLE FOR RESEARCH. WE ARE MOVING FORWARD WITH A PARADIGM SHIFT IN THE STUDY OF GWI, WHICH UTILIZES CONTEMPORARY STEM CELL TECHNOLOGY TO CONVERT SOMATIC CELLS FROM GULF WAR VETERANS INTO PLURIPOTENT CELL LINES THAT CAN BE DIFFERENTIATED INTO VARIOUS CELL TYPES, INCLUDING NEURONS, GLIA, MUSCLE, OR OTHER RELEVANT CELL TYPES. SUCH CELL LINES ARE IMMORTAL AND WILL BE A RESOURCE FOR GWI RESEARCHERS TO PURSUE MECHANISTIC HYPOTHESES AND THERAPEUTICS.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
13  1598  39 DNA METHYLATION SIGNATURE IN MONONUCLEAR CELLS AND PROINFLAMMATORY CYTOKINES MAY DEFINE MOLECULAR SUBTYPES IN SPORADIC MENIERE DISEASE. MENIERE DISEASE (MD) IS A MULTIFACTORIAL DISORDER OF THE INNER EAR CHARACTERIZED BY VERTIGO ATTACKS ASSOCIATED WITH SENSORINEURAL HEARING LOSS AND TINNITUS WITH A SIGNIFICANT HERITABILITY. ALTHOUGH MD HAS BEEN ASSOCIATED WITH SEVERAL GENES, NO EPIGENETIC STUDIES HAVE BEEN PERFORMED ON MD. HERE WE PERFORMED WHOLE-GENOME BISULFITE SEQUENCING IN 14 MD PATIENTS AND SIX HEALTHY CONTROLS, WITH THE AIM OF IDENTIFYING AN MD METHYLATION SIGNATURE AND POTENTIAL DISEASE MECHANISMS. WE OBSERVED A HIGH NUMBER OF DIFFERENTIALLY METHYLATED CPGS (DMC) WHEN COMPARING MD PATIENTS TO CONTROLS (N= 9545), SEVERAL OF THEM IN HEARING LOSS GENES, SUCH AS PCDH15,&NBSP;ADGRV1 AND CDH23. BIOINFORMATIC ANALYSES OF DMCS AND CIS-REGULATORY REGIONS PREDICTED PHENOTYPES RELATED TO ABNORMAL EXCITATORY POSTSYNAPTIC CURRENTS, ABNORMAL NMDA-MEDIATED RECEPTOR CURRENTS AND ABNORMAL GLUTAMATE-MEDIATED RECEPTOR CURRENTS WHEN COMPARING MD TO CONTROLS. MOREOVER, WE IDENTIFIED VARIOUS DMCS IN GENES PREVIOUSLY ASSOCIATED WITH COCHLEOVESTIBULAR PHENOTYPES IN MICE. WE HAVE ALSO FOUND 12 UNDERMETHYLATED REGIONS (UMR) THAT WERE EXCLUSIVE TO MD, INCLUDING TWO UMR IN AN INTER CPG ISLAND IN THE PHB GENE. WE SUGGEST THAT THE DNA METHYLATION SIGNATURE ALLOWS DISTINGUISHING BETWEEN MD PATIENTS AND CONTROLS. THE ENRICHMENT ANALYSIS CONFIRMS PREVIOUS FINDINGS OF A CHRONIC INFLAMMATORY PROCESS UNDERLYING MD.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
14  3496  51 IDENTIFICATION OF MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME-ASSOCIATED DNA METHYLATION PATTERNS. BACKGROUND: MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A COMPLEX CONDITION INVOLVING MULTIPLE ORGAN SYSTEMS AND CHARACTERIZED BY PERSISTENT/RELAPSING DEBILITATING FATIGUE, IMMUNE DYSFUNCTION, NEUROLOGICAL PROBLEMS, AND OTHER SYMPTOMS NOT CURABLE FOR AT LEAST 6 MONTHS. DISRUPTION OF DNA METHYLATION PATTERNS HAS BEEN TIED TO VARIOUS IMMUNE AND NEUROLOGICAL DISEASES; HOWEVER, ITS STATUS IN ME/CFS REMAINS UNCERTAIN. OUR STUDY AIMED AT IDENTIFYING CHANGES IN THE DNA METHYLATION PATTERNS THAT ASSOCIATE WITH ME/CFS. METHODS: WE EXTRACTED GENOMIC DNA FROM PERIPHERAL BLOOD MONONUCLEAR CELLS FROM 13 ME/CFS STUDY SUBJECTS AND 12 HEALTHY CONTROLS AND MEASURED GLOBAL DNA METHYLATION BY ELISA-LIKE METHOD AND SITE-SPECIFIC METHYLATION STATUS USING ILLUMINA METHYLATIONEPIC MICROARRAYS. PYROSEQUENCING VALIDATION INCLUDED 33 ME/CFS CASES AND 31 CONTROLS FROM TWO GEOGRAPHICALLY DISTANT COHORTS. RESULTS: GLOBAL DNA METHYLATION LEVELS OF ME/CFS CASES WERE SIMILAR TO THOSE OF CONTROLS. HOWEVER, MICROARRAY-BASED APPROACH ALLOWED DETECTION OF 17,296 DIFFERENTIALLY METHYLATED CPG SITES IN 6,368 GENES ACROSS REGULATORY ELEMENTS AND WITHIN CODING REGIONS OF GENES. ANALYSIS OF DNA METHYLATION IN PROMOTER REGIONS REVEALED 307 DIFFERENTIALLY METHYLATED PROMOTERS. INGENUITY PATHWAY ANALYSIS INDICATED THAT GENES ASSOCIATED WITH DIFFERENTIALLY METHYLATED PROMOTERS PARTICIPATED IN AT LEAST 15 DIFFERENT PATHWAYS MOSTLY RELATED TO CELL SIGNALING WITH A STRONG IMMUNE COMPONENT. CONCLUSIONS: THIS IS THE FIRST STUDY THAT HAS EXPLORED GENOME-WIDE EPIGENETIC CHANGES ASSOCIATED WITH ME/CFS USING THE ADVANCED ILLUMINA METHYLATIONEPIC MICROARRAYS COVERING ABOUT 850,000 CPG SITES IN TWO GEOGRAPHICALLY DISTANT COHORTS OF ME/CFS CASES AND MATCHED CONTROLS. OUR RESULTS ARE ALIGNED WITH PREVIOUS STUDIES THAT INDICATE A DYSREGULATION OF THE IMMUNE SYSTEM IN ME/CFS. THEY ALSO SUGGEST A POTENTIAL ROLE OF EPIGENETIC DE-REGULATION IN THE PATHOBIOLOGY OF ME/CFS. WE PROPOSE SCREENING OF LARGER COHORTS OF ME/CFS CASES TO DETERMINE THE EXTERNAL VALIDITY OF THESE EPIGENETIC CHANGES IN ORDER TO IMPLEMENT THEM AS POSSIBLE DIAGNOSTIC MARKERS IN CLINICAL SETTING.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
15  2123  45 EPIGENETIC IMPACTS OF STRESS PRIMING OF THE NEUROINFLAMMATORY RESPONSE TO SARIN SURROGATE IN MICE: A MODEL OF GULF WAR ILLNESS. BACKGROUND: GULF WAR ILLNESS (GWI) IS AN ARCHETYPAL, MEDICALLY UNEXPLAINED, CHRONIC CONDITION CHARACTERISED BY PERSISTENT SICKNESS BEHAVIOUR AND NEUROIMMUNE AND NEUROINFLAMMATORY COMPONENTS. AN ESTIMATED 25-32% OF THE OVER 900,000 VETERANS OF THE 1991 GULF WAR FULFIL THE REQUIREMENTS OF A GWI DIAGNOSIS. IT HAS BEEN HYPOTHESISED THAT THE HIGH PHYSICAL AND PSYCHOLOGICAL STRESS OF COMBAT MAY HAVE INCREASED VULNERABILITY TO IRREVERSIBLE ACETYLCHOLINESTERASE (ACHE) INHIBITORS LEADING TO A PRIMING OF THE NEUROIMMUNE SYSTEM. A NUMBER OF STUDIES HAVE LINKED HIGH LEVELS OF PSYCHOPHYSIOLOGICAL STRESS AND TOXICANT EXPOSURES TO EPIGENETIC MODIFICATIONS THAT REGULATE GENE EXPRESSION. RECENT RESEARCH IN A MOUSE MODEL OF GWI HAS SHOWN THAT PRE-EXPOSURE WITH THE STRESS HORMONE CORTICOSTERONE (CORT) CAUSES AN INCREASE IN EXPRESSION OF SPECIFIC CHEMOKINES AND CYTOKINES IN RESPONSE TO DIISOPROPYL FLUOROPHOSPHATE (DFP), A SARIN SURROGATE AND IRREVERSIBLE ACHE INHIBITOR. METHODS: C57BL/6J MICE WERE EXPOSED TO CORT FOR 4 DAYS, AND EXPOSED TO DFP ON DAY 5, BEFORE SACRIFICE 6 H LATER. THE TRANSCRIPTOME WAS EXAMINED USING RNA-SEQ, AND THE EPIGENOME WAS EXAMINED USING REDUCED REPRESENTATION BISULFITE SEQUENCING AND H3K27AC CHIP-SEQ. RESULTS: WE SHOW TRANSCRIPTIONAL, HISTONE MODIFICATION (H3K27AC) AND DNA METHYLATION CHANGES IN GENES RELATED TO THE IMMUNE AND NEURONAL SYSTEM, POTENTIALLY RELEVANT TO NEUROINFLAMMATORY AND COGNITIVE SYMPTOMS OF GWI. FURTHER EVIDENCE SUGGESTS ALTERED PROPORTIONS OF MYELINATING OLIGODENDROCYTES IN THE FRONTAL CORTEX, PERHAPS CONNECTED TO WHITE MATTER DEFICITS SEEN IN GWI SUFFERERS. CONCLUSIONS: OUR FINDINGS MAY REFLECT THE EARLY CHANGES WHICH OCCURRED IN GWI VETERANS, AND WE OBSERVE ALTERATIONS IN SEVERAL PATHWAYS ALTERED IN GWI SUFFERERS. THESE CLOSE LINKS TO CHANGES SEEN IN VETERANS WITH GWI INDICATES THAT THIS MODEL REFLECTS THE ENVIRONMENTAL EXPOSURES RELATED TO GWI AND MAY PROVIDE A MODEL FOR BIOMARKER DEVELOPMENT AND TESTING FUTURE TREATMENTS.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
16  1571  42 DNA METHYLATION PATTERNS IN CD8(+) T CELLS DISCERN PSORIASIS FROM PSORIATIC ARTHRITIS AND CORRELATE WITH CUTANEOUS DISEASE ACTIVITY. BACKGROUND: PSORIASIS IS A T CELL-MEDIATED CHRONIC AUTOIMMUNE/INFLAMMATORY DISEASE. WHILE SOME PATIENTS EXPERIENCE DISEASE LIMITED TO THE SKIN (SKIN PSORIASIS), OTHERS DEVELOP JOINT INVOLVEMENT (PSORIATIC ARTHRITIS; PSA). IN THE ABSENCE OF DISEASE- AND/OR OUTCOME-SPECIFIC BIOMARKERS, AND AS ARTHRITIS CAN PRECEDE SKIN MANIFESTATIONS, DIAGNOSTIC AND THERAPEUTIC DELAYS ARE COMMON AND CONTRIBUTE TO DISEASE BURDEN AND DAMAGE ACCRUAL. OBJECTIVE: ALTERED EPIGENETIC MARKS, INCLUDING DNA METHYLATION, CONTRIBUTE TO EFFECTOR T CELL PHENOTYPES AND ALTERED CYTOKINE EXPRESSION IN AUTOIMMUNE/INFLAMMATORY DISEASES. THIS PROJECT AIMED AT THE IDENTIFICATION OF DISEASE-/OUTCOME-SPECIFIC DNA METHYLATION SIGNATURES IN CD8(+) T CELLS FROM PATIENTS WITH PSORIASIS AND PSA AS COMPARED TO HEALTHY CONTROLS. METHOD: PERIPHERAL BLOOD CD8(+) T CELLS FROM NINE HEALTHY CONTROLS, 10 PSORIASIS, AND SEVEN PSA PATIENTS WERE COLLECTED TO ANALYZE DNA METHYLATION MARKS USING ILLUMINA HUMAN METHYLATION EPIC BEADCHIPS (>850,000 CPGS PER SAMPLE). BIOINFORMATIC ANALYSIS WAS PERFORMED USING R (MINFI, LIMMA, CHAMP, AND DMRCATE PACKAGES). RESULTS: DNA METHYLATION PROFILES IN CD8(+) T CELLS DIFFERENTIATE HEALTHY CONTROLS FROM PSORIASIS PATIENTS [397 DIFFERENTIALLY METHYLATED POSITIONS (DMPS); 9 DIFFERENTIALLY METHYLATED REGIONS (DMRS) WHEN >/=CPGS PER DMR WERE CONSIDERED; 2 DMRS FOR >/=10 CPGS]. FURTHERMORE, PATIENTS WITH SKIN PSORIASIS CAN BE DISCRIMINATED FROM PSA PATIENTS [1,861 DMPS, 20 DMRS (>/=5 CPGS PER REGION), 4 DMRS (>/=10 CPGS PER REGION)]. GENE ONTOLOGY (GO) ANALYSES CONSIDERING GENES WITH >/=1 DMP IN THEIR PROMOTER DELIVERED METHYLATION DEFECTS IN SKIN PSORIASIS AND PSA PRIMARILY AFFECTING THE BMP SIGNALING PATHWAY AND ENDOPEPTIDASE REGULATOR ACTIVITY, RESPECTIVELY. GO ANALYSIS OF GENES ASSOCIATED WITH DMRS BETWEEN SKIN PSORIASIS AND PSA DEMONSTRATED AN ENRICHMENT OF GABAERGIC NEURON AND CORTEX NEURON DEVELOPMENT PATHWAYS. TREATMENT WITH CYTOKINE BLOCKERS ASSOCIATED WITH DNA METHYLATION CHANGES [2,372 DMPS; 1,907 DMPS WITHIN PROMOTERS, 7 DMRS (>/=5 CPG PER REGIONS)] AFFECTING TRANSFORMING GROWTH FACTOR BETA RECEPTOR AND TRANSMEMBRANE RECEPTOR PROTEIN SERINE/THREONINE KINASE SIGNALING PATHWAYS. LASTLY, A METHYLATION SCORE INCLUDING TNF AND IL-17 PATHWAY ASSOCIATED DMPS INVERSE CORRELATES WITH SKIN DISEASE ACTIVITY SCORES (PASI). CONCLUSION: PATIENTS WITH SKIN PSORIASIS EXHIBIT DNA METHYLATION PATTERNS IN CD8(+) T CELLS THAT ALLOW DIFFERENTIATION FROM PSA PATIENTS AND HEALTHY INDIVIDUALS, AND REFLECT CLINICAL ACTIVITY OF SKIN DISEASE. THUS, DNA METHYLATION PROFILING PROMISES POTENTIAL AS DIAGNOSTIC AND PROGNOSTIC TOOL TO BE USED FOR MOLECULAR PATIENT STRATIFICATION TOWARD INDIVIDUALIZED TREATMENT.	2021	
                                                                                                                                                                                                                             
17  3487  44 IDENTIFICATION OF DIFFERENTIALLY METHYLATED SITES WITH WEAK METHYLATION EFFECTS. DEOXYRIBONUCLEIC ACID (DNA) METHYLATION IS AN EPIGENETIC ALTERATION CRUCIAL FOR REGULATING STRESS RESPONSES. IDENTIFYING LARGE-SCALE DNA METHYLATION AT SINGLE NUCLEOTIDE RESOLUTION IS MADE POSSIBLE BY WHOLE GENOME BISULFITE SEQUENCING. AN ESSENTIAL TASK FOLLOWING THE GENERATION OF BISULFITE SEQUENCING DATA IS TO DETECT DIFFERENTIALLY METHYLATED CYTOSINES (DMCS) AMONG TREATMENTS. MOST STATISTICAL METHODS FOR DMC DETECTION DO NOT CONSIDER THE DEPENDENCY OF METHYLATION PATTERNS ACROSS THE GENOME, THUS POSSIBLY INFLATING TYPE I ERROR. FURTHERMORE, SMALL SAMPLE SIZES AND WEAK METHYLATION EFFECTS AMONG DIFFERENT PHENOTYPE CATEGORIES MAKE IT DIFFICULT FOR THESE STATISTICAL METHODS TO ACCURATELY DETECT DMCS. TO ADDRESS THESE ISSUES, THE WAVELET-BASED FUNCTIONAL MIXED MODEL (WFMM) WAS INTRODUCED TO DETECT DMCS. TO FURTHER EXAMINE THE PERFORMANCE OF WFMM IN DETECTING WEAK DIFFERENTIAL METHYLATION EVENTS, WE USED BOTH SIMULATED AND EMPIRICAL DATA AND COMPARE WFMM PERFORMANCE TO A POPULAR DMC DETECTION TOOL METHYLKIT. ANALYSES OF SIMULATED DATA THAT REPLICATED THE EFFECTS OF THE HERBICIDE GLYPHOSATE ON DNA METHYLATION IN ARABIDOPSIS THALIANA SHOW THAT WFMM RESULTS IN HIGHER SENSITIVITY AND SPECIFICITY IN DETECTING DMCS COMPARED TO METHYLKIT, ESPECIALLY WHEN THE METHYLATION DIFFERENCES AMONG PHENOTYPE GROUPS ARE SMALL. MOREOVER, THE PERFORMANCE OF WFMM IS ROBUST WITH RESPECT TO SMALL SAMPLE SIZES, MAKING IT PARTICULARLY ATTRACTIVE CONSIDERING THE CURRENT HIGH COSTS OF BISULFITE SEQUENCING. ANALYSIS OF EMPIRICAL ARABIDOPSIS THALIANA DATA UNDER VARYING GLYPHOSATE DOSAGES, AND THE ANALYSIS OF MONOZYGOTIC (MZ) TWINS WHO HAVE DIFFERENT PAIN SENSITIVITIES-BOTH DATASETS HAVE WEAK METHYLATION EFFECTS OF <1%-SHOW THAT WFMM CAN IDENTIFY MORE RELEVANT DMCS RELATED TO THE PHENOTYPE OF INTEREST THAN METHYLKIT. DIFFERENTIALLY METHYLATED REGIONS (DMRS) ARE GENOMIC REGIONS WITH DIFFERENT DNA METHYLATION STATUS ACROSS BIOLOGICAL SAMPLES. DMRS AND DMCS ARE ESSENTIALLY THE SAME CONCEPTS, WITH THE ONLY DIFFERENCE BEING HOW METHYLATION INFORMATION ACROSS THE GENOME IS SUMMARIZED. IF METHYLATION LEVELS ARE DETERMINED BY GROUPING NEIGHBORING CYTOSINE SITES, THEN THEY ARE DMRS; IF METHYLATION LEVELS ARE CALCULATED BASED ON SINGLE CYTOSINES, THEY ARE DMCS.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
18   336  44 ALTERATIONS IN DNA METHYLATION STATUS ASSOCIATED WITH GULF WAR ILLNESS. GULF WAR ILLNESS (GWI) AFFECTS ABOUT 25% OF PERSIAN GULF VETERANS WITH A CLUSTER OF CHRONIC SYMPTOMS, INCLUDING IMMUNE DYSFUNCTION AND NEUROLOGICAL ISSUES. RECENT STUDIES IMPLICATE GENE EXPRESSION CHANGES IN IMMUNE FUNCTION TO BE ASSOCIATED WITH GWI. SINCE DNA METHYLATION CAN REGULATE SUCH CHANGES IN GENE EXPRESSION, AND DISRUPTION OF DNA METHYLATION PATTERN IS IMPLICATED IN VARIOUS IMMUNE AND NEUROLOGICAL DISEASES, WE AIMED TO STUDY THE DNA METHYLATION PATTERNS IN PERIPHERAL BLOOD MONONUCLEAR CELLS FROM GWI PATIENTS. GLOBAL DNA METHYLATION LEVELS WERE SIMILAR IN GWI PATIENTS AND CONTROLS. HOWEVER, THE GENOME-WIDE MICROARRAY TECHNOLOGY DETECTED 10,767 DIFFERENTIALLY METHYLATED CPG SITES ACROSS GENE REGULATORY ELEMENTS AND WITHIN CODING REGIONS. APPROXIMATELY 88% OF THEM WERE HYPERMETHYLATED IN GWI PATIENTS. THE SEPARATE ANALYSIS FOUND 776 DIFFERENTIALLY METHYLATED GENE PROMOTERS (DMP), WHICH WERE PREDOMINANTLY HYPERMETHYLATED. PYROSEQUENCING VALIDATION CONFIRMED MICROARRAY RESULTS. FUNCTIONAL ANALYSIS REVEALED THAT MAJORITY OF THE DMPS BELONGED TO GENES RESPONSIBLE FOR METABOLISM AND IMMUNE SYSTEM. THIS IS THE FIRST PILOT HUMAN STUDY CHARACTERIZING GENOME-WIDE EPIGENETIC CHANGES ASSOCIATED WITH GWI. IT SUGGESTS A SIGNIFICANT CONTRIBUTION OF EPIGENETIC DYSFUNCTION IN GWI. MOREOVER, IT SUPPORTS THE DYSREGULATION OF IMMUNE FUNCTION IN GWI. LASTLY, IT SUGGESTS STUDIES WITH THE LARGER COHORT TO VALIDATE OUR FINDINGS.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
19  2643  44 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
20  1988  46 EPIGENETIC ANALYSIS IN A MURINE GENETIC MODEL OF GULF WAR ILLNESS. OF THE NEARLY 1 MILLION MILITARY PERSONNEL WHO PARTICIPATED IN THE 1990-1991 GULF WAR, BETWEEN 25% AND 35% BECAME ILL WITH WHAT NOW IS REFERRED TO AS GULF WAR ILLNESS (GWI) BY THE DEPARTMENT OF DEFENSE. SYMPTOMS VARIED FROM GASTROINTESTINAL DISTRESS TO LETHARGY, MEMORY LOSS, INABILITY TO CONCENTRATE, DEPRESSION, RESPIRATORY, AND REPRODUCTIVE PROBLEMS. THE SYMPTOMS HAVE PERSISTED FOR 30 YEARS IN THOSE AFFLICTED BUT THE BASIS OF THE ILLNESS REMAINS LARGELY UNKNOWN. NERVE AGENTS AND OTHER CHEMICAL EXPOSURES IN THE WAR ZONE HAVE BEEN IMPLICATED BUT THE LONG-TERM EFFECTS OF THESE ACUTE EXPOSURES HAVE LEFT FEW IF ANY IDENTIFIABLE SIGNATURES. THE MAJOR AIM OF THIS STUDY IS TO ELUCIDATE THE POSSIBLE GENOMIC BASIS FOR THE PERSISTENCE OF SYMPTOMS, ESPECIALLY OF THE NEUROLOGICAL AND BEHAVIORAL EFFECTS. TO ADDRESS THIS, WE PERFORMED A WHOLE GENOME EPIGENETIC ANALYSIS OF THE PROPOSED CAUSE OF GWI, VIZ., EXPOSURE TO ORGANOPHOSPHATE NEUROTOXICANTS COMBINED WITH HIGH CIRCULATING GLUCOCORTICOIDS IN TWO INBRED MOUSE STRAINS, C57BL/6J AND DBA/2J. THE ANIMALS RECEIVED CORTICOSTERONE IN THEIR DRINKING WATER FOR 7 DAYS FOLLOWED BY INJECTION OF DIISOPROPYLFLUOROPHOSPHATE, A NERVE AGENT SURROGATE. SIX WEEKS AFTER DFP INJECTION, THE ANIMALS WERE EUTHANIZED AND MEDIAL PREFRONTAL CORTEX HARVESTED FOR GENOME-WIDE DNA METHYLATION ANALYSIS USING HIGH-THROUGHPUT SEQUENCING. WE OBSERVED 67 DIFFERENTIALLY METHYLATED GENES, NOTABLY AMONG THEM, TTLL7, AKR1C14, SLC44A4, AND RUSC2, ALL RELATED TO DIFFERENT SYMPTOMS OF GWI. OUR RESULTS SUPPORT PROOF OF PRINCIPLE OF GENETIC DIFFERENCES IN THE CHRONIC EFFECTS OF GWI-RELATED EXPOSURES AND MAY REVEAL WHY THE DISEASE HAS PERSISTED IN MANY OF THE NOW AGING GULF WAR VETERANS.	2023