1   919 128 CHRONIC HYPOXIA DURING GESTATION CAUSES EPIGENETIC REPRESSION OF THE ESTROGEN RECEPTOR-ALPHA GENE IN OVINE UTERINE ARTERIES VIA HEIGHTENED PROMOTER METHYLATION. ESTROGEN RECEPTOR-ALPHA (ERALPHA) PLAYS A KEY ROLE IN THE ADAPTATION OF INCREASED UTERINE BLOOD FLOW IN PREGNANCY. CHRONIC HYPOXIA IS A COMMON STRESS TO MATERNAL CARDIOVASCULAR HOMEOSTASIS AND CAUSES INCREASED RISK OF PREECLAMPSIA. STUDIES IN PREGNANT SHEEP DEMONSTRATED THAT HYPOXIA DURING GESTATION DOWNREGULATED ERALPHA GENE EXPRESSION IN UTERINE ARTERIES. THE PRESENT STUDY TESTED THE HYPOTHESIS THAT HYPOXIA CAUSES EPIGENETIC REPRESSION OF THE ERALPHA GENE IN UTERINE ARTERIES VIA HEIGHTENED PROMOTER METHYLATION. OVINE ERALPHA PROMOTER OF 2035 BP SPANNING FROM -2000 TO +35 OF THE TRANSCRIPTION START SITE WAS CLONED. NO ESTROGEN OR HYPOXIA-INDUCIBLE FACTOR RESPONSE ELEMENTS WERE FOUND AT THE PROMOTER. TWO TRANSCRIPTION FACTOR BINDING SITES, USF(-15) AND SP1(-520), CONTAINING CPG DINUCLEOTIDES WERE IDENTIFIED, WHICH HAD SIGNIFICANT EFFECTS ON THE PROMOTER ACTIVITY. THE USF ELEMENT BINDS TRANSCRIPTION FACTORS USF1 AND USF2, AND THE SP1 ELEMENT BINDS SP1, AS WELL AS ERALPHA THROUGH SP1. DELETION OF THE SP1 SITE ABROGATED 17BETA-ESTRADIOL-INDUCED INCREASE IN THE PROMOTER ACTIVITY. IN NORMOXIC CONTROL SHEEP, CPG METHYLATION AT THE SP1 BUT NOT THE USF SITE WAS SIGNIFICANTLY DECREASED IN UTERINE ARTERIES OF PREGNANT AS COMPARED WITH NONPREGNANT ANIMALS. IN PREGNANT SHEEP EXPOSED TO LONG-TERM HIGH-ALTITUDE HYPOXIA, CPG METHYLATION AT BOTH SP1 AND USF SITES IN UTERINE ARTERIES WAS SIGNIFICANTLY INCREASED. METHYLATION INHIBITED TRANSCRIPTION FACTOR BINDING AND THE PROMOTER ACTIVITY. THE RESULTS PROVIDE EVIDENCE OF HYPOXIA CAUSING HEIGHTENED PROMOTER METHYLATION AND RESULTANT ERALPHA GENE REPRESSION IN UTERINE ARTERIES AND SUGGEST NEW INSIGHTS OF MOLECULAR MECHANISMS LINKING GESTATIONAL HYPOXIA TO ABERRANT UTEROPLACENTAL CIRCULATION AND INCREASED RISK OF PREECLAMPSIA.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
2  6589  33 TUMOR NECROSIS FACTOR-ALPHA GENE PROMOTER METHYLATION IN JAPANESE ADULTS WITH CHRONIC PERIODONTITIS AND RHEUMATOID ARTHRITIS. BACKGROUND AND OBJECTIVE: OVER-EXPRESSION OF TUMOR NECROSIS FACTOR-ALPHA (TNF-ALPHA) PLAYS A PATHOLOGICAL ROLE IN CHRONIC PERIODONTITIS (CP) AND RHEUMATOID ARTHRITIS (RA), WHICH MIGHT BE REGULATED BY THE EPIGENETIC MECHANISM. THE AIM OF THE PRESENT STUDY WAS TO EVALUATE WHETHER THERE IS A UNIQUE METHYLATION PROFILE OF THE TNF-ALPHA GENE PROMOTER IN BLOOD CELLS OF INDIVIDUALS WITH CP AND RA. MATERIAL AND METHODS: THE STUDY PARTICIPANTS CONSISTED OF 30 JAPANESE ADULTS WITH RA (RA GROUP), 30 RACE-MATCHED ADULTS WITH CP ONLY (CP GROUP) AND 30 RACE-MATCHED HEALTHY CONTROLS (H GROUP). GENOMIC DNA ISOLATED FROM PERIPHERAL BLOOD WAS MODIFIED BY SODIUM BISULFITE AND ANALYZED, BY DIRECT SEQUENCING, TO INVESTIGATE DNA METHYLATION OF THE TNF-ALPHA GENE PROMOTER REGION. THE LEVEL OF TNF-ALPHA PRODUCED IN MONONUCLEAR CELLS STIMULATED WITH PORPHYROMONAS GINGIVALIS LIPOPOLYSACCHARIDE WAS DETERMINED USING ELISA. RESULTS: TWELVE CYTOSINE-GUANINE DINUCLEOTIDE (CPG) MOTIFS WERE IDENTIFIED IN THE TNF-ALPHA PROMOTER FRAGMENT FROM -343 TO +57 BP. THE CP GROUP SHOWED A SIGNIFICANTLY HIGHER METHYLATION RATE AND FREQUENCY AT -72 BP THAN THE H GROUP (P < 0.01). THE RA GROUP EXHIBITED SIGNIFICANTLY HIGHER METHYLATION RATES AT SEVEN CPG MOTIFS (-302, -163, -119, -72, -49, -38 AND +10 BP), AND SIGNIFICANTLY HIGHER METHYLATION FREQUENCIES AT SIX CPG MOTIFS (-163, -119, -72, -49, -38 AND +10 BP), THAN THE H GROUP (P < 0.01 FOR ALL COMPARISONS). THE LEVELS OF TNF-ALPHA PRODUCED WERE SIGNIFICANTLY DIFFERENT BETWEEN INDIVIDUALS WITH AND WITHOUT METHYLATION AT -163 BP (P = 0.03). CONCLUSION: THESE RESULTS SUGGEST THAT THE HYPERMETHYLATED STATUS OF CPG MOTIFS IN THE TNF-ALPHA GENE PROMOTER IN BLOOD CELLS MAY BE UNIQUE TO JAPANESE ADULTS WITH CP AND RA.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
3  2480  70 EPIGENETIC UPREGULATION OF LARGE-CONDUCTANCE CA2+-ACTIVATED K+ CHANNEL EXPRESSION IN UTERINE VASCULAR ADAPTATION TO PREGNANCY. OUR PREVIOUS STUDY DEMONSTRATED THAT PREGNANCY INCREASED LARGE-CONDUCTANCE CA(2+)-ACTIVATED POTASSIUM CHANNEL BETA1 SUBUNIT (BKBETA1) EXPRESSION AND LARGE-CONDUCTANCE CA(2+)-ACTIVATED POTASSIUM CHANNEL ACTIVITY IN UTERINE ARTERIES, WHICH WERE ABROGATED BY CHRONIC HYPOXIA. THE PRESENT STUDY TESTED THE HYPOTHESIS THAT PROMOTER METHYLATION/DEMETHYLATION IS A KEY MECHANISM IN EPIGENETIC REPROGRAMMING OF BKBETA1 EXPRESSION PATTERNS IN UTERINE ARTERIES. OVINE BKBETA1 PROMOTER OF 2315 BP SPANNING FROM -2211 TO +104 OF THE TRANSCRIPTION START SITE WAS CLONED, AND AN SP1-380 BINDING SITE THAT CONTAINS CPG DINUCLEOTIDE IN ITS CORE BINDING SEQUENCES WAS IDENTIFIED. SITE-DIRECTED DELETION OF THE SP1 SITE SIGNIFICANTLY DECREASED THE BKBETA1 PROMOTER ACTIVITY. ESTROGEN RECEPTOR-ALPHA BOUND TO THE SP1 SITE THROUGH TETHERING TO SP1 AND UPREGULATED THE EXPRESSION OF BKBETA1. THE SP1 BINDING SITE AT BKBETA1 PROMOTER WAS HIGHLY METHYLATED IN UTERINE ARTERIES OF NONPREGNANT SHEEP, AND METHYLATION INHIBITED TRANSCRIPTION FACTOR BINDING AND BKBETA1 PROMOTER ACTIVITY. PREGNANCY CAUSED A SIGNIFICANT DECREASE IN CPG METHYLATION AT THE SP1 BINDING SITE AND INCREASED SP1 BINDING TO THE BKBETA1 PROMOTER AND BKBETA1 MRNA ABUNDANCE. CHRONIC HYPOXIA DURING GESTATION ABROGATED THIS PREGNANCY-INDUCED DEMETHYLATION AND UPREGULATION OF BKBETA1 EXPRESSION. THE RESULTS PROVIDE EVIDENCE OF A NOVEL MECHANISM OF PROMOTER DEMETHYLATION IN PREGNANCY-INDUCED REPROGRAMMING OF LARGE-CONDUCTANCE CA(2+)-ACTIVATED POTASSIUM CHANNEL EXPRESSION AND FUNCTION IN UTERINE ARTERIES AND SUGGEST NEW INSIGHTS OF EPIGENETIC MECHANISMS LINKING GESTATIONAL HYPOXIA TO ABERRANT UTEROPLACENTAL CIRCULATION AND INCREASED RISK OF PREECLAMPSIA.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
4   849  37 CHILDHOOD TRAUMATIZATION IS ASSOCIATED WITH DIFFERENCES IN TRPA1 PROMOTER METHYLATION IN FEMALE PATIENTS WITH MULTISOMATOFORM DISORDER WITH PAIN AS THE LEADING BODILY SYMPTOM. BACKGROUND: THE CONSTRUCT OF MULTISOMATOFORM DISORDER (MSD) IS A COMMON POINT OF REFERENCE FOR PATIENTS IN DIFFERENT SOMATIC AND PSYCHOSOMATIC SPECIALTIES AND THEREFORE USEFUL IN STUDYING LARGE WELL-CHARACTERIZED COHORTS OF A PROTOTYPE OF A SOMATOFORM DISORDER AND IN PARALLEL AS A FUNCTIONAL SOMATIC SYNDROME (FSS). THIS DISORDER IS CHARACTERIZED BY DISTRESSING AND FUNCTIONALLY DISABLING SOMATIC SYMPTOMS WITH CHRONIC PAIN AS THE MOST FREQUENT AND CLINICALLY RELEVANT COMPLAINT. PAIN IS PERCEIVED BY NOCICEPTIVE NERVE FIBERS AND TRANSFERRED THROUGH THE GENERATION OF ACTION POTENTIALS BY DIFFERENT RECEPTOR MOLECULES KNOWN TO DETERMINE PAIN SENSITIVITY IN PATHOPHYSIOLOGICAL PROCESSES. PREVIOUS STUDIES HAVE SHOWN THAT FOR THE TRANSIENT RECEPTOR POTENTIAL ANKYRIN 1 (TRPA1), RECEPTOR METHYLATION OF A PARTICULAR CPG DINUCLEOTIDE IN THE PROMOTER REGION IS INVERSELY ASSOCIATED WITH BOTH HEAT PAIN AND PRESSURE PAIN THRESHOLDS. IN THIS STUDY, WE HYPOTHESIZED THAT TRPA1 PROMOTER METHYLATION REGULATES PAIN SENSITIVITY OF PATIENTS WITH MULTISOMATOFORM DISORDER (MSD). A COHORT OF 151 PATIENTS WITH MSD AND 149 MATCHED HEALTHY VOLUNTEERS WERE EVALUATED USING QUANTITATIVE SENSORY TESTING, CLINICAL AND PSYCHOMETRIC ASSESSMENT, AND METHYLATION ANALYSIS USING DNA ISOLATED FROM WHOLE BLOOD. RESULTS: WE FOUND CPG -628 TO BE CORRELATED WITH MECHANICAL PAIN THRESHOLD AND CPG -411 TO BE CORRELATED WITH MECHANICAL PAIN THRESHOLD IN FEMALE VOLUNTEERS, I.E., HIGHER METHYLATION LEVELS LEAD TO HIGHER PAIN THRESHOLDS. A NOVEL FINDING IS THAT METHYLATION LEVELS WERE SIGNIFICANTLY DIFFERENT BETWEEN PATIENTS WITH NO AND SEVERE LEVELS OF CHILDHOOD TRAUMA. CPG METHYLATION ALSO CORRELATED WITH PSYCHOMETRIC ASSESSMENT OF PAIN AND PAIN LEVELS RATED ON A VISUAL ANALOG SCALE. CONCLUSION: OUR FINDINGS SUPPORT THE HYPOTHESIS THAT EPIGENETIC REGULATION OF TRPA1 PLAYS A ROLE IN MECHANICAL PAIN SENSITIVITIES IN HEALTHY VOLUNTEERS. THEY FURTHER PROVIDE EVIDENCE FOR THE POSSIBLE INFLUENCE OF CHILDHOOD TRAUMATIC EXPERIENCES ON THE EPIGENETIC REGULATION OF TRPA1 IN PATIENTS WITH MSD.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
5    63  33 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
6  2078  32 EPIGENETIC DIVERGENCE IN THE TRPA1 PROMOTER CORRELATES WITH PRESSURE PAIN THRESHOLDS IN HEALTHY INDIVIDUALS. THE EXPRESSION PATTERN OF IMPORTANT TRANSDUCTION MOLECULES IN NOCICEPTIVE SENSORY NEURONS IS LIKELY TO DICTATE PAIN SENSITIVITY. WHILE THIS NOTION IS WELL ESTABLISHED FOR INCREASED PAIN SENSITIVITIES UNDER CONDITIONS LIKE INFLAMMATION AND NEUROPATHY, LESS IS KNOWN AS TO WHICH MOLECULES ARE DEFINING INTERINDIVIDUAL DIFFERENCES IN PAIN SENSITIVITY IN HEALTHY SUBJECTS. A GENOME-WIDE METHYLATION ANALYSIS ON MONOZYGOTIC TWINS FOUND THAT METHYLATION OF A CPG DINUCLEOTIDE IN THE PROMOTER OF TRANSIENT RECEPTOR POTENTIAL ANKYRIN 1 (TRPA1) IS INVERSELY ASSOCIATED WITH THE THRESHOLD FOR HEAT-INDUCED PAIN. SEVERAL IN VITRO STUDIES ALSO SUGGEST THAT TRPA1 MEDIATES MECHANICAL SENSITIVITY OF SENSORY AFFERENTS, THUS POTENTIALLY MEDIATING PRESSURE-EVOKED PAIN. IN THE PRESENT STUDY, WE THEREFORE INVESTIGATED THE EPIGENETIC PREDISPOSITION FOR PRESSURE PAIN BY ANALYZING THE METHYLATION STATUS OF 47 CPG SITES IN THE PROMOTER REGION OF TRPA1. USING DNA FROM WHOLE-BLOOD SAMPLES OF 75 HEALTHY VOLUNTEERS, WE FOUND THAT THE SAME CPG SITE PREVIOUSLY FOUND TO AFFECT THE THRESHOLD FOR HEAT-EVOKED PAIN IS HYPERMETHYLATED IN SUBJECTS WITH A LOW THRESHOLD FOR PRESSURE PAIN. WE ALSO FOUND GENDER DIFFERENCES, WITH FEMALES DISPLAYING HIGHER METHYLATION RATES COMBINED WITH HIGHER PRESSURE PAIN SENSITIVITIES AS COMPARED WITH MALES. IN CONCLUSION, OUR FINDINGS SUPPORT THE NOTION THAT EPIGENETIC REGULATION OF TRPA1 SEEMS TO REGULATE THERMAL AND MECHANICAL PAIN SENSITIVITIES.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
7  2374  44 EPIGENETIC REGULATION OF TNFA EXPRESSION IN PERIODONTAL DISEASE. BACKGROUND: TUMOR NECROSIS FACTOR-ALPHA (TNF-ALPHA) PLAYS A CENTRAL ROLE IN THE MOLECULAR PATHOGENESIS OF PERIODONTAL DISEASE. HOWEVER, THE EPIGENETIC REGULATION ATTRIBUTABLE TO MICROBIAL AND INFLAMMATORY SIGNALS AT THE BIOFILM-GINGIVAL INTERFACE ARE POORLY UNDERSTOOD. IN THIS STUDY, THE DNA METHYLATION ALTERATION WITHIN THE TNFA PROMOTER IN HUMAN GINGIVAL BIOPSIES FROM DIFFERENT STAGES OF PERIODONTAL DISEASE IS INVESTIGATED AND THE REGULATORY MECHANISM OF TNFA TRANSCRIPTION BY DNA METHYLATION IS EXPLORED. METHODS: GINGIVAL BIOPSIES WERE OBTAINED FROM 17 PATIENTS WITH CHRONIC PERIODONTITIS (CP) AND 18 PERIODONTALLY HEALTHY INDIVIDUALS. ANOTHER 11 INDIVIDUALS PARTICIPATED IN AN EXPERIMENTALLY INDUCED GINGIVITIS STUDY, AND GINGIVAL BIOPSIES WERE COLLECTED AT THE BASELINE, INDUCTION, AND RESOLUTION PHASE. TO CONFIRM THAT TNFA PROMOTER METHYLATION MODULATED TNFA TRANSCRIPTION, THP.1 CELLS WERE TREATED WITH A DNA METHYLTRANSFERASE INHIBITOR, 5-AZA-2-DEOXYCYTIDINE (5-AZA-2DC), AND AN RAW294.7 CELL LINE TRANSFECTED WITH A TNFA PROMOTER-SPECIFIC LUCIFERASE REPORTER SYSTEM WITH OR WITHOUT METHYLATION WAS USED. RESULTS: IN GINGIVAL BIOPSIES FROM INDIVIDUALS WITH SEVERE CP, TWO INDIVIDUAL CYTOSINE-GUANINE DINUCLEOTIDES (CPG SITES) WITHIN THE TNFA PROMOTER (AT -163 AND -161 BP) DISPLAYED INCREASED METHYLATION IN CP SAMPLES COMPARED TO THOSE WITH GINGIVAL HEALTH (16.1% +/- 5.1% VERSUS 11.0% +/- 4.6%, P = 0.02 AND 19.8% +/- 4.1% VERSUS 15.4% +/- 3.6%, P = 0.04, RESPECTIVELY). THE METHYLATION LEVEL AT -163 BP WAS INVERSELY ASSOCIATED WITH THE TRANSCRIPTION LEVEL OF TNFA (P = 0.018). HOWEVER, NO SIGNIFICANT DIFFERENCE IN THE TNFA PROMOTER METHYLATION PATTERN WAS OBSERVED IN SAMPLES BIOPSIED DURING THE INDUCTION OR RESOLUTION PHASE OF EXPERIMENTALLY INDUCED GINGIVITIS, WHICH REPRESENTED A REVERSIBLE PERIODONTAL LESION. THP.1 CELLS TREATED WITH 5-AZA-2DC DEMONSTRATED A TIME-DEPENDENT INCREASE IN TNFA MESSENGER LEVEL. IT WAS ALSO FOUND THAT THE LUCIFERASE ACTIVITY DECREASED 2.6-FOLD IN A CONSTRUCT CONTAINING AN IN VITRO METHYLATED TNFA PROMOTER WHEN COMPARED TO THE UNMETHYLATED INSERT (P = 0.03). CONCLUSION: ALTHOUGH THE BIOPSY SAMPLES REPRESENTED A MIXED CELL POPULATION, THE CHANGE IN PROMOTER METHYLATION STATUS IN CHRONIC PERIODONTAL DISEASE SUGGESTED THAT DNA METHYLATION MAY BE AN IMPORTANT REGULATORY MECHANISM IN CONTROLLING TNFA TRANSCRIPTIONAL EXPRESSION IN PERIODONTAL DISEASE.	2013	
                                                                                                                                                                                                                                                                             
8   500  24 ASSOCIATION BETWEEN NEUROPATHIC PAIN CHARACTERISTICS AND DNA METHYLATION OF TRANSIENT RECEPTOR POTENTIAL ANKYRIN 1 IN HUMAN PERIPHERAL BLOOD. ELUCIDATION OF EPIGENETIC MECHANISMS CORRELATING WITH NEUROPATHIC PAIN IN HUMANS IS CRUCIAL FOR THE PREVENTION AND TREATMENT OF THIS TREATMENT-RESISTANT PAIN STATE. IN THE PRESENT STUDY, ASSOCIATIONS BETWEEN NEUROPATHIC PAIN CHARACTERISTICS AND DNA METHYLATION OF THE TRANSIENT RECEPTOR POTENTIAL ANKYRIN 1 (TRPA1) GENE WERE EVALUATED IN CHRONIC PAIN PATIENTS AND PREOPERATIVE PATIENTS. PAIN AND PSYCHOLOGICAL STATES WERE PROSPECTIVELY ASSESSED IN PATIENTS WHO SUFFERED CHRONIC PAIN OR WERE SCHEDULED FOR THORACIC SURGERY. NEUROPATHIC CHARACTERISTICS WERE ASSESSED USING THE DOULEUR NEUROPATHIQUE 4 (DN4) QUESTIONNAIRE. DNA METHYLATION LEVELS OF THE CPG ISLANDS IN THE TRPA1 GENE WERE EXAMINED USING WHOLE BLOOD. FORTY-EIGHT ADULT PATIENTS WERE ENROLLED IN THIS STUDY. INCREASES IN DNA METHYLATION RATES AT CPG -51 SHOWED POSITIVE CORRELATIONS WITH INCREASES IN THE DN4 SCORE BOTH IN PREOPERATIVE AND CHRONIC PAIN PATIENTS. COMBINED METHYLATION RATES AT CPG -51 IN THESE PATIENTS ALSO SIGNIFICANTLY INCREASED TOGETHER WITH INCREASE IN DN4 SCORES. NEUROPATHIC PAIN CHARACTERISTICS ARE LIKELY ASSOCIATED WITH METHYLATION RATES AT THE PROMOTER REGION OF THE TRPA1 GENE IN HUMAN PERIPHERAL BLOOD.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
9  1580  33 DNA METHYLATION PROFILES ARE ASSOCIATED WITH COMPLEX REGIONAL PAIN SYNDROME AFTER TRAUMATIC INJURY. FACTORS CONTRIBUTING TO DEVELOPMENT OF COMPLEX REGIONAL PAIN SYNDROME (CRPS) ARE NOT FULLY UNDERSTOOD. THIS STUDY EXAMINED POSSIBLE EPIGENETIC MECHANISMS THAT MAY CONTRIBUTE TO CRPS AFTER TRAUMATIC INJURY. DNA METHYLATION PROFILES WERE COMPARED BETWEEN INDIVIDUALS DEVELOPING CRPS (N = 9) AND THOSE DEVELOPING NON-CRPS NEUROPATHIC PAIN (N = 38) AFTER UNDERGOING AMPUTATION FOLLOWING MILITARY TRAUMA. LINEAR MODELS FOR MICROARRAY (LIMMA) ANALYSES REVEALED 48 DIFFERENTIALLY METHYLATED CYTOSINE-PHOSPHATE-GUANINE DINUCLEOTIDE (CPG) SITES BETWEEN GROUPS (UNADJUSTED P'S < 0.005), WITH THE TOP GENE COL11A1 MEETING BONFERRONI-ADJUSTED P < 0.05. THE SECOND LARGEST DIFFERENTIAL METHYLATION WAS OBSERVED FOR THE HLA-DRB6 GENE, AN IMMUNE-RELATED GENE LINKED PREVIOUSLY TO CRPS IN A SMALL GENE EXPRESSION STUDY. FOR ALL BUT 7 OF THE SIGNIFICANT CPG SITES, THE CRPS GROUP WAS HYPOMETHYLATED. NUMEROUS FUNCTIONAL GENE ONTOLOGY-BIOLOGICAL PROCESS CATEGORIES WERE SIGNIFICANTLY ENRICHED (FALSE DISCOVERY RATE-ADJUSTED Q VALUE <0.15), INCLUDING MULTIPLE IMMUNE-RELATED CATEGORIES (EG, ACTIVATION OF IMMUNE RESPONSE, IMMUNE SYSTEM DEVELOPMENT, REGULATION OF IMMUNE SYSTEM PROCESSES, AND ANTIGEN PROCESSING AND PRESENTATION). DIFFERENTIALLY METHYLATED GENES WERE MORE HIGHLY CONNECTED IN HUMAN PROTEIN-PROTEIN NETWORKS THAN EXPECTED BY CHANCE (P < 0.05), SUPPORTING THE BIOLOGICAL RELEVANCE OF THE FINDINGS. RESULTS WERE VALIDATED IN AN INDEPENDENT SAMPLE LINKING A DNA BIOBANK WITH ELECTRONIC HEALTH RECORDS (N = 126 CRPS PHENOTYPE, N = 19,768 NON-CRPS CHRONIC PAIN PHENOTYPE). ANALYSES USING PREDIXCAN METHODOLOGY INDICATED DIFFERENCES IN THE GENETICALLY DETERMINED COMPONENT OF GENE EXPRESSION IN 7 OF 48 GENES IDENTIFIED IN METHYLATION ANALYSES (P'S < 0.02). RESULTS SUGGEST THAT IMMUNE- AND INFLAMMATORY-RELATED FACTORS MIGHT CONFER RISK OF DEVELOPING CRPS AFTER TRAUMATIC INJURY. VALIDATION FINDINGS DEMONSTRATE THE POTENTIAL OF USING ELECTRONIC HEALTH RECORDS LINKED TO DNA FOR GENOMIC STUDIES OF CRPS.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
10  3783  29 INTERFERON-GAMMA PROMOTER HYPOMETHYLATION AND INCREASED EXPRESSION IN CHRONIC PERIODONTITIS. AIM: THE GOAL OF THIS INVESTIGATION WAS TO DETERMINE WHETHER EPIGENETIC MODIFICATIONS IN THE IFNG PROMOTER ARE ASSOCIATED WITH AN INCREASE OF IFNG TRANSCRIPTION IN DIFFERENT STAGES OF PERIODONTAL DISEASES. MATERIALS AND METHODS: DNA WAS EXTRACTED FROM GINGIVAL BIOPSY SAMPLES COLLECTED FROM 47 TOTAL SITES FROM 47 DIFFERENT SUBJECTS: 23 PERIODONTALLY HEALTHY SITES, 12 EXPERIMENTALLY INDUCED GINGIVITIS SITES AND 12 CHRONIC PERIODONTITIS SITES. LEVELS OF DNA METHYLATION WITHIN THE IFNG PROMOTER CONTAINING SIX CPG DINUCLEOTIDES WERE DETERMINED USING PYROSEQUENCING TECHNOLOGY. INTERFERON GAMMA MRNA EXPRESSION WAS ANALYSED BY QUANTITATIVE POLYMERASE CHAIN REACTIONS USING ISOLATED RNA FROM PART OF THE BIOLOGICAL SAMPLES MENTIONED ABOVE. RESULTS: THE METHYLATION LEVEL OF ALL SIX ANALYSED CPG SITES WITHIN THE IFNG PROMOTER REGION IN THE PERIODONTITIS BIOPSIES 52% [INTERQUARTILE RANGE, IQR (43.8%, 63%)] WAS SIGNIFICANTLY LOWER THAN PERIODONTALLY HEALTHY SAMPLES 62% [IQR (51.3%, 74%)], P=0.007 AND GINGIVITIS BIOPSIES 63% [IQR (55%, 74%)], P=0.02. THE TRANSCRIPTIONAL LEVEL OF IFNG IN PERIODONTITIS BIOPSIES WAS 1.96-FOLD AND SIGNIFICANTLY HIGHER THAN TISSUES WITH PERIODONTAL HEALTH (P=0.04). ALTHOUGH THE MRNA LEVEL FROM EXPERIMENTAL GINGIVITIS SAMPLES EXHIBITED AN 8.5-FOLD INCREASE AS COMPARED WITH PERIODONTALLY HEALTHY SAMPLES, NO SIGNIFICANT METHYLATION DIFFERENCE WAS OBSERVED IN EXPERIMENTAL GINGIVITIS SAMPLE. CONCLUSIONS: A HYPOMETHYLATION PROFILE WITHIN IFNG PROMOTER REGION IS RELATED TO AN INCREASE OF IFNG TRANSCRIPTION PRESENT IN THE CHRONIC PERIODONTITIS BIOPSIES, WHILE SUCH AN INCREASE OF IFNG IN EXPERIMENTALLY INDUCED GINGIVITIS SEEMS INDEPENDENT OF PROMOTER METHYLATION ALTERATION.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
11   308  31 ALCOHOL AND DNA METHYLATION: AN EPIGENOME-WIDE ASSOCIATION STUDY IN BLOOD AND NORMAL BREAST TISSUE. THE BIOLOGICAL MECHANISMS DRIVING ASSOCIATIONS BETWEEN ALCOHOL CONSUMPTION AND CHRONIC DISEASES MIGHT INCLUDE EPIGENETIC MODIFICATION OF DNA METHYLATION. WE EXPLORED THE HYPOTHESIS THAT ALCOHOL CONSUMPTION IS ASSOCIATED WITH METHYLATION IN AN EPIGENOME-WIDE ASSOCIATION STUDY OF BLOOD AND NORMAL BREAST TISSUE DNA. INFINIUM HUMANMETHYLATION450 BEADCHIP (ILLUMINA INC., SAN DIEGO, CALIFORNIA) ARRAY DATA ON BLOOD DNA METHYLATION WAS EXAMINED IN A DISCOVERY SET OF 2,878 NON-HISPANIC WHITE WOMEN FROM THE SISTER STUDY (UNITED STATES, 2004-2015) WHO PROVIDED DETAILED QUESTIONNAIRE INFORMATION ON LIFETIME ALCOHOL USE. ROBUST LINEAR REGRESSION MODELING WAS USED TO IDENTIFY SIGNIFICANT ASSOCIATIONS (FALSE DISCOVERY RATE OF Q < 0.05) BETWEEN THE NUMBER OF ALCOHOLIC DRINKS PER WEEK AND DNA METHYLATION AT 5,458 CYTOSINE-PHOSPHATE-GUANINE (CPG) SITES. ASSOCIATIONS WERE REPLICATED (P < 0.05) FOR 677 CPGS IN AN INDEPENDENT SET OF 187 BLOOD DNA SAMPLES FROM THE SISTER STUDY AND FOR 628 CPGS IN AN INDEPENDENT SET OF 171 NORMAL BREAST DNA SAMPLES; 1,207 CPGS WERE REPLICATED IN EITHER BLOOD OR NORMAL BREAST, WITH 98 CPGS REPLICATED IN BOTH TISSUES. INDIVIDUAL GENE EFFECTS WERE NOTABLE FOR PHOSPHOGLYCERATE DEHYDROGENASE (PGHDH), PEPTIDYL-PROLYL CIS-TRANS ISOMERASE (PPIF), SOLUTE CARRIER 15 (SLC15), SOLUTE CARRIER FAMILY 43 MEMBER 1 (SLC43A1), AND SOLUTE CARRIER FAMILY 7 MEMBER 11 (SLC7A11). WE ALSO FOUND THAT HIGH ALCOHOL CONSUMPTION WAS ASSOCIATED WITH SIGNIFICANTLY LOWER GLOBAL METHYLATION AS MEASURED BY THE AVERAGE OF CPGS ON THE ENTIRE ARRAY.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
12  2762  26 EXPRESSION OF TET2 ENZYME INDICATES ENHANCED EPIGENETIC MODIFICATION OF CELLS IN PERIODONTITIS. DNA METHYLATION IS AN IMPORTANT EPIGENETIC MECHANISM INVOLVED IN THE REGULATION OF GENE EXPRESSION, AND A REDUCTION IN DNA METHYLATION INFLUENCES CELL-CYCLE PROGRESSION AND CELL DIFFERENTIATION IN INFLAMMATORY CELLS. THE AIM OF THE PRESENT STUDY WAS TO ANALYZE THE DNA-METHYLATION PATTERN AT LOCAL AND GLOBAL/SYSTEMIC LEVELS IN PATIENTS WITH PERIODONTITIS AND GINGIVITIS. TWENTY-ONE SUBJECTS WITH GENERALIZED, SEVERE PERIODONTITIS AND 17 SUBJECTS WITH GINGIVAL INFLAMMATION BUT NO ATTACHMENT LOSS WERE RECRUITED. GINGIVAL BIOPSIES AND PERIPHERAL BLOOD SAMPLES WERE COLLECTED AND PREPARED FOR IMMUNOHISTOCHEMICAL ANALYSIS OF 5-METHYLCYTOSINE (5MC), 5-HYDROXYMETHYLCYTOSINE (5HMC), TEN-ELEVEN TRANSLOCATION 2 (TET2), AND DNA METHYLTRANSFERASE 1 (DNMT1). WHILST A SIMILAR PATTERN FOR 5MC AND 5HMC DNA METHYLATION WAS FOUND IN BOTH TYPES OF LESIONS, A SIGNIFICANTLY LARGER PROPORTION OF TET2-POSITIVE CELLS WAS FOUND IN PERIODONTITIS LESIONS THAN IN GINGIVITIS LESIONS. QUANTITATIVE REAL-TIME PCR ANALYSIS SHOWED NO DIFFERENCES BETWEEN GINGIVITIS AND PERIODONTITIS LESIONS REGARDING EXPRESSION OF TET2 AND ISOCITRATE DEHYDROGENASE (IDH) GENES, WHILE THE GLOBAL LEVEL OF 5HMC WAS SIGNIFICANTLY HIGHER IN BLOOD THAN IN TISSUE IN PATIENTS WITH PERIODONTITIS. IT IS SUGGESTED THAT EPIGENETIC CHANGES ARE MORE COMMON IN PERIODONTITIS LESIONS THAN IN GINGIVITIS LESIONS AND THAT SUCH CHANGES ARE TISSUE SPECIFIC.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
13   101  31 A RAT METHYL-SEQ PLATFORM TO IDENTIFY EPIGENETIC CHANGES ASSOCIATED WITH STRESS EXPOSURE. AS GENOMES OF A WIDER VARIETY OF ANIMALS BECOME AVAILABLE, THERE IS AN INCREASING NEED FOR TOOLS THAT CAN CAPTURE DYNAMIC EPIGENETIC CHANGES IN THESE ANIMAL MODELS. THE RAT IS ONE PARTICULAR MODEL ANIMAL WHERE AN EPIGENETIC TOOL CAN COMPLEMENT MANY PHARMACOLOGICAL AND BEHAVIORAL STUDIES TO PROVIDE INSIGHTFUL MECHANISTIC INFORMATION. TO THIS END, WE ADAPTED THE SURESELECT TARGET CAPTURE SYSTEM (REFERRED TO AS METHYL-SEQ) FOR THE RAT, WHICH CAN ASSESS DNA METHYLATION LEVELS ACROSS THE RAT GENOME. THE RAT DESIGN TARGETED PROMOTERS, CPG ISLANDS, ISLAND SHORES, AND GC-RICH REGIONS FROM ALL REFSEQ GENES. TO IMPLEMENT THE PLATFORM ON A RAT EXPERIMENT, MALE SPRAGUE DAWLEY RATS WERE EXPOSED TO CHRONIC VARIABLE STRESS FOR 3 WEEKS, AFTER WHICH BLOOD SAMPLES WERE COLLECTED FOR GENOMIC DNA EXTRACTION. METHYL-SEQ LIBRARIES WERE CONSTRUCTED FROM THE RAT DNA SAMPLES BY SHEARING, ADAPTER LIGATION, TARGET ENRICHMENT, BISULFITE CONVERSION, AND MULTIPLEXING. LIBRARIES WERE SEQUENCED ON A NEXT-GENERATION SEQUENCING PLATFORM AND THE SEQUENCED READS WERE ANALYZED TO IDENTIFY DMRS BETWEEN DNA OF STRESSED AND UNSTRESSED RATS. TOP CANDIDATE DMRS WERE INDEPENDENTLY VALIDATED BY BISULFITE PYROSEQUENCING TO CONFIRM THE ROBUSTNESS OF THE PLATFORM. RESULTS DEMONSTRATE THAT THE RAT METHYL-SEQ PLATFORM IS A USEFUL EPIGENETIC TOOL THAT CAN CAPTURE METHYLATION CHANGES INDUCED BY EXPOSURE TO STRESS.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
14  3460  34 HYPOMETHYLATION OF THE IL8 PROMOTER IN NASAL EPITHELIAL CELLS OF PATIENTS WITH CHRONIC RHINOSINUSITIS WITH NASAL POLYPS. BACKGROUND: IL-8 IS AN IMPORTANT CHEMOKINE IMPLICATED IN THE PATHOGENESIS OF CHRONIC RHINOSINUSITIS (CRS), BUT LITTLE IS KNOWN ABOUT EPIGENETIC REGULATION OF IL8 IN THE PATHOGENESIS OF CRS. OBJECTIVE: WE SOUGHT TO INVESTIGATE THE RELATIONSHIP BETWEEN THE DNA METHYLATION LEVEL IN THE IL8 PROXIMAL PROMOTER AND CRS IN HAN CHINESE SUBJECTS. METHODS: PATIENTS WITH CHRONIC RHINOSINUSITIS WITH NASAL POLYPS (CRSWNP; N = 187), PATIENTS WITH CHRONIC RHINOSINUSITIS WITHOUT NASAL POLYPS (CRSSNP; N = 89), AND CONTROL SUBJECTS (N = 57) WERE ENROLLED IN 2 INDEPENDENT COHORTS. PURIFIED HUMAN NASAL EPITHELIAL CELLS FROM EACH PARTICIPANT WERE ASSESSED FOR PERCENTAGE DNA METHYLATION OF CPG SITES IN THE IL8 PROXIMAL PROMOTER BY USING BISULFITE PYROSEQUENCING AND FOR FUNCTIONAL ASPECTS OF METHYLATION STATUS BY USING IN VITRO ASSAYS. RESULTS: DNA METHYLATION OF CPG SITES 1, 2, AND 3, RESPECTIVELY, IN THE IL8 PROXIMAL PROMOTER WAS SIGNIFICANTLY DECREASED IN HUMAN NASAL EPITHELIAL CELLS OF PATIENTS WITH CRSWNP COMPARED WITH THAT IN PATIENTS WITH CRSSNP (P < .001) AND CONTROL SUBJECTS (P < .001). PERCENTAGE OF DNA METHYLATION OF THE CPG3 SITE WAS CORRELATED NEGATIVELY WITH BOTH TISSUE EOSINOPHILIC CATIONIC PROTEIN (P < .01) AND MYELOPEROXIDASE (P < .05) LEVELS. IL-1BETA (P < .001) AND TNF-ALPHA (P < .01) SIGNIFICANTLY INCREASED IL8 EXPRESSION ACCOMPANIED BY A REDUCTION IN METHYLATION AT THE CPG3 SITE (P < .001). ELECTROPHORETIC MOBILITY SHIFT ASSAYS DEMONSTRATED THAT METHYLATION STATUS OF CPG3 CHANGED THE BINDING OF OCTAMER-BINDING TRANSCRIPTION FACTOR 1 AND NUCLEAR FACTOR KAPPAB. CONCLUSION: DECREASED DNA METHYLATION OF PARTICULARLY CPG SITES IN THE IL8 PROXIMAL PROMOTER MIGHT PLAY A ROLE IN THE PATHOGENESIS OF CRSWNP.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
15  1620  35 DNA METHYLTRANSFERASE-MEDIATED TRANSCRIPTIONAL SILENCING IN MALIGNANT GLIOMA: A COMBINED WHOLE-GENOME MICROARRAY AND PROMOTER ARRAY ANALYSIS. EPIGENETIC INACTIVATION OF TUMOR SUPPRESSOR GENES IS A COMMON FEATURE IN HUMAN CANCER. PROMOTER HYPERMETHYLATION AND HISTONE DEACETYLATION ARE REVERSIBLE EPIGENETIC MECHANISMS ASSOCIATED WITH TRANSCRIPTIONAL REGULATION. DNA METHYLTRANSFERASES (DNMT1 AND DNMT3B) REGULATE AND MAINTAIN PROMOTER METHYLATION AND ARE OVEREXPRESSED IN HUMAN CANCER. WE PERFORMED WHOLE-GENOME MICROARRAY ANALYSIS TO IDENTIFY GENES WITH ALTERED EXPRESSION AFTER RNAI-INDUCED SUPPRESSION OF DNMT IN A GLIOBLASTOMA MULTIFORME (GBM) CELL LINE. WE THEN IDENTIFIED GENES WITH BOTH DECREASED EXPRESSION AND EVIDENCE OF PROMOTER CPG ISLAND HYPERMETHYLATION IN GBM TISSUE SAMPLES USING A COMBINED WHOLE-GENOME MICROARRAY TRANSCRIPTOME ANALYSIS IN CONJUNCTION WITH A PROMOTER ARRAY ANALYSIS AFTER DNA IMMUNOPRECIPITATION WITH ANTI-5-METHYLCYTIDINE. DNMT1 AND 3B KNOCKDOWN RESULTED IN THE RESTORED EXPRESSION OF 308 GENES THAT ALSO CONTAINED PROMOTER REGION HYPERMETHYLATION. OF THESE, 43 WERE ALSO FOUND TO BE DOWNREGULATED IN GBM TISSUE SAMPLES. THREE DOWNREGULATED GENES WITH HYPERMETHYLATED PROMOTERS AND RESTORED EXPRESSION IN RESPONSE TO ACUTE DNMT SUPPRESSION WERE ASSAYED FOR METHYLATION CHANGES USING BISULFITE SEQUENCE ANALYSIS OF THE PROMOTER REGION AFTER CHRONIC DNMT SUPPRESSION. RESTORATION OF GENE EXPRESSION WAS NOT ASSOCIATED WITH CHANGES IN PROMOTER REGION METHYLATION, BUT RATHER WITH CHANGES IN HISTONE METHYLATION AND CHROMATIN CONFORMATION. TWO OF THE IDENTIFIED GENES EXHIBITED GROWTH SUPPRESSIVE ACTIVITY IN IN VITRO ASSAYS. COMBINING TARGETED GENETIC MANIPULATIONS WITH COMPREHENSIVE GENOMIC AND EXPRESSION ANALYSES PROVIDES A POTENTIALLY POWERFUL NEW APPROACH FOR IDENTIFYING EPIGENETICALLY REGULATED GENES IN GBM.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
16  2633  30 EPIGENOME-WIDE DNA METHYLATION PATTERNS ASSOCIATED WITH FATIGUE IN PRIMARY SJOGREN'S SYNDROME. OBJECTIVE: CHRONIC FATIGUE IS A COMMON, DISABLING AND POORLY UNDERSTOOD PHENOMENON. RECENT STUDIES INDICATE THAT EPIGENETIC MECHANISMS MAY BE INVOLVED IN THE EXPRESSION OF FATIGUE, A PROMINENT FEATURE OF PRIMARY SS (PSS). THE AIM OF THIS STUDY WAS TO INVESTIGATE WHETHER DNA METHYLATION PROFILES OF WHOLE BLOOD ARE ASSOCIATED WITH FATIGUE IN PATIENTS WITH PSS. METHODS: FORTY-EIGHT PSS PATIENTS WITH HIGH (N = 24) OR LOW (N = 24) FATIGUE AS MEASURED BY A VISUAL ANALOGUE SCALE WERE INCLUDED. GENOME-WIDE DNA METHYLATION WAS INVESTIGATED USING THE ILLUMINA HUMANMETHYLATION450 BEADCHIP ARRAY. AFTER QUALITY CONTROL, A TOTAL OF 383 358 CYTOSINE-PHOSPHATE-GUANINE (CPG) SITES REMAINED FOR FURTHER ANALYSIS. AGE, SEX AND DIFFERENTIAL CELL COUNT ESTIMATES WERE INCLUDED AS COVARIATES IN THE ASSOCIATION MODEL. A FALSE DISCOVERY RATE-CORRECTED P < 0.05 WAS CONSIDERED SIGNIFICANT, AND A CUT-OFF OF 3% AVERAGE DIFFERENCE IN METHYLATION LEVELS BETWEEN HIGH- AND LOW-FATIGUE PATIENTS WAS APPLIED. RESULTS: A TOTAL OF 251 DIFFERENTIALLY METHYLATED CPG SITES WERE ASSOCIATED WITH FATIGUE. THE CPG SITE WITH THE MOST PRONOUNCED HYPOMETHYLATION IN PSS HIGH FATIGUE ANNOTATED TO THE SBF2-ANTISENSE RNA1 GENE. THE MOST DISTINCT HYPERMETHYLATION WAS OBSERVED AT A CPG SITE ANNOTATED TO THE LYMPHOTOXIN ALPHA GENE. FUNCTIONAL PATHWAY ANALYSIS OF GENES WITH DIFFERENTLY METHYLATED CPG SITES IN SUBJECTS WITH HIGH VS LOW FATIGUE REVEALED ENRICHMENT IN SEVERAL PATHWAYS ASSOCIATED WITH INNATE AND ADAPTIVE IMMUNITY. CONCLUSION: SOME GENES INVOLVED IN REGULATION OF THE IMMUNE SYSTEM AND IN INFLAMMATION ARE DIFFERENTLY METHYLATED IN PSS PATIENTS WITH HIGH VS LOW FATIGUE. THESE FINDINGS POINT TO FUNCTIONAL NETWORKS THAT MAY UNDERLIE FATIGUE. EPIGENETIC CHANGES COULD CONSTITUTE A FATIGUE-REGULATING MECHANISM IN PSS.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
17   812  34 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	

18  1161  40 CONTINUOUS DEVELOPMENTAL AND EARLY LIFE TRICHLOROETHYLENE EXPOSURE PROMOTED DNA METHYLATION ALTERATIONS IN POLYCOMB PROTEIN BINDING SITES IN EFFECTOR/MEMORY CD4(+) T CELLS. TRICHLOROETHYLENE (TCE) IS AN INDUSTRIAL SOLVENT AND DRINKING WATER POLLUTANT ASSOCIATED WITH CD4(+) T CELL-MEDIATED AUTOIMMUNITY. IN OUR MOUSE MODEL, DISCONTINUATION OF TCE EXPOSURE DURING ADULTHOOD AFTER DEVELOPMENTAL EXPOSURE DID NOT PREVENT IMMUNOTOXICITY. TO DETERMINE WHETHER PERSISTENT EFFECTS WERE LINKED TO EPIGENETIC CHANGES WE CONDUCTED WHOLE GENOME REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS) TO EVALUATE METHYLATION OF CPG SITES IN AUTOSOMAL CHROMOSOMES IN ACTIVATED EFFECTOR/MEMORY CD4(+) T CELLS. FEMALE MRL+/+ MICE WERE EXPOSED TO VEHICLE CONTROL OR TCE IN THE DRINKING WATER FROM GESTATION UNTIL ~37 WEEKS OF AGE [POSTNATAL DAY (PND) 259]. IN A SUBSET OF MICE, TCE EXPOSURE WAS DISCONTINUED AT ~22 WEEKS OF AGE (PND 154). AT PND 259, RRBS ASSESSMENT REVEALED MORE GLOBAL METHYLATION CHANGES IN THE CONTINUOUS EXPOSURE GROUP VS. THE DISCONTINUOUS EXPOSURE GROUP. A MAJORITY OF THE DIFFERENTIALLY METHYLATED CPG REGIONS (DMRS) ACROSS PROMOTERS, ISLANDS, AND REGULATORY ELEMENTS WERE HYPERMETHYLATED (~90%). HOWEVER, CONTINUOUS DEVELOPMENTAL TCE EXPOSURE ALTERED THE METHYLATION OF 274 CPG SITES IN PROMOTERS AND CPG ISLANDS. IN CONTRAST, ONLY 4 CPG ISLAND REGIONS WERE DIFFERENTIALLY METHYLATED (HYPERMETHYLATED) IN THE DISCONTINUOUS GROUP. INTERESTINGLY, 2 OF THESE 4 SITES WERE ALSO HYPERMETHYLATED IN THE CONTINUOUS EXPOSURE GROUP, AND BOTH OF THESE ISLAND REGIONS ARE ASSOCIATED WITH LYSINE 27 ON HISTONE H3 (H3K27) INVOLVED IN POLYCOMB COMPLEX-DEPENDENT TRANSCRIPTIONAL REPRESSION VIA H3K27 TRI-METHYLATION. CPG SITES WERE OVERLAPPED WITH THE OPEN REGULATORY ANNOTATION DATABASE. UNLIKE THE DISCONTINUOUS GROUP, CONTINUOUS TCE TREATMENT RESULTED IN 129 DMRS INCLUDING 12 UNIQUE TRANSCRIPTION FACTORS AND REGULATORY ELEMENTS; 80% OF WHICH WERE ENRICHED FOR ONE OR MORE POLYCOMB GROUP (PCG) PROTEIN BINDING REGIONS (I.E., SUZ12, EZH2, JARID2, AND MTF2). PATHWAY ANALYSIS OF THE DMRS INDICATED THAT TCE PRIMARILY ALTERED THE METHYLATION OF GENES ASSOCIATED WITH REGULATION OF CELLULAR METABOLISM AND CELL SIGNALING. THE RESULTS DEMONSTRATED THAT CONTINUOUS DEVELOPMENTAL EXPOSURE TO TCE DIFFERENTIALLY METHYLATED BINDING SITES OF PCG PROTEINS IN EFFECTOR/MEMORY CD4(+) CELLS. THERE WERE MINIMAL YET POTENTIALLY BIOLOGICALLY SIGNIFICANT EFFECTS THAT OCCURRED WHEN EXPOSURE WAS DISCONTINUED. THESE RESULTS POINT TOWARD A NOVEL MECHANISM BY WHICH CHRONIC DEVELOPMENTAL TCE EXPOSURE MAY ALTER TERMINALLY DIFFERENTIATED CD4(+) T CELL FUNCTION IN ADULTHOOD.	2019	
                                                                                            
19  2079  26 EPIGENETIC DNA METHYLATION CHANGES ASSOCIATED WITH HEADACHE CHRONIFICATION: A RETROSPECTIVE CASE-CONTROL STUDY. BACKGROUND THE BIOLOGICAL MECHANISMS OF HEADACHE CHRONIFICATION ARE POORLY UNDERSTOOD. WE AIMED TO IDENTIFY CHANGES IN DNA METHYLATION ASSOCIATED WITH THE TRANSFORMATION FROM EPISODIC TO CHRONIC HEADACHE. METHODS PARTICIPANTS WERE RECRUITED FROM THE POPULATION-BASED NORWEGIAN HUNT STUDY. THIRTY-SIX FEMALE HEADACHE PATIENTS WHO TRANSFORMED FROM EPISODIC TO CHRONIC HEADACHE BETWEEN BASELINE AND FOLLOW-UP 11 YEARS LATER WERE MATCHED AGAINST 35 CONTROLS WITH EPISODIC HEADACHE. DNA METHYLATION WAS QUANTIFIED AT 485,000 CPG SITES, AND CHANGES IN METHYLATION LEVEL AT THESE SITES WERE COMPARED BETWEEN CASES AND CONTROLS BY LINEAR REGRESSION ANALYSIS. DATA WERE ANALYZED IN TWO STAGES (STAGES 1 AND 2) AND IN A COMBINED META-ANALYSIS. RESULTS NONE OF THE TOP 20 CPG SITES IDENTIFIED IN STAGE 1 REPLICATED IN STAGE 2 AFTER MULTIPLE TESTING CORRECTION. IN THE COMBINED META-ANALYSIS THE STRONGEST ASSOCIATED CPG SITES WERE RELATED TO SH2D5 AND NPTX2, TWO BRAIN-EXPRESSED GENES INVOLVED IN THE REGULATION OF SYNAPTIC PLASTICITY. FUNCTIONAL ENRICHMENT ANALYSIS POINTED TO PROCESSES INCLUDING CALCIUM ION BINDING AND ESTROGEN RECEPTOR PATHWAYS. CONCLUSION IN THIS FIRST GENOME-WIDE STUDY OF DNA METHYLATION IN HEADACHE CHRONIFICATION SEVERAL POTENTIALLY IMPLICATED LOCI AND PROCESSES WERE IDENTIFIED. THE STUDY EXEMPLIFIES THE USE OF PROSPECTIVELY COLLECTED POPULATION COHORTS TO SEARCH FOR EPIGENETIC MECHANISMS OF DISEASE.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
20   344  39 ALTERED BDNF METHYLATION IN PATIENTS WITH CHRONIC MUSCULOSKELETAL PAIN AND HIGH BIOPSYCHOSOCIAL COMPLEXITY. PURPOSE: THE INTERMED INSTRUMENT, WHICH WAS DEVELOPED TO MEASURE PATIENT'S BIOPSYCHOSOCIAL (BPS) COMPLEXITY, REPRESENTS A POWERFUL DIAGNOSTIC AND THERAPEUTIC TOOL. EPIGENETIC CHANGES ARE THE INTERFACE BETWEEN SIGNALS FROM THE ENVIRONMENT AND GENETIC MODIFICATIONS, AFFECTING GENE EXPRESSION, IN PARTICULAR, BY DNA METHYLATION OF CPG DINUCLEOTIDES IN PROMOTOR REGIONS OF THE CORRESPONDING GENES. THE BRAIN-DERIVED NEUROTROPHIC FACTOR (BDNF) GENE PLAYS A CRUCIAL ROLE IN THE CENTRAL SENSITIZATION (CS) OF PAIN. IN THIS STUDY, WE HYPOTHESIZED THAT CHRONIC PAIN MODIFIES THE METHYLATION LEVELS OF THE BDNF GENE IN A MANNER THAT IS INTERCONNECTED WITH THE BPS STATUS. PATIENTS AND METHODS: FIFTY-EIGHT CHRONIC MUSCULOSKELETAL PAIN PATIENTS (CMSP) WERE ENROLLED IN THE STUDY. DNA WAS EXTRACTED FROM BLOOD SAMPLES, THE METHYLATION LEVELS OF 13 CPG SITES IN THE BDNF PROMOTER WERE MEASURED BY PYROSEQUENCING, AND ASSOCIATION STUDIES WITH VARIOUS PATIENT PARAMETERS AND THE INTERMED SCORES WERE PERFORMED. RESULTS: INTERESTINGLY, A NEGATIVE CORRELATION (-0.40) WAS FOUND BETWEEN THE TOTAL INTERMED SCORES AND THE AVERAGE CPG METHYLATION VALUES OF THE BDNF GENE, BUT NO CORRELATION WAS OBSERVED WITH THE SEVERITY OF PAIN, DEGREE OF ANXIETY, DEPRESSION, OR KINESIOPHOBIA AND CATASTROPHISM. MOREOVER, THE ASSOCIATION WAS INDEPENDENT OF AGE, SEX AND LEVEL OF COMORBIDITIES. CONCLUSION: THIS RESULT SHOWS THAT CMSP, IN ASSOCIATION WITH ITS BIOPSYCHOSOCIAL CONTEXT, EPIGENETICALLY DECREASES THE DEGREE OF METHYLATION OF THE BDNF PROMOTER AND SHOULD THEREFORE INCREASE THE LEVEL OF BDNF TRANSCRIPTION. IT ALSO SUGGESTS A ROLE OF THE INTERMED TOOL TO DETECT A RELATIONSHIP BETWEEN THE BPS COMPLEXITY AND THE EPIGENETIC CONTROL OF A TARGET GENE. THE POSSIBLE UPREGULATION OF BDNF EXPRESSION MIGHT BE, AT LEAST IN PART, THE SIGNAL FOR CHRONIC PAIN-INDUCED CENTRAL SENSITIZATION (CS). THIS COULD PARTLY EXPLAIN WHY PATIENTS WITH A HIGHER LEVEL OF COMPLEXITY FEEL MORE PAIN THAN THOSE WITH LOWER COMPLEXITY.	2020