1  972 143 CHRONIC OBSTRUCTIVE PULMONARY DISEASE IS ASSOCIATED WITH EPIGENOME-WIDE DIFFERENTIAL METHYLATION IN BAL LUNG CELLS. DNA METHYLATION PATTERNS IN CHRONIC PULMONARY OBSTRUCTIVE DISEASE (COPD) MIGHT OFFER NEW INSIGHTS INTO DISEASE PATHOGENESIS. TO ASSESS METHYLATION PROFILES IN THE MAIN COPD TARGET ORGAN, WE PERFORMED AN EPIGENOME-WIDE ASSOCIATION STUDY ON BAL CELLS. BRONCHOSCOPIES WERE PERFORMED IN 18 SUBJECTS WITH COPD AND 15 CONTROL SUBJECTS (EX- AND CURRENT SMOKERS). DNA METHYLATION WAS MEASURED USING THE ILLUMINA METHYLATIONEPIC BEADCHIP KIT, COVERING MORE THAN 850,000 CPGS. DIFFERENTIALLY METHYLATED POSITIONS (DMPS) WERE EXAMINED FOR 1) ENRICHMENT IN PATHWAYS AND FUNCTIONAL GENE RELATIONSHIPS USING THE KYOTO ENCYCLOPEDIA OF GENES AND GENOMES AND GENE ONTOLOGY, 2) ACCELERATED AGING USING HORVATH'S EPIGENETIC CLOCK, 3) CORRELATION WITH GENE EXPRESSION, AND 4) COLOCALIZATION WITH GENETIC VARIATION. WE FOUND 1,155 BONFERRONI-SIGNIFICANT (P < 6.74 X 10(-8)) DMPS ASSOCIATED WITH COPD, MANY WITH LARGE EFFECT SIZES. FUNCTIONAL ANALYSIS IDENTIFIED BIOLOGICALLY PLAUSIBLE PATHWAYS AND GENE RELATIONSHIPS, INCLUDING ENRICHMENT FOR TRANSCRIPTION FACTOR ACTIVITY. STRONG CORRELATION WAS FOUND BETWEEN DNA METHYLATION AND CHRONOLOGICAL AGE BUT NOT BETWEEN COPD AND ACCELERATED AGING. FOR 79 UNIQUE DMPS, DNA METHYLATION CORRELATED SIGNIFICANTLY WITH GENE EXPRESSION IN BAL CELLS. THIRTY-NINE PERCENT OF DMPS WERE COLOCALIZED WITH COPD-ASSOCIATED SNPS. TO THE BEST OF OUR KNOWLEDGE, THIS IS THE FIRST EPIGENOME-WIDE ASSOCIATION STUDY OF COPD ON BAL CELLS, AND OUR ANALYSES REVEALED MANY DIFFERENTIAL METHYLATION SITES. INTEGRATION WITH MRNA DATA SHOWED A STRONG FUNCTIONAL READOUT FOR RELEVANT GENES, IDENTIFYING SITES WHERE DNA METHYLATION MIGHT DIRECTLY AFFECT EXPRESSION. ALMOST HALF OF DMPS WERE COLOCATED WITH SNPS IDENTIFIED IN PREVIOUS GENOME-WIDE ASSOCIATION STUDIES OF COPD, SUGGESTING JOINT GENETIC AND EPIGENETIC PATHWAYS RELATED TO DISEASE.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
2  348  47 ALTERED DNA METHYLATION IS ASSOCIATED WITH ABERRANT GENE EXPRESSION IN PARENCHYMAL BUT NOT AIRWAY FIBROBLASTS ISOLATED FROM INDIVIDUALS WITH COPD. BACKGROUND: CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS A HETEROGENEOUS DISEASE OF THE LUNGS THAT IS CURRENTLY THE FOURTH LEADING CAUSE OF DEATH WORLDWIDE. GENETIC FACTORS ACCOUNT FOR ONLY A SMALL AMOUNT OF COPD RISK, BUT EPIGENETIC MECHANISMS, INCLUDING DNA METHYLATION, HAVE THE POTENTIAL TO MEDIATE THE INTERACTIONS BETWEEN AN INDIVIDUAL'S GENETICS AND ENVIRONMENTAL EXPOSURE. DNA METHYLATION IS HIGHLY CELL TYPE-SPECIFIC, AND INDIVIDUAL CELL TYPE STUDIES OF DNA METHYLATION IN COPD ARE SPARSE. FIBROBLASTS ARE PRESENT WITHIN THE AIRWAY AND PARENCHYMA OF THE LUNG AND CONTRIBUTE TO THE ABERRANT DEPOSITION OF EXTRACELLULAR MATRIX IN COPD. NO ASSESSMENT OR COMPARISON OF GENOME-WIDE DNA METHYLATION PROFILES IN THE AIRWAY AND PARENCHYMAL FIBROBLASTS FROM INDIVIDUALS WITH AND WITHOUT COPD HAS BEEN UNDERTAKEN. THESE DATA PROVIDE VALUABLE INSIGHT INTO THE MOLECULAR MECHANISMS CONTRIBUTING TO COPD AND THE DIFFERING PATHOLOGIES OF SMALL AIRWAYS DISEASE AND EMPHYSEMA IN COPD. METHODS: GENOME-WIDE DNA METHYLATION WAS EVALUATED AT OVER 485,000 CPG SITES USING THE ILLUMINA INFINIUM HUMANMETHYLATION450 BEADCHIP ARRAY IN THE AIRWAY (NON-COPD N = 8, COPD N = 7) AND PARENCHYMAL FIBROBLASTS (NON-COPD N = 17, COPD N = 29) ISOLATED FROM INDIVIDUALS WITH AND WITHOUT COPD. TARGETED GENE EXPRESSION WAS ASSESSED BY QPCR IN MATCHED RNA SAMPLES. RESULTS: DIFFERENTIALLY METHYLATED DNA REGIONS WERE IDENTIFIED BETWEEN CELLS ISOLATED FROM INDIVIDUALS WITH AND WITHOUT COPD IN BOTH AIRWAY AND PARENCHYMAL FIBROBLASTS. ONLY IN PARENCHYMAL FIBROBLASTS WAS DIFFERENTIAL DNA METHYLATION ASSOCIATED WITH DIFFERENTIAL GENE EXPRESSION. A SECOND ANALYSIS OF DIFFERENTIAL DNA METHYLATION VARIABILITY IDENTIFIED 359 INDIVIDUAL DIFFERENTIALLY VARIABLE CPG SITES IN PARENCHYMAL FIBROBLASTS. NO DIFFERENTIALLY VARIABLE CPG SITES WERE IDENTIFIED IN THE AIRWAY FIBROBLASTS. FIVE DIFFERENTIALLY VARIABLE-METHYLATED CPG SITES, ASSOCIATED WITH THREE GENES, WERE SUBSEQUENTLY ASSESSED FOR GENE EXPRESSION DIFFERENCES. TWO GENES (OAT AND GRIK2) DISPLAYED SIGNIFICANTLY INCREASED GENE EXPRESSION IN CELLS ISOLATED FROM INDIVIDUALS WITH COPD. CONCLUSIONS: DIFFERENTIAL AND VARIABLE DNA METHYLATION WAS ASSOCIATED WITH COPD STATUS IN THE PARENCHYMAL FIBROBLASTS BUT NOT AIRWAY FIBROBLASTS. ABERRANT DNA METHYLATION WAS ASSOCIATED WITH ALTERED GENE EXPRESSION IMPARTING BIOLOGICAL FUNCTION TO DNA METHYLATION CHANGES. CHANGES IN DNA METHYLATION ARE THEREFORE IMPLICATED IN THE MOLECULAR MECHANISMS UNDERLYING COPD PATHOGENESIS AND MAY REPRESENT NOVEL THERAPEUTIC TARGETS.	2018	

3 3079  53 GENOME-WIDE METHYLATION AND EXPRESSION ANALYSES REVEAL THE EPIGENETIC LANDSCAPE OF IMMUNE-RELATED DISEASES FOR TOBACCO SMOKING. BACKGROUND: SMOKING IS A MAJOR CAUSAL RISK FACTOR FOR LUNG CANCER, CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD), CARDIOVASCULAR DISEASE (CVD), AND IS THE MAIN PREVENTABLE CAUSE OF DEATHS IN THE WORLD. THE COMPONENTS OF CIGARETTE SMOKE ARE INVOLVED IN IMMUNE AND INFLAMMATORY PROCESSES, WHICH MAY INCREASE THE PREVALENCE OF CIGARETTE SMOKE-RELATED DISEASES. HOWEVER, THE UNDERLYING MOLECULAR MECHANISMS LINKING SMOKING AND DISEASES HAVE NOT BEEN WELL EXPLORED. THIS STUDY WAS AIMED TO DEPICT A GLOBAL MAP OF DNA METHYLATION AND GENE EXPRESSION CHANGES INDUCED BY TOBACCO SMOKING AND TO EXPLORE THE MOLECULAR MECHANISMS BETWEEN SMOKING AND HUMAN DISEASES THROUGH WHOLE-GENOME BISULFITE SEQUENCING (WGBS) AND RNA-SEQUENCING (RNA-SEQ). RESULTS: WE PERFORMED WGBS ON 72 SAMPLES (36 SMOKERS AND 36 NONSMOKERS) AND RNA-SEQ ON 75 SAMPLES (38 SMOKERS AND 37 NONSMOKERS), AND CYTOKINE IMMUNOASSAY ON PLASMA FROM 22 MALES (9 SMOKERS AND 13 NONSMOKERS) WHO WERE RECRUITED FROM THE CITY OF JINCHENG IN CHINA. BY COMPARING THE DATA OF THE TWO GROUPS, WE DISCOVERED A GENOME-WIDE METHYLATION LANDSCAPE OF DIFFERENTIALLY METHYLATED REGIONS (DMRS) ASSOCIATED WITH SMOKING. FUNCTIONAL ENRICHMENT ANALYSES REVEALED THAT BOTH SMOKING-RELATED HYPER-DMR GENES (DMGS) AND HYPO-DMGS WERE RELATED TO SYNAPSE-RELATED PATHWAYS, WHEREAS THE HYPO-DMGS WERE SPECIFICALLY RELATED TO CANCER AND ADDICTION. THE DIFFERENTIALLY EXPRESSED GENES (DEGS) REVEALED BY RNA-SEQ ANALYSIS WERE SIGNIFICANTLY ENRICHED IN THE "IMMUNOSUPPRESSION" PATHWAY. CORRELATION ANALYSIS OF DMRS WITH THEIR CORRESPONDING GENE EXPRESSION SHOWED THAT GENES AFFECTED BY TOBACCO SMOKING WERE MOSTLY RELATED TO IMMUNE SYSTEM DISEASES. FINALLY, BY COMPARING CYTOKINE CONCENTRATIONS BETWEEN SMOKERS AND NONSMOKERS, WE FOUND THAT VASCULAR ENDOTHELIAL GROWTH FACTOR (VEGF) WAS SIGNIFICANTLY UPREGULATED IN SMOKERS. CONCLUSIONS: IN SUM, WE FOUND THAT SMOKING-INDUCED DMRS HAVE DIFFERENT DISTRIBUTION PATTERNS IN HYPERMETHYLATED AND HYPOMETHYLATED AREAS BETWEEN SMOKERS AND NONSMOKERS. WE FURTHER IDENTIFIED AND VERIFIED SMOKING-RELATED DMGS AND DEGS THROUGH MULTI-OMICS INTEGRATION ANALYSIS OF DNA METHYLOME AND TRANSCRIPTOME DATA. THESE FINDINGS PROVIDE US A COMPREHENSIVE GENOMIC MAP OF THE MOLECULAR CHANGES INDUCED BY SMOKING WHICH WOULD ENHANCE OUR UNDERSTANDING OF THE HARMS OF SMOKING AND ITS RELATIONSHIP WITH DISEASES.	2021	
                                                                                                                                                                                                        
4 2418  38 EPIGENETIC SIGNATURE OF CHRONIC LOW BACK PAIN IN HUMAN T CELLS. OBJECTIVE: DETERMINE IF CHRONIC LOW BACK PAIN (LBP) IS ASSOCIATED WITH DNA METHYLATION SIGNATURES IN HUMAN T CELLS THAT WILL REVEAL NOVEL MECHANISMS AND POTENTIAL THERAPEUTIC TARGETS AND EXPLORE THE FEASIBILITY OF EPIGENETIC DIAGNOSTIC MARKERS FOR PAIN-RELATED PATHOPHYSIOLOGY. METHODS: GENOME-WIDE DNA METHYLATION ANALYSIS OF 850,000 CPG SITES IN WOMEN AND MEN WITH CHRONIC LBP AND PAIN-FREE CONTROLS WAS PERFORMED. T CELLS WERE ISOLATED (DISCOVERY COHORT, N = 32) AND USED TO IDENTIFY DIFFERENTIALLY METHYLATED CPG SITES, AND GENE ONTOLOGIES AND MOLECULAR PATHWAYS WERE IDENTIFIED. A POLYGENIC DNA METHYLATION SCORE FOR LBP WAS GENERATED IN BOTH WOMEN AND MEN. VALIDATION WAS PERFORMED IN AN INDEPENDENT COHORT (VALIDATION COHORT, N = 63) OF CHRONIC LBP AND HEALTHY CONTROLS. RESULTS: ANALYSIS WITH THE DISCOVERY COHORT REVEALED A TOTAL OF 2,496 AND 419 DIFFERENTIALLY METHYLATED CPGS IN WOMEN AND MEN, RESPECTIVELY. IN WOMEN, MOST OF THESE SITES WERE HYPOMETHYLATED AND ENRICHED IN GENES WITH FUNCTIONS IN THE EXTRACELLULAR MATRIX, IN THE IMMUNE SYSTEM (IE, CYTOKINES), OR IN EPIGENETIC PROCESSES. IN MEN, A UNIQUE CHRONIC LBP DNA METHYLATION SIGNATURE WAS IDENTIFIED CHARACTERIZED BY SIGNIFICANT ENRICHMENT FOR GENES FROM THE MAJOR HISTOCOMPATIBILITY COMPLEX. SEX-SPECIFIC POLYGENIC DNA METHYLATION SCORES WERE GENERATED TO ESTIMATE THE PAIN STATUS OF EACH INDIVIDUAL AND CONFIRMED IN THE VALIDATION COHORT USING PYROSEQUENCING. CONCLUSION: THIS STUDY REVEALS SEX-SPECIFIC DNA METHYLATION SIGNATURES IN HUMAN T CELLS THAT DISCRIMINATES CHRONIC LBP PARTICIPANTS FROM HEALTHY CONTROLS.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
5  304  46 AIRWAY AGING AND METHYLATION DISRUPTIONS IN HIV-ASSOCIATED CHRONIC OBSTRUCTIVE PULMONARY DISEASE. RATIONALE: AGE-RELATED DISEASES LIKE CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) OCCUR AT HIGHER RATES IN PEOPLE LIVING WITH HUMAN IMMUNODEFICIENCY VIRUS (PLWH) THAN IN UNINFECTED POPULATIONS. OBJECTIVES: TO IDENTIFY WHETHER ACCELERATED AGING CAN BE OBSERVED IN THE AIRWAYS OF PLWH WITH COPD, MANIFEST BY A UNIQUE DNA METHYLATION SIGNATURE. METHODS: BRONCHIAL EPITHELIAL BRUSHINGS FROM PLWH WITH AND WITHOUT COPD AND HIV-UNINFECTED ADULTS WITH AND WITHOUT COPD (N = 76) WERE PROFILED FOR DNA METHYLATION AND GENE EXPRESSION. WE EVALUATED GLOBAL ALU AND LINE-1 METHYLATION AND CALCULATED THE EPIGENETIC AGE USING THE HORVATH CLOCK AND THE METHYLATION TELOMERE LENGTH ESTIMATOR. TO IDENTIFY GENOME-WIDE DIFFERENTIAL DNA METHYLATION AND GENE EXPRESSION ASSOCIATED WITH HIV AND COPD, ROBUST LINEAR MODELS WERE USED FOLLOWED BY AN EXPRESSION QUANTITATIVE TRAIT METHYLATION (EQTM) ANALYSIS. MEASUREMENTS AND MAIN RESULTS: EPIGENETIC AGE ACCELERATION AND SHORTER METHYLATION ESTIMATES OF TELOMERE LENGTH WERE FOUND IN PLWH WITH COPD COMPARED WITH PLWH WITHOUT COPD AND UNINFECTED PATIENTS WITH AND WITHOUT COPD. GLOBAL HYPOMETHYLATION WAS IDENTIFIED IN PLWH. WE IDENTIFIED 7,970 CYTOSINE BASES LOCATED NEXT TO A GUANINE BASE (CPG SITES), 293 GENES, AND 9 EXPRESSION QUANTITATIVE TRAIT METHYLATION-GENE PAIRS ASSOCIATED WITH THE INTERACTION BETWEEN HIV AND COPD. ACTIN BINDING LIM PROTEIN FAMILY MEMBER 3 (ABLIM3) WAS ONE OF THE NOVEL CANDIDATE GENES FOR HIV-ASSOCIATED COPD HIGHLIGHTED BY OUR ANALYSIS. CONCLUSIONS: METHYLATION AGE ACCELERATION IS OBSERVED IN THE AIRWAY EPITHELIUM OF PLWH WITH COPD, A PROCESS THAT MAY BE RESPONSIBLE FOR THE HEIGHTENED RISK OF COPD IN THIS POPULATION. THEIR DISTINCT METHYLATION PROFILE, DIFFERING FROM THAT OBSERVED IN PATIENTS WITH COPD ALONE, SUGGESTS A UNIQUE PATHOGENESIS TO HIV-ASSOCIATED COPD. THE ASSOCIATIONS WARRANT FURTHER INVESTIGATION TO ESTABLISH CAUSALITY.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
6 1551  47 DNA METHYLATION IS GLOBALLY DISRUPTED AND ASSOCIATED WITH EXPRESSION CHANGES IN CHRONIC OBSTRUCTIVE PULMONARY DISEASE SMALL AIRWAYS. DNA METHYLATION IS AN EPIGENETIC MODIFICATION THAT IS HIGHLY DISRUPTED IN RESPONSE TO CIGARETTE SMOKE AND INVOLVED IN A WIDE SPECTRUM OF MALIGNANT AND NONMALIGNANT DISEASES, BUT SURPRISINGLY NOT PREVIOUSLY ASSESSED IN SMALL AIRWAYS OF PATIENTS WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD). SMALL AIRWAYS ARE THE PRIMARY SITES OF AIRFLOW OBSTRUCTION IN COPD. WE SOUGHT TO DETERMINE WHETHER DNA METHYLATION PATTERNS ARE DISRUPTED IN SMALL AIRWAY EPITHELIA OF PATIENTS WITH COPD, AND EVALUATE WHETHER CHANGES IN GENE EXPRESSION ARE ASSOCIATED WITH THESE DISRUPTIONS. GENOME-WIDE METHYLATION AND GENE EXPRESSION ANALYSIS WERE PERFORMED ON SMALL AIRWAY EPITHELIAL DNA AND RNA OBTAINED FROM THE SAME PATIENT DURING BRONCHOSCOPY, USING ILLUMINA'S INFINIUM HM27 AND AFFYMETRIX'S GENECHIP HUMAN GENE 1.0 ST ARRAYS. TO CONTROL FOR KNOWN EFFECTS OF CIGARETTE SMOKING ON DNA METHYLATION, METHYLATION AND GENE EXPRESSION PROFILES WERE COMPARED BETWEEN FORMER SMOKERS WITH AND WITHOUT COPD MATCHED FOR AGE, PACK-YEARS, AND YEARS OF SMOKING CESSATION. OUR RESULTS INDICATE THAT ABERRANT DNA METHYLATION IS (1) A GENOME-WIDE PHENOMENON IN SMALL AIRWAYS OF PATIENTS WITH COPD, AND (2) ASSOCIATED WITH ALTERED EXPRESSION OF GENES AND PATHWAYS IMPORTANT TO COPD, SUCH AS THE NF-E2-RELATED FACTOR 2 OXIDATIVE RESPONSE PATHWAY. DNA METHYLATION IS LIKELY AN IMPORTANT MECHANISM CONTRIBUTING TO MODULATION OF GENES IMPORTANT TO COPD PATHOLOGY. BECAUSE THESE METHYLATION EVENTS MAY UNDERLIE DISEASE-SPECIFIC GENE EXPRESSION CHANGES, THEIR CHARACTERIZATION IS A CRITICAL FIRST STEP TOWARD THE DEVELOPMENT OF EPIGENETIC MARKERS AND AN OPPORTUNITY FOR DEVELOPING NOVEL EPIGENETIC THERAPEUTIC INTERVENTIONS FOR COPD.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
7 1528  36 DNA METHYLATION CHANGES IN REGIONAL LUNG MACROPHAGES ARE ASSOCIATED WITH METABOLIC DIFFERENCES. A NUMBER OF PULMONARY DISEASES OCCUR WITH UPPER LOBE PREDOMINANCE, INCLUDING CYSTIC FIBROSIS AND SMOKING-RELATED CHRONIC OBSTRUCTIVE PULMONARY DISEASE. IN THE HEALTHY LUNG, SEVERAL PHYSIOLOGIC AND METABOLIC FACTORS EXHIBIT DISPARITY WHEN COMPARING THE UPPER LOBE OF THE LUNG TO LOWER LOBE, INCLUDING DIFFERENCES IN OXYGENATION, VENTILATION, LYMPHATIC FLOW, PH, AND BLOOD FLOW. IN THIS STUDY, WE ASKED WHETHER THESE REGIONAL DIFFERENCES IN THE LUNG ARE ASSOCIATED WITH DNA METHYLATION CHANGES IN LUNG MACROPHAGES THAT COULD POTENTIALLY LEAD TO ALTERED CELL RESPONSIVENESS UPON SUBSEQUENT ENVIRONMENTAL CHALLENGE. ALL ANALYSES WERE PERFORMED USING PRIMARY LUNG MACROPHAGES COLLECTED VIA BRONCHOALVEOLAR LAVAGE FROM HEALTHY HUMAN SUBJECTS WITH NORMAL PULMONARY FUNCTION. EPIGENOME-WIDE DNA METHYLATION WAS EXAMINED VIA INFINIUM METHYLATIONEPIC (850K) ARRAY AND VALIDATED BY TARGETED NEXT-GENERATION BISULFITE SEQUENCING. WE OBSERVED 95 CPG LOCI WITH SIGNIFICANT DIFFERENTIAL METHYLATION IN LUNG MACROPHAGES, COMPARING UPPER LOBE TO LOWER LOBE (ALL FALSE DISCOVERY RATE < 0.05). SEVERAL OF THESE GENES, INCLUDING CLIP4, HSH2D, NR4A1, SNX10, AND TYK2, HAVE BEEN IMPLICATED AS PARTICIPANTS IN INFLAMMATORY/IMMUNE-RELATED BIOLOGICAL PROCESSES. FUNCTIONALLY, WE IDENTIFIED PHENOTYPIC DIFFERENCES IN OXYGEN USE, COMPARING UPPER VERSUS LOWER LUNG MACROPHAGES. OUR RESULTS SUPPORT A HYPOTHESIS THAT EPIGENETIC CHANGES, SPECIFICALLY DNA METHYLATION, AT A MULTITUDE OF GENE LOCI IN LUNG MACROPHAGES ARE ASSOCIATED WITH METABOLIC DIFFERENCES REGIONALLY IN LUNG.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
8 1185  43 COORDINATED CHANGES IN AHRR METHYLATION IN LYMPHOBLASTS AND PULMONARY MACROPHAGES FROM SMOKERS. SMOKING IS ASSOCIATED WITH A WIDE VARIETY OF ADVERSE HEALTH OUTCOMES INCLUDING CANCER, CHRONIC OBSTRUCTIVE PULMONARY DISEASE, DIABETES, DEPRESSION, AND HEART DISEASE. UNFORTUNATELY, THE MOLECULAR MECHANISMS THROUGH WHICH THESE EFFECTS ARE CONVEYED ARE NOT CLEARLY UNDERSTOOD. TO EXAMINE THE POTENTIAL ROLE OF EPIGENETIC FACTORS IN THESE PROCESSES, WE EXAMINED THE RELATIONSHIP OF SMOKING TO GENOME WIDE METHYLATION AND GENE EXPRESSION USING BIOMATERIAL FROM TWO INDEPENDENT SAMPLES, LYMPHOBLAST DNA AND RNA (N = 119) AND LUNG ALVEOLAR MACROPHAGE DNA (N = 19). WE FOUND THAT IN BOTH SAMPLES CURRENT SMOKING STATUS WAS ASSOCIATED WITH SIGNIFICANT CHANGES IN DNA METHYLATION, IN PARTICULAR AT THE ARYL HYDROCARBON RECEPTOR REPRESSOR (AHRR), A KNOWN TUMOR SUPPRESSOR. BOTH BASELINE DNA METHYLATION AND SMOKER ASSOCIATED DNA METHYLATION SIGNATURES AT AHRR WERE HIGHLY CORRELATED (R = 0.94 AND 0.45, RESPECTIVELY). DNA METHYLATION AT THE MOST DIFFERENTIALLY METHYLATED AHRR CPG RESIDUE IN BOTH SAMPLES, CG0557592, WAS SIGNIFICANTLY ASSOCIATED WITH AHRR GENE EXPRESSION. PATHWAY ANALYSIS OF LYMPHOBLAST DATA (GENES WITH MOST SIGNIFICANT METHYLATION CHANGES) DEMONSTRATED ENRICHMENT IN PROTEIN KINASE C PATHWAYS AND IN TGF BETA SIGNALING PATHWAYS. FOR ALVEOLAR MACROPHAGES, PATHWAY ANALYSIS DEMONSTRATED ALTERATIONS IN INFLAMMATION-RELATED PROCESSES. WE CONCLUDE THAT SMOKING IS ASSOCIATED WITH FUNCTIONALLY SIGNIFICANT GENOME WIDE CHANGES IN DNA METHYLATION IN BOTH LYMPHOBLASTS AND PULMONARY MACROPHAGES AND THAT FURTHER INTEGRATED INVESTIGATIONS OF THESE EPIGENETIC EFFECTS OF SMOKING ON CARCINOGENESIS AND OTHER RELATED CO-MORBIDITIES ARE INDICATED.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
9 2079  35 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
10 1589  44 DNA METHYLATION PROFILING IN A CIGARETTE SMOKE-EXPOSED MOUSE MODEL OF AIRWAY INFLAMMATION. PURPOSE: DNA METHYLATION, A MAJOR EPIGENETIC MODIFICATION, HAS BEEN DOCUMENTED TO PLAY AN IMPORTANT ROLE IN CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD). IN THIS STUDY, WE AIMED TO PROFILE THE DNA METHYLATION PATTERNS IN A MOUSE MODEL OF AIRWAY INFLAMMATION INDUCED BY CIGARETTE SMOKE (CS), A FOREMOST RISK FACTOR OF COPD. MATERIAL AND METHODS: TO ESTABLISH A MODEL OF AIRWAY INFLAMMATION, WILD-TYPE MICE WERE EXPOSED TO MAINSTREAM CS OR ROOM AIR FOR 2 HOURS TWICE DAILY, 6 DAYS PER WEEK FOR CONSECUTIVE 4 WEEKS. LUNG TISSUES OF THE MICE WERE COLLECTED FOR GENOME-WIDE DNA METHYLATION ANALYSIS BY LIQUID HYBRIDIZATION CAPTURE-BASED BISULFITE SEQUENCING, WHICH WERE USED FOR INTERSECTION ANALYSIS WITH GENE EXPRESSION BY CDNA MICROARRAY TO IDENTIFY CANDIDATE METHYLATED GENES. THEN, FUNCTIONAL ENRICHMENT ANALYSES WITH PROTEIN-PROTEIN INTERACTION (PPI) NETWORK REGARDING THESE GENES WERE CONDUCTED TO EXPLORE THE POTENTIAL MECHANISMS. RESULTS: AFTER 4-WEEK CS EXPOSURE, THE LEVEL OF DNA METHYLATION ACCOMPANIED BY A SUBACUTE AIRWAY INFLAMMATION WAS MARKEDLY ENHANCED, AND 2002 DIFFERENTIALLY METHYLATED GENES (DMGS) WERE ANNOTATED, INCLUDING 565 DMGS CONTAINED METHYLATIONS IN GENE PROMOTERS, WHICH WERE USED FOR INTERSECTION WITH THE DIFFERENTIALLY EXPRESSED GENES. THEN, 135 CANDIDATE METHYLATED GENES WERE FURTHER SELECTED BY THE INTERSECTION, AMONG WHICH 58 GENES WITH FUNCTIONAL METHYLATED MODIFICATION WERE FINALLY IDENTIFIED. FURTHER ANALYSES REVEALED CANDIDATE METHYLATED GENES WERE SIGNIFICANTLY ENRICHED IN A COMPLICATED NETWORK OF SIGNALS AND PROCESSES, INCLUDING INTERLEUKINS, TOLL-LIKE RECEPTORS, T-CELLS DIFFERENTIATION, OXIDATIVE STRESS, MAST CELLS ACTIVATION, STEM CELLS PROLIFERATION, ETC., AS WELL AS THE 58 FUNCTIONAL METHYLATED GENES WERE PARTIALLY LOCATED AT KEY POSITIONS IN PPI NETWORK, ESPECIALLY CXCL1, DDX58 AND JAK3. CONCLUSION: THIS STUDY SUGGESTS CS EXPOSURE SIGNIFICANTLY ENHANCES DNA METHYLATED LEVEL, AND THE POTENTIAL FUNCTIONAL METHYLATED GENES ARE CLOSELY RELATED TO COMPLICATED INFLAMMATORY-IMMUNE RESPONSES, WHICH MAY PROVIDE SOME NEW EXPERIMENTAL EVIDENCE IN UNDERSTANDING THE EPIGENETIC MECHANISMS OF CS-INDUCED AIRWAY INFLAMMATION IN COPD.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                 
11 2633  44 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
12 1705  43 DYNAMICS OF SMOKING-INDUCED GENOME-WIDE METHYLATION CHANGES WITH TIME SINCE SMOKING CESSATION. SEVERAL STUDIES HAVE RECENTLY IDENTIFIED STRONG EPIGENETIC SIGNALS RELATED TO TOBACCO SMOKING. HOWEVER, AN ASPECT THAT DID NOT RECEIVE MUCH ATTENTION IS THE EVOLUTION OF EPIGENETIC CHANGES WITH TIME SINCE SMOKING CESSATION. WE CONDUCTED A SERIES OF EPIGENOME-WIDE ASSOCIATION STUDIES TO CAPTURE THE DYNAMICS OF SMOKING-INDUCED EPIGENETIC CHANGES AFTER SMOKING CESSATION, USING GENOME-WIDE METHYLATION PROFILES OBTAINED FROM BLOOD SAMPLES IN 745 WOMEN FROM 2 EUROPEAN POPULATIONS. TWO DISTINCT CLASSES OF CPG SITES WERE IDENTIFIED: SITES WHOSE METHYLATION REVERTS TO LEVELS TYPICAL OF NEVER SMOKERS WITHIN DECADES AFTER SMOKING CESSATION, AND SITES REMAINING DIFFERENTIALLY METHYLATED, EVEN MORE THAN 35 YEARS AFTER SMOKING CESSATION. OUR RESULTS SUGGEST THAT THE DYNAMICS OF METHYLATION CHANGES FOLLOWING SMOKING CESSATION ARE DRIVEN BY A DIFFERENTIAL AND SITE-SPECIFIC MAGNITUDE OF THE SMOKING-INDUCED ALTERATIONS (WITH PERSISTENT SITES BEING MOST AFFECTED) IRRESPECTIVE OF THE INTENSITY AND DURATION OF SMOKING. ANALYSES OF THE LINK BETWEEN METHYLATION AND EXPRESSION LEVELS REVEALED THAT METHYLATION PREDOMINANTLY AND REMOTELY DOWN-REGULATES GENE EXPRESSION. AMONG GENES WHOSE EXPRESSION WAS ASSOCIATED WITH OUR CANDIDATE CPG SITES, LRRN3 APPEARED TO BE PARTICULARLY INTERESTING AS IT WAS ONE OF THE FEW GENES WHOSE METHYLATION AND EXPRESSION WERE DIRECTLY ASSOCIATED, AND THE ONLY GENE IN WHICH BOTH METHYLATION AND GENE EXPRESSION WERE FOUND ASSOCIATED WITH SMOKING. OUR STUDY HIGHLIGHTS PERSISTENT EPIGENETIC MARKERS OF SMOKING, WHICH CAN POTENTIALLY BE DETECTED DECADES AFTER CESSATION. SUCH HISTORICAL SIGNATURES ARE PROMISING BIOMARKERS TO REFINE INDIVIDUAL RISK PROFILING OF SMOKING-INDUCED CHRONIC DISEASE SUCH AS LUNG CANCER.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
13 6311  36 THE RELATION BETWEEN DNA METHYLATION PATTERNS AND SERUM CYTOKINE LEVELS IN COMMUNITY-DWELLING ADULTS: A PRELIMINARY STUDY. BACKGROUND: THE LEVELS OF CIRCULATING CYTOKINES FLUCTUATE WITH AGE, ACUTE ILLNESS, AND CHRONIC DISEASE, AND ARE PREDICTIVE OF MORTALITY; THIS IS ALSO TRUE FOR PATTERNS OF DNA (CPG) METHYLATION. GIVEN THAT IMMUNE CELLS ARE PARTICULARLY SENSITIVE TO CHANGES IN THE CONCENTRATION OF CYTOKINES IN THEIR MICROENVIRONMENT, WE HYPOTHESIZED THAT SERUM LEVELS OF TNF, IL-6, IL-8 AND IL-10 WOULD CORRELATE WITH GENOME-WIDE ALTERATIONS IN THE DNA METHYLATION LEVELS OF BLOOD LEUKOCYTES. TO TEST THIS, WE EVALUATED COMMUNITY-DWELLING ADULTS (N = 14; 48-78 YEARS OLD) RECRUITED TO A PILOT STUDY FOR THE CANADIAN LONGITUDINAL STUDY ON AGING (CLSA), EXAMINING DNA METHYLATION PATTERNS IN PERIPHERAL BLOOD MONONUCLEAR CELLS USING THE ILLUMINA HUMANMETHYLATION 450 K BEADCHIP. RESULTS: WE SHOW THAT, APART FROM AGE, SERUM IL-10 LEVELS EXHIBITED THE MOST SUBSTANTIAL ASSOCIATION TO DNA METHYLATION PATTERNS, FOLLOWED BY TNF, IL-6 AND IL-8. FURTHERMORE, WHILE THE LEVELS OF THESE CYTOKINES WERE HIGHER IN ELDERLY ADULTS, NO ASSOCIATIONS WITH EPIGENETIC ACCELERATED AGING, DERIVED USING THE EPIGENETIC CLOCK, WERE OBSERVED. CONCLUSIONS: AS A PRELIMINARY STUDY WITH A SMALL SAMPLE SIZE, THE CONCLUSIONS DRAWN FROM THIS WORK MUST BE VIEWED WITH CAUTION; HOWEVER, OUR OBSERVATIONS ARE ENCOURAGING AND CERTAINLY WARRANT MORE SUITABLY POWERED STUDIES OF THIS RELATIONSHIP.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
14 6027  32 THE BLOOD DNA METHYLATION CLOCK GRIMAGE IS A ROBUST SURROGATE FOR AIRWAY EPITHELIA AGING. ONE KEY FEATURE OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS THAT ITS PREVALENCE INCREASES EXPONENTIALLY WITH AGE. DNA METHYLATION CLOCKS HAVE BECOME POWERFUL BIOMARKERS TO DETECT ACCELERATED AGING IN A VARIETY OF DISEASES AND CAN HELP PROGNOSE OUTCOMES IN SEVERE COPD. THIS STUDY INVESTIGATED WHICH DNA METHYLATION CLOCK COULD BEST REFLECT AIRWAY EPIGENETIC AGE WHEN USED IN MORE ACCESSIBLE BLOOD SAMPLES. OUR ANALYSES SHOWED THAT OUT OF SIX DNA METHYLATION CLOCKS INVESTIGATED, DNAMGRIMAGE DEMONSTRATED THE STRONGEST CORRELATION AND THE SMALLEST DIFFERENCE BETWEEN THE AIRWAY EPITHELIUM AND BLOOD. OUR FINDINGS SUGGESTS THAT BLOOD DNAMGRIMAGE ACCURATELY REFLECTS AIRWAY EPIGENETIC AGE OF INDIVIDUALS AND THAT ITS ELEVATION IS HIGHLY ASSOCIATED WITH COPD.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
15  274  34 AGE-RELATED CHANGES IN DNA METHYLATION AFFECT RENAL HISTOLOGY AND POST-TRANSPLANT FIBROSIS. DURING AGEING, KIDNEY FUNCTION DECREASES DUE TO RENAL TUBULAR ATROPHY, INTERSTITIAL FIBROSIS, GLOMERULOSCLEROSIS AND ARTERIOSCLEROSIS. RECENTLY, CHANGES IN DNA METHYLATION WERE SHOWN TO CONTRIBUTE TO VARIOUS AGEING PROCESSES. HOWEVER, IT IS UNKNOWN WHETHER SUCH CHANGES ALSO CONTRIBUTE TO AGE-RELATED KIDNEY DYSFUNCTION. TO ASSESS THIS, WE PROFILED GENOME-WIDE CHANGES IN DNA METHYLATION (OVER 800 000 CPG SITES) IN 95 RENAL BIOPSIES OBTAINED PRIOR TO KIDNEY TRANSPLANTATION FROM DONORS AGED 16 TO 73 YEARS. DONOR AGE SIGNIFICANTLY ASSOCIATED WITH THE METHYLATION OF 92 778 CPGS (FALSE DISCOVERY RATE UNDER 0.05), CORRESPONDING TO 10 285 DIFFERENTIALLY METHYLATED REGIONS. THESE REGIONS WERE MOST FREQUENTLY LOCATED IN GENES INVOLVED IN THE WNT/BETA-CATENIN SIGNALING PATHWAY. USING AN INDEPENDENT COHORT OF 67 BIOPSIES, WE AUTONOMOUSLY VALIDATED THESE FINDINGS. INTERESTINGLY, THE METHYLATION STATUS OF THESE 92 778 AGE-RELATED CPGS WAS ASSOCIATED WITH GLOMERULOSCLEROSIS (34.4% OF CPGS AT A FALSE DISCOVERY RATE UNDER 0.05) AND INTERSTITIAL FIBROSIS (0.9%) AND GRAFT FUNCTION AT ONE YEAR AFTER TRANSPLANTATION, BUT NOT WITH TUBULAR ATROPHY AND ARTERIOSCLEROSIS. NO ASSOCIATION WAS OBSERVED WITH ANY OF THESE PATHOLOGIES AT THE TIME OF TRANSPLANTATION (0% AT A FALSE DISCOVERY RATE UNDER 0.05). THUS, AGE-ASSOCIATED CHANGES IN DNA METHYLATION AT THE TIME OF TRANSPLANTATION PREDICT FUTURE INJURY OF TRANSPLANTED KIDNEYS. SPECIFICALLY, OUR EPIGENOME-WIDE ASSOCIATION STUDY DEMONSTRATES THAT EPIGENETIC RENAL AGEING IS IMPLICATED IN PROGRESSIVE FIBROSIS IN BOTH THE GLOMERULUS AND THE INTERSTITIUM.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
16 6761  35 X CHROMOSOME-WIDE ANALYSIS IDENTIFIES DNA METHYLATION SITES INFLUENCED BY CIGARETTE SMOKING. BACKGROUND: TOBACCO SMOKING IS A MAJOR CAUSE OF CHRONIC DISEASE WORLDWIDE. SMOKING MAY INDUCE CELLULAR AND MOLECULAR CHANGES INCLUDING EPIGENETIC MODIFICATION, WITH BOTH SHORT-TERM AND LONG-TERM MODIFICATION PATTERNS THAT MAY CONTRIBUTE TO PHENOTYPIC EXPRESSION OF DISEASES. RECENT EPIGENOME-WIDE ASSOCIATION STUDIES (EWAS) HAVE IDENTIFIED DOZENS OF SMOKING-RELATED DNA METHYLATION (DNAM) SITES. HOWEVER, THE X CHROMOSOMAL DNAM SITES HAVE BEEN LARGELY OVERLOOKED DUE TO A LACK OF AN ANALYTICAL FRAMEWORK FOR DEALING WITH THE SEX-DIMORPHIC DISTRIBUTION. TO IDENTIFY NOVEL SMOKING-RELATED DNAM SITES ON THE X CHROMOSOME, WE EXAMINED THE MODALITY OF EACH X CHROMOSOMAL DNAM SITE AND CONDUCTED A SEX-SPECIFIC ASSOCIATION STUDY OF CIGARETTE SMOKING. RESULTS: WE USED A DISCOVERY SAMPLE OF 139 MIDDLE-AGE TWINS, AND THREE REPLICATION SAMPLES OF 78 TWINS, 464 AND 333 UNRELATED INDIVIDUALS INCLUDING 47, 17, 22, AND 89 CURRENT SMOKERS, RESPECTIVELY. AFTER CORRECTION FOR MULTIPLE TESTING, THE TOP SMOKING-RELATED DNAM SITES IN BCOR AND TSC22D3 WERE SIGNIFICANTLY HYPERMETHYLATED AND HYPOMETHYLATED, RESPECTIVELY, AMONG CURRENT SMOKERS. THESE SMOKING-ASSOCIATED SITES WERE REPLICATED WITH META-ANALYSIS P-VALUES OF 9.17 X 10(-12) AND 1.61 X 10(-9). FOR BOTH SITES, THE SMOKING EFFECTS ON METHYLATION LEVELS WERE LARGER IN MALES THAN THAT IN FEMALES. CONCLUSIONS: OUR FINDINGS HIGHLIGHT THE IMPORTANCE OF INVESTIGATING X CHROMOSOME METHYLATION PATTERNS AND THEIR ASSOCIATIONS WITH ENVIRONMENTAL EXPOSURES AND DISEASE PHENOTYPES AND DEMONSTRATE A ROBUST STATISTICAL METHODOLOGY FOR SUCH STUDY. EXISTING EWAS OF HUMAN DISEASES SHOULD INCORPORATE THE X CHROMOSOMAL SITES TO COMPLETE A COMPREHENSIVE EPIGENOME-WIDE SCAN.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
17 1552  43 DNA METHYLATION IS PREDICTIVE OF MORTALITY IN CURRENT AND FORMER SMOKERS. RATIONALE: SMOKING RESULTS IN AT LEAST A DECADE LOWER LIFE EXPECTANCY. MORTALITY AMONG CURRENT SMOKERS IS TWO TO THREE TIMES AS HIGH AS NEVER SMOKERS. DNA METHYLATION IS AN EPIGENETIC MODIFICATION OF THE HUMAN GENOME THAT HAS BEEN ASSOCIATED WITH BOTH CIGARETTE SMOKING AND MORTALITY.OBJECTIVES: WE SOUGHT TO IDENTIFY DNA METHYLATION MARKS IN BLOOD THAT ARE PREDICTIVE OF MORTALITY IN A SUBSET OF THE COPDGENE (GENETIC EPIDEMIOLOGY OF COPD) STUDY, REPRESENTING 101 DEATHS AMONG 667 CURRENT AND FORMER SMOKERS.METHODS: WE ASSAYED GENOME-WIDE DNA METHYLATION IN NON-HISPANIC WHITE SMOKERS WITH AND WITHOUT CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) USING BLOOD SAMPLES FROM THE COPDGENE ENROLLMENT VISIT. WE TESTED WHETHER DNA METHYLATION WAS ASSOCIATED WITH MORTALITY IN MODELS ADJUSTED FOR COPD STATUS, AGE, SEX, CURRENT SMOKING STATUS, AND PACK-YEARS OF CIGARETTE SMOKING. REPLICATION WAS PERFORMED IN A SUBSET OF 231 INDIVIDUALS FROM THE ECLIPSE (EVALUATION OF COPD LONGITUDINALLY TO IDENTIFY PREDICTIVE SURROGATE ENDPOINTS) STUDY.MEASUREMENTS AND MAIN RESULTS: WE IDENTIFIED SEVEN CPG SITES ASSOCIATED WITH MORTALITY (FALSE DISCOVERY RATE < 20%) THAT REPLICATED IN THE ECLIPSE COHORT (P < 0.05). NONE OF THESE MARKS WERE ASSOCIATED WITH LONGITUDINAL LUNG FUNCTION DECLINE IN SURVIVORS, SMOKING HISTORY, OR CURRENT SMOKING STATUS. HOWEVER, DIFFERENTIAL METHYLATION OF TWO REPLICATED PIK3CD (PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA) SITES WERE ASSOCIATED WITH LUNG FUNCTION AT ENROLLMENT (P < 0.05). WE ALSO OBSERVED ASSOCIATIONS BETWEEN DNA METHYLATION AND GENE EXPRESSION FOR THE PIK3CD SITES.CONCLUSIONS: THIS STUDY IS THE FIRST TO IDENTIFY VARIABLE DNA METHYLATION ASSOCIATED WITH ALL-CAUSE MORTALITY IN SMOKERS WITH AND WITHOUT COPD. EVALUATING PREDICTIVE EPIGENOMIC MARKS OF SMOKERS IN PERIPHERAL BLOOD MAY ALLOW FOR TARGETED RISK STRATIFICATION AND AID IN DELIVERY OF FUTURE TAILORED THERAPEUTIC INTERVENTIONS.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
18 2400  40 EPIGENETIC REPROGRAMMING OF IMMUNE CELLS IN WOMEN WITH PCOS IMPACT GENES CONTROLLING REPRODUCTIVE FUNCTION. CONTEXT: POLYCYSTIC OVARY SYNDROME (PCOS) IS A CHRONIC DISEASE AFFECTING REPRODUCTIVE FUNCTION AND WHOLE-BODY METABOLISM. ALTHOUGH THE ETIOLOGY IS UNCLEAR, EMERGING EVIDENCE INDICATES THAT THE EPIGENETICS MAY BE A CONTRIBUTING FACTOR. OBJECTIVE: TO DETERMINE THE ROLE OF GLOBAL AND GENOME-WIDE EPIGENETIC MODIFICATIONS IN SPECIFIC IMMUNE CELLS IN PCOS COMPARED WITH CONTROLS AND WHETHER THESE COULD BE RELATED TO CLINICAL FEATURES OF PCOS. DESIGN: CROSS-SECTIONAL STUDY. PARTICIPANTS: WOMEN WITH (N = 17) OR WITHOUT PCOS (N = 17). SETTING: RECRUITED FROM THE GENERAL COMMUNITY. MAIN OUTCOME MEASURES: ISOLATED PERIPHERAL BLOOD MONONUCLEAR CELLS WERE ANALYZED USING MULTICOLOR FLOW CYTOMETRY METHODS TO DETERMINE GLOBAL DNA METHYLATION LEVELS IN A CELL-SPECIFIC FASHION. TRANSCRIPTOMIC AND GENOME-WIDE DNA METHYLATION ANALYSES WERE PERFORMED ON T HELPER CELLS USING RNA SEQUENCING AND REDUCED REPRESENTATION BISULFITE SEQUENCING. RESULTS: WOMEN WITH PCOS HAD LOWER GLOBAL DNA METHYLATION IN MONOCYTES (P = 0.006) AND IN T HELPER (P = 0.004), T CYTOTOXIC (P = 0.004), AND B CELLS (P = 0.03). SPECIFIC GENOME-WIDE DNA METHYLATION ANALYSIS OF T HELPER CELLS FROM WOMEN WITH PCOS IDENTIFIED 5581 DIFFERENTIALLY METHYLATED CPG SITES. FUNCTIONAL GENE ONTOLOGY ENRICHMENT ANALYSIS SHOWED THAT GENES LOCATED AT THE PROXIMITY OF DIFFERENTIALLY METHYLATED CPG SITES BELONG TO PATHWAYS RELATED TO REPRODUCTIVE FUNCTION AND IMMUNE CELL FUNCTION. HOWEVER, THESE GENES WERE NOT ALTERED AT THE TRANSCRIPTOMIC LEVEL. CONCLUSIONS: IT WAS SHOWN THAT PCOS IS ASSOCIATED WITH GLOBAL AND GENE-SPECIFIC DNA METHYLATION REMODELING IN A CELL TYPE-SPECIFIC MANNER. FURTHER INVESTIGATION IS WARRANTED TO DETERMINE WHETHER EPIGENETIC REPROGRAMMING OF IMMUNE CELLS IS IMPORTANT IN DETERMINING THE DIFFERENT PHENOTYPES OF PCOS.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
19 6691  49 VARIABLE DNA METHYLATION IS ASSOCIATED WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE AND LUNG FUNCTION. RATIONALE: CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS ASSOCIATED WITH LOCAL (LUNG) AND SYSTEMIC (BLOOD) INFLAMMATION AND MANIFESTATIONS. DNA METHYLATION IS AN IMPORTANT REGULATOR OF GENE TRANSCRIPTION, AND GLOBAL AND SPECIFIC GENE METHYLATION MARKS MAY VARY WITH CIGARETTE SMOKE EXPOSURE. OBJECTIVES: TO PERFORM A COMPREHENSIVE ASSESSMENT OF METHYLATION MARKS IN DNA FROM SUBJECTS WELL PHENOTYPED FOR NONNEOPLASTIC LUNG DISEASE. METHODS: WE CONDUCTED ARRAY-BASED METHYLATION SCREENS, USING A TEST-REPLICATION APPROACH, IN TWO FAMILY-BASED COHORTS (N = 1,085 AND 369 SUBJECTS). MEASUREMENTS AND MAIN RESULTS: WE OBSERVED 349 CPG SITES SIGNIFICANTLY ASSOCIATED WITH THE PRESENCE AND SEVERITY OF COPD IN BOTH COHORTS. SEVENTY PERCENT OF THE ASSOCIATED CPG SITES WERE OUTSIDE OF CPG ISLANDS, WITH THE MAJORITY OF CPG SITES RELATIVELY HYPOMETHYLATED. GENE ONTOLOGY ANALYSIS BASED ON THESE 349 CPGS (330 GENES) SUGGESTED THE INVOLVEMENT OF A NUMBER OF GENES RESPONSIBLE FOR IMMUNE AND INFLAMMATORY SYSTEM PATHWAYS, RESPONSES TO STRESS AND EXTERNAL STIMULI, AS WELL AS WOUND HEALING AND COAGULATION CASCADES. INTERESTINGLY, OUR OBSERVATIONS INCLUDE SIGNIFICANT, REPLICABLE ASSOCIATIONS BETWEEN SERPINA1 HYPOMETHYLATION AND COPD AND LOWER AVERAGE LUNG FUNCTION PHENOTYPES (COMBINED P VALUES: COPD, 1.5 X 10(-23); FEV(1)/FVC, 1.5 X 10(-35); FEV(1), 2.2 X 10(-40)). CONCLUSIONS: GENETIC AND EPIGENETIC PATHWAYS MAY BOTH CONTRIBUTE TO COPD. MANY OF THE TOP ASSOCIATIONS BETWEEN COPD AND DNA METHYLATION OCCUR IN BIOLOGICALLY PLAUSIBLE PATHWAYS. THIS LARGE-SCALE ANALYSIS SUGGESTS THAT DNA METHYLATION MAY BE A BIOMARKER OF COPD AND MAY HIGHLIGHT NEW PATHWAYS OF COPD PATHOGENESIS.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
20    3  39 "EPIGENOME-WIDE METHYLATION PROFILE OF CHRONIC KIDNEY DISEASE-DERIVED ARTERIAL DNA UNCOVERS NOVEL PATHWAYS IN DISEASE-ASSOCIATED CARDIOVASCULAR PATHOLOGY.". CHRONIC KIDNEY DISEASE (CKD) RELATED CARDIOVASCULAR DISEASE (CVD) IS CHARACTERIZED BY VASCULAR REMODELLING WITH WELL-ESTABLISHED STRUCTURAL AND FUNCTIONAL CHANGES IN THE VASCULAR WALL SUCH AS ARTERIAL STIFFNESS, MATRIX DEPOSITION, AND CALCIFICATION. THESE PHENOTYPIC CHANGES RESEMBLE PATHOLOGY SEEN IN AGEING, AND ARE LIKELY TO BE MEDIATED BY SUSTAINED ALTERATIONS IN GENE EXPRESSION, WHICH MAY BE CAUSED BY EPIGENETIC CHANGES SUCH AS TISSUE-SPECIFIC DNA METHYLATION. WE AIMED TO INVESTIGATE TISSUE SPECIFIC CHANGES IN DNA METHYLATION THAT OCCUR IN CKD-RELATED CVD. GENOME-WIDE DNA METHYLATION CHANGES WERE EXAMINED IN BISULPHITE CONVERTED GENOMIC DNA ISOLATED FROM THE VASCULAR MEDIA OF CKD AND HEALTHY ARTERIES. METHYLATION-SPECIFIC PCR WAS USED TO VALIDATE THE ARRAY DATA, AND THE ASSOCIATION BETWEEN DNA METHYLATION AND GENE AND PROTEIN EXPRESSION WAS EXAMINED. THE DNA METHYLATION AGE WAS COMPARED TO THE CHRONOLOGICAL AGE IN BOTH CASES AND CONTROLS. THREE HUNDRED AND NINETEEN DIFFERENTIALLY METHYLATED REGIONS (DMR) WERE IDENTIFIED SPREAD ACROSS THE GENOME. PATHWAY ANALYSIS REVEALED THAT DMRS ASSOCIATED WITH GENES WERE INVOLVED IN EMBRYONIC AND VASCULAR DEVELOPMENT, AND SIGNALLING PATHWAYS SUCH AS TGFBETA AND FGF. EXPRESSION OF TOP DIFFERENTIALLY METHYLATED GENE HOXA5 SHOWED A SIGNIFICANT NEGATIVE CORRELATION WITH DNA METHYLATION. INTERESTINGLY, DNA METHYLATION AGE AND CHRONOLOGICAL AGE WERE HIGHLY CORRELATED, BUT THERE WAS NO EVIDENCE OF ACCELERATED AGE-RELATED DNA METHYLATION IN THE ARTERIES OF CKD PATIENTS. IN CONCLUSION, WE DEMONSTRATED THAT DIFFERENTIAL DNA METHYLATION IN THE ARTERIAL TISSUE OF CKD PATIENTS REPRESENTS A POTENTIAL MEDIATOR OF ARTERIAL PATHOLOGY AND MAY BE USED TO UNCOVER NOVEL PATHWAYS IN THE GENESIS OF CKD-ASSOCIATED COMPLICATIONS.	2021