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  3056  43 GENOME-WIDE DNA METHYLATION ANALYSIS IMPLICATES ENRICHMENT OF INTERFERON PATHWAY IN AFRICAN AMERICAN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS AND EUROPEAN AMERICANS WITH LUPUS NEPHRITIS. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC, MULTISYSTEM, INFLAMMATORY AUTOIMMUNE DISEASE THAT DISPROPORTIONATELY AFFECTS WOMEN. TRENDS IN SLE PREVALENCE AND CLINICAL COURSE DIFFER BY ANCESTRY, WITH THOSE OF AFRICAN AMERICAN ANCESTRY PRESENTING WITH MORE ACTIVE, SEVERE AND RAPIDLY PROGRESSIVE DISEASE THAN EUROPEAN AMERICANS. PREVIOUS RESEARCH ESTABLISHED ALTERED EPIGENETIC SIGNATURES IN SLE PATIENTS COMPARED TO CONTROLS. HOWEVER, THE CONTRIBUTION OF ABERRANT DNA METHYLATION (DNAM) TO THE RISK OF SLE BY ANCESTRY AND DIFFERENCES AMONG PATIENTS WITH SLE-ASSOCIATED LUPUS NEPHRITIS (LN) HAS NOT BEEN WELL DESCRIBED. WE EVALUATED THE DNA METHYLOMES OF 87 INDIVIDUALS INCLUDING 41 SLE PATIENTS, WITH AND WITHOUT LN, AND 46 CONTROLS ENROLLED IN AN ANCESTRY DIVERSE, WELL-CHARACTERIZED COHORT STUDY OF ESTABLISHED SLE (41 SLE PATIENTS [20 SLE-LN+, 21 SLE-LN-] AND 46 SEX-, RACE- AND AGE-MATCHED CONTROLS; 55% AFRICAN AMERICAN, 45% EUROPEAN AMERICAN). PARTICIPANTS WERE GENOTYPED USING THE INFINIUM GLOBAL DIVERSITY ARRAY (GDA), AND GENETIC ANCESTRY WAS ESTIMATED USING PRINCIPAL COMPONENTS. GENOME-WIDE DNA METHYLATION WAS INITIALLY MEASURED USING THE ILLUMINA METHYLATIONEPIC 850K BEADCHIP ARRAY FOLLOWED BY METHYLATION-SPECIFIC QPCR TO VALIDATE THE METHYLATION STATUS AT PUTATIVE LOCI. DIFFERENTIALLY METHYLATED POSITIONS (DMP) WERE IDENTIFIED USING A CASE-CONTROL APPROACH ADJUSTED FOR ANCESTRY. WE IDENTIFIED A TOTAL OF 51 DMPS IN CPGS AMONG SLE PATIENTS COMPARED TO CONTROLS. GENES PROXIMAL TO THESE CPGS WERE HIGHLY ENRICHED FOR INVOLVEMENT IN TYPE I INTERFERON SIGNALING. DMPS AMONG EUROPEAN AMERICAN SLE PATIENTS WITH LN WERE SIMILAR TO AFRICAN AMERICAN SLE PATIENTS WITH AND WITHOUT LN. OUR FINDINGS WERE VALIDATED USING AN ORTHOGONAL, METHYL-SPECIFIC PCR FOR THREE SLE-ASSOCIATED DMPS NEAR OR PROXIMAL TO MX1, USP18, AND IFITM1. OUR STUDY CONFIRMS PREVIOUS REPORTS THAT DMPS IN CPGS ASSOCIATED WITH SLE ARE ENRICHED IN TYPE I INTERFERON GENES. HOWEVER, WE SHOW THAT EUROPEAN AMERICAN SLE PATIENTS WITH LN HAVE SIMILAR DNAM PATTERNS TO AFRICAN AMERICAN SLE PATIENTS IRRESPECTIVE OF LN, SUGGESTING THAT ABERRANT DNAM ALTERS ACTIVITY OF TYPE I INTERFERON PATHWAY LEADING TO MORE SEVERE DISEASE INDEPENDENT OF ANCESTRY.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                           
3  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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
4  1910  43 ENRICHMENT OF GENOMIC PATHWAYS BASED ON DIFFERENTIAL DNA METHYLATION PROFILES ASSOCIATED WITH KNEE OSTEOARTHRITIS PAIN. OUR STUDY AIMED TO IDENTIFY DIFFERENTIALLY METHYLATED REGIONS (I.E., GENOMIC REGION WHERE MULTIPLE ADJACENT CPG SITES SHOW DIFFERENTIAL METHYLATION) AND THEIR ENRICHED GENOMIC PATHWAYS ASSOCIATED WITH KNEE OSTEOARTHRITIS PAIN (KOA). WE RECRUITED COGNITIVELY HEALTHY MIDDLE TO OLDER AGED (AGE 45-85) ADULTS WITH (N = 182) AND WITHOUT (N = 31) SELF-REPORTED KOA PAIN. WE ALSO EXTRACTED DNA FROM PERIPHERAL BLOOD THAT WAS ANALYZED USING METHYLATIONEPIC ARRAYS. THE R PACKAGE MINFI (ARYEE ET AL., 2014) WAS USED TO PERFORM METHYLATION DATA PREPROCESSING AND QUALITY CONTROL. TO INVESTIGATE BIOLOGICAL PATHWAYS IMPACTED BY DIFFERENTIAL METHYLATION, WE PERFORMED PATHWAY ENRICHMENT ANALYSIS USING INGENUITY PATHWAY ANALYSIS (IPA) TO IDENTIFY CANONICAL PATHWAYS AND UPSTREAM REGULATORS. ANNOTATED GENES WITHIN +/- 5 KB OF THE PUTATIVE DIFFERENTIALLY METHYLATED REGIONS (DMRS, P < 0.05) WERE SUBJECTED TO THE IPA ANALYSIS. THERE WAS NO SIGNIFICANT DIFFERENCE IN AGE, SEX, STUDY SITE BETWEEN NO PAIN AND PAIN GROUP (P > 0.05). NON-HISPANIC BLACK INDIVIDUALS WERE OVERREPRESENTED IN THE PAIN GROUP (P = 0.003). AT RAW P < 0.05 CUTOFF, WE IDENTIFIED A TOTAL OF 19,710 CPG PROBES, INCLUDING 13,951 HYPERMETHYLATED CPG PROBES, FOR WHICH DNA METHYLATION LEVEL WAS HIGHER IN THE GROUPS WITH HIGHEST PAIN GRADES. WE ALSO IDENTIFIED 5,759 HYPOMETHYLATED CPG PROBES FOR WHICH DNA METHYLATION LEVEL WAS LOWER IN THE PAIN GROUPS WITH HIGHER PAIN GRADES. IPA REVEALED THAT PAIN-RELATED DMRS WERE ENRICHED ACROSS MULTIPLE PATHWAYS AND UPSTREAM REGULATORS. THE TOP 10 CANONICAL PATHWAYS WERE LINKED TO CELLULAR SIGNALING PROCESSES RELATED TO IMMUNE RESPONSES (I.E., ANTIGEN PRESENTATION, PD-1, PD-L1 CANCER IMMUNOTHERAPY, B CELL DEVELOPMENT, IL-4 SIGNALING, TH1 AND TH2 ACTIVATION PATHWAY, AND PHAGOSOME MATURATION). MOREOVER, IN TERMS OF UPSTREAM REGULATORS, NDUFAF3 WAS THE MOST SIGNIFICANT (P = 8.6E-04) UPSTREAM REGULATOR. OUR FINDINGS SUPPORT PREVIOUS PRELIMINARY WORK SUGGESTING THE IMPORTANCE OF EPIGENETIC REGULATION OF THE IMMUNE SYSTEM IN KNEE PAIN AND THE NEED FOR FUTURE WORK TO UNDERSTAND THE EPIGENETIC CONTRIBUTIONS TO CHRONIC PAIN.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
5  3501  40 IDENTIFICATION OF POTENTIAL BIOMARKERS FOR SYSTEMIC LUPUS ERYTHEMATOSUS BY INTEGRATED ANALYSIS OF GENE EXPRESSION AND METHYLATION DATA. INTRODUCTION: SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A HETEROGENEOUS AND CHRONIC AUTOIMMUNE DISEASE. ABERRANT DNA METHYLATION OCCURS DURING VARIOUS PROCESSES OF SLE DEVELOPMENT REGULATING THE MRNA EXPRESSION OF INTERRELATED GENES. THIS STUDY AIMS TO SCREEN POTENTIAL DNA METHYLATION MARKERS FOR SLE. METHODS: GENE EXPRESSION AND METHYLATION DATASETS WERE DOWNLOADED FROM THE GENE EXPRESSION OMNIBUS (GEO) DATABASE. DIFFERENTIALLY EXPRESSED GENES (DEGS) BETWEEN SLE PATIENTS AND HEALTHY CONTROLS WERE SCREENED USING THE LIMMA R PACKAGE, AND DIFFERENTIALLY METHYLATED POSITIONS (DMPS) AND REGIONS (DMRS) WERE IDENTIFIED USING DMPFINDER AND BUMPHUNTER (MINFI). ADDITIONALLY, THE DNA METHYLATION MARKERS TO DISTINGUISH SLE PATIENTS FROM HEALTHY CONTROLS WERE EXPLORED THROUGH RECEIVER OPERATING CHARACTERISTIC (ROC) CURVES AND LOGISTIC REGRESSION ANALYSES. FINALLY, WE VALIDATED THE RESULTS OF THE BIOINFORMATIC ANALYSIS BY PYROSEQUENCING. RESULTS: IN TOTAL, 91 DEGS, 90,092 DMPS, 15 DMRS, AND 13 DMR-ASSOCIATED GENES WERE IDENTIFIED. THROUGH THE INTEGRATIVE ANALYSIS OF DEG- AND DMR-ASSOCIATED GENES, WE IDENTIFIED FIVE TYPE I INTERFERON (IFN)-RELATED GENES AS KEY EPIGENETIC-DRIVEN GENES IN SLE. GO ENRICHMENT ANALYSIS SHOWED THAT THE FIVE SLE-ASSOCIATED EPIGENETIC-DRIVEN GENES WERE MAINLY ENRICHED IN THE TYPE I IFN SIGNALING PATHWAY INVOLVED IN IMMUNE RESPONSE AND DEFENSE RESPONSE TO VIRUS. MOREOVER, WE IDENTIFIED TWO SLE-SPECIFIC DNA METHYLATION MARKERS, THREE SLE WITHOUT LUPUS NEPHRITIS (SLE-LN(-))-SPECIFIC DNA METHYLATION MARKERS, AND TWO SLE WITH LUPUS NEPHRITIS (SLE-LN(+))-SPECIFIC DNA METHYLATION MARKERS BY STEPWISE LOGISTIC REGRESSION. CONCLUSIONS: OVERALL, OUR STUDY DEMONSTRATES POTENTIAL DNA METHYLATION MARKERS OF SLE, SLE-LN(-), AND SLE-LN(+), WHICH MAY HELP THE DIAGNOSIS, BOOST THE DEVELOPMENT OF NEW EPIGENETIC THERAPY, AND CONTRIBUTE TO INDIVIDUALIZED TREATMENT. KEY POINTS * THIS STUDY IDENTIFIED FIVE TYPE I IFN-RELATED GENES AS KEY EPIGENETIC-DRIVEN GENES IN SLE, WHICH SUPPORT THE IMPORTANCE OF THE TYPE I IFN PATHWAY IN THE PATHOGENESIS OF SLE * WE IDENTIFIED NOVEL DNA METHYLATION BIOMARKERS IN SLE, SLE-LN-, AND SLE-LN+ BY A COMPREHENSIVE ANALYSIS OF BIOINFORMATICS METHODS AND EXECUTED EXPERIMENTAL VALIDATION, AND BINARY LOGISTIC REGRESSION ANALYSIS SHOWED THAT THEY HAVE EXCELLENT POTENTIAL * THESE RESULTS MAY PROVIDE NEW INSIGHTS INTO THE BIOLOGICAL MECHANISMS OF SLE, AND IDENTIFY RELIABLE BIOMARKERS FOR SLE, SLE-LN-, AND SLE-LN+, WHICH MAY CONTRIBUTE TO DIAGNOSIS AND INDIVIDUALIZED TREATMENT.	2023	
                                                                                                                                                                                 
6  3070  37 GENOME-WIDE DNA METHYLATION PROFILING IN CD8 T-CELLS AND GAMMA DELTA T-CELLS OF ASIAN INDIAN PATIENTS WITH TAKAYASU ARTERITIS. BACKGROUND: TAKAYASU'S ARTERITIS (TA) IS A CHRONIC INFLAMMATORY DISEASE THAT AFFECTS AORTA AND ITS MAIN BRANCHES AT THEIR ORIGIN. GENETIC, PATHOLOGICAL AND FUNCTIONAL STUDIES HAVE SHOWN THAT CD8 AND GAMMA DELTA (GAMMA/DELTA) T-LYMPHOCYTES ARE INVOLVED IN INFLAMMATORY PROCESSES IN AFFECTED REGIONS OF ARTERIES CAUSING VASCULAR DAMAGE. THE MOLECULAR FUNCTION OF THESE LYMPHOCYTES REMAINS UNCLEAR AND CURRENTLY NO EPIGENETIC STUDIES ARE AVAILABLE IN TA. WE PRIMARILY PERFORMED GENOME WIDE METHYLATION ANALYSIS IN CD8 T CELLS AND GAMMADELTA T CELLS OF PATIENTS WITH TA AND COMPARED WITH HEALTHY CONTROLS. METHODS: WE RECRUITED 12 SUBJECTS IN EACH GROUP NAMELY TA PATIENT AND HEALTHY CONTROLS. BLOOD SAMPLES WERE COLLECTED AFTER OBTAINING INFORMED WRITTEN CONSENT. CD8 T CELLS AND GAMMADELTA T CELLS WERE SEPARATED FROM WHOLE BLOOD. DNA EXTRACTED FROM THESE CELLS AND WERE SUBJECTED TO BISULFITE TREATMENT. FINALLY, BISULFITE TREATED DNA WAS LOADED IN INFINIUM METHYLATION EPIC ARRAY. BIOINFORMATICS ANALYSIS WAS USED TO IDENTIFY DIFFERENTIAL METHYLATION REGIONS WHICH WERE THEN MAPPED TO GENES. RESULTS: INTERLEUKIN (IL)-32 AND LYMPHOTOXIN-A WERE GENES SIGNIFICANTLY HYPOMETHYLATED IN CD8 T-CELLS. ANTI-INFLAMMATORY CYTOKINE GENES, IL-10, IL-1RN AND IL-27 WERE HYPOMETHYLATED IN GAMMADELTA T CELLS OF TA PATIENTS AS COMPARED TO HEALTHY CONTROLS. GENE ENRICHMENT ANALYSIS USING GENE ONTOLOGY (GO) DATABASE AND KYOTO ENCYCLOPAEDIA OF GENES AND GENOMES (KEGG) IDENTIFIED THAT GENES INVOLVED IN T-CELL RECEPTOR SIGNALLING PATHWAYS WERE HYPOMETHYLATED IN CD8 T-CELLS AND HYPERMETHYLATED IN GAMMADELTA T CELLS OF TA PATIENTS. CONCLUSION: CD8 T-CELLS MIGHT PLAY A MAJOR ROLE IN IMMUNOPATHOGENESIS OF INFLAMMATION IN TA, WHEREAS GAMMADELTA T CELLS MAY PLAY A REGULATORY ROLE.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
7  1908  45 ENRICHMENT OF GENOMIC PATHWAYS BASED ON DIFFERENTIAL DNA METHYLATION ASSOCIATED WITH CHRONIC POSTSURGICAL PAIN AND ANXIETY IN CHILDREN: A PROSPECTIVE, PILOT STUDY. WE HAVE REPORTED CHILD ANXIETY SENSITIVITY (CHILD ANXIETY SENSITIVITY INDEX [CASI]) PREDICTS CHRONIC POSTSURGICAL PAIN (CPSP). HEREIN, WE EVALUATED DNA METHYLATION PROFILES TO UNDERSTAND THE GENE-ENVIRONMENT INTERACTIONS UNDERLYING CPSP AND CASI, TO IDENTIFY SHARED, ENRICHED, GENOMIC PATHWAYS. IN 73 PROSPECTIVELY RECRUITED ADOLESCENTS UNDERGOING SPINE FUSION, PREOPERATIVE CASI AND PAIN DATA OVER 12 MONTHS AFTER SURGERY WERE COLLECTED. DNA FROM THE PERIPHERAL BLOOD OF EVALUABLE SUBJECTS WITH (N = 16) AND WITHOUT CPSP (N = 40) WERE ANALYZED USING METHYLATIONEPIC ARRAYS. WE IDENTIFIED 637 AND 2,445 DIFFERENTIALLY DNA METHYLATED POSITIONS (DMPS) ASSOCIATED WITH CPSP AND CASI, RESPECTIVELY (P </= .05). INGENUITY PATHWAY ANALYSIS OF 39 GENES WITH DMPS FOR BOTH CPSP AND CASI REVEALED ENRICHMENT OF SEVERAL CANONICAL PATHWAYS, INCLUDING GABA RECEPTOR (P = .00016 FOR CPSP; P =.0008 FOR CASI) AND DOPAMINE-DARPP32 FEEDBACK IN CYCLIC ADENOSINE MONOPHOSPHATE (P = .004 FOR CPSP AND P =.00003 FOR CASI) SIGNALING. GENE-GENE INTERACTION NETWORK ENRICHMENT ANALYSIS REVEALED PARTICIPATION OF PATHWAYS IN CELL SIGNALING, MOLECULAR TRANSPORT, METABOLISM, AND NEUROLOGIC DISEASES (P < 10(-8)). BIOINFORMATIC APPROACHES TO IDENTIFY HISTONE MARKS AND TRANSCRIPTION FACTOR (TF) BINDING EVENTS UNDERLYING DMPS, SHOWED THEIR LOCATION IN ACTIVE REGULATORY REGIONS IN PAIN PATHWAY RELEVANT BRAIN CELLS. USING ENRICHR/PINET ENRICHMENT AND LIBRARY OF INTEGRATED NETWORK-BASED CELLULAR SIGNATURES KNOCKDOWN SIGNATURES, WE IDENTIFIED TFS REGULATING GENES WITH DMPS IN ASSOCIATION WITH CPSP AND CASI. IN CONCLUSION, WE IDENTIFIED EPIGENETICALLY ENRICHED PATHWAYS ASSOCIATED WITH CPSP AND ANXIETY SENSITIVITY IN CHILDREN UNDERGOING SURGERY. OUR FINDINGS SUPPORT GABA HYPOFUNCTION AND THE ROLES OF THE DOPAMINE-DARPP32 PATHWAY IN EMOTION/REWARD AND PAIN. THIS PILOT STUDY PROVIDES NEW EPIGENETIC INSIGHTS INTO THE PATHOPHYSIOLOGY OF CPSP AND A BASIS FOR FUTURE STUDIES IN BIOMARKER DEVELOPMENT AND TARGETABLE INTERVENTIONS. PERSPECTIVE: DIFFERENTIAL DNA METHYLATION IN REGULATORY GENOMIC REGIONS ENRICHING SHARED NEURAL PATHWAYS WERE ASSOCIATED WITH CPSP AND CASI IN ADOLESCENTS UNDERGOING SPINE SURGERY. OUR FINDINGS SUPPORT GABA HYPOFUNCTION AND THE ROLES OF THE DOPAMINE-DARPP32 PATHWAY IN EMOTION/REWARD CONTRIBUTING TO BEHAVIORAL MAINTENANCE OF PAIN 10 TO 12 MONTHS AFTER SURGERY.	2019	
                                                                                                                                                                                                                                                                                                                          
8   812  51 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	
                                                                                                       
9  1571  47 DNA METHYLATION PATTERNS IN CD8(+) T CELLS DISCERN PSORIASIS FROM PSORIATIC ARTHRITIS AND CORRELATE WITH CUTANEOUS DISEASE ACTIVITY. BACKGROUND: PSORIASIS IS A T CELL-MEDIATED CHRONIC AUTOIMMUNE/INFLAMMATORY DISEASE. WHILE SOME PATIENTS EXPERIENCE DISEASE LIMITED TO THE SKIN (SKIN PSORIASIS), OTHERS DEVELOP JOINT INVOLVEMENT (PSORIATIC ARTHRITIS; PSA). IN THE ABSENCE OF DISEASE- AND/OR OUTCOME-SPECIFIC BIOMARKERS, AND AS ARTHRITIS CAN PRECEDE SKIN MANIFESTATIONS, DIAGNOSTIC AND THERAPEUTIC DELAYS ARE COMMON AND CONTRIBUTE TO DISEASE BURDEN AND DAMAGE ACCRUAL. OBJECTIVE: ALTERED EPIGENETIC MARKS, INCLUDING DNA METHYLATION, CONTRIBUTE TO EFFECTOR T CELL PHENOTYPES AND ALTERED CYTOKINE EXPRESSION IN AUTOIMMUNE/INFLAMMATORY DISEASES. THIS PROJECT AIMED AT THE IDENTIFICATION OF DISEASE-/OUTCOME-SPECIFIC DNA METHYLATION SIGNATURES IN CD8(+) T CELLS FROM PATIENTS WITH PSORIASIS AND PSA AS COMPARED TO HEALTHY CONTROLS. METHOD: PERIPHERAL BLOOD CD8(+) T CELLS FROM NINE HEALTHY CONTROLS, 10 PSORIASIS, AND SEVEN PSA PATIENTS WERE COLLECTED TO ANALYZE DNA METHYLATION MARKS USING ILLUMINA HUMAN METHYLATION EPIC BEADCHIPS (>850,000 CPGS PER SAMPLE). BIOINFORMATIC ANALYSIS WAS PERFORMED USING R (MINFI, LIMMA, CHAMP, AND DMRCATE PACKAGES). RESULTS: DNA METHYLATION PROFILES IN CD8(+) T CELLS DIFFERENTIATE HEALTHY CONTROLS FROM PSORIASIS PATIENTS [397 DIFFERENTIALLY METHYLATED POSITIONS (DMPS); 9 DIFFERENTIALLY METHYLATED REGIONS (DMRS) WHEN >/=CPGS PER DMR WERE CONSIDERED; 2 DMRS FOR >/=10 CPGS]. FURTHERMORE, PATIENTS WITH SKIN PSORIASIS CAN BE DISCRIMINATED FROM PSA PATIENTS [1,861 DMPS, 20 DMRS (>/=5 CPGS PER REGION), 4 DMRS (>/=10 CPGS PER REGION)]. GENE ONTOLOGY (GO) ANALYSES CONSIDERING GENES WITH >/=1 DMP IN THEIR PROMOTER DELIVERED METHYLATION DEFECTS IN SKIN PSORIASIS AND PSA PRIMARILY AFFECTING THE BMP SIGNALING PATHWAY AND ENDOPEPTIDASE REGULATOR ACTIVITY, RESPECTIVELY. GO ANALYSIS OF GENES ASSOCIATED WITH DMRS BETWEEN SKIN PSORIASIS AND PSA DEMONSTRATED AN ENRICHMENT OF GABAERGIC NEURON AND CORTEX NEURON DEVELOPMENT PATHWAYS. TREATMENT WITH CYTOKINE BLOCKERS ASSOCIATED WITH DNA METHYLATION CHANGES [2,372 DMPS; 1,907 DMPS WITHIN PROMOTERS, 7 DMRS (>/=5 CPG PER REGIONS)] AFFECTING TRANSFORMING GROWTH FACTOR BETA RECEPTOR AND TRANSMEMBRANE RECEPTOR PROTEIN SERINE/THREONINE KINASE SIGNALING PATHWAYS. LASTLY, A METHYLATION SCORE INCLUDING TNF AND IL-17 PATHWAY ASSOCIATED DMPS INVERSE CORRELATES WITH SKIN DISEASE ACTIVITY SCORES (PASI). CONCLUSION: PATIENTS WITH SKIN PSORIASIS EXHIBIT DNA METHYLATION PATTERNS IN CD8(+) T CELLS THAT ALLOW DIFFERENTIATION FROM PSA PATIENTS AND HEALTHY INDIVIDUALS, AND REFLECT CLINICAL ACTIVITY OF SKIN DISEASE. THUS, DNA METHYLATION PROFILING PROMISES POTENTIAL AS DIAGNOSTIC AND PROGNOSTIC TOOL TO BE USED FOR MOLECULAR PATIENT STRATIFICATION TOWARD INDIVIDUALIZED TREATMENT.	2021	

10  1161  38 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	
                                                                                                                                                                                                  
11  3460  37 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
12  6589  28 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
13  1581  30 DNA METHYLATION PROFILES IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS TREATED WITH CHEMOIMMUNOTHERAPY. BACKGROUND: IN ORDER TO GAIN INSIGHT INTO THE CONTRIBUTION OF DNA METHYLATION TO DISEASE PROGRESSION OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), USING 450K ILLUMINA ARRAYS, WE DETERMINED THE DNA METHYLATION PROFILES IN PAIRED PRE-TREATMENT/RELAPSE SAMPLES FROM 34 CLL PATIENTS TREATED WITH CHEMOIMMUNOTHERAPY, MOSTLY (N = 31) WITH THE FLUDARABINE-CYCLOPHOSPHAMIDE-RITUXIMAB (FCR) REGIMEN. RESULTS: THE EXTENT OF IDENTIFIED CHANGES IN CLL CELLS VERSUS MEMORY B CELLS FROM HEALTHY DONORS WAS TERMED "EPIGENETIC BURDEN" (EB) WHEREAS THE NUMBER OF CHANGES BETWEEN THE PRE-TREATMENT VERSUS THE RELAPSE SAMPLE WAS TERMED "RELAPSE CHANGES" (RC). SIGNIFICANT (P < 0.05) ASSOCIATIONS WERE IDENTIFIED BETWEEN (I) HIGH EB AND SHORT TIME-TO-FIRST-TREATMENT (TTFT); AND, (II) FEW RCS AND SHORT TIME-TO-RELAPSE. BOTH THE EB AND THE RC CLUSTERED IN SPECIFIC GENOMIC REGIONS AND CHROMATIN STATES, INCLUDING REGULATORY REGIONS CONTAINING BINDING SITES OF TRANSCRIPTION FACTORS IMPLICATED IN B CELL AND CLL BIOLOGY. CONCLUSIONS: OVERALL, WE SHOW THAT DNA METHYLATION IN CLL FOLLOWS DIFFERENT DYNAMICS IN RESPONSE TO CHEMOIMMUNOTHERAPY. THESE EPIGENETIC ALTERATIONS WERE LINKED WITH SPECIFIC CLINICAL AND BIOLOGICAL FEATURES.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
14   408  39 ANALYSIS OF GENE EXPRESSION AND METHYLATION DATASETS IDENTIFIED ADAMTS9, FKBP5, AND PFKBF3 AS BIOMARKERS FOR OSTEOARTHRITIS. BACKGROUND: OSTEOARTHRITIS (OA) IS A KIND OF CHRONIC OSTEOARTHROPATHY AND DEGENERATIVE JOINT DISEASE. EPIGENETIC REGULATION IN THE GENE EXPRESSION DYNAMICS HAS BECOME INCREASINGLY IMPORTANT IN OA. WE PERFORMED A COMBINED ANALYSIS OF TWO TYPES OF MICROARRAY DATASETS (GENE EXPRESSION AND DNA METHYLATION) TO IDENTIFY METHYLATION-BASED KEY BIOMARKERS TO PROVIDE A BETTER UNDERSTANDING OF MOLECULAR BIOLOGICAL MECHANISMS OF OA. METHODS: WE OBTAINED TWO EXPRESSION PROFILING DATASETS (GSE55235, GSE55457) AND ONE DNA METHYLATION PROFILING DATA SET (GSE63695) FROM THE GENE EXPRESSION OMNIBUS. FIRST, DIFFERENTIALLY EXPRESSED GENES (DEGS) BETWEEN PATIENTS WITH OA AND CONTROLS WERE IDENTIFIED USING THE LIMMA PACKAGE IN R(V3.4.4). THEN, FUNCTION ENRICHMENT ANALYSIS OF DEGS WAS PERFORMED USING A DAVID DATABASE. FOR DNA METHYLATION DATASETS, CHAMP METHYLATION ANALYSIS PACKAGE WAS USED TO IDENTIFY DIFFERENTIAL METHYLATION GENES (DMGS). FINALLY, A COMPREHENSIVE ANALYSIS OF DEGS AND DMGS WAS CONDUCTED TO IDENTIFY GENES THAT EXHIBITED DIFFERENTIAL EXPRESSION AND METHYLATION SIMULTANEOUSLY. RESULTS: WE IDENTIFIED 112 DEGS AND 2,896 DMGS IN PATIENTS WITH OA COMPARED WITH CONTROLS. FUNCTIONAL ANALYSIS OF DEGS OBTAINED THAT INFLAMMATORY RESPONSES, IMMUNE RESPONSES, AND POSITIVE REGULATION OF APOPTOSIS, TUMOR NECROSIS FACTOR (TNF) SIGNALING PATHWAY, AND OSTEOCLAST DIFFERENTIATION MAY BE INVOLVED IN THE PATHOGENESIS OF OA. CROSS-ANALYSIS REVEALED 26 GENES THAT EXHIBITED DIFFERENTIAL EXPRESSION AND METHYLATION IN OA. AMONG THEM, ADAMTS9, FKBP5, AND PFKBF3 WERE IDENTIFIED AS VALUABLE METHYLATION-BASED BIOMARKERS FOR OA. CONCLUSION: IN SUMMARY, OUR STUDY IDENTIFIED DIFFERENT MOLECULAR FEATURES BETWEEN PATIENTS WITH OA AND CONTROLS. THIS MAY PROVIDE NEW CLUES FOR CLARIFYING THE PATHOGENETIC MECHANISMS OF OA.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
15  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	
                                                                                                                                                                                                                                                                                                                                                                   
16  1620  32 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
17  1132  29 COMPREHENSIVE DNA METHYLATION ANALYSIS USING A METHYL-CPG-BINDING DOMAIN CAPTURE-BASED METHOD IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS. THE ROLE OF LONG NONCODING RNAS (LNCRNAS) IN CANCER IS COMING TO THE FOREFRONT DUE TO GROWING INTEREST IN UNDERSTANDING THEIR MECHANISTIC FUNCTIONS DURING CANCER DEVELOPMENT AND PROGRESSION. DESPITE THIS, THE GLOBAL EPIGENETIC REGULATION OF LNCRNAS AND REPETITIVE SEQUENCES IN CANCER HAS NOT BEEN WELL INVESTIGATED, PARTICULARLY IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). THIS STUDY FOCUSES ON A UNIQUE APPROACH: THE IMMUNOPRECIPITATION-BASED CAPTURE OF DOUBLE-STRANDED, METHYLATED DNA FRAGMENTS USING METHYL-BINDING DOMAIN (MBD) PROTEINS, FOLLOWED BY NEXT-GENERATION SEQUENCING (MBD-SEQ). CLL PATIENT SAMPLES BELONGING TO TWO PROGNOSTIC SUBGROUPS (5 IGVH MUTATED SAMPLES + 5 IGVH UNMUTATED SAMPLES) WERE USED IN THIS STUDY. ANALYSIS REVEALED 5,800 HYPERMETHYLATED AND 12,570 HYPOMETHYLATED CLL-SPECIFIC DIFFERENTIALLY METHYLATED GENES (CLLDMGS) COMPARED TO NORMAL HEALTHY CONTROLS. IMPORTANTLY, THESE RESULTS IDENTIFIED SEVERAL CLL-SPECIFIC, DIFFERENTIALLY METHYLATED LNCRNAS, REPETITIVE ELEMENTS, AND PROTEIN-CODING GENES WITH POTENTIAL PROGNOSTIC VALUE. THIS WORK OUTLINES A DETAILED PROTOCOL FOR AN MBD-SEQ AND BIOINFORMATICS PIPELINE DEVELOPED FOR THE COMPREHENSIVE ANALYSIS OF GLOBAL METHYLATION PROFILES IN HIGHLY CPG-RICH REGIONS USING CLL PATIENT SAMPLES. FINALLY, A PROTEIN-CODING GENE AND AN LNCRNA WERE VALIDATED USING PYROSEQUENCING, WHICH IS A HIGHLY QUANTITATIVE METHOD TO ANALYZE CPG METHYLATION LEVELS TO FURTHER CORROBORATE THE FINDINGS FROM THE MBD-SEQ PROTOCOL.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
18  2406  37 EPIGENETIC RESPONSES TO RHINOVIRUS EXPOSURE IN AIRWAY EPITHELIAL CELLS ARE CORRELATED WITH KEY TRANSCRIPTIONAL PATHWAYS IN CHRONIC RHINOSINUSITIS. BACKGROUND: VIRUSES MAY DRIVE IMMUNE MECHANISMS RESPONSIBLE FOR CHRONIC RHINOSINUSITIS WITH NASAL POLYPOSIS (CRSWNP), BUT LITTLE IS KNOWN ABOUT THE UNDERLYING MOLECULAR MECHANISMS. OBJECTIVES: TO IDENTIFY EPIGENETIC AND TRANSCRIPTIONAL RESPONSES TO A COMMON UPPER RESPIRATORY PATHOGEN, RHINOVIRUS (RV), THAT ARE SPECIFIC TO PATIENTS WITH CRSWNP USING A PRIMARY SINONASAL EPITHELIAL CELL CULTURE MODEL. METHODS: AIRWAY EPITHELIAL CELLS WERE COLLECTED AT SURGERY FROM PATIENTS WITH CRSWNP (CASES) AND FROM CONTROLS WITHOUT SINUS DISEASE, CULTURED, AND THEN EXPOSED TO RV OR VEHICLE FOR 48 H. DIFFERENTIAL GENE EXPRESSION AND DNA METHYLATION (DNAM) BETWEEN CASES AND CONTROLS IN RESPONSE TO RV WERE DETERMINED USING LINEAR MIXED MODELS. WEIGHTED GENE CO-EXPRESSION ANALYSIS (WGCNA) WAS USED TO IDENTIFY (A) CO-REGULATED GENE EXPRESSION AND DNAM SIGNATURES, AND (B) GENES, PATHWAYS, AND REGULATORY MECHANISMS SPECIFIC TO CRSWNP. RESULTS: WE IDENTIFIED 5585 DIFFERENTIAL TRANSCRIPTIONAL AND 261 DNAM RESPONSES (FDR <0.10) TO RV BETWEEN CRSWNP CASES AND CONTROLS. THESE DIFFERENTIAL RESPONSES FORMED THREE CO-EXPRESSION/CO-METHYLATION MODULES THAT WERE RELATED TO CRSWNP AND THREE THAT WERE RELATED TO RV (BONFERRONI CORRECTED P < .01). MOST (95%) OF THE DIFFERENTIALLY METHYLATED CPGS (DMCS) WERE IN MODULES RELATED TO CRSWNP, WHEREAS THE DIFFERENTIALLY EXPRESSED GENES (DEGS) WERE MORE EQUALLY DISTRIBUTED BETWEEN THE CRSWNP- AND RV-RELATED MODULES. GENES IN THE CRSWNP-RELATED MODULES WERE ENRICHED IN KNOWN CRS AND/OR VIRAL RESPONSE IMMUNE PATHWAYS. CONCLUSION: RV ACTIVATES SPECIFIC EPIGENETIC PROGRAMS AND CORRELATED TRANSCRIPTIONAL NETWORKS IN THE SINONASAL EPITHELIUM OF INDIVIDUALS WITH CRSWNP. THESE NOVEL OBSERVATIONS SUGGEST EPIGENETIC SIGNATURES SPECIFIC TO PATIENTS WITH CRSWNP MODULATE RESPONSE TO VIRAL PATHOGENS AT THE MUCOSAL ENVIRONMENTAL INTERFACE. DETERMINING HOW VIRAL RESPONSE PATHWAYS ARE INVOLVED IN EPITHELIAL INFLAMMATION IN CRSWNP COULD LEAD TO THERAPEUTIC TARGETS FOR THIS BURDENSOME AIRWAY DISORDER.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
19  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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
20  3410  37 HOXA5 UNDERGOES DYNAMIC DNA METHYLATION AND TRANSCRIPTIONAL REPRESSION IN THE ADIPOSE TISSUE OF MICE EXPOSED TO HIGH-FAT DIET. BACKGROUND/OBJECTIVES: THE GENOMIC BASES OF THE ADIPOSE TISSUE ABNORMALITIES INDUCED BY CHRONIC POSITIVE CALORIE EXCESS HAVE BEEN ONLY PARTIALLY ELUCIDATED. WE ADOPTED A GENOME-WIDE APPROACH TO DIRECTLY TEST WHETHER LONG-TERM HIGH-FAT DIET (HFD) EXPOSURE AFFECTS THE DNA METHYLATION PROFILE OF THE MOUSE ADIPOSE TISSUE AND TO IDENTIFY THE FUNCTIONAL CONSEQUENCES OF THESE CHANGES. SUBJECTS/METHODS: WE HAVE USED EPIDIDYMAL FAT OF MICE FED EITHER HIGH-FAT (HFD) OR REGULAR CHOW (STD) DIET FOR 5 MONTHS AND PERFORMED GENOME-WIDE DNA METHYLATION ANALYSES BY METHYLATED DNA IMMUNOPRECIPITATION SEQUENCING (MEDIP-SEQ). MOUSE HOMEOBOX (HOX) GENE DNA METHYLATION PCR, RT-QPCR AND BISULPHITE SEQUENCING ANALYSES WERE THEN PERFORMED. RESULTS: MICE FED THE HFD PROGRESSIVELY EXPANDED THEIR ADIPOSE MASS ACCOMPANIED BY A SIGNIFICANT DECREASE IN GLUCOSE TOLERANCE (P<0.001) AND INSULIN SENSITIVITY (P<0.05). MEDIP-SEQ DATA ANALYSIS REVEALED A UNIFORM DISTRIBUTION OF DIFFERENTIALLY METHYLATED REGIONS (DMR) THROUGH THE ENTIRE ADIPOCYTE GENOME, WITH A HIGHER NUMBER OF HYPERMETHYLATED REGIONS IN HFD MICE (P<0.005). THIS DIFFERENT METHYLATION PROFILE WAS ACCOMPANIED BY INCREASED EXPRESSION OF THE DNMT3A DNA METHYLTRANSFERASE (DNMT; P<0.05) AND THE METHYL-CPG-BINDING DOMAIN PROTEIN MBD3 (P<0.05) GENES IN HFD MICE. GENE ONTOLOGY ANALYSIS REVEALED THAT, IN THE HFD-TREATED MICE, THE HOX FAMILY OF DEVELOPMENT GENES WAS HIGHLY ENRICHED IN DIFFERENTIALLY METHYLATED GENES (P=0.008). TO VALIDATE THIS FINDING, HOXA5, WHICH IS IMPLICATED IN FAT TISSUE DIFFERENTIATION AND REMODELING, HAS BEEN SELECTED AND ANALYZED BY BISULPHITE SEQUENCING, CONFIRMING HYPERMETHYLATION IN THE ADIPOSE TISSUE FROM THE HFD MICE. HOXA5 HYPERMETHYLATION WAS ASSOCIATED WITH DOWNREGULATION OF HOXA5 MRNA AND PROTEIN EXPRESSION. FEEDING ANIMALS PREVIOUSLY EXPOSED TO THE HFD WITH A STANDARD CHOW DIET FOR TWO FURTHER MONTHS IMPROVED THE METABOLIC PHENOTYPE OF THE ANIMALS, ACCOMPANIED BY RETURN OF HOXA5 METHYLATION AND EXPRESSION LEVELS (P<0.05) TO VALUES SIMILAR TO THOSE OF THE CONTROL MICE MAINTAINED UNDER STANDARD CHOW. CONCLUSIONS: HFD INDUCES ADIPOSE TISSUE ABNORMALITIES ACCOMPANIED BY EPIGENETIC CHANGES AT THE HOXA5 ADIPOSE TISSUE REMODELING GENE.	2016