1  5556 119 ROLE OF FLUORIDE INDUCED HISTONE TRIMETHYLATION IN DEVELOPMENT OF SKELETAL FLUOROSIS. CHRONIC EXPOSURE TO FLUORIDE HAS BEEN ASSOCIATED WITH THE DEVELOPMENT OF SKELETAL FLUOROSIS. LIMITED REPORTS ARE AVAILABLE ON FLUORIDE INDUCED HISTONE MODIFICATION. HOWEVER, THE ROLE OF HISTONE MODIFICATION IN THE PATHOGENESIS OF SKELETAL FLUOROSIS IS NOT INVESTIGATED. IN THE PRESENT STUDY, WE HAVE INVESTIGATED THE ROLE OF FLUORIDE INDUCED HISTONE MODIFICATION ON FLUOROSIS DEVELOPMENT USING HUMAN OSTEOSARCOMA (HOS) CELL LINE. THE EXPRESSION OF HISTONE METHYLTRANSFERASES (EHMT1 AND EHZ2) AND LEVEL OF GLOBAL HISTONE TRIMETHYLATION (H3K9 AND H3K27) HAVE BEEN ASSESSED AND OBSERVED TO BE INCREASED SIGNIFICANTLY AFTER FLUORIDE EXPOSURE (8 MG/L). EPITECT CHROMATIN IMMUNOPRECIPITATION (CHIP) QPCR ARRAY (HUMAN TGFBETA/BMP SIGNALING PATHWAY) WAS PERFORMED TO ASSESS THE H3K9 TRIMETHYLATION AT PROMOTER REGIONS OF PATHWAY-SPECIFIC GENES. H3K9 CHIP PCR ARRAY ANALYSIS IDENTIFIED HYPER H3K9 TRIMETHYLATION IN PROMOTER REGIONS OF TGFBR2 AND SMAD3. QPCR AND STRING ANALYSIS WAS CARRIED OUT TO DETERMINE THE REPRESSIVE EPIGENETIC EFFECT OF H3K9 TRIMETHYLATION ON EXPRESSION PATTERN AND FUNCTIONAL ASSOCIATION OF IDENTIFIED GENES. IDENTIFIED GENES (TGFBR2 AND SMAD3) SHOWED DOWN-REGULATION WHICH CONFIRMS THE REPRESSIVE EPIGENETIC EFFECT OF PROMOTER H3K9 HYPER TRIMETHYLATION. EXPRESSION OF TWO OTHER VITAL GENES COL1A1 AND MMP13 INVOLVED IN TGFBR2-SMAD SIGNALING PATHWAY WAS ALSO FOUND TO BE DOWN-REGULATED WITH A DECREASE IN EXPRESSION OF TGFBR2 AND SMAD3. STRING ANALYSIS REVEALED FUNCTIONAL ASSOCIATION AND INVOLVEMENT OF IDENTIFIED GENES TGFBR2, SMAD3, COL1A1 AND MMP13 IN THE COLLAGEN AND CARTILAGE DEVELOPMENT/MORPHOGENESIS, CONNECTIVE TISSUE FORMATION, BIO-MINERAL TISSUE DEVELOPMENT, ENDOCHONDRAL BONE FORMATION, BONE AND SKELETAL MORPHOGENESIS. IN CONCLUSION, PRESENT INVESTIGATION IS A FIRST ATTEMPT TO LINK FLUORIDE INDUCED HYPER H3K9 TRI-METHYLATION MEDIATED REPRESSION OF TGFBR2 AND SMAD3 WITH THE DEVELOPMENT OF SKELETAL FLUOROSIS.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
2  3488  30 IDENTIFICATION OF DNA METHYLATION ASSOCIATED ENRICHMENT PATHWAYS IN ADULTS WITH NON-SPECIFIC CHRONIC LOW BACK PAIN. CHRONIC LOW BACK PAIN (CLBP) THAT CANNOT BE ATTRIBUTABLE TO A SPECIFIC PATHOANATOMICAL CHANGE IS ASSOCIATED WITH HIGH PERSONAL AND SOCIETAL COSTS. STILL, THE UNDERLYING MECHANISM THAT CAUSES AND SUSTAINS SUCH A PHENOTYPE IS LARGELY UNKNOWN. EMERGING EVIDENCE SUGGESTS THAT EPIGENETIC CHANGES PLAY A ROLE IN CHRONIC PAIN CONDITIONS. USING REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS), WE EVALUATED DNA METHYLATION PROFILES OF ADULTS WITH NON-SPECIFIC CLBP (N = 50) AND PAIN-FREE CONTROLS (N = 48). WE IDENTIFIED 28,325 HYPERMETHYLATED AND 36,936 HYPOMETHYLATED CPG SITES (P < 0.05). AFTER CORRECTING FOR MULTIPLE TESTING, WE IDENTIFIED 159 DMRS (Q < 0.01AND METHYLATION DIFFERENCE > 10%), THE MAJORITY OF WHICH WERE LOCATED IN CPG ISLAND (50%) AND PROMOTER REGIONS (48%) ON THE ASSOCIATED GENES. THE GENES ASSOCIATED WITH THE DIFFERENTIALLY METHYLATED REGIONS WERE HIGHLY ENRICHED IN BIOLOGICAL PROCESSES THAT HAVE PREVIOUSLY BEEN IMPLICATED IN IMMUNE SIGNALING, ENDOCHONDRAL OSSIFICATION, AND G-PROTEIN COUPLED TRANSMISSIONS. OUR FINDINGS SUPPORT INFLAMMATORY ALTERATIONS AND THE ROLE OF BONE MATURATION IN CLBP. THIS STUDY SUGGESTS THAT EPIGENETIC REGULATION HAS AN IMPORTANT ROLE IN THE PATHOPHYSIOLOGY OF NON-SPECIFIC CLBP AND A BASIS FOR FUTURE STUDIES IN BIOMARKER DEVELOPMENT AND TARGETED INTERVENTIONS.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
3  5555  47 ROLE OF FLUORIDE INDUCED EPIGENETIC ALTERATIONS IN THE DEVELOPMENT OF SKELETAL FLUOROSIS. FLUORIDE IS AN ESSENTIAL TRACE ELEMENT REQUIRED FOR PROPER BONE AND TOOTH DEVELOPMENT. SYSTEMIC HIGH EXPOSURE TO FLUORIDE THROUGH ENVIRONMENTAL EXPOSURE (DRINKING WATER AND FOOD) MAY RESULT IN TOXICITY CAUSING A DISORDER CALLED FLUOROSIS. IN THE PRESENT STUDY, WE INVESTIGATED THE ALTERATION IN DNA METHYLATION PROFILE WITH CHRONIC EXPOSURE (30 DAYS) TO FLUORIDE (8 MG/L) AND ITS RELEVANCE IN THE DEVELOPMENT OF FLUOROSIS. WHOLE GENOME BISULFITE SEQUENCING (WGBS) WAS CARRIED OUT IN HUMAN OSTEOSARCOMA CELLS (HOS) EXPOSED TO FLUORIDE. WHOLE GENOME BISULFITE SEQUENCING (WGBS) AND FUNCTIONAL ANNOTATION OF DIFFERENTIALLY METHYLATED GENES INDICATE ALTERATIONS IN METHYLATION STATUS OF GENES INVOLVED IN BIOLOGICAL PROCESSES ASSOCIATED WITH BONE DEVELOPMENT PATHWAYS. COMBINED ANALYSIS OF PROMOTER DNA HYPER METHYLATION, STRING: FUNCTIONAL PROTEIN ASSOCIATION NETWORKS AND GENE EXPRESSION ANALYSIS REVEALED EPIGENETIC ALTERATIONS IN BMP1, METAP2, MMP11 AND BACH1 GENES, WHICH PLAYS A ROLE IN THE EXTRACELLULAR MATRIX DISASSEMBLY, COLLAGEN CATABOLIC/ORGANIZATION PROCESS, SKELETAL MORPHOGENESIS/DEVELOPMENT, OSSIFICATION AND OSTEOBLAST DEVELOPMENT. THE PRESENT STUDY SHOWS THAT FLUORIDE CAUSES PROMOTER DNA HYPERMETHYLATION IN BMP1, METAP2, MMP11 AND BACH1 GENES WITH SUBSEQUENT DOWN-REGULATION IN THEIR EXPRESSION LEVEL (RNA LEVEL). THE RESULTS IMPLIES THAT FLUORIDE INDUCED DNA HYPERMETHYLATION OF THESE GENES MAY HAMPER EXTRACELLULAR MATRIX DEPOSITION, CARTILAGE FORMATION, ANGIOGENESIS, VASCULAR SYSTEM DEVELOPMENT AND POROSITY OF BONE, THUS PROMOTE SKELETAL FLUOROSIS.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
4  2634  38 EPIGENOME-WIDE DNA METHYLATION PROFILING OF CONDITIONED PAIN MODULATION IN INDIVIDUALS WITH NON-SPECIFIC CHRONIC LOW BACK PAIN. BACKGROUND: THE PATHOANATOMIC CAUSE OF CHRONIC LOW BACK PAIN (CLBP) CANNOT BE IDENTIFIED FOR UP TO 90% OF INDIVIDUALS. HOWEVER, DYSFUNCTIONAL PROCESSING OF ENDOGENOUS NOCICEPTIVE INPUT, MEASURED AS CONDITIONED PAIN MODULATION (CPM), HAS BEEN ASSOCIATED WITH CLBP AND MAY INVOLVE CHANGES IN NEURONAL GENE EXPRESSION. EPIGENETIC-INDUCED CHANGES SUCH AS DNA METHYLATION (DNAM) HAVE BEEN ASSOCIATED WITH CLBP. METHODS: IN THE PRESENT STUDY, THE RELATIONSHIP BETWEEN CPM AND DNAM CHANGES IN A SAMPLE OF COMMUNITY-DWELLING ADULTS WITH NONSPECIFIC CLBP (N = 48) AND PAIN-FREE CONTROLS (PFC; N = 50) WAS EXAMINED USING REDUCED REPRESENTATION BISULFITE SEQUENCING. GENE ONTOLOGY (GO) TERM ENRICHMENT AND KYOTO ENCYCLOPEDIA OF GENES AND GENOMES (KEGG) PATHWAY ANALYSIS WERE APPLIED TO IDENTIFY KEY PATHWAYS INVOLVED IN EFFICIENT VERSUS DEFICIENT CPM. RESULTS: BASED ON CPM EFFICIENCY, WE IDENTIFIED 6006 AND 18,305 DIFFERENTIALLY METHYLATED CPG SITES (DMCS) WITH Q VALUES < 0.01 AMONG INDIVIDUALS WITH CLBP AND PFCS, RESPECTIVELY. MOST OF THE DMCS WERE HYPOMETHYLATED AND ANNOTATED TO GENES OF RELEVANCE TO PAIN, INCLUDING OPRM1, ADRB2, CACNA2D3, GNA12, LPL, NAXD, AND ASPHD1. IN BOTH CLBP AND PFC GROUPS, THE DMCS ANNOTATED GENES ENRICHED MANY GO TERMS RELEVANT TO PAIN PROCESSING, INCLUDING TRANSCRIPTION REGULATION BY RNA POLYMERASE II, NERVOUS SYSTEM DEVELOPMENT, GENERATION OF NEURONS, NEURON DIFFERENTIATION, AND NEUROGENESIS. BOTH GROUPS ALSO ENRICHED THE PATHWAYS INVOLVED IN RAP1-SIGNALING, CANCER, AND DOPAMINERGIC NEUROGENESIS. HOWEVER, MAPK-RAS SIGNALING PATHWAYS WERE ENRICHED IN THE CLBP, NOT THE PFC GROUP. CONCLUSIONS: THIS IS THE FIRST STUDY TO INVESTIGATE THE GENOME-SCALE DNA METHYLATION PROFILES OF CPM PHENOTYPE IN ADULTS WITH CLBP AND PFCS. BASED ON CPM EFFICIENCY, FEWER DMC ENRICHMENT PATHWAYS WERE UNIQUE TO THE CLBP THAN THE PFCS GROUP. OUR RESULTS SUGGEST THAT EPIGENETICALLY INDUCED MODIFICATION OF NEURONAL DEVELOPMENT/DIFFERENTIATION PATHWAYS MAY AFFECT CPM EFFICIENCY, SUGGESTING NOVEL POTENTIAL THERAPEUTIC TARGETS FOR CENTRAL SENSITIZATION. HOWEVER, CPM EFFICIENCY AND THE EXPERIENCE OF NONSPECIFIC CLBP MAY BE INDEPENDENT. FURTHER MECHANISTIC STUDIES ARE REQUIRED TO CONFIRM THE RELATIONSHIP BETWEEN CPM, CENTRAL SENSITIZATION, AND NONSPECIFIC CLBP.	2022	
                                                                                                                                                                                                                                                       
5   122  28 A SYSTEMATIC REVIEW ON FLUORIDE-INDUCED EPIGENETIC TOXICITY IN MAMMALS. FLUORIDE, ONE OF THE GLOBAL GROUNDWATER CONTAMINANTS, IS UBIQUITOUS IN OUR DAY-TO-DAY LIFE FROM VARIOUS NATURAL AND ANTHROPOGENIC SOURCES. NUMEROUS IN VITRO, IN VIVO, AND EPIDEMIOLOGICAL STUDIES ARE CONDUCTED TO UNDERSTAND THE EFFECT OF FLUORIDE ON BIOLOGICAL SYSTEMS. A LOW CONCENTRATION OF FLUORIDE IS REPORTED TO INCREASE ORAL HEALTH, WHEREAS CHRONIC EXPOSURE TO HIGHER CONCENTRATIONS CAUSES FLUORIDE TOXICITY (FLUOROSIS). IT INCLUDES DENTAL FLUOROSIS, SKELETAL FLUOROSIS, AND FLUORIDE TOXICITY IN SOFT TISSUES. THE MECHANISM OF FLUORIDE TOXICITY HAS BEEN REVIEWED EXTENSIVELY. HOWEVER, EPIGENETIC REGULATION IN FLUORIDE TOXICITY HAS NOT BEEN REVIEWED. THIS SYSTEMATIC REVIEW SUMMARIZES THE CURRENT KNOWLEDGE REGARDING FLUORIDE-INDUCED EPIGENETIC TOXICITY IN THE IN VITRO, IN VIVO, AND EPIDEMIOLOGICAL STUDIES IN MAMMALIAN SYSTEMS. WE EXAMINED FOUR DATABASES FOR THE ASSOCIATION BETWEEN EPIGENETICS AND FLUORIDE EXPOSURE. OUT OF 932 ARTICLES (AS OF 31 MARCH 2022), 39 MET OUR INCLUSION CRITERIA. MOST OF THE STUDIES FOCUSED ON DIFFERENT GENES, AND OVERALL, PRELIMINARY EVIDENCE FOR EPIGENETIC REGULATION OF FLUORIDE TOXICITY WAS IDENTIFIED. WE FURTHER HIGHLIGHT THE NEED FOR EPIGENOME STUDIES RATHER THAN CANDIDATE GENES AND PROVIDE RECOMMENDATIONS FOR FUTURE RESEARCH. OUR RESULTS INDICATE A CORRELATION BETWEEN FLUORIDE EXPOSURE AND EPIGENETIC PROCESSES. FURTHER STUDIES ARE WARRANTED TO ELUCIDATE AND CONFIRM THE MECHANISM OF EPIGENETIC ALTERATIONS MEDIATED FLUORIDE TOXICITY.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
6   112  29 A ROLE FOR GLOBAL DNA METHYLATION LEVEL AND IL2 EXPRESSION IN THE TRANSITION FROM ACUTE TO CHRONIC LOW BACK PAIN. OBJECTIVES: THE TRANSITION FROM ACUTE LOW BACK PAIN (ALBP) TO CHRONIC LBP (CLBP) RESULTS FROM A VARIETY OF FACTORS, INCLUDING EPIGENETIC MODIFICATIONS OF DNA. THE AIM OF THIS STUDY WAS TO (1) COMPARE GLOBAL DNA (GDNA) METHYLATION AND HISTONE ACETYLATION AT LBP ONSET BETWEEN THE ALBP AND CLBP PARTICIPANTS, (2) COMPARE MRNA EXPRESSION OF GENES WITH KNOWN ROLES IN THE TRANSDUCTION, MAINTENANCE, AND/OR MODULATION OF PAIN BETWEEN THE ALBP AND CLBP PARTICIPANTS, (3) COMPARE SOMATOSENSORY FUNCTION AND PAIN RATINGS IN OUR PARTICIPANTS, AND (4) DETERMINE IF THE AFOREMENTIONED MEASUREMENTS WERE ASSOCIATED. METHODS: A TOTAL OF 220 PARTICIPANTS WERE RECRUITED FOR THIS PROSPECTIVE OBSERVATIONAL STUDY FOLLOWING RECENT ONSET OF AN EPISODE OF LBP. WE RETAINED 45 INDIVIDUALS WHOSE GDNA WAS OF SUFFICIENT QUALITY FOR ANALYSIS. THE FINAL SAMPLE INCLUDED 14 PARTICIPANTS WHOSE PAIN RESOLVED WITHIN 6 WEEKS OF ONSET (ALBP),15 PARTICIPANTS THAT REPORTED PAIN FOR 6 MONTHS (CLBP), AND 16 HEALTHY CONTROLS. PARTICIPANTS WERE SUBJECTED TO QUANTITATIVE SENSORY TESTING (QST), BLOOD WAS DRAWN VIA VENIPUNCTURE, GDNA ISOLATED, AND GLOBAL DNA METHYLATION AND HISTONE ACETYLATION, AS WELL AS MRNA EXPRESSION OF 84 CANDIDATE GENES, WERE MEASURED. RESULTS: INDIVIDUALS THAT DEVELOP CLBP DISPLAY MULTIMODAL SOMATOSENSORY HYPERSENSITIVITY RELATIVE TO ALBP PARTICIPANTS. CLBP PARTICIPANTS ALSO HAD SIGNIFICANTLY LOWER GLOBAL DNA METHYLATION, WHICH WAS NEGATIVELY CORRELATED WITH INTERLEUKIN-2 (IL2) MRNA EXPRESSION. DISCUSSION: CLBP IS CHARACTERIZED BY SOMATOSENSORY HYPERSENSITIVITY, LOWER GLOBAL DNA METHYLATION, AND HIGHER IL2 EXPRESSION LEVEL COMPARED TO THOSE WHOSE PAIN WILL RESOLVE QUICKLY (ALBP). THESE RESULTS SUGGEST POTENTIAL DIAGNOSTIC AND THERAPEUTIC RELEVANCE FOR GLOBAL DNA METHYLATION AND IL2 EXPRESSION IN THE PATHOLOGY UNDERLYING THE TRANSITION FROM ACUTE TO CHRONIC LBP.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
7   908  40 CHRONIC EXPOSURE TO ENVIRONMENTALLY RELEVANT CONCENTRATION OF FLUORIDE IMPAIRS OSTEOBLAST'S COLLAGEN SYNTHESIS AND MATRIX MINERALIZATION: INVOLVEMENT OF EPIGENETIC REGULATION IN SKELETAL FLUOROSIS. GLOBALLY, 200 MILLION PEOPLE ARE SUFFERING FROM TOXIC MANIFESTATIONS OF FLUORIDE(F), DENTAL AND SKELETAL FLUOROSIS; UNFORTUNATELY, THERE IS NO TREATMENT. TO UNRAVEL THE PATHOGENESIS OF SKELETAL FLUOROSIS, WE ESTABLISHED FLUOROSIS MICE BY TREATING ENVIRONMENTALLY RELEVANT CONCENTRATION OF F (15 PPM NAF) THROUGH DRINKING WATER FOR 4 MONTHS. AS IN SKELETAL FLUOROSIS, LOCOMOTOR DISABILITY, CRIPPLING DEFORMITIES OCCUR AND THUS, OUR HYPOTHESIS WAS F MIGHT ADVERSELY AFFECTS COLLAGEN WHICH GIVES THE BONE TENSILE STRENGTH. THIS WORK INEVITABLY HAD TO BE CARRIED OUT ON OSTEOBLAST CELLS, RESPONSIBLE FOR SYNTHESIS, DEPOSITION, AND MINERALIZATION OF BONE MATRIX. ISOLATED OSTEOBLAST CELLS WERE CONFIRMED BY ALP ACTIVITY AND MINERALIZED NODULES FORMATION. EXPRESSION OF COLLAGEN COL1A1, COL1A2, COL1A1 WAS SIGNIFICANTLY REDUCED IN TREATED MICE. FURTHER, A STUDY REVEALED THE INVOLVEMENT OF EPIGENETIC REGULATION BY PROMOTER HYPERMETHYLATION OF COL1A1; EXPRESSIONAL ALTERATIONS OF TRANSCRIPTION FACTORS, CALCIUM CHANNELS AND OTHER GENES E.G., CBFA-1, TGF-BETA1, BMP1, SP1, SP7, NF-(K)B P65, BMP-2, BGLAP, GPRC6A AND CAV(1.2) ARE ASSOCIATED WITH IMPAIRMENT OF COLLAGEN SYNTHESIS, DEPOSITION AND DECREASED MINERALIZATION THUS, ENFEEBLING BONE HEALTH. THIS STUDY INDICATES THE POSSIBLE ASSOCIATION OF EPIGENETIC REGULATION IN SKELETAL FLUOROSIS. HOWEVER, NO ASSOCIATION WAS FOUND BETWEEN POLYMORPHISMS IN THE COL1A1 (RSAI, HINDIII) AND COL1A2 (RSAI, HINDIII) GENES WITH FLUOROSIS IN MICE.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
8  4021  28 LOWERED DNA METHYLTRANSFERASE (DNMT-3B) MRNA EXPRESSION IS ASSOCIATED WITH GENOMIC DNA HYPERMETHYLATION IN PATIENTS WITH CHRONIC ALCOHOLISM. DNA METHYLTRANSFERASES (DNMTS) ARE INVOLVED WITHIN THE EPIGENETIC CONTROL OF DNA METHYLATION PROCESSES. RECENTLY, IT HAS BEEN SHOWN THAT THE GENOMIC DNA METHYLATION IN PATIENTS WITH ALCOHOLISM IS INCREASED. IN THE PRESENT CONTROLLED STUDY WE OBSERVED A SIGNIFICANT DECREASE OF MRNA EXPRESSION OF DNMT-3A AND DNMT-3B WHEN COMPARING ALCOHOLIC PATIENTS (N = 59) WITH HEALTHY CONTROLS (N = 66): DNMT-3A (T = -2.38, P = 0.019), DNMT-3B (T = -2.65, P = 0.008). NO SIGNIFICANT DIFFERENCES WERE SEEN FOR DNMT-1 AND MBD-2 (METHYL-CPG-BINDING-DOMAIN PROTEIN 2) EXPRESSION. ADDITIONALLY, WE OBSERVED A SIGNIFICANT NEGATIVE CORRELATION BETWEEN DNMT-3B EXPRESSION AND THE BLOOD ALCOHOL CONCENTRATION (R = -0.45, P = 0.003) WHICH MIGHT EXPLAIN THE DECREASE OF DNMT-3B MRNA EXPRESSION IN ALCOHOLIC PATIENTS. USING A MULTIVARIATE MODEL WE OBSERVED THAT THE INCREASE (10%) OF GENOMIC DNA METHYLATION IN PATIENTS WITH ALCOHOLISM WAS SIGNIFICANTLY ASSOCIATED WITH THEIR LOWERED DNMT-3B MRNA EXPRESSION (MULTIPLE LINEAR REGRESSION, P = 0.014). SINCE METHYLATION OF DNA IS AN IMPORTANT EPIGENETIC FACTOR IN REGULATION OF GENE EXPRESSION THESE FINDINGS MAY HAVE IMPORTANT IMPLICATIONS FOR A POSSIBLE SUBSEQUENT DERANGEMENT OF EPIGENETIC CONTROL IN THESE PATIENTS.	2006	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
9  1161  40 CONTINUOUS DEVELOPMENTAL AND EARLY LIFE TRICHLOROETHYLENE EXPOSURE PROMOTED DNA METHYLATION ALTERATIONS IN POLYCOMB PROTEIN BINDING SITES IN EFFECTOR/MEMORY CD4(+) T CELLS. TRICHLOROETHYLENE (TCE) IS AN INDUSTRIAL SOLVENT AND DRINKING WATER POLLUTANT ASSOCIATED WITH CD4(+) T CELL-MEDIATED AUTOIMMUNITY. IN OUR MOUSE MODEL, DISCONTINUATION OF TCE EXPOSURE DURING ADULTHOOD AFTER DEVELOPMENTAL EXPOSURE DID NOT PREVENT IMMUNOTOXICITY. TO DETERMINE WHETHER PERSISTENT EFFECTS WERE LINKED TO EPIGENETIC CHANGES WE CONDUCTED WHOLE GENOME REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS) TO EVALUATE METHYLATION OF CPG SITES IN AUTOSOMAL CHROMOSOMES IN ACTIVATED EFFECTOR/MEMORY CD4(+) T CELLS. FEMALE MRL+/+ MICE WERE EXPOSED TO VEHICLE CONTROL OR TCE IN THE DRINKING WATER FROM GESTATION UNTIL ~37 WEEKS OF AGE [POSTNATAL DAY (PND) 259]. IN A SUBSET OF MICE, TCE EXPOSURE WAS DISCONTINUED AT ~22 WEEKS OF AGE (PND 154). AT PND 259, RRBS ASSESSMENT REVEALED MORE GLOBAL METHYLATION CHANGES IN THE CONTINUOUS EXPOSURE GROUP VS. THE DISCONTINUOUS EXPOSURE GROUP. A MAJORITY OF THE DIFFERENTIALLY METHYLATED CPG REGIONS (DMRS) ACROSS PROMOTERS, ISLANDS, AND REGULATORY ELEMENTS WERE HYPERMETHYLATED (~90%). HOWEVER, CONTINUOUS DEVELOPMENTAL TCE EXPOSURE ALTERED THE METHYLATION OF 274 CPG SITES IN PROMOTERS AND CPG ISLANDS. IN CONTRAST, ONLY 4 CPG ISLAND REGIONS WERE DIFFERENTIALLY METHYLATED (HYPERMETHYLATED) IN THE DISCONTINUOUS GROUP. INTERESTINGLY, 2 OF THESE 4 SITES WERE ALSO HYPERMETHYLATED IN THE CONTINUOUS EXPOSURE GROUP, AND BOTH OF THESE ISLAND REGIONS ARE ASSOCIATED WITH LYSINE 27 ON HISTONE H3 (H3K27) INVOLVED IN POLYCOMB COMPLEX-DEPENDENT TRANSCRIPTIONAL REPRESSION VIA H3K27 TRI-METHYLATION. CPG SITES WERE OVERLAPPED WITH THE OPEN REGULATORY ANNOTATION DATABASE. UNLIKE THE DISCONTINUOUS GROUP, CONTINUOUS TCE TREATMENT RESULTED IN 129 DMRS INCLUDING 12 UNIQUE TRANSCRIPTION FACTORS AND REGULATORY ELEMENTS; 80% OF WHICH WERE ENRICHED FOR ONE OR MORE POLYCOMB GROUP (PCG) PROTEIN BINDING REGIONS (I.E., SUZ12, EZH2, JARID2, AND MTF2). PATHWAY ANALYSIS OF THE DMRS INDICATED THAT TCE PRIMARILY ALTERED THE METHYLATION OF GENES ASSOCIATED WITH REGULATION OF CELLULAR METABOLISM AND CELL SIGNALING. THE RESULTS DEMONSTRATED THAT CONTINUOUS DEVELOPMENTAL EXPOSURE TO TCE DIFFERENTIALLY METHYLATED BINDING SITES OF PCG PROTEINS IN EFFECTOR/MEMORY CD4(+) CELLS. THERE WERE MINIMAL YET POTENTIALLY BIOLOGICALLY SIGNIFICANT EFFECTS THAT OCCURRED WHEN EXPOSURE WAS DISCONTINUED. THESE RESULTS POINT TOWARD A NOVEL MECHANISM BY WHICH CHRONIC DEVELOPMENTAL TCE EXPOSURE MAY ALTER TERMINALLY DIFFERENTIATED CD4(+) T CELL FUNCTION IN ADULTHOOD.	2019	

10  1910  31 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	
                                                                                                                                                                                                                                                                                                                                                                                                                   
11  1485  17 DMRFUSION: A DIFFERENTIALLY METHYLATED REGION DETECTION TOOL BASED ON THE RANKED FUSION METHOD. DNA METHYLATION IS AN IMPORTANT EPIGENETIC MODIFICATION INVOLVED IN MANY BIOLOGICAL PROCESSES AND DISEASES. COMPUTATIONAL ANALYSIS OF DIFFERENTIALLY METHYLATED REGIONS (DMRS) COULD EXPLORE THE UNDERLYING REASONS OF METHYLATION. DMRFUSION IS PRESENTED AS A USEFUL TOOL FOR COMPREHENSIVE DNA METHYLATION ANALYSIS OF DMRS ON METHYLATION SEQUENCING DATA. THIS TOOL IS DESIGNED BASE ON THE INTEGRATION OF SEVERAL RANKING METHODS; INFORMATION GAIN, BETWEEN VERSUS WITHIN CLASS SCATTER RATIO, FISHER RATIO, Z-SCORE AND WELCH'S T-TEST. IN THIS STUDY, DMRFUSION ON REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS) DATA IN CHRONIC LYMPHOCYTIC LEUKEMIA CANCER DISPLAYED 30 NOMINATED REGIONS AND CPG SITES WITH A MAXIMUM METHYLATION DIFFERENCE DETECTED IN THE HYPERMETHYLATION DMRS. WE REALIZED THAT DMRFUSION IS ABLE TO PROCESS METHYLATION SEQUENCING DATA IN AN EFFICIENT AND ACCURATE MANNER AND TO PROVIDE ANNOTATION AND VISUALIZATION FOR DMRS WITH HIGH FOLD DIFFERENCE SCORE (P-VALUE AND FDR<0.05 AND TYPE I ERROR: 0.04).	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
12  3609  35 IN UTERO ARSENIC EXPOSURE AND EPIGENOME-WIDE ASSOCIATIONS IN PLACENTA, UMBILICAL ARTERY, AND HUMAN UMBILICAL VEIN ENDOTHELIAL CELLS. EXPOSURE TO ARSENIC EARLY IN LIFE HAS BEEN ASSOCIATED WITH INCREASED RISK OF SEVERAL CHRONIC DISEASES AND IS BELIEVED TO ALTER EPIGENETIC PROGRAMMING IN UTERO. IN THE PRESENT STUDY, WE EVALUATE THE EPIGENOME-WIDE ASSOCIATION OF ARSENIC EXPOSURE IN UTERO AND DNA METHYLATION IN PLACENTA (N = 37), UMBILICAL ARTERY (N = 45) AND HUMAN UMBILICAL VEIN ENDOTHELIAL CELLS (HUVEC) (N = 52) IN A BIRTH COHORT USING THE INFINIUM HUMANMETHYLATION450 BEADCHIP ARRAY. UNADJUSTED AND CELL MIXTURE ADJUSTED ASSOCIATIONS FOR EACH TISSUE WERE EXAMINED ALONG WITH ENRICHMENT ANALYSES RELATIVE TO CPG ISLAND LOCATION AND OMNIBUS PERMUTATION TESTS OF ASSOCIATION AMONG BIOLOGICAL PATHWAYS. ONE CPG IN ARTERY (CG26587014) AND 4 CPGS IN PLACENTA (CG12825509; CG20554753; CG23439277; CG21055948) REACHED A BONFERRONI ADJUSTED LEVEL OF SIGNIFICANCE. SEVERAL CPGS WERE DIFFERENTIALLY METHYLATED IN ARTERY AND PLACENTA WHEN CONTROLLING THE FALSE DISCOVERY RATE (Q-VALUE<0.05), BUT NONE IN HUVEC. ENRICHMENT OF HYPOMETHYLATED CPG ISLANDS WAS OBSERVED FOR ARTERY WHILE HYPERMETHYLATION OF OPEN SEA REGIONS WERE PRESENT IN PLACENTA RELATIVE TO PRENATAL ARSENIC EXPOSURE. THE MELANOGENESIS PATHWAY WAS DIFFERENTIALLY METHYLATED IN ARTERY (MAX F P < 0.001), PLACENTA (MAX F P < 0.001), AND HUVEC (MAX F P = 0.02). SIMILARLY, THE INSULIN-SIGNALING PATHWAY WAS DIFFERENTIALLY METHYLATED IN ARTERY (MAX F P = 0.02), PLACENTA (MAX F P = 0.02), AND HUVEC (MAX F P = 0.02). OUR RESULTS SHOW THAT PRENATAL ARSENIC EXPOSURE CAN ALTER DNA METHYLATION IN ARTERY AND PLACENTA BUT NOT IN HUVEC. FURTHER STUDIES ARE NEEDED TO DETERMINE IF THESE ALTERATIONS IN DNA METHYLATION MEDIATE THE EFFECT OF PRENATAL ARSENIC EXPOSURE AND HEALTH OUTCOMES LATER IN LIFE.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
13  1620  37 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
14  4231  34 METHYLATION OF PROTOCADHERIN 10, A NOVEL TUMOR SUPPRESSOR, IS ASSOCIATED WITH POOR PROGNOSIS IN PATIENTS WITH GASTRIC CANCER. BACKGROUND & AIMS: BY USING METHYLATION-SENSITIVE REPRESENTATIONAL DIFFERENCE ANALYSIS, WE IDENTIFIED PROTOCADHERIN 10 (PCDH10), A GENE THAT ENCODES A PROTOCADHERIN AND IS SILENCED IN A TUMOR-SPECIFIC MANNER. WE ANALYZED ITS EPIGENETIC INACTIVATION, BIOLOGICAL EFFECTS, AND PROGNOSTIC SIGNIFICANCE IN GASTRIC CANCER. METHODS: METHYLATION STATUS WAS EVALUATED BY COMBINED BISULFITE RESTRICTION ANALYSIS AND BISULFITE SEQUENCING. THE EFFECTS OF PCDH10 RE-EXPRESSION WERE DETERMINED IN GROWTH, APOPTOSIS, PROLIFERATION, AND INVASION ASSAYS. PCDH10 TARGET GENES WERE IDENTIFIED BY COMPLEMENTARY DNA MICROARRAY ANALYSIS. RESULTS: PCDH10 WAS SILENCED OR DOWN-REGULATED IN 94% (16 OF 17) OF GASTRIC CANCER CELL LINES; EXPRESSION LEVELS WERE RESTORED BY EXPOSURE TO DEMETHYLATING AGENTS. RE-EXPRESSION OF PCDH10 IN MKN45 GASTRIC CANCER CELLS REDUCED COLONY FORMATION IN VITRO AND TUMOR GROWTH IN MICE; IT ALSO INHIBITED CELL PROLIFERATION (P < .01), INDUCED CELL APOPTOSIS (P < .001), AND REPRESSED CELL INVASION (P < .05), UP-REGULATING THE PRO-APOPTOSIS GENES FAS, CASPASE 8, JUN, AND CDKN1A; THE ANTIPROLIFERATION GENE FGFR; AND THE ANTI-INVASION GENE HTATIP2. PCDH10 METHYLATION WAS DETECTED IN 82% (85 OF 104) OF GASTRIC TUMORS COMPARED WITH 37% (38 OF 104) OF PAIRED NONTUMOR TISSUES (P < .0001). IN THE LATTER, PCDH10 METHYLATION WAS HIGHER IN PRECANCEROUS LESIONS (27 OF 45; 60%) THAN IN CHRONIC GASTRITIS SAMPLES (11 OF 59; 19%) (P < .0001). AFTER A MEDIAN FOLLOW-UP PERIOD OF 16.8 MONTHS, MULTIVARIATE ANALYSIS REVEALED THAT PATIENTS WITH PCDH10 METHYLATION IN ADJACENT NONTUMOR AREAS HAD A SIGNIFICANT DECREASE IN OVERALL SURVIVAL. KAPLAN-MEIER SURVIVAL CURVES SHOWED THAT PCDH10 METHYLATION WAS ASSOCIATED SIGNIFICANTLY WITH SHORTENED SURVIVAL IN STAGE I-III GASTRIC CANCER PATIENTS. CONCLUSIONS: PCDH10 IS A GASTRIC TUMOR SUPPRESSOR; ITS METHYLATION AT EARLY STAGES OF GASTRIC CARCINOGENESIS IS AN INDEPENDENT PROGNOSTIC FACTOR.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
15   143  28 ABERRANT DNA METHYLATION OF TWO TUMOR SUPPRESSOR GENES, P14(ARF) AND P15(INK4B), AFTER CHRONIC OCCUPATIONAL EXPOSURE TO LOW LEVEL OF BENZENE. BACKGROUND: EXPOSURE TO BENZENE WOULD BE ASSOCIATED WITH MANY DISEASES INCLUDING LEUKEMIA. EPIGENETIC ALTERATIONS SEEM TO BE AMONG THE MAIN MECHANISMS INVOLVED. OBJECTIVE: TO DETERMINE IF CHRONIC OCCUPATIONAL EXPOSURE TO LOW LEVEL OF BENZENE WOULD BE ASSOCIATED WITH DNA METHYLATION. METHODS: GLOBAL DNA METHYLATION AND PROMOTER-SPECIFIC METHYLATION OF THE TWO TUMOR SUPPRESSOR GENES, P14(ARF) AND P15(INK4B), WERE ASSESSED EMPLOYING METHYLATION-SPECIFIC PCR USING THE DNA EXTRACTED FROM 40 PETROCHEMICAL WORKERS EXPOSED TO AMBIENT BENZENE LEVELS OF <1 PPM, AND 31 OFFICE WORKERS NOT EXPOSED TO BENZENE OR ITS DERIVATIVES. RESULTS: WHILE AN INCREASE IN GLOBAL DNA METHYLATION OF 5% IN P14(ARF) (P=0.501) AND 28% IN P15(INK4B) (P=0.02) GENES WAS OBSERVED IN THE EXPOSED GROUP, NO HYPERMETHYLATION IN EITHER OF THE STUDIED GENES WAS OBSERVED IN THE UNEXPOSED GROUP. NO SIGNIFICANT ASSOCIATION WAS FOUND BETWEEN THE FREQUENCY OF ABERRANT METHYLATION AND EITHER OF AGE, WORK EXPERIENCE, AND SMOKING HABIT IN THE EXPOSED GROUP. CONCLUSION: CHRONIC OCCUPATIONAL EXPOSURE TO LOWER THAN THE PERMISSIBLE EXPOSURE LIMIT OF BENZENE MAY STILL RESULT IN DNA METHYLATION OF TUMOR SUPPRESSOR GENES THAT MAY ULTIMATELY LEAD TO DEVELOPMENT OF CANCER.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
16  3783  26 INTERFERON-GAMMA PROMOTER HYPOMETHYLATION AND INCREASED EXPRESSION IN CHRONIC PERIODONTITIS. AIM: THE GOAL OF THIS INVESTIGATION WAS TO DETERMINE WHETHER EPIGENETIC MODIFICATIONS IN THE IFNG PROMOTER ARE ASSOCIATED WITH AN INCREASE OF IFNG TRANSCRIPTION IN DIFFERENT STAGES OF PERIODONTAL DISEASES. MATERIALS AND METHODS: DNA WAS EXTRACTED FROM GINGIVAL BIOPSY SAMPLES COLLECTED FROM 47 TOTAL SITES FROM 47 DIFFERENT SUBJECTS: 23 PERIODONTALLY HEALTHY SITES, 12 EXPERIMENTALLY INDUCED GINGIVITIS SITES AND 12 CHRONIC PERIODONTITIS SITES. LEVELS OF DNA METHYLATION WITHIN THE IFNG PROMOTER CONTAINING SIX CPG DINUCLEOTIDES WERE DETERMINED USING PYROSEQUENCING TECHNOLOGY. INTERFERON GAMMA MRNA EXPRESSION WAS ANALYSED BY QUANTITATIVE POLYMERASE CHAIN REACTIONS USING ISOLATED RNA FROM PART OF THE BIOLOGICAL SAMPLES MENTIONED ABOVE. RESULTS: THE METHYLATION LEVEL OF ALL SIX ANALYSED CPG SITES WITHIN THE IFNG PROMOTER REGION IN THE PERIODONTITIS BIOPSIES 52% [INTERQUARTILE RANGE, IQR (43.8%, 63%)] WAS SIGNIFICANTLY LOWER THAN PERIODONTALLY HEALTHY SAMPLES 62% [IQR (51.3%, 74%)], P=0.007 AND GINGIVITIS BIOPSIES 63% [IQR (55%, 74%)], P=0.02. THE TRANSCRIPTIONAL LEVEL OF IFNG IN PERIODONTITIS BIOPSIES WAS 1.96-FOLD AND SIGNIFICANTLY HIGHER THAN TISSUES WITH PERIODONTAL HEALTH (P=0.04). ALTHOUGH THE MRNA LEVEL FROM EXPERIMENTAL GINGIVITIS SAMPLES EXHIBITED AN 8.5-FOLD INCREASE AS COMPARED WITH PERIODONTALLY HEALTHY SAMPLES, NO SIGNIFICANT METHYLATION DIFFERENCE WAS OBSERVED IN EXPERIMENTAL GINGIVITIS SAMPLE. CONCLUSIONS: A HYPOMETHYLATION PROFILE WITHIN IFNG PROMOTER REGION IS RELATED TO AN INCREASE OF IFNG TRANSCRIPTION PRESENT IN THE CHRONIC PERIODONTITIS BIOPSIES, WHILE SUCH AN INCREASE OF IFNG IN EXPERIMENTALLY INDUCED GINGIVITIS SEEMS INDEPENDENT OF PROMOTER METHYLATION ALTERATION.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
17  1908  28 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	
                                                                                                                      
18  2374  38 EPIGENETIC REGULATION OF TNFA EXPRESSION IN PERIODONTAL DISEASE. BACKGROUND: TUMOR NECROSIS FACTOR-ALPHA (TNF-ALPHA) PLAYS A CENTRAL ROLE IN THE MOLECULAR PATHOGENESIS OF PERIODONTAL DISEASE. HOWEVER, THE EPIGENETIC REGULATION ATTRIBUTABLE TO MICROBIAL AND INFLAMMATORY SIGNALS AT THE BIOFILM-GINGIVAL INTERFACE ARE POORLY UNDERSTOOD. IN THIS STUDY, THE DNA METHYLATION ALTERATION WITHIN THE TNFA PROMOTER IN HUMAN GINGIVAL BIOPSIES FROM DIFFERENT STAGES OF PERIODONTAL DISEASE IS INVESTIGATED AND THE REGULATORY MECHANISM OF TNFA TRANSCRIPTION BY DNA METHYLATION IS EXPLORED. METHODS: GINGIVAL BIOPSIES WERE OBTAINED FROM 17 PATIENTS WITH CHRONIC PERIODONTITIS (CP) AND 18 PERIODONTALLY HEALTHY INDIVIDUALS. ANOTHER 11 INDIVIDUALS PARTICIPATED IN AN EXPERIMENTALLY INDUCED GINGIVITIS STUDY, AND GINGIVAL BIOPSIES WERE COLLECTED AT THE BASELINE, INDUCTION, AND RESOLUTION PHASE. TO CONFIRM THAT TNFA PROMOTER METHYLATION MODULATED TNFA TRANSCRIPTION, THP.1 CELLS WERE TREATED WITH A DNA METHYLTRANSFERASE INHIBITOR, 5-AZA-2-DEOXYCYTIDINE (5-AZA-2DC), AND AN RAW294.7 CELL LINE TRANSFECTED WITH A TNFA PROMOTER-SPECIFIC LUCIFERASE REPORTER SYSTEM WITH OR WITHOUT METHYLATION WAS USED. RESULTS: IN GINGIVAL BIOPSIES FROM INDIVIDUALS WITH SEVERE CP, TWO INDIVIDUAL CYTOSINE-GUANINE DINUCLEOTIDES (CPG SITES) WITHIN THE TNFA PROMOTER (AT -163 AND -161 BP) DISPLAYED INCREASED METHYLATION IN CP SAMPLES COMPARED TO THOSE WITH GINGIVAL HEALTH (16.1% +/- 5.1% VERSUS 11.0% +/- 4.6%, P = 0.02 AND 19.8% +/- 4.1% VERSUS 15.4% +/- 3.6%, P = 0.04, RESPECTIVELY). THE METHYLATION LEVEL AT -163 BP WAS INVERSELY ASSOCIATED WITH THE TRANSCRIPTION LEVEL OF TNFA (P = 0.018). HOWEVER, NO SIGNIFICANT DIFFERENCE IN THE TNFA PROMOTER METHYLATION PATTERN WAS OBSERVED IN SAMPLES BIOPSIED DURING THE INDUCTION OR RESOLUTION PHASE OF EXPERIMENTALLY INDUCED GINGIVITIS, WHICH REPRESENTED A REVERSIBLE PERIODONTAL LESION. THP.1 CELLS TREATED WITH 5-AZA-2DC DEMONSTRATED A TIME-DEPENDENT INCREASE IN TNFA MESSENGER LEVEL. IT WAS ALSO FOUND THAT THE LUCIFERASE ACTIVITY DECREASED 2.6-FOLD IN A CONSTRUCT CONTAINING AN IN VITRO METHYLATED TNFA PROMOTER WHEN COMPARED TO THE UNMETHYLATED INSERT (P = 0.03). CONCLUSION: ALTHOUGH THE BIOPSY SAMPLES REPRESENTED A MIXED CELL POPULATION, THE CHANGE IN PROMOTER METHYLATION STATUS IN CHRONIC PERIODONTAL DISEASE SUGGESTED THAT DNA METHYLATION MAY BE AN IMPORTANT REGULATORY MECHANISM IN CONTROLLING TNFA TRANSCRIPTIONAL EXPRESSION IN PERIODONTAL DISEASE.	2013	
                                                                                                                                                                               
19  3294  21 HIGH INCIDENCE OF MGMT AND RARBETA PROMOTER METHYLATION IN PRIMARY GLIOBLASTOMAS: ASSOCIATION WITH HISTOPATHOLOGICAL CHARACTERISTICS, INFLAMMATORY MEDIATORS AND CLINICAL OUTCOME. GLIOBLASTOMAS, THE MOST FREQUENT PRIMARY BRAIN TUMORS IN ADULTS, ARE CHARACTERIZED BY A HIGHLY AGGRESSIVE, INFLAMMATORY AND ANGIOGENIC PHENOTYPE. METHYLATION OF CPG ISLANDS IN CANCER-RELATED GENES MAY SERVE AS AN EPIGENETIC BIOMARKER FOR GLIOBLASTOMA DIAGNOSIS AND PROGNOSIS. THE AIM OF THIS STUDY WAS TO ANALYZE THE METHYLATION STATUS OF FOUR CRITICAL TUMOR-ASSOCIATED GENES (MGMT, RARBETA, RASSF1A, CDH13), AND INVESTIGATE POSSIBLE LINKS WITH INFLAMMATORY (INTERLEUKIN [IL]-6, IL-8) AND ANGIOGENIC MEDIATORS (VASCULAR ENDOTHELIAL GROWTH FACTOR [VEGF], CYCLOOXYGENASE [COX]-2) AND CLINICAL OUTCOME IN 23 GLIOMA SAMPLES (6 GRADE II ASTROCYTOMAS, 17 GRADE IV GLIOBLASTOMAS). RARBETA AND MGMT GENES WERE MORE FREQUENTLY METHYLATED IN 70.58% AND 58.8% OF GLIOBLASTOMAS, RESPECTIVELY. RASSF1A AND CDH13 DISPLAYED A SIMILAR METHYLATION FREQUENCY (23.52%) IN GLIOBLASTOMAS. NO GENE METHYLATION WAS OBSERVED IN GRADE II ASTROCYTOMAS. TUMOR GRADE CORRELATED POSITIVELY WITH MGMT AND RARBETA METHYLATION (P = 0.005 AND P = 0.019, RESPECTIVELY) AND THE EXTENT OF NECROSIS (P = 0.001 AND P = 0.003). INTERESTINGLY, THE MARKER OF CHRONIC INFLAMMATION, IL-6, WAS POSITIVELY ASSOCIATED WITH METHYLATION OF MGMT (P = 0.004), RARBETA (P = 0.002), AND RASSF1A (P = 0.0081) AS WELL AS THE TOTAL NUMBER OF METHYLATED GENES (P < 0.0001), INDICATING THE IMPORTANT ROLE OF IL-6 IN MAINTAINING PROMOTER METHYLATION OF THESE GENES. VEGF EXPRESSION CORRELATED POSITIVELY WITH MGMT AND RARBETA METHYLATION ALTHOUGH THESE RELATIONSHIPS WERE OF MARGINAL SIGNIFICANCE (P = 0.0679 AND P = 0.0757). KAPLAN-MEIER UNIVARIATE SURVIVAL ANALYSIS INDICATED AN UNFAVORABLE SURVIVAL PERIOD IN PATIENTS WITH MGMT METHYLATION COMPARED WITH THOSE WITHOUT METHYLATION (P = 0.0474). OUR STUDY HIGHLIGHTS THE IMPLICATION OF MGMT AND RARBETA METHYLATION IN THE AGGRESSIVE PHENOTYPE OF PRIMARY GLIOBLASTOMAS. THE ASSOCIATION OF MGMT METHYLATION WITH CLINICAL OUTCOME INDICATES ITS POTENTIAL PROGNOSTIC VALUE.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
20   159  31 ABERRANT PROMOTER HYPERMETHYLATION OF MULTIPLE GENES IN GALLBLADDER CARCINOMA AND CHRONIC CHOLECYSTITIS. PURPOSE: ABERRANT METHYLATION OF 5' GENE PROMOTER REGIONS IS AN EPIGENETIC PHENOMENON THAT IS A MAJOR MECHANISM FOR SILENCING OF TUMOR SUPPRESSOR GENES IN MANY CANCER TYPES. THERE IS LIMITED INFORMATION ABOUT THE MOLECULAR CHANGES INVOLVED IN THE PATHOGENESIS OF GALLBLADDER CARCINOMA (GBC), INCLUDING METHYLATION STATUS. EXPERIMENTAL DESIGN: WE INVESTIGATED THE ABERRANT PROMOTER METHYLATION PROFILE OF 24 KNOWN OR SUSPECTED TUMOR SUPPRESSOR GENES IN 50 GBCS AND COMPARED THOSE RESULTS WITH THE FINDINGS IN 25 CHRONIC CHOLECYSTITIS (CC) SPECIMENS WITHOUT CANCER. THE METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION AND COMBINED RESTRICTION ANALYSIS METHODS WERE USED TO DETECT METHYLATION, AND THE RESULTS WERE CONFIRMED BY SEQUENCING OF CLONED POLYMERASE CHAIN REACTION PRODUCTS. RESULTS: IN GBC, GENE METHYLATION FREQUENCIES VARIED FROM 0% TO 80%. TEN GENES DEMONSTRATED RELATIVELY HIGH FREQUENCIES OF ABERRANT METHYLATION: SHP1 (80%), 3-OST-2 (72%), CDH13 (44%), P15INK4B (44%), CDH1 (38%), RUNX3 (32%), APC (30%), RIZ1 (26%), P16INK4A (24%), AND HPP1 (20%). EIGHT GENES (P73, RARBETA2, SOCS-1, DAPK, DCR2, DCR1, HIN1, AND CHFR) SHOWED LOW FREQUENCIES (2-14%) OF METHYLATION, AND NO METHYLATION OF THE REMAINING SIX GENES (TIMP-3, P57, RASSF1A, CRBP1, SYK, AND NORE1) WAS DETECTED. IN CC, METHYLATION WAS DETECTED FOR SEVEN GENES: SHP1 (88%), P15INK4B (28%), 3-OST-2 (12%), CDH1 (12%), CDH13 (8%), DCR2 (4%), AND P16INK4A (4%). SIGNIFICANTLY HIGHER FREQUENCIES OF METHYLATION IN GBC COMPARED WITH CC WERE DETECTED FOR EIGHT GENES (3-OST-2, CDH13, CDH1, RUNX3, APC, RIZ1, P16INK4A, AND HPP1). OF THOSE, FOUR GENES SHOWED FREQUENT METHYLATION (>30%) IN GBCS. THE MEAN METHYLATION INDEX, AN EXPRESSION OF THE AMOUNT OF METHYLATED GENES BY CASE, WAS SIGNIFICANTLY HIGHER IN GBC (0.196 +/- 0.013) COMPARED WITH CC (0.065 +/- 0.008; P < 0.001). CONCLUSIONS: OUR STUDY CONSTITUTES THE MOST COMPREHENSIVE METHYLATION PROFILE REPORT AVAILABLE IN GBC AND DEMONSTRATES THAT THIS NEOPLASM HAS A DISTINCT PATTERN OF ABNORMAL GENE METHYLATION. WHEREAS GALLBLADDERS FROM HEALTHY INDIVIDUAL WERE NOT AVAILABLE, OUR FINDING OF METHYLATION IN CC CASES WITHOUT CANCER SUGGESTS THAT THIS PHENOMENON REPRESENTS AN EARLY EVENT IN THE PATHOGENESIS OF GBC.	2004