1   772 101 CDYL DEFICIENCY BRAKES NEURONAL EXCITABILITY AND NOCICEPTION THROUGH PROMOTING KCNB1 TRANSCRIPTION IN PERIPHERAL SENSORY NEURONS. EPIGENETIC MODIFICATIONS ARE INVOLVED IN THE ONSET, DEVELOPMENT, AND MAINTENANCE OF PAIN; HOWEVER, THE PRECISE EPIGENETIC MECHANISM UNDERLYING PAIN REGULATION REMAINS ELUSIVE. HERE IT IS REPORTED THAT THE EPIGENETIC FACTOR CHROMODOMAIN Y-LIKE (CDYL) IS CRUCIAL FOR PAIN PROCESSING. SELECTIVE KNOCKOUT OF CDYL IN SENSORY NEURONS RESULTS IN DECREASED NEURONAL EXCITABILITY AND NOCICEPTION. MOREOVER, CDYL FACILITATES HISTONE 3 LYSINE 27 TRIMETHYLATION (H3K27ME3) DEPOSITION AT THE KCNB1 INTRON REGION THUS SILENCING VOLTAGE-GATED POTASSIUM CHANNEL (K(V) ) SUBFAMILY MEMBER K(V) 2.1 TRANSCRIPTION. LOSS FUNCTION OF CDYL ENHANCES TOTAL K(V) AND K(V) 2.1 CURRENT DENSITY IN DORSAL ROOT GANGLIA AND KNOCKDOWN OF K(V) 2.1 REVERSES THE PAIN-RELATED PHENOTYPES OF CDYL DEFICIENCY MICE. FURTHERMORE, FOCAL ADMINISTRATION OF A NOVEL POTENT CDYL ANTAGONIST BLUNTS NOCICEPTION AND ATTENUATES NEUROPATHIC PAIN. THESE FINDINGS REVEAL THAT CDYL IS A CRITICAL REGULATOR OF PAIN SENSATION AND SHED LIGHT ON THE DEVELOPMENT OF NOVEL ANALGESICS TARGETING EPIGENETIC MECHANISMS.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
2  5553  21 ROLE OF EPIGENETICS IN THE PATHOGENESIS OF CHRONIC RHINOSINUSITIS WITH NASAL POLYPS. CHRONIC RHINOSINUSITIS (CRS) IS A HIGHLY PREVALENT DISEASE CHARACTERIZED BY MUCOSAL INFLAMMATION OF THE NOSE AND PARANASAL SINUSES. CRS CAN BE DIVIDED INTO TWO MAIN CATEGORIES, CRS WITH NASAL POLYPS (NPS; CRSWNP) AND CRS WITHOUT NPS (CRSSNP). ALTHOUGH THE PATHOPHYSIOLOGY OF CRS REMAINS UNCLEAR, DNA METHYLATION HAS BEEN IMPLICATED IN THE ETIOLOGY OF CRSWNP. THE AIM OF THE PRESENT STUDY WAS TO ELUCIDATE WHETHER DNA METHYLATION OF SPECIFIC GENES IS INVOLVED IN THE DEVELOPMENT OF NPS. IN TOTAL, 18 INDIVIDUALS WERE INCLUDED IN THE PRESENT STUDY, AND WERE DIVIDED INTO THREE GROUPS: CRSWNP (N=7), CRSSNP (N=7) AND HEALTHY CONTROLS (N=4). NP TISSUES WERE OBTAINED FROM THE SEVEN PATIENTS WITH CRSWNP AND BIOPSIES OF THE INFERIOR TURBINATE MUCOSA FROM ALL THREE GROUPS WERE USED AS CONTROLS. METHYLATED GENES DETECTED BY METHYL?CPG?BINDING DOMAIN SEQUENCING WERE VALIDATED BY METHYLATION?SPECIFIC POLYMERASE CHAIN REACTION (PCR), BISULFITE SEQUENCING, AND REVERSE TRANSCRIPTION?QUANTITATIVE PCR (RT?QPCR). METHYL?CPG?BINDING DOMAIN SEQUENCING IDENTIFIED 43,674 CPG ISLANDS IN 518 GENES. THE PROMOTOR REGIONS OF 10 AND 30 GENES WERE HYPERMETHYLATED AND HYPOMETHYLATED, RESPECTIVELY, IN NP SAMPLES COMPARED WITH CONTROLS. THE TOP FOUR GENES WITH ALTERED HYPOMETHYLATION IN NP TISSUES WERE, KERATIN 19 (KRT19), NUCLEAR RECEPTOR SUBFAMILY 2 GROUP F MEMBER 2 (NR2F2), A DISINTEGRIN?LIKE AND METALLOPEPTIDASE (REPROLYSIN TYPE) WITH THROMBOSPONDIN TYPE 1 MOTIF 1 (ADAMTS1) AND ZINC FINGER PROTEIN 222 (ZNF222). RT?QPCR DEMONSTRATED THAT THE EXPRESSION LEVELS OF KRT19, NR2F2 AND ADAMTS1 WERE SIGNIFICANTLY INCREASED IN NP TISSUES; HOWEVER, THERE WAS NO DIFFERENCE IN THE LEVELS OF ZNF222 BETWEEN NP AND CONTROL TISSUES. FURTHER STUDIES ARE REQUIRED TO CONFIRM THE RELEVANCE OF THESE EPIGENETIC MODIFICATIONS IN THE MECHANISMS UNDERLYING NP FORMATION.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
3   415  17 ANALYSIS OF RETROTRANSPOSON SUBFAMILY DNA METHYLATION REVEALS NOVEL EARLY EPIGENETIC CHANGES IN CHRONIC LYMPHOCYTIC LEUKEMIA. RETROTRANSPOSONS SUCH AS LINE-1 AND ALU COMPRISE >25% OF THE HUMAN GENOME. WHILE GLOBAL HYPOMETHYLATION OF THESE ELEMENTS HAS BEEN WIDELY REPORTED IN SOLID TUMOURS, THEIR EPIGENETIC DYSREGULATION IS YET TO BE CHARACTERISED IN CHRONIC LYMPHOCYTIC LEUKAEMIA, AND THERE HAS BEEN SCANT CONSIDERATION OF THEIR EVOLUTIONARY HISTORY THAT MEDIATES SENSITIVITY TO HYPOMETHYLATION. HERE, WE DEVELOPED AN APPROACH FOR LOCUS- AND EVOLUTIONARY SUBFAMILY-SPECIFIC ANALYSIS OF RETROTRANSPOSONS USING THE ILLUMINA INFINIUM HUMAN METHYLATION 450K MICROARRAY PLATFORM, WHICH WE APPLIED TO PUBLICLY-AVAILABLE DATASETS FROM CHRONIC LYMPHOCYTIC LEUKAEMIA AND OTHER HAEMATOLOGICAL MALIGNANCIES. WE IDENTIFIED 9,797 MICROARRAY PROBES MAPPING TO 117 LINE-1 SUBFAMILIES AND 13,130 MAPPING TO 37 ALU SUBFAMILIES. OF THESE, 10,782 WERE DIFFERENTIALLY METHYLATED (PFDR<0.05) IN CHRONIC LYMPHOCYTIC LEUKAEMIA PATIENTS (N=139) COMPARED WITH HEALTHY INDIVIDUALS (N=14), WITH ENRICHMENT AT ENHANCERS (P=0.002). DIFFERENTIAL METHYLATION WAS ASSOCIATED WITH EVOLUTIONARY AGE OF LINE-1 (R2=0.31, P=0.003) AND ALU (R2=0.74, P=0.002) ELEMENTS, WITH GREATER HYPOMETHYLATION OF OLDER SUBFAMILIES (L1M, ALUJ). LOCUS-SPECIFIC HYPOMETHYLATION WAS ASSOCIATED WITH DIFFERENTIAL EXPRESSION OF PROXIMAL GENES, INCLUDING DCLK2, HK1, ILRUN, TANK, TBCD, TNFRSF1B AND TXNRD2, WITH HIGHER EXPRESSION OF DCLK2 AND TNFRSF1B ASSOCIATED WITH REDUCED PATIENT SURVIVAL. HYPOMETHYLATION AT NINE LOCI WAS HIGHLY FREQUENT IN CHRONIC LYMPHOCYTIC LEUKAEMIA (>90% PATIENTS) BUT NOT OBSERVED IN HEALTHY INDIVIDUALS OR OTHER LEUKAEMIAS, AND WAS DETECTABLE IN BLOOD SAMPLES TAKEN PRIOR TO CHRONIC LYMPHOCYTIC LEUKAEMIA DIAGNOSIS IN 9 OF 82 INDIVIDUALS FROM THE MELBOURNE COLLABORATIVE COHORT STUDY. OUR RESULTS DEMONSTRATE DIFFERENTIAL METHYLATION OF RETROTRANSPOSONS IN CHRONIC LYMPHOCYTIC LEUKAEMIA BY THEIR EVOLUTIONARY HERITAGE THAT MODULATES EXPRESSION OF PROXIMAL GENES.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                       
4  3433  35 HYDROXYMETHYLATION OF MICRORNA-365-3P REGULATES NOCICEPTIVE BEHAVIORS VIA KCNH2. DNA 5-HYDROXYLMETHYLCYTOSINE (5HMC) CATALYZED BY TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE (TET) OCCURS ABUNDANTLY IN NEURONS OF MAMMALS. HOWEVER, THE IN VIVO CAUSAL LINK BETWEEN TET DYSREGULATION AND NOCICEPTIVE MODULATION HAS NOT BEEN ESTABLISHED. HERE, WE FOUND THAT SPINAL TET1 AND TET3 WERE SIGNIFICANTLY INCREASED IN THE MODEL OF FORMALIN-INDUCED ACUTE INFLAMMATORY PAIN, WHICH WAS ACCOMPANIED WITH THE AUGMENT OF GENOME-WIDE 5HMC CONTENT IN SPINAL CORD. KNOCKDOWN OF SPINAL TET1 OR TET3 ALLEVIATED THE FORMALIN-INDUCED NOCICEPTIVE BEHAVIOR AND OVEREXPRESSION OF SPINAL TET1 OR TET3 IN NAIVE MICE PRODUCED PAIN-LIKE BEHAVIOR AS EVIDENCED BY DECREASED THERMAL PAIN THRESHOLD. FURTHERMORE, WE FOUND THAT TET1 OR TET3 REGULATED THE NOCICEPTIVE BEHAVIOR BY TARGETING MICRORNA-365-3P (MIR-365-3P). FORMALIN INCREASED 5HMC IN THE MIR-365-3P PROMOTER, WHICH WAS INHIBITED BY KNOCKDOWN OF TET1 OR TET3 AND MIMICKED BY OVEREXPRESSION OF TET1 OR TET3 IN NAIVE MICE. NOCICEPTIVE BEHAVIOR INDUCED BY FORMALIN OR OVEREXPRESSION OF SPINAL TET1 OR TET3 COULD BE PREVENTED BY DOWNREGULATION OF MIR-365-3P, AND MIMICKED BY OVEREXPRESSION OF SPINAL MIR-365-3P. FINALLY, WE DEMONSTRATED THAT A POTASSIUM CHANNEL, VOLTAGE-GATED EAG-RELATED SUBFAMILY H MEMBER 2 (KCNH2), VALIDATED AS A TARGET OF MIR-365-3P, PLAYED A CRITICAL ROLE IN NOCICEPTIVE MODULATION BY SPINAL TET OR MIR-365-3P. TOGETHER, WE CONCLUDED THAT TET-MEDIATED HYDROXYMETHYLATION OF MIR-365-3P REGULATES NOCICEPTIVE BEHAVIOR VIA KCNH2. SIGNIFICANCE STATEMENT: MOUNTING EVIDENCE INDICATES THAT EPIGENETIC MODIFICATIONS IN THE NOCICEPTIVE PATHWAY CONTRIBUTE TO PAIN PROCESSES AND ANALGESIA RESPONSE. HERE, WE FOUND THAT THE INCREASE OF 5HMC CONTENT MEDIATED BY TET1 OR TET3 IN MIR-365-3P PROMOTER IN THE SPINAL CORD IS INVOLVED IN NOCICEPTIVE MODULATION THROUGH TARGETING A POTASSIUM CHANNEL, KCNH2. OUR STUDY REVEALS A NEW EPIGENETIC MECHANISM UNDERLYING NOCICEPTIVE INFORMATION PROCESSING, WHICH MAY BE A NOVEL TARGET FOR DEVELOPMENT OF ANTINOCICEPTIVE DRUGS.	2016	
                                                                                                                                                                                                                                                                                                                                      
5  6674  15 USE OF METHYLATION PROFILING TO IDENTIFY SIGNIFICANT DIFFERENTIALLY METHYLATED GENES IN BONE MARROW MESENCHYMAL STROMAL CELLS FROM ACUTE MYELOID LEUKEMIA. THE PRESENT STUDY AIMED TO CHARACTERIZE THE EPIGENETIC ARCHITECTURE BY STUDYING THE DNA METHYLATION SIGNATURE IN BONE MARROW MESENCHYMAL STEM CELLS (BM?MSCS) FROM PATIENTS WITH ACUTE MYELOID LEUKEMIA (AML). MICROARRAY DATASET GSE79695 WAS DOWNLOADED FROM THE GENE EXPRESSION OMNIBUS DATABASE. DIFFERENTIALLY METHYLATED SITES AND DIFFERENTIALLY METHYLATED CPG ISLANDS WERE IDENTIFIED IN BM?MSC SAMPLES FROM PATIENTS WITH AML COMPARED WITH CONTROLS. MICRORNAS (MIRS) ENCODING GENES COVERING DIFFERENTIALLY METHYLATED SITES WERE FOUND AND THE REGULATION NETWORK WAS CONSTRUCTED. PATHWAY ENRICHMENT ANALYSIS OF HYPERMETHYLATED GENES AND HYPOMETHYLATED GENES WAS PERFORMED, FOLLOWED BY PROTEIN?PROTEIN INTERACTION (PPI) NETWORK CONSTRUCTION. MOREOVER, THE IDENTIFIED DIFFERENTIALLY METHYLATED GENES WERE COMPARED WITH THE LEUKEMIA?RELATED MARKER/THERAPEUTIC GENES FROM THE LITERATURE. OVERALL, 228 HYPERMETHYLATED CPG SITE PROBES COVERING 183 GENE SYMBOLS AND 523 HYPOMETHYLATED CPG SITES PROBES COVERING 362 GENE SYMBOLS WERE IDENTIFIED IN THE BM?MSCS FROM AML PATIENTS. FURTHERMORE, 4 GENES WITH CPG ISLAND HYPERMETHYLATION WERE IDENTIFIED, INCLUDING PEPTIDASE M20 DOMAIN CONTAINING 1 (PM20D1). THE HSA?MIR?596?ENCODING GENE MIR596 WAS FOUND TO BE HYPERMETHYLATED AND THE REGULATION NETWORK BASED ON HSA?MIR?596 AND ITS TARGETS (SUCH AS CYTOCHROME P450 FAMILY 1 SUBFAMILY B MEMBER 1) WAS CONSTRUCTED. HYPERMETHYLATED AND HYPOMETHYLATED GENES WERE ENRICHED IN DIFFERENT KYOTO ENCYCLOPEDIA OF GENES AND GENOMES PATHWAYS, INCLUDING 'HSA05221: ACUTE MYELOID LEUKEMIA' AND 'HSA05220: CHRONIC MYELOID LEUKEMIA', WHICH THE HYPOMETHYLATED GENE MITOGEN?ACTIVATED PROTEIN KINASE 3 (MAPK3) WAS INVOLVED IN. IN ADDITION, MAPK3, LYSINE DEMETHYLASE 2B AND RAP1A, MEMBER OF RAS ONCOGENE FAMILY WERE HUBS IN THE PPI NETWORK OF METHYLATED GENES. IN CONCLUSION, PM20D1 WITH HYPERMETHYLATION OF CPG ISLANDS MAY BE ASSOCIATED WITH THE ENERGY EXPENDITURE OF PATIENTS WITH AML. FURTHERMORE, THE ABERRANTLY HYPERMETHYLATED MIR?159?ENCODING GENE MIR159 MAY BE A POTENTIAL BIOMARKER OF AML.	2018	
                                                                                                                                                                                                                  
6    83  18 A NOVEL EPIGENETIC MARKER, TEN-ELEVEN TRANSLOCATION FAMILY MEMBER 2 (TET2), IS IDENTIFIED IN THE INTRACTABLE EPILEPTIC BRAIN AND REGULATES ATP BINDING CASSETTE SUBFAMILY B MEMBER 1 (ABCB1) IN THE BLOOD-BRAIN BARRIER. DRUG-RESISTANT EPILEPSY (DRE) IS A CHRONIC CONDITION DERIVED FROM SPONTANEOUS CHANGES AND REGULATORY EFFECTS IN THE EPILEPTIC BRAIN. AS DEMETHYLATION FACTORS, TEN-ELEVEN TRANSLOCATION (TET) FAMILY MEMBERS HAVE BECOME A FOCUS IN RECENT STUDIES OF NEUROLOGICAL DISORDERS. HERE, WE QUANTIFIED AND LOCALIZED TET1, TET2 AND 5-HYDROXYMETHYLCYTOSINE (5-HMC) IN THE TEMPORAL LOBE CORTEX OF DRE PATIENTS (N = 27) AND TRAUMATIC BRAIN HEMORRHAGE CONTROLS (N = 10) BY IMMUNOCHEMICAL STAINING. TET2 AND ATP BINDING CASSETTE SUBFAMILY B MEMBER 1 (ABCB1) EXPRESSION PATTERNS WERE DETERMINED IN THE ISOLATED BRAIN CAPILLARIES OF DRE PATIENTS. TET2 EXPRESSION WAS SIGNIFICANTLY INCREASED IN THE TEMPORAL CORTICAL TISSUE OF DRE PATIENTS WITH OR WITHOUT HIPPOCAMPAL SCLEROSIS (HS) COMPARED TO CONTROL PATIENTS, WHILE TET1 AND 5-HMC SHOWED NO DIFFERENCES IN EXPRESSION. WE ALSO FOUND THAT A PARTICULARLY STRONG EXPRESSION OF TET2 IN THE VASCULAR TISSUE OF DRE PATIENTS. ABCB1 AND TET2 HAVE EVIDENTLY HIGHER EXPRESSION IN THE VASCULAR ENDOTHELIUM FROM THE NEOCORTEX OF DRE PATIENTS. IN BLOOD-BRAIN BARRIER (BBB) MODEL, TET2 DEPLETION CAN CAUSE ATTENUATED EXPRESSION AND FUNCTION OF ABCB1. DATA FROM A COHORT STUDY AND EXPERIMENTS IN A BBB MODEL SUGGEST THAT TET2 HAS A SPECIFIC REGULATORY EFFECT ON ABCB1, WHICH MAY SERVE AS A POTENTIAL MECHANISM AND TARGET IN DRE.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
7  1839  18 EFFECTS OF PRENATAL NICOTINE EXPOSURE ON HEPATIC GLUCOSE AND LIPID METABOLISM IN OFFSPRING RATS AND ITS HEREDITABILITY. PRENATAL NICOTINE EXPOSURE (PNE) COULD INDUCE AN INCREASED SUSCEPTIBILITY TO MULTIPLE CHRONIC DISEASES IN ADULT OFFSPRING, THAT MAINLY CAUSED BY INTRAUTERINE MATERNAL GLUCOCORTICOID (GC) OVER-EXPOSURE. WE INVESTIGATED THE CHANGES AND INHERITABILITY OF HEPATIC GLUCOSE AND LIPID METABOLISM CAUSED BY PNE, TO DECIPHER THE POSSIBLE INTRAUTERINE PROGRAMMING MECHANISM. PREGNANT WISTAR RATS WERE ADMINISTERED SUBCUTANEOUSLY WITH 2 MG/KG.D NICOTINE FROM GESTATIONAL DAY (GD) 9 APPROXIMATELY 20, AND SECOND-GENERATION (F2) WERE SET ACCORDING TO THE MATING BETWEEN CONTROL FEMALES AND PNE MALES. THE RESULTS SHOWED THAT SERUM PHENOTYPES AND HEPATIC ENZYMES OF GLUCOSE AND LIPID METABOLISM WERE LOWER IN F1 FETAL RATS OF PNE BUT HIGHER IN THE F1 ADULT RATS. MEANWHILE, THE ACTIVATED STATES OF HEPATIC GLUCOCORTICOID-ACTIVATION SYSTEM, INCLUDING TYPE 1 AND TYPE 2 11BETA-HYDROXYSTEROID DEHYDROGENASES (HSD11B1/2), NUCLEAR RECEPTOR SUBFAMILY 3, GROUP C, MEMBER 1 (NR3C1) AND CCAAT ENHANCER BINDING PROTEIN ALPHA (CEBPA), WERE POSITIVELY CORRELATED WITH SERUM CORTICOSTERONE LEVELS BUT NEGATIVELY CORRELATED WITH THE HISTONE ACETYLATION (H3K27AC) AND EXPRESSION LEVELS OF INSULIN-LIKE GROWTH FACTOR 1 (IGF1) BEFORE AND AFTER BIRTH. FURTHERMORE, SERUM PHENOTYPES AND HEPATIC ENZYMES OF GLUCOSE AND LIPID METABOLISM WERE LOWER IN BOTH F2 FETAL AND ADULT RATS OF PNE, WHICH WERE CONSISTENT WITH THE HEPATIC CHANGES OF GC-IGF1 AXIS AND THE GLUCOCORTICOID-ACTIVATION SYSTEM. IN CONCLUSION, PNE COULD LEAD TO INHERITABLE CHANGES OF HEPATIC GLUCOSE AND LIPID METABOLISM, WHICH ARE RELATED TO THE INTRAUTERINE PROGRAMMING OF GC-IGF1 AXIS INDUCED BY THE GLUCOCORTICOID-ACTIVATION SYSTEM.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
8  2053  24 EPIGENETIC CONNECTIONS OF THE TRPA1 ION CHANNEL IN PAIN TRANSMISSION AND NEUROGENIC INFLAMMATION - A THERAPEUTIC PERSPECTIVE IN MIGRAINE? PERSISTENT REPROGRAMMING OF EPIGENETIC PATTERN LEADS TO CHANGES IN GENE EXPRESSION OBSERVED IN MANY NEUROLOGICAL DISORDERS. TRANSIENT RECEPTOR POTENTIAL CATION CHANNEL SUBFAMILY A MEMBER 1 (TRPA1), A MEMBER OF THE TRP CHANNELS SUPERFAMILY, IS ACTIVATED BY MANY MIGRAINE TRIGGERS AND EXPRESSED IN TRIGEMINAL NEURONS AND BRAIN REGIONS THAT ARE IMPORTANT IN MIGRAINE PATHOGENESIS. TRP CHANNELS CHANGE NOXIOUS STIMULI INTO PAIN SIGNALS WITH THE INVOLVEMENT OF EPIGENETIC REGULATION. THE EXPRESSION OF THE TRPA1 ENCODING GENE, TRPA1, IS MODULATED IN PAIN-RELATED SYNDROMES BY EPIGENETIC ALTERATIONS, INCLUDING DNA METHYLATION, HISTONE MODIFICATIONS, AND EFFECTS OF NON-CODING RNAS: MICRO RNAS (MIRNAS), LONG NON-CODING RNAS, AND CIRCULAR RNAS. TRPA1 MAY CHANGE EPIGENETIC PROFILE OF MANY PAIN-RELATED GENES AS IT MAY MODIFY ENZYMES RESPONSIBLE FOR EPIGENETIC MODIFICATIONS AND EXPRESSION OF NON-CODING RNAS. TRPA1 MAY INDUCE THE RELEASE OF CALCITONIN GENE RELATED PEPTIDE (CGRP), FROM TRIGEMINAL NEURONS AND DURAL TISSUE. THEREFORE, EPIGENETIC REGULATION OF TRPA1 MAY PLAY A ROLE IN EFFICACY AND SAFETY OF ANTI-MIGRAINE THERAPIES TARGETING TRP CHANNELS AND CGRP. TRPA1 IS ALSO INVOLVED IN NEUROGENIC INFLAMMATION, IMPORTANT IN MIGRAINE PATHOGENESIS. THE FUNDAMENTAL ROLE OF TRPA1 IN INFLAMMATORY PAIN TRANSMISSION MAY BE EPIGENETICALLY REGULATED. IN CONCLUSION, EPIGENETIC CONNECTIONS OF TRPA1 MAY PLAY A ROLE IN EFFICACY AND SAFETY OF ANTI-MIGRAINE THERAPY TARGETING TRP CHANNELS OR CGRP AND THEY SHOULD BE FURTHER EXPLORED FOR EFFICIENT AND SAFE ANTIMIGRAINE TREATMENT. THIS NARRATIVE/PERSPECTIVE REVIEW PRESENTS INFORMATION ON THE STRUCTURE AND FUNCTIONS OF TRPA1 AS WELL AS ROLE OF ITS EPIGENETIC CONNECTIONS IN PAIN TRANSMISSION AND POTENTIAL IN MIGRAINE THERAPY.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
9  5976  28 TET1-DEPENDENT EPIGENETIC MODIFICATION OF BDNF EXPRESSION IN DORSAL HORN NEURONS MEDIATES NEUROPATHIC PAIN IN RATS. TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE 1 (TET1) MEDIATES THE CONVERSION OF 5-METHYLCYTOSINE (5 MC) TO 5-HYDROXYMETHYLCYTOSINE (5 HMC), HENCE PROMOTING DNA DEMETHYLATION. ALTHOUGH RECENT STUDIES HAVE LINKED THE DNA DEMETHYLATION OF SPECIFIC GENES TO PAIN HYPERSENSITIVITY, THE ROLE OF SPINAL TET1-DEPENDENT DNA DEMETHYLATION IN NOCICEPTION HYPERSENSITIVITY DEVELOPMENT REMAINS ELUSIVE. HERE, WE REPORT CORRELATED WITH BEHAVIORAL ALLODYNIA, SPINAL NERVE LIGATION (SNL) UPREGULATED TET1 EXPRESSION IN DORSAL HORN NEURONS THAT HYDROXYLATE 5 MC TO 5 HMC AT CPG DINUCLEOTIDES IN THE BDNF PROMOTER TO PROMOTE SPINAL BDNF EXPRESSION AT DAY 7 AFTER OPERATION. FOCAL KNOCKDOWN OF SPINAL TET1 EXPRESSION DECREASED TET1 BINDING AND 5 HMC ENRICHMENT, FURTHER INCREASED 5 MC ENRICHMENT AT CPG SITES IN THE BDNF PROMOTER AND DECREASED SPINAL BDNF EXPRESSION ACCOMPANIED BY THE ALLEVIATION OF THE DEVELOPED ALLODYNIA. MOREOVER, AT DAY 7 AFTER OPERATION, SNL-ENHANCED TET1 EXPRESSION ALSO INHIBITED THE BINDING OF DNA METHYLTRANSFERASES (DNMTS, I.E., DNMT1, DNMT3A, AND DNMT3B) TO THE BDNF PROMOTER, A REQUIREMENT FOR TRANSCRIPTIONAL SILENCING BY CATALYSING 5-CYTOSINE (5C) TO 5 MC. TOGETHER, THESE DATA SUGGEST AT CPG SITES OF THE BDNF PROMOTER, SNL-ENHANCED TET1 EXPRESSION PROMOTES DNA DEMETHYLATION BOTH BY CONVERTING 5 MC TO 5 HMC AND INHIBITING DNMT BINDING TO REGULATE SPINAL BDNF EXPRESSION, HENCE CONTRIBUTING TO BEHAVIORAL ALLODYNIA DEVELOPMENT.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
10  2258  11 EPIGENETIC PRIMING IN CHRONIC LIVER DISEASE IMPACTS THE TRANSCRIPTIONAL AND GENETIC LANDSCAPES OF HEPATOCELLULAR CARCINOMA. HEPATOCELLULAR CARCINOMAS (HCCS) USUALLY ARISE FROM CHRONIC LIVER DISEASE (CLD). PRECANCEROUS CELLS IN CHRONICALLY INFLAMED ENVIRONMENTS MAY BE 'EPIGENETICALLY PRIMED', SENSITISING THEM TO ONCOGENIC TRANSFORMATION. WE INVESTIGATED WHETHER EPIGENETIC PRIMING IN CLD MAY AFFECT HCC OUTCOMES BY INFLUENCING THE GENOMIC AND TRANSCRIPTOMIC LANDSCAPES OF HCC. ANALYSIS OF DNA METHYLATION ARRAYS FROM 10 PAIRED CLD-HCC IDENTIFIED 339 SHARED DYSREGULATED CPG SITES AND 18 SHARED DIFFERENTIALLY METHYLATED REGIONS COMPARED WITH HEALTHY LIVERS. THESE REGIONS WERE ASSOCIATED WITH DYSREGULATED EXPRESSION OF GENES WITH RELEVANCE IN HCC, INCLUDING UBIQUITIN D (UBD), CYTOCHROME P450 FAMILY 2 SUBFAMILY C MEMBER 19 (CYP2C19) AND O-6-METHYLGUANINE-DNA METHYLTRANSFERASE (MGMT). METHYLATION CHANGES WERE RECAPITULATED IN AN INDEPENDENT COHORT OF NINE PAIRED CLD-HCC. HIGH CLD METHYLATION SCORE, DEFINED USING THE 124 DYSREGULATED CPGS IN CLD AND HCC IN BOTH COHORTS, WAS ASSOCIATED WITH POOR SURVIVAL, INCREASED SOMATIC GENETIC ALTERATIONS AND TP53 MUTATIONS IN TWO INDEPENDENT HCC COHORTS. ONCOGENIC TRANSCRIPTIONAL AND METHYLATION DYSREGULATION IS EVIDENT IN CLD AND COMPOUNDED IN HCC. EPIGENETIC PRIMING IN CLD SCULPTS THE TRANSCRIPTIONAL LANDSCAPE OF HCC AND CREATES AN ENVIRONMENT FAVOURING THE ACQUISITION OF GENETIC ALTERATIONS, SUGGESTING THAT THE EXTENT OF EPIGENETIC PRIMING IN CLD COULD INFLUENCE DISEASE OUTCOME.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
11  1564  18 DNA METHYLATION OF PROXIMAL PLAT PROMOTER IN CHRONIC RHINOSINUSITIS WITH NASAL POLYPS. BACKGROUND NASAL POLYPS (NP) ARE CHARACTERIZED BY PSEUDOCYSTS DERIVED FROM STROMAL TISSUE EDEMA AND CAUSE PERSISTENT INFECTIONS IN PATIENTS WITH CHRONIC RHINOSINUSITIS (CRS). A LOW LEVEL OF TISSUE-TYPE PLASMINOGEN ACTIVATOR (GENE NAME PLAT) IS CONSIDERED A CAUSE OF STROMAL TISSUE EDEMA BECAUSE OF INSUFFICIENT PLASMIN ACTIVATION IN NP; HOWEVER, THE MECHANISM REGULATING PLAT GENE EXPRESSION LEVELS IS STILL UNCLEAR. THE EPIGENETIC MECHANISM REGULATING THE PLAT GENE EXPRESSION HAS BEEN STUDIED IN OTHER TISSUES. OBJECTIVE WE AIMED TO INVESTIGATE THE METHYLATION LEVELS IN THE PROXIMAL PLAT PROMOTER AND THEIR EFFECTS ON GENE EXPRESSION IN NP TISSUE. METHODS WE INVESTIGATED THE METHYLATION LEVELS AT 3 CPG SITES IN THE PROXIMAL PLAT PROMOTER REGIONS (-618, -121, AND -105 WITH RESPECT TO THE TRANSCRIPTION INITIATION SITE) BY BISULFITE PYROSEQUENCING AND THEIR EFFECTS ON THE GENE EXPRESSION BY QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION (QPCR) IN 20 PAIRED SAMPLES OF NP AND INFERIOR TURBINATE TISSUE (IT) FROM PATIENTS WITH CRS. RESULTS THE DNA METHYLATION LEVELS AT ALL CPG SITES WERE HIGHER ( P < .01), AND THE PLAT EXPRESSION WAS LOWER ( P < .001) IN NP COMPARED WITH IT. THE METHYLATION CHANGES AT THE -618 SITE SHOWED A NEGATIVE CORRELATION WITH THE GENE EXPRESSION CHANGES BETWEEN NP AND IT ( R = -.65, P < .01). CONCLUSIONS HYPERMETHYLATION OF PLAT PROMOTER MAY DOWNREGULATE THE GENE EXPRESSION IN NP, LEADING TO EXCESSIVE FIBRIN DEPOSITION BY ABERRANT COAGULATION CASCADE. DNA METHYLATION OF PROXIMAL PLAT PROMOTER MAY CONTRIBUTE TO NP GROWTH AND HAVE A POTENTIAL AS A NEW THERAPEUTIC TARGET.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
12  3460  17 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
13  5086  15 PILOT STUDY OF DNA METHYLATION IN THE PATHOGENESIS OF CHRONIC RHINOSINUSITIS WITH NASAL POLYPS. BACKGROUND: DNA METHYLATION HAS BEEN IMPLICATED IN THE PATHOGENESIS OF ALLERGY AND ATOPY. THIS STUDY AIMED TO IDENTIFY WHETHER DNA METHYLATION ALSO PLAYS AN IMPORTANT ROLE IN THE PATHOGENESIS OF NASAL POLYPS (NP). METHODOLOGY: NP TISSUES WERE OBTAINED FROM 32 PATIENTS WITH CHRONIC RHINOSINUSITIS WITH BILATERAL NP. BIOPSIES OF INFERIOR TURBINATE MUCOSA (ITM) WERE TAKEN FROM 18 PATIENTS WHO UNDERWENT RHINOSEPTOPLASTY (CONTROL GROUP). THE METHYLATED GENES, WHICH WERE DETECTED BY DNA METHYLATION MICROARRAY, WERE VALIDATED BY METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION, BISULPHITE SEQUENCING, REAL-TIME POLYMERASE CHAIN REACTION AND IMMUNOHISTOCHEMISTRY. RESULTS: DNA METHYLATION MICROARRAY IDENTIFIED 8,008 CPG ISLANDS IN 2,848 GENES. ONE HUNDRED AND NINETY-EIGHT GENES WERE FOUND TO HAVE A METHYLATED SIGNAL IN THE PROMOTER REGION IN NP SAMPLES COMPARED WITH ITM SAMPLES. THE FOUR TOP GENES THAT CHANGED, COL18A1, EP300, GNAS AND SMURF1, WERE SELECTED FOR FURTHER STUDY. THE METHYLATION FREQUENCY OF COL18A1 WAS SIGNIFICANTLY HIGHER IN NP SAMPLES THAN IN ITM SAMPLES. CONCLUSIONS: DNA METHYLATION MIGHT PLAY AN IMPORTANT ROLE IN THE PATHOGENESIS OF NP. PROMOTER METHYLATION OF COL18A1 WAS FOUND TO BE SIGNIFICANTLY INCREASED IN NP TISSUES, FURTHER STUDIES ARE NECESSARY TO CONFIRM THE SIGNIFICANCE OF THESE EPIGENETIC FACTORS IN THE MECHANISMS UNDERLYING THE DEVELOPMENT OR PERSISTENCE OF NP.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
14  1492  23 DNA HYDROXYMETHYLATION BY TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE 1 AND 3 REGULATES NOCICEPTIVE SENSITIZATION IN A CHRONIC INFLAMMATORY PAIN MODEL. BACKGROUND: TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE CONVERTS 5-METHYLCYTOSINE IN DNA TO 5-HYDROXYMETHYLCYTOSINE, WHICH PLAYS AN IMPORTANT ROLE IN GENE TRANSCRIPTION. ALTHOUGH 5-HYDROXYMETHYLCYTOSINE IS ENRICHED IN MAMMALIAN NEURONS, ITS REGULATORY FUNCTION IN NOCICEPTIVE INFORMATION PROCESSING IS UNKNOWN. METHODS: THE GLOBAL LEVELS OF 5-HYDROXYMETHYLCYTOSINE AND TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE WERE MEASURED IN SPINAL CORDS IN MICE TREATED WITH COMPLETE FREUND'S ADJUVANT. IMMUNOBLOTTING, IMMUNOHISTOCHEMISTRY, AND BEHAVIORAL TESTS WERE USED TO EXPLORE THE DOWNSTREAM TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE-DEPENDENT SIGNALING PATHWAY. RESULTS: COMPLETE FREUND'S ADJUVANT-INDUCED NOCICEPTION INCREASED THE MEAN LEVELS (+/- SD) OF SPINAL 5-HYDROXYMETHYLCYTOSINE (178 +/- 34 VS. 100 +/- 21; P = 0.0019), TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE-1 (0.52 +/- 0.11 VS. 0.36 +/- 0.064; P = 0.0088), AND TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE-3 (0.61 +/- 0.13 VS. 0.39 +/- 0.08; P = 0.0083) COMPARED WITH LEVELS IN CONTROL MICE (N = 6/GROUP). THE KNOCKDOWN OF TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE-1 OR TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE-3 ALLEVIATED THERMAL HYPERALGESIA AND MECHANICAL ALLODYNIA, WHEREAS OVEREXPRESSION CYTOSINETHEM IN NAIVE MICE (N = 6/GROUP). DOWN-REGULATION OF SPINAL TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE-1 AND TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE-3 ALSO REVERSED THE INCREASES IN FOS EXPRESSION (123 +/- 26 VS. 294 +/- 6; P = 0.0031; AND 140 +/- 21 VS. 294 +/- 60; P = 0.0043, RESPECTIVELY; N = 6/GROUP), 5-HYDROXYMETHYLCYTOSINE LEVELS IN THE STAT3 PROMOTER (75 +/- 16.1 VS. 156 +/- 28.9; P = 0.0043; AND 91 +/- 19.1 VS. 156 +/- 28.9; P = 0.0066, RESPECTIVELY; N = 5/GROUP), AND CONSEQUENT STAT3 EXPRESSION (93 +/- 19.6 VS. 137 +/- 27.5; P = 0.035; AND 72 +/- 15.2 VS. 137 +/- 27.5; P = 0.0028, RESPECTIVELY; N = 5/GROUP) IN COMPLETE FREUND'S ADJUVANT-TREATED MICE. CONCLUSIONS: THIS STUDY REVEALS A NOVEL EPIGENETIC MECHANISM FOR TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE-1 AND TEN-ELEVEN TRANSLOCATION METHYLCYTOSINE DIOXYGENASE-3 IN THE MODULATION OF SPINAL NOCICEPTIVE INFORMATION VIA TARGETING OF STAT3.	2017	

15  3138  16 GLOBAL DNA METHYLATION PROFILING REVEALS NEW INSIGHTS INTO EPIGENETICALLY DEREGULATED PROTEIN CODING AND LONG NONCODING RNAS IN CLL. BACKGROUND: METHYL-CPG-BINDING DOMAIN PROTEIN ENRICHED GENOME-WIDE SEQUENCING (MBD-SEQ) IS A ROBUST AND POWERFUL METHOD FOR ANALYZING METHYLATED CPG-RICH REGIONS WITH COMPLETE GENOME-WIDE COVERAGE. IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), THE ROLE OF CPG METHYLATED REGIONS ASSOCIATED WITH TRANSCRIBED LONG NONCODING RNAS (LNCRNA) AND REPETITIVE GENOMIC ELEMENTS ARE POORLY UNDERSTOOD. BASED ON MBD-SEQ, WE CHARACTERIZED THE GLOBAL METHYLATION PROFILE OF HIGH CPG-RICH REGIONS IN DIFFERENT CLL PROGNOSTIC SUBGROUPS BASED ON IGHV MUTATIONAL STATUS. RESULTS: OUR STUDY IDENTIFIED 5800 HYPERMETHYLATED AND 12,570 HYPOMETHYLATED CLL-SPECIFIC DIFFERENTIALLY METHYLATED GENES (CLLDMGS) COMPARED TO NORMAL CONTROLS. FROM CLLDMGS, 40 % OF HYPERMETHYLATED AND 60 % OF HYPOMETHYLATED GENES WERE MAPPED TO NONCODING RNAS. IN ADDITION, WE FOUND THAT THE MAJOR REPETITIVE ELEMENTS SUCH AS SHORT INTERSPERSED ELEMENTS (SINE) AND LONG INTERSPERSED ELEMENTS (LINE) HAVE A HIGH PERCENTAGE OF CLLDMRS (DIFFERENTIALLY METHYLATED REGIONS) IN IGHV SUBGROUPS COMPARED TO NORMAL CONTROLS. FINALLY, TWO NOVEL LNCRNAS (HYPERMETHYLATED CRNDE AND HYPOMETHYLATED AC012065.7) WERE VALIDATED IN AN INDEPENDENT CLL SAMPLE COHORT (48 SAMPLES) COMPARED WITH 6 NORMAL SORTED B CELL SAMPLES USING QUANTITATIVE PYROSEQUENCING ANALYSIS. THE METHYLATION LEVELS SHOWED AN INVERSE CORRELATION TO GENE EXPRESSION LEVELS ANALYZED BY REAL-TIME QUANTITATIVE PCR. NOTABLY, SURVIVAL ANALYSIS REVEALED THAT HYPERMETHYLATION OF CRNDE AND HYPOMETHYLATION OF AC012065.7 CORRELATED WITH AN INFERIOR OUTCOME. CONCLUSIONS: THUS, OUR COMPREHENSIVE METHYLATION ANALYSIS BY MBD-SEQ PROVIDED NOVEL HYPER AND HYPOMETHYLATED LONG NONCODING RNAS, REPETITIVE ELEMENTS, ALONG WITH PROTEIN CODING GENES AS POTENTIAL EPIGENETIC-BASED CLL-SIGNATURE GENES INVOLVED IN DISEASE PATHOGENESIS AND PROGNOSIS.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
16  2262  13 EPIGENETIC PROFILING IN CHRONIC LYMPHOCYTIC LEUKEMIA REVEALS NOVEL METHYLATION TARGETS. CPG ISLAND METHYLATION IS AN EPIGENETIC ALTERATION THAT CONTRIBUTES TO TUMORIGENESIS BY TRANSCRIPTIONAL INACTIVATION OF GENES. LITTLE IS KNOWN ABOUT THE OVERALL LEVELS OF CPG ISLAND METHYLATION IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). TO PROVIDE A BASELINE ESTIMATE OF GLOBAL ABERRANT METHYLATION AND IDENTIFY TARGET SEQUENCES FOR ADDITIONAL INVESTIGATION, WE PERFORMED RESTRICTION LANDMARK GENOMIC SCANNING ON 10 CLL SAMPLES. TWO METHYLATION-SENSITIVE LANDMARK ENZYMES WERE USED (NOTI AND ASCI), ALLOWING ASSESSMENT OF OVER 3000 CPG ISLANDS IN EACH SAMPLE. TUMOR-DERIVED RESTRICTION LANDMARK GENOMIC SCANNING PROFILES WERE COMPARED WITH PROFILES FROM CD19-SELECTED B CELLS FROM NORMAL VOLUNTEERS AND MATCHED NORMAL NEUTROPHILS FROM 4 CLL PATIENTS. WE FOUND 2.5-8.1% (MEAN 4.8%) OF THE CPG ISLANDS IN CLL SAMPLES WERE ABERRANTLY METHYLATED COMPARED WITH CONTROLS, AND THE METHYLATION EVENTS HAD A NONRANDOM DISTRIBUTION (P < 0.0001). FURTHERMORE, WE IDENTIFIED 193 ABERRANTLY METHYLATED SEQUENCES, OF WHICH 93% HAVE CPG ISLAND CHARACTERISTICS AND 90% HAVE HOMOLOGY TO GENES OR EXPRESSED SEQUENCES. ONE SUCH GENE, THE G PROTEIN-COUPLED METABOTROPIC GLUTAMATE RECEPTOR 7 (GRM7), POSSIBLY INHIBITS CYCLIC AMP SIGNALING IN THE INDUCTION OF APOPTOSIS. BISULFITE SEQUENCING OF GRM7 CONFIRMED EXTENSIVE CPG ISLAND METHYLATION, AND TREATMENT WITH 5-AZA-2'-DEOXYCYTIDINE (DECITABINE) RESULTED IN UP-REGULATED EXPRESSION OF SEVERAL GENES IN VITRO WITH CONCURRENT CELLULAR DEPLETION OF DNMT1 PROTEIN. OUR DUAL-ENZYME GLOBAL METHYLATION STUDY SHOWS THAT CLL IS CHARACTERIZED BY WIDESPREAD NONRANDOM CPG ISLAND METHYLATION SIMILAR TO OTHER TUMORS AND PROVIDES A PANEL OF NOVEL METHYLATION TARGETS THAT CAN BE USED IN LARGER STUDIES DESIGNED TO ASSESS IMPACT ON DISEASE PROGRESSION AND SURVIVAL.	2004	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
17   411  12 ANALYSIS OF GENOME-WIDE DNA METHYLATION PATTERNS IN OBESITY. OBESITY IS A CHRONIC AND COMPLEX PSYCHOSOMATIC DISEASE THAT IS BECOMING INCREASINGLY PREVALENT WORLDWIDE. THIS STUDY AIMED TO ANALYZE WHOLE METHYLATION PROFILES TO UNCOVER THE EPIGENETIC MECHANISMS ASSOCIATED WITH OBESITY. DNA METHYLATION PROFILES IN BLOOD SAMPLES FROM PATIENTS WITH OBESITY AND NORMAL CONTROLS WERE STUDIED USING THE ILLUMINA 850 K METHYLATION MICROARRAY. THE DIAGNOSTIC VALUE OF THE DIFFERENTIALLY METHYLATED GENES WAS DETERMINED USING RECEIVER OPERATING CHARACTERISTIC (ROC) ANALYSIS. THE EXPRESSION OF SELECTED CANDIDATE GENES WAS VERIFIED USING REVERSE TRANSCRIPTION QUANTITATIVE POLYMERASE CHAIN REACTION (RT-QPCR) AND PYROSEQUENCING. A TOTAL OF 9,371 SIGNIFICANTLY DIFFERENTIALLY METHYLATED SITES (7,974 HYPERMETHYLATED SITES AND 1,397 HYPOMETHYLATED SITES) WERE IDENTIFIED IN 4,571 GENES. A DIFFERENCE IN THE DISTRIBUTION OF DIFFERENTIALLY METHYLATED SITES (HYPERMETHYLATED AND HYPOMETHYLATED) IN BOTH GENE STRUCTURES AND CPG ISLANDS WAS OBSERVED. A TOTAL OF 114 KEY DIFFERENTIALLY METHYLATED SITES WERE IDENTIFIED IN THE CPG ISLANDS. ROC RESULTS INDICATED THAT INHIBIN SUBUNIT BETA B (INHBB), HOMEOBOX A9 (HOXA9), TROPONIN T3 (TNNT3), CYCLIC ADENOSINE MONOPHOSPHATE (CAMP)-RESPONSIVE ELEMENT BINDING PROTEIN (CREB)-REGULATED TRANSCRIPTION COACTIVATOR 1 (CRTC1) AND ZINC FINGER AND BTB DOMAIN-CONTAINING 7 B (ZBTB7B) COULD DISCRIMINATE PATIENTS WITH OBESITY FROM NORMAL CONTROLS. RT-QPCR RESULTS OF CRTC1 AND ZBTB7B WERE CONSISTENT WITH OUR METHYLATION PROFILE RESULTS. THE PYROSEQUENCING RESULTS SHOWED THAT THE METHYLATION LEVELS OF CRTC1 CPG SITES (CPG1 AND CPG2-CG11660071) AND INHBB CPG SITES (CPG2) WERE SIGNIFICANTLY CHANGED IN PATIENTS WITH OBESITY COMPARED WITH NORMAL CONTROLS, WHICH WAS CONSISTENT WITH OUR DNA METHYLATION PROFILE RESULTS. OUR STUDY PROVIDES NEW INSIGHTS INTO THE PATHOLOGICAL MECHANISM OF OBESITY.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
18  4243  17 METHYLATION STATUS OF CEBPA GENE PROMOTER IN CHRONIC MYELOID LEUKEMIA. CCAAT/ENHANCER BINDING PROTEIN ALPHA IS ONE OF THE CRUCIAL TRANSCRIPTION FACTORS FOR MYELOID CELL DEVELOPMENT THAT HAS BEEN FOUND TO BE INVOLVED IN HEMATOPOIETIC DIFFERENTIATION AND LEUKEMIOGENESIS. RECENTLY, EPIGENETIC REGULATION OF CEBPA EXPRESSION THROUGH DNA METHYLATION HAS BEEN DEMONSTRATED IN LEUKEMIA. THE AIM OF THIS STUDY WAS TO INVESTIGATE THE METHYLATION STATUS OF CEBPA GENE IN CHRONIC MYELOID LEUKEMIA (CML) PATIENTS. THE METHYLATION STATUS OF CEBPA PROMOTER WAS STUDIED IN 100 PATIENTS WITH CML AND 98 NORMAL HEALTHY INDIVIDUALS FROM HYDERABAD, INDIA, USING METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION. THE ABERRANT METHYLATION OF CEBPA GENE PROMOTER WAS FOUND IN 32 OF THE 100 CML CASES. A HIGHLY SIGNIFICANT ASSOCIATION WAS FOUND BETWEEN THE FREQUENCY OF CEBPA GENE PROMOTER HYPERMETHYLATION AND THE CML STAGES (P = 0.017), BUT ASSOCIATION WITH RESPECT TO AGE AND GENDER OF THE PATIENT WAS NOT FOUND. THE RESULTS SUGGEST THAT ABERRANT METHYLATION IN THE CPG ISLAND OF THE PROMOTER REGION OF THIS GENE MIGHT BE A COMMON EVENT IN CML, AND SYSTEMIC EXPRESSION STUDIES WILL BE NEEDED TO UNFOLD THE ROLE OF CEBPA PROMOTER METHYLATION IN THE DEVELOPMENT, PROGRESSION, AND PROGNOSIS OF CML.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
19   885  27 CHRONIC CONSTRICTION INJURY-INDUCED CHANGES IN CIRCULAR RNA EXPRESSION PROFILING OF THE DORSAL ROOT GANGLION IN A RAT MODEL OF NEUROPATHIC PAIN. BACKGROUND: THE PATHOGENESIS OF NEUROPATHIC PAIN (NP) HAS NOT BEEN FULLY ELUCIDATED. GENE CHANGES IN DORSAL ROOT GANGLIA (DRG) MAY CONTRIBUTE TO THE DEVELOPMENT OF NP. CIRCULAR RNAS (CIRCRNAS) ARE A CLASS OF ENDOGENOUS NONCODING RNAS THAT FORM COVALENTLY CLOSED LOOP STRUCTURES AND ARE CRUCIAL FOR GENETIC AND EPIGENETIC REGULATION. HOWEVER, LITTLE IS KNOWN ABOUT CIRCRNA CHANGES IN DRG NEURONS AFTER PERIPHERAL NERVE INJURY. METHODS: A SCIATIC NERVE CHRONIC CONSTRICTION INJURY (CCI) MODEL WAS ESTABLISHED TO INDUCE NEUROPATHIC PAIN. WE PERFORMED GENOME-WIDE CIRCRNA ANALYSIS OF FOUR PAIRED DORSAL ROOT GANGLION (DRG) SAMPLES (L4-L5) FROM CCI AND NEGATIVE CONTROL (NC) RATS USING NEXT-GENERATION SEQUENCING TECHNOLOGY. THE DIFFERENTIALLY EXPRESSED CIRCRNAS (DECIRCRNAS) WERE IDENTIFIED BY DIFFERENTIAL EXPRESSION ANALYSIS, AND THE EXPRESSION PROFILE OF CIRCRNAS WAS VALIDATED BY QUANTITATIVE PCR. GENE ONTOLOGY AND KYOTO ENCYCLOPEDIA OF GENES AND GENOMES ANALYSES WERE PERFORMED TO PREDICT THE FUNCTION OF DECIRCRNAS. RESULTS: A TOTAL OF 374 DECIRCRNAS WERE IDENTIFIED BETWEEN CCI AND NC RATS USING CIRCRNA HIGH-THROUGHPUT SEQUENCING. AMONG THEM, 290 WERE UPREGULATED AND 84 WERE DOWNREGULATED IN THE CCI GROUP. THE EXPRESSION LEVELS OF NINE DECIRCRNAS WERE VALIDATED BY QPCR. FUNCTIONAL ANNOTATION ANALYSIS SHOWED THAT THE DECIRCRNAS WERE MAINLY ENRICHED IN PATHWAYS AND FUNCTIONS, INCLUDING 'DOPAMINERGIC SYNAPSE,' 'RENIN SECRETION,' 'MITOGEN-ACTIVATED PROTEIN KINASE SIGNALING PATHWAY,' AND 'NEUROGENESIS.' COMPETING ENDOGENOUS RNA ANALYSIS SHOWED THAT THE TOP 50 CIRCRNAS EXHIBITED INTERACTIONS WITH FOUR PAIN-RELATED MICRORNAS (MIRNAS). CIRC:CHR2:33950934-33955969 WAS THE LARGEST NODE IN THE CIRCRNA-MIRNA INTERACTION NETWORK. CONCLUSIONS: PERIPHERAL NERVE INJURY-INDUCED NEUROPATHIC PAIN LED TO CHANGES IN THE COMPREHENSIVE EXPRESSION PROFILE OF CIRCRNAS IN THE DRG OF RATS. DECIRCRNAS MAY ADVANCE OUR UNDERSTANDING OF THE MOLECULAR MECHANISMS UNDERLYING NEUROPATHIC PAIN.	2022	
                                                                                                                                                                                                                                                                                                             
20  1718  14 DYSREGULATED LONG NON-CODING RNAS IN THE TEMPORAL LOBE EPILEPSY MOUSE MODEL. PURPOSE: TO PERFORM COMPREHENSIVE PROFILING OF LONG NON-CODING RNAS (LNCRNAS) IN TEMPORAL LOBE EPILEPSY. METHODS: WE PERFORMED EXTENSIVE PROFILING OF LNCRNAS AND MRNAS IN THE MOUSE PILOCARPINE MODEL IN SPECIFIC BRAIN REGIONS, THE HIPPOCAMPUS AND CORTEX, AND COMPARED THE RESULTS TO THOSE OF THE CONTROL MOUSE. DIFFERENTIALLY EXPRESSED LNCRNAS AND MRNAS WERE IDENTIFIED WITH A MICROARRAY ANALYSIS (ARRAYSTAR MOUSE LNCRNA EXPRESSION MICROARRAY V3.0). THEN, GENE ONTOLOGY (GO) AND PATHWAY ANALYSIS WERE PERFORMED TO INVESTIGATE THE POTENTIAL ROLES OF THE DIFFERENTIALLY EXPRESSED MRNAS IN THE PILOCARPINE MODEL. PROTEIN-PROTEIN INTERACTIONS TRANSCRIBED BY DYSREGULATED MRNAS WITH/WITHOUT CO-DYSREGULATED LNCRNAS WERE ANALYZED USING STRING V10 (HTTP://STRING-DB.ORG/). RESULTS: A TOTAL OF 22 AND 83 LNCRNAS WERE UP- AND DOWN-REGULATED (>/=2.0-FOLD, ALL P < .05), RESPECTIVELY, IN THE HIPPOCAMPUS OF THE EPILEPSY MODEL, WHILE 46 AND 659 LNCRNAS WERE UP- AND DOWN-REGULATED, RESPECTIVELY, IN THE CORTEX OF THE EPILEPSY MODEL. GO AND PATHWAY ANALYSIS REVEALED THAT THE DYSREGULATED MRNAS WERE CLOSELY ASSOCIATED WITH A PROCESS ALREADY KNOWN TO BE INVOLVED IN EPILEPTOGENESIS: ACUTE INFLAMMATION, CALCIUM ION REGULATION, EXTRACELLULAR MATRIX REMODELING, AND NEURONAL DIFFERENTIATION. AMONG THE LNCRNAS, WE IDENTIFIED 10 LNCRNAS COMMONLY DYSREGULATED WITH CORRESPONDING MRNAS IN THE CORTEX. THE STRING ANALYSIS SHOWED THAT THE DYSREGULATED MRNAS WERE INTERCONNECTED AROUND TWO CENTERS: THE MTOR PATHWAY-RELATED GENES AND REST PATHWAY-RELATED GENES. CONCLUSION: LNCRNAS WERE DYSREGULATED IN THE PILOCARPINE MOUSE MODEL ACCORDING TO THE BRAIN REGIONS OF THE HIPPOCAMPUS AND CORTEX. THE DYSREGULATED LNCRNAS WITH CO-DYSREGULATED MRNAS MIGHT BE POSSIBLE THERAPEUTIC TARGETS FOR THE EPIGENETIC REGULATION OF CHRONIC EPILEPSY.	2018