1 4076 134 MATERNAL HIGH-FAT DIET MODIFIES EPIGENETIC MARKS H3K27ME3 AND H3K27AC IN BONE TO REGULATE OFFSPRING OSTEOBLASTOGENESIS IN MICE. STUDIES FROM BOTH HUMANS AND ANIMAL MODELS INDICATED THAT MATERNAL CHRONIC POOR-QUALITY DIET, ESPECIALLY A HIGH FAT DIET (HFD), IS SIGNIFICANTLY ASSOCIATED WITH REDUCED BONE DENSITY AND CHILDHOOD FRACTURES IN OFFSPRING. WHEN PREVIOUSLY STUDIED IN A RAT MODEL, OUR DATA SUGGESTED THAT MATERNAL HFD CHANGES EPIGENETIC MARKS SUCH AS DNA METHYLATION AND HISTONE MODIFICATIONS TO CONTROL OSTEOBLAST METABOLISM. IN MOUSE EMBRYONIC AND POSTNATAL OFFSPRING BONE SAMPLES, A CHIP-SEQUENCING (CHIP-SEQ)-BASED GENOME-WIDE METHOD WAS USED TO LOCATE THE REPRESSIVE HISTONE MARK H3K27ME3 (MEDIATED VIA THE POLYCOMB HISTONE METHYLTRANSFERASE, EZH2) AND EXPRESSIVE HISTONE MARK H3K27AC (P300/CBP MEDIATED) THROUGHOUT THE GENOME. USING ISOLATED MOUSE EMBRYONIC CELLS FROM FOETAL CALVARIA (OSTEOBLAST-LIKE CELLS), H3K27ME3 CHIP-SEQ SHOWED THAT 147 GENE BODIES AND 26 GENE PROMOTERS IN HFD EMBRYOTIC SAMPLES HAD A GREATER THAN TWOFOLD INCREASE IN H3K27ME PEAKS COMPARED TO CONTROLS. AMONG THE HFD SAMPLES, PTHLH AND COL2A1 THAT ARE IMPORTANT GENES PLAYING ROLES DURING CHONDRO- AND OSTEOGENESIS HAD SIGNIFICANTLY ENRICHED LEVELS OF H3K27ME3. THEIR DECREASED MRNA EXPRESSION WAS CONFIRMED BY REAL-TIME PCR AND STANDARD CHIP ANALYSIS, INDICATING A STRONG ASSOCIATION WITH EZH2 MEDIATED H3K27ME3 EPIGENETIC CHANGES. USING EMBRYONIC CALVARIA OSTEOBLASTIC CELLS AND OFFSPRING BONE SAMPLES, H3K27AC CHIP-SEQ ANALYSIS SHOWED THAT OSTEOBLAST INHIBITOR GENES TNFAIP3 AND TWIST1 HAD SIGNIFICANTLY ENRICHED PEAKS OF H3K27AC IN HFD SAMPLES COMPARED TO CONTROLS. THEIR INCREASED GENE EXPRESSION AND ASSOCIATION WITH H3K27AC WERE ALSO CONFIRMED BY REAL-TIME PCR AND STANDARD CHIP ANALYSIS. THESE FINDINGS INDICATE THAT CHRONIC MATERNAL HFD CHANGES HISTONE TRIMETHYLATION AND ACETYLATION EPIGENETIC MARKS TO REGULATE EXPRESSION OF GENES CONTROLLING OSTEOBLASTOGENESIS.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
2 3658  38 INDUCTION OF ABERRANT TRIMETHYLATION OF HISTONE H3 LYSINE 27 BY INFLAMMATION IN MOUSE COLONIC EPITHELIAL CELLS. A FIELD FOR CANCERIZATION (FIELD DEFECT), WHERE GENETIC AND EPIGENETIC ALTERATIONS ARE ACCUMULATED IN NORMAL-APPEARING TISSUES, IS INVOLVED IN HUMAN CARCINOGENESIS, ESPECIALLY CANCERS ASSOCIATED WITH CHRONIC INFLAMMATION. ALTHOUGH ABERRANT DNA METHYLATION IS INVOLVED IN THE FIELD DEFECT AND INDUCED BY CHRONIC INFLAMMATION, IT IS STILL UNCLEAR FOR TRIMETHYLATION OF HISTONE H3 LYSINE 27 (H3K27ME3), WHICH IS INVOLVED IN GENE REPRESSION INDEPENDENT OF DNA METHYLATION AND FUNCTIONS AS A PRE-MARK FOR ABERRANT DNA METHYLATION. IN THIS STUDY, USING A MOUSE COLITIS MODEL INDUCED BY DEXTRAN SULFATE SODIUM (DSS), WE AIMED TO CLARIFY WHETHER ABERRANT H3K27ME3 IS INDUCED BY INFLAMMATION AND INVOLVED IN A FIELD DEFECT. CHIP-ON-CHIP ANALYSIS OF COLONIC EPITHELIAL CELLS REVEALED THAT H3K27ME3 LEVELS WERE INCREASED OR DECREASED FOR 266 GENOMIC REGIONS BY AGING, AND MORE EXTENSIVELY (23 INCREASED AND 3574 DECREASED REGIONS) BY COLITIS. SUCH INCREASE OR DECREASE OF H3K27ME3 WAS INDUCED AS EARLY AS 2 WEEKS AFTER THE INITIATION OF DSS TREATMENT, AND PERSISTED AT LEAST FOR 16 WEEKS EVEN AFTER THE INFLAMMATION DISAPPEARED. SOME OF THE ABERRANT H3K27ME3 IN COLONIC EPITHELIAL CELLS WAS CARRIED OVER INTO COLON TUMORS. FURTHERMORE, H3K27ME3 ACQUIRED AT DAPK1 BY COLITIS WAS FOLLOWED BY INCREASED DNA METHYLATION, SUPPORTING ITS FUNCTION AS A PRE-MARK FOR ABERRANT DNA METHYLATION. THESE RESULTS DEMONSTRATED THAT ABERRANT H3K27ME3 CAN BE INDUCED BY EXPOSURE TO A SPECIFIC ENVIRONMENT, SUCH AS COLITIS, AND SUGGESTED THAT ABERRANT HISTONE MODIFICATION, IN ADDITION TO ABERRANT DNA METHYLATION, IS INVOLVED IN THE FORMATION OF A FIELD DEFECT.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
3 4497  41 MORPHINE LEADS TO GLOBAL GENOME CHANGES IN H3K27ME3 LEVELS VIA A POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) SELF-REGULATORY MECHANISM IN MESCS. BACKGROUND: ENVIRONMENTALLY INDUCED EPIGENETIC CHANGES CAN LEAD TO HEALTH PROBLEMS OR DISEASE, BUT THE MECHANISMS INVOLVED REMAIN UNCLEAR. MORPHINE CAN PASS THROUGH THE PLACENTAL BARRIER LEADING TO ABNORMAL EMBRYO DEVELOPMENT. HOWEVER, THE MECHANISM BY WHICH MORPHINE CAUSES THESE EFFECTS AND HOW THEY SOMETIMES PERSIST INTO ADULTHOOD IS NOT WELL KNOWN. TO UNRAVEL THE MORPHINE-INDUCED CHROMATIN ALTERATIONS INVOLVED IN ABERRANT EMBRYO DEVELOPMENT, WE EXPLORED THE ROLE OF THE H3K27ME3/PRC2 REPRESSIVE COMPLEX IN GENE EXPRESSION AND ITS TRANSMISSION ACROSS CELLULAR GENERATIONS IN RESPONSE TO MORPHINE. RESULTS: USING MOUSE EMBRYONIC STEM CELLS AS A MODEL SYSTEM, WE FOUND THAT CHRONIC MORPHINE TREATMENT INDUCES A GLOBAL DOWNREGULATION OF THE HISTONE MODIFICATION H3K27ME3. CONVERSELY, CHIP-SEQ SHOWED A REMARKABLE INCREASE IN H3K27ME3 LEVELS AT SPECIFIC GENOMIC SITES, PARTICULARLY PROMOTERS, DISRUPTING SELECTIVE TARGET GENES RELATED TO EMBRYO DEVELOPMENT, CELL CYCLE AND METABOLISM. THROUGH A SELF-REGULATORY MECHANISM, MORPHINE DOWNREGULATED THE TRANSCRIPTION OF PRC2 COMPONENTS RESPONSIBLE FOR H3K27ME3 BY ENRICHING HIGH H3K27ME3 LEVELS AT THE PROMOTER REGION. DOWNREGULATION OF PRC2 COMPONENTS PERSISTED FOR AT LEAST 48 H (4 CELL CYCLES) FOLLOWING MORPHINE REMOVAL, THOUGH PROMOTER H3K27ME3 LEVELS RETURNED TO CONTROL LEVELS. CONCLUSIONS: MORPHINE INDUCES TARGETING OF THE PRC2 COMPLEX TO SELECTED PROMOTERS, INCLUDING THOSE OF PRC2 COMPONENTS, LEADING TO CHARACTERISTIC CHANGES IN GENE EXPRESSION AND A GLOBAL REDUCTION IN H3K27ME3. FOLLOWING MORPHINE REMOVAL, ENHANCED PROMOTER H3K27ME3 LEVELS REVERT TO NORMAL SOONER THAN GLOBAL H3K27ME3 OR PRC2 COMPONENT TRANSCRIPT LEVELS. WE SUGGEST THAT H3K27ME3 IS INVOLVED IN INITIATING MORPHINE-INDUCED CHANGES IN GENE EXPRESSION, BUT NOT IN THEIR MAINTENANCE. MODEL OF POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) AND H3K27ME3 ALTERATIONS INDUCED BY CHRONIC MORPHINE EXPOSURE. MORPHINE INDUCES H3K27ME3 ENRICHMENT AT PROMOTERS OF GENES ENCODING CORE MEMBERS OF THE PRC2 COMPLEX AND IS ASSOCIATED WITH THEIR TRANSCRIPTIONAL DOWNREGULATION.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
4 5791  40 STABLE HISTONE METHYLATION CHANGES AT PROTEOGLYCAN NETWORK GENES FOLLOWING ETHANOL EXPOSURE. ALCOHOL USE DISORDER (AUD) IS A CHRONIC MENTAL ILLNESS IN WHICH PATIENTS OFTEN ACHIEVE PROTRACTED PERIODS OF ABSTINENCE PRIOR TO RELAPSE. EPIGENETIC MECHANISMS MAY PROVIDE AN EXPLANATION FOR THE PERSISTING GENE EXPRESSION CHANGES THAT CAN BE OBSERVED EVEN AFTER LONG PERIODS OF ABSTINENCE AND MAY CONTRIBUTE TO RELAPSE. IN THIS STUDY, WE EXAMINED TWO HISTONE MODIFICATIONS, HISTONE 3 LYSINE 4 TRI-METHYLATION (H3K4ME3) AND HISTONE 3 LYSINE 27 TRI-METHYLATION (H3K27ME3), IN THE PREFRONTAL CORTEX OF WITHDRAWAL SEIZURE RESISTANT (WSR) MICE 21 DAYS AFTER 72 H OF ETHANOL VAPOR EXPOSURE. THESE HISTONE MODIFICATIONS WERE SELECTED BECAUSE THEY ARE ASSOCIATED WITH ACTIVE PROMOTERS (H3K4ME3) AND REPRESSED GENE EXPRESSION IN A EUCHROMATIC ENVIRONMENT (H3K27ME3). WE PERFORMED A GENOME-WIDE ANALYSIS TO IDENTIFY DIFFERENCES IN H3K4ME3 AND H3K27ME3 LEVELS IN POST-ETHANOL EXPOSURE VS. CONTROL MICE BY CHIP-SEQ. WE DETECTED A GLOBAL REDUCTION IN H3K4ME3 PEAKS AND INCREASE IN H3K27ME3 PEAKS IN POST-ETHANOL EXPOSURE MICE COMPARED TO CONTROLS, THESE CHANGES ARE CONSISTENT WITH PERSISTENT REDUCTIONS IN GENE EXPRESSION. PATHWAY ANALYSIS OF GENES DISPLAYING CHANGES IN H3K4ME3 AND H3K27ME3 REVEALED ENRICHMENT FOR GENES INVOLVED IN PROTEOGLYCAN AND CALCIUM SIGNALING PATHWAYS, RESPECTIVELY. MICROARRAY ANALYSIS OF 7,683 GENES AND QPCR ANALYSIS IDENTIFIED EIGHT GENES DISPLAYING CONCORDANT REGULATION OF GENE EXPRESSION AND H3K4ME3/H3K27ME3. WE ALSO COMPARED CHANGES IN H3K4ME3 AND/OR H3K27ME3 FROM OUR STUDY WITH CHANGES IN GENE EXPRESSION IN RESPONSE TO ETHANOL FROM PUBLISHED LITERATURE AND WE FOUND THAT THE EXPRESSION OF 52% OF THE GENES WITH ALTERED H3K4ME3 BINDING AND 40% OF GENES WITH H3K27ME3 DIFFERENCES ARE ALTERED BY ETHANOL EXPOSURE. THE CHROMATIN CHANGES ASSOCIATED WITH THE 21-DAY POST-EXPOSURE PERIOD SUGGEST THAT THIS PERIOD IS A UNIQUE STATE IN THE ADDICTION CYCLE THAT DIFFERS FROM ETHANOL INTOXICATION AND ACUTE WITHDRAWAL. THESE RESULTS PROVIDE INSIGHTS INTO THE ENDURING EFFECTS OF ETHANOL ON PROTEOGLYCAN AND CALCIUM SIGNALING GENES IN THE BRAIN.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
5 2297  30 EPIGENETIC REGULATION OF ACUTE INFLAMMATORY PAIN. ACUTE PAIN IS ASSOCIATED WITH TISSUE DAMAGE, WHICH RESULTS IN THE RELEASE OF INFLAMMATORY MEDIATORS. RECENT STUDIES POINT TO THE INVOLVEMENT OF EPIGENETIC MECHANISMS (DNA METHYLATION) IN THE DEVELOPMENT OF PAIN. WE HAVE FOUND THAT DURING ACUTE INFLAMMATORY PAIN INDUCED BY THE APPLICATION OF 10% MUSTARD OIL ON THE TONGUES OF RATS, LEVELS OF DNMT3A AND 3B WERE ELEVATED MARKEDLY (36 AND 42 % RESPECTIVELY), WHEREAS THE LEVEL OF DNMT1 WAS NOT CHANGED SIGNIFICANTLY. PREVIOUS INJECTION OF XEFOCAM WITH 0,4 MG/KG DOSE DECREASED LEVELS OF DNMT3A AND 3B (25 AND 24% RESPECTIVELY). THE LEVEL OF DNMT1 WAS NOT CHANGED SIGNIFICANTLY COMPARED TO THE CONTROL GROUP. THE FINDINGS SUPPORT THE IDEA THAT INHIBITORS OF DNA-METHYLTRANSFERASES COULD BE USEFUL FOR PAIN MANAGEMENT. OUR DATA SUGGEST THAT NSAIDS (ALONE OR IN COMBINATION WITH DNMT INHIBITORS) MAY BE PROPOSED AS POSSIBLE EPIGENETIC REGULATORY AGENTS, WHICH MAY PLAY A ROLE IN EPIGENETIC MECHANISMS INDIRECTLY THROUGH ALTERING THE ACTIVITY OF INFLAMMATORY MEDIATORS INVOLVED IN PAIN DEVELOPMENT.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
6 1731  47 DYSREGULATION OF THE HISTONE DEMETHYLASE KDM6B IN ALCOHOL DEPENDENCE IS ASSOCIATED WITH EPIGENETIC REGULATION OF INFLAMMATORY SIGNALING PATHWAYS. EPIGENETIC ENZYMES OVERSEE LONG-TERM CHANGES IN GENE EXPRESSION BY INTEGRATING GENETIC AND ENVIRONMENTAL CUES. WHILE THERE ARE HUNDREDS OF ENZYMES THAT CONTROL HISTONE AND DNA MODIFICATIONS, THEIR POTENTIAL ROLES IN SUBSTANCE ABUSE AND ALCOHOL DEPENDENCE REMAIN UNDEREXPLORED. A FEW RECENT STUDIES HAVE SUGGESTED THAT EPIGENETIC PROCESSES COULD UNDERLIE TRANSCRIPTOMIC AND BEHAVIORAL HALLMARKS OF ALCOHOL ADDICTION. IN THE PRESENT STUDY, WE SOUGHT TO IDENTIFY EPIGENETIC ENZYMES IN THE BRAIN THAT ARE DYSREGULATED DURING PROTRACTED ABSTINENCE AS A CONSEQUENCE OF CHRONIC AND INTERMITTENT ALCOHOL EXPOSURE. THROUGH QUANTITATIVE MRNA EXPRESSION ANALYSIS OF OVER 100 EPIGENETIC ENZYMES, WE IDENTIFIED 11 THAT ARE SIGNIFICANTLY ALTERED IN ALCOHOL-DEPENDENT RATS COMPARED WITH CONTROLS. FOLLOW-UP STUDIES OF ONE OF THESE ENZYMES, THE HISTONE DEMETHYLASE KDM6B, SHOWED THAT THIS ENZYME EXHIBITS REGION-SPECIFIC DYSREGULATION IN THE PREFRONTAL CORTEX AND NUCLEUS ACCUMBENS OF ALCOHOL-DEPENDENT RATS. KDM6B WAS ALSO UPREGULATED IN THE HUMAN ALCOHOLIC BRAIN. UPREGULATION OF KDM6B PROTEIN IN ALCOHOL-DEPENDENT RATS WAS ACCOMPANIED BY A DECREASE OF TRIMETHYLATION LEVELS AT HISTONE H3, LYSINE 27 (H3K27ME3), CONSISTENT WITH THE KNOWN DEMETHYLASE SPECIFICITY OF KDM6B. SUBSEQUENT EPIGENETIC (CHROMATIN IMMUNOPRECIPITATION [CHIP]-SEQUENCING) ANALYSIS SHOWED THAT ALCOHOL-INDUCED CHANGES IN H3K27ME3 WERE SIGNIFICANTLY ENRICHED AT GENES IN THE IL-6 SIGNALING PATHWAY, CONSISTENT WITH THE WELL-CHARACTERIZED ROLE OF KDM6B IN MODULATION OF INFLAMMATORY RESPONSES. KNOCKDOWN OF KDM6B IN CULTURED MICROGLIAL CELLS DIMINISHED IL-6 INDUCTION IN RESPONSE TO AN INFLAMMATORY STIMULUS. OUR FINDINGS IMPLICATE A NOVEL KDM6B-MEDIATED EPIGENETIC SIGNALING PATHWAY INTEGRATED WITH INFLAMMATORY SIGNALING PATHWAYS THAT ARE KNOWN TO UNDERLIE THE DEVELOPMENT OF ALCOHOL ADDICTION.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
7 3455  40 HYPOMETHYLATION COORDINATES ANTAGONISTICALLY WITH HYPERMETHYLATION IN CANCER DEVELOPMENT: A CASE STUDY OF LEUKEMIA. BACKGROUND: METHYLATION CHANGES ARE FREQUENT IN CANCERS, BUT UNDERSTANDING HOW HYPER- AND HYPOMETHYLATED REGION CHANGES COORDINATE, ASSOCIATE WITH GENOMIC FEATURES, AND AFFECT GENE EXPRESSION IS NEEDED TO BETTER UNDERSTAND THEIR BIOLOGICAL SIGNIFICANCE. THE FUNCTIONAL SIGNIFICANCE OF HYPERMETHYLATION IS WELL STUDIED, BUT THAT OF HYPOMETHYLATION REMAINS LIMITED. HERE, WITH PAIRED EXPRESSION AND METHYLATION SAMPLES GATHERED FROM A PATIENT/CONTROL COHORT, WE ATTEMPT TO BETTER CHARACTERIZE THE GENE EXPRESSION AND METHYLATION CHANGES THAT TAKE PLACE IN CANCER FROM B CELL CHRONIC LYMPHOCYTE LEUKEMIA (B-CLL) SAMPLES. RESULTS: ACROSS THE DATASET, WE FOUND THAT CONSISTENT DIFFERENTIALLY HYPOMETHYLATED REGIONS (C-DMRS) ACROSS SAMPLES WERE RELATIVELY FEW COMPARED TO THE MANY POORLY CONSISTENT HYPO- AND HIGHLY CONSERVED HYPER-DMRS. HOWEVER, GENES IN THE HYPO-C-DMRS TENDED TO BE ASSOCIATED WITH FUNCTIONS ANTAGONISTIC TO THOSE IN THE HYPER-C-DMRS, LIKE DIFFERENTIATION, CELL-CYCLE REGULATION AND PROLIFERATION, SUGGESTING COORDINATED REGULATION OF METHYLATION CHANGES. HYPO-C-DMRS IN B-CLL WERE FOUND ENRICHED IN KEY SIGNALING PATHWAYS LIKE B CELL RECEPTOR AND P53 PATHWAYS AND GENES/MOTIFS ESSENTIAL FOR B LYMPHOPOIESIS. HYPO-C-DMRS TENDED TO BE PROXIMAL TO GENES WITH ELEVATED EXPRESSION IN CONTRAST TO THE TRANSCRIPTION SILENCING-MECHANISM IMPOSED BY HYPERMETHYLATION. HYPO-C-DMRS TENDED TO BE ENRICHED IN THE REGIONS OF ACTIVATING H4K4ME1/2/3, H3K79ME2, AND H3K27AC HISTONE MODIFICATIONS. IN COMPARISON, THE POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) SIGNATURE, MARKED BY EZH2, SUZ12, CTCF BINDING-SITES, REPRESSIVE H3K27ME3 MARKS, AND "REPRESSED/POISED PROMOTER" STATES WERE ASSOCIATED WITH HYPER-C-DMRS. MOST HYPO-C-DMRS WERE FOUND IN INTRONS (36 %), 3' UNTRANSLATED REGIONS (29 %), AND INTERGENIC REGIONS (24 %). MANY OF THESE GENIC REGIONS ALSO OVERLAPPED WITH ENHANCERS. THE METHYLATION OF CPGS FROM 3'UTR EXONS WAS FOUND TO HAVE WEAK BUT POSITIVE CORRELATION WITH GENE EXPRESSION. IN CONTRAST, METHYLATION IN THE 5'UTR WAS NEGATIVELY CORRELATED WITH EXPRESSION. TO BETTER CHARACTERIZE THE OVERLAP BETWEEN METHYLATION AND EXPRESSION CHANGES, WE IDENTIFIED CORRELATION MODULES THAT ASSOCIATE WITH "APOPTOSIS" AND "LEUKOCYTE ACTIVATION". CONCLUSIONS: DESPITE CLINICAL HETEROGENEITY IN DISEASE PRESENTATION, A NUMBER OF METHYLATION CHANGES, BOTH HYPO AND HYPER, APPEAR TO BE COMMON IN B-CLL. HYPOMETHYLATION APPEARS TO PLAY AN ACTIVE, TARGETED, AND COMPLEMENTARY ROLE IN CANCER PROGRESSION, AND IT INTERPLAYS WITH HYPERMETHYLATION IN A COORDINATED FASHION IN THE CANCER PROCESS.	2016	

8 1144  41 CONCOMITANT HETEROCHROMATINISATION AND DOWN-REGULATION OF GENE EXPRESSION UNVEILS EPIGENETIC SILENCING OF RELB IN AN AGGRESSIVE SUBSET OF CHRONIC LYMPHOCYTIC LEUKEMIA IN MALES. BACKGROUND: THE SENSITIVITY OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) CELLS TO CURRENT TREATMENTS, BOTH IN VITRO AND IN VIVO, RELIES ON THEIR ABILITY TO ACTIVATE APOPTOTIC DEATH. CLL CELLS RESISTANT TO DNA DAMAGE-INDUCED APOPTOSIS DISPLAY DEREGULATION OF A SPECIFIC SET OF GENES. METHODS: MICROARRAY HYBRIDIZATION (HUMAN GENECHIP, AFFYMETRIX), IMMUNOFLUORESCENT IN SITU LABELING COUPLED WITH VIDEO-MICROSCOPY RECORDING/ANALYSES, CHROMATIN-IMMUNOPRECIPITATION (CHIP), POLYMERASE CHAIN REACTIONS (PCR), REAL-TIME QUANTITATIVE PCR (RT-QPCR) AND BISULFITE GENOME SEQUENCING WERE THE MAIN METHODS APPLIED. STATISTICAL ANALYSES WERE PERFORMED BY APPLYING GCRMA AND SAM ANALYSIS (MICROARRAY DATA) AND STUDENT'S T-TEST OR MANN & WHITNEY'S U-TEST. RESULTS: HEREIN WE SHOW THAT, REMARKABLY, IN A RESISTANT MALE CLL CELLS THE VAST MAJORITY OF GENES WERE DOWN-REGULATED COMPARED WITH SENSITIVE CELLS, WHEREAS THIS WAS NOT THE CASE IN CELLS DERIVED FROM FEMALES. THIS GENE DOWN-REGULATION WAS FOUND TO BE ASSOCIATED WITH AN OVERALL GAIN OF HETEROCHROMATIN AS EVIDENCED BY IMMUNOFLUORESCENT LABELING OF HETEROCHROMATIN PROTEIN 1ALPHA (HP-1), TRIMETHYLATED HISTONE 3 LYSINE 9 (3METH3K9), AND 5-METHYLCYTIDINE (5METC). NOTABLY, 17 GENES WERE FOUND TO BE COMMONLY DEREGULATED IN RESISTANT MALE AND FEMALE CELL SAMPLES. AMONG THESE, RELB WAS IDENTIFIED AS A DISCRIMINATORY CANDIDATE GENE REPRESSED IN THE MALE AND UPREGULATED IN THE FEMALE RESISTANT CELLS. CONCLUSION: THE MOLECULAR DEFECTS IN THE SILENCING OF RELB INVOLVE AN INCREASE IN H3K9- BUT NOT CPG-ISLAND METHYLATION IN THE PROMOTER REGIONS. INCREASE IN ACETYL-H3 IN RESISTANT FEMALE BUT NOT MALE CLL SAMPLES AS WELL AS A DECREASE OF TOTAL CELLULAR LEVEL OF RELB AFTER AN INHIBITION OF HISTONE DEACETYLASE (HDAC) BY TRICHOSTATIN A (TSA), FURTHER EMPHASIZE THE ROLE OF EPIGENETIC MODIFICATIONS WHICH COULD DISCRIMINATE TWO CLL SUBSETS. TOGETHER, THESE RESULTS HIGHLIGHTED THE EPIGENETIC RELB SILENCING AS A NEW MARKER OF THE PROGRESSIVE DISEASE IN MALES.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
9 2747  41 EXPRESSION ANALYSIS OF THE EPIGENETIC METHYLTRANSFERASES AND METHYL-CPG BINDING PROTEIN FAMILIES IN THE NORMAL B-CELL AND B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). THE IMPORTANCE OF EPIGENETIC MODIFICATIONS IN CARCINOGENESIS HAS BEEN A SOURCE OF CONTROVERSY FOR SOME TIME. THERE IS LITTLE DOUBT THAT CHANGES IN GENOMIC HYPERMETHYLATION CONTRIBUTE TO THE SILENCING OF TUMOR SUPPRESSOR GENES. FURTHERMORE, RECENT STUDIES HAVE ALSO IDENTIFIED THE SIGNIFICANCE OF GENOMIC HYPOMETHYLATION ASSOCIATED WITH CHROMOSOMAL INSTABILITY AND TUMORIGENESIS. ONE OF THE MOST PERPLEXING QUESTIONS REGARDING EPIGENETIC MODIFICATIONS AND LEUKEMOGENESIS IS THE RELATIONSHIP WITH DNA METHYLTRANSFERASES (DNMT'S). THE PRIMARY FUNCTION OF THE DNMT ENZYMES IS TO METHYLATE GENOMIC DNA, WHEREAS THE METHYL-CPG BINDING DOMAIN PROTEINS (MBD) INTERPRET THIS METHYLATION SIGNAL AND REGULATE GENE EXPRESSION AND CHROMATIN BEHAVIOR. IN THIS STUDY WE ANALYSE THESE GENE FAMILIES BY QUANTITATIVE REAL-TIME PCR TO INVESTIGATE WHETHER EXPRESSION LEVELS AND THE B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (B-CLL) PHENOTYPE ARE ASSOCIATED. FURTHERMORE, GIVEN THE EPIGENETIC CROSSTALK BETWEEN GENOME STABILITY AND THE HISTONE CHROMATIN CODE WE HAVE ANALYSED EUKARYOTIC HISTONE METHYLTRANSFERASE (EU-HMTASEI). SURPRISINGLY, WE DID NOT OBSERVE SIGNIFICANT CHANGES IN DNMT1 EXPRESSION IN B-CLL CASES WHEN COMPARED TO NORMAL LYMPHOCYTES, REGARDLESS OF WHETHER WE NORMALISE AGAINST GAPDH OR PCNA AS REFERENCE STANDARDS. INDEED, EXPRESSION OF THE MAINTENANCE AND DE NOVO METHYLASES WERE INDEPENDENTLY REGULATED. OF PARTICULAR NOTE WAS THE SIGNIFICANT DOWN REGULATION OF DNMT3B. FURTHERMORE, WE OBSERVED A POSITIVE CORRELATION BETWEEN HMTASEI EXPRESSION LEVELS AND STAGE OF LEUKEMIA SUGGESTING THAT CHANGES IN THE METHYLATION PATTERNS IN B-CLL MAY REPRESENT DEREGULATION OF THE EPIGENETIC REPERTOIRE THAT ALSO INCLUDE THE METHYLATION DEPENDENT BINDING PROTEINS, MBD2 AND MECP2. WE ENVISAGE CHANGES IN THE EPIGENETIC PROGRAM ARE MULTIFACTORIAL IN NATURE AND POSTULATE THAT THE PREVALENT GENOMIC METHYLASES JUST ONE COMPONENT OF A LARGER EPIGENETIC REPERTOIRE.	2004	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
10 6411  35 THE SITE SPECIFIC DEMETHYLATION IN THE 5'-REGULATORY AREA OF NMDA RECEPTOR 2B SUBUNIT GENE ASSOCIATED WITH CIE-INDUCED UP-REGULATION OF TRANSCRIPTION. BACKGROUND: THE NMDA RECEPTOR REPRESENTS A PARTICULARLY IMPORTANT SITE OF ETHANOL ACTION IN THE CNS. WE RECENTLY REPORTED THAT NMDA RECEPTOR 2B (NR2B) GENE EXPRESSION WAS PERSISTENTLY UP-REGULATED FOLLOWING CHRONIC INTERMITTENT ETHANOL (CIE) TREATMENT. INCREASING EVIDENCE THAT EPIGENETIC MECHANISMS ARE INVOLVED IN DYNAMIC AND LONG-LASTING REGULATION OF GENE EXPRESSION IN MULTIPLE NEUROADAPTIVE PROCESSES PROMPTED US TO INVESTIGATE THE ROLE OF DNA METHYLATION IN MEDIATING CIE-INDUCED UP-REGULATION OF NR2B GENE TRANSCRIPTION. TO DISSECT THE CHANGES OF DNA METHYLATION IN THE NR2B GENE, WE HAVE SCREENED A LARGE NUMBER OF CPG SITES WITHIN ITS 5'-REGULATORY AREA FOLLOWING CIE TREATMENT. METHODS: PRIMARY CORTICAL CULTURED NEURONS WERE SUBJECTED TO ETHANOL TREATMENT IN A CIE PARADIGM. BISULFITE CONVERSION FOLLOWED BY PYROSEQUENCING WAS USED FOR QUANTITATIVE MEASUREMENT AND ANALYSIS OF CPG METHYLATION STATUS WITHIN THE 5'-REGULATORY AREA OF THE NR2B GENE; CHROMATIN IMMUNOPRECIPITATION (CHIP) ASSAY WAS USED TO EXAMINE DNA LEVELS ASSOCIATED WITH METHYLATION AND TRANSCRIPTION FACTOR BINDING. ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA) AND IN VITRO DNA METHYLATION ASSAYS WERE PERFORMED TO DETERMINE THE DIRECT IMPACT OF DNA METHYLATION ON THE INTERACTION BETWEEN DNA AND TRANSCRIPTION FACTOR AND PROMOTER ACTIVITY. RESULTS: ANALYSIS OF INDIVIDUAL CPG METHYLATION SITES WITHIN THE NR2B 5'REGULATORY AREA REVEALED THREE REGIONS WITH CLUSTERS OF SITE-SPECIFIC CPG DEMETHYLATION FOLLOWING CIE TREATMENT AND WITHDRAWAL. THIS WAS CONFIRMED BY CHIP SHOWING SIMILAR DECREASES OF METHYLATED DNA IN THE SAME REGIONS. THE CIE-INDUCED DEMETHYLATION IS CHARACTERIZED BY BEING LOCATED NEAR CERTAIN TRANSCRIPTION FACTOR BINDING SEQUENCES, AP-1 AND CRE, AND OCCURRED DURING TREATMENT AS WELL AS AFTER ETHANOL WITHDRAWAL. FURTHERMORE, THE INCREASE IN VITRO OF METHYLATED DNA DECREASED TRANSCRIPTION FACTOR BINDING ACTIVITY AND PROMOTER ACTIVITY. AN ADDITIONAL CHIP ASSAY INDICATED THAT THE CIE-INDUCED DNA DEMETHYLATION IS ACCOMPANIED BY INCREASED OCCUPATION BY TRANSCRIPTION FACTORS. CONCLUSIONS: THESE RESULTS SUGGEST AN IMPORTANT ROLE OF DNA DEMETHYLATION IN MEDIATING CIE-INDUCED NR2B GENE UP-REGULATION, THUS IMPLICATING A NOVEL MOLECULAR SITE OF ALCOHOL ACTION.	2010	
                                                                                                                                                                                                                                                                                               
11 1117  35 COMPARATIVE AND EXPERIMENTAL STUDIES ON THE GENES ALTERED BY CHRONIC HYPOXIA IN HUMAN BRAIN MICROENDOTHELIAL CELLS. BACKGROUND : HYPOXIA INDUCIBLE FACTOR 1 ALPHA (HIF1A) IS A MASTER REGULATOR OF ACUTE HYPOXIA; HOWEVER, WITH CHRONIC HYPOXIA, HIF1A LEVELS RETURN TO THE NORMOXIC LEVELS. IMPORTANTLY, THE GENES THAT ARE INVOLVED IN THE CELL SURVIVAL AND VIABILITY UNDER CHRONIC HYPOXIA ARE NOT KNOWN. THEREFORE, WE TESTED THE HYPOTHESIS THAT CHRONIC HYPOXIA LEADS TO THE UPREGULATION OF A CORE GROUP OF GENES WITH ASSOCIATED CHANGES IN THE PROMOTER DNA METHYLATION THAT MEDIATES THE CELL SURVIVAL UNDER HYPOXIA. RESULTS : WE EXAMINED THE EFFECT OF CHRONIC HYPOXIA (3 DAYS; 0.5% OXYGEN) ON HUMAN BRAIN MICRO ENDOTHELIAL CELLS (HBMEC) VIABILITY AND APOPTOSIS. HYPOXIA CAUSED A SIGNIFICANT REDUCTION IN CELL VIABILITY AND AN INCREASE IN APOPTOSIS. NEXT, WE EXAMINED CHRONIC HYPOXIA ASSOCIATED CHANGES IN TRANSCRIPTOME AND GENOME-WIDE PROMOTER METHYLATION. THE DATA OBTAINED WAS COMPARED WITH 16 OTHER MICROARRAY STUDIES ON CHRONIC HYPOXIA. NINE GENES WERE ALTERED IN RESPONSE TO CHRONIC HYPOXIA IN ALL 17 STUDIES. INTERESTINGLY, HIF1A WAS NOT ALTERED WITH CHRONIC HYPOXIA IN ANY OF THE STUDIES. FURTHERMORE, WE COMPARED OUR DATA TO THREE OTHER STUDIES THAT IDENTIFIED HIF-RESPONSIVE GENES BY VARIOUS APPROACHES. ONLY TWO GENES WERE FOUND TO BE HIF DEPENDENT. WE SILENCED EACH OF THESE 9 GENES USING CRISPR/CAS9 SYSTEM. DOWNREGULATION OF EGLN3 SIGNIFICANTLY INCREASED THE CELL DEATH UNDER CHRONIC HYPOXIA, WHEREAS DOWNREGULATION OF ERO1L, ENO2, ADRENOMEDULLIN, AND SPAG4 REDUCED THE CELL DEATH UNDER HYPOXIA. CONCLUSIONS : WE PROVIDE A CORE GROUP OF GENES THAT REGULATES CELLULAR ACCLIMATIZATION UNDER CHRONIC HYPOXIC STRESS, AND MOST OF THEM ARE HIF INDEPENDENT.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
12  273  43 AGE-INDUCED SUPPRESSION OF EZH2 MEDIATES INJURY OF PODOCYTES BY REDUCING H3K27ME3. BACKGROUND: CHRONIC HYPERGLYCEMIA, A PIVOTAL FEATURE OF DIABETES MELLITUS (DM), INITIATES THE FORMATION OF ADVANCED GLYCATION END PRODUCTS (AGES) AND THE DYSREGULATION OF EPIGENETIC MECHANISMS, WHICH MAY CAUSE INJURY TO RENAL PODOCYTES, A CENTRAL FEATURE OF DIABETIC KIDNEY DISEASE (DKD). PREVIOUS DATA OF OUR GROUP SHOWED THAT AGES SIGNIFICANTLY REDUCE THE EXPRESSION OF NIPP1 (NUCLEAR INHIBITOR OF PROTEIN PHOSPHATASE 1) IN PODOCYTES IN VITRO AS WELL AS IN HUMAN AND MURINE DKD. NIPP1 WAS SHOWN BY OTHERS TO INTERACT WITH ENHANCER OF ZESTE HOMOLOG 2 (EZH2), WHICH CATALYZES THE REPRESSIVE METHYLATION OF H3K27ME3 ON HISTONE 3. THEREFORE, WE HYPOTHESIZED THAT AGES CAN DIRECTLY INDUCE EPIGENETIC CHANGES IN PODOCYTES. METHODS: WE ANALYZED THE RELEVANCE OF AGES ON EZH2 EXPRESSION AND ACTIVITY IN A MURINE PODOCYTE CELL LINE. CELLS WERE TREATED WITH 5 MG/ML GLYCATED BSA FOR 24 H. TO DETERMINE THE MEANING OF EZH2 SUPPRESSION, EZH2 ACTIVITY WAS INHIBITED BY INCUBATING THE CELLS WITH THE PHARMACOLOGICAL METHYLTRANSFERASE INHIBITOR 3-DEAZANEPLANOCIN A; EZH2 EXPRESSION WAS REPRESSED WITH SIRNA. MRNA EXPRESSION WAS ANALYZED WITH REAL-TIME PCR, AND PROTEIN EXPRESSION WITH WESTERN BLOT. EZH2 EXPRESSION AND LEVEL OF H3K27 TRIMETHYLATION IN PODOCYTES OF DIABETIC DB/DB MICE, A MOUSE MODEL FOR TYPE 2 DM, WERE ANALYZED USING IMMUNOFLUORESCENCE. RESULTS: OUR DATA DEMONSTRATED THAT AGES DECREASE EZH2 EXPRESSION IN PODOCYTES AND CONSEQUENTLY REDUCE H3K27ME3. THIS SUPPRESSION OF EZH2 MIMICKED THE AGE EFFECTS AND CAUSED AN UPREGULATED EXPRESSION OF PATHOLOGICAL FACTORS THAT CONTRIBUTE TO PODOCYTE INJURY IN DKD. IN ADDITION, ANALYSES OF DB/DB MICE SHOWED SIGNIFICANTLY REDUCED H3K27ME3 AND EZH2 EXPRESSION IN PODOCYTES. MOREOVER, THE SUPPRESSION OF NIPP1 AND EZH2 SHOWED SIMILAR EFFECTS REGARDING PODOCYTE INJURY. CONCLUSIONS: OUR STUDIES PROVIDE A NOVEL PATHWAY HOW AGES CONTRIBUTE TO PODOCYTE INJURY AND THE FORMATION OF THE SO-CALLED METABOLIC MEMORY IN DKD.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
13 2590  39 EPIGENETICS OF PROTEASOME INHIBITION IN THE LIVER OF RATS FED ETHANOL CHRONICALLY. AIM: TO EXAMINE THE EFFECTS OF ETHANOL-INDUCED PROTEASOME INHIBITION, AND THE EFFECTS OF PROTEASOME INHIBITION IN THE REGULATION OF EPIGENETIC MECHANISMS. METHODS: RATS WERE FED ETHANOL FOR 1 MO USING THE TSUKAMOTO-FRENCH MODEL AND WERE COMPARED TO RATS GIVEN THE PROTEASOME INHIBITOR PS-341 (BORTEZOMIB, VELCADE(TM)) BY INTRAPERITONEAL INJECTION. MICROARRAY ANALYSIS AND REAL TIME PCR WERE PERFORMED AND PROTEASOME ACTIVITY ASSAYS AND WESTERN BLOT ANALYSIS WERE PERFORMED USING ISOLATED NUCLEI. RESULTS: CHRONIC ETHANOL FEEDING CAUSED A SIGNIFICANT INHIBITION OF THE UBIQUITIN PROTEASOME PATHWAY IN THE NUCLEUS, WHICH LED TO CHANGES IN THE TURNOVER OF TRANSCRIPTIONAL FACTORS, HISTONE-MODIFYING ENZYMES, AND, THEREFORE, AFFECTED EPIGENETIC MECHANISMS. CHRONIC ETHANOL FEEDING WAS RELATED TO AN INCREASE IN HISTONE ACETYLATION, AND IT IS HYPOTHESIZED THAT THE PROTEASOME PROTEOLYTIC ACTIVITY REGULATED HISTONE MODIFICATIONS BY CONTROLLING THE STABILITY OF HISTONE MODIFYING ENZYMES, AND, THEREFORE, REGULATED THE CHROMATIN STRUCTURE, ALLOWING EASY ACCESS TO CHROMATIN BY RNA POLYMERASE, AND, THUS, PROPER GENE EXPRESSION. PROTEASOME INHIBITION BY PS-341 INCREASED HISTONE ACETYLATION SIMILAR TO CHRONIC ETHANOL FEEDING. IN ADDITION, PROTEASOME INHIBITION CAUSED DRAMATIC CHANGES IN HEPATIC REMETHYLATION REACTIONS AS THERE WAS A SIGNIFICANT DECREASE IN THE ENZYMES RESPONSIBLE FOR THE REGENERATION OF S-ADENOSYLMETHIONINE, AND, IN PARTICULAR, A SIGNIFICANT DECREASE IN THE BETAINE-HOMOCYSTEINE METHYLTRANSFERASE ENZYME. THIS SUGGESTED THAT HYPOMETHYLATION WAS ASSOCIATED WITH PROTEASOME INHIBITION, AS INDICATED BY THE DECREASE IN HISTONE METHYLATION. CONCLUSION: THE ROLE OF PROTEASOME INHIBITION IN REGULATING EPIGENETIC MECHANISMS, AND ITS LINK TO LIVER INJURY IN ALCOHOLIC LIVER DISEASE, IS THUS A PROMISING APPROACH TO STUDY LIVER INJURY DUE TO CHRONIC ETHANOL CONSUMPTION.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
14  531  37 ASTROCYTE REACTIVITY FOLLOWING BLAST EXPOSURE INVOLVES ABERRANT HISTONE ACETYLATION. BLAST INDUCED NEUROTRAUMA (BINT) IS A PREVALENT INJURY WITHIN MILITARY AND CIVILIAN POPULATIONS. THE INJURY IS CHARACTERIZED BY PERSISTENT INFLAMMATION AT THE CELLULAR LEVEL WHICH MANIFESTS AS A MULTITUDE OF COGNITIVE AND FUNCTIONAL IMPAIRMENTS. EPIGENETIC REGULATION OF TRANSCRIPTION OFFERS AN IMPORTANT CONTROL MECHANISM FOR GENE EXPRESSION AND CELLULAR FUNCTION WHICH MAY UNDERLIE CHRONIC INFLAMMATION AND RESULT IN NEURODEGENERATION. WE HYPOTHESIZE THAT ALTERED HISTONE ACETYLATION PATTERNS MAY BE INVOLVED IN BLAST INDUCED INFLAMMATION AND THE CHRONIC ACTIVATION OF GLIAL CELLS. THIS STUDY AIMED TO ELUCIDATE CHANGES TO HISTONE ACETYLATION OCCURRING FOLLOWING INJURY AND THE ROLES THESE CHANGES MAY HAVE WITHIN THE PATHOLOGY. SPRAGUE DAWLEY RATS WERE SUBJECTED TO EITHER A 10 OR 17 PSI BLAST OVERPRESSURE WITHIN AN ADVANCED BLAST SIMULATOR (ABS). SHAM ANIMALS UNDERWENT THE SAME PROCEDURES WITHOUT BLAST EXPOSURE. MEMORY IMPAIRMENTS WERE MEASURED USING THE NOVEL OBJECT RECOGNITION (NOR) TEST AT 2 AND 7 DAYS POST-INJURY. TISSUES WERE COLLECTED AT 7 DAYS FOR WESTERN BLOT AND IMMUNOHISTOCHEMISTRY (IHC) ANALYSIS. SHAM ANIMALS SHOWED INTACT MEMORY AT EACH TIME POINT. THE NOVEL OBJECT DISCRIMINATION DECREASED SIGNIFICANTLY BETWEEN TWO AND 7 DAYS FOR EACH INJURY GROUP (P < 0.05). THIS IS INDICATIVE OF THE ONSET OF MEMORY IMPAIRMENT. WESTERN BLOT ANALYSIS SHOWED GLIAL FIBRILLARY ACIDIC PROTEIN (GFAP), A KNOWN MARKER OF ACTIVATED ASTROCYTES, WAS ELEVATED IN THE PREFRONTAL CORTEX (PFC) FOLLOWING BLAST EXPOSURE FOR BOTH INJURY GROUPS. ANALYSIS OF HISTONE PROTEIN EXTRACT SHOWED NO CHANGES IN THE LEVEL OF ANY TOTAL HISTONE PROTEINS WITHIN THE PFC. HOWEVER, ACETYLATION LEVELS OF HISTONE H2B, H3, AND H4 WERE DECREASED IN BOTH GROUPS (P < 0.05). CO-LOCALIZATION IMMUNOFLUORESCENCE WAS USED TO FURTHER INVESTIGATE ANY POTENTIAL CORRELATION BETWEEN DECREASED HISTONE ACETYLATION AND ASTROCYTE ACTIVATION. THESE EXPERIMENTS SHOWED A SIMILAR DECREASE IN H3 ACETYLATION IN ASTROCYTES EXPOSED TO A 17 PSI BLAST BUT NOT A 10 PSI BLAST. FURTHER INVESTIGATION OF GENE EXPRESSION BY POLYMERASE CHAIN REACTION (PCR) ARRAY, SHOWED DYSREGULATION OF SEVERAL CYTOKINE AND CYTOKINE RECEPTORS THAT ARE INVOLVED IN NEUROINFLAMMATORY PROCESSES. WE HAVE SHOWN ABERRANT HISTONE ACETYLATION PATTERNS INVOLVED IN BLAST INDUCED ASTROGLIOSIS AND COGNITIVE IMPAIRMENTS. FURTHER UNDERSTANDING OF THEIR ROLE IN THE INJURY PROGRESSION MAY LEAD TO NOVEL THERAPEUTIC TARGETS.	2016	
                                                                                                                                                               
15 4014  38 LOW-DOSE CD INDUCES HEPATIC GENE HYPERMETHYLATION, ALONG WITH THE PERSISTENT REDUCTION OF CELL DEATH AND INCREASE OF CELL PROLIFERATION IN RATS AND MICE. BACKGROUND: CADMIUM (CD) IS CLASSIFIED AS A HUMAN CARCINOGEN PROBABLY ASSOCIATED WITH EPIGENETIC CHANGES. DNA METHYLATION IS ONE OF EPIGENETIC MECHANISMS BY WHICH CELLS CONTROL GENE EXPRESSION. THEREFORE, THE PRESENT STUDY GENOME-WIDELY SCREENED THE METHYLATION-ALTERED GENES IN THE LIVER OF RATS PREVIOUSLY EXPOSED TO LOW-DOSE CD. METHODOLOGY PRINCIPAL FINDINGS: RATS WERE EXPOSED TO CD AT 20 NMOL/KG EVERY OTHER DAY FOR 4 WEEKS AND GENE METHYLATION WAS ANALYZED AT THE 48(TH) WEEK WITH METHYLATED DNA IMMUNOPRECIPITATION-CPG ISLAND MICROARRAY. AMONG THE 1629 ALTERED GENES, THERE WERE 675 GENES WHOSE PROMOTER CPG ISLANDS (CGIS) WERE HYPERMETHYLATED, 899 GENES WHOSE PROMOTER CGIS WERE HYPOMETHYLATED, AND 55 GENES WHOSE PROMOTER CGIS WERE MIXED WITH HYPER- AND HYPO-METHYLATION. CASPASE-8 GENE PROMOTER CGIS AND TNF GENE PROMOTER CGIS WERE HYPERMETHYLATED AND HYPOMETHYLATED, RESPECTIVELY, ALONG WITH A LOW APOPTOSIS RATE IN CD-TREATED RAT LIVERS. TO LINK THE ABERRANT METHYLATION OF CASPASE-8 AND TNF GENES TO THE LOW APOPTOSIS INDUCED BY LOW-DOSE CD, MICE WERE GIVEN CHRONIC EXPOSURE TO LOW-DOSE CD WITH AND WITHOUT METHYLATION INHIBITOR (5-AZA-2'-DEOXYCTIDENE, 5-AZA). AT THE 48(TH) WEEK AFTER CD EXPOSURE, LIVERS FROM CD-TREATED MICE DISPLAYED THE INCREASED CASPASE-8 CGI METHYLATION AND DECREASED CASPASE-8 PROTEIN EXPRESSION, ALONG WITH SIGNIFICANT INCREASES IN CELL PROLIFERATION AND OVEREXPRESSION OF TGF-BETA1 AND CYTOKERATIN 8/18 (THE LATTER IS A NEW MARKER OF MOUSE LIVER PRENEOPLASTIC LESIONS), ALL WHICH WERE PREVENTED BY 5-AZA TREATMENT. CONCLUSION/SIGNIFICANCE: THESE RESULTS SUGGEST THAT CD-INDUCED GLOBAL GENE HYPERMETHYLATION, MOST LIKELY CASPASE-8 GENE PROMOTER HYPERMETHYLATION THAT DOWN-REGULATED ITS EXPRESSION, LEADING TO THE DECREASED HEPATIC APOPTOSIS AND INCREASED PRENEOPLASTIC LESIONS.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
16 2825  46 FLOW-DEPENDENT EPIGENETIC REGULATION OF IGFBP5 EXPRESSION BY H3K27ME3 CONTRIBUTES TO ENDOTHELIAL ANTI-INFLAMMATORY EFFECTS. RATIONALE: ATHEROSCLEROSIS IS A CHRONIC INFLAMMATORY AND EPIGENETIC DISEASE THAT IS INFLUENCED BY DIFFERENT PATTERNS OF BLOOD FLOW. HOWEVER, THE EPIGENETIC MECHANISM WHEREBY ATHEROPROTECTIVE FLOW CONTROLS ENDOTHELIAL GENE PROGRAMMING REMAINS ELUSIVE. HERE, WE INVESTIGATED THE POSSIBILITY THAT FLOW ALTERS ENDOTHELIAL GENE EXPRESSION THROUGH EPIGENETIC MECHANISMS. METHODS: EN FACE STAINING AND WESTERN BLOT WERE USED TO DETECT PROTEIN EXPRESSION. REAL-TIME PCR WAS USED TO DETERMINE RELATIVE GENE EXPRESSION. RNA-SEQUENCING OF HUMAN UMBILICAL VEIN ENDOTHELIAL CELLS TREATED WITH SIRNA OF ENHANCER OF ZESTE HOMOLOG 2 (EZH2) OR LAMINAR FLOW WAS USED FOR TRANSCRIPTIONAL PROFILING. RESULTS: WE FOUND THAT TRIMETHYLATION OF HISTONE 3 LYSINE 27 (H3K27ME3), A REPRESSIVE EPIGENETIC MARK THAT ORCHESTRATES GENE REPRESSION, WAS REDUCED IN LAMINAR FLOW AREAS OF MOUSE AORTA AND FLOW-TREATED HUMAN ENDOTHELIAL CELLS. THE DECREASE OF H3K27ME3 PARALLELED A REDUCTION IN THE EPIGENETIC "WRITER"-EZH2, THE CATALYTIC SUBUNIT OF THE POLYCOMB REPRESSIVE COMPLEX 2 (PRC2). MOREOVER, LAMINAR FLOW DECREASED EXPRESSION OF EZH2 VIA MECHANOSENSITIVE MIR101. GENOME-WIDE TRANSCRIPTOME PROFILING STUDIES IN ENDOTHELIAL CELLS TREATED WITH EZH2 SIRNA AND FLOW REVEALED THE UPREGULATION OF NOVEL MECHANOSENSITIVE GENE IGFBP5 (INSULIN-LIKE GROWTH FACTOR-BINDING PROTEIN 5), WHICH IS EPIGENETICALLY SILENCED BY H3K27ME3. FUNCTIONALLY, INHIBITION OF H3K27ME3 BY EZH2 SIRNA OR GSK126 (A SPECIFIC EZH2 INHIBITOR) REDUCED H3K27ME3 LEVELS AND MONOCYTE ADHESION TO ENDOTHELIAL CELLS. ADENOVIRAL OVEREXPRESSION OF IGFBP5 ALSO RECAPITULATED THE ANTI-INFLAMMATORY EFFECTS OF H3K27ME3 INHIBITION. MORE IMPORTANTLY, WE OBSERVED EZH2 UPREGULATION, AND IGFBP5 DOWNREGULATION, IN ADVANCED ATHEROSCLEROTIC PLAQUES FROM HUMAN PATIENTS. CONCLUSION: TAKEN TOGETHER, OUR FINDINGS REVEAL THAT ATHEROPROTECTIVE FLOW REDUCES H3K27ME3 AS A CHROMATIN-BASED MECHANISM TO AUGMENT THE EXPRESSION OF GENES THAT CONFER AN ANTI-INFLAMMATORY RESPONSE IN THE ENDOTHELIUM. OUR STUDY EXEMPLIFIES FLOW-DEPENDENT EPIGENETIC REGULATION OF ENDOTHELIAL GENE EXPRESSION, AND ALSO SUGGESTS THAT TARGETING THE EZH2/H3K27ME3/IGFBP5 PATHWAY MAY OFFER NOVEL THERAPEUTICS FOR INFLAMMATORY DISORDERS SUCH AS ATHEROSCLEROSIS.	2018	
                                                                                                                                                                                                                                                                                                                                
17 5177  39 PREFRONTAL CORTEX EXPRESSION OF CHROMATIN MODIFIER GENES IN MALE WSP AND WSR MICE CHANGES ACROSS ETHANOL DEPENDENCE, WITHDRAWAL, AND ABSTINENCE. ALCOHOL-USE DISORDER (AUD) IS A RELAPSING DISORDER ASSOCIATED WITH EXCESSIVE ETHANOL CONSUMPTION. RECENT STUDIES SUPPORT THE INVOLVEMENT OF EPIGENETIC MECHANISMS IN THE DEVELOPMENT OF AUD. STUDIES CARRIED OUT SO FAR HAVE FOCUSED ON A FEW SPECIFIC EPIGENETIC MODIFICATIONS. THE GOAL OF THIS PROJECT WAS TO INVESTIGATE GENE EXPRESSION CHANGES OF EPIGENETIC REGULATORS THAT MEDIATE A BROAD ARRAY OF CHROMATIN MODIFICATIONS AFTER CHRONIC ALCOHOL EXPOSURE, CHRONIC ALCOHOL EXPOSURE FOLLOWED BY 8 H WITHDRAWAL, AND CHRONIC ALCOHOL EXPOSURE FOLLOWED BY 21 DAYS OF ABSTINENCE IN WITHDRAWAL-RESISTANT (WSR) AND WITHDRAWAL SEIZURE-PRONE (WSP) SELECTED MOUSE LINES. WE FOUND THAT CHRONIC VAPOR EXPOSURE TO HIGHLY INTOXICATING LEVELS OF ETHANOL ALTERS THE EXPRESSION OF SEVERAL CHROMATIN REMODELING GENES MEASURED BY QUANTITATIVE PCR ARRAY ANALYSES. THE IDENTIFIED EFFECTS WERE INDEPENDENT OF SELECTED LINES, WHICH, HOWEVER, DISPLAYED BASELINE DIFFERENCES IN EPIGENETIC GENE EXPRESSION. WE REPORTED DYSREGULATION IN THE EXPRESSION OF GENES INVOLVED IN HISTONE ACETYLATION, DEACETYLATION, LYSINE AND ARGININE METHYLATION AND UBIQUITINATIONHYLATION DURING CHRONIC ETHANOL EXPOSURE AND WITHDRAWAL, BUT NOT AFTER 21 DAYS OF ABSTINENCE. ETHANOL-INDUCED CHANGES ARE CONSISTENT WITH DECREASED HISTONE ACETYLATION AND WITH DECREASED DEPOSITION OF THE PERMISSIVE UBIQUITINATION MARK H2BK120UB, ASSOCIATED WITH REDUCED TRANSCRIPTION. ON THE OTHER HAND, ETHANOL-INDUCED CHANGES IN THE EXPRESSION OF GENES INVOLVED IN HISTONE LYSINE METHYLATION ARE CONSISTENT WITH INCREASED TRANSCRIPTION. THE NET RESULT OF THESE MODIFICATIONS ON GENE EXPRESSION IS LIKELY TO DEPEND ON THE COMBINATION OF THE SPECIFIC HISTONE TAIL MODIFICATIONS PRESENT AT A GIVEN TIME ON A GIVEN PROMOTER. SINCE ALCOHOL DOES NOT MODULATE GENE EXPRESSION UNIDIRECTIONALLY, IT IS NOT SURPRISING THAT ALCOHOL DOES NOT UNIDIRECTIONALLY ALTER CHROMATIN STRUCTURE TOWARD A CLOSED OR OPEN STATE, AS SUGGESTED BY THE RESULTS OF THIS STUDY.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
18 1236  33 CURCUMIN AMELIORATES NEPHROSCLEROSIS VIA SUPPRESSION OF HISTONE ACETYLATION INDEPENDENT OF HYPERTENSION. BACKGROUND: ALTHOUGH HISTONE ACETYLATION, AN EPIGENETIC MODIFICATION, HAS BEEN REPORTED TO BE RELATED TO THE PROGRESSION OF VARIOUS DISEASES, ITS INVOLVEMENT IN NEPHROSCLEROSIS IS UNCLEAR. METHODS: DAHL SALT-SENSITIVE RATS WERE USED AS A MODEL OF NEPHROSCLEROSIS IN THIS STUDY. THE RATS WERE DIVIDED INTO THREE GROUPS: (I) NORMAL-SALT DIET GROUP, (II) HIGH-SALT DIET GROUP (HS), AND (III) HS ADMINISTERED DAILY WITH CURCUMIN, A HISTONE ACETYLTRANSFERASE INHIBITOR (HS+C). AT 6 WEEKS AFTER THE TREATMENT, THE KIDNEYS WERE DISSECTED. MORPHOLOGIC CHANGES WERE ASSESSED BY MASSON'S TRICHROME STAINING. THE NUMBER OF MACROPHAGES, FIBROBLASTS AND THE CELLS EXPRESSING ACETYLATED HISTONE H3 AT LYS 9 (H3K9) WERE ASSESSED BY IMMUNOHISTOCHEMISTRY. RESULTS: ALTHOUGH BOTH HS AND HS+C RATS REVEALED A MARKED INCREASE IN SYSTOLIC BLOOD PRESSURE, SERUM CREATININE WAS INCREASED ONLY IN HS RATS AT 6 WEEKS. IN THE HS RATS, NEPHROSCLEROSIS WAS INDUCED, ACCOMPANYING A SIGNIFICANT ACCUMULATION OF MACROPHAGES AND FIBROBLASTS. THE INFLAMMATION AND FIBROSIS WAS MARKEDLY SUPPRESSED IN THE HS+C GROUP. THE LEVEL OF HISTONE ACETYLATION AT LYS 9 WAS ENHANCED IN THE HS RATS, WHEREAS CURCUMIN ADMINISTRATION SUPPRESSED THE HISTONE ACETYLATION. MOREOVER, IN THE HS RATS, INTERLEUKIN-6 GENE EXPRESSION WAS ASSOCIATED WITH ACETYLATED H3K9, AS REVEALED BY CHROMATIN IMMUNOPRECIPITATION ASSAY. CONCLUSIONS: OUR RESULTS SUGGESTED THAT CURCUMIN AMELIORATES NEPHROSCLEROSIS VIA SUPPRESSION OF HISTONE ACETYLATION, INDEPENDENTLY OF HYPERTENSION.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
19 6794  34 [EFFECT OF BENZO(A)PYRENE ON THE EXPRESSION OF AHR-REGULATED MICRORNA IN FEMALE AND MALE RAT LUNGS]. SMOKING IS THE MAIN RISK FACTOR FOR LUNG CANCER, MAINLY DUE TO PRESENCE OF NITROSAMINES AND POLYCYCLIC AROMATIC HYDROCARBONS, INCLUDING BENZO[A]PYRENE (BP) IN TOBACCO SMOKE COMPOSITION. THE GENOTOXIC EFFECT OF BP IS BASED ON THE HIGH DNA-BINDING ABILITY OF ITS METABOLITES, WHILE THE EPIGENETIC EFFECTS ARE MEDIATED BY A CHANGE IN THE EXPRESSION OF CANCER RELATED GENES OR REGULATORY RNAS. IT HAS BEEN SHOWN THAT WOMEN HAVE A HIGHER RISK TO DEVELOP LUNG CANCER UPON SMOKING RATHER THAN MEN. WE HYPOTHESIZED THAT CROSSTALK BETWEEN SIGNALING PATHWAYS ACTIVATED BY BP AND ESTROGENS COULD UNDERLIE THE SEX-DEPENDENT DIFFERENCES IN MIRNAS EXPRESSION. TO TEST THIS HYPOTHESIS, MALE AND FEMALE RATS WERE SUBJECTED TO SHORT-TERM OR LONG-TERM BP EXPOSURE. USING IN SILICO ANALYSIS, MIRNAS CONTAINING THE ER- AND AHR-BINDING SITES IN THE PROMOTERS OF THE GENES (OR HOST GENES) WERE SELECTED. DURING CHRONIC EXPOSURE OF BP THE EXPRESSION OF MIR-22-3P, -29A-3P, -126A-3P, -193B-5P IN THE LUNGS OF MALE RATS WERE SIGNIFICANTLY INCREASED, WHILE THE LEVEL OF MIRNA-483-3P WERE DECREASED. EXPRESSION OF MIRNA-483-3P WAS UP-REGULATED DURING CHRONIC BP EXPOSURE IN THE LUNGS OF FEMALE RATS AND THE LEVELS OF OTHER STUDIED MIRNAS WERE UNCHANGED. IN TURN, CHANGES IN THE EXPRESSION OF MIRNAS WERE FOLLOWED BY CHANGES IN THE EXPRESSION OF THEIR TARGET GENES, INCLUDING PTEN, EMP2, IGF1, ITGA6, SLC34A2, AND THE OBSERVED CHANGES IN FEMALE AND MALE RAT LUNGS WERE VARIED. THUS, OUR RESULTS SUGGEST THAT SEX-DEPENDENT EPIGENETIC EFFECTS OF BP MAY BE BASED ON DIFFERENT EXPRESSION OF AHR- AND ER- REGULATED MIRNAS.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
20 6419  32 THE TET2-UPF1 COMPLEX MODULATES MRNA STABILITY UNDER STRESS CONDITIONS. INTRODUCTION: ENVIRONMENTAL STRESS PROMOTES EPIGENETIC ALTERATIONS THAT IMPACT GENE EXPRESSION AND SUBSEQUENTLY PARTICIPATE IN THE PATHOLOGICAL PROCESSES OF THE DISORDER. AMONG EPIGENETIC REGULATIONS, TEN-ELEVEN TRANSLOCATION (TET) ENZYMES OXIDIZE 5-METHYLCYTOSINE (5MC) TO 5-HYDROXYMETHYLCYTOSINE (5HMC) IN DNA AND RNA AND FUNCTION AS CRITICAL PLAYERS IN THE PATHOGENESIS OF DISEASES. OUR PREVIOUS RESULTS SHOWED THAT CHRONIC STRESS INCREASES THE EXPRESSION OF CYTOPLASMIC TET2 IN THE HIPPOCAMPUS OF MICE EXPOSED TO CHRONIC MILD STRESS (CMS). WHETHER THE CYTOPLASMIC TET2 ALTERS RNA 5HMC MODIFICATION IN CHRONIC STRESS-RELATED PROCESSES REMAINS LARGELY UNKNOWN. METHODS: TO EXPLORE THE ROLE OF CYTOPLASMIC TET2 UNDER CMS CONDITIONS, WE ESTABLISHED CMS MICE MODEL AND DETECTED THE EXPRESSION OF RNA 5HMC BY DOT BLOT. WE VERIFIED THE INTERACTION OF TET2 AND ITS INTERACTING PROTEIN BY CO-IMMUNOPRECIPITATION COMBINED WITH MASS SPECTROMETRY AND SCREENED DOWNSTREAM TARGET GENES BY CLUSTER ANALYSIS OF TET2 AND UPSTREAM FRAMESHIFT 1 (UPF1) INTERACTING RNA. THE EXPRESSION OF PROTEIN WAS DETECTED BY WESTERN BLOT AND THE EXPRESSION OF THE SCREENED TARGET GENES WAS DETECTED BY QRT-PCR. RESULTS: IN THIS STUDY, WE FOUND THAT INCREASED CYTOPLASMIC TET2 EXPRESSION UNDER CMS CONDITIONS LEADS TO INCREASE IN TOTAL RNA 5HMC MODIFICATION. TET2 INTERACTED WITH THE KEY NON-SENSE-MEDIATED MRNA DECAY (NMD) FACTOR UPF1, REGULATED THE STABILITY OF STRESS-RELATED GENES SUCH AS UNC5B MRNA, AND MIGHT THEREBY AFFECT NEURODEVELOPMENT. DISCUSSION: IN SUMMARY, THIS STUDY REVEALED THAT TET2-MEDIATED RNA 5HMC MODIFICATION IS INVOLVED IN STRESS-RELATED MRNA STABILITY REGULATION AND MAY SERVE AS A POTENTIAL THERAPEUTIC TARGET FOR CHRONIC STRESS-RELATED DISEASES SUCH AS DEPRESSION.	2023