1  3235 137 HEMIN AVAILABILITY INDUCES COORDINATED DNA METHYLATION AND GENE EXPRESSION CHANGES IN PORPHYROMONAS GINGIVALIS. PERIODONTAL DISEASE IS A CHRONIC INFLAMMATORY DISEASE IN WHICH THE ORAL PATHOGEN PORPHYROMONAS GINGIVALIS PLAYS AN IMPORTANT ROLE. PORPHYROMONAS GINGIVALIS EXPRESSES VIRULENCE DETERMINANTS IN RESPONSE TO HIGHER HEMIN CONCENTRATIONS, BUT THE UNDERLYING REGULATORY PROCESSES REMAIN UNCLEAR. BACTERIAL DNA METHYLATION HAS THE POTENTIAL TO FULFIL THIS MECHANISTIC ROLE. WE CHARACTERIZED THE METHYLOME OF P. GINGIVALIS, AND COMPARED ITS VARIATION TO TRANSCRIPTOME CHANGES IN RESPONSE TO HEMIN AVAILABILITY. PORPHYROMONAS GINGIVALIS W50 WAS GROWN IN CHEMOSTAT CONTINUOUS CULTURE WITH EXCESS OR LIMITED HEMIN, PRIOR TO WHOLE-METHYLOME AND TRANSCRIPTOME PROFILING USING NANOPORE AND ILLUMINA RNA-SEQ. DNA METHYLATION WAS QUANTIFIED FOR DAM/DCM MOTIFS AND ALL-CONTEXT N6-METHYLADENINE (6MA) AND 5-METHYLCYTOSINE (5MC). OF ALL 1,992 GENES ANALYZED, 161 AND 268 WERE RESPECTIVELY OVER- AND UNDER-EXPRESSED WITH EXCESS HEMIN. NOTABLY, WE DETECTED DIFFERENTIAL DNA METHYLATION SIGNATURES FOR THE DAM "GATC" MOTIF AND BOTH ALL-CONTEXT 6MA AND 5MC IN RESPONSE TO HEMIN AVAILABILITY. JOINT ANALYSES IDENTIFIED A SUBSET OF COORDINATED CHANGES IN GENE EXPRESSION, 6MA, AND 5MC METHYLATION THAT TARGET GENES INVOLVED IN LACTATE UTILIZATION AND ABC TRANSPORTERS. THE RESULTS IDENTIFY ALTERED METHYLATION AND EXPRESSION RESPONSES TO HEMIN AVAILABILITY IN P. GINGIVALIS, WITH INSIGHTS INTO MECHANISMS REGULATING ITS VIRULENCE IN PERIODONTAL DISEASE. IMPORTANCE DNA METHYLATION HAS IMPORTANT ROLES IN BACTERIA, INCLUDING IN THE REGULATION OF TRANSCRIPTION. PORPHYROMONAS GINGIVALIS, AN ORAL PATHOGEN IN PERIODONTITIS, EXHIBITS WELL-ESTABLISHED GENE EXPRESSION CHANGES IN RESPONSE TO HEMIN AVAILABILITY. HOWEVER, THE REGULATORY PROCESSES UNDERLYING THESE EFFECTS REMAIN UNKNOWN. WE PROFILED THE NOVEL P. GINGIVALIS EPIGENOME, AND ASSESSED EPIGENETIC AND TRANSCRIPTOME VARIATION UNDER LIMITED AND EXCESS HEMIN CONDITIONS. AS EXPECTED, MULTIPLE GENE EXPRESSION CHANGES WERE DETECTED IN RESPONSE TO LIMITED AND EXCESS HEMIN THAT REFLECT HEALTH AND DISEASE, RESPECTIVELY. NOTABLY, WE ALSO DETECTED DIFFERENTIAL DNA METHYLATION SIGNATURES FOR THE DAM "GATC" MOTIF AND BOTH ALL-CONTEXT 6MA AND 5MC IN RESPONSE TO HEMIN. JOINT ANALYSES IDENTIFIED COORDINATED CHANGES IN GENE EXPRESSION, 6MA, AND 5MC METHYLATION THAT TARGET GENES INVOLVED IN LACTATE UTILIZATION AND ABC TRANSPORTERS. THE RESULTS IDENTIFY NOVEL REGULATORY PROCESSES UNDERLYING THE MECHANISM OF HEMIN REGULATED GENE EXPRESSION IN P. GINGIVALIS, WITH PHENOTYPIC IMPACTS ON ITS VIRULENCE IN PERIODONTAL DISEASE.	2023	

2  3984  41 LONG-TERM IMPACT OF MATERNAL HIGH-FAT DIET ON OFFSPRING CARDIAC HEALTH: ROLE OF MICRO-RNA BIOGENESIS. HEART FAILURE IS A WORLDWIDE LEADING CAUSE OF DEATH. DIET AND OBESITY ARE PARTICULARLY OF HIGH CONCERN IN HEART DISEASE ETIOLOGY. GRAVELY, ALTERED NUTRITION DURING DEVELOPMENTAL WINDOWS OF VULNERABILITY CAN HAVE LONG-TERM IMPACT ON HEART HEALTH; HOWEVER, THE UNDERLYING MECHANISMS ARE POORLY UNDERSTOOD. IN THE UNDERSTANDING OF THE INITIATION OF CHRONIC DISEASES RELATED TO DEVELOPMENTAL EXPOSURE TO ENVIRONMENTAL CHALLENGES, DEREGULATIONS IN EPIGENETIC MECHANISMS INCLUDING MICRO-RNAS HAVE BEEN PROPOSED AS KEY EVENTS. IN THIS CONTEXT, WE AIMED AT DELINEATING THE ROLE OF MICRO-RNAS IN THE PROGRAMMING OF CARDIAC ALTERATIONS INDUCED BY EARLY DEVELOPMENTAL EXPOSURE TO NUTRITIONAL IMBALANCE. TO REACH OUR AIM, WE DEVELOPED A HUMAN RELEVANT MODEL OF DEVELOPMENTAL EXPOSURE TO NUTRITIONAL IMBALANCE BY MATERNALLY EXPOSING RAT TO HIGH-FAT DIET DURING GESTATION AND LACTATION. IN THIS MODEL, OFFSPRING EXPOSED TO MATERNAL HIGH-FAT DIET DEVELOPED CARDIAC HYPERTROPHY AND INCREASED EXTRACELLULAR MATRIX DEPOT COMPARED TO THOSE EXPOSED TO CHOW DIET. MICROARRAY APPROACH PERFORMED ON CARDIAC TISSUE ALLOWED THE IDENTIFICATION OF A MICRO-RNA SUBSET WHICH WAS DOWN-REGULATED IN HIGH-FAT DIET-EXPOSED ANIMALS AND WHICH WERE PREDICTED TO REGULATE TRANSFORMING GROWTH FACTOR-BETA (TGFBETA)-MEDIATED REMODELING. AS INDICATED BY IN VITRO APPROACHES AND GENE EXPRESSION MEASUREMENT IN THE HEART OF OUR ANIMALS, DECREASE IN DIGEORGE CRITICAL REGION 8 (DGCR8) EXPRESSION, INVOLVED IN MICRO-RNA BIOGENESIS, SEEMS TO BE A CRITICAL POINT IN THE ALTERATIONS OF THE MICRO-RNA PROFILE AND THE TGFBETA-MEDIATED REMODELING INDUCED BY MATERNAL EXPOSURE TO HIGH-FAT DIET. FINALLY, INCREASING DGCR8 ACTIVITY AND/OR EXPRESSION THROUGH HEMIN TREATMENT IN VITRO REVEALED ITS POTENTIAL IN THE RESCUE OF THE PRO-FIBROTIC PHENOTYPE IN CARDIOMYOCYTES DRIVEN BY DGCR8 DECREASE. THESE FINDINGS SUGGEST THAT CARDIAC ALTERATIONS INDUCED BY MATERNAL EXPOSURE TO HIGH-FAT DIET IS RELATED TO ABNORMALITIES IN TGFBETA PATHWAY AND ASSOCIATED WITH DOWN-REGULATED MICRO-RNA PROCESSING. OUR STUDY HIGHLIGHTED DGCR8 AS A POTENTIAL THERAPEUTIC TARGET FOR HEART DISEASES RELATED TO EARLY EXPOSURE TO DIETARY CHALLENGE.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                  
3   323  33 ALKBH4 STABILIZATION IS REQUIRED FOR ARSENIC-INDUCED 6MA DNA METHYLATION INHIBITION, KERATINOCYTE MALIGNANT TRANSFORMATION, AND TUMORIGENICITY. INORGANIC ARSENIC IS ONE OF THE WELL-KNOWN HUMAN SKIN CARCINOGENS. HOWEVER, THE MOLECULAR MECHANISM BY WHICH ARSENIC PROMOTES CARCINOGENESIS REMAINS UNCLEAR. PREVIOUS STUDIES HAVE ESTABLISHED THAT EPIGENETIC CHANGES, INCLUDING CHANGES IN DNA METHYLATION, ARE AMONG THE CRITICAL MECHANISMS THAT DRIVE CARCINOGENESIS. N(6)-METHYLADENINE (6MA) METHYLATION ON DNA IS A WIDESPREAD EPIGENETIC MODIFICATION THAT WAS INITIALLY FOUND ON BACTERIAL AND PHAGE DNA. ONLY RECENTLY HAS 6MA BEEN IDENTIFIED IN MAMMALIAN GENOMES. HOWEVER, THE FUNCTION OF 6MA IN GENE EXPRESSION AND CANCER DEVELOPMENT IS NOT WELL UNDERSTOOD. HERE, WE SHOW THAT CHRONIC LOW DOSES OF ARSENIC INDUCE MALIGNANT TRANSFORMATION AND TUMORIGENESIS IN KERATINOCYTES AND LEAD TO THE UPREGULATION OF ALKBH4 AND DOWNREGULATION OF 6MA ON DNA. WE FOUND THAT REDUCED 6MA LEVELS IN RESPONSE TO LOW LEVELS OF ARSENIC WERE MEDIATED BY THE UPREGULATION OF THE 6MA DNA DEMETHYLASE ALKBH4. MOREOVER, WE FOUND THAT ARSENIC INCREASED ALKBH4 PROTEIN LEVELS AND THAT ALKBH4 DELETION IMPAIRED ARSENIC-INDUCED TUMORIGENICITY IN VITRO AND IN MICE. MECHANISTICALLY, WE FOUND THAT ARSENIC PROMOTED ALKBH4 PROTEIN STABILITY THROUGH REDUCED AUTOPHAGY. TOGETHER, OUR FINDINGS REVEAL THAT THE DNA 6MA DEMETHYLASEALKBH4 PROMOTES ARSENIC TUMORIGENICITY AND ESTABLISHES ALKBH4 AS A PROMISING TARGET FOR ARSENIC-INDUCED TUMORIGENESIS.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
4  3036  32 GENISTEIN AMELIORATES RENAL FIBROSIS THROUGH REGULATION SNAIL VIA M6A RNA DEMETHYLASE ALKBH5. RENAL TUBULE-INTERSTITIAL FIBROSIS IS RELATED TO CHRONIC KIDNEY DISEASE PROGRESSION AND A TYPICAL FEATURE OF THE AGING KIDNEY. EPIGENETIC MODIFICATIONS OF FIBROSIS-PRONE GENES REGULATE THE DEVELOPMENT OF RENAL FIBROSIS. AS A KIND OF "EPIGENETIC DIET", SOY ISOFLAVONE GENISTEIN WAS REPORTED TO HAVE RENAL PROTECTIVE ACTION AND EPIGENETIC-MODULATING EFFECTS. HOWEVER, ITS RENAL PROTECTION ROLE AND UNDERLYING MECHANISMS ARE YET TO BE FULLY CLARIFIED. HEREIN, WE SHOWED THAT GENISTEIN EXHIBITS A DEMONSTRABLE ANTI-FIBROTIC EFFECT ON KIDNEY IN VIVO UUO (UNILATERAL URETERAL OCCLUSION) MODEL AND RENAL EPITHELIAL CELLS IN VITRO MODEL. THE MECHANISM IS STRONGLY ASSOCIATED WITH EPITHELIAL-TO-MESENCHYMAL TRANSITION AND M6A RNA DEMETHYLASE ALKBH5. MOUSE FIBROTIC KIDNEYS INDUCED BY UUO EXHIBITED ADVERSE EXPRESSION OF RENAL FIBROSIS-RELATED PROTEINS AND SIGNIFICANT INCREASES IN THE TOTAL M6A LEVEL. AS AN ERASER, ALKBH5 SHOWED SEVERER SUPPRESSION IN THE RENAL FIBROSIS PROCESS. HOWEVER, GENISTEIN PRETREATMENT RESTORED ALKBH5 LOSS REMARKABLY AND REDUCED RENAL FIBROSIS, ABNORMAL PROTEIN, AND INFLAMMATORY MARKERS. THE EXAMINATION OF POSSIBLE MECHANISMS REVEALED THAT GENISTEIN PROMOTED ALKBH5 AND MAYBE INDUCED THE LEVEL OF MRNA M6A METHYLATION IN SOME EPITHELIAL-TO-MESENCHYMAL TRANSITION-RELATED TRANSCRIPTION FACTORS. WE FOUND SNAIL WAS THE CRITICAL REGULATOR AND CRITICAL FOR THE PROTECTIVE ROLE OF GENISTEIN. TO VERIFY THE RELATIONSHIP BETWEEN ALKBH5 AND SNAIL, WE GENERATED KNOCKDOWN AND OVEREXPRESSION OF ALKBH5 CELLS IN VITRO. ALKBH5 KNOCKDOWN ENHANCED THE MESENCHYMAL PHENOTYPE MARKER ALPHA-SMOOTH MUSCLE ACTIN AND SNAIL EXPRESSION. IN AGREEMENT, OVEREXPRESSION ALKBH5 INCREASED EPITHELIAL ADHESION MOLECULE E-CADHERIN AND REDUCED SNAIL EXPRESSION. IN CONCLUSION, GENISTEIN INCREASED RENAL ALKBH5 EXPRESSION IN UUO-INDUCED RENAL FIBROSIS AND REDUCED RNA M6A LEVELS AND AMELIORATES RENAL DAMAGES.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
5  3410  37 HOXA5 UNDERGOES DYNAMIC DNA METHYLATION AND TRANSCRIPTIONAL REPRESSION IN THE ADIPOSE TISSUE OF MICE EXPOSED TO HIGH-FAT DIET. BACKGROUND/OBJECTIVES: THE GENOMIC BASES OF THE ADIPOSE TISSUE ABNORMALITIES INDUCED BY CHRONIC POSITIVE CALORIE EXCESS HAVE BEEN ONLY PARTIALLY ELUCIDATED. WE ADOPTED A GENOME-WIDE APPROACH TO DIRECTLY TEST WHETHER LONG-TERM HIGH-FAT DIET (HFD) EXPOSURE AFFECTS THE DNA METHYLATION PROFILE OF THE MOUSE ADIPOSE TISSUE AND TO IDENTIFY THE FUNCTIONAL CONSEQUENCES OF THESE CHANGES. SUBJECTS/METHODS: WE HAVE USED EPIDIDYMAL FAT OF MICE FED EITHER HIGH-FAT (HFD) OR REGULAR CHOW (STD) DIET FOR 5 MONTHS AND PERFORMED GENOME-WIDE DNA METHYLATION ANALYSES BY METHYLATED DNA IMMUNOPRECIPITATION SEQUENCING (MEDIP-SEQ). MOUSE HOMEOBOX (HOX) GENE DNA METHYLATION PCR, RT-QPCR AND BISULPHITE SEQUENCING ANALYSES WERE THEN PERFORMED. RESULTS: MICE FED THE HFD PROGRESSIVELY EXPANDED THEIR ADIPOSE MASS ACCOMPANIED BY A SIGNIFICANT DECREASE IN GLUCOSE TOLERANCE (P<0.001) AND INSULIN SENSITIVITY (P<0.05). MEDIP-SEQ DATA ANALYSIS REVEALED A UNIFORM DISTRIBUTION OF DIFFERENTIALLY METHYLATED REGIONS (DMR) THROUGH THE ENTIRE ADIPOCYTE GENOME, WITH A HIGHER NUMBER OF HYPERMETHYLATED REGIONS IN HFD MICE (P<0.005). THIS DIFFERENT METHYLATION PROFILE WAS ACCOMPANIED BY INCREASED EXPRESSION OF THE DNMT3A DNA METHYLTRANSFERASE (DNMT; P<0.05) AND THE METHYL-CPG-BINDING DOMAIN PROTEIN MBD3 (P<0.05) GENES IN HFD MICE. GENE ONTOLOGY ANALYSIS REVEALED THAT, IN THE HFD-TREATED MICE, THE HOX FAMILY OF DEVELOPMENT GENES WAS HIGHLY ENRICHED IN DIFFERENTIALLY METHYLATED GENES (P=0.008). TO VALIDATE THIS FINDING, HOXA5, WHICH IS IMPLICATED IN FAT TISSUE DIFFERENTIATION AND REMODELING, HAS BEEN SELECTED AND ANALYZED BY BISULPHITE SEQUENCING, CONFIRMING HYPERMETHYLATION IN THE ADIPOSE TISSUE FROM THE HFD MICE. HOXA5 HYPERMETHYLATION WAS ASSOCIATED WITH DOWNREGULATION OF HOXA5 MRNA AND PROTEIN EXPRESSION. FEEDING ANIMALS PREVIOUSLY EXPOSED TO THE HFD WITH A STANDARD CHOW DIET FOR TWO FURTHER MONTHS IMPROVED THE METABOLIC PHENOTYPE OF THE ANIMALS, ACCOMPANIED BY RETURN OF HOXA5 METHYLATION AND EXPRESSION LEVELS (P<0.05) TO VALUES SIMILAR TO THOSE OF THE CONTROL MICE MAINTAINED UNDER STANDARD CHOW. CONCLUSIONS: HFD INDUCES ADIPOSE TISSUE ABNORMALITIES ACCOMPANIED BY EPIGENETIC CHANGES AT THE HOXA5 ADIPOSE TISSUE REMODELING GENE.	2016	
                                                                                                                                                                                                                                                                                                                     
6  6058  45 THE DEFICIENCY OF N6-METHYLADENOSINE DEMETHYLASE ALKBH5 ENHANCES THE NEURODEGENERATIVE DAMAGE INDUCED BY COBALT. COBALT EXPOSURE, EVEN AT LOW CONCENTRATIONS, INDUCES NEURODEGENERATIVE DAMAGE, SUCH AS ALZHEIMER'S DISEASE (AD). THE SPECIFIC UNDERLYING MECHANISMS REMAIN UNCLEAR. OUR PREVIOUS STUDY DEMONSTRATED THAT M(6)A METHYLATION ALTERATION IS INVOLVED IN COBALT-INDUCED NEURODEGENERATIVE DAMAGE, SUCH AS IN AD. HOWEVER, THE ROLE OF M(6)A RNA METHYLATION AND ITS UNDERLYING MECHANISMS ARE POORLY UNDERSTOOD. IN THIS STUDY, BOTH EPIDEMIOLOGICAL AND LABORATORY STUDIES SHOWED THAT COBALT EXPOSURE COULD DOWNREGULATE THE EXPRESSION OF THE M(6)A DEMETHYLASE ALKBH5, SUGGESTING A KEY ROLE FOR ALKBH5. MOREOVER, METHYLATED RNA IMMUNOPRECIPITATION AND SEQUENCING (MERIP-SEQ) ANALYSIS REVEALED THAT ALKBH5 DEFICIENCY IS ASSOCIATED WITH NEURODEGENERATIVE DISEASES. KEGG PATHWAY AND GENE ONTOLOGY ANALYSES FURTHER REVEALED THAT THE DIFFERENTIALLY M(6)A-MODIFIED GENES RESULTING FROM ALKBH5 DOWNREGULATION AND COBALT EXPOSURE WERE AGGREGATED IN THE PATHWAYS OF PROLIFERATION, APOPTOSIS, AND AUTOPHAGY. SUBSEQUENTLY, ALKBH5 DEFICIENCY WAS SHOWN TO EXACERBATE CELL VIABILITY DECLINE, MOTIVATE CELL APOPTOSIS AND ATTENUATE CELL AUTOPHAGY INDUCED BY COBALT WITH EXPERIMENTAL TECHNIQUES OF GENE OVEREXPRESSION/INHIBITION. IN ADDITION, MORPHOLOGICAL CHANGES IN NEURONS AND THE EXPRESSION OF AD-RELATED PROTEINS, SUCH AS APP, P-TAU, AND TAU, IN THE CEREBRAL HIPPOCAMPUS OF WILD-TYPE AND ALKBH5 KNOCKOUT MICE AFTER CHRONIC COBALT EXPOSURE WERE ALSO INVESTIGATED. BOTH IN VITRO AND IN VIVO RESULTS SHOWED THAT LOWER EXPRESSION OF ALKBH5 AGGRAVATED COBALT-INDUCED NEURODEGENERATIVE DAMAGE. THESE RESULTS SUGGEST THAT ALKBH5, AS AN EPIGENETIC REGULATOR, COULD BE A POTENTIAL TARGET FOR ALLEVIATING COBALT-INDUCED NEURODEGENERATIVE DAMAGE. IN ADDITION, WE PROPOSE A NOVEL STRATEGY FOR THE PREVENTION AND TREATMENT OF ENVIRONMENTAL TOXICANT-RELATED NEURODEGENERATION FROM AN EPIGENETIC PERSPECTIVE.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
7  5438  33 REMOVAL OF EPIGENETIC REPRESSIVE MARK ON INFLAMMATORY GENES IN FAT LIVER. NONALCOHOLIC FATTY LIVER DISEASE (NAFLD) IS THE MOST COMMON CHRONIC LIVER DISEASE WORLDWIDE. THE DETAILED EPIGENOMIC CHANGES DURING FAT ACCUMULATION IN LIVER ARE NOT CLEAR YET. HERE, WE PERFORMED CHIP-SEQ ANALYSIS IN THE LIVER TISSUES OF HIGH-FAT DIET AND REGULAR CHOW DIET MICE AND INVESTIGATED THE DYNAMIC LANDSCAPES OF H3K27AC AND H3K9ME3 MARKS ON CHROMATIN. WE FIND THAT THE ACTIVATED TYPICAL ENHANCERS MARKED WITH H3K27AC ARE ENRICHED ON LIPID METABOLIC PATHWAYS IN FAT LIVER; HOWEVER, SUPER ENHANCERS DO NOT CHANGE MUCH. THE REGIONS COVERED WITH H3K9ME3 REPRESSIVE MARK SEEM TO UNDERGO GREAT CHANGES, AND ITS PEAK NUMBER AND INTENSITY BOTH DECREASE IN FAT LIVER. THE ENHANCERS LOCATED IN LOST H3K9ME3 REGIONS ARE ENRICHED IN LIPID METABOLISM AND INFLAMMATORY PATHWAYS; AND MOTIF ANALYSIS SHOWS THAT THEY ARE POTENTIAL TARGETS FOR TRANSCRIPTION FACTORS INVOLVED IN METABOLIC AND INFLAMMATORY PROCESSES. OUR STUDY HAS REVEALED THAT H3K9ME3 MAY PLAY AN IMPORTANT ROLE DURING THE PATHOGENESIS OF NAFLD THROUGH REGULATING THE ACCESSIBILITY OF ENHANCERS.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
8  3064  39 GENOME-WIDE DNA METHYLATION ENCODES CARDIAC TRANSCRIPTIONAL REPROGRAMMING IN HUMAN ISCHEMIC HEART FAILURE. ISCHEMIC CARDIOMYOPATHY (ICM) IS THE CLINICAL ENDPOINT OF CORONARY HEART DISEASE AND A LEADING CAUSE OF HEART FAILURE. DESPITE GROWING DEMANDS TO DEVELOP PERSONALIZED APPROACHES TO TREAT ICM, PROGRESS IS LIMITED BY INADEQUATE KNOWLEDGE OF ITS PATHOGENESIS. SINCE EPIGENETICS HAS BEEN IMPLICATED IN THE DEVELOPMENT OF OTHER CHRONIC DISEASES, THE CURRENT STUDY WAS DESIGNED TO DETERMINE WHETHER TRANSCRIPTIONAL AND/OR EPIGENETIC CHANGES ARE SUFFICIENT TO DISTINGUISH ICM FROM OTHER ETIOLOGIES OF HEART FAILURE. SPECIFICALLY, WE HYPOTHESIZE THAT GENOME-WIDE DNA METHYLATION ENCODES TRANSCRIPTIONAL REPROGRAMMING IN ICM. RNA-SEQUENCING ANALYSIS WAS PERFORMED ON HUMAN ISCHEMIC LEFT VENTRICULAR TISSUE OBTAINED FROM PATIENTS WITH END-STAGE HEART FAILURE, WHICH ENRICHED KNOWN TARGETS OF THE POLYCOMB METHYLTRANSFERASE EZH2 COMPARED TO NON-ISCHEMIC HEARTS. COMBINED RNA SEQUENCING AND GENOME-WIDE DNA METHYLATION ANALYSIS REVEALED A ROBUST GENE EXPRESSION PATTERN CONSISTENT WITH SUPPRESSION OF OXIDATIVE METABOLISM, INDUCED ANAEROBIC GLYCOLYSIS, AND ALTERED CELLULAR REMODELING. LASTLY, KLF15 WAS IDENTIFIED AS A PUTATIVE UPSTREAM REGULATOR OF METABOLIC GENE EXPRESSION THAT WAS ITSELF REGULATED BY EZH2 IN A SET DOMAIN-DEPENDENT MANNER. OUR OBSERVATIONS THEREFORE DEFINE A NOVEL ROLE OF DNA METHYLATION IN THE METABOLIC REPROGRAMMING OF ICM. FURTHERMORE, WE IDENTIFY EZH2 AS AN EPIGENETIC REGULATOR OF KLF15 ALONG WITH DNA HYPERMETHYLATION, AND WE PROPOSE A NOVEL MECHANISM THROUGH WHICH CORONARY HEART DISEASE REPROGRAMS THE EXPRESSION OF BOTH INTERMEDIATE ENZYMES AND UPSTREAM REGULATORS OF CARDIAC METABOLISM SUCH AS KLF15.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
9  1122  41 COMPARISON OF GENE EXPRESSION PROFILES IN CHROMATE TRANSFORMED BEAS-2B CELLS. BACKGROUND: HEXAVALENT CHROMIUM [CR(VI)] IS A POTENT HUMAN CARCINOGEN. OCCUPATIONAL EXPOSURE HAS BEEN ASSOCIATED WITH INCREASED RISK OF RESPIRATORY CANCER. MULTIPLE MECHANISMS HAVE BEEN SHOWN TO CONTRIBUTE TO CR(VI) INDUCED CARCINOGENESIS, INCLUDING DNA DAMAGE, GENOMIC INSTABILITY, AND EPIGENETIC MODULATION, HOWEVER, THE MOLECULAR MECHANISM AND DOWNSTREAM GENES MEDIATING CHROMIUM'S CARCINOGENICITY REMAIN TO BE ELUCIDATED. METHODS/RESULTS: WE ESTABLISHED CHROMATE TRANSFORMED CELL LINES BY CHRONIC EXPOSURE OF NORMAL HUMAN BRONCHIAL EPITHELIAL BEAS-2B CELLS TO LOW DOSES OF CR(VI) FOLLOWED BY ANCHORAGE-INDEPENDENT GROWTH. THESE TRANSFORMED CELL LINES NOT ONLY EXHIBITED CONSISTENT MORPHOLOGICAL CHANGES BUT ALSO ACQUIRED ALTERED AND DISTINCT GENE EXPRESSION PATTERNS COMPARED WITH NORMAL BEAS-2B CELLS AND CONTROL CELL LINES (UNTREATED) THAT AROSE SPONTANEOUSLY IN SOFT AGAR. INTERESTINGLY, THE GENE EXPRESSION PROFILES OF SIX CR(VI) TRANSFORMED CELL LINES WERE REMARKABLY SIMILAR TO EACH OTHER YET DIFFERED SIGNIFICANTLY FROM THAT OF EITHER CONTROL CELL LINES OR NORMAL BEAS-2B CELLS. A TOTAL OF 409 DIFFERENTIALLY EXPRESSED GENES WERE IDENTIFIED IN CR(VI) TRANSFORMED CELLS COMPARED TO CONTROL CELLS. GENES RELATED TO CELL-TO-CELL JUNCTION WERE UPREGULATED IN ALL CR(VI) TRANSFORMED CELLS, WHILE GENES ASSOCIATED WITH THE INTERACTION BETWEEN CELLS AND THEIR EXTRACELLULAR MATRICES WERE DOWN-REGULATED. ADDITIONALLY, EXPRESSION OF GENES INVOLVED IN CELL PROLIFERATION AND APOPTOSIS WERE ALSO CHANGED. CONCLUSION: THIS STUDY IS THE FIRST TO REPORT GENE EXPRESSION PROFILING OF CR(VI) TRANSFORMED CELLS. THE GENE EXPRESSION CHANGES ACROSS INDIVIDUAL CHROMATE EXPOSED CLONES WERE REMARKABLY SIMILAR TO EACH OTHER BUT DIFFERED SIGNIFICANTLY FROM THE GENE EXPRESSION FOUND IN ANCHORAGE-INDEPENDENT CLONES THAT AROSE SPONTANEOUSLY. OUR ANALYSIS IDENTIFIED MANY NOVEL GENE EXPRESSION CHANGES THAT MAY CONTRIBUTE TO CHROMATE INDUCED CELL TRANSFORMATION, AND COLLECTIVELY THIS TYPE OF INFORMATION WILL PROVIDE A BETTER UNDERSTANDING OF THE MECHANISM UNDERLYING CHROMATE CARCINOGENICITY.	2011	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
10   701  28 BROWN FAT DNMT3B DEFICIENCY AMELIORATES OBESITY IN FEMALE MICE. OBESITY RESULTS FROM A CHRONIC ENERGY IMBALANCE DUE TO ENERGY INTAKE EXCEEDING ENERGY EXPENDITURE. ACTIVATION OF BROWN FAT THERMOGENESIS HAS BEEN SHOWN TO COMBAT OBESITY. EPIGENETIC REGULATION, INCLUDING DNA METHYLATION, HAS EMERGED AS A KEY REGULATOR OF BROWN FAT THERMOGENIC FUNCTION. HERE WE AIMED TO STUDY THE ROLE OF DNMT3B, A DNA METHYLTRANSFERASE INVOLVED IN DE NOVO DNA METHYLATION, IN THE REGULATION OF BROWN FAT THERMOGENESIS AND OBESITY. WE FOUND THAT THE SPECIFIC DELETION OF DNMT3B IN BROWN FAT PROMOTES THE THERMOGENIC AND MITOCHONDRIAL PROGRAM IN BROWN FAT, ENHANCES ENERGY EXPENDITURE, AND DECREASES ADIPOSITY IN FEMALE MICE FED A REGULAR CHOW DIET. WITH A LEAN PHENOTYPE, THE FEMALE KNOCKOUT MICE ALSO EXHIBIT INCREASED INSULIN SENSITIVITY. IN ADDITION, DNMT3B DEFICIENCY IN BROWN FAT ALSO PREVENTS DIET-INDUCED OBESITY AND INSULIN RESISTANCE IN FEMALE MICE. INTERESTINGLY, OUR RNA-SEQ ANALYSIS REVEALED AN UPREGULATION OF THE PI3K-AKT PATHWAY IN THE BROWN FAT OF FEMALE DNMT3B KNOCKOUT MICE. HOWEVER, MALE DNMT3B KNOCKOUT MICE HAVE NO CHANGE IN THEIR BODY WEIGHT, SUGGESTING THE EXISTENCE OF SEXUAL DIMORPHISM IN THE BROWN FAT DNMT3B KNOCKOUT MODEL. OUR DATA DEMONSTRATE THAT DNMT3B PLAYS AN IMPORTANT ROLE IN THE REGULATION OF BROWN FAT FUNCTION, ENERGY METABOLISM AND OBESITY IN FEMALE MICE.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
11  1129  38 COMPREHENSIVE ANALYSIS OF MRNA-LNCRNA CO-EXPRESSION PROFILES IN MOUSE BRAIN DURING INFECTION WITH TOXOPLASMA GONDII. TOXOPLASMA GONDII IS AN OBLIGATE INTRACELLULAR PROTOZOAN PARASITE WHICH SERIOUSLY THREATENS THE HEALTH OF DOMESTIC ANIMALS AND HUMANS. LONG NON-CODING RNAS (LNCRNAS) ARE NON-PROTEIN-CODING TRANSCRIPTS GREATER THAN 200 NUCLEOTIDES, WHICH ARE WIDELY INVOLVED IN TRANSCRIPTIONAL AND EPIGENETIC REGULATIONS. HOWEVER, LITTLE IS KNOWN ABOUT THE ROLES OF HOST LNCRNAS IN THE RESPONSE TO T. GONDII INFECTIONS. IN THIS STUDY, USING ILLUMINA SEQUENCING TECHNOLOGY, WE ANALYZED THE EXPRESSION PROFILES OF MRNAS AND LNCRNAS IN BALB/C MOUSE BRAIN FOLLOWING INFECTION BY T. GONDII PRU STRAIN (TYPE II GENOTYPE) CYSTS. THE IDENTIFIED DIFFERENTIALLY EXPRESSED (DE) RNAS WERE SUBJECTED TO BIOINFORMATICS ANALYSIS. A TOTAL OF 2,090 ANNOTATED LNCRNAS ALONG WITH 3,577 NOVEL LNCRNAS WERE IDENTIFIED. IN THE ACUTELY INFECTED MOUSE BRAIN, A TOTAL OF 330 MRNAS AND 19 LNCRNAS WERE DYS-REGULATED, WHEREAS 136 DE MRNAS AND 9 DE LNCRNAS WERE IDENTIFIED IN CHRONICALLY INFECTED MOUSE BRAIN. GO ANALYSIS REVEALED THAT THESE DE MRNAS IDENTIFIED AT ACUTE INFECTION STAGE WERE INVOLVED IN IMMUNE RESPONSE, WHEREAS DE MRNAS FOUND AT CHRONIC INFECTION STAGE WERE MOSTLY ENRICHED IN RESPONSE TO PROTOZOAN. KEGG ANALYSIS SHOWED THAT DE MRNAS WERE SIGNIFICANTLY ENRICHED IN DISEASE RELATED PATHWAYS. IN ADDITION, THE PUTATIVE MRNA-LNCRNA CO-EXPRESSION NETWORK WAS CONSTRUCTED, AND SEVERAL HUB REGULATORY RNAS WERE IDENTIFIED BASED ON THE TRANSCRIPTOME DATA. THIS STUDY FIRSTLY CHARACTERIZED THE CO-EXPRESSION PROFILE OF MRNAS AND LNCRNAS IN MOUSE BRAIN INFECTED WITH T. GONDII AND PROVIDED A FRAMEWORK FOR FURTHER STUDIES OF THE ROLES OF LNCRNAS IN HOST NEUROPATHOLOGY DURING TOXOPLASMOSIS PROGRESSION.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
12  4015  45 LOW-DOSE EXPOSURE TO BISPHENOLS A, F AND S OF HUMAN PRIMARY ADIPOCYTE IMPACTS CODING AND NON-CODING RNA PROFILES. BISPHENOL A (BPA) EXPOSURE HAS BEEN SUSPECTED TO BE ASSOCIATED WITH DELETERIOUS EFFECTS ON HEALTH INCLUDING OBESITY AND METABOLICALLY-LINKED DISEASES. ALTHOUGH BISPHENOLS F (BPF) AND S (BPS) ARE BPA STRUCTURAL ANALOGS COMMONLY USED IN MANY MARKETED PRODUCTS AS A REPLACEMENT FOR BPA, ONLY SPARSE TOXICOLOGICAL DATA ARE AVAILABLE YET. OUR OBJECTIVE WAS TO COMPREHENSIVELY CHARACTERIZE BISPHENOLS GENE TARGETS IN A HUMAN PRIMARY ADIPOCYTE MODEL, IN ORDER TO DETERMINE WHETHER THEY MAY INDUCE CELLULAR DYSFUNCTION, USING CHRONIC EXPOSURE AT TWO CONCENTRATIONS: A "LOW-DOSE" SIMILAR TO THE DOSE USUALLY ENCOUNTERED IN HUMAN BIOLOGICAL FLUIDS AND A HIGHER DOSE. THEREFORE, BPA, BPF AND BPS HAVE BEEN ADDED AT 10 NM OR 10 MUM DURING THE DIFFERENTIATION OF HUMAN PRIMARY ADIPOCYTES FROM SUBCUTANEOUS FAT OF THREE NON-DIABETIC CAUCASIAN FEMALE PATIENTS. GENE EXPRESSION (MRNA/LNCRNA) ARRAYS AND MICRORNA ARRAYS, HAVE BEEN USED TO ASSESS CODING AND NON-CODING RNA CHANGES. WE DETECTED SIGNIFICANTLY DEREGULATED MRNA/LNCRNA AND MIRNA AT LOW AND HIGH DOSES. ENRICHMENT IN "CANCER" AND "ORGANISMAL INJURY AND ABNORMALITIES" RELATED PATHWAYS WAS FOUND IN RESPONSE TO THE THREE PRODUCTS. SOME LONG INTERGENIC NON-CODING RNAS AND SMALL NUCLEOLAR RNAS WERE DIFFERENTIALLY EXPRESSED SUGGESTING THAT BISPHENOLS MAY ALSO ACTIVATE MULTIPLE CELLULAR PROCESSES AND EPIGENETIC MODIFICATIONS. THE ANALYSIS OF UPSTREAM REGULATORS OF DEREGULATED GENES HIGHLIGHTED HORMONES OR HORMONE-LIKE CHEMICALS SUGGESTING THAT BPS AND BPF CAN BE SUSPECTED TO INTERFERE, JUST LIKE BPA, WITH HORMONAL REGULATION AND HAVE TO BE CONSIDERED AS ENDOCRINE DISRUPTORS. ALL THESE RESULTS SUGGEST THAT AS BPA, ITS SUBSTITUTES BPS AND BPF SHOULD BE USED WITH THE SAME RESTRICTIONS.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
13  5994  29 TGFBETA-INCURRED EPIGENETIC ABERRATIONS OF MIRNA AND DNA METHYLTRANSFERASE SUPPRESS KLOTHO AND POTENTIATE RENAL FIBROSIS. RENAL FIBROSIS IS A COMMON PATHOLOGICAL FEATURE OF CHRONIC KIDNEY DISEASES (CKD) AND ITS DEVELOPMENT AND PROGRESSION ARE SIGNIFICANTLY AFFECTED BY EPIGENETIC MODIFICATIONS SUCH AS ABERRANT MIRNA AND DNA METHYLATION. KLOTHO IS AN ANTI-AGING AND ANTI-FIBROTIC PROTEIN AND ITS EARLY DECLINE AFTER RENAL INJURY IS REPORTEDLY ASSOCIATED WITH ABERRANT DNA METHYLATION. HOWEVER, THE KEY UPSTREAM PATHOLOGICAL MEDIATORS AND THE MOLECULAR CASCADE LEADING TO EPIGENETIC KLOTHO SUPPRESSION ARE NOT EXCLUSIVELY ESTABLISHED. HERE WE INVESTIGATE THE EPIGENETIC MECHANISM OF KLOTHO DEFICIENCY AND ITS FUNCTIONAL RELEVANCE IN RENAL FIBROGENESIS. FIBROTIC KIDNEYS INDUCED BY UNILATERAL URETERAL OCCLUSION (UUO) DISPLAYED MARKED KLOTHO SUPPRESSION AND THE PROMOTER HYPERMETHYLATION. THESE ABNORMALITIES WERE LIKELY DUE TO DEREGULATED TRANSFORMING GROWTH FACTOR-BETA (TGFBETA) SINCE TGFBETA ALONE CAUSED THE SIMILAR EPIGENETIC ABERRATIONS IN CULTURED RENAL CELLS AND TGFBETA BLOCKADE PREVENTED THE ALTERATIONS IN UUO KIDNEY. FURTHER INVESTIGATION REVEALED THAT TGFBETA ENHANCED DNA METHYLTRANSFERASE (DNMT) 1 AND DNMT3A VIA INHIBITING MIR-152 AND MIR-30A IN BOTH RENAL CELLS AND FIBROTIC KIDNEYS. ACCORDINGLY THE BLOCKADE OF EITHER TGFBETA SIGNALING OR DNMT1/3A ACTIVITIES SIGNIFICANTLY RECOVERED THE KLOTHO LOSS AND ATTENUATED PRO-FIBROTIC PROTEIN EXPRESSION AND RENAL FIBROSIS. MOREOVER, KLOTHO KNOCKDOWN BY RNA INTERFERENCES ABOLISHED THE ANTI-FIBROTIC EFFECTS OF DNMT INHIBITION IN BOTH TGFBETA-TREATED RENAL CELL AND UUO KIDNEY, INDICATING THAT TGFBETA-MEDIATED MIR-152/30A INHIBITIONS, DNMT1/3A ABERRATIONS AND SUBSEQUENT KLOTHO LOSS CONSTITUTE A CRITICAL REGULATORY LOOP THAT ELIMINATES KLOTHO'S ANTI-FIBROTIC ACTIVITIES AND POTENTIATES RENAL FIBROGENESIS. THUS, OUR STUDY ELABORATES A NOVEL EPIGENETIC CASCADE OF RENAL FIBROGENESIS AND REVEALS THE POTENTIAL THERAPEUTIC TARGETS FOR TREATING THE RENAL FIBROSIS-ASSOCIATED KIDNEY DISEASES.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
14  1468  30 DISTINCT EPIGENETIC PROGRAMS REGULATE CARDIAC MYOCYTE DEVELOPMENT AND DISEASE IN THE HUMAN HEART IN VIVO. EPIGENETIC MECHANISMS AND TRANSCRIPTION FACTOR NETWORKS ESSENTIAL FOR DIFFERENTIATION OF CARDIAC MYOCYTES HAVE BEEN UNCOVERED. HOWEVER, RESHAPING OF THE EPIGENOME OF THESE TERMINALLY DIFFERENTIATED CELLS DURING FETAL DEVELOPMENT, POSTNATAL MATURATION, AND IN DISEASE REMAINS UNKNOWN. HERE, WE INVESTIGATE THE DYNAMICS OF THE CARDIAC MYOCYTE EPIGENOME DURING DEVELOPMENT AND IN CHRONIC HEART FAILURE. WE FIND THAT PRENATAL DEVELOPMENT AND POSTNATAL MATURATION ARE CHARACTERIZED BY A COOPERATION OF ACTIVE CPG METHYLATION AND HISTONE MARKS AT CIS-REGULATORY AND GENIC REGIONS TO SHAPE THE CARDIAC MYOCYTE TRANSCRIPTOME. IN CONTRAST, PATHOLOGICAL GENE EXPRESSION IN TERMINAL HEART FAILURE IS ACCOMPANIED BY CHANGES IN ACTIVE HISTONE MARKS WITHOUT MAJOR ALTERATIONS IN CPG METHYLATION AND REPRESSIVE CHROMATIN MARKS. NOTABLY, CIS-REGULATORY REGIONS IN CARDIAC MYOCYTES ARE SIGNIFICANTLY ENRICHED FOR CARDIOVASCULAR DISEASE-ASSOCIATED VARIANTS. THIS STUDY UNCOVERS DISTINCT LAYERS OF EPIGENETIC REGULATION NOT ONLY DURING PRENATAL DEVELOPMENT AND POSTNATAL MATURATION BUT ALSO IN DISEASED HUMAN CARDIAC MYOCYTES.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
15  5120  36 POSSIBLE EPIGENETIC REGULATORY EFFECT OF DYSREGULATED CIRCULAR RNAS IN EPILEPSY. CIRCULAR RNAS (CIRCRNAS) INVOLVE IN THE EPIGENETIC REGULATION AND ITS MAJOR MECHANISM IS THE SEQUESTRATION OF THE TARGET MICRO RNAS (MIRNAS). WE HYPOTHESIZED THAT CIRCRNAS MIGHT BE RELATED WITH THE PATHOPHYSIOLOGY OF CHRONIC EPILEPSY AND EVALUATED THE ALTERED CIRCRNA EXPRESSIONS AND THEIR POSSIBLE REGULATORY EFFECTS ON THEIR TARGET MIRNAS AND MRNAS IN A MOUSE EPILEPSY MODEL. THE CIRCRNA EXPRESSION PROFILE IN THE HIPPOCAMPUS OF THE PILOCARPINE MICE WAS ANALYZED AND COMPARED WITH CONTROL. THE CORRELATION BETWEEN THE EXPRESSION OF MIRNA BINDING SITES (MIRNA RESPONSE ELEMENTS, MRE) IN THE DYSREGULATED CIRCRNAS AND THE EXPRESSION OF THEIR TARGET MIRNAS WAS EVALUATED. AS MIRNAS ALSO INHIBIT THEIR TARGET MRNAS, CIRCRNA-MIRNA-MRNA REGULATORY NETWORK, COMPRISED OF DYSREGULATED RNAS THAT TARGETS ONE ANOTHER WERE SEARCHED. FOR THE IDENTIFIED NETWORKS, BIOINFORMATICS ANALYSES WERE PERFORMED. AS THE RESULT, FORTY-THREE CIRCRNAS WERE DYSREGULATED IN THE HIPPOCAMPUS (UP-REGULATED, 26; DOWN-REGULATED, 17). THE CHANGE IN THE EXPRESSION OF MRE IN THOSE CIRCRNAS NEGATIVELY CORRELATED WITH THE CHANGE IN THE RELEVANT TARGET MIRNA EXPRESSION (R = -0.461, P<0.001), SUPPORTING THAT CIRCRNAS INHIBIT THEIR TARGET MIRNA. 333 DYSREGULATED CIRCRNA-MIRNA-MRNA NETWORKS WERE IDENTIFIED. GENE ONTOLOGY AND PATHWAY ANALYSES DEMONSTRATED THAT THE UP-REGULATED MRNAS IN THOSE NETWORKS WERE CLOSELY RELATED TO THE MAJOR PROCESSES IN EPILEPSY. AMONG THEM, STRING ANALYSIS IDENTIFIED 37 KEY MRNAS WITH ABUNDANT (>/=4) INTERACTIONS WITH OTHER DYSREGULATED TARGET MRNAS. THE DYSREGULATION OF THE CIRCRNAS WHICH HAD MULTIPLE INTERACTIONS WITH KEY MRNAS WERE VALIDATED BY PCR. WE CONCLUDED THAT DYSREGULATED CIRCRNAS MIGHT HAVE A PATHOPHYSIOLOGIC ROLE IN CHRONIC EPILEPSY BY REGULATING MULTIPLE DISEASE RELEVANT MRNAS VIA CIRCRNA-MIRNA-MRNA INTERACTIONS.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
16  3292  45 HIGH FAT DIET AND EXERCISE LEAD TO A DISRUPTED AND PATHOGENIC DNA METHYLOME IN MOUSE LIVER. HIGH-FAT DIET CONSUMPTION AND SEDENTARY LIFESTYLE ELEVATES RISK FOR OBESITY, NON-ALCOHOLIC FATTY LIVER DISEASE, AND CANCER. EXERCISE TRAINING CONVEYS HEALTH BENEFITS IN POPULATIONS WITH OR WITHOUT THESE CHRONIC CONDITIONS. DIET AND EXERCISE REGULATE GENE EXPRESSION BY MEDIATING EPIGENETIC MECHANISMS IN MANY TISSUES; HOWEVER, SUCH EFFECTS ARE POORLY DOCUMENTED IN THE LIVER, A CENTRAL METABOLIC ORGAN. TO DISSECT THE CONSEQUENCES OF DIET AND EXERCISE ON THE LIVER EPIGENOME, WE MEASURED DNA METHYLATION, USING REDUCED REPRESENTATION BISULFITE SEQUENCING, AND TRANSCRIPTION, USING RNA-SEQ, IN MICE MAINTAINED ON A FAST FOOD DIET WITH SEDENTARY LIFESTYLE OR EXERCISE, COMPARED WITH CONTROL DIET WITH AND WITHOUT EXERCISE. OUR ANALYSES REVEAL THAT GENOME-WIDE DIFFERENTIAL DNA METHYLATION AND EXPRESSION OF GENE CLUSTERS ARE INDUCED BY DIET AND/OR EXERCISE. A COMBINATION OF FAST FOOD AND EXERCISE TRIGGERS EXTENSIVE GENE ALTERATIONS, WITH ENRICHMENT OF CARBOHYDRATE/LIPID METABOLIC PATHWAYS AND MUSCLE DEVELOPMENTAL PROCESSES. THROUGH EVALUATION OF PUTATIVE PROTECTIVE EFFECTS OF EXERCISE ON DIET-INDUCED DNA METHYLATION, WE SHOW THAT HYPERMETHYLATION IS EFFECTIVELY PREVENTED, ESPECIALLY AT PROMOTERS AND ENHANCERS, WHEREAS HYPOMETHYLATION IS ONLY PARTIALLY ATTENUATED. WE ASSESSED DIET-INDUCED DNA METHYLATION CHANGES ASSOCIATED WITH LIVER CANCER-RELATED EPIGENETIC MODIFICATIONS AND IDENTIFIED SIGNIFICANT INCREASES AT LIVER-SPECIFIC ENHANCERS IN FAST FOOD GROUPS, SUGGESTING PARTIAL LOSS OF LIVER CELL IDENTITY. HYPERMETHYLATION AT A SUBSET OF GENE PROMOTERS WAS ASSOCIATED WITH INHIBITION OF TISSUE DEVELOPMENT AND PROMOTION OF CARCINOGENIC PROCESSES. OUR STUDY DEMONSTRATES EXTENSIVE REPROGRAMMING OF THE EPIGENOME BY DIET AND EXERCISE, EMPHASIZING THE FUNCTIONAL RELEVANCE OF EPIGENETIC MECHANISMS AS AN INTERFACE BETWEEN LIFESTYLE MODIFICATIONS AND PHENOTYPIC ALTERATIONS.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
17  6672  35 USE OF A MOUSE IN VITRO FERTILIZATION MODEL TO UNDERSTAND THE DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE HYPOTHESIS. THE DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE HYPOTHESIS HOLDS THAT ALTERATIONS TO HOMEOSTASIS DURING CRITICAL PERIODS OF DEVELOPMENT CAN PREDISPOSE INDIVIDUALS TO ADULT-ONSET CHRONIC DISEASES SUCH AS DIABETES AND METABOLIC SYNDROME. IT REMAINS CONTROVERSIAL WHETHER PREIMPLANTATION EMBRYO MANIPULATION, CLINICALLY USED TO TREAT PATIENTS WITH INFERTILITY, DISTURBS HOMEOSTASIS AND AFFECTS LONG-TERM GROWTH AND METABOLISM. TO ADDRESS THIS CONTROVERSY, WE HAVE ASSESSED THE EFFECTS OF IN VITRO FERTILIZATION (IVF) ON POSTNATAL PHYSIOLOGY IN MICE. WE DEMONSTRATE THAT IVF AND EMBRYO CULTURE, EVEN UNDER CONDITIONS CONSIDERED OPTIMAL FOR MOUSE EMBRYO CULTURE, ALTER POSTNATAL GROWTH TRAJECTORY, FAT ACCUMULATION, AND GLUCOSE METABOLISM IN ADULT MICE. UNBIASED METABOLIC PROFILING IN SERUM AND MICROARRAY ANALYSIS OF PANCREATIC ISLETS AND INSULIN SENSITIVE TISSUES (LIVER, SKELETAL MUSCLE, AND ADIPOSE TISSUE) REVEALED BROAD CHANGES IN METABOLIC HOMEOSTASIS, CHARACTERIZED BY SYSTEMIC OXIDATIVE STRESS AND MITOCHONDRIAL DYSFUNCTION. ADOPTING A CANDIDATE APPROACH, WE IDENTIFY THIOREDOXIN-INTERACTING PROTEIN (TXNIP), A KEY MOLECULE INVOLVED IN INTEGRATING CELLULAR NUTRITIONAL AND OXIDATIVE STATES WITH METABOLIC RESPONSE, AS A MARKER FOR PREIMPLANTATION STRESS AND DEMONSTRATE TISSUE-SPECIFIC EPIGENETIC AND TRANSCRIPTIONAL TXNIP MISREGULATION IN SELECTED ADULT TISSUES. IMPORTANTLY, DYSREGULATION OF TXNIP EXPRESSION IS ASSOCIATED WITH ENRICHMENT FOR H4 ACETYLATION AT THE TXNIP PROMOTER THAT PERSISTS FROM THE BLASTOCYST STAGE THROUGH ADULTHOOD IN ADIPOSE TISSUE. OUR DATA SUPPORT THE VULNERABILITY OF PREIMPLANTATION EMBRYOS TO ENVIRONMENTAL DISTURBANCE AND DEMONSTRATE THAT CONCEPTION BY IVF CAN REPROGRAM METABOLIC HOMEOSTASIS THROUGH METABOLIC, TRANSCRIPTIONAL, AND EPIGENETIC MECHANISMS WITH LASTING EFFECTS FOR ADULT GROWTH AND FITNESS. THIS STUDY HAS WIDE CLINICAL RELEVANCE AND UNDERSCORES THE IMPORTANCE OF CONTINUED FOLLOW-UP OF IVF-CONCEIVED OFFSPRING.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
18  4010  31 LOW MATERNAL ADHERENCE TO A MEDITERRANEAN DIET IS ASSOCIATED WITH INCREASE IN METHYLATION AT THE MEG3-IG DIFFERENTIALLY METHYLATED REGION IN FEMALE INFANTS. DIET IS DICTATED BY THE SURROUNDING ENVIRONMENT, AS FOOD ACCESS AND AVAILABILITY MAY CHANGE DEPENDING ON WHERE ONE LIVES. MATERNAL DIET DURING PREGNANCY IS AN IMPORTANT PART OF THE IN UTERO ENVIRONMENT, AND MAY AFFECT THE EPIGENOME. STUDIES LOOKING AT OVERALL DIET PATTERN IN RELATION TO DNA METHYLATION HAVE BEEN LACKING. THE MEDITERRANEAN DIET IS KNOWN FOR ITS HEALTH BENEFITS, INCLUDING DECREASED INFLAMMATION, WEIGHT LOSS, AND MANAGEMENT OF CHRONIC DISEASES. THIS STUDY ASSESSES THE ASSOCIATION BETWEEN MATERNAL ADHERENCE TO A MEDITERRANEAN DIET PATTERN DURING PREGNANCY AND INFANT DNA METHYLATION AT BIRTH. MEDITERRANEAN DIET ADHERENCE IN EARLY PREGNANCY WAS MEASURED IN 390 WOMEN ENROLLED IN THE NEWBORN EPIGENETIC STUDY, AND DNA METHYLATION WAS ASSESSED IN THEIR INFANTS AT BIRTH. MULTINOMIAL LOGISTIC REGRESSION WAS USED TO ASSESS THE ASSOCIATION BETWEEN ADHERENCE TO A MEDITERRANEAN DIET AND INFANT METHYLATION AT THE MEG3, MEG3-IG, PLEIOMORPHIC ADENOMA GENE-LIKE 1, INSULIN-LIKE GROWTH FACTOR 2 GENE, H19, MESODERM-SPECIFIC TRANSCRIPT, NEURONATIN, PATERNALLY EXPRESSED GENE 3, SARCOGLYCAN AND PATERNALLY EXPRESSED GENE 10 REGIONS, MEASURED BY PYROSEQUENCING. INFANTS OF MOTHERS WITH A LOW ADHERENCE TO A MEDITERRANEAN DIET HAD A GREATER ODDS OF HYPO-METHYLATION AT THE MEG3-IG DIFFERENTIALLY METHYLATED REGION (DMR). SEX-STRATIFIED MODELS SHOWED THAT THIS ASSOCIATION WAS PRESENT IN GIRLS ONLY. THIS STUDY PROVIDES EARLY EVIDENCE ON THE ASSOCIATION BETWEEN OVERALL DIET PATTERN AND METHYLATION AT THE 9 DMRS INCLUDED IN THIS STUDY, AND SUGGESTS THAT MATERNAL DIET CAN HAVE A SEX-SPECIFIC IMPACT ON INFANT DNA METHYLATION AT SPECIFIC IMPRINTED DMRS.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
19  1764  32 EARLY-IMMEDIATE GENE EGR1 IS ASSOCIATED WITH TGFBETA1 REGULATION OF EPIGENETIC READER BROMODOMAIN-CONTAINING PROTEIN 4 VIA THE CANONICAL SMAD3 SIGNALING IN HEPATIC STELLATE CELLS IN VITRO AND IN VIVO. UPON CHRONIC DAMAGE TO THE LIVER, MULTIPLE CYTOKINES STIMULATE HEPATIC STELLATE CELLS (HSCS), CAUSING THE ALTERATIONS OF GENE EXPRESSION PROFILES AND THUS LEADING TO HSC ACTIVATION, A KEY STEP IN LIVER FIBROGENESIS. ACTIVATED HSCS ARE THE DOMINANT CONTRIBUTORS TO LIVER FIBROSIS. BROMODOMAIN CONTAINING PROTEIN 4 (BRD4), AN IMPORTANT EPIGENETIC READER, WAS DEMONSTRATED TO CONCENTRATE ON HUNDREDS OF ENHANCERS ASSOCIATED WITH GENES INVOLVED IN MULTIPLE PROFIBROTIC PATHWAYS, THEREBY DIRECTING HSC ACTIVATION AND THE FIBROTIC RESPONSES. THE PRESENT STUDIES WERE DESIGNED TO EXAMINE THE EFFECT OF TRANSFORMING GROWTH FACTOR BETA-1 (TGFBETA1), THE MOST POTENT PRO-FIBROTIC CYTOKINE, ON BRD4 EXPRESSION IN HSCS AND, IF SO, ELUCIDATED THE UNDERLYING MECHANISMS IN VITRO AND IN VIVO. THE EXPERIMENTS EMPLOYED THE HETEROGENEOUS TGFBETA1 KNOCKOUT (TGFBETA1(+/-) ) MICE, GENE KNOCKDOWN IN VIVO, AND A MODEL OF THIOACETAMIDE (TAA)-INDUCED LIVER INJURY. THE RESULTS REVEALED THAT TGFBETA1 ENHANCED BRD4 EXPRESSION IN HSCS, WHICH WAS MEDIATED, AT LEAST, BY SMAD3 SIGNALING AND EARLY-IMMEDIATE GENE EGR1 (EARLY GROWTH RESPONSE-1). TGFBETA1-INDUCED SMAD3 SIGNALING INCREASED EGR1 EXPRESSION AND PROMOTED EGR1 BINDING TO BRD4 PROMOTER AT A SITE AROUND -111 BP, PROMOTING BRD4 EXPRESSION. EGR1 KNOCKDOWN REDUCED BRD4 EXPRESSION IN HSCS IN A MOUSE MODEL OF TAA-INDUCED LIVER INJURY AND LESSENED LIVER FIBROSIS. DOUBLE FLUORESCENCE STAINING DEMONSTRATED A STRONG INCREASE IN BRD4 EXPRESSION IN ACTIVATED HSCS IN FIBROTIC AREAS OF THE HUMAN LIVERS, PARALLELING THE UPREGULATION OF P-SMAD3 AND EGR1. THIS RESEARCH SUGGESTED NOVEL MOLECULAR EVENTS UNDERLYING THE ROLES OF THE MASTER PRO-FIBROTIC CYTOKINE TGFBETA1 IN HSC ACTIVATION AND LIVER FIBROGENESIS.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
20   917  33 CHRONIC HIGH-FAT DIET DRIVES POSTNATAL EPIGENETIC REGULATION OF MU-OPIOID RECEPTOR IN THE BRAIN. OPIOID SYSTEM DYSREGULATION HAS BEEN OBSERVED IN BOTH GENETIC AND HIGH-FAT DIET (HFD)-INDUCED MODELS OF OBESITY. AN UNDERSTANDING OF THE MOLECULAR MECHANISMS OF MOR TRANSCRIPTIONAL REGULATION, PARTICULARLY WITHIN AN IN VIVO CONTEXT, IS LACKING. USING A DIET-INDUCED MODEL OF OBESITY (DIO), MICE WERE FED A HIGH-FAT DIET (60% CALORIES FROM FAT) FROM WEANING TO >18 WEEKS OF AGE. COMPARED WITH MICE FED THE CONTROL DIET, DIO MICE HAD A DECREASED PREFERENCE FOR SUCROSE. MOR MRNA EXPRESSION WAS DECREASED IN REWARD-RELATED CIRCUITRY (VENTRAL TEGMENTAL AREA (VTA), NUCLEUS ACCUMBENS (NAC), AND PREFRONTAL CORTEX (PFC)) BUT NOT THE HYPOTHALAMUS, IMPORTANT IN THE HOMEOSTATIC REGULATION OF FEEDING. DNA METHYLATION IS AN EPIGENETIC MODIFICATION THAT LINKS ENVIRONMENTAL EXPOSURES TO ALTERED GENE EXPRESSION. WE FOUND A SIGNIFICANT INCREASE IN DNA METHYLATION IN THE MOR PROMOTER REGION WITHIN THE REWARD-RELATED BRAIN REGIONS. METHYL CPG-BINDING PROTEIN 2 (MECP2) CAN BIND METHYLATED DNA AND REPRESS TRANSCRIPTION, AND DIO MICE SHOWED INCREASED BINDING OF MECP2 TO THE MOR PROMOTER IN REWARD-RELATED REGIONS OF THE BRAIN. FINALLY, USING CHIP ASSAYS WE EXAMINED H3K9 METHYLATION (INACTIVE CHROMATIN) AND H3 ACETYLATION (ACTIVE CHROMATIN) WITHIN THE MOR PROMOTER REGION AND FOUND INCREASED H3K9 METHYLATION AND DECREASED H3 ACETYLATION. THESE DATA ARE THE FIRST TO IDENTIFY DNA METHYLATION, MECP2 RECRUITMENT, AND CHROMATIN REMODELING AS MECHANISMS LEADING TO TRANSCRIPTIONAL REPRESSION OF MOR IN THE BRAINS OF MICE FED A HIGH-FAT DIET.	2011