1 1987 137 EPIGENETIC ALTERATIONS OF CXCL5 IN CR(VI)-INDUCED CARCINOGENESIS. CHRONIC EXPOSURE TO HEXAVALENT CHROMIUM COMPOUNDS [CR(VI)] IS ASSOCIATED WITH AN INCREASED RISK OF CANCERS, BUT THE MOLECULAR MECHANISMS REMAIN TO BE ELUCIDATED. IN THIS STUDY, WE FOUND THAT CXCL5 LEVELS IN PERIPHERAL BLOOD MONOCYTES (PBMCS) AND PLASMA FROM WORKERS WITH OCCUPATIONAL EXPOSURE TO CR(VI) WERE DRAMATICALLY UPREGULATED COMPARED TO NON-EXPOSURE HEALTHY SUBJECTS, AND PLASMA C-X-C MOTIF CHEMOKINE LIGAND 5 (CXCL5) CXCL5 LEVELS WERE POSITIVELY CORRELATED WITH CR CONCENTRATIONS IN SUBJECTS' TOENAILS. ZINC CHROMATE EXPOSED MICE SHOWED HIGHER LEVELS OF CXCL5 AND ITS RECEPTOR CXCR2 IN LUNG TISSUES, AND IN PBMCS. SIMILAR CXCL5 UPREGULATION WAS EVIDENT IN CR(VI)-INDUCED TRANSFORMED (CR-T) CELLS WITH LONG-TERM CR(VI) TREATMENT. MECHANISTIC STUDIES SHOWED THAT ELEVATED CXCL5 EXPRESSION LEVELS WERE REGULATED BY CR(VI)-INDUCED HISTONE MODIFICATIONS AND DNA HYPOMETHYLATION, AND THAT THE C-MYC/P300 COMPLEX WAS A KEY UPSTREAM REGULATOR OF HISTONE H3 ACETYLATION. CXCL5 OVEREXPRESSION PROMOTED CR(VI)-INDUCED THE EPITHELIAL TO MESENCHYME TRANSITION (EMT) BY UPREGULATING ZINC FINGER E-BOX BINDING HOMEOBOX 1 (ZEB1) TO PROMOTE TUMOR DEVELOPMENT. OUR FINDINGS IDENTIFY A NOVEL MECHANISM BY WHICH CXCL5 IS UPREGULATED AND PROMOTES EMT AND CARCINOGENESIS UPON CHRONIC CR(VI) EXPOSURE. OUR WORK ALSO IMPLIES THAT CXCL5 MRNA AND PROTEIN LEVELS WILL ELEVATE IN PBMCS AND SERUM AFTER OCCUPATIONAL CR(VI) EXPOSURE, WHICH MAY BE A POTENTIAL TARGET AND BIOMARKER FOR CANCER PREVENTION AND HEALTH SURVEILLANCE AMONG POPULATIONS EXPOSED TO CR(VI). 2022 2 2425 35 EPIGENETIC SILENCING OF IRF1 DYSREGULATES TYPE III INTERFERON RESPONSES TO RESPIRATORY VIRUS INFECTION IN EPITHELIAL TO MESENCHYMAL TRANSITION. CHRONIC OXIDATIVE INJURY PRODUCED BY AIRWAY DISEASE TRIGGERS A TRANSFORMING GROWTH FACTOR-BETA (TGF-BETA)-MEDIATED EPIGENETIC REPROGRAMMING KNOWN AS THE EPITHELIAL-MESENCHYMAL TRANSITION (EMT). WE OBSERVE THAT EMT SILENCES PROTECTIVE MUCOSAL INTERFERON (IFN)-I AND III PRODUCTION ASSOCIATED WITH ENHANCED RHINOVIRUS (RV) AND RESPIRATORY SYNCYTIAL VIRUS (RSV) REPLICATION. MESENCHYMAL TRANSITIONED CELLS ARE DEFECTIVE IN INDUCIBLE INTERFERON REGULATORY FACTOR 1 (IRF1) EXPRESSION BY OCCLUDING RELA AND IRF3 ACCESS TO THE PROMOTER. IRF1 IS NECESSARY FOR THE EXPRESSION OF TYPE III IFNS (IFNLS 1 AND 2/3). INDUCED BY THE EMT, ZINC FINGER E-BOX BINDING HOMEOBOX 1 (ZEB1) BINDS AND SILENCES IRF1. ECTOPIC ZEB1 IS SUFFICIENT FOR IRF1 SILENCING, WHEREAS ZEB1 KNOCKDOWN PARTIALLY RESTORES IRF1-IFNL UPREGULATION. ZEB1 SILENCES IRF1 THROUGH THE CATALYTIC ACTIVITY OF THE ENHANCER OF ZESTE 2 POLYCOMB REPRESSIVE COMPLEX 2 SUBUNIT (EZH2), FORMING REPRESSIVE H3K27(ME3) MARKS. WE OBSERVE THAT IRF1 EXPRESSION IS MEDIATED BY ZEB1 DE-REPRESSION, AND OUR STUDY DEMONSTRATES HOW AIRWAY REMODELLING/FIBROSIS IS ASSOCIATED WITH A DEFECTIVE MUCOSAL ANTIVIRAL RESPONSE THROUGH ZEB1-INITIATED EPIGENETIC SILENCING. 2017 3 3410 38 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 4 1056 34 CLINICAL MANIFESTATIONS AND EPIGENETIC MECHANISMS OF GASTRIC MUCOSA ASSOCIATED LYMPHOID TISSUE LYMPHOMA AND LONG-TERM FOLLOW-UP FOLLOWING HELICOBACTER PYLORI ERADICATION. THE CURRENT STUDY AIMED TO SUMMARIZE THE CLINICAL MANIFESTATIONS AND IDENTIFY THE EPIGENETIC MECHANISMS OF GASTRIC MUCOSA ASSOCIATED LYMPHOID TISSUE (MALT) LYMPHOMA, AS WELL AS EVALUATE THE LONG-TERM EFFECTS OF HELICOBACTER PYLORI (H. PYLORI) ERADICATION. A TOTAL OF 122 PATIENTS WITH MARGINAL ZONE B-CELL LYMPHOMA OF PRIMARY GASTRIC MALT LYMPHOMA WERE ENROLLED IN THE PRESENT STUDY. THE CLINICAL MANIFESTATIONS OF GASTRIC MALT LYMPHOMA, INCLUDING SYMPTOMS, H. PYLORI STATE AND ENDOSCOPIC TYPE, WERE SUMMARIZED. THE RESPONSE TO THERAPY WAS EVALUATED IN PATIENTS THAT UNDERWENT H. PYLORI ERADICATION. SURVIVAL ANALYSIS WAS ESTIMATED USING THE KAPLAN-MEIER METHOD. THE EXPRESSION OF MICRORNA-383 (MIR-383) IN TUMOR TISSUES AND CELL LINES WAS DETERMINED USING REVERSE TRANSCRIPTION QUANTITATIVE POLYMERASE CHAIN REACTION. FURTHERMORE, BIOINFORMATIC ANALYSES, LUCIFERASE REPORTER ASSAYS. AND WESTERN BLOT ANALYSIS IDENTIFIED ZINC FINGER E-BOX BINDING HOMEOBOX 2 (ZEB2) AS A DIRECT TARGET GENE OF MIR-383. AN MTT ASSAY WAS USED TO EXAMINE THE FUNCTION OF MIR-383 AND ZEB2 IN MALT LYMPHOMA. THE CLINICAL SYMPTOMS OF PATIENTS WITH GASTRIC MALT LYMPHOMA WERE NON-SPECIFIC AND INCLUDED EPIGASTRIC PAIN, ABDOMINAL DISCOMFORT AND BLEEDING. THE MAJORITY OF ENDOSCOPIC TYPES WERE CLASSIFIED AS ULCER, EROSION AND MUCOSA EDEMA. THE H. PYLORI INFECTION RATE WAS 79.5% (97/122) AND A TOTAL OF 47 PATIENTS UNDERWENT ERADICATION THERAPY. LYMPHOMA REMISSION WAS ACHIEVED IN 93.6% (44/47) OF PATIENTS AND COMPLETE REMISSION (CR) WAS ACHIEVED IN 74.4% (35/47). THE MEDIAN FOLLOW-UP TIME WAS 38 MONTHS (RANGE, 10-132 MONTHS) AND THE MEDIAN TIME TAKEN TO ACHIEVE CR WAS 4 MONTHS (RANGE, 3-7 MONTHS). THE ESTIMATED 3-YEAR SURVIVAL RATE WAS 90.3% AND THE 5-YEAR SURVIVAL RATE WAS 76.2%. THEREFORE, IT WAS DETERMINED THAT PATIENTS WITH STAGE I OR II GASTRIC MALT LYMPHOMA ARE ABLE TO UNDERGO H. PYLORI ERADICATION AS A FIRST-LINE TREATMENT AND THAT THE SURVIVAL RATE OF PATIENTS UNDERGOING THIS TREATMENT IS HIGH. FURTHERMORE, IT WAS DETERMINED THAT THE MECHANISM BY WHICH MIR-383 AND ZEB2 CONTRIBUTE TO MALT LYMPHOMA PROGRESSION IS BY THE TARGETING OF ZEB2 BY MIR-383, WHICH INHIBITS THE PROLIFERATION OF CANCER CELLS. 2018 5 411 37 ANALYSIS OF GENOME-WIDE DNA METHYLATION PATTERNS IN OBESITY. OBESITY IS A CHRONIC AND COMPLEX PSYCHOSOMATIC DISEASE THAT IS BECOMING INCREASINGLY PREVALENT WORLDWIDE. THIS STUDY AIMED TO ANALYZE WHOLE METHYLATION PROFILES TO UNCOVER THE EPIGENETIC MECHANISMS ASSOCIATED WITH OBESITY. DNA METHYLATION PROFILES IN BLOOD SAMPLES FROM PATIENTS WITH OBESITY AND NORMAL CONTROLS WERE STUDIED USING THE ILLUMINA 850 K METHYLATION MICROARRAY. THE DIAGNOSTIC VALUE OF THE DIFFERENTIALLY METHYLATED GENES WAS DETERMINED USING RECEIVER OPERATING CHARACTERISTIC (ROC) ANALYSIS. THE EXPRESSION OF SELECTED CANDIDATE GENES WAS VERIFIED USING REVERSE TRANSCRIPTION QUANTITATIVE POLYMERASE CHAIN REACTION (RT-QPCR) AND PYROSEQUENCING. A TOTAL OF 9,371 SIGNIFICANTLY DIFFERENTIALLY METHYLATED SITES (7,974 HYPERMETHYLATED SITES AND 1,397 HYPOMETHYLATED SITES) WERE IDENTIFIED IN 4,571 GENES. A DIFFERENCE IN THE DISTRIBUTION OF DIFFERENTIALLY METHYLATED SITES (HYPERMETHYLATED AND HYPOMETHYLATED) IN BOTH GENE STRUCTURES AND CPG ISLANDS WAS OBSERVED. A TOTAL OF 114 KEY DIFFERENTIALLY METHYLATED SITES WERE IDENTIFIED IN THE CPG ISLANDS. ROC RESULTS INDICATED THAT INHIBIN SUBUNIT BETA B (INHBB), HOMEOBOX A9 (HOXA9), TROPONIN T3 (TNNT3), CYCLIC ADENOSINE MONOPHOSPHATE (CAMP)-RESPONSIVE ELEMENT BINDING PROTEIN (CREB)-REGULATED TRANSCRIPTION COACTIVATOR 1 (CRTC1) AND ZINC FINGER AND BTB DOMAIN-CONTAINING 7 B (ZBTB7B) COULD DISCRIMINATE PATIENTS WITH OBESITY FROM NORMAL CONTROLS. RT-QPCR RESULTS OF CRTC1 AND ZBTB7B WERE CONSISTENT WITH OUR METHYLATION PROFILE RESULTS. THE PYROSEQUENCING RESULTS SHOWED THAT THE METHYLATION LEVELS OF CRTC1 CPG SITES (CPG1 AND CPG2-CG11660071) AND INHBB CPG SITES (CPG2) WERE SIGNIFICANTLY CHANGED IN PATIENTS WITH OBESITY COMPARED WITH NORMAL CONTROLS, WHICH WAS CONSISTENT WITH OUR DNA METHYLATION PROFILE RESULTS. OUR STUDY PROVIDES NEW INSIGHTS INTO THE PATHOLOGICAL MECHANISM OF OBESITY. 2021 6 6663 46 UPREGULATION OF HISTONE-LYSINE METHYLTRANSFERASES PLAYS A CAUSAL ROLE IN HEXAVALENT CHROMIUM-INDUCED CANCER STEM CELL-LIKE PROPERTY AND CELL TRANSFORMATION. WHILE HEXAVALENT CHROMIUM [CR(VI)] IS GENERALLY CONSIDERED AS A GENOTOXIC ENVIRONMENTAL CARCINOGEN, STUDIES SHOWED THAT CR(VI) EXPOSURE ALSO CAUSES EPIGENETIC CHANGES. HOWEVER, WHETHER CR(VI)-CAUSED EPIGENETIC DYSREGULATIONS PLAYS AN IMPORTANT ROLE IN CR(VI) CARCINOGENICITY REMAIN LARGELY UNKNOWN. THE AIM OF THIS STUDY WAS TO DETERMINE IF CHRONIC LOW DOSE CR(VI) EXPOSURE CAUSES EPIGENETIC CHANGES, THE UNDERLYING MECHANISM AND WHETHER CHRONIC LOW DOSE CR(VI) EXPOSURE-CAUSED EPIGENETIC DYSREGULATION CONTRIBUTES CAUSALLY TO CR(VI)-INDUCED CANCER STEM CELL (CSC)-LIKE PROPERTY AND CELL TRANSFORMATION. TWO IMMORTALIZED HUMAN BRONCHIAL EPITHELIAL CELL LINES (BEAS-2B AND 16HBE) WERE EXPOSED TO 0.25 MUM OF K(2)CR(2)O(7) FOR 20 AND 40 WEEKS TO INDUCE CELL TRANSFORMATION, RESPECTIVELY. CR(VI)-INDUCED EPIGENETIC CHANGES WERE EXAMINED IN CR(VI)-TRANSFORMED CELLS AND CR(VI) EXPOSURE-CAUSED HUMAN LUNG CANCER TISSUES. PHARMACOLOGICAL INHIBITORS AND GENE KNOCKDOWN EXPERIMENTS WERE USED TO DETERMINE THE ROLE OF EPIGENETIC DYSREGULATION IN CR(VI) CARCINOGENICITY. WE FOUND THAT CHRONIC CR(VI) EXPOSURE CAUSES EPIGENETIC DYSREGULATION AS EVIDENCED BY THE INCREASED LEVELS OF HISTONE H3 REPRESSIVE METHYLATION MARKS (H3K9ME2 AND H3K27ME3) AND THE RELATED HISTONE-LYSING METHYLTRANSFERASES (HMTASES). PHARMACOLOGICAL INHIBITION OR KNOCKDOWN OF HMTASES REDUCES H3 REPRESSIVE METHYLATION MARKS AND MALIGNANT PHENOTYPES OF CR(VI)-TRANSFORMED CELLS. MOREOVER, KNOCKDOWN OF HMTASES IN PARENTAL CELLS SIGNIFICANTLY REDUCES CHRONIC CR(VI) EXPOSURE-INDUCED CSC-LIKE PROPERTY AND CELL TRANSFORMATION. FURTHER MECHANISTIC STUDY REVEALED THAT KNOCKDOWN OF HMTASES DECREASES CR(VI) EXPOSURE-CAUSED DNA DAMAGE. OUR FINDINGS INDICATE THAT CHRONIC CR(VI) EXPOSURE INCREASES H3 REPRESSIVE METHYLATION MARKS BY INCREASING THE RELATED HMTASES EXPRESSION; AND THAT INCREASED EXPRESSION OF HMTASES PLAYS A CAUSAL ROLE IN CR(VI)-INDUCED CSC-LIKE PROPERTY AND CELL TRANSFORMATION. 2018 7 3460 35 HYPOMETHYLATION OF THE IL8 PROMOTER IN NASAL EPITHELIAL CELLS OF PATIENTS WITH CHRONIC RHINOSINUSITIS WITH NASAL POLYPS. BACKGROUND: IL-8 IS AN IMPORTANT CHEMOKINE IMPLICATED IN THE PATHOGENESIS OF CHRONIC RHINOSINUSITIS (CRS), BUT LITTLE IS KNOWN ABOUT EPIGENETIC REGULATION OF IL8 IN THE PATHOGENESIS OF CRS. OBJECTIVE: WE SOUGHT TO INVESTIGATE THE RELATIONSHIP BETWEEN THE DNA METHYLATION LEVEL IN THE IL8 PROXIMAL PROMOTER AND CRS IN HAN CHINESE SUBJECTS. METHODS: PATIENTS WITH CHRONIC RHINOSINUSITIS WITH NASAL POLYPS (CRSWNP; N = 187), PATIENTS WITH CHRONIC RHINOSINUSITIS WITHOUT NASAL POLYPS (CRSSNP; N = 89), AND CONTROL SUBJECTS (N = 57) WERE ENROLLED IN 2 INDEPENDENT COHORTS. PURIFIED HUMAN NASAL EPITHELIAL CELLS FROM EACH PARTICIPANT WERE ASSESSED FOR PERCENTAGE DNA METHYLATION OF CPG SITES IN THE IL8 PROXIMAL PROMOTER BY USING BISULFITE PYROSEQUENCING AND FOR FUNCTIONAL ASPECTS OF METHYLATION STATUS BY USING IN VITRO ASSAYS. RESULTS: DNA METHYLATION OF CPG SITES 1, 2, AND 3, RESPECTIVELY, IN THE IL8 PROXIMAL PROMOTER WAS SIGNIFICANTLY DECREASED IN HUMAN NASAL EPITHELIAL CELLS OF PATIENTS WITH CRSWNP COMPARED WITH THAT IN PATIENTS WITH CRSSNP (P < .001) AND CONTROL SUBJECTS (P < .001). PERCENTAGE OF DNA METHYLATION OF THE CPG3 SITE WAS CORRELATED NEGATIVELY WITH BOTH TISSUE EOSINOPHILIC CATIONIC PROTEIN (P < .01) AND MYELOPEROXIDASE (P < .05) LEVELS. IL-1BETA (P < .001) AND TNF-ALPHA (P < .01) SIGNIFICANTLY INCREASED IL8 EXPRESSION ACCOMPANIED BY A REDUCTION IN METHYLATION AT THE CPG3 SITE (P < .001). ELECTROPHORETIC MOBILITY SHIFT ASSAYS DEMONSTRATED THAT METHYLATION STATUS OF CPG3 CHANGED THE BINDING OF OCTAMER-BINDING TRANSCRIPTION FACTOR 1 AND NUCLEAR FACTOR KAPPAB. CONCLUSION: DECREASED DNA METHYLATION OF PARTICULARLY CPG SITES IN THE IL8 PROXIMAL PROMOTER MIGHT PLAY A ROLE IN THE PATHOGENESIS OF CRSWNP. 2019 8 3983 38 LONG-TERM EXPOSURE TO CIGARETTE SMOKE EXTRACT INDUCES HYPOMETHYLATION AT THE RUNX3 AND IGF2-H19 LOCI IN IMMORTALIZED HUMAN UROTHELIAL CELLS. CIGARETTE SMOKING IS THE SINGLE MOST IMPORTANT EPIDEMIOLOGICAL RISK FACTOR FOR BLADDER CANCER BUT IT IS NOT KNOWN WHETHER EXPOSURE OF UROTHELIAL CELLS TO THE SYSTEMIC SOLUBLE CONTENTS OF CIGARETTE SMOKE IS DIRECTLY CAUSATIVE TO BLADDER CANCER AND THE ASSOCIATED EPIGENETIC CHANGES SUCH AS TUMOR SUPPRESSOR GENE HYPERMETHYLATION. WE UNDERTOOK THIS STUDY TO INVESTIGATE IF LONG-TERM TREATMENT OF HUMAN UROTHELIAL CELLS WITH CIGARETTE SMOKE EXTRACT (CSE) RESULTS IN TUMOR SUPPRESSOR GENE HYPERMETHYLATION, A PHENOTYPE THAT WAS PREVIOUSLY ASSOCIATED WITH LONG-TERM CONSTANT CSE TREATMENT OF AIRWAY EPITHELIAL CELLS. WE CHRONICALLY TREATED AN IMMORTALIZED HUMAN UROTHELIAL CELL LINE UROTSA WITH CSE USING A CYCLIC DAILY REGIMEN BUT THE CELLS WERE CULTURED IN CSE-FREE MEDIUM BETWEEN DAILY TREATMENTS. BISULFITE SEQUENCING AND REAL-TIME PCR ARRAY-BASED METHYLATION PROFILING WERE EMPLOYED TO EVALUATE METHYLATION CHANGES AT TUMOR SUPPRESSOR GENE LOCI IN THE CHRONICALLY CSE-TREATED CELLS VERSUS THE PASSAGE-MATCHED UNTREATED CONTROL CELLS. THE RUNX3 TUMOR SUPPRESSOR GENE PROMOTER WAS HYPOMETHYLATED WITH A SIGNIFICANT INCREASE IN PROPORTION OF THE COMPLETELY UNMETHYLATED HAPLOTYPE AFTER THE LONG-TERM CSE TREATMENT; WHEREAS RUNX3 PROMOTER HYPERMETHYLATION WAS PREVIOUSLY REPORTED FOR BLADDER CANCERS OF SMOKERS. HYPOMETHYLATION INDUCED BY THE LONG-TERM CSE TREATMENT WAS ALSO OBSERVED FOR THE IGF2-H19 LOCUS. THE METHYLATION STATUS AT THE PRSS8/PROSTASIN AND 16 ADDITIONAL LOCI HOWEVER, WAS UNAFFECTED BY THE CHRONIC CSE TREATMENT. TRANSIENT CSE TREATMENT OVER 1 DAILY REGIMEN RESULTED IN TRANSCRIPTIONAL DOWN-REGULATION OF RUNX3 AND H19, BUT ONLY THE H19 TRANSCRIPTION WAS DOWN-REGULATED IN THE CHRONICALLY CSE-TREATED UROTHELIAL CELLS. TRANSCRIPTION OF A KEY ENZYME IN ONE-CARBON METABOLISM, DIHYDROFOLATE REDUCTASE (DHFR) WAS GREATLY REDUCED BY THE LONG-TERM CSE TREATMENT, POTENTIALLY SERVING AS A MECHANISM FOR THE HYPOMETHYLATION PHENOTYPE VIA A REDUCED SUPPLY OF METHYL DONOR. IN CONCLUSION, CHRONIC CYCLIC CSE TREATMENT OF UROTHELIAL CELLS INDUCED HYPOMETHYLATION RATHER THAN HYPERMETHYLATION AT SPECIFIC LOCI. 2013 9 1122 50 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 1089 31 COCAINE-RELATED DNA METHYLATION IN CAUDATE NEURONS ALTERS 3D CHROMATIN STRUCTURE OF THE IRXA GENE CLUSTER. EPIGENETIC MECHANISMS, LIKE THOSE INVOLVING DNA METHYLATION, ARE THOUGHT TO MEDIATE THE RELATIONSHIP BETWEEN CHRONIC COCAINE DEPENDENCE AND MOLECULAR CHANGES IN ADDICTION-RELATED NEUROCIRCUITRY, BUT HAVE BEEN UNDERSTUDIED IN HUMAN BRAIN. WE INITIALLY USED REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS) TO GENERATE A METHYLOME-WIDE PROFILE OF COCAINE DEPENDENCE IN HUMAN POST-MORTEM CAUDATE TISSUE. WE FOCUSED ON THE IROQUOIS HOMEOBOX A (IRXA) GENE CLUSTER, WHERE HYPOMETHYLATION IN EXON 3 OF IRX2 IN NEURONAL NUCLEI WAS ASSOCIATED WITH COCAINE DEPENDENCE. WE REPLICATED THIS FINDING IN AN INDEPENDENT COHORT AND FOUND SIMILAR RESULTS IN THE DORSAL STRIATUM FROM COCAINE SELF-ADMINISTERING MICE. USING EPIGENOME EDITING AND 3C ASSAYS, WE DEMONSTRATED A CAUSAL RELATIONSHIP BETWEEN METHYLATION WITHIN THE IRX2 GENE BODY, CTCF PROTEIN BINDING, THREE-DIMENSIONAL (3D) CHROMATIN INTERACTION, AND GENE EXPRESSION. TOGETHER, THESE FINDINGS SUGGEST THAT COCAINE-RELATED HYPOMETHYLATION OF IRX2 CONTRIBUTES TO THE DEVELOPMENT AND MAINTENANCE OF COCAINE DEPENDENCE THROUGH ALTERATIONS IN 3D CHROMATIN STRUCTURE IN THE CAUDATE NUCLEUS. 2021 11 3231 30 HELICOBACTER PYLORI-INDUCED MODULATION OF THE PROMOTER METHYLATION OF WNT ANTAGONIST GENES IN GASTRIC CARCINOGENESIS. BACKGROUND: THIS STUDY AIMED TO INVESTIGATE THE CHANGES IN THE PROMOTER METHYLATION AND GENE EXPRESSION OF MULTIPLE WNT ANTAGONISTS BETWEEN THE CHRONIC INFECTION AND ERADICATION OF HELICOBACTER PYLORI (H. PYLORI) IN GASTRIC CARCINOGENESIS. METHODS: THE LEVELS OF METHYLATION AND CORRESPONDING MRNA EXPRESSION OF SEVEN WNT ANTAGONIST GENES (SFRP1, -2, -5, DKK1, -2, -3, WIF1) WERE COMPARED AMONG THE PATIENTS WITH H. PYLORI-POSITIVE GASTRIC CANCERS (GCS), AND H. PYLORI-POSITIVE AND H. PYLORI-NEGATIVE CONTROLS, BY QUANTITATIVE METHYLIGHT ASSAY AND REAL-TIME REVERSE TRANSCRIPTION (RT)-POLYMERASE CHAIN REACTION (PCR), RESPECTIVELY. THE CHANGES OF THE METHYLATION AND EXPRESSION LEVELS OF THE GENES WERE ALSO COMPARED BETWEEN THE H. PYLORI ERADICATION AND H. PYLORI-PERSISTENT GROUPS 1 YEAR AFTER ENDOSCOPIC RESECTION OF GCS. RESULTS: THE METHYLATION LEVELS OF SFRP AND DKK FAMILY GENES WERE SIGNIFICANTLY INCREASED IN THE PATIENTS WITH H. PYLORI-POSITIVE GCS AND FOLLOWED BY H. PYLORI-POSITIVE CONTROLS COMPARED WITH H. PYLORI-NEGATIVE CONTROLS (P < 0.001). SFRP1, -2, AND DKK3 GENE EXPRESSION WAS STEPWISE DOWNREGULATED FROM H. PYLORI-NEGATIVE CONTROLS, H. PYLORI-POSITIVE CONTROLS, AND TO H. PYLORI-POSITIVE GCS (P < 0.05). AMONG THE WNT ANTAGONISTS, ONLY THE DEGREES OF METHYLATION AND DOWNREGULATION OF DKK3 WERE SIGNIFICANTLY REDUCED AFTER H. PYLORI ERADICATION (P < 0.05). CONCLUSION: EPIGENETIC SILENCING OF SFRP AND DKK FAMILY GENES MAY FACILITATE THE FORMATION OF AN EPIGENETIC FIELD DURING H. PYLORI-ASSOCIATED GASTRIC CARCINOGENESIS. THE EPIGENETIC FIELD MAY NOT BE REVERSED EVEN AFTER H. PYLORI ERADICATION EXCEPT BY DKK3 METHYLATION. 2018 12 4349 34 MIR-155 AND MIR-122 EXPRESSION OF SPERMATOZOA IN OBESE SUBJECTS. OBESITY IS CHARACTERIZED BY MILD CHRONIC INFLAMMATION THAT IS LINKED WITH IMPAIRED IRON HOMEOSTASIS. STUDIES IN HUMAN AND MURINE SHOW THAT THERE IS A TRANSGENERATIONAL EPIGENETIC INHERITANCE VIA THE GAMETES IN OBESITY; HOWEVER, THERE IS LITTLE INFORMATION ON CHANGES IN THE EXPRESSION OF MICRORNAS RELATED TO INFLAMMATION AND IRON HOMEOSTASIS IN SPERMATOZOA FROM OBESE SUBJECTS. THE PRESENT STUDY INVESTIGATED THE EXPRESSION OF MICRORNAS RELATED TO INFLAMMATION (MIR-21 Y MIR-155) AND IRON NUTRITION (MIR-122 AND MIR-200B) IN PLASMA, PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMC) AND SPERMATOZOA FROM NORMOZOOSPERMIC CONTROLS (CN; N = 17; BMI: 24.6 +/- 2.0) AND OBESE (OB; N = 17; BMI: 32.6 +/- 4.4) MEN. TO DETERMINE THE INFLAMMATION LEVELS, WE MEASURED IL-6, TNF-ALPHA, AND MONOCYTE CHEMOATTRACTANT PROTEIN-1 (MCP1) BY MAGNETIC LUMINEX((R)) ASSAY. MRNA EXPRESSION OF IL6, TNF-ALPHA, AND HEPCIDIN (HAMP) IN PBMC WERE EVALUATED BY RT-QPCR. THE ANALYSIS OF MICRORNAS WAS PERFORMED USING THE TAQMAN((R)) ASSAYS. THE IRON CONTENT IN PBMC, SEMINAL PLASMA, AND SPERMATOZOA WAS DETERMINED BY INDUCTIVELY COUPLED PLASMA MASS SPECTROMETRY (ICP-MS). HIGH SERUM IL6, TNF-ALPHA, AND MCP1 LEVELS WERE OBSERVED IN OB GROUP (P < 0.05). GENE EXPRESSION ANALYSIS SHOWED AN INCREASED ABUNDANCE RELATIVE OF TNF-ALPHA (P = 0.018), HAMP (P = 0.03), AND IL6 (P = 0.02) IN PBMC FROM OBESE SUBJECTS. ALSO, WE OBSERVED HIGH LEVELS OF SERUM FERRITIN (P = 0.03), IRON CONTENT IN SEMINAL PLASMA (P = 0.04), AND SPERMATOZOA (P = 0.002), BUT LOWER SERUM FE (P = 0.007) IN OBESE SUBJECTS. IN THE OB GROUP, A HIGH EXPRESSION OF MIR-155 (P = 0.02) AND MIR-21 (P = 0.03) WAS OBSERVED IN PBMC AND MIR-122 (P = 0.03) IN PLASMA. IN SPERM, BOTH MIR-155 (P = 0.004) AND MIR-122 (P = 0.028) WERE HIGH IN THE OB GROUP. OUR RESULTS SHOWED THAT OBESE SUBJECTS HAVE INCREASED EXPRESSIONS OF MIR-155 AND MIR-122, TWO MICRORNAS THAT WERE PREVIOUSLY RELATED WITH INFLAMMATION AND IRON METABOLISM, RESPECTIVELY, AT BOTH THE SYSTEMIC AND SPERM LEVELS. 2018 13 672 27 BRAF, KRAS AND HELICOBACTER PYLORI EPIGENETIC CHANGES-ASSOCIATED CHRONIC GASTRITIS IN EGYPTIAN PATIENTS WITH AND WITHOUT GASTRIC CANCER. WE AIMED TO STUDY MLH1 AND MGMT METHYLATION STATUS IN HELICOBACTER PYLORI-ASSOCIATED CHRONIC GASTRITIS IN EGYPTIAN PATIENTS WITH AND WITHOUT GASTRIC CANCER. 39 PATIENTS WERE INCLUDED IN OUR STUDY. THEY WERE DIVIDED INTO 2 GROUPS; PATIENTS WITHOUT (GROUP I) AND WITH GASTRIC ADENOCARCINOMA (GROUP II). PATIENTS WERE SUBJECTED TO CLINICAL EXAMINATION, ABDOMINAL ULTRASOUND AND UPPER ENDOSCOPY FOR GASTRIC BIOPSY. BIOPSIES WERE SUBJECTED TO UREASE TEST, HISTOLOGICAL EXAMINATION, AND DNA PURIFICATION. H. PYLORI, BRAF, KRAS, MLH1 AND MGMT METHYLATION WERE ASSESSED BY QUANTITATIVE PCR. DNA SEQUENCING WAS PERFORMED TO ASSESS BRAF AND KRAS GENES MUTATION. QPCR OF H. PYLORI WAS SIGNIFICANTLY HIGHER IN PATIENTS WITH ADENOCARCINOMA (GROUP II) THAN THOSE WITHOUT ADENOCARCINOMA (GROUP I); WITH A P < 0.001 AS WELL AS IN PATIENTS WITH AGE ABOVE 50 YEARS WITH A P VALUE = 0.008. BY APPLYING LOGISTIC REGRESSION ANALYSIS IT WAS REPORTED THAT THE H. PYLORI QPCR IS A SIGNIFICANT PREDICTOR TO THE ADENOCARCINOMA WITH OR = 1.025 (95 % CI: 1. 002-1.048), WITH SENSITIVITY OF 90 % AND SPECIFICITY OF 100 %. ADENOCARCINOMA PATIENTS HAD A SIGNIFICANTLY HIGHER MEAN AGE AND LEVELS OF H. PYLORI, BRAF, K-RAS, METHYLATED MGMT AND METHYLATED MLH1 THAN THOSE OF GASTRITIS PATIENTS. DNA SEQUENCE ANALYSIS OF BRAF (CODON 12) AND KRAS (CODON 600) HAD GENES MUTATION IN GASTRIC ADENOCARCINOMA VERSUS CHRONIC GASTRITIS. CONCLUSION: H. PYLORI MAY CAUSE EPIGENETIC CHANGES PREDISPOSING THE PATIENTS TO CANCER STOMACH. ESTIMATION OF H. PYLORI BY QPCR CAN BE A GOOD PREDICTOR TO ADENOCARCINOMA. BRAF AND KRAS GENES MUTATION WERE REVELED IN GASTRITIS AND ADENOCARCINOMA PATIENTS. 2016 14 5701 28 SINGLE NUCLEOTIDE POLYMORPHISMS OF CAUDAL TYPE HOMEOBOX 1 AND 2 ARE ASSOCIATED WITH BARRETT'S ESOPHAGUS. BACKGROUND: BARRETT'S ESOPHAGUS (BE), THE PREMALIGNANT LESION OF ESOPHAGEAL ADENOCARCINOMA, IS BELIEVED TO DEVELOP AS A RESULT OF CHRONIC GASTROESOPHAGEAL REFLUX DISEASE (GERD). APPROXIMATELY 10 % OF SUBJECTS WITH GERD PROGRESS TO BE. GENETIC, EPIGENETIC AND OTHER RISK FACTORS MAY CONTRIBUTE TO THIS INTER-INDIVIDUAL VARIABILITY. CAUDAL TYPE HOMEOBOX 1 (CDX1) AND CAUDAL TYPE HOMEOBOX 2 (CDX2) PLAY IMPORTANT REGULATORY ROLES IN THE DEVELOPMENT OF HUMAN BE. AIMS: TO DETERMINE ASSOCIATIONS BETWEEN CDX1 AND CDX2 SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) AND BE. METHODS: GENOMIC DNA WAS EXTRACTED FROM BLOOD SAMPLES COLLECTED FROM BE (N = 109) AND GERD (N = 223) PATIENTS FOR GENOTYPING OF 5 SNPS EACH OF CDX1 AND CDX2 USING TAQMAN ALLELIC DISCRIMINATION ASSAYS. ODDS RATIOS AND 95 % CONFIDENCE INTERVALS OF SNPS AND HAPLOTYPES WERE CALCULATED WITH A LOGISTIC REGRESSION MODEL ADJUSTED FOR FACTORS INCLUDING AGE, SEX AND HIATAL HERNIA. INTERACTIONS BETWEEN GENETIC VARIANTS AND THESE THREE RISK FACTORS WERE ALSO ANALYZED. RESULTS: OLDER AGE (>/=50 YEARS), MALE SEX AND HIATAL HERNIA WERE SIGNIFICANTLY ASSOCIATED WITH BE (P < 0.001). FIVE VARIANTS OF CDX1 SNPS (RS3776082, RS717746 AND RS3776083), ONE CDX1 HAPLOTYPE, AND THREE VARIANTS OF CDX2 SNPS (RS4769585 AND RS3812863) WERE ASSOCIATED WITH BE (P < 0.05). STATISTICALLY SIGNIFICANT INTERACTIONS WERE DETECTED BETWEEN MOST OF THESE SNPS AND THE THREE RISK FACTORS (P < 0.05). CONCLUSION: CERTAIN SNPS OF CDX1 AND CDX2 AND THEIR INTERACTIONS WITH OTHER RISK FACTORS ARE ASSOCIATED WITH BE, AND MAY CONTRIBUTE TO HUMAN SUSCEPTIBILITY TO BE. 2014 15 3792 33 INTERLEUKIN-1BETA INCREASES THE RISK OF GASTRIC CANCER THROUGH INDUCTION OF ABERRANT DNA METHYLATION IN A MOUSE MODEL. INTERLEUKIN-1BETA (IL-1BETA) HAS A SIGNIFICANT ROLE IN CHRONIC GASTRIC INFLAMMATION AND MANIFESTATIONS OF GASTRIC DISEASES. THE PRESENT STUDY AIMED TO ELUCIDATE THE SPECIFIC ROLE OF IL-1BETA IN INDUCTION OF DNA METHYLATION USING IL-1 RECEPTOR TYPE 1 KNOCKOUT (IL-1R1(-)/(-)) MICE. IN THE PRESENT STUDY, WILD-TYPE (WT) AND IL-1R1(-)/(-) MICE WERE INJECTED WITH IL-1BETA (5 MICROG/KG/DAY). SERUM LEVELS OF IL-1BETA, INTERLEUKIN-6 (IL-6) AND NITRIC OXIDE (NO) WERE MEASURED BY ENZYME-LINKED IMMUNOSORBENT OR NO ASSAYS. E-CADHERIN (E-CAD) METHYLATION STATUS AND MESSENGER (M)RNA EXPRESSION OF IL-1BETA, IL-6, E-CAD AND INDUCIBLE NITRIC OXIDE SYNTHASE (INOS) WERE ANALYZED. RESULTS FROM THE PRESENT STUDY INDICATED SIGNIFICANTLY HIGHER IL-1BETA MRNA EXPRESSION (P<0.001) IN WT MICE COMPARED WITH IL-1R1(-)/(-) MICE. IL-1BETA AND IL-6 RELEASE WAS SIGNIFICANTLY INCREASED IN TREATED WT MICE COMPARED WITH IL-1R1(-)/(-) MICE AT 1 H, 4 H AND 8 H (ALL P<0.005). IL-1BETA RELEASE WAS ONLY DETECTED IN WT MICE FOLLOWING A SECOND DOSE MEASURED AT DAY 3, WEEK 1 AND WEEK 2 WHEN COMPARED WITH IL-1R1(-)/(-) MICE. PROMOTER METHYLATION OF E-CAD AND A DECREASE IN GENE EXPRESSION WAS OBSERVED IN TREATED WT MICE. MRNA EXPRESSION OF INOS IN WT MICE WAS SIGNIFICANTLY INCREASED AT WEEK 1 COMPARED WITH IL-1R1(-)/(-) MICE (P=0.0411). FURTHERMORE, A SIGNIFICANTLY INCREASED LEVEL OF NO PRODUCTION WAS OBSERVED IN TREATED WT MICE (P<0.005 AT 8 H AND WEEK 1; P<0.001 AT 4 H AND DAY 3) WHEN COMPARED WITH IL-1R1(-)/(-) MICE. THE PRESENT RESULTS INDICATED THAT IL-1BETA WAS ABLE TO DIRECTLY INDUCE DNA METHYLATION, WHICH MAY LINK INFLAMMATION-INDUCED EPIGENETIC CHANGES AND THE DEVELOPMENT OF GASTRIC DISEASES. 2016 16 2439 37 EPIGENETIC SILENCING OF THE MLH1 PROMOTER IN RELATION TO THE DEVELOPMENT OF GASTRIC CANCER AND ITS USE AS A BIOMARKER FOR PATIENTS WITH MICROSATELLITE INSTABILITY: A SYSTEMATIC ANALYSIS. BACKGROUND/AIMS: HUMAN MUTL HOMOLOG 1 (MLH1) PROMOTER METHYLATION WAS REPORTED IN GASTRIC CANCER (GC). THIS STUDY DETERMINED THE CLINICOPATHOLOGICAL, PROGNOSTIC, AND DIAGNOSTIC EFFECTS OF MLH1 PROMOTER METHYLATION IN GC. METHODS: THE COMBINED ODDS RATIO (OR) OR HAZARD RATIO (HR) AND THEIR CORRESPONDING 95% CONFIDENCE INTERVALS (95% CI) WERE CALCULATED. THE POOLED SENSITIVITY, SPECIFICITY, AND AREA UNDER THE CURVE (AUC) WERE ANALYZED. RESULTS: A TOTAL OF 4654 GC PATIENTS AND 3669 NON-MALIGNANT CONTROLS WERE IDENTIFIED IN THIS SYSTEMATIC ANALYSIS. MLH1 PROMOTER METHYLATION WAS SIGNIFICANTLY HIGHER IN GC SAMPLES THAN IN GASTRIC ADENOMAS, CHRONIC GASTRITIS, ADJACENT TISSUES, NORMAL GASTRIC MUCOSA, AND NORMAL HEALTHY BLOOD SAMPLES, BUT IT EXHIBITED A SIMILAR FREQUENCY IN GC VS. INTESTINAL METAPLASIA AND DYSPLASIA SAMPLES. MLH1 PROMOTER METHYLATION CORRELATED WITH AGE AND MICROSATELLITE INSTABILITY (MSI), BUT IT WAS NOT ASSOCIATED WITH GENDER, H. PYLORI INFECTION, SMOKING, DRINKING BEHAVIORS, PATHOLOGICAL HISTOLOGY, TUMOR DIFFERENTIATION, CLINICAL STAGE, LYMPH NODE STATUS, DISTANT METASTASIS, OR OVERALL SURVIVAL OF GC. MLH1 PROMOTER METHYLATION EXHIBITED A POOR SENSITIVITY VALUE (< 0.5) IN PATIENTS WITH GC COMPARED WITH ADJACENT TISSUES, GASTRIC ADENOMAS, CHRONIC GASTRITIS, NORMAL GASTRIC MUCOSA, AND NORMAL HEALTHY BLOOD SAMPLES. THE POOLED SENSITIVITY, SPECIFICITY, AND AUC OF MLH1 PROMOTER METHYLATION IN GC WITH MSI VS. GC WITH MICROSATELLITE STABILITY (MSS) SAMPLES WERE 0.64, 0.96, AND 0.90, RESPECTIVELY. CONCLUSIONS: OUR RESULTS SUGGEST THAT THE DETECTION OF MLH1 PROMOTER METHYLATION MAY BE A POTENTIAL PROGNOSTIC BIOMARKER FOR GC PATIENTS WITH MSI. 2018 17 3531 38 IMATINIB CAUSES EPIGENETIC ALTERATIONS OF PTEN GENE VIA UPREGULATION OF DNA METHYLTRANSFERASES AND POLYCOMB GROUP PROTEINS. WE HAVE RECENTLY REPORTED THE POSSIBLE IMATINIB-RESISTANT MECHANISM; LONG-TERM EXPOSURE OF LEUKEMIA CELLS TO IMATINIB DOWNREGULATED LEVELS OF PHOSPHATASE AND TENSIN HOMOLOG DELETED ON CHROMOSOME 10 (PTEN) VIA HYPERMETHYLATION OF ITS PROMOTER REGION (LEUKEMIA 2010; 24: 1631). THE PRESENT STUDY EXPLORED THE MOLECULAR MECHANISMS BY WHICH IMATINIB CAUSED METHYLATION ON THE PROMOTER REGION OF THIS TUMOR SUPPRESSOR GENE IN LEUKEMIA CELLS. REAL-TIME REVERSE TRANSCRIPTION PCR FOUND THAT LONG-TERM EXPOSURE OF CHRONIC EOSINOPHILIC LEUKEMIA EOL-1 CELLS EXPRESSING FIP1L1/PLATELET-DERIVED GROWTH FACTOR RECEPTOR-ALPHA TO IMATINIB INDUCED EXPRESSION OF DNA METHYLTRANSFERASE 3A (DNMT3A) AND HISTONE-METHYLTRANSFERASE ENHANCER OF ZESTE HOMOLOG 2 (EZH2), A FAMILY OF POLYCOMB GROUP, THEREBY INCREASING METHYLATION OF THE GENE. IMMUNOPRECIPITATION ASSAY FOUND THE INCREASED COMPLEX FORMATION OF DNMT3A AND EZH2 PROTEINS IN THESE CELLS. MOREOVER, CHROMATIN IMMUNOPRECIPITATION ASSAY SHOWED THAT AMOUNTS OF BOTH DNMT3A AND EZH2 PROTEINS BOUND AROUND THE PROMOTER REGION OF PTEN GENE WERE INCREASED IN EOL-1 CELLS AFTER EXPOSURE TO IMATINIB. FURTHERMORE, WE FOUND THAT LEVELS OF DNMT3A AND EZH2 WERE STRIKINGLY INCREASED IN LEUKEMIA CELLS ISOLATED FROM INDIVIDUALS WITH CHRONIC MYELOGENOUS LEUKEMIA (N=1) AND PHILADELPHIA CHROMOSOME-POSITIVE ACUTE LYMPHOBLASTIC LEUKEMIA (N=2), WHO RELAPSED AFTER TREATMENT WITH IMATINIB COMPARED WITH THOSE ISOLATED AT THEIR INITIAL PRESENTATION. TAKEN TOGETHER, IMATINIB COULD CAUSE DRUG-RESISTANCE VIA RECRUITMENT OF POLYCOMB GENE COMPLEX TO THE PROMOTER REGION OF THE PTEN AND DOWNREGULATION OF THIS GENE'S TRANSCRIPTS IN LEUKEMIA PATIENTS. 2011 18 1620 33 DNA METHYLTRANSFERASE-MEDIATED TRANSCRIPTIONAL SILENCING IN MALIGNANT GLIOMA: A COMBINED WHOLE-GENOME MICROARRAY AND PROMOTER ARRAY ANALYSIS. EPIGENETIC INACTIVATION OF TUMOR SUPPRESSOR GENES IS A COMMON FEATURE IN HUMAN CANCER. PROMOTER HYPERMETHYLATION AND HISTONE DEACETYLATION ARE REVERSIBLE EPIGENETIC MECHANISMS ASSOCIATED WITH TRANSCRIPTIONAL REGULATION. DNA METHYLTRANSFERASES (DNMT1 AND DNMT3B) REGULATE AND MAINTAIN PROMOTER METHYLATION AND ARE OVEREXPRESSED IN HUMAN CANCER. WE PERFORMED WHOLE-GENOME MICROARRAY ANALYSIS TO IDENTIFY GENES WITH ALTERED EXPRESSION AFTER RNAI-INDUCED SUPPRESSION OF DNMT IN A GLIOBLASTOMA MULTIFORME (GBM) CELL LINE. WE THEN IDENTIFIED GENES WITH BOTH DECREASED EXPRESSION AND EVIDENCE OF PROMOTER CPG ISLAND HYPERMETHYLATION IN GBM TISSUE SAMPLES USING A COMBINED WHOLE-GENOME MICROARRAY TRANSCRIPTOME ANALYSIS IN CONJUNCTION WITH A PROMOTER ARRAY ANALYSIS AFTER DNA IMMUNOPRECIPITATION WITH ANTI-5-METHYLCYTIDINE. DNMT1 AND 3B KNOCKDOWN RESULTED IN THE RESTORED EXPRESSION OF 308 GENES THAT ALSO CONTAINED PROMOTER REGION HYPERMETHYLATION. OF THESE, 43 WERE ALSO FOUND TO BE DOWNREGULATED IN GBM TISSUE SAMPLES. THREE DOWNREGULATED GENES WITH HYPERMETHYLATED PROMOTERS AND RESTORED EXPRESSION IN RESPONSE TO ACUTE DNMT SUPPRESSION WERE ASSAYED FOR METHYLATION CHANGES USING BISULFITE SEQUENCE ANALYSIS OF THE PROMOTER REGION AFTER CHRONIC DNMT SUPPRESSION. RESTORATION OF GENE EXPRESSION WAS NOT ASSOCIATED WITH CHANGES IN PROMOTER REGION METHYLATION, BUT RATHER WITH CHANGES IN HISTONE METHYLATION AND CHROMATIN CONFORMATION. TWO OF THE IDENTIFIED GENES EXHIBITED GROWTH SUPPRESSIVE ACTIVITY IN IN VITRO ASSAYS. COMBINING TARGETED GENETIC MANIPULATIONS WITH COMPREHENSIVE GENOMIC AND EXPRESSION ANALYSES PROVIDES A POTENTIALLY POWERFUL NEW APPROACH FOR IDENTIFYING EPIGENETICALLY REGULATED GENES IN GBM. 2009 19 3289 41 HIF-1ALPHA MEDIATES TUMOR HYPOXIA TO CONFER A PERPETUAL MESENCHYMAL PHENOTYPE FOR MALIGNANT PROGRESSION. ALTHOUGH TUMOR PROGRESSION INVOLVES GENETIC AND EPIGENETIC ALTERATIONS TO NORMAL CELLULAR BIOLOGY, THE UNDERLYING MECHANISMS OF THESE CHANGES REMAIN OBSCURE. NUMEROUS STUDIES HAVE SHOWN THAT HYPOXIA-INDUCIBLE FACTOR 1ALPHA (HIF-1ALPHA) IS OVEREXPRESSED IN MANY HUMAN CANCERS AND UP-REGULATES A HOST OF HYPOXIA-RESPONSIVE GENES FOR CANCER GROWTH AND SURVIVAL. WE RECENTLY IDENTIFIED AN ALTERNATIVE MECHANISM OF HIF-1ALPHA FUNCTION THAT INDUCES GENETIC ALTERATIONS BY SUPPRESSING DNA REPAIR. HERE, WE SHOW THAT LONG-TERM HYPOXIA, WHICH MIMICS THE TUMOR MICROENVIRONMENT, DRIVES A PERPETUAL EPITHELIAL-MESENCHYMAL TRANSITION (EMT) THROUGH UP-REGULATION OF THE ZINC FINGER E-BOX BINDING HOMEOBOX PROTEIN ZEB2, WHEREAS SHORT-TERM HYPOXIA INDUCES A REVERSIBLE EMT THAT REQUIRES THE TRANSCRIPTION FACTOR TWIST1. MOREOVER, WE SHOW THAT THE PERPETUAL EMT DRIVEN BY CHRONIC HYPOXIA DEPENDS ON HIF-1ALPHA INDUCTION OF GENETIC ALTERATIONS RATHER THAN ITS CANONICAL TRANSCRIPTIONAL ACTIVATOR FUNCTION. THESE MESENCHYMAL TUMOR CELLS NOT ONLY ACQUIRE TUMORIGENICITY BUT ALSO DISPLAY CHARACTERISTICS OF ADVANCED CANCERS, INCLUDING NECROSIS, AGGRESSIVE INVASION, AND METASTASIS. HENCE, THESE RESULTS REVEAL A MECHANISM BY WHICH HIF-1ALPHA PROMOTES A PERPETUAL MESENCHYMAL PHENOTYPE, THEREBY ADVANCING TUMOR PROGRESSION. 2011 20 4076 35 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