1 3058 140 GENOME-WIDE DNA METHYLATION ANALYSIS IN RENAL ISCHEMIA REPERFUSION INJURY. RENAL ISCHEMIA REPERFUSION INJURY (IRI) IS FREQUENTLY ENCOUNTERED AFTER KIDNEY TRANSPLANTATION AND IS A LEADING CAUSE OF ACUTE RENAL FAILURE. ABERRANT GENE EXPRESSION AND EPIGENETIC REGULATION OCCUR DURING THE PATHOPHYSIOLOGY OF IRI. IN THIS STUDY, WE USED REDUCED REPRESENTATION BISULFITE SEQUENCING TO IDENTIFY THE DNA METHYLOME OF RENAL TISSUES DURING IRI AND THE SHAM-OPERATED TISSUES IN C57BL/6. THE METHYLATION STATUS OF APPROXIMATELY 1.29 MILLION CPGS LOCATED IN AN AVERAGE OF 11554 CPG ISLANDS AND 17113 PROMOTERS IN GENOME WAS DETERMINED. COMPARED WITH SHAM-OPERATED KIDNEY, BOTH ACUTE AND CHRONIC IRI SIGNIFICANTLY DECREASED THE GENOME-WIDE METHYLATION LEVEL (1.1-1.8%) AND THE CPG METHYLATION LEVEL IN THE PROMOTER (0.4-0.5%), CPG ISLAND (0.5-1.3%), EXON (1.3-1.9%), AND INTRON (0.8-1.1%; ALL P<10(-153)). THE PROMOTERS OF 200, 191, AND 79 GENES WERE DIFFERENTIALLY METHYLATED IN THE RENAL TISSUES AT 24H, 7DAYS, AND AT BOTH THE TIME POINTS AFTER IRI, RESPECTIVELY. AMONG THE 79 GENES, WHICH WERE CONSISTENTLY EPIGENETICALLY REGULATED AT TWO TIME POINTS, 18 GENES (22.8%) SHOWED DIFFERENTIAL EXPRESSION AFTER IRI IN A PREVIOUS STUDY OF RENAL EXPRESSION. WE VALIDATED THE PROMOTER METHYLATION STATUS AND EXPRESSION OF FIVE OUT OF THE 18 GENES, INCLUDING 2700049A03RIK, CCR9, FGD2, PFKFB3, AND SDC4 IN AN INDEPENDENT RENAL TISSUE COHORT. WE FOUND THAT ALL THE FIVE GENES EXHIBITED ALTERED METHYLATION OF PROMOTER (P=0.009-0.0001) FOLLOWING RENAL INJURY. THE PROMOTER METHYLATION OF 2700049A03RIK AND CCR9 WAS NEGATIVELY CORRELATED WITH THEIR MRNA EXPRESSION IN RENAL TISSUES (P<0.001 AND P<0.0001, RESPECTIVELY). OUR STUDY NOT ONLY DEMONSTRATED A GENOME-WIDE DNA METHYLATION PATTERN IN THE IR-INJURED RENAL TISSUE FOR THE FIRST TIME, BUT ALSO INDICATED THAT THE REGULATION OF PROMOTER METHYLATION IS AN IMPORTANT MECHANISM UNDERLYING PERSISTENT ALTERATION OF GENE EXPRESSION. 2017 2 3125 29 GHSR DNA HYPERMETHYLATION IS A COMMON EPIGENETIC ALTERATION OF HIGH DIAGNOSTIC VALUE IN A BROAD SPECTRUM OF CANCERS. IDENTIFICATION OF A SINGLE MOLECULAR TRAIT THAT IS DETERMINANT OF COMMON MALIGNANCIES MAY SERVE AS A POWERFUL DIAGNOSTIC SUPPLEMENT TO CANCER TYPE-SPECIFIC MARKERS. HERE, WE REPORT A DNA METHYLATION MARK THAT IS CHARACTERISTIC OF SEVEN STUDIED MALIGNANCIES, NAMELY CANCERS OF LUNG, BREAST, PROSTATE, PANCREAS, COLORECTUM, GLIOBLASTOMA AND B CELL CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) (N = 137). THIS MARK WAS DEFINED BY SUBSTANTIAL HYPERMETHYLATION AT THE PROMOTER AND FIRST EXON OF GROWTH HORMONE SECRETAGOUGE RECEPTOR (GHSR) THROUGH BISULFITE PYROSEQUENCING. THE DEGREE OF ABERRANT METHYLATION WAS CAPABLE OF ACCURATE DISCRIMINATION BETWEEN CANCER AND CONTROL SAMPLES. THE HIGHEST SENSITIVITY AND SPECIFICITY OF CANCER DETECTION WAS ACHIEVED FOR CANCERS OF PANCREAS, LUNG, BREAST AND CLL YIELDING THE AREA UNDER THE CURVE (AUC) VALUES OF 1.0000, 0.9952, 0.9800 AND 0.9400, RESPECTIVELY. NARROWING TO A SINGLE CPG SITE WITHIN THE GENE'S PROMOTER OR FOUR CONSECUTIVE CPG UNITS OF THE HIGHEST METHYLATION LEVELS WITHIN THE FIRST EXON IMPROVED THE DETECTION POWER. GHSR HYPERMETHYLATION WAS DETECTED ALREADY AT THE EARLY STAGE TUMORS. THE ACCURATE PERFORMANCE OF THIS MARKER WAS FURTHER REPLICATED IN AN INDEPENDENT SET OF PANCREATIC CANCER AND CONTROL SAMPLES (N = 78). THESE FINDINGS SUPPORT THE CANDIDATURE OF GHSR METHYLATION AS A HIGHLY ACCURATE PAN-CANCER MARKER. 2015 3 3858 42 ISCHEMIA-INDUCED DNA HYPERMETHYLATION DURING KIDNEY TRANSPLANT PREDICTS CHRONIC ALLOGRAFT INJURY. BACKGROUND ISCHEMIA DURING KIDNEY TRANSPLANT CAUSES CHRONIC ALLOGRAFT INJURY AND ADVERSELY AFFECTS OUTCOME, BUT THE UNDERLYING MECHANISMS ARE INCOMPLETELY UNDERSTOOD. IN TUMORS, OXYGEN SHORTAGE REDUCES THE DNA DEMETHYLATING ACTIVITY OF THE TEN-11 TRANSLOCATION (TET) ENZYMES, YIELDING HYPERMETHYLATED GENOMES THAT PROMOTE TUMOR PROGRESSION. WE INVESTIGATED WHETHER ISCHEMIA SIMILARLY INDUCES DNA HYPERMETHYLATION IN KIDNEY TRANSPLANTS AND CONTRIBUTES TO CHRONIC INJURY.METHODS WE PROFILED GENOME-WIDE DNA METHYLATION IN THREE COHORTS OF BRAIN-DEAD DONOR KIDNEY ALLOGRAFT BIOPSY SPECIMENS: A LONGITUDINAL COHORT WITH PAIRED BIOPSY SPECIMENS OBTAINED AT ALLOGRAFT PROCUREMENT (PREISCHEMIA; N=13), AFTER IMPLANTATION AND REPERFUSION (POSTISCHEMIA; N=13), AND AT 3 OR 12 MONTHS AFTER TRANSPLANT (N=5 EACH); A CROSS-SECTIONAL COHORT WITH PREIMPLANTATION BIOPSY SPECIMENS (N=82); AND A CROSS-SECTIONAL COHORT WITH POSTREPERFUSION BIOPSY SPECIMENS (N=46).RESULTS ANALYSIS OF THE PAIRED PREISCHEMIA AND POSTISCHEMIA SPECIMENS REVEALED THAT METHYLATION INCREASED DRASTICALLY IN ALL ALLOGRAFTS ON ISCHEMIA. HYPERMETHYLATION WAS CAUSED BY LOSS OF 5-HYDROXYMETHYLCYTOSINE, THE PRODUCT OF TET ACTIVITY, AND IT WAS STABLE 1 YEAR AFTER TRANSPLANT. IN THE PREIMPLANTATION COHORT, CPG HYPERMETHYLATION DIRECTLY CORRELATED WITH ISCHEMIA TIME AND FOR SOME CPGS, INCREASED 2.6% PER ADDITIONAL HOUR OF ISCHEMIA. HYPERMETHYLATION PREFERENTIALLY AFFECTED AND REDUCED THE EXPRESSION OF GENES INVOLVED IN SUPPRESSING KIDNEY INJURY AND FIBROSIS. MOREOVER, CPG HYPERMETHYLATION IN PREIMPLANTATION SPECIMENS PREDICTED CHRONIC INJURY, PARTICULARLY FIBROSIS AND GLOMERULOSCLEROSIS, 1 YEAR AFTER TRANSPLANT. THIS FINDING WAS VALIDATED IN THE INDEPENDENT POSTREPERFUSION COHORT, IN WHICH HYPERMETHYLATION ALSO PREDICTED REDUCED ALLOGRAFT FUNCTION 1 YEAR AFTER TRANSPLANT, OUTPERFORMING ESTABLISHED CLINICAL VARIABLES.CONCLUSIONS WE HIGHLIGHT A NOVEL EPIGENETIC BASIS FOR ISCHEMIA-INDUCED CHRONIC ALLOGRAFT INJURY WITH BIOMARKER POTENTIAL. 2018 4 1990 33 EPIGENETIC ANALYSIS OF PAGET'S DISEASE OF BONE IDENTIFIES DIFFERENTIALLY METHYLATED LOCI THAT PREDICT DISEASE STATUS. PAGET'S DISEASE OF BONE (PDB) IS CHARACTERIZED BY FOCAL INCREASES IN DISORGANIZED BONE REMODELING. THIS STUDY AIMS TO CHARACTERIZE PDB-ASSOCIATED CHANGES IN DNA METHYLATION PROFILES IN PATIENTS' BLOOD. META-ANALYSIS OF DATA FROM THE DISCOVERY AND CROSS-VALIDATION SET, EACH COMPRISING 116 PDB CASES AND 130 CONTROLS, REVEALED SIGNIFICANT DIFFERENCES IN DNA METHYLATION AT 14 CPG SITES, 4 CPG ISLANDS, AND 6 GENE-BODY REGIONS. THESE LOCI, INCLUDING TWO CHARACTERIZED AS FUNCTIONAL THROUGH EXPRESSION QUANTITATIVE TRAIT-METHYLATION ANALYSIS, WERE ASSOCIATED WITH FUNCTIONS RELATED TO OSTEOCLAST DIFFERENTIATION, MECHANICAL LOADING, IMMUNE FUNCTION, AND VIRAL INFECTION. A MULTIVARIATE CLASSIFIER BASED ON DISCOVERY SAMPLES WAS FOUND TO DISCRIMINATE PDB CASES AND CONTROLS FROM THE CROSS-VALIDATION WITH A SENSITIVITY OF 0.84, SPECIFICITY OF 0.81, AND AN AREA UNDER CURVE OF 92.8%. IN CONCLUSION, THIS STUDY HAS SHOWN FOR THE FIRST TIME THAT EPIGENETIC FACTORS CONTRIBUTE TO THE PATHOGENESIS OF PDB AND MAY OFFER DIAGNOSTIC MARKERS FOR PREDICTION OF THE DISEASE. 2021 5 3468 37 HYPOXIA-INDUCED DNA HYPERMETHYLATION IN HUMAN PULMONARY FIBROBLASTS IS ASSOCIATED WITH THY-1 PROMOTER METHYLATION AND THE DEVELOPMENT OF A PRO-FIBROTIC PHENOTYPE. BACKGROUND: PULMONARY FIBROSIS IS A DEBILITATING AND LETHAL DISEASE WITH NO EFFECTIVE TREATMENT OPTIONS. UNDERSTANDING THE PATHOLOGICAL PROCESSES AT PLAY WILL DIRECT THE APPLICATION OF NOVEL THERAPEUTIC AVENUES. HYPOXIA HAS BEEN IMPLICATED IN THE PATHOGENESIS OF PULMONARY FIBROSIS YET THE PRECISE MECHANISM BY WHICH IT CONTRIBUTES TO DISEASE PROGRESSION REMAINS TO BE FULLY ELUCIDATED. IT HAS BEEN SHOWN THAT CHRONIC HYPOXIA CAN ALTER DNA METHYLATION PATTERNS IN TUMOUR-DERIVED CELL LINES. THIS EPIGENETIC ALTERATION CAN INDUCE CHANGES IN CELLULAR PHENOTYPE WITH PROMOTER METHYLATION BEING ASSOCIATED WITH GENE SILENCING. OF PARTICULAR RELEVANCE TO IDIOPATHIC PULMONARY FIBROSIS (IPF) IS THE OBSERVATION THAT THY-1 PROMOTER METHYLATION IS ASSOCIATED WITH A MYOFIBROBLAST PHENOTYPE WHERE LOSS OF THY-1 OCCURS ALONGSIDE INCREASED ALPHA SMOOTH MUSCLE ACTIN (ALPHA-SMA) EXPRESSION. THE INITIAL AIM OF THIS STUDY WAS TO DETERMINE WHETHER HYPOXIA REGULATES DNA METHYLATION IN NORMAL HUMAN LUNG FIBROBLASTS (CCD19LU). AS IT HAS BEEN REPORTED THAT HYPOXIA SUPPRESSES THY-1 EXPRESSION DURING LUNG DEVELOPMENT WE ALSO STUDIED THE EFFECT OF HYPOXIA ON THY-1 PROMOTER METHYLATION AND GENE EXPRESSION. METHODS: CCD19LU WERE GROWN FOR UP TO 8 DAYS IN HYPOXIA AND ASSESSED FOR GLOBAL CHANGES IN DNA METHYLATION USING FLOW CYTOMETRY. REAL-TIME PCR WAS USED TO QUANTIFY EXPRESSION OF THY-1, ALPHA-SMA, COLLAGEN I AND III. GENOMIC DNA WAS BISULPHITE TREATED AND METHYLATION SPECIFIC PCR (MSPCR) WAS USED TO EXAMINE THE METHYLATION STATUS OF THE THY-1 PROMOTER. RESULTS: SIGNIFICANT GLOBAL HYPERMETHYLATION WAS DETECTED IN HYPOXIC FIBROBLASTS RELATIVE TO NORMOXIC CONTROLS AND WAS ACCOMPANIED BY INCREASED EXPRESSION OF MYOFIBROBLAST MARKERS. THY-1 MRNA EXPRESSION WAS SUPPRESSED IN HYPOXIC CELLS, WHICH WAS RESTORED WITH THE DEMETHYLATING AGENT 5-AZA-2'-DEOXYCYTIDINE. MSPCR REVEALED THAT THY-1 BECAME METHYLATED FOLLOWING FIBROBLAST EXPOSURE TO 1% O2. CONCLUSION: THESE DATA SUGGEST THAT GLOBAL AND GENE-SPECIFIC CHANGES IN DNA METHYLATION MAY PLAY AN IMPORTANT ROLE IN FIBROBLAST FUNCTION IN HYPOXIA. 2012 6 4221 34 METHYLATION AND SILENCING OF PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE O IN CHRONIC LYMPHOCYTIC LEUKEMIA. PURPOSE: PREVIOUS STUDIES IN OUR LABORATORY HAVE SHOWN THE PROGRESSIVE METHYLATION AND SUPPRESSION OF THE GENE ENCODING PROTEIN TYROSINE PHOSPHATASE, PTPRO, IN THE LIVERS OF RATS FED A METHYL-DEFICIENT DIET THAT INDUCES HEPATOCARCINOGENESIS. SUBSEQUENTLY, WE OBSERVED THE METHYLATION OF PTPRO IN PRIMARY HUMAN LUNG TUMORS AND ALSO SHOWED ITS POTENTIAL TUMOR SUPPRESSOR CHARACTERISTICS. THE PRESENT STUDY WAS UNDERTAKEN TO INVESTIGATE WHETHER THE TRUNCATED FORM OF PTPRO (PTPROT), SPECIFICALLY EXPRESSED IN NAIVE B LYMPHOCYTES, WAS ALSO METHYLATED AND SUPPRESSED IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), A DISEASE GENERALLY AFFECTING B LYMPHOCYTES. EXPERIMENTAL DESIGN AND RESULTS: INITIAL SCREENING SHOWED THAT 60% OF THE 52 CLL SAMPLES ANALYZED USING METHYLATION-SPECIFIC PCR ASSAY WERE METHYLATED COMPARED WITH B LYMPHOCYTES FROM NORMAL INDIVIDUALS, WHICH WERE NOT METHYLATED. THE EXPRESSION OF PTPROT, AS MEASURED BY SEMIQUANTITATIVE REVERSE TRANSCRIPTION-PCR, INVERSELY CORRELATED WITH METHYLATION IN THE FEW SAMPLES TESTED. ANALYSIS OF ADDITIONAL SAMPLES (N = 50) BY COMBINED BISULFITE RESTRICTION ANALYSIS SHOWED THAT THE PTPRO CPG ISLAND WAS METHYLATED IN 82% OF PATIENTS WITH CLL COMPARED WITH B LYMPHOCYTES FROM NORMAL INDIVIDUALS. FURTHERMORE, OVERALL EXPRESSION OF PTPRO WAS REDUCED IN CLL RELATIVE TO NORMAL LYMPHOCYTES. THE PTPRO GENE WAS ALSO SUPPRESSED BY METHYLATION IN THE CLL CELL LINE WAC3CD5, WHERE IT COULD BE REACTIVATED UPON TREATMENT WITH THE DNA HYPOMETHYLATING AGENT 5-AZAC. ECTOPIC EXPRESSION OF PTPROT IN A NONEXPRESSING CELL LINE INCREASED GROWTH INHIBITION WITH FLUDARABINE TREATMENT, A THERAPY COMMONLY USED FOR CLL. CONCLUSION: THIS STUDY REVEALS THE POTENTIAL ROLE OF PTPRO METHYLATION AND SILENCING IN CLL TUMORIGENESIS AND ALSO PROVIDES A NOVEL MOLECULAR TARGET IN THE EPIGENETIC THERAPY. 2007 7 11 41 15Q12 VARIANTS, SPUTUM GENE PROMOTER HYPERMETHYLATION, AND LUNG CANCER RISK: A GWAS IN SMOKERS. BACKGROUND: LUNG CANCER IS THE LEADING CAUSE OF CANCER-RELATED MORTALITY WORLDWIDE. DETECTION OF PROMOTER HYPERMETHYLATION OF TUMOR SUPPRESSOR GENES IN EXFOLIATED CELLS FROM THE LUNG PROVIDES AN ASSESSMENT OF FIELD CANCERIZATION THAT IN TURN PREDICTS LUNG CANCER. THE IDENTIFICATION OF GENETIC DETERMINANTS FOR THIS VALIDATED CANCER BIOMARKER SHOULD PROVIDE NOVEL INSIGHTS INTO MECHANISMS UNDERLYING EPIGENETIC REPROGRAMMING DURING LUNG CARCINOGENESIS. METHODS: A GENOME-WIDE ASSOCIATION STUDY USING GENERALIZED ESTIMATING EQUATIONS AND LOGISTIC REGRESSION MODELS WAS CONDUCTED IN TWO GEOGRAPHICALLY INDEPENDENT SMOKER COHORTS TO IDENTIFY LOCI AFFECTING THE PROPENSITY FOR CANCER-RELATED GENE METHYLATION THAT WAS ASSESSED BY A 12-GENE PANEL INTERROGATED IN SPUTUM. ALL STATISTICAL TESTS WERE TWO-SIDED. RESULTS: TWO SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) AT 15Q12 (RS73371737 AND RS7179575) THAT DROVE GENE METHYLATION WERE DISCOVERED AND REPLICATED WITH RS73371737 REACHING GENOME-WIDE SIGNIFICANCE (P = 3.3X10(-8)). A HAPLOTYPE CARRYING RISK ALLELES FROM THE TWO 15Q12 SNPS CONFERRED 57% INCREASED RISK FOR GENE METHYLATION (P = 2.5X10(-9)). RS73371737 REDUCED GABRB3 EXPRESSION IN LUNG CELLS AND INCREASED RISK FOR SMOKING-INDUCED CHRONIC MUCOUS HYPERSECRETION. FURTHERMORE, SUBJECTS WITH VARIANT HOMOZYGOTE OF RS73371737 HAD A TWO-FOLD INCREASE IN RISK FOR LUNG CANCER (P = .0043). PATHWAY ANALYSIS IDENTIFIED DNA DOUBLE-STRAND BREAK REPAIR BY HOMOLOGOUS RECOMBINATION (DSBR-HR) AS A MAJOR PATHWAY AFFECTING SUSCEPTIBILITY FOR GENE METHYLATION THAT WAS VALIDATED BY MEASURING CHROMATID BREAKS IN LYMPHOCYTES CHALLENGED BY BLEOMYCIN. CONCLUSIONS: A FUNCTIONAL 15Q12 VARIANT WAS IDENTIFIED AS A RISK FACTOR FOR GENE METHYLATION AND LUNG CANCER. THE ASSOCIATIONS COULD BE MEDIATED BY GABAERGIC SIGNALING THAT DRIVES THE SMOKING-INDUCED MUCOUS CELL METAPLASIA. OUR FINDINGS ALSO SUBSTANTIATE DSBR-HR AS A CRITICAL PATHWAY DRIVING EPIGENETIC GENE SILENCING. 2015 8 1846 34 EFFECTS OF TWO TYPES OF ENERGY RESTRICTION ON METHYLATION LEVELS OF ADIPONECTIN RECEPTOR 1 AND LEPTIN RECEPTOR OVERLAPPING TRANSCRIPT IN A MOUSE MAMMARY TUMOUR VIRUS-TRANSFORMING GROWTH FACTOR-ALPHA BREAST CANCER MOUSE MODEL. THE ROLE OF ADIPONECTIN AND LEPTIN SIGNALLING PATHWAYS HAS BEEN SUGGESTED TO PLAY IMPORTANT ROLES IN THE PROTECTIVE EFFECTS OF ENERGY RESTRICTION (ER) ON MAMMARY TUMOUR (MT) DEVELOPMENT. TO STUDY THE EFFECTS OF ER ON THE METHYLATION LEVELS IN ADIPONECTIN RECEPTOR 1 (ADIPOR1) AND LEPTIN RECEPTOR OVERLAPPING TRANSCRIPT (LEPROT) GENES USING THE PYROSEQUENCING METHOD IN MAMMARY FAT PAD TISSUE, MOUSE MAMMARY TUMOUR VIRUS-TRANSFORMING GROWTH FACTOR-ALPHA (MMTV-TGF-ALPHA) FEMALE MICE WERE RANDOMLY ASSIGNED TO AD LIBITUM (AL), CHRONIC ER (CER, 15 % ER) OR INTERMITTENT ER (3 WEEKS AL AND 1 WEEK 60 % ER IN CYCLIC PERIODS) GROUPS AT 10 WEEKS OF AGE UNTIL 82 WEEKS OF AGE. THE METHYLATION LEVELS OF ADIPOR1 IN THE CER GROUP WERE HIGHER THAN THOSE IN THE AL GROUP AT WEEK 49/50 (P < 0.05), WHILE THE LEVELS OF METHYLATION FOR ADIPOR1 AND LEPROT GENES WERE SIMILAR AMONG THE OTHER GROUPS. ALSO, THE METHYLATION LEVELS AT CPG2 AND CPG3 REGIONS OF THE PROMOTER REGION OF THE ADIPOR1 GENE IN THE CER GROUP WERE THREE TIMES HIGHER (P < 0.05), WHILE CPG1 ISLAND OF LEPROT METHYLATION WAS SIGNIFICANTLY LOWER COMPARED WITH THE OTHER GROUPS (P < 0.05). ADIPONECTIN AND LEPTIN GENE EXPRESSION LEVELS WERE CONSISTENT WITH THE METHYLATION LEVELS. WE ALSO OBSERVED A CHANGE WITH AGEING IN METHYLATION LEVELS OF THESE GENES. THESE RESULTS INDICATE THAT DIFFERENT TYPES OF ER MODIFY METHYLATION LEVELS OF ADIPOR1 AND LEPROT IN DIFFERENT WAYS AND CER HAD A MORE SIGNIFICANT EFFECT ON METHYLATION LEVELS OF BOTH GENES. EPIGENETIC REGULATION OF THESE GENES MAY PLAY IMPORTANT ROLES IN THE PREVENTIVE EFFECTS OF ER AGAINST MT DEVELOPMENT AND AGEING PROCESSES. 2021 9 3638 38 INCREASED EXPRESSION OF BETA-DEFENSIN 1 (DEFB1) IN CHRONIC OBSTRUCTIVE PULMONARY DISEASE. ON-GOING AIRWAY INFLAMMATION IS CHARACTERISTIC FOR THE PATHOPHYSIOLOGY OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD). HOWEVER, THE KEY FACTORS DETERMINING THE DECREASE IN LUNG FUNCTION, AN IMPORTANT CLINICAL PARAMETER OF COPD, ARE NOT CLEAR. GENOME-WIDE LINKAGE ANALYSES PROVIDE EVIDENCE FOR SIGNIFICANT LINKAGE TO AIRWAY OBSTRUCTION SUSCEPTIBILITY LOCI ON CHROMOSOME 8P23, THE LOCATION OF THE HUMAN DEFENSIN GENE CLUSTER. MOREOVER, A GENETIC VARIATION IN THE DEFENSIN BETA 1 (DEFB1) GENE WAS FOUND TO BE ASSOCIATED WITH COPD. THEREFORE, WE HYPOTHESIZED THAT DEFB1 IS DIFFERENTLY REGULATED AND EXPRESSED IN HUMAN LUNGS DURING COPD PROGRESSION. GENE EXPRESSION OF DEFB1 WAS ASSESSED IN BRONCHIAL EPITHELIUM AND BAL FLUID CELLS OF HEALTHY CONTROLS AND PATIENTS WITH COPD AND USING BISULFITE SEQUENCING AND CHIP ANALYSIS, THE EPIGENETIC CONTROL OF DEFB1 MRNA EXPRESSION WAS INVESTIGATED. WE CAN DEMONSTRATE THAT DEFB1 MRNA EXPRESSION WAS SIGNIFICANTLY INCREASED IN BRONCHOPULMONARY SPECIMEN OF PATIENTS WITH COPD (N = 34) VS. HEALTHY CONTROLS (N = 10) (P<0.0001). FURTHERMORE, A SIGNIFICANT CORRELATION COULD BE DETECTED BETWEEN DEFB1 AND FUNCTIONAL PARAMETERS SUCH AS FEV(1) (P = 0.0024) AND THE FEV(1)/VC RATIO (P = 0.0005). UPREGULATION OF DEFB1 MRNA WAS PARALLELED BY CHANGES IN HDAC1-3, HDAC5 AND HDAC8 MRNA EXPRESSION. WHEREAS BISULFITE SEQUENCING REVEALED NO DIFFERENCES IN THE METHYLATION STATE OF DEFB1 PROMOTER BETWEEN PATIENTS WITH COPD AND CONTROLS, CHIP ANALYSIS SHOWED THAT ENHANCED DEFB1 MRNA EXPRESSION WAS ASSOCIATED WITH THE ESTABLISHMENT OF AN ACTIVE HISTONE CODE. THUS, EXPRESSION OF HUMAN DEFB1 IS UPREGULATED AND RELATED TO THE DECREASE IN PULMONARY FUNCTION IN PATIENTS WITH COPD. 2011 10 155 32 ABERRANT METHYLATION OF POLO-LIKE KINASE CPG ISLANDS IN PLK4 HETEROZYGOUS MICE. BACKGROUND: HEPATOCELLULAR CARCINOMA (HCC), ONE OF THE MOST COMMON CANCERS WORLD-WIDE OCCURS TWICE AS OFTEN IN MEN COMPARED TO WOMEN. PREDISPOSING CONDITIONS SUCH AS ALCOHOLISM, CHRONIC VIRAL HEPATITIS, AFLATOXIN B1 INGESTION, AND CIRRHOSIS ALL CONTRIBUTE TO THE DEVELOPMENT OF HCC. METHODS: WE USED A COMBINATION OF METHYLATION SPECIFIC PCR AND BISULFITE SEQUENCING, QREAL-TIME PCR (QPCR), AND WESTERN BLOT ANALYSIS TO EXAMINE EPIGENETIC CHANGES FOR THE POLO-LIKE KINASES (PLKS) DURING THE DEVELOPMENT OF HEPATOCELLULAR CARCINOMA (HCC) IN PLK4 HETEROZYGOUS MICE AND MURINE EMBRYONIC FIBROBLASTS (MEFS). RESULTS: HERE WE REPORT THAT THE PROMOTER METHYLATION OF PLK4 CPG ISLANDS INCREASES WITH AGE, WAS MORE PREVALENT IN MALES AND THAT PLK4 EPIGENETIC MODIFICATION AND SUBSEQUENT DOWNREGULATION OF EXPRESSION WAS ASSOCIATED WITH THE DEVELOPMENT OF HCC IN PLK4 MUTANT MICE. INTERESTINGLY, THE OPPOSITE OCCURS WITH ANOTHER PLK FAMILY MEMBER, PLK1 WHICH WAS TYPICALLY HYPERMETHYLATED IN NORMAL LIVER TISSUE BUT BECAME HYPOMETHYLATED AND UPREGULATED IN LIVER TUMOURS. FURTHERMORE, UPON ALCOHOL EXPOSURE MURINE EMBRYONIC FIBROBLASTS EXHIBITED INCREASED PLK4 HYPERMETHYLATION AND DOWNREGULATION ALONG WITH INCREASED CENTROSOME NUMBERS AND MULTINUCLEATION. CONCLUSIONS: THESE RESULTS SUGGEST THAT ABERRANT PLK METHYLATION IS CORRELATED WITH THE DEVELOPMENT OF HCC IN MICE. 2011 11 3049 37 GENOME-WIDE ANALYSIS REVEALS ZINC TRANSPORTER ZIP9 REGULATED BY DNA METHYLATION PROMOTES RADIATION-INDUCED SKIN FIBROSIS VIA THE TGF-BETA SIGNALING PATHWAY. RADIATION-INDUCED SKIN FIBROSIS IS A DETRIMENTAL AND CHRONIC DISORDER THAT OCCURS AFTER RADIATION EXPOSURE. DNA METHYLATION HAS BEEN CHARACTERIZED AS AN IMPORTANT REGULATORY MECHANISM OF MULTIPLE PATHOLOGICAL PROCESSES. IN THIS STUDY, WE COMPARED THE GENOME-WIDE DNA METHYLATION STATUS IN RADIATION-INDUCED FIBROTIC SKIN AND ADJACENT NORMAL TISSUES OF RATS BY METHYLATED DNA IMMUNOPRECIPITATION SEQUENCING. RADIATION-INDUCED FIBROTIC SKIN SHOWED DIFFERENTIALLY METHYLATED REGIONS ASSOCIATED WITH 3,650 PROTEIN-CODING GENES, 72 MICRORNAS, 5,836 LONG NONCODING RNAS AND 3 PIWI-INTERACTING RNAS. BY INTEGRATING THE MRNA AND METHYLATION PROFILES, THE ZINC TRANSPORTER SLC39A9/ZIP9 WAS INVESTIGATED IN GREATER DETAIL. THE PROTEIN LEVEL OF ZIP9 WAS INCREASED IN IRRADIATED SKIN TISSUES OF HUMANS, MONKEYS, AND RATS, ESPECIALLY IN RADIOGENIC FIBROTIC SKIN TISSUES. RADIATION INDUCED THE DEMETHYLATION OF A CPG DINUCLEOTIDE IN EXON 1 OF ZIP9 THAT RESULTED IN RECRUITMENT OF THE TRANSCRIPTIONAL FACTOR SP1 AND INCREASED ZIP9 EXPRESSION. OVEREXPRESSION OF ZIP9 RESULTED IN ACTIVATION OF THE PROFIBROTIC TRANSFORMING GROWTH FACTOR-BETA SIGNALING PATHWAY THROUGH PROTEIN KINASE B IN HUMAN FIBROBLASTS. IN ADDITION, RADIATION-INDUCED SKIN FIBROSIS WAS ASSOCIATED WITH INCREASED ZINC ACCUMULATION. THE ZINC CHELATOR N,N,N',N'-TETRAKIS(2-PYRIDYLMETHYL)-1,2-ETHYLENEDIAMINE ABROGATED ZIP9-INDUCED ACTIVATION OF THE TRANSFORMING GROWTH FACTOR-BETA SIGNALING PATHWAY AND ATTENUATED RADIATION-INDUCED SKIN FIBROSIS IN A RAT MODEL. IN SUMMARY, OUR FINDINGS ILLUSTRATE EPIGENETIC REGULATION OF ZIP9 AND ITS CRITICAL ROLE IN PROMOTING RADIATION-INDUCED SKIN FIBROSIS. 2020 12 546 36 ATTENUATED EXPRESSION OF SLCO2A1 CAUSED BY DNA METHYLATION IN PEDIATRIC INFLAMMATORY BOWEL DISEASE. BACKGROUND: SLCO2A1 ENCODES A PROSTAGLANDIN (PG) TRANSPORTER, AND AUTOSOMAL RECESSIVE PATHOGENIC VARIANTS OF THIS GENE CAUSE CHRONIC ENTEROPATHY ASSOCIATED WITH SLCO2A1. IT IS UNCLEAR WHETHER A HETEROZYGOUS PATHOGENIC VARIANT OF SLCO2A1 HAS A ROLE IN THE PATHOGENESIS OF OTHER TYPES OF INFLAMMATORY BOWEL DISEASE (IBD). IN THIS STUDY, WE INVESTIGATED THE POSSIBLE INVOLVEMENT OF A LOCAL EPIGENETIC ALTERATION IN SLCO2A1 IN PATIENTS WITH A HETEROZYGOUS PATHOGENIC VARIANT. METHODS: WE CONDUCTED WHOLE-EXOME SEQUENCING OF SAMPLES FROM 2 SISTERS WITH SUSPECTED MONOGENIC IBD. IN ADDITION, WE PERFORMED BISULFITE SEQUENCING USING DNA EXTRACTED FROM THEIR SMALL AND LARGE INTESTINE SAMPLES TO EXPLORE EPIGENETIC ALTERATIONS. RESULTS: A HETEROZYGOUS SPLICING SITE VARIANT, SLCO2A1:C.940 + 1G > A, WAS DETECTED IN BOTH PATIENTS. TO EXPLORE THE POSSIBLE INVOLVEMENT OF EPIGENETIC ALTERATIONS, WE ANALYZED PROTEIN AND MESSENGER RNA EXPRESSION OF SLCO2A1, AND OBSERVED ATTENUATED SLCO2A1 EXPRESSION IN THE INFLAMED LESIONS OF THESE PATIENTS COMPARED WITH THAT IN THE CONTROL INDIVIDUALS. FURTHERMORE, BISULFITE SEQUENCING INDICATED DENSE METHYLATION IN THE PROMOTER REGION OF SLCO2A1 ONLY IN THE INFLAMED LESIONS OF BOTH PATIENTS. THE URINARY PG METABOLITE LEVELS IN THESE PATIENTS WERE COMPARABLE TO THOSE IN PATIENTS WITH CHRONIC ENTEROPATHY ASSOCIATED WITH SLCO2A1 AND HIGHER THAN THOSE IN THE CONTROL INDIVIDUALS. WE FOUND CONSIDERABLY HIGHER LEVELS OF THE METABOLITES IN PATIENT 1, WHO SHOWED MORE SEVERE SYMPTOMS THAN PATIENT 2. CONCLUSIONS: LOCAL DNA METHYLATION ATTENUATED SLCO2A1 EXPRESSION, WHICH MAY EVOKE LOCAL INFLAMMATION OF THE MUCOSA BY THE UNINCORPORATED PG. THESE FINDINGS MAY IMPROVE OUR UNDERSTANDING OF THE EPIGENETIC MECHANISMS UNDERLYING IBD DEVELOPMENT. 2023 13 658 35 BLOOD DNA METHYLATION PREDICTS DIABETIC KIDNEY DISEASE PROGRESSION IN HIGH FAT DIET-FED MICE. DIABETIC KIDNEY DISEASE (DKD) PROGRESSES AT DIFFERENT RATES AMONG PATIENTS WITH TYPE 2 DIABETES MELLITUS (T2D). EARLY IDENTIFICATION OF PATIENTS WITH A HIGHER RISK OF DKD PROGRESSION IS ESSENTIAL TO IMPROVE PROGNOSIS. EPIGENETIC MODIFICATIONS, PARTICULARLY DNA METHYLATION, HAVE BEEN INDEPENDENTLY IMPLICATED IN T2D AND CHRONIC KIDNEY DISEASE. THE CURRENT STUDY AIMED TO DETERMINE CHANGES IN BLOOD DNA METHYLATION THAT REFLECTS AND PREDICTS DKD PROGRESSION. C57BL/6 MICE WERE FED A HIGH-FAT DIET (HFD) FROM WEANING AND SUBCLASSIFIED INTO TWO GROUPS, HFD-1 AND HFD-2, ACCORDING TO URINARY KIDNEY INJURY MARKER KIM-1/CREATININE RATIOS (LOW VS. HIGH) AND HISTOLOGICAL ABNORMALITIES (MILD-MODERATE VS. ADVANCED). DNA METHYLATION PROFILES WERE DETERMINED BY REDUCED REPRESENTATIVE BISULFIDE SEQUENCING (RRBS). OUR RESULTS CONFIRMED EARLY AND ESTABLISHED DKD AT WEEK 9 AND WEEK 32, RESPECTIVELY. AT WEEK 32, ADVANCED KIDNEY INJURY WAS ASSOCIATED WITH DYSREGULATION OF METHYLATION AND DEMETHYLATION ENZYMES IN THE KIDNEY. BLOOD RRBS REVEALED 579 AND 203 DIFFERENTIALLY METHYLATED SITES (DMS) BETWEEN HFD-1 AND HFD-2 ANIMALS AT WEEK 32 AND WEEK 9, RESPECTIVELY, AMONG WHICH 11 WERE COMMON. THE DMS IN BLOOD AND KIDNEY AT WEEK 32 WERE BOTH RELATED TO ORGAN DEVELOPMENT, NEUROGENESIS, CELL JUNCTION, AND WNT SIGNALLING, WHILE THE DMS IN BLOOD AT WEEK 9 SUGGESTED A SPECIFIC ENRICHMENT OF KIDNEY DEVELOPMENT PROCESSES. IN CONCLUSION, OUR DATA STRONGLY SUPPORT THE IMPLICATION OF EARLY BLOOD DNA METHYLATION MODIFICATIONS AND DKD PROGRESSION IN T2D THAT COULD BE USED TO IMPROVE THE DISEASE'S PROGNOSTICATION. 2022 14 3084 42 GENOME-WIDE SCREEN OF DNA METHYLATION IDENTIFIES NOVEL MARKERS IN CHILDHOOD OBESITY. EPIGENETIC MODIFICATIONS HAVE BEEN HIGHLIGHTED IN CHRONIC NON-COMMUNICABLE DISEASES. THE AIM OF THIS STUDY WAS TO INVESTIGATE GENOME-WIDE DNA METHYLATION FOR THE IDENTIFICATION OF METHYLATION MARKERS IN OBESITY. WITH OBESE CHINESE PRESCHOOL CHILDREN, WE PERFORMED COMPREHENSIVE DNA METHYLATION PROFILING OF GENE PROMOTERS AND CPG ISLANDS TO DETERMINE THE DIFFERENTIALLY METHYLATED GENES USING METHYLATED DNA IMMUNOPRECIPITATION FOLLOWED BY HYBRIDIZATION TO THE NIMBLEGEN HUMAN DNA METHYLATION 385K PROMOTER PLUS CPG ISLAND MICROARRAY. WE FOUND THAT COMPARED TO LEAN CHILDREN, 251 PROMOTERS AND 575 CGIS WERE DEMETHYLATED, AND 141 PROMOTERS AND 277 CGIS WERE HYPERMETHYLATED IN OBESE CHILDREN, AND THEIR DISTRIBUTION ON CHROMOSOMES WAS IMBALANCED, SHOWING MORE PROMOTERS AND CGIS WITH DEMETHYLATION ON CHROMOSOMES 3, 16, 17 AND 19 AND MORE DIFFERENTIALLY METHYLATED PROMOTERS AND CGIS ON CHROMOSOME X COMPARED WITH CHROMOSOME Y. FURTHER ANALYSIS INDICATED THAT ABERRANT METHYLATIONS OCCURRED MOSTLY IN HCP PROMOTERS AND PROMOTER CGIS. AMONG THE TOP 80 PROMOTERS AND CGIS THAT HAD DIFFERENTIATED METHYLATION BETWEEN OBESE AND LEAN CHILDREN, NEARLY HALF HAVE BEEN PREVIOUSLY STUDIED, AND ALMOST ALL OF THEM ARE INVOLVED IN THE PATHOGENESIS OF CANCERS THAT ARE ASSOCIATED WITH MANY ORGANS. FURTHERMORE, FOUR GENES (FZD7, PRLHR, EXOSC4, AND EIF6) WITH DIFFERENTIAL PROMOTER METHYLATION WERE VALIDATED, AND THEIR ASSOCIATIONS WITH OBESITY MUST BE CLARIFIED. IN CONCLUSION, THIS STUDY REPRESENTS THE FIRST EFFORT TO DETERMINE METHYLATION MARKERS IN OBESE CHINESE CHILDREN, WHICH HAS POTENTIAL RELEVANCE FOR IDENTIFYING MARKERS THAT ARE USEFUL IN ELUCIDATING THE MECHANISMS OF OBESITY PATHOGENESIS AND ITS COMPLICATIONS. 2015 15 4516 31 MULTI-OMICS CHARACTERIZATION OF INFLAMMATORY BOWEL DISEASE-INDUCED HYPERPLASIA/DYSPLASIA IN THE RAG2(-/-)/IL10(-/-) MOUSE MODEL. EPIGENETIC DYSREGULATION IS HYPOTHESIZED TO PLAY A ROLE IN THE OBSERVED ASSOCIATION BETWEEN INFLAMMATORY BOWEL DISEASE (IBD) AND COLON TUMOR DEVELOPMENT. IN THE PRESENT WORK, DNA METHYLOME, HYDROXYMETHYLOME, AND TRANSCRIPTOME ANALYSES WERE CONDUCTED IN PROXIMAL COLON TISSUES HARVESTED FROM THE HELICOBACTER HEPATICUS (H. HEPATICUS)-INFECTED MURINE MODEL OF IBD. REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS) AND OXIDATIVE RRBS (OXRRBS) ANALYSES IDENTIFIED 1606 DIFFERENTIALLY METHYLATED REGIONS (DMR) AND 3011 DIFFERENTIALLY HYDROXYMETHYLATED REGIONS (DHMR). THESE DMR/DHMR OVERLAPPED WITH GENES THAT ARE ASSOCIATED WITH GASTROINTESTINAL DISEASE, INFLAMMATORY DISEASE, AND CANCER. RNA-SEQ REVEALED PRONOUNCED EXPRESSION CHANGES OF A NUMBER OF GENES ASSOCIATED WITH INFLAMMATION AND CANCER. SEVERAL GENES INCLUDING DUOX2, TGM2, CDHR5, AND HK2 EXHIBITED CHANGES IN BOTH DNA METHYLATION/HYDROXYMETHYLATION AND GENE EXPRESSION LEVELS. OVERALL, OUR RESULTS SUGGEST THAT CHRONIC INFLAMMATION TRIGGERS CHANGES IN METHYLATION AND HYDROXYMETHYLATION PATTERNS IN THE GENOME, ALTERING THE EXPRESSION OF KEY TUMORIGENESIS GENES AND POTENTIALLY CONTRIBUTING TO THE INITIATION OF COLORECTAL CANCER. 2020 16 4694 39 NEXT-GENERATION SEQUENCING IDENTIFIES MAJOR DNA METHYLATION CHANGES DURING PROGRESSION OF PH+ CHRONIC MYELOID LEUKEMIA. LITTLE IS KNOWN ABOUT THE IMPACT OF DNA METHYLATION ON THE EVOLUTION/PROGRESSION OF PH+ CHRONIC MYELOID LEUKEMIA (CML). WE INVESTIGATED THE METHYLOME OF CML PATIENTS IN CHRONIC PHASE (CP-CML), ACCELERATED PHASE (AP-CML) AND BLAST CRISIS (BC-CML) AS WELL AS IN CONTROLS BY REDUCED REPRESENTATION BISULFITE SEQUENCING. ALTHOUGH ONLY ~600 DIFFERENTIALLY METHYLATED CPG SITES WERE IDENTIFIED IN SAMPLES OBTAINED FROM CP-CML PATIENTS COMPARED WITH CONTROLS, ~6500 DIFFERENTIALLY METHYLATED CPG SITES WERE FOUND IN SAMPLES FROM BC-CML PATIENTS. IN THE MAJORITY OF AFFECTED CPG SITES, METHYLATION WAS INCREASED. IN CP-CML PATIENTS WHO PROGRESSED TO AP-CML/BC-CML, WE IDENTIFIED UP TO 897 GENES THAT WERE METHYLATED AT THE TIME OF PROGRESSION BUT NOT AT THE TIME OF DIAGNOSIS. USING RNA-SEQUENCING, WE OBSERVED DOWNREGULATED EXPRESSION OF MANY OF THESE GENES IN BC-CML COMPARED WITH CP-CML SAMPLES. SEVERAL OF THEM ARE WELL-KNOWN TUMOR-SUPPRESSOR GENES OR REGULATORS OF CELL PROLIFERATION, AND GENE RE-EXPRESSION WAS OBSERVED BY THE USE OF EPIGENETIC ACTIVE DRUGS. TOGETHER, OUR RESULTS DEMONSTRATE THAT CPG SITE METHYLATION CLEARLY INCREASES DURING CML PROGRESSION AND THAT IT MAY PROVIDE A USEFUL BASIS FOR REVEALING NEW TARGETS OF THERAPY IN ADVANCED CML. 2016 17 494 29 ASSESSMENT OF PROMOTER METHYLATION IDENTIFIES PTCH AS A PUTATIVE TUMOR-SUPPRESSOR GENE IN HUMAN CLL. BACKGROUND: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS CHARACTERIZED BY A CLONAL ACCUMULATION OF NEOPLASTIC LYMPHOCYTES, INDICATING DISRUPTION OF APOPTOSIS. PATIENTS AND METHODS: DIFFERENTIAL METHYLATION HYBRIDIZATION ANALYSIS WAS PERFORMED TO IDENTIFY NOVEL TARGET GENES SILENCED BY CPG ISLAND METHYLATION IN PATIENTS WITH CLL. RESULTS: PATCHED (PTCH), A TUMOR-SUPPRESSOR GENE, WAS FOUND TO BE FREQUENTLY METHYLATED IN CLL SAMPLES COMPARED TO SAMPLES DERIVED FROM HEALTHY INDIVIDUALS. DE NOVO METHYLATION OF A CPG ISLAND REGION LOCATED UPSTREAM OF PTCH EXON 1 WAS CONFIRMED BY PYROSEQUENCING IN 17/37 (46%) OF PERIPHERAL BLOOD MONONUCLEAR CELLS OF PATIENTS WITH CLL, BUT IN NONE ISOLATED FROM SEVEN HEALTHY INDIVIDUALS. NO ASSOCIATION WAS FOUND BETWEEN PTCH HYPERMETHYLATION AND CURRENTLY USED PROGNOSTIC CLL FACTORS. CONCLUSION: OUR INVESTIGATION SUGGESTS THAT EPIGENETIC SILENCING OF PTCH IS A MECHANISM CONTRIBUTING TO CLL TUMORIGENESIS. 2016 18 3296 34 HIGH RESOLUTION INTEGRATIVE ANALYSIS REVEALS WIDESPREAD GENETIC AND EPIGENETIC CHANGES AFTER CHRONIC IN-VITRO ACID AND BILE EXPOSURE IN BARRETT'S EPITHELIUM CELLS. BARRETT'S EPITHELIUM (BE) IS A PREMALIGNANT CONDITION RESULTING FROM CHRONIC GASTROESOPHAGEAL REFLUX THAT MAY PROGRESS TO ESOPHAGEAL ADENOCARCINOMA (EAC). EARLY INTERVENTION HOLDS PROMISE IN PREVENTING BE PROGRESSION. HOWEVER, IDENTIFICATION OF HIGH-RISK BE PATIENTS REMAINS CHALLENGING DUE TO INADEQUATE BIOMARKERS FOR EARLY DIAGNOSIS. WE INVESTIGATED THE EFFECT OF PROLONGED CHRONIC ACID AND BILE EXPOSURE ON TRANSCRIPTOME, METHYLOME, AND MUTATOME OF CELLS IN AN IN-VITRO BE CARCINOGENESIS (BEC) MODEL. TWENTY WEEKS ACID AND BILE EXPOSED CELLS FROM THE BEC MODEL (BEC20W) WERE COMPARED WITH THEIR NAIVE PREDECESSORS HISEQ ILLUMINA BASED RNA SEQUENCING WAS PERFORMED ON RNA FROM BOTH THE CELLS FOR GENE EXPRESSION AND MUTATIONAL ANALYSIS. HELP TAGGING ASSAY WAS PERFORMED FOR DNA METHYLATION ANALYSIS. INGENUITY PATHWAY, GENE ONTOLOGY, AND KEGG PATHWAY ANALYSES WERE THEN PERFORMED ON DATASETS. WIDESPREAD ABERRANT GENETIC AND EPIGENETIC CHANGES WERE OBSERVED IN THE BEC20W CELLS. COMBINATORIAL ANALYSES REVEALED 433 FROM A TOTAL OF 863 DOWNREGULATED GENES HAD ACCOMPANYING HYPERMETHYLATION OF PROMOTERS. SIMULTANEOUSLY, 690 GENES FROM A TOTAL OF 1,492 WERE UPREGULATED WITH ACCOMPANYING PROMOTER HYPOMETHYLATION. IN ADDITION, 763 MUTATIONS WERE IDENTIFIED ON 637 GENES. INGENUITY PATHWAY ANALYSIS, GENE ONTOLOGY, AND KEGG PATHWAY ANALYSES ASSOCIATED THE GENETIC AND EPIGENETIC CHANGES IN BEC20W CELLS WITH CELLULAR AND BIOLOGICAL FUNCTIONS. INTEGRATION OF HIGH RESOLUTION COMPARATIVE ANALYSES OF NAIVE BAR-T AND BEC20W CELLS REVEALED STRIKING GENETIC AND EPIGENETIC CHANGES INDUCED BY CHRONIC ACID AND BILE EXPOSURE THAT MAY DISRUPT NORMAL CELLULAR FUNCTIONS AND PROMOTE CARCINOGENESIS. THIS NOVEL STUDY REVEALS SEVERAL POTENTIAL TARGETS FOR FUTURE BIOMARKERS AND THERAPEUTIC DEVELOPMENT. 2013 19 411 36 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 20 2453 35 EPIGENETIC SUPPRESSION OF THE IMMUNOREGULATOR MZB1 IS ASSOCIATED WITH THE MALIGNANT PHENOTYPE OF GASTRIC CANCER. PREDICTION OF TUMOR RECURRENCE AFTER CURATIVE RESECTION IS CRITICAL FOR DETERMINING THE PROGNOSIS OF PATIENTS WITH GASTRIC CANCER (GC). THE INITIATION AND PROGRESSION OF GC ARE ASSOCIATED WITH INAPPROPRIATE IMMUNE RESPONSES CAUSED BY CHRONIC INFLAMMATION OF THE GASTRIC MUCOSA. TO IDENTIFY IMMUNOREGULATORY MOLECULES INVOLVED IN GC PROGRESSION, GC CELL LINES AND 200 PAIRS OF TUMOR AND NORMAL TISSUES FROM PATIENTS WITH GC WERE ANALYZED FOR GENE EXPRESSION, AMPLIFICATION AND METHYLATION AS WELL AS FUNCTION OF A DIFFERENTIALLY EXPRESSED GENE. THE TRANSCRIPTOME ANALYSIS REVEALED THAT MARGINAL ZONE B AND B1 CELL SPECIFIC PROTEIN (MZB1) WAS EXPRESSED AT SIGNIFICANTLY DECREASED LEVELS IN PRIMARY GC TISSUES WHEN COMPARED WITH THE CORRESPONDING NORMAL GASTRIC MUCOSA. PCR ARRAY ANALYSIS EXPLORING GENES EXPRESSED COOPERATIVELY WITH MZB1 REVEALED THAT DIFFERENTIAL EXPRESSION OF MZB1 MRNA IN GC CELL LINES CORRELATED POSITIVELY WITH THE LEVELS OF THE MRNAS ENCODING ESTROGEN RECEPTOR 1 AND DESUMOYLATING ISOPEPTIDASE 1. HYPERMETHYLATION OF THE MZB1 PROMOTER WAS FREQUENT IN CELL LINES WITH DECREASED LEVELS OF MZB1 MRNA. SIRNA-MEDIATED KNOCKDOWN OF MZB1 SIGNIFICANTLY INCREASED PROLIFERATION, INVASION AND MIGRATION OF GC CELL LINES. LOW MZB1 EXPRESSION WAS AN INDEPENDENT PROGNOSTIC FACTOR FOR RECURRENCE AFTER CURATIVE GASTRECTOMY AND WAS ASSOCIATED SIGNIFICANTLY WITH INCREASED HEMATOGENOUS RECURRENCE. MZB1 ACTS AS A SUPPRESSOR OF GC. LOW MZB1 EXPRESSION IN THE PRIMARY GC TISSUE IS PREDICTIVE OF RECURRENCE AFTER CURATIVE RESECTION. 2016