1 1499 113 DNA METHYLATION ANALYSIS IN NONALCOHOLIC FATTY LIVER DISEASE SUGGESTS DISTINCT DISEASE-SPECIFIC AND REMODELING SIGNATURES AFTER BARIATRIC SURGERY. NONALCOHOLIC FATTY LIVER DISEASE (NAFLD) IS THE MOST COMMON CHRONIC LIVER DISORDER IN INDUSTRIALIZED COUNTRIES. LIVER SAMPLES FROM MORBIDLY OBESE PATIENTS (N = 45) WITH ALL STAGES OF NAFLD AND CONTROLS (N = 18) WERE ANALYZED BY ARRAY-BASED DNA METHYLATION AND MRNA EXPRESSION PROFILING. NAFLD-SPECIFIC EXPRESSION AND METHYLATION DIFFERENCES WERE SEEN FOR NINE GENES CODING FOR KEY ENZYMES IN INTERMEDIATE METABOLISM (INCLUDING PC, ACLY, AND PLCG1) AND INSULIN/INSULIN-LIKE SIGNALING (INCLUDING IGF1, IGFBP2, AND PRKCE) AND REPLICATED BY BISULFITE PYROSEQUENING (INDEPENDENT N = 39). TRANSCRIPTION FACTOR BINDING SITES AT NAFLD-SPECIFIC CPG SITES WERE >1,000-FOLD ENRICHED FOR ZNF274, PGC1A, AND SREBP2. INTRAINDIVIDUAL COMPARISON OF LIVER BIOPSIES BEFORE AND AFTER BARIATRIC SURGERY SHOWED NAFLD-ASSOCIATED METHYLATION CHANGES TO BE PARTIALLY REVERSIBLE. POSTBARIATRIC AND NAFLD-SPECIFIC METHYLATION SIGNATURES WERE CLEARLY DISTINCT BOTH IN GENE ONTOLOGY AND TRANSCRIPTION FACTOR BINDING SITE ANALYSES, WITH >400-FOLD ENRICHMENT OF NRF1, HSF1, AND ESRRA SITES. OUR FINDINGS PROVIDE AN EXAMPLE OF TREATMENT-INDUCED EPIGENETIC ORGAN REMODELING IN HUMANS. 2013 2 3354 34 HISTONE DEMETHYLATION PROFILES IN NONALCOHOLIC FATTY LIVER DISEASE AND PROGNOSTIC VALUES IN HEPATOCELLULAR CARCINOMA: A BIOINFORMATIC ANALYSIS. NONALCOHOLIC FATTY LIVER DISEASE (NAFLD) IS THE MOST COMMON CHRONIC LIVER DISEASE WITH MULTIFACTORIAL PATHOGENESIS; HISTONE DEMETHYLASES (HDMS) ARE EMERGING AS ATTRACTIVE TARGETS. WE IDENTIFIED HDM GENES (INCLUDING KDM5C, KDM6B, KDM8, KDM4A, AND JMJD7) THAT WERE DIFFERENTIALLY EXPRESSED IN NAFLD AND NORMAL SAMPLES BY EXPLORING GENE EXPRESSION PROFILING DATASETS. THERE WAS NO SIGNIFICANT DIFFERENCE IN THE EXPRESSION OF GENES RELATED TO HISTONE DEMETHYLATION BETWEEN MILD AND ADVANCED NAFLD. IN VITRO AND IN VIVO STUDIES INDICATED THAT KDM6B AND JMJD7 WERE UPREGULATED AT THE MRNA LEVEL IN NAFLD. WE EXPLORED THE EXPRESSION LEVELS AND PROGNOSTIC VALUES OF THE IDENTIFIED HDM GENES IN HEPATOCELLULAR CARCINOMA (HCC). KDM5C AND KDM4A WERE UPREGULATED IN HCC COMPARED TO NORMAL TISSUE, WHILE KDM8 SHOWED DOWNREGULATION. THE ABNORMAL EXPRESSION LEVELS OF THESE HDMS COULD PROVIDE PROGNOSTIC VALUES. FURTHERMORE, KDM5C AND KDM4A WERE ASSOCIATED WITH IMMUNE CELL INFILTRATION IN HCC. HDMS WERE ASSOCIATED WITH CELLULAR AND METABOLIC PROCESSES AND MAY BE INVOLVED IN THE REGULATION OF GENE EXPRESSION. DIFFERENTIALLY EXPRESSED HDM GENES IDENTIFIED IN NAFLD MAY PROVIDE VALUE TO UNDERSTANDING PATHOGENESIS AND IN THE DEVELOPMENT OF EPIGENETIC THERAPEUTIC TARGETS. HOWEVER, ON THE BASIS OF THE INCONSISTENT RESULTS OF IN VITRO STUDIES, FUTURE IN VIVO EXPERIMENTS COMBINED WITH TRANSCRIPTOMIC ANALYSIS ARE NEEDED FOR FURTHER VALIDATION. 2023 3 3084 22 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 4 2809 33 FGF1 AMELIORATES OBESITY-ASSOCIATED HEPATIC STEATOSIS BY REVERSING IGFBP2 HYPERMETHYLATION. OBESITY IS A MAJOR CONTRIBUTING FACTOR FOR METABOLIC-ASSOCIATED FATTY LIVER DISEASE (MAFLD). FIBROBLAST GROWTH FACTOR (FGF) 1 IS THE FIRST PARACRINE FGF FAMILY MEMBER IDENTIFIED TO EXHIBIT PROMISING METABOLIC REGULATORY PROPERTIES CAPABLE OF CONFERRING GLUCOSE-LOWERING AND INSULIN-SENSITIZING EFFECT. THIS STUDY EXPLORES THE ROLE AND MOLECULAR UNDERPINNINGS OF FGF1 IN OBESITY-ASSOCIATED HEPATIC STEATOSIS. IN A MOUSE HIGH-FAT DIET (HFD)-INDUCED MAFLD MODEL, CHRONIC TREATMENT WITH RECOMBINANT FGF1(RFGF1) WAS FOUND TO EFFECTIVELY REDUCE THE SEVERITY OF INSULIN RESISTANCE, HYPERLIPIDEMIA, AND INFLAMMATION. FGF1 TREATMENT DECREASED LIPID ACCUMULATION IN THE MOUSE LIVER AND PALMITIC ACID-TREATED AML12 CELLS. THESE EFFECTS WERE ASSOCIATED WITH DECREASED MATURE FORM SREBF1 EXPRESSION AND ITS TARGET GENES FASN AND SCD1. INTERESTINGLY, WE UNCOVERED THAT RFGF1 SIGNIFICANTLY INDUCED IGFBP2 EXPRESSION AT BOTH MRNA AND PROTEIN LEVELS IN HFD-FED MOUSE LIVERS AND CULTURED HEPATOCYTES TREATED WITH PALMITIC ACID. ADENO-ASSOCIATED VIRUS-MEDIATED IGFBP2 SUPPRESSION SIGNIFICANTLY DIMINISHED THE THERAPEUTIC BENEFIT OF RFGF1 ON MAFLD-ASSOCIATED PHENOTYPES, INDICATING THAT IGFBP2 PLAYS A CRUCIAL ROLE IN THE FGF1-MEDIATED REDUCTION OF HEPATIC STEATOSIS. FURTHER ANALYSIS REVEALED THAT RFGF1 TREATMENT REDUCES THE RECRUITMENT OF DNA METHYLTRANSFERASE 3 ALPHA TO THE IGFBP2 GENOMIC LOCUS, LEADING TO DECREASED IGFBP2 GENE METHYLATION AND INCREASED MRNA AND PROTEIN EXPRESSION. COLLECTIVELY, OUR FINDINGS REVEAL FGF1 MODULATION OF LIPID METABOLISM VIA EPIGENETIC REGULATION OF IGFBP2 EXPRESSION, AND UNRAVEL THE THERAPEUTIC POTENTIAL OF THE FGF1-IGFBP2 AXIS IN METABOLIC DISEASES ASSOCIATED WITH OBESITY. 2023 5 658 30 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 6 1590 31 DNA METHYLATION PROFILING IN HUMAN LUNG TISSUE IDENTIFIES GENES ASSOCIATED WITH COPD. CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS A SMOKING-RELATED DISEASE CHARACTERIZED BY GENETIC AND PHENOTYPIC HETEROGENEITY. ALTHOUGH ASSOCIATION STUDIES HAVE IDENTIFIED MULTIPLE GENOMIC REGIONS WITH REPLICATED ASSOCIATIONS TO COPD, GENETIC VARIATION ONLY PARTIALLY EXPLAINS THE SUSCEPTIBILITY TO LUNG DISEASE, AND SUGGESTS THE RELEVANCE OF EPIGENETIC INVESTIGATIONS. WE PERFORMED GENOME-WIDE DNA METHYLATION PROFILING IN HOMOGENIZED LUNG TISSUE SAMPLES FROM 46 CONTROL SUBJECTS WITH NORMAL LUNG FUNCTION AND 114 SUBJECTS WITH COPD, ALL FORMER SMOKERS. THE DIFFERENTIALLY METHYLATED LOCI WERE INTEGRATED WITH PREVIOUS GENOME-WIDE ASSOCIATION STUDY RESULTS. THE TOP 535 DIFFERENTIALLY METHYLATED SITES, FILTERED FOR A MINIMUM MEAN METHYLATION DIFFERENCE OF 5% BETWEEN CASES AND CONTROLS, WERE ENRICHED FOR CPG SHELVES AND SHORES. PATHWAY ANALYSIS REVEALED ENRICHMENT FOR TRANSCRIPTION FACTORS. THE TOP DIFFERENTIALLY METHYLATED SITES FROM THE INTERSECTION WITH PREVIOUS GWAS WERE IN CHRM1, GLT1D1, AND C10ORF11; SORTED BY GWAS P-VALUE, THE TOP SITES INCLUDED FRMD4A, THSD4, AND C10ORF11. EPIGENETIC ASSOCIATION STUDIES COMPLEMENT GENETIC ASSOCIATION STUDIES TO IDENTIFY GENES POTENTIALLY INVOLVED IN COPD PATHOGENESIS. ENRICHMENT FOR GENES IMPLICATED IN ASTHMA AND LUNG FUNCTION AND FOR TRANSCRIPTION FACTORS SUGGESTS THE POTENTIAL PATHOGENIC RELEVANCE OF GENES IDENTIFIED THROUGH DIFFERENTIAL METHYLATION AND THE INTERSECTION WITH A BROADER RANGE OF GWAS ASSOCIATIONS. 2016 7 3296 27 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 8 3125 24 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 9 3764 30 INTEGRATIVE ANALYSIS OF DNA METHYLATION AND GENE EXPRESSION DATA IDENTIFIES EPAS1 AS A KEY REGULATOR OF COPD. CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS A COMPLEX DISEASE. GENETIC, EPIGENETIC, AND ENVIRONMENTAL FACTORS ARE KNOWN TO CONTRIBUTE TO COPD RISK AND DISEASE PROGRESSION. THEREFORE WE DEVELOPED A SYSTEMATIC APPROACH TO IDENTIFY KEY REGULATORS OF COPD THAT INTEGRATES GENOME-WIDE DNA METHYLATION, GENE EXPRESSION, AND PHENOTYPE DATA IN LUNG TISSUE FROM COPD AND CONTROL SAMPLES. OUR INTEGRATIVE ANALYSIS IDENTIFIED 126 KEY REGULATORS OF COPD. WE IDENTIFIED EPAS1 AS THE ONLY KEY REGULATOR WHOSE DOWNSTREAM GENES SIGNIFICANTLY OVERLAPPED WITH MULTIPLE GENES SETS ASSOCIATED WITH COPD DISEASE SEVERITY. EPAS1 IS DISTINCT IN COMPARISON WITH OTHER KEY REGULATORS IN TERMS OF METHYLATION PROFILE AND DOWNSTREAM TARGET GENES. GENES PREDICTED TO BE REGULATED BY EPAS1 WERE ENRICHED FOR BIOLOGICAL PROCESSES INCLUDING SIGNALING, CELL COMMUNICATIONS, AND SYSTEM DEVELOPMENT. WE CONFIRMED THAT EPAS1 PROTEIN LEVELS ARE LOWER IN HUMAN COPD LUNG TISSUE COMPARED TO NON-DISEASE CONTROLS AND THAT EPAS1 GENE EXPRESSION IS REDUCED IN MICE CHRONICALLY EXPOSED TO CIGARETTE SMOKE. AS EPAS1 DOWNSTREAM GENES WERE SIGNIFICANTLY ENRICHED FOR HYPOXIA RESPONSIVE GENES IN ENDOTHELIAL CELLS, WE TESTED EPAS1 FUNCTION IN HUMAN ENDOTHELIAL CELLS. EPAS1 KNOCKDOWN BY SIRNA IN ENDOTHELIAL CELLS IMPACTED GENES THAT SIGNIFICANTLY OVERLAPPED WITH EPAS1 DOWNSTREAM GENES IN LUNG TISSUE INCLUDING HYPOXIA RESPONSIVE GENES, AND GENES ASSOCIATED WITH EMPHYSEMA SEVERITY. OUR FIRST INTEGRATIVE ANALYSIS OF GENOME-WIDE DNA METHYLATION AND GENE EXPRESSION PROFILES ILLUSTRATES THAT NOT ONLY DOES DNA METHYLATION PLAY A 'CAUSAL' ROLE IN THE MOLECULAR PATHOPHYSIOLOGY OF COPD, BUT IT CAN BE LEVERAGED TO DIRECTLY IDENTIFY NOVEL KEY MEDIATORS OF THIS PATHOPHYSIOLOGY. 2015 10 155 20 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 1846 20 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 12 3583 30 IMPACT OF SHORT- AND LONG-TERM ELECTRICALLY INDUCED MUSCLE EXERCISE ON GENE SIGNALING PATHWAYS, GENE EXPRESSION, AND PGC1A METHYLATION IN MEN WITH SPINAL CORD INJURY. EXERCISE ATTENUATES THE DEVELOPMENT OF CHRONIC NONCOMMUNICABLE DISEASES (NCDS). GENE SIGNALING PATHWAY ANALYSIS OFFERS AN OPPORTUNITY TO DISCOVER IF ELECTRICALLY INDUCED MUSCLE EXERCISE REGULATES KEY PATHWAYS AMONG PEOPLE LIVING WITH SPINAL CORD INJURY (SCI). WE EXAMINED SHORT-TERM AND LONG-TERM DURATIONS OF ELECTRICALLY INDUCED SKELETAL MUSCLE EXERCISE ON COMPLEX GENE SIGNALING PATHWAYS, SPECIFIC GENE REGULATION, AND EPIGENETIC TAGGING OF PGC1A, A MAJOR TRANSCRIPTION FACTOR IN SKELETAL MUSCLE OF MEN WITH SCI. AFTER SHORT- OR LONG-TERM ELECTRICALLY INDUCED EXERCISE TRAINING, PARTICIPANTS UNDERWENT BIOPSIES OF THE TRAINED AND UNTRAINED MUSCLES. RNA WAS HYBRIDIZED TO AN EXON MICROARRAY AND ANALYZED BY A GENE SET ENRICHMENT ANALYSIS. WE DISCOVERED THAT LONG-TERM EXERCISE TRAINING REGULATED THE REACTOME GENE SETS FOR METABOLISM (38 GENE SETS), CELL CYCLE (36 GENE SETS), DISEASE (27 GENE SETS), GENE EXPRESSION AND TRANSCRIPTION (22 GENE SETS), ORGANELLE BIOGENESIS (4 GENE SETS), CELLULAR RESPONSE TO STIMULI (8 GENE SETS), IMMUNE SYSTEM (8 GENE SETS), VESICLE-MEDIATED TRANSPORT (4 GENE SETS), AND TRANSPORT OF SMALL MOLECULES (3 GENE SETS). SPECIFIC GENE EXPRESSION INCLUDED: OXIDATIVE CATABOLISM OF GLUCOSE INCLUDING PDHB (P < 0.001), PDHX (P < 0.001), MPC1 (P < 0.009), AND MPC2 (P < 0.007); OXIDATIVE PHOSPHORYLATION GENES INCLUDING SDHA (P < 0.006), SDHB (P < 0.001), NDUFB1 (P < 0.002), NDUFA2 (P < 0.001); TRANSCRIPTION GENES INCLUDING PGC1ALPHA (P < 0.030) AND PRKAB2 (P < 0.011); HYPERTROPHY GENE MSTN (P < 0.001); AND THE MYOKINE GENERATING FNDC5 GENE (P < 0.008). LONG-TERM ELECTRICALLY INDUCED EXERCISE DEMETHYLATED THE MAJOR TRANSCRIPTION FACTOR PGC1A. TAKEN TOGETHER, THESE FINDINGS SUPPORT THAT LONG-TERM ELECTRICALLY INDUCED MUSCLE ACTIVITY REGULATES KEY PATHWAYS ASSOCIATED WITH MUSCLE HEALTH AND SYSTEMIC METABOLISM. 2020 13 1909 32 ENRICHMENT OF GENOMIC PATHWAYS BASED ON DIFFERENTIAL DNA METHYLATION PROFILES ASSOCIATED WITH CHRONIC MUSCULOSKELETAL PAIN IN OLDER ADULTS: AN EXPLORATORY STUDY. OUR STUDY AIMED TO IDENTIFY DIFFERENTIALLY METHYLATED CPGS/REGIONS AND THEIR ENRICHED GENOMIC PATHWAYS ASSOCIATED WITH UNDERLYING CHRONIC MUSCULOSKELETAL PAIN IN OLDER INDIVIDUALS. WE RECRUITED COGNITIVELY HEALTHY OLDER ADULTS WITH (N = 20) AND WITHOUT (N = 9) SELF-REPORTED MUSCULOSKELETAL PAIN AND COLLECTED DNA FROM PERIPHERAL BLOOD THAT WAS ANALYZED USING METHYLATIONEPIC ARRAYS. WE IDENTIFIED 31,739 HYPERMETHYLATED CPG AND 10,811 HYPOMETHYLATED CPG PROBES (PS 25% OF ENRICHMENT SITES ARE FOUND WITHIN, DOWNSTREAM OR BETWEEN ANNOTATED GENES. LESS THAN 10% OF THESE SITES WERE ALTERED IN MIST1(-/-) ACINI, WITH MOST CHANGES IN H3K4ME3 ENRICHMENT NOT REFLECTING ALTERED GENE EXPRESSION. INGENUITY PATHWAY ANALYSIS OF GENES DIFFERENTIALLY-ENRICHED FOR H3K4ME3 REVEALED AN ASSOCIATION WITH PANCREATITIS AND PANCREATIC DUCTAL ADENOCARCINOMA IN MIST1(-/-) TISSUE. MOST OF THESE GENES WERE NOT DIFFERENTIALLY EXPRESSED BUT SEVERAL WERE READILY INDUCED BY ACUTE EXPERIMENTAL PANCREATITIS, WITH SIGNIFICANTLY INCREASED EXPRESSION IN MIST1(-/-) TISSUE RELATIVE TO WILD TYPE MICE. WE SUGGEST THAT THE CHRONIC CELL STRESS OBSERVED IN THE ABSENCE OF MIST1 RESULTS IN EPIGENETIC REPROGRAMMING OF GENES INVOLVED IN PROMOTING PANCREATITIS TO A POISED STATE, THEREBY INCREASING THE SENSITIVITY TO EVENTS THAT PROMOTE DISEASE. 2014 20 5205 27 PRENATAL STRESS CHANGES THE GLYCOPROTEIN GPM6A GENE EXPRESSION AND INDUCES EPIGENETIC CHANGES IN RAT OFFSPRING BRAIN. PRENATAL STRESS (PS) EXERTS STRONG IMPACT ON FETAL BRAIN DEVELOPMENT AND ON ADULT OFFSPRING BRAIN FUNCTIONS. PREVIOUS WORK DEMONSTRATED THAT CHRONIC STRESS ALTERS THE MRNA EXPRESSION OF GPM6A, A NEURONAL GLYCOPROTEIN INVOLVED IN FILOPODIUM EXTENSION. IN THIS WORK, WE ANALYZED THE EFFECT OF PS ON GPM6A EXPRESSION AND THE EPIGENETIC MECHANISMS INVOLVED. PREGNANT WISTAR RATS RECEIVED RESTRAINT STRESS DURING THE LAST WEEK OF GESTATION. MALE OFFSPRING WERE SACRIFICED ON POSTNATAL DAYS 28 AND 60. HIPPOCAMPUS AND PREFRONTAL CORTEX SAMPLES WERE ANALYZED FOR GENE EXPRESSION (QPCR FOR MRNAS AND MICRORNAS), METHYLATION STATUS (BISULFITE CONVERSION) AND PROTEIN LEVELS. HIPPOCAMPAL NEURONS IN CULTURE WERE USED TO ANALYZE MICRORNA OVEREXPRESSION EFFECTS. PRENATAL STRESS INDUCED CHANGES IN GPM6A LEVELS IN BOTH TISSUES AND AT BOTH AGES ANALYZED, INDICATING A PERSISTENT EFFECT. TWO CPG ISLANDS IN THE GPM6A GENE WERE IDENTIFIED. VARIATIONS IN THE METHYLATION PATTERN AT THREE SPECIFIC CPGS WERE FOUND IN HIPPOCAMPUS, BUT NOT IN PFC SAMPLES FROM PS OFFSPRING. MICRORNAS PREDICTED TO TARGET GPM6A WERE IDENTIFIED IN SILICO. QPCR MEASUREMENTS SHOWED THAT PS MODIFIED THE EXPRESSION OF SEVERAL MICRORNAS IN BOTH TISSUES, BEING MICRORNA-133B THE MOST SIGNIFICANTLY ALTERED. FURTHER STUDIES OVEREXPRESSING THIS MICRORNA IN NEURONAL CULTURES SHOWED A REDUCTION IN GMP6A MRNA AND PROTEIN LEVEL. MOREOVER FILOPODIUM DENSITY WAS ALSO REDUCED, SUGGESTING THAT GPM6A FUNCTION WAS AFFECTED. GESTATIONAL STRESS AFFECTED GPM6A GENE EXPRESSION IN OFFSPRING LIKELY THROUGH CHANGES IN METHYLATION STATUS AND IN POSTTRANSCRIPTIONAL REGULATION BY MICRORNAS. THUS, OUR FINDINGS PROPOSE GPM6A AS A NOVEL TARGET FOR EPIGENETIC REGULATION DURING PRENATAL STRESS. 2014