1 6746 132 WHOLE EXOME SEQUENCING OF ULCERATIVE COLITIS-ASSOCIATED COLORECTAL CANCER BASED ON NOVEL SOMATIC MUTATIONS IDENTIFIED IN CHINESE PATIENTS. BACKGROUND: CARCINOGENESIS IS A SEVERE CONSEQUENCE OF CHRONIC ULCERATIVE COLITIS. WE INVESTIGATED THE SOMATIC MUTATIONS AND PATHWAY ALTERATIONS IN ULCERATIVE COLITIS-ASSOCIATED COLORECTAL CANCER (CRC) IN CHINESE PATIENTS COMPARED WITH SPORADIC CRCS TO REVEAL POTENTIAL THERAPEUTIC TARGETS IN ULCERATIVE COLITIS-ASSOCIATED CRC. METHODS: WHOLE EXOME SEQUENCING WAS PERFORMED ON ARCHIVAL TUMOR TISSUES AND PAIRED ADJACENT NONDYSPLASTIC MUCOSA FROM 10 ULCERATIVE COLITIS-ASSOCIATED CRC PATIENTS AT A HIGH RISK OF CARCINOGENESIS. GENOMIC ALTERATION PROFILES FROM 223 PRIMARY CRCS FROM THE CANCER GENOME ATLAS SERVED AS SPORADIC CRC CONTROLS. A META-ANALYSIS WAS PERFORMED TO INVESTIGATE DIFFERENCES IN MAJOR GENETIC MUTATIONS BETWEEN ULCERATIVE COLITIS-ASSOCIATED AND CROHN'S DISEASE-ASSOCIATED CRCS. RESULTS: WE IDENTIFIED 44 NONSILENT RECURRENT SOMATIC MUTATIONS VIA WHOLE EXOME SEQUENCING, INCLUDING 25 DELETERIOUS MUTATIONS INVOLVED IN APOPTOSIS AND THE PI3K-AKT PATHWAY (COL6A3, FN1), AUTOPHAGY (ULK1), CELL ADHESION (PODXL, PTPRT, ZFHX4), AND EPIGENETIC REGULATION (ARID1A, NCOR2, KMT2D, NCOA6, MECP2, SUPT6H). IN TOTAL, 11 OF THE 25 MUTATED GENES SIGNIFICANTLY DIFFERED BETWEEN ULCERATIVE COLITIS-ASSOCIATED CRC AND SPORADIC CRC (APC, APOB, MECP2, NCOR2, NTRK2, PODXL, RABGAP1, SIK3, SUPT6H, ULK1, USP48). SOMATIC TP53 MUTATIONS OCCURRED IN 33% OF ULCERATIVE COLITIS-ASSOCIATED CRCS. SUBSEQUENT META-ANALYSIS REVEALED DISTINCT MUTATION PROFILES FOR CROHN'S DISEASE- AND ULCERATIVE COLITIS-ASSOCIATED CRCS. MUTATIONS INVOLVING THE NF-KB PATHWAY AND EPIGENETIC REGULATION WERE MORE COMMON IN ULCERATIVE COLITIS-ASSOCIATED CRCS THAN IN SPORADIC CRCS. CONCLUSION: DISTINCT GENOMIC ALTERATION PROFILES OF DELETERIOUS SOMATIC MUTATIONS WERE FOUND IN ULCERATIVE COLITIS-ASSOCIATED AND SPORADIC CRCS. MUTATIONS OF EPIGENETIC REGULATORS, SUCH AS KMT2D AND NCOA6, WERE COMMON, SUGGESTING AN EPIGENETIC PATHOMECHANISM FOR COLITIS-ASSOCIATED CARCINOMA IN CHINESE PATIENTS. 2019 2 499 38 ASSOCIATION BETWEEN HMLH1 HYPERMETHYLATION AND JC VIRUS (JCV) INFECTION IN HUMAN COLORECTAL CANCER (CRC). INCORPORATION OF VIRAL DNA MAY INTERFERE WITH THE NORMAL SEQUENCE OF HUMAN DNA BASES ON THE GENETIC LEVEL OR CAUSE SECONDARY EPIGENETIC CHANGES SUCH AS GENE PROMOTER METHYLATION OR HISTONE ACETYLATION. COLORECTAL CANCER (CRC) IS THE SECOND LEADING CAUSE OF CANCER MORTALITY IN THE USA. CHROMOSOMAL INSTABILITY (CIN) WAS ESTABLISHED AS THE KEY MECHANISM IN CANCER DEVELOPMENT. LATER, IT WAS FOUND THAT CRC RESULTS NOT ONLY FROM THE PROGRESSIVE ACCUMULATION OF GENETIC ALTERATIONS BUT ALSO FROM EPIGENETIC CHANGES. JC VIRUS (JCV) IS A CANDIDATE ETIOLOGIC FACTOR IN SPORADIC CRC. IT MAY ACT BY STABILIZING BETA-CATENIN, FACILITATING ITS ENTRANCE TO THE CELL NUCLEUS, INITIALING PROLIFERATION AND CANCER DEVELOPMENT. DIPLOID CRC CELL LINES TRANSFECTED WITH JCV-CONTAINING PLASMIDS DEVELOPED CIN. THIS RESULT PROVIDES DIRECT EXPERIMENTAL EVIDENCE FOR THE ABILITY OF JCV T-AG TO INDUCE CIN IN THE GENOME OF COLONIC EPITHELIAL CELLS. THE ASSOCIATION OF CRC HMLH1 METHYLATION AND TUMOR POSITIVITY FOR JCV WAS RECENTLY DOCUMENTED. JC VIRUS T-AG DNA SEQUENCES WERE FOUND IN 77% OF CRCS AND ARE ASSOCIATED WITH PROMOTER METHYLATION OF MULTIPLE GENES. HMLH1 WAS METHYLATED IN 25 OUT OF 80 CRC PATIENTS POSITIVE FOR T-AG (31%) IN COMPARISON WITH ONLY ONE OUT OF 11 T-AG NEGATIVE CASES (9%). THUS, JCV CAN MEDIATE BOTH CIN AND ABERRANT METHYLATION IN CRC. LIKE OTHER VIRUSES, CHRONIC INFECTION WITH JCV MAY INDUCE CRC BY DIFFERENT MECHANISMS WHICH SHOULD BE FURTHER INVESTIGATED. THUS, GENE PROMOTER METHYLATION INDUCED BY JCV MAY BE AN IMPORTANT PROCESS IN CRC AND THE POLYP-CARCINOMA SEQUENCE. 2011 3 2948 45 GENETIC AND EPIGENETIC CHARACTERISTICS OF INFLAMMATORY BOWEL DISEASE-ASSOCIATED COLORECTAL CANCER. BACKGROUND & AIMS: INFLAMMATORY BOWEL DISEASE (IBD) IS A CHRONIC, RELAPSING INFLAMMATORY DISORDER ASSOCIATED WITH AN ELEVATED RISK OF COLORECTAL CANCER (CRC). IBD-ASSOCIATED CRC (IBD-CRC) MAY REPRESENT A DISTINCT PATHWAY OF TUMORIGENESIS COMPARED TO SPORADIC CRC (SCRC). OUR AIM WAS TO COMPREHENSIVELY CHARACTERIZE IBD-ASSOCIATED TUMORIGENESIS INTEGRATING MULTIPLE HIGH-THROUGHPUT APPROACHES, AND TO COMPARE THE RESULTS WITH IN-HOUSE DATA SETS FROM SCRCS. METHODS: WHOLE-GENOME SEQUENCING, SINGLE NUCLEOTIDE POLYMORPHISM ARRAYS, RNA SEQUENCING, GENOME-WIDE METHYLATION ANALYSIS, AND IMMUNOHISTOCHEMISTRY WERE PERFORMED USING FRESH-FROZEN AND FORMALIN-FIXED TISSUE SAMPLES OF TUMOR AND CORRESPONDING NORMAL TISSUES FROM 31 PATIENTS WITH IBD-CRC. RESULTS: TRANSCRIPTOME-BASED TUMOR SUBTYPING REVEALED THE COMPLETE ABSENCE OF CANONICAL EPITHELIAL TUMOR SUBTYPE ASSOCIATED WITH WNT SIGNALING IN IBD-CRCS, DOMINATED INSTEAD BY MESENCHYMAL STROMA-RICH SUBTYPE. NEGATIVE WNT REGULATORS AXIN2 AND RNF43 WERE STRONGLY DOWN-REGULATED IN IBD-CRCS AND CHROMOSOMAL GAINS AT HNF4A, A NEGATIVE REGULATOR OF WNT-INDUCED EPITHELIAL-MESENCHYMAL TRANSITION (EMT), WERE LESS FREQUENT COMPARED TO SCRCS. ENRICHMENT OF HYPOMETHYLATION AT HNF4ALPHA BINDING SITES WAS DETECTED SOLELY IN SCRC GENOMES. PIGR AND OSMR INVOLVED IN MUCOSAL IMMUNITY WERE DYSREGULATED VIA EPIGENETIC MODIFICATIONS IN IBD-CRCS. GENOME-WIDE ANALYSIS SHOWED SIGNIFICANT ENRICHMENT OF NONCODING MUTATIONS TO 5'UNTRANSLATED REGION OF TP53 IN IBD-CRCS. AS REPORTED PREVIOUSLY, SOMATIC MUTATIONS IN APC AND KRAS WERE LESS FREQUENT IN IBD-CRCS COMPARED TO SCRCS. CONCLUSIONS: DISTINCT MECHANISMS OF WNT PATHWAY DYSREGULATION SKEW IBD-CRCS TOWARD MESENCHYMAL TUMOR SUBTYPE, WHICH MAY AFFECT PROGNOSIS AND TREATMENT OPTIONS. INCREASED OSMR SIGNALING MAY FAVOR THE ESTABLISHMENT OF MESENCHYMAL TUMORS IN PATIENTS WITH IBD. 2021 4 2637 34 EPIGENOME-WIDE STUDY IDENTIFIES EPIGENETIC OUTLIERS IN NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER. NONGENETIC PREDISPOSITION TO COLORECTAL CANCER CONTINUES TO BE DIFFICULT TO MEASURE PRECISELY, HAMPERING EFFORTS IN TARGETED PREVENTION AND SCREENING. EPIGENETIC CHANGES IN THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER CAN SERVE AS A TOOL IN PREDICTING COLORECTAL CANCER OUTCOMES. WE IDENTIFIED EPIGENETIC CHANGES AFFECTING THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER. DNA METHYLATION PROFILING ON NORMAL COLON MUCOSA FROM 77 PATIENTS WITH COLORECTAL CANCER AND 68 CONTROLS IDENTIFIED A DISTINCT SUBGROUP OF NORMALLY-APPEARING MUCOSA WITH MARKEDLY DISRUPTED DNA METHYLATION AT A LARGE NUMBER OF CPGS, TERMED AS "OUTLIER METHYLATION PHENOTYPE" (OMP) AND ARE PRESENT IN 15 OF 77 PATIENTS WITH CANCER VERSUS 0 OF 68 CONTROLS (P < 0.001). SIMILAR FINDINGS WERE ALSO SEEN IN PUBLICLY AVAILABLE DATASETS. COMPARISON OF NORMAL COLON MUCOSA TRANSCRIPTION PROFILES OF PATIENTS WITH OMP CANCER WITH THOSE OF PATIENTS WITH NON-OMP CANCER INDICATES GENES WHOSE PROMOTERS ARE HYPERMETHYLATED IN THE OMP PATIENTS ARE ALSO TRANSCRIPTIONALLY DOWNREGULATED, AND THAT MANY OF THE GENES MOST AFFECTED ARE INVOLVED IN INTERACTIONS BETWEEN EPITHELIAL CELLS, THE MUCUS LAYER, AND THE MICROBIOME. ANALYSIS OF 16S RRNA PROFILES SUGGESTS THAT NORMAL COLON MUCOSA OF OMPS ARE ENRICHED IN BACTERIAL GENERA ASSOCIATED WITH COLORECTAL CANCER RISK, ADVANCED TUMOR STAGE, CHRONIC INTESTINAL INFLAMMATION, MALIGNANT TRANSFORMATION, NOSOCOMIAL INFECTIONS, AND KRAS MUTATIONS. IN CONCLUSION, OUR STUDY IDENTIFIES AN EPIGENETICALLY DISTINCT OMP GROUP IN THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER THAT IS CHARACTERIZED BY A DISRUPTED METHYLOME, ALTERED GENE EXPRESSION, AND MICROBIAL DYSBIOSIS. PROSPECTIVE STUDIES ARE NEEDED TO DETERMINE WHETHER OMP COULD SERVE AS A BIOMARKER FOR AN ELEVATED EPIGENETIC RISK FOR COLORECTAL CANCER DEVELOPMENT. PREVENTION RELEVANCE: OUR STUDY IDENTIFIES AN EPIGENETICALLY DISTINCT OMP GROUP IN THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER THAT IS CHARACTERIZED BY A DISRUPTED METHYLOME, ALTERED GENE EXPRESSION, AND MICROBIAL DYSBIOSIS. IDENTIFICATION OF OMPS IN HEALTHY CONTROLS AND PATIENTS WITH COLORECTAL CANCER WILL LEAD TO PREVENTION AND BETTER PROGNOSIS, RESPECTIVELY. 2022 5 546 31 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 6 5864 27 SUPPRESSION OF ELF4 IN ULCERATIVE COLITIS PREDISPOSES HOST TO COLORECTAL CANCER. ULCERATIVE COLITIS (UC) IS A CHRONIC INFLAMMATORY BOWEL DISEASE, CHARACTERIZED BY RELAPSING AND REMITTING COLON MUCOSAL INFLAMMATION. FOR PATIENTS SUFFERING FROM UC, A HIGHER RISK OF COLON CANCER HAS BEEN WIDELY RECOGNIZED. HERE, WE FOUND THAT ELF4 (-/-) MICE DEVELOPED COLON TUMORS WITH 3 CYCLES OF DEXTRAN SULFATE SODIUM SALT (DSS) TREATMENT ALONE. WE FURTHER SHOWED THAT ELF4 SUPPRESSION WAS PREVALENT IN BOTH PATIENTS WITH UC AND DSS-INDUCED MICE MODELS, AND THIS SUPPRESSION WAS CAUSED BY PROMOTER REGION METHYLATION. ELF4, UPON PARYLATION BY PARP1, TRANSCRIPTIONALLY REGULATED MULTIPLE DNA DAMAGE REPAIR MACHINERY COMPONENTS. CONSISTENTLY, ELF4 DEFICIENCY LEADS TO MORE SEVERE DNA DAMAGE BOTH IN VITRO AND IN VIVO. ORAL ADMINISTRATION OF MONTMORILLONITE POWDER CAN PREVENT THE REDUCTION OF ELF4 IN DSS-INDUCED COLITIS MODELS AND LOWER THE RISK OF COLON TUMOR DEVELOPMENT DURING AZOXYMETHANE (AOM) AND DSS INDUCED COLITIS-ASSOCIATED CANCER (CAC). THESE DATA PROVIDED ADDITIONAL MECHANISM OF CAC INITIATION AND SUPPORTED THE "EPIGENETIC PRIMING MODEL OF TUMOR INITIATION". 2021 7 11 33 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 4516 28 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 9 2453 32 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 10 1990 31 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 11 3125 23 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 12 2088 35 EPIGENETIC DYSREGULATION OF SECRETED FRIZZLED-RELATED PROTEINS IN MYELOPROLIFERATIVE NEOPLASMS COMPLEMENTS THE JAK2V617F-MUTATION. BACKGROUND: SECRETED FRIZZLED-RELATED PROTEINS (SFRPS) ARE ANTAGONISTS OF THE WNT SIGNALING PATHWAY, WHICH PLAYS A CENTRAL ROLE IN STEM CELL MAINTENANCE AND DIFFERENTIATION OF STEM CELLS AND HEMATOPOIETIC PROGENITORS. EPIGENETIC DOWNREGULATION OF SFRPS BY PROMOTER HYPERMETHYLATION HAS BEEN DESCRIBED TO BE INVOLVED IN THE PATHOGENESIS OF HEMATOPOIETIC MALIGNANCIES. THERE IS AN ASSOCIATION BETWEEN ABERRANT WNT SIGNALING AND THE ESTABLISHED CANCER STEM CELL CONCEPT. IN CONTRAST TO BCR-ABL1-POSITIVE CHRONIC MYELOID LEUKEMIA CML, BCR-ABL1-NEGATIVE MYELOPROLIFERATIVE NEOPLASMS (PH-MPN) ARE CHARACTERIZED BY THE FREQUENT OCCURRENCE OF AN AUTOACTIVATING MUTATION IN THE JAK2 TYROSINE KINASE (JAK2V617F) OR OTHER MUTATIONS IN THE JAK-STAT PATHWAY. HOWEVER, PATHOGENETIC MECHANISMS OF JAK2 MUTATED OR UNMUTATED PH-MPN REMAIN NOT COMPLETELY UNDERSTOOD. WE DETERMINED THE PROMOTER METHYLATION STATUS OF SFRP-1, -2, -4, AND -5 IN 57 MPN PATIENT SAMPLES BY METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (PCR) (MSP). JAK2V617F WAS ASSESSED BY ALLELE-SPECIFIC PCR. RESULTS: ABERRANT METHYLATION AMONG PRIMARY MPN SAMPLES WAS 4% FOR SFRP-1, 25% FOR SFRP-2, 2% FOR SFRP-4, AND 0% FOR SFRP-5. HYPERMETHYLATION OF SFRP-2, WHICH WAS THE MOST FREQUENTLY HYPERMETHYLATED GENE IN OUR STUDY, COULD NOT BE CORRELATED TO ANY SPECIFIC MPN SUBTYPE. HOWEVER, WE DETECTED A SIGNIFICANT CORRELATION BETWEEN SFRP-2 METHYLATION AND PRESENCE OF A JAK2V617F MUTATION (P = 0.008). NONE OF THE 10 CML SAMPLES SHOWED ANY SFRP-METHYLATION. CONCLUSIONS: OUR DATA INDICATE THAT EPIGENETIC DYSREGULATION OF THE WNT SIGNALING PATHWAY IS A COMMON EVENT IN MPN WITH ABERRANT METHYLATION OF AT LEAST ONE SFRP BEING DETECTED IN 25% OF THE PRIMARY PATIENT SAMPLES AND IN 30% IF ONLY ACCOUNTING FOR PH-MPN. A SIGNIFICANT CORRELATION BETWEEN SFRP-2 METHYLATION AND PRESENCE OF JAK2V617F IN OUR DATA SUPPORTS THE HYPOTHESIS THAT EPIGENETIC DYSREGULATION MAY BE A COMPLEMENTARY MECHANISM TO GENETIC ABERRATIONS. ABERRANT METHYLATION OF CRUCIAL STEM CELL MAINTENANCE GENES SEEMS TO CONTRIBUTE TO DISEASE PATHOGENESIS IN PH-MPN. 2012 13 6052 25 THE CROHN'S DISEASE ASSOCIATED SNP RS6651252 IMPACTS MYC GENE EXPRESSION IN HUMAN COLONIC EPITHELIAL CELLS. CROHN'S DISEASE (CD) IS A DEBILITATING INFLAMMATORY BOWEL DISEASE (IBD) THAT ARISES FROM CHRONIC INFLAMMATION IN THE GASTROINTESTINAL TRACT. GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE IDENTIFIED OVER 200 SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) THAT ARE ASSOCIATED WITH A PREDISPOSITION FOR DEVELOPING IBD. FOR THE MAJORITY, THE CAUSAL VARIANT AND TARGET GENES AFFECTED ARE UNKNOWN. HERE, WE INVESTIGATED THE CD-ASSOCIATED SNP RS6651252 THAT MAPS TO A GENE DESERT REGION ON CHROMOSOME 8. WE DEMONSTRATE THAT RS6651252 RESIDES WITHIN A WNT RESPONSIVE DNA ENHANCER ELEMENT (WRE) AND THAT THE DISEASE ASSOCIATED ALLELE AUGMENTS BINDING OF THE TCF7L2 TRANSCRIPTION FACTOR TO THIS REGION. USING CRISPR/CAS9 DIRECTED GENE EDITING AND EPIGENETIC MODULATION, WE FIND THAT THE RS6651252 ENHANCER REGULATES EXPRESSION OF THE C-MYC PROTO-ONCOGENE (MYC). FURTHERMORE, WE FOUND MYC TRANSCRIPT LEVELS ARE ELEVATED IN PATIENT-DERIVED COLONIC SEGMENTS HARBORING THE DISEASE-ASSOCIATED ALLELE IN COMPARISON TO THOSE CONTAINING THE ANCESTRAL ALLELE. THESE RESULTS SUGGEST THAT WNT/MYC SIGNALING CONTRIBUTES TO CD PATHOGENESIS AND THAT PATIENTS HARBORING THE DISEASE-ASSOCIATED ALLELE MAY BENEFIT FROM THERAPIES THAT TARGET MYC OR MYC-REGULATED GENES. 2019 14 3296 36 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 15 2974 37 GENETIC AND METHYLATION STATUS OF CDKN2A (P14(ARF)/P16(INK4A)) AND TP53 GENES IN RECURRENT RESPIRATORY PAPILLOMATOSIS. RECURRENT RESPIRATORY PAPILLOMATOSIS (RRP) IS A RARE AND CHRONIC DISEASE AFFECTING THE UPPER AIRWAY WITH PAPILLOMATOUS LESIONS CAUSED BY THE HUMAN PAPILLOMAVIRUS (HPV) INFECTION, ESPECIALLY HPV-6 AND/OR HPV-11 TYPES. LITTLE IS KNOWN ABOUT THE GENETIC AND EPIGENETIC DRIVERS IN RRP PATHOPHYSIOLOGY. FOR THIS PURPOSE, WE ANALYZED 27 PAPILLOMATOUS LESIONS FROM PATIENTS WITH RRP TO EVALUATE SOMATIC MUTATIONS AND METHYLATION STATUS IN CDKN2A (P14(ARF)/P16(INK4A)) AND TP53, WHICH ARE KEY TUMOR SUPPRESSOR GENES FOR THE CELL CYCLE CONTROL. SANGER SEQUENCING ANALYSIS REVEALED ONE SOMATIC MUTATION IN TP53 (C.733_734INSA) AND FOUR MUTATIONS IN CDKN2A (C.-30G > T, C.29_30INSA, C.69DELT, AND C.300C > A). THESE MUTATIONS WERE OBSERVED IN 10 PATIENTS, 6 OF WHICH CARRIED DOUBLE MUTATION. FURTHERMORE, 50% (5/10) OF THESE PATIENTS CARRYING SOMATIC MUTATIONS HAD RRP SEVERITY, REPRESENTING 62.5% (5/8) OF THE SEVERITY CASES IN THIS STUDY, ALBEIT NO SIGNIFICANT ASSOCIATION WAS FOUND BETWEEN SOMATIC MUTATIONS AND DISEASE SEVERITY. METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION ASSAYS REVEALED P14(ARF) PROMOTER HYPERMETHYLATION IN 100% OF CASES, FOLLOWED BY TP53 (96.3%) AND P16(INK4A) (55.6%), SUGGESTING THE INFLUENCE OF HPV IN THE DNA METHYLATION MACHINERY. IN CONCLUSION, SOMATIC MUTATIONS WERE NOT COMMON EVENTS IDENTIFIED IN PATIENTS WITH RRP. HOWEVER, EPIGENETIC MODULATION BY HIGH METHYLATION RATES, PARTICULARLY FOR THE P14(ARF)/TP53 PATHWAY, SEEMS TO BE IN THE COURSE OF RRP DEVELOPMENT. 2022 16 152 30 ABERRANT METHYLATION OF DAPK IN LONG-STANDING ULCERATIVE COLITIS AND ULCERATIVE COLITIS-ASSOCIATED CARCINOMA. DEATH-ASSOCIATED PROTEIN KINASE (DAPK) HAS PRO-APOPTOTIC FUNCTIONS AND PARTICIPATES IN VARIOUS APOPTOTIC SYSTEMS. DAPK ACTS AS A TUMOR SUPPRESSOR, AND ITS INACTIVATION BY PROMOTER HYPERMETHYLATION HAS BEEN FREQUENTLY OBSERVED IN VARIOUS HUMAN CANCERS. AS ALTERATIONS OF PRO-APOPTOTIC GENES MIGHT CAUSE INSTABILITY IN THE BALANCE OF CELL-TURNOVER DURING CHRONIC INFLAMMATORY PROCESSES, EPIGENETIC SILENCING OF DAPK MIGHT BE INVOLVED IN THE CARCINOGENESIS OF ULCERATIVE COLITIS-ASSOCIATED CARCINOMA (UCC). TO EVALUATE THE ROLE OF DAPK IN THE INFLAMMATION-DRIVEN CARCINOGENESIS OF ULCERATIVE COLITIS (UC), WE ANALYZED PROMOTER HYPERMETHYLATION AND PROTEIN EXPRESSION OF DAPK USING METHYLATION-SPECIFIC PCR AND IMMUNOHISTOCHEMISTRY IN 43 UCCS AND PAIRED UC-BACKGROUND MUCOSA, AS WELL AS IN UC-BACKGROUND MUCOSA OF 50 PATIENTS WITHOUT UCC. THE FREQUENCY OF METHYLATION OF DAPK IN UCCS WAS LOW (27.6%) COMPARED TO OVERALL NON-NEOPLASTIC UC-BACKGROUND MUCOSA (48.3%; P=0.02) AND SPORADIC COLORECTAL CARCINOMA (57.4%, P=0.019). THE DIFFERENCE IN THE METHYLATION FREQUENCY IN UC-BACKGROUND MUCOSA IN PATIENTS WITHOUT UCC (54.2%), COMPARED TO THOSE WITH UCC (40.0%), WAS NOT SIGNIFICANT (P=0.141). PROMOTER METHYLATION CORRELATED SIGNIFICANTLY WITH DECREASED DAPK PROTEIN EXPRESSION (P<0.001) AND SEVERITY OF INFLAMMATORY ACTIVITY (P=0.024). IN UNMETHYLATED UC-BACKGROUND MUCOSA, DAPK PROTEIN EXPRESSION INCREASED WITH ACTIVITY OF UC-ASSOCIATED INFLAMMATION, SUGGESTING A PROTECTIVE ROLE OF THE PRO-APOPTOTIC DAPK DURING THE CHRONIC INFLAMMATORY PROCESS OF UC. THUS, INACTIVATION OF DAPK BY PROMOTER HYPERMETHYLATION MIGHT BE CRUCIAL FOR ACCUMULATION OF DNA DAMAGE IN INFLAMED MUCOSA OF UC, AND MIGHT THEREFORE CONTRIBUTE TO THE INITIATION OF THE NEOPLASTIC PROCESS AND DEVELOPMENT OF UC-ASSOCIATED CARCINOMA. 2010 17 6686 28 VALIDATION OF EPIGENETIC MARKERS TO IDENTIFY COLITIS ASSOCIATED CANCER: RESULTS OF MODULE 1 OF THE ENDCAP-C STUDY. BACKGROUND: CHRONIC INFLAMMATION CAUSED BY ULCERATIVE COLITIS (UC) CAUSES A PRO-NEOPLASTIC DRIVE IN THE INFLAMED COLON, LEADING TO A MARKEDLY GREATER RISK OF INVASIVE MALIGNANCY COMPARED TO THE GENERAL POPULATION. DESPITE SURVEILLANCE PROTOCOLS, 50% OF CASES PROCEED TO CANCER BEFORE NEOPLASIA IS DETECTED. THE ENHANCED NEOPLASIA DETECTION AND CANCER PREVENTION IN CHRONIC COLITIS (ENDCAP-C) TRIAL IS AN OBSERVATIONAL MULTI-CENTRE TEST ACCURACY STUDY TO ASCERTAIN THE ROLE OF MOLECULAR MARKERS IN IMPROVING THE DETECTION OF DYSPLASIA. WE AIMED TO VALIDATE PREVIOUSLY IDENTIFIED BIOMARKERS OF NEOPLASIA IN A RETROSPECTIVE COHORT AND CREATE PREDICTIVE MODELS FOR LATER VALIDATION IN A PROSPECTIVE COHORT. METHODS: A RETROSPECTIVE ANALYSIS USING BISULPHITE PYROSEQUENCING OF AN 11 MARKER PANEL (SFRP1, SFRP2, SRP4, SRP5, WIF1, TUBB6, SOX7, APC1A, APC2, MINT1, RUNX3) IN SAMPLES FROM 35 PATIENTS WITH CANCER, 78 WITH DYSPLASIA AND 343 WITHOUT NEOPLASIA UNDERGOING SURVEILLANCE FOR UC ASSOCIATED NEOPLASIA ACROSS 6 MEDICAL CENTRES. PREDICTIVE MODELS FOR UC ASSOCIATED CANCER/DYSPLASIA WERE CREATED IN THE SETTING OF NEOPLASTIC AND NON-NEOPLASTIC MUCOSA. FINDINGS: FOR NEOPLASTIC MUCOSA A FIVE MARKER PANEL (SFRP2, SFRP4, WIF1, APC1A, APC2) WAS ACCURATE IN DETECTING PRE-CANCEROUS AND INVASIVE NEOPLASIA (AUC = 0.83; 95% CI: 0.79, 0.88), AND DYSPLASIA (AUC = 0.88; (0.84, 0.91). FOR NON-NEOPLASTIC MUCOSA A FOUR MARKER PANEL (APC1A, SFRP4, SFRP5, SOX7) HAD MODEST ACCURACY (AUC = 0.68; 95% CI: 0.62,0.73) IN PREDICTING ASSOCIATED BOWEL NEOPLASIA THROUGH THE METHYLATION SIGNATURE OF DISTANT NON-NEOPLASTIC COLONIC MUCOSA. INTERPRETATION: THIS MULTIPLEX METHYLATION MARKER PANEL IS ACCURATE IN THE DETECTION OF ULCERATIVE COLITIS ASSOCIATED DYSPLASIA AND NEOPLASIA AND IS CURRENTLY BEING VALIDATED IN A PROSPECTIVE CLINICAL TRIAL. FUNDING: THE ENDCAP-C STUDY WAS FUNDED BY THE NATIONAL INSTITUTE FOR HEALTH RESEARCH EFFICACY AND MECHANISM EVALUATION (EME) PROGRAMME (11/100/29). 2019 18 2037 32 EPIGENETIC CHANGES OF TIMP-3, GSTP-1 AND 14-3-3 SIGMA GENES AS INDICATION OF STATUS OF CHRONIC INFLAMMATION AND CANCER. OBJECTIVES: THIS STUDY AIMED TO COMPARE THE EPIGENETIC CHANGES VIA HYPERMETHYLATION STATUS OF TIMP-3, GSTP-1 AND 14-3-3SIGMA GENES, BETWEEN HEALTHY SUBJECTS AND PATIENTS WITH REVERSIBLE CHRONIC INFLAMMATORY DISEASE, AND BETWEEN HEALTHY SUBJECTS AND PATIENTS WITH IRREVERSIBLE MALIGNANT DISEASE, TO HIGHLIGHT THE GENETIC CHANGES THAT OCCUR IN THE PROGRESSION FROM AN INFLAMMATORY CONDITION TO IRREVERSIBLE GENETIC CHANGES COMMONLY OBSERVED IN CANCER PATIENTS. METHODS: DNA WAS EXTRACTED FROM THE BLOOD OF 680 HEALTHY SUBJECTS, AND TISSUES AND BLOOD OF 110 PATIENTS WITH CHRONIC INFLAMMATION DISEASE OF THE GUMS, AS WELL AS NEOPLASTIC TISSUES OF 108 BREAST CANCER PATIENTS. METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (PCR) FOR TIMP-3, GSTP-1 AND 14-3-3SIGMA WAS PERFORMED, AND HYPERMETHYLATION STATUS WAS ANALYZED AND COMPARED BETWEEN THE 3 GROUPS. RESULTS: THE HYPERMETHYLATION FREQUENCIES OF TIMP-3 AND GSTP-1 OF REVERSIBLE CHRONIC INFLAMMATORY GUM DISEASE AND THE CONTROL GROUP WERE SIMILAR, BUT BOTH WERE SIGNIFICANTLY LOWER THAN THOSE FOR MALIGNANT DISEASE PATIENTS (P<0.0001). THE METHYLATION FREQUENCY OF 14-3-3SIGMA IN CHRONIC INFLAMMATORY GUM DISEASE WAS HIGHER THAN IN THE CANCER AND CONTROL GROUPS (P<0.0001). THE METHYLATION OF CPG ISLANDS IN TIMP-3 AND GSTP-1 IN CHRONIC INFLAMMATION PATIENTS OCCURRED AS FREQUENTLY AS IN THE CONTROL GROUP, BUT LESS FREQUENTLY THAN IN BREAST CANCER PATIENTS. HOWEVER, THE EPIGENETIC SILENCING OF 14-3-3SIGMA OCCURRED MORE FREQUENTLY IN THE CHRONIC INFLAMMATION GROUP THAN IN CANCER PATIENTS AND HEALTHY CONTROLS. CONCLUSIONS: THE EPIGENETIC SILENCING OF 14-3-3SIGMA MIGHT BE ESSENTIAL FOR CHRONIC INFLAMMATORY GUM DISEASE. THE EPIGENETIC CHANGES PRESENTED IN CHRONIC INFLAMMATION PATIENTS MIGHT DEMONSTRATE AN IRREVERSIBLE DESTRUCTION IN THE TISSUES OR ORGANS SIMILAR TO CANCER. 2014 19 493 20 ASSESSMENT OF P53 AND ATM FUNCTIONALITY IN CHRONIC LYMPHOCYTIC LEUKEMIA BY MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION. THE ATM-P53 DNA-DAMAGE RESPONSE (DDR) PATHWAY HAS A CRUCIAL ROLE IN CHEMORESISTANCE IN CLL, AS INDICATED BY THE ADVERSE PROGNOSTIC IMPACT OF GENETIC ABERRATIONS OF TP53 AND ATM. IDENTIFYING AND DISTINGUISHING TP53 AND ATM FUNCTIONAL DEFECTS HAS BECOME RELEVANT AS EPIGENETIC AND POSTTRANSCRIPTIONAL DYSREGULATION OF THE ATM/P53 AXIS IS INCREASINGLY BEING RECOGNIZED AS THE UNDERLYING CAUSE OF CHEMORESISTANCE. ALSO, SPECIFIC TREATMENTS SENSITIZING TP53- OR ATM-DEFICIENT CLL CELLS ARE EMERGING. WE THEREFORE DEVELOPED A NEW ATM-P53 FUNCTIONAL ASSAY WITH THE AIM TO (I) IDENTIFY AND (II) DISTINGUISH ABNORMALITIES OF TP53 VERSUS ATM AND (III) ENABLE THE IDENTIFICATION OF ADDITIONAL DEFECTS IN THE ATM-P53 PATHWAY. REVERSED TRANSCRIPTASE MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION (RT-MLPA) WAS USED TO MEASURE ATM AND/OR P53-DEPENDENT GENES AT THE RNA LEVEL FOLLOWING DNA DAMAGE USING IRRADIATION. HERE, WE SHOWED THAT THIS ASSAY IS ABLE TO IDENTIFY AND DISTINGUISH THREE SUBGROUPS OF CLL TUMORS (I.E., TP53-DEFECTIVE, ATM-DEFECTIVE AND WT) AND IS ALSO ABLE TO DETECT ADDITIONAL SAMPLES WITH A DEFECTIVE DDR, WITHOUT MOLECULAR ABERRATIONS IN TP53 AND/OR ATM. THESE FINDINGS MAKE THE ATM-P53 RT-MLPA FUNCTIONAL ASSAY A PROMISING PROGNOSTIC TOOL FOR PREDICTING TREATMENT RESPONSES IN CLL. 2015 20 3439 26 HYPERMETHYLATION AND LOSS OF EXPRESSION OF GLUTATHIONE PEROXIDASE-3 IN BARRETT'S TUMORIGENESIS. CHRONIC GASTROESOPHAGEAL REFLUX DISEASE IS A KNOWN RISK FACTOR FOR BARRETT'S ESOPHAGUS (BE), WHICH INDUCES OXIDATIVE MUCOSAL DAMAGE. GLUTATHIONE PEROXIDASE-3 (GPX3) IS A SECRETORY PROTEIN WITH POTENT EXTRACELLULAR ANTIOXIDANT ACTIVITY. IN THIS STUDY, WE HAVE INVESTIGATED THE MRNA AND PROTEIN EXPRESSION OF GPX3, AND EXPLORED PROMOTER HYPERMETHYLATION AS AN EPIGENETIC MECHANISM FOR GPX3 GENE INACTIVATION DURING BARRETT'S CARCINOGENESIS. QUANTITATIVE REAL-TIME REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION ON 42 BARRETT'S ADENOCARCINOMAS (BAS) REVEALED CONSISTENTLY REDUCED LEVELS OF GPX3 MRNA IN 91% OF TUMOR SAMPLES. GPX3 PROMOTER HYPERMETHYLATION WAS DETECTED IN 62% OF BARRETT'S METAPLASIA, 82% OF DYSPLASIA, AND 88% OF BA SAMPLES. HYPERMETHYLATION OF BOTH ALLELES OF GPX3 WAS MOST FREQUENTLY SEEN IN BAS (P = .001). IMMUNOHISTOCHEMICAL STAINING OF GPX3 IN MATCHING TISSUE SECTIONS (NORMAL, BE, BARRETT'S DYSPLASIA, AND BA) REVEALED STRONG IMMUNOSTAINING FOR GPX3 IN NORMAL ESOPHAGEAL AND GASTRIC TISSUES. HOWEVER, WEAK TO ABSENT GPX3 STAINING WAS OBSERVED IN BARRETT'S DYSPLASIA AND ADENOCARCINOMA SAMPLES WHERE THE PROMOTER WAS HYPERMETHYLATED. THE DEGREE OF LOSS OF IMMUNOHISTOCHEMISTRY CORRELATED WITH THE HYPERMETHYLATION PATTERN (MONOALLELIC VERSUS BIALLELIC). THE OBSERVED HIGH FREQUENCY OF PROMOTER HYPERMETHYLATION AND PROGRESSIVE LOSS OF GPX3 EXPRESSION IN BA AND ITS ASSOCIATED LESIONS, TOGETHER WITH ITS KNOWN FUNCTION AS A POTENT ANTIOXIDANT, SUGGEST THAT EPIGENETIC INACTIVATION AND REGULATION OF GLUTATHIONE PATHWAY MAY BE CRITICAL IN THE DEVELOPMENT AND PROGRESSION OF BE. 2005