1 2843 153 FREQUENT CPG ISLAND METHYLATION IN PRECURSOR LESIONS AND EARLY GASTRIC ADENOCARCINOMAS. GASTRIC CARCINOGENESIS INVOLVES MULTIPLE GENETIC AND EPIGENETIC ALTERATIONS. EPIGENETIC SILENCING OF TUMOR-RELATED GENES DUE TO CPG ISLAND METHYLATION (CIM) HAS BEEN RECENTLY REPORTED IN GASTRIC CANCER, BUT THE ROLE IN PRECURSOR LESIONS IS NOT WELL UNDERSTOOD. WE ANALYSED THE METHYLATION STATUS OF THE TUMOR SUPPRESSOR GENE P16, THE DNA MISMATCH REPAIR GENE HMLH1, AND FOUR CPG ISLANDS (MINT1, MINT2, MINT25, AND MINT31) USING METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION IN 35 POLYPOID ADENOMAS AND 46 FLAT DYSPLASIAS UNASSOCIATED WITH CARCINOMA, 34 EARLY ADENOCARCINOMAS (T1N0M0) AND ASSOCIATED ADENOMAS/DYSPLASIAS, AND CORRESPONDING ADJACENT NON-NEOPLASTIC MUCOSA. THE EXTENT OF CIM WAS DEFINED BY THE FRACTION OF METHYLATED LOCI (METHYLATION INDEX), AND COMPARED WITH PREVIOUSLY CHARACTERIZED GENETIC ALTERATIONS (MICROSATELLITE INSTABILITY (MSI) AND APC GENE MUTATION). WE FOUND THAT METHYLATION OF P16 WAS MORE FREQUENT IN ADENOCARCINOMA-ASSOCIATED DYSPLASIAS/ADENOMAS (29%) AND ADENOCARCINOMAS (44%) AS COMPARED TO FLAT DYSPLASIAS (4%) AND ADENOMAS (18%) UNASSOCIATED WITH ADENOCARCINOMA (P=0.001). THE MEAN METHYLATION INDEX INCREASED FROM NORMAL/CHRONIC GASTRITIS (CG) MUCOSA (0.09) TO INTESTINAL METAPLASIA (IM) (0.16), FLAT DYSPLASIAS (0.40) OR POLYPOID ADENOMAS (0.41) UNASSOCIATED WITH CARCINOMA, DYSPLASIAS/ADENOMAS ASSOCIATED WITH CARCINOMA (0.44), AND ADENOCARCINOMAS (0.44). THERE WAS NO DIFFERENCE IN FREQUENCIES OF HIGH-LEVEL CPG ISLAND METHYLATION (CIM-H, METHYLATION INDEX > OR =0.5) AMONG FLAT DYSPLASIAS (50%) AND POLYPOID ADENOMAS (51%) UNASSOCIATED WITH CARCINOMA, DYSPLASIAS/ADENOMAS ASSOCIATED WITH ADENOCARCINOMA (47%), AND ADENOCARCINOMA (47%). CIM-H WAS PRESENT IN 15% OF IM, BUT NOT IN NORMAL/CG MUCOSA. THERE WAS A SIGNIFICANT CORRELATION BETWEEN METHYLATION OF HMLH1 AND HIGH-LEVEL OF MICROSATELLITE INSTABILITY (MSI-H): METHYLATION OF HMLH1 WAS PRESENT IN 71% OF MSI-H TUMORS, BUT ONLY 8% OF MSI-LOW TUMORS AND 13% OF MICROSATELLITE-STABLE TUMORS (P=0.0001). THERE WAS NO STATISTICAL DIFFERENCE BETWEEN METHYLATION INDEX AND APC MUTATION. OUR RESULTS INDICATE THAT CONCURRENT PROMOTER METHYLATION IS AN EARLY AND FREQUENT EVENT IN GASTRIC TUMORIGENESIS, INCLUDING BOTH MSI-H AND MICROSATELLITE-STABLE NEOPLASMS. METHYLATION OF THE P16 GENE MAY CONTRIBUTE TO THE MALIGNANT TRANSFORMATION OF GASTRIC PRECURSOR LESIONS.	2004	

2 4232  48 METHYLATION OF RUNX3 IN VARIOUS TYPES OF HUMAN CANCERS AND PREMALIGNANT STAGES OF GASTRIC CARCINOMA. ACCUMULATING EVIDENCE HAS IDENTIFIED A MECHANISM POTENTIALLY RESPONSIBLE FOR THE INACTIVATION OF TUMOR SUPPRESSOR GENES, NAMELY TRANSCRIPTIONAL SILENCING BY ABERRANT METHYLATION OF CPG ISLANDS. A PREVIOUS STUDY HAS SHOWN THE LOSS OF RUNX3 EXPRESSION, DUE TO ABERRANT METHYLATION OF ITS CPG ISLAND, IN GASTRIC CANCER CELL LINES, SUGGESTING THAT RUNX3 IS A TARGET FOR EPIGENETIC GENE SILENCING IN GASTRIC CARCINOGENESIS. HOWEVER, THERE ARE LIMITED DATA ON THE METHYLATION STATUS OF RUNX3 IN THE NEOPLASTIC AND NON-NEOPLASTIC TISSUES IN VARIOUS TYPES OF HUMAN CANCERS, INCLUDING GASTRIC CANCER. HERE, WE REPORT THAT 60% OF GASTRIC CANCER CELL LINES AND 64% OF PRIMARY GASTRIC CARCINOMAS (N=75) WERE METHYLATED AT THE RUNX3 CPG ISLAND. RUNX3 METHYLATION WAS ALSO DETECTED IN HEPATOCELLULAR CARCINOMAS (73%, N=48), LARYNX CANCERS (62%, N=37), LUNG CANCERS (46%, N=24), BREAST CANCERS (25%, N=25), PROSTATE CANCERS (23%, N=44), ENDOMETRIAL CANCERS (12.5%, N=24), COLON CANCERS (4.9%, N=61) AND UTERINE CERVICAL CANCERS (2.5%, N=40), SHOWING THAT RUNX3 METHYLATION IS NOT RESTRICTED TO GASTRIC CANCER. INTERESTINGLY, THE RUNX3 METHYLATION WAS ESPECIALLY FREQUENT IN TUMORS FROM TISSUES OF A FOREGUT DERIVATIVE, THAT IS, THE STOMACH, LIVER, LARYNX AND LUNG. NEXT, THE METHYLATION STATUS OF RUNX3 IN VARIOUS NON-NEOPLASTIC TISSUES WAS EXAMINED, INCLUDING THE PREMALIGNANT LESIONS OF GASTRIC CARCINOMAS. THE RUNX3 METHYLATION WAS FOUND IN 8.1% OF CHRONIC GASTRITIS (N=99), 28.1% OF INTESTINAL METAPLASIA (N=32), 27.3% OF GASTRIC ADENOMAS (N=77) AND 64% OF GASTRIC CARCINOMAS (N=75), BUT NOT IN CHRONIC HEPATITIS B, NORMAL PROSTATE AND COLON MUCOSA, EVEN THOUGH IN CASES OF CHRONIC HEPATITIS, THE METHYLATION FREQUENCY OF ITS NEOPLASTIC TISSUES WAS VERY HIGH. IN CONCLUSION, RUNX3 METHYLATION IS FREQUENTLY FOUND IN HUMAN CANCERS, INCLUDING GASTRIC CANCER, AND IS MOSTLY CANCER SPECIFIC, WITH THE EXCEPTION OF THE STOMACH, AND THUS, MIGHT BE USEFUL AS A POTENTIAL DIAGNOSTIC BIOMARKER OF CANCER.	2004	
                                                                                                                                                                                                                                                                                                                                                                    
3  185  42 ACCUMULATION OF ABERRANT CPG HYPERMETHYLATION BY HELICOBACTER PYLORI INFECTION PROMOTES DEVELOPMENT AND PROGRESSION OF GASTRIC MALT LYMPHOMA. ABERRANT DNA HYPERMETHYLATION IS AN IMPORTANT MECHANISM FOR THE INACTIVATION OF TUMOR-RELATED GENES IN HUMAN TUMORS. GASTRIC MUCOSA-ASSOCIATED LYMPHOID TISSUE (MALT) LYMPHOMAS ARISE FROM HELICOBACTER PYLORI-ASSOCIATED CHRONIC GASTRITIS; MOST PATIENTS ARE H. PYLORI-POSITIVE AND ERADICATION THERAPY IS HIGHLY EFFECTIVE. IN THE PRESENT STUDY, WE USED METHYLATION-SPECIFIC PCR TO ANALYZE THE DNA METHYLATION STATUS OF 11 TUMOR-RELATED GENES (KIP2, P16, HMLH-1, P15, P73, MGMT, DAPK, MINT1, MINT2, MINT31 AND HCAD) IN 21 SPECIMENS OF MALT LYMPHOMA, 5 SPECIMENS OF MALT LYMPHOMA WITH LARGE CELL COMPONENT (HIGH-GRADE MALT LYMPHOMA), 15 SPECIMENS OF DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL), 8 SPECIMENS OF COMPLETE REMISSION OF MALT LYMPHOMA AFTER ERADICATION THERAPY, 5 SPECIMENS WITH NO EVIDENCE OF MALIGNANCY AND PBMCS FROM 10 HEALTHY DONORS. THE AVERAGE NUMBER OF METHYLATED GENES WAS SIGNIFICANTLY GREATER IN GASTRIC LYMPHOMAS AS COMPARED TO NORMAL CONTROLS (P<0.001). THE CPG ISLAND METHYLATOR PHENOTYPE (CIMP) WAS OBSERVED IN 93.3% (14/15) OF DLBCLS, 100% (5/5) OF HIGH-GRADE MALT LYMPHOMAS AND 61.9% (13/21) OF MALT LYMPHOMAS; IN CONTRAST, CIMP WAS NOT FOUND IN THE CONTROL GROUP (0%). THE AVERAGE NUMBER OF METHYLATED GENES AND THE CIMP INCIDENCE SIGNIFICANTLY INCREASED WITH H. PYLORI INFECTION. FURTHERMORE, ABERRANT CPG METHYLATION OF SPECIFIC GENES, SUCH AS P16, MGMT AND MINT31, WAS CONSISTENTLY ASSOCIATED WITH H. PYLORI INFECTION. THESE FINDINGS STRONGLY SUGGEST THAT H. PYLORI INFECTION CAUSES THE ABERRANT DNA HYPERMETHYLATION OF SPECIFIC GENES AND INDUCES CIMP, WHICH IS AN IMPORTANT EPIGENETIC MECHANISM FOR THE DEVELOPMENT AND PROGRESSION OF GASTRIC MALT LYMPHOMA; ADDITIONALLY, OUR FINDINGS PROVIDE NEW EPIGENETIC MARKERS.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
4 3298  49 HIGH-DEFINITION CPG METHYLATION OF NOVEL GENES IN GASTRIC CARCINOGENESIS IDENTIFIED BY NEXT-GENERATION SEQUENCING. GASTRIC CANCERS ARE THE MOST FREQUENT GASTRIC MALIGNANCY AND USUALLY ARISE IN THE SEQUENCE OF HELICOBACTER PYLORI-ASSOCIATED CHRONIC GASTRITIS. CPG METHYLATION IS A CENTRAL MECHANISM OF EPIGENETIC GENE REGULATION AFFECTING CANCER-RELATED GENES, AND OCCURS EARLY IN GASTRIC CARCINOGENESIS. DNA SAMPLES FROM NON-METAPLASTIC GASTRIC MUCOSA WITH VARIABLE LEVELS OF GASTRITIS (NON-METAPLASTIC MUCOSA), INTESTINAL METAPLASIA, OR GASTRIC CANCER WERE SCREENED WITH METHYLATION ARRAYS FOR CPG METHYLATION OF CANCER-RELATED GENES AND 30 GENE TARGETS WERE FURTHER CHARACTERIZED BY HIGH-DEFINITION BISULFITE NEXT-GENERATION SEQUENCING. IN ADDITION, DATA FROM THE CANCER GENOME ATLAS WERE ANALYZED FOR CORRELATION OF METHYLATION WITH GENE EXPRESSION. OVERALL, 13 GENES HAD SIGNIFICANTLY INCREASED CPG METHYLATION IN GASTRIC CANCER VS NON-METAPLASTIC MUCOSA (BRINP1, CDH11, CHFR, EPHA5, EPHA7, FGF2, FLI1, GALR1, HS3ST2, PDGFRA, SEZ6L, SGCE, AND SNRPN). FURTHER, MOST OF THESE GENES HAD CORRESPONDING REDUCED EXPRESSION LEVELS IN GASTRIC CANCER COMPARED WITH INTESTINAL METAPLASIA, INCLUDING NOVEL HYPERMETHYLATED GENES IN GASTRIC CANCER (FLI1, GALR1, SGCE, AND SNRPN), SUGGESTING THAT THEY MAY REGULATE NEOPLASTIC TRANSFORMATION FROM NON-MALIGNANT INTESTINAL METAPLASIA TO CANCER. OUR DATA SUGGEST A TUMOR-SUPPRESSOR ROLE FOR FLI1 IN GASTRIC CANCER, CONSISTENT WITH RECENTLY REPORTED DATA IN BREAST CANCER. FOR THE GENES WITH STRONGEST METHYLATION/EXPRESSION CORRELATION, NAMELY FLI1, THE EXPRESSION WAS LOWEST IN MICROSATELLITE-UNSTABLE TUMORS COMPARED WITH OTHER GASTRIC CANCER MOLECULAR SUBTYPES. IMPORTANTLY, REDUCED EXPRESSION OF HYPERMETHYLATED BRINP1 AND SGCE WAS SIGNIFICANTLY ASSOCIATED WITH FAVORABLE SURVIVAL IN GASTRIC CANCER. IN SUMMARY, WE REPORT NOVEL METHYLATION GENE TARGETS THAT MAY HAVE FUNCTIONAL ROLES IN DISCRETE STAGES OF GASTRIC CARCINOGENESIS AND MAY SERVE AS BIOMARKERS FOR DIAGNOSIS AND PROGNOSIS OF GASTRIC CANCER.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                             
5 3439  32 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
6  494  35 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
7 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
8 2453  34 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
9 6686  32 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	
                                                                                                                                                                                                                                                                                                                                                                   
10 2037  38 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
11  159  53 ABERRANT PROMOTER HYPERMETHYLATION OF MULTIPLE GENES IN GALLBLADDER CARCINOMA AND CHRONIC CHOLECYSTITIS. PURPOSE: ABERRANT METHYLATION OF 5' GENE PROMOTER REGIONS IS AN EPIGENETIC PHENOMENON THAT IS A MAJOR MECHANISM FOR SILENCING OF TUMOR SUPPRESSOR GENES IN MANY CANCER TYPES. THERE IS LIMITED INFORMATION ABOUT THE MOLECULAR CHANGES INVOLVED IN THE PATHOGENESIS OF GALLBLADDER CARCINOMA (GBC), INCLUDING METHYLATION STATUS. EXPERIMENTAL DESIGN: WE INVESTIGATED THE ABERRANT PROMOTER METHYLATION PROFILE OF 24 KNOWN OR SUSPECTED TUMOR SUPPRESSOR GENES IN 50 GBCS AND COMPARED THOSE RESULTS WITH THE FINDINGS IN 25 CHRONIC CHOLECYSTITIS (CC) SPECIMENS WITHOUT CANCER. THE METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION AND COMBINED RESTRICTION ANALYSIS METHODS WERE USED TO DETECT METHYLATION, AND THE RESULTS WERE CONFIRMED BY SEQUENCING OF CLONED POLYMERASE CHAIN REACTION PRODUCTS. RESULTS: IN GBC, GENE METHYLATION FREQUENCIES VARIED FROM 0% TO 80%. TEN GENES DEMONSTRATED RELATIVELY HIGH FREQUENCIES OF ABERRANT METHYLATION: SHP1 (80%), 3-OST-2 (72%), CDH13 (44%), P15INK4B (44%), CDH1 (38%), RUNX3 (32%), APC (30%), RIZ1 (26%), P16INK4A (24%), AND HPP1 (20%). EIGHT GENES (P73, RARBETA2, SOCS-1, DAPK, DCR2, DCR1, HIN1, AND CHFR) SHOWED LOW FREQUENCIES (2-14%) OF METHYLATION, AND NO METHYLATION OF THE REMAINING SIX GENES (TIMP-3, P57, RASSF1A, CRBP1, SYK, AND NORE1) WAS DETECTED. IN CC, METHYLATION WAS DETECTED FOR SEVEN GENES: SHP1 (88%), P15INK4B (28%), 3-OST-2 (12%), CDH1 (12%), CDH13 (8%), DCR2 (4%), AND P16INK4A (4%). SIGNIFICANTLY HIGHER FREQUENCIES OF METHYLATION IN GBC COMPARED WITH CC WERE DETECTED FOR EIGHT GENES (3-OST-2, CDH13, CDH1, RUNX3, APC, RIZ1, P16INK4A, AND HPP1). OF THOSE, FOUR GENES SHOWED FREQUENT METHYLATION (>30%) IN GBCS. THE MEAN METHYLATION INDEX, AN EXPRESSION OF THE AMOUNT OF METHYLATED GENES BY CASE, WAS SIGNIFICANTLY HIGHER IN GBC (0.196 +/- 0.013) COMPARED WITH CC (0.065 +/- 0.008; P < 0.001). CONCLUSIONS: OUR STUDY CONSTITUTES THE MOST COMPREHENSIVE METHYLATION PROFILE REPORT AVAILABLE IN GBC AND DEMONSTRATES THAT THIS NEOPLASM HAS A DISTINCT PATTERN OF ABNORMAL GENE METHYLATION. WHEREAS GALLBLADDERS FROM HEALTHY INDIVIDUAL WERE NOT AVAILABLE, OUR FINDING OF METHYLATION IN CC CASES WITHOUT CANCER SUGGESTS THAT THIS PHENOMENON REPRESENTS AN EARLY EVENT IN THE PATHOGENESIS OF GBC.	2004	
                                                                                                    
12 4220  33 METHYLATED CYSTEINE DIOXYGENASE-1 GENE PROMOTER IN THE SERUM IS A POTENTIAL BIOMARKER FOR HEPATITIS B VIRUS-RELATED HEPATOCELLULAR CARCINOMA. HEPATOCELLULAR CARCINOMA (HCC) IS THE THIRD LEADING CAUSE OF CANCER-RELATED MORTALITY WORLDWIDE. EPIGENETIC ANALYSIS HAS ATTRACTED INCREASING ATTENTION IN THE MOLECULAR DIAGNOSIS OF HCC. CYSTEINE DIOXYGENASE 1 (CDO1) IS A KEY ENZYME IN THE TAURINE BIOSYNTHETIC PATHWAY AND CONVERTS CYSTEINE TO CYSTEINE SULFINATE. THE CDO1 GENE IS A TUMOR SUPPRESSOR GENE AND IS USUALLY SILENCED BY THE METHYLATION OF ITS PROMOTER IN CARCINOGENESIS. IN THIS STUDY, WE EVALUATED WHETHER THE METHYLATION STATUS OF CDO1 GENE PROMOTER IS OF DIAGNOSTIC VALUE FOR HEPATITIS B VIRUS (HBV)-RELATED HCC. THE CDO1 PROMOTER METHYLATION STATUS WAS DETERMINED IN SERUM SAMPLES USING METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (MSP) IN A COHORT OF 123 PATIENTS WITH HBV-RELATED HCC, 28 WITH LIVER CIRRHOSIS (LC), 29 WITH CHRONIC HEPATITIS B (CHB) AND 20 HEALTHY CONTROLS. THE FREQUENCY OF THE CDO1 PROMOTER METHYLATION IN HBV-RELATED HCC (42.3%) WAS SIGNIFICANTLY HIGHER THAN THAT IN LC (14.3%), CHB (6.9%) AND HEALTHY CONTROLS (0%) (P = 0.006; P < 0.0001; P < 0.0001; RESPECTIVELY). FURTHERMORE, IN HCC PATIENTS, THE FREQUENCY OF CDO1 PROMOTER METHYLATION WAS HIGHER IN ADVANCED STAGES (III-IV) (53%) THAN THE EARLY STAGES (I-II) (20%) (P = 0.001). EVALUATION OF THE CDO1 PROMOTER METHYLATION STATUS IN SERUM, IN COMBINATION WITH AFP (> 20 NG/ML), SIGNIFICANTLY IMPROVED THE DIAGNOSTIC VALUE, WITH SENSITIVITY AND SPECIFICITY OF 82.9% AND 75.4%, RESPECTIVELY IN DISTINGUISHING HCC FROM LC AND CHB. IN CONCLUSION, METHYLATION STATUS OF SERUM CDO1 GENE PROMOTER MAY BE HELPFUL IN THE DIAGNOSIS OF HCC AND THE ESTIMATION OF THE HCC STAGES.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
13  388  37 AN INTEGRATED ANALYSIS OF SOCS1 DOWN-REGULATION IN HBV INFECTION-RELATED HEPATOCELLULAR CARCINOMA. PERSISTENT INFLAMMATION TOGETHER WITH GENETIC/EPIGENETIC ABERRATIONS IS STRONGLY ASSOCIATED WITH CHRONIC HEPATITIS B VIRUS (HBV) INFECTION-RELATED HEPATOCARCINOGENESIS. HERE, WE INVESTIGATED THE ALTERATIONS OF THE SUPPRESSOR OF CYTOKINE SIGNALLING (SOCS) FAMILY GENES IN HBV-RELATED HEPATOCELLULAR CARCINOMA (HCC). A TOTAL OF 116 PATIENTS WITH HCC WERE ENROLLED IN THIS STUDY. THE METHYLATION STATUSES OF SOCS1-7 AND CISH GENES WERE QUANTITATIVELY MEASURED AND CLINICOPATHOLOGICAL SIGNIFICANCE OF SOCS1 METHYLATION WAS STATISTICALLY ANALYSED. THE GENE COPY NUMBER VARIATION WAS ASSAYED BY ACGH. LUCIFERASE REPORTER ASSAY AND WESTERN BLOT WERE USED TO DETECT THE INVOLVEMENT OF SOCS1 IN P53 SIGNALLING. WE FOUND HIGH FREQUENCIES OF SOCS1 GENE HYPERMETHYLATION IN BOTH TUMOUR (56.03%) AND ADJACENT NONTUMOUR TISSUES (54.31%), BUT TUMOUR TISSUES EXHIBITED INCREASED METHYLATION INTENSITY (24.01% VS 13.11%, P < 0.0001), PARTICULARLY IN PATIENTS WITH LARGER TUMOUR SIZE OR CIRRHOSIS BACKGROUND (P < 0.0001). IN ADDITION, THE FREQUENCY AND INTENSITY OF SOCS1 HYPERMETHYLATION IN TUMOUR TISSUES WERE BOTH SIGNIFICANTLY HIGHER THAN THOSE IN NONTUMOUR TISSUES IN MALE GENDER PATIENTS AND IN PATIENTS >/=45 YEARS OLD (P = 0.0214 AND P < 0.0001, P = 0.0232 AND P < 0.0001, RESPECTIVELY). SOCS1 GENE DELETION WAS FOUND IN 8 OF 25 ACGH ASSAYED TUMOUR SPECIMENS, WHICH WAS ASSOCIATED WITH LOWER SOCS1 MRNA EXPRESSION (P = 0.0448). FURTHERMORE, ECTOPIC SOCS1 OVEREXPRESSION COULD ACTIVATE THE P53 SIGNALLING PATHWAY IN HCC CELL LINES. HYPERMETHYLATION OF SOCS2-7 AND CISH GENES WAS SELDOM FOUND IN HCC. OUR RESULTS SUGGESTED THAT THE GENE LOSS AND EPIGENETIC SILENCING OF SOCS1 WERE STRONGLY ASSOCIATED WITH HBV-RELATED HCC.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
14 5349  35 RASSF1A AND DOK1 PROMOTER METHYLATION LEVELS IN HEPATOCELLULAR CARCINOMA, CIRRHOTIC AND NON-CIRRHOTIC LIVER, AND CORRELATION WITH LIVER CANCER IN BRAZILIAN PATIENTS. HEPATOCELLULAR CARCINOMA (HCC) IS THE SECOND MOST COMMON CAUSE OF CANCER MORTALITY WORLDWIDE. MOST CASES OF HCC ARE ASSOCIATED WITH CIRRHOSIS RELATED TO CHRONIC HEPATITIS B VIRUS OR HEPATITIS C VIRUS INFECTIONS. HYPERMETHYLATION OF PROMOTER REGIONS IS THE MAIN EPIGENETIC MECHANISM OF GENE SILENCING AND HAS BEEN INVOLVED IN HCC DEVELOPMENT. THE AIM OF THIS STUDY WAS TO DETERMINE WHETHER ABERRANT METHYLATION OF RASSF1A AND DOK1 GENE PROMOTERS IS ASSOCIATED WITH THE PROGRESSION OF LIVER DISEASE IN BRAZILIAN PATIENTS. METHYLATION LEVELS WERE MEASURED BY PYROSEQUENCING IN 41 (20 HCC, 9 CIRRHOTIC, AND 12 NON-CIRRHOTIC) LIVER TISSUE SAMPLES. MEAN RATES OF METHYLATION IN RASSF1A AND DOK1 WERE 16.2% AND 12.0% IN NON-CIRRHOTIC, 26.1% AND 19.6% IN CIRRHOTIC, AND 59.1% AND 56.0% IN HCC TISSUES, RESPECTIVELY, SHOWING A GRADUAL INCREASE ACCORDING TO THE PROGRESSION OF THE DISEASE, WITH SIGNIFICANTLY HIGHER LEVELS IN TUMOR TISSUES. IN ADDITION, HYPERMETHYLATION OF RASSF1A AND DOK1 WAS FOUND IN THE VAST MAJORITY (88%) OF THE HCC CASES. INTERESTINGLY, DOK1 METHYLATION LEVELS IN HCC SAMPLES WERE SIGNIFICANTLY HIGHER IN THE GROUP OF YOUNGER (<40 YEARS) PATIENTS, AND HIGHER IN MODERATELY DIFFERENTIATED THAN IN POORLY DIFFERENTIATED TUMORS (P < 0.05). OUR RESULTS REINFORCE THE HYPOTHESIS THAT HYPERMETHYLATION OF RASSF1A AND DOK1 CONTRIBUTES TO HEPATOCARCINOGENESIS AND IS ASSOCIATED TO CLINICOPATHOLOGICAL CHARACTERISTICS. RASSF1A AND DOK1 PROMOTER HYPERMETHYLATION MAY BE A VALUABLE BIOMARKER FOR EARLY DIAGNOSIS OF HCC AND A POTENTIAL MOLECULAR TARGET FOR EPIGENETIC-BASED THERAPY.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
15 2637  33 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	
                                                                                                                               
16 5270  42 PROMOTER DNA METHYLATION FREQUENCY AND CLINICOPATHOLOGICAL ROLE OF MIR-129-2 GENE IN PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA. OBJECTIVES: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS CHARACTERIZED BY THE ACCUMULATION OF APPARENTLY MATURE B-TYPE LYMPHOCYTES IN THE LYMPHOHEMATOPOIETIC ORGANS. METHYLATION IN PROMOTERS OF TUMOR SUPPRESSOR GENES IS ONE OF THE MECHANISMS THAT CAUSES BLOOD MALIGNANCY. IN THIS STUDY, WE EVALUATED THE PROMOTER DNA METHYLATION STATUS OF MIR-129-2 TUMOR SUPPRESSOR GENE AND ITS ASSOCIATION WITH CLINICAL AND LABORATORY PARAMETERS OF PATIENTS WITH CLL. METHODS: WE STUDIED THE PROMOTER DNA METHYLATION FREQUENCY OF THE MIR-129-2 GENE IN 50 PATIENTS WITH CLL AND 50 HEALTHY CONTROLS USING METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION METHODS. STATISTICAL ANALYSIS WAS PERFORMED USING SPSS-18 SOFTWARE, AND A P-VALUE < 0.050 WAS CONSIDERED STATISTICALLY SIGNIFICANT. RESULTS: THE FREQUENCY OF PROMOTER DNA METHYLATION OF THE MIR-129-2 GENE WAS SIGNIFICANTLY HIGHER IN THE CLL GROUP COMPARED WITH CONTROL GROUP (38.0% VS. 0.0%, P < 0.001; CHI(2) = 23.457). THE PROMOTER DNA METHYLATION FREQUENCY OF MIR-129-2 GENE WAS NOT SIGNIFICANTLY DIFFERENT BETWEEN THE TWO SEXES (P = 0.236). A SIGNIFICANT BUT WEAK CORRELATION WAS SEEN BETWEEN THE METHYLATED STATE OF THE MIR-129-2 GENE AND ORGANOMEGALY (P = 0.019, R = 0.330) AS WELL AS HEMOGLOBIN LEVELS (P = 0.020, R = -0.233). HOWEVER, BINARY LOGISTIC REGRESSION ANALYSIS INDICATED ORGANOMEGALY AS THE ONLY CLINICAL BIOMARKER WITH A STATISTICALLY SIGNIFICANT ASSOCIATION WITH THE HYPERMETHYLATED MIR-129-2 GENE STATE (P = 0.046). CONCLUSIONS: THE HIGH FREQUENCY OF PROMOTER DNA METHYLATION OF THE MIR-129-2 GENE IN THE CLL GROUP COMPARED TO THE CONTROL GROUP, AS WELL AS ITS SIGNIFICANT ASSOCIATION WITH ORGANOMEGALY, SUGGESTS THE IMPORTANCE OF THIS EPIGENETIC BIOMARKER IN THE PATHOGENESIS AND PROGNOSIS OF CLL DISEASE.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
17  672  31 BRAF, KRAS AND HELICOBACTER PYLORI EPIGENETIC CHANGES-ASSOCIATED CHRONIC GASTRITIS IN EGYPTIAN PATIENTS WITH AND WITHOUT GASTRIC CANCER. WE AIMED TO STUDY MLH1 AND MGMT METHYLATION STATUS IN HELICOBACTER PYLORI-ASSOCIATED CHRONIC GASTRITIS IN EGYPTIAN PATIENTS WITH AND WITHOUT GASTRIC CANCER. 39 PATIENTS WERE INCLUDED IN OUR STUDY. THEY WERE DIVIDED INTO 2 GROUPS; PATIENTS WITHOUT (GROUP I) AND WITH GASTRIC ADENOCARCINOMA (GROUP II). PATIENTS WERE SUBJECTED TO CLINICAL EXAMINATION, ABDOMINAL ULTRASOUND AND UPPER ENDOSCOPY FOR GASTRIC BIOPSY. BIOPSIES WERE SUBJECTED TO UREASE TEST, HISTOLOGICAL EXAMINATION, AND DNA PURIFICATION. H. PYLORI, BRAF, KRAS, MLH1 AND MGMT METHYLATION WERE ASSESSED BY QUANTITATIVE PCR. DNA SEQUENCING WAS PERFORMED TO ASSESS BRAF AND KRAS GENES MUTATION. QPCR OF H. PYLORI WAS SIGNIFICANTLY HIGHER IN PATIENTS WITH ADENOCARCINOMA (GROUP II) THAN THOSE WITHOUT ADENOCARCINOMA (GROUP I); WITH A P < 0.001 AS WELL AS IN PATIENTS WITH AGE ABOVE 50 YEARS WITH A P VALUE = 0.008. BY APPLYING LOGISTIC REGRESSION ANALYSIS IT WAS REPORTED THAT THE H. PYLORI QPCR IS A SIGNIFICANT PREDICTOR TO THE ADENOCARCINOMA WITH OR = 1.025 (95 % CI: 1. 002-1.048), WITH SENSITIVITY OF 90 % AND SPECIFICITY OF 100 %. ADENOCARCINOMA PATIENTS HAD A SIGNIFICANTLY HIGHER MEAN AGE AND LEVELS OF H. PYLORI, BRAF, K-RAS, METHYLATED MGMT AND METHYLATED MLH1 THAN THOSE OF GASTRITIS PATIENTS. DNA SEQUENCE ANALYSIS OF BRAF (CODON 12) AND KRAS (CODON 600) HAD GENES MUTATION IN GASTRIC ADENOCARCINOMA VERSUS CHRONIC GASTRITIS. CONCLUSION: H. PYLORI MAY CAUSE EPIGENETIC CHANGES PREDISPOSING THE PATIENTS TO CANCER STOMACH. ESTIMATION OF H. PYLORI BY QPCR CAN BE A GOOD PREDICTOR TO ADENOCARCINOMA. BRAF AND KRAS GENES MUTATION WERE REVELED IN GASTRITIS AND ADENOCARCINOMA PATIENTS.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
18 2327  42 EPIGENETIC REGULATION OF HUMAN CANCER/TESTIS ANTIGEN GENE, HAGE, IN CHRONIC MYELOID LEUKEMIA. BACKGROUND AND OBJECTIVES: CANCER TESTIS ANTIGENS (CTA) PROVIDE ATTRACTIVE TARGETS FOR CANCER-SPECIFIC IMMUNOTHERAPY. ALTHOUGH CTA GENES ARE EXPRESSED IN SOME NORMAL TISSUES, SUCH AS THE TESTIS, THIS IMMUNOLOGICALLY PROTECTED SITE LACKS MHC I EXPRESSION AND AS SUCH, DOES NOT PRESENT SELF ANTIGENS TO T CELLS. TO DATE, CTA GENES HAVE BEEN SHOWN TO BE EXPRESSED IN A RANGE OF SOLID TUMORS VIA DEMETHYLATION OF THEIR PROMOTER CPG ISLANDS, BUT RARELY IN CHRONIC MYELOID LEUKEMIA (CML) OR OTHER HEMATOLOGIC MALIGNANCIES. DESIGN AND METHODS: IN THIS STUDY, THE METHYLATION STATUS OF THE HAGE CTA GENE PROMOTER WAS ANALYZED BY QUANTITATIVE METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (MSP) AND SEQUENCING IN FOUR PHILADELPHIA-POSITIVE CELL LINES (TCC-S, K562, KU812 AND KYO-1) AND IN CML SAMPLES TAKEN FROM PATIENTS IN CHRONIC PHASE (CP N=215) OR BLAST CRISIS (BC N=47). HAGE EXPRESSION WAS ASSESSED BY QUANTITATIVE REVERSE TRANSCRIPTASE-POLYMERASE CHAIN REACTION. RESULTS: THE TCC-S CELL LINE SHOWED DEMETHYLATION OF HAGE THAT WAS ASSOCIATED WITH OVER-EXPRESSION OF THIS GENE. HAGE HYPOMETHYLATION WAS SIGNIFICANTLY MORE FREQUENT IN BC (46%) THAN IN CP (22%) (P=0.01) AND WAS CORRELATED WITH HIGH EXPRESSION LEVELS OF HAGE TRANSCRIPTS (P<0.0001). OF NOTE, IN CP-CML, EXTENSIVE HAGE HYPOMETHYLATION WAS ASSOCIATED WITH POORER PROGNOSIS IN TERMS OF CYTOGENETIC RESPONSE TO INTERFERON (P=0.01) OR IMATINIB (P=0.01), MOLECULAR RESPONSE TO IMATINIB (P=0.003) AND PROGRESSION-FREE SURVIVAL (P=0.05). INTERPRETATIONS AND CONCLUSION: THE METHYLATION STATUS OF THE HAGE PROMOTER DIRECTLY CORRELATES WITH ITS EXPRESSION IN BOTH CML CELL LINES AND PATIENTS AND IS ASSOCIATED WITH ADVANCED DISEASE AND POOR OUTCOME.	2007	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
19 4221  37 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
20  152  41 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