1 564 149 BASAL CELL CARCINOMAS OF THE SCALP AFTER RADIOTHERAPY FOR TINEA CAPITIS IN CHILDHOOD: A GENETIC AND EPIGENETIC STUDY WITH COMPARISON WITH BASAL CELL CARCINOMAS EVOLVING IN CHRONICALLY SUN-EXPOSED AREAS. BACKGROUND: BASAL CELL CARCINOMA (BCC) HAS BEEN MOSTLY ASSOCIATED WITH SUN EXPOSURE, BUT IONIZING RADIATION IS ALSO A KNOWN RISK FACTOR. IT IS NOT CLEAR IF THE PATHOGENESIS OF BCC, NAMELY AT A GENOMIC AND EPIGENETIC LEVEL, DIFFERS ACCORDING TO THE UNDERLYING TRIGGERING FACTORS. OBJECTIVE: THE PRESENT STUDY AIMS TO COMPARE GENETIC AND EPIGENETIC CHANGES IN BCCS RELATED TO IONIZING RADIATION AND CHRONIC SUN EXPOSURE. METHODS: TUMOR SAMPLES FROM BCCS OF THE SCALP IN PATIENTS SUBMITTED TO RADIOTHERAPY TO TREAT TINEA CAPITIS IN CHILDHOOD AND BCCS FROM SUN-EXPOSED AREAS WERE ANALYSED THROUGH ARRAY COMPARATIVE GENOMIC HYBRIDIZATION (ARRAY-CGH) AND METHYLATION-SPECIFIC MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION (MS-MLPA) TO DETECT COPY NUMBER ALTERATIONS AND METHYLATION STATUS OF SPECIFIC GENES. RESULTS: GENOMIC CHARACTERIZATION OF TUMOR SAMPLES REVEALED SEVERAL COPY NUMBER GAINS AND LOSSES IN ALL CHROMOSOMES, WITH THE MOST FREQUENT GAINS OBSERVED AT 2P, 6P, 12P, 14Q, 15Q, 18Q, XP AND YP, AND THE MOST FREQUENT LOSSES OBSERVED AT 3Q, 14Q, 16P, 17Q, 22Q, XP, YP AND YQ. WE DEVELOPED A STATISTICAL MODEL, ENCOMPASSING GAINS IN 3P AND 16P AND LOSSES IN 14Q AND 20P, WITH POTENTIAL TO DISCRIMINATE BCC SAMPLES WITH SPORADIC AETIOLOGY FROM BCC SAMPLES THAT EVOLVE AFTER RADIOTHERAPY IN CHILDHOOD FOR THE TREATMENT OF TINEA CAPITIS, WHICH PRESENTED STATISTICAL SIGNIFICANCE (P = 0.003). FEW METHYLATED GENES WERE DETECTED THROUGH MS-MLPA, MOST FREQUENTLY RARB AND CD44. CONCLUSIONS: OUR STUDY REPRESENTS A STEP FORWARD IN THE UNDERSTANDING OF THE GENETIC MECHANISMS UNDERLYING THE PATHOGENESIS OF BCC AND SUGGESTS POTENTIAL DIFFERENCES ACCORDING TO THE UNDERLYING RIS K FACTORS. 2021 2 2261 34 EPIGENETIC PROFILE IN CHRONIC LYMPHOCYTIC LEUKEMIA USING METHYLATION-SPECIFIC MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION. AIM: TO ANALYZE THE METHYLATION STATUS OF 35 TUMOR SUPPRESSOR GENES USING METHYLATION-SPECIFIC MULTIPLEX LIGATION-DEPENDENT PROBE AMPLIFICATION (MS-MLPA) IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). MATERIALS & METHODS: THE DNA OF 37 SAMPLES FROM PATIENTS WITH CLL, SIX HEALTHY DONORS, AND JURKAT AND RAMOS CELL LINES WAS ANALYZED BY MS-MLPA. RESULTS: OUR RESULTS CONFIRM THAT HYPERMETHYLATION IS A COMMON AND NOT RANDOMLY DISTRIBUTED EVENT IN CLL, AND SOME GENES, SUCH AS WT1, CDH13, IGSF4/TSLC1, GATA5, DAPK1 AND RARB, ARE HYPERMETHYLATED IN MORE THAN 25% OF THE ANALYZED SAMPLES. IMPORTANTLY, MS-MLPA ALSO DETECTED HYPERMETHYLATION OF SOME GENES NOT REPORTED PREVIOUSLY IN CLL, AND THEIR METHYLATION STATUS WAS CONFIRMED BY BISULFITE SEQUENCING. CONCLUSION: THESE RESULTS INDICATE THAT MS-MLPA IS A USEFUL TECHNIQUE FOR THE DETECTION OF METHYLATION IN CLL SAMPLES. SELECTING CLL-SPECIFIC METHYLATION TARGETS IN ORDER TO GENERATE A CLL-SPECIFIC MS-MLPA PROBE SET COULD ENHANCE ITS USEFULNESS AS A TOOL IN STUDIES OF RISK STRATIFICATION AND GUIDING THE BEST THERAPEUTIC DECISION. 2012 3 2830 37 FOCAL 9P INSTABILITY IN HEMATOLOGIC NEOPLASIAS REVEALED BY COMPARATIVE GENOMIC HYBRIDIZATION AND SINGLE-NUCLEOTIDE POLYMORPHISM MICROARRAY ANALYSES. COPY NUMBER LOSSES IN CHROMOSOME ARM 9P ARE WELL-KNOWN ABERRATIONS IN MALIGNANCIES, INCLUDING LEUKEMIAS. THE CDKN2A GENE IS SUGGESTED TO PLAY A KEY ROLE IN THESE ABERRATIONS. IN THIS STUDY OVERVIEWING 9P LOSSES IN HEMATOLOGIC NEOPLASIAS, WE INTRODUCE THE TERM FOCAL 9P INSTABILITY TO INDICATE MULTIPLE AREAS OF COPY NUMBER LOSS OR HOMOZYGOUS LOSS WITHIN A LARGER HETEROZYGOUS ONE IN 9P. WE HAVE USED MICROARRAY COMPARATIVE GENOMIC HYBRIDIZATION TO STUDY PATIENTS WITH ACUTE LYMPHOBLASTIC LEUKEMIA (ALL, N = 140), ACUTE MYELOID LEUKEMIA (N = 50), CHRONIC LYMPHOCYTIC LEUKEMIA (N = 20), AND MYELODYSPLASTIC SYNDROMES (N = 37). OUR RESULTS SHOW THAT 9P INSTABILITY IS RESTRICTED TO ALL. IN TOTAL, 58/140 (41%) PATIENTS WITH ALL HAD A LOSS IN 9P. THE 9P INSTABILITY WAS DETECTED IN 19% OF THE PATIENTS WITH ALL AND ALWAYS INCLUDED HOMOZYGOUS LOSS OF CDKN2A ALONG WITH LOSS OF CDKN2B. OTHER POSSIBLY IMPORTANT GENES INCLUDED MTAP, IFN, MLLT3, JAK2, PTPLAD2, AND PAX5. 13/27 (48%) PATIENTS WITH THE INSTABILITY HAD THE BCR/ABL1 FUSION GENE OR OTHER ONCOGENE-ACTIVATING TRANSLOCATION OR STRUCTURAL ABERRATIONS. TWO PATIENTS HAD HOMOZYGOUS LOSS OF HSA-MIR -31, A MICRORNA KNOWN TO REGULATE IKZF1. IKZF1 DELETION AT 7P12.1 WAS SEEN IN 10 (37%) PATIENTS WITH THE 9P INSTABILITY. THESE FINDINGS SUGGEST THAT, IN ALL LEUKEMOGENESIS, LOSS OF CDKN2A AND OTHER TARGET GENES IN THE INSTABILITY REGION IS FREQUENTLY ASSOCIATED WITH BCR/ABL1 AND IKZF1 DYSFUNCTION. THE MULTIPLE MECHANISMS LEADING TO 9P INSTABILITY INCLUDING PHYSICAL OR EPIGENETIC LOSS OF THE TARGET GENES, LOSS OF THE MICRORNA CLUSTER, AND THE ROLE OF FRA9G FRAGILE SITE ARE DISCUSSED. 2010 4 1659 34 DOWN-REGULATION OF CANDIDATE TUMOR SUPPRESSOR GENES WITHIN CHROMOSOME BAND 13Q14.3 IS INDEPENDENT OF THE DNA METHYLATION PATTERN IN B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA. LOSS OF GENOMIC MATERIAL FROM CHROMOSOMAL BAND 13Q14.3 IS THE MOST COMMON GENETIC IMBALANCE IN B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (B-CLL) AND MANTLE CELL LYMPHOMA, POINTING TO THE INVOLVEMENT OF THIS REGION IN A TUMOR SUPPRESSOR MECHANISM. FROM THE MINIMALLY DELETED REGION, 3 CANDIDATE GENES HAVE BEEN ISOLATED, RFP2, BCMS, AND BCMSUN. DNA SEQUENCE ANALYSES HAVE FAILED TO DETECT SMALL MUTATIONS IN ANY OF THESE GENES, SUGGESTING A DIFFERENT PATHOMECHANISM, MOST LIKELY HAPLOINSUFFICIENCY. WE, THEREFORE, TESTED B-CLL PATIENTS FOR EPIGENETIC ABERRATIONS BY MEASURING EXPRESSION OF GENES FROM 13Q14.3 AND METHYLATION OF THEIR PROMOTOR REGION. RB1, CLLD7, KPNA3, CLLD6, AND RFP2 WERE DOWN-REGULATED IN B-CLL PATIENTS AS COMPARED WITH B CELLS OF HEALTHY DONORS, WITH RFP2 SHOWING THE MOST PRONOUNCED LOSS OF EXPRESSION. TO TEST WHETHER THIS LOSS OF GENE EXPRESSION IS ASSOCIATED WITH METHYLATION OF CPG ISLANDS IN THE RESPECTIVE PROMOTOR REGIONS, WE PERFORMED METHYLATION-SENSITIVE QUANTITATIVE POLYMERASE CHAIN REACTION ANALYSES AND BISULFITE SEQUENCING ON DNA FROM B-CLL PATIENTS. NO DIFFERENCE IN THE METHYLATION PATTERNS COULD BE DETECTED IN ANY CPG ISLAND OF THE MINIMALLY DELETED REGION. DOWN-REGULATION OF GENES WITHIN CHROMOSOMAL BAND 13Q14.3 IN B-CLL IS IN LINE WITH THE CONCEPT OF HAPLOINSUFFICIENCY, BUT THIS TUMOR-SPECIFIC PHENOMENON IS NOT ASSOCIATED WITH DNA METHYLATION. 2002 5 326 37 ALLELIC SILENCING AT THE TUMOR-SUPPRESSOR LOCUS 13Q14.3 SUGGESTS AN EPIGENETIC TUMOR-SUPPRESSOR MECHANISM. GENOMIC MATERIAL FROM CHROMOSOME BAND 13Q14.3 DISTAL TO THE RETINOBLASTOMA LOCUS IS RECURRENTLY LOST IN A VARIETY OF HUMAN NEOPLASMS, INDICATING AN AS-YET-UNIDENTIFIED TUMOR-SUPPRESSOR MECHANISM. NO PATHOGENIC MUTATIONS HAVE BEEN FOUND IN THE MINIMALLY DELETED REGION UNTIL NOW. HOWEVER, IN B CELL CHRONIC LYMPHOCYTIC LEUKEMIA TUMORS WITH LOSS OF ONE COPY OF THE CRITICAL REGION, RESPECTIVE CANDIDATE TUMOR-SUPPRESSOR GENES ARE DOWN-REGULATED BY A FACTOR >2, WHICH WOULD BE EXPECTED BY A NORMAL GENE-DOSAGE EFFECT. THIS FINDING POINTS TO AN EPIGENETIC PATHOMECHANISM. WE FIND THAT THE TWO COPIES OF THE CRITICAL REGION REPLICATE ASYNCHRONOUSLY, SUGGESTING DIFFERENTIAL CHROMATIN PACKAGING OF THE TWO COPIES OF 13Q14.3. ALTHOUGH WE ALSO DETECT MONOALLELIC SILENCING OF GENES LOCALIZED IN THE CRITICAL REGION, MONOALLELIC EXPRESSION ORIGINATES FROM EITHER THE MATERNAL OR PATERNAL COPY, EXCLUDING AN IMPRINTING MECHANISM. DNA METHYLATION ANALYSES REVEALED ONE CPG ISLAND OF THE REGION TO BE METHYLATED. DNA DEMETHYLATION OF THIS CPG ISLAND AND GLOBAL HISTONE HYPERACETYLATION INDUCED BIALLELIC EXPRESSION, WHEREAS REPLICATION TIMING WAS NOT AFFECTED. WE PROPOSE THAT DIFFERENTIAL REPLICATION TIMING REPRESENTS AN EARLY EPIGENETIC MARK THAT DISTINGUISHES THE TWO COPIES OF 13Q14.3, RESULTING IN DIFFERENTIAL CHROMATIN PACKAGING AND MONOALLELIC EXPRESSION. ACCORDINGLY, DELETION OF THE SINGLE ACTIVE COPY OF 13Q14.3 RESULTS IN SIGNIFICANT DOWN-REGULATION OF THE CANDIDATE GENES AND LOSS OF FUNCTION, PROVIDING A MODEL FOR THE INTERACTION OF GENETIC LESIONS AND EPIGENETIC SILENCING AT 13Q14.3 IN B CELL CHRONIC LYMPHOCYTIC LEUKEMIA. 2006 6 159 42 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 7 1062 26 CLINICAL SIGNIFICANCE OF DNA METHYLATION IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS: RESULTS FROM 3 UK CLINICAL TRIALS. CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS WITH MUTATED IMMUNOGLOBULIN HEAVY-CHAIN GENES (IGHV-M), PARTICULARLY THOSE LACKING POOR-RISK GENOMIC LESIONS, OFTEN RESPOND WELL TO CHEMOIMMUNOTHERAPY (CIT). DNA METHYLATION PROFILING CAN SUBDIVIDE EARLY-STAGE PATIENTS INTO NAIVE B-CELL-LIKE CLL (N-CLL), MEMORY B-CELL-LIKE CLL (M-CLL), AND INTERMEDIATE CLL (I-CLL), WITH DIFFERING TIMES TO FIRST TREATMENT AND OVERALL SURVIVAL. HOWEVER, WHETHER DNA METHYLATION CAN IDENTIFY PATIENTS DESTINED TO RESPOND FAVORABLY TO CIT HAS NOT BEEN ASCERTAINED. WE CLASSIFIED TREATMENT-NAIVE PATIENTS (N = 605) FROM 3 UK CHEMO AND CIT CLINICAL TRIALS INTO THE 3 EPIGENETIC SUBGROUPS, USING PYROSEQUENCING AND MICROARRAY ANALYSIS, AND PERFORMED EXPANSIVE SURVIVAL ANALYSIS. THE N-CLL, I-CLL, AND M-CLL SIGNATURES WERE FOUND IN 80% (N = 245/305), 17% (53/305), AND 2% (7/305) OF IGHV-UNMUTATED (IGHV-U) CASES, RESPECTIVELY, AND IN 9%, (19/216), 50% (108/216), AND 41% (89/216) OF IGHV-M CASES, RESPECTIVELY. MULTIVARIATE COX PROPORTIONAL ANALYSIS IDENTIFIED M-CLL AS AN INDEPENDENT PROGNOSTIC FACTOR FOR OVERALL SURVIVAL (HAZARD RATIO [HR], 0.46; 95% CONFIDENCE INTERVAL [CI], 0.24-0.87; P = .018) IN CLL4, AND FOR PROGRESSION-FREE SURVIVAL (HR, 0.25; 95% CI, 0.10-0.57; P = .002) IN ARCTIC AND ADMIRE PATIENTS. THE ANALYSIS OF EPIGENETIC SUBGROUPS IN PATIENTS ENTERED INTO 3 FIRST-LINE UK CLL TRIALS IDENTIFIES M-CLL AS AN INDEPENDENT MARKER OF PROLONGED SURVIVAL AND MAY AID IN THE IDENTIFICATION OF PATIENTS DESTINED TO DEMONSTRATE PROLONGED SURVIVAL AFTER CIT. 2019 8 1996 36 EPIGENETIC AND GENETIC ALTERATIONS OF THE EDNRB GENE IN NASOPHARYNGEAL CARCINOMA. BACKGROUND: LOSS OF HETEROZYGOSITY (LOH) AT 13Q22 IS A COMMON EVENT IN NASOPHARYNGEAL CARCINOMA (NPC). EDNRB GENE LOCATED AT 13Q22 HAS BEEN DEMONSTRATED TO BE HYPERMETHYLATED IN SOME KINDS OF TUMORS. IN THE CURRENT STUDY, WE FOCUSED ON THE EPIGENETIC AND GENETIC ALTERATIONS OF EDNRB IN NPC. METHODS: THE MRNA EXPRESSION OF EDNRB WAS DETECTED BY SEMIQUANTITATIVE RT-PCR AND REAL-TIME QUANTITATIVE PCR IN 49 NPC AND 12 CHRONIC NASOPHARYNGITIS BIOPSIES. THE METHYLATION AND LOH STATUS OF EDNRB WERE EXAMINED BY METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION, MICROSATELLITE PCR AND SEQUENCING. WE ALSO EXAMINED THE MRNA EXPRESSION OF EDNRB IN FOUR NPC CELL LINES AFTER 5-AZA-2'-DEOXYCYTIDINE TREATMENT. RESULTS: EDNRB WAS DOWNREGULATED IN PRIMARY NPC TISSUES AND NPC CELL LINES, AND A RELATIVELY HIGHER METHYLATION LEVEL OF EDNRB WAS FOUND IN NPC BIOPSIES (84%) COMPARED TO THAT IN CHRONIC NASOPHARYNGITIS BIOPSIES (42%). TREATMENT OF NPC CELL LINES WITH 5-AZA-2'-DEOXYCYTIDINE ACTIVATED EDNRB EXPRESSION. LOH OF EDNRB GENE WAS ALSO FOUND AT TWO MICROSATELLITE SITES WITH RATIOS OF 6.25 AND 16.67% IN NPC. CONCLUSION: OUR RESULTS SUGGESTED THAT EDNRB EXPRESSION MAY BE AFFECTED BY ABERRANT PROMOTER METHYLATION AND GENE DELETION AND MAY PLAY A ROLE IN THE DEVELOPMENT OF NPC. 2007 9 2481 31 EPIGENETIC UPREGULATION OF LNCRNAS AT 13Q14.3 IN LEUKEMIA IS LINKED TO THE IN CIS DOWNREGULATION OF A GENE CLUSTER THAT TARGETS NF-KB. NON-CODING RNAS ARE MUCH MORE COMMON THAN PREVIOUSLY THOUGHT. HOWEVER, FOR THE VAST MAJORITY OF NON-CODING RNAS, THE CELLULAR FUNCTION REMAINS ENIGMATIC. THE TWO LONG NON-CODING RNA (LNCRNA) GENES DLEU1 AND DLEU2 MAP TO A CRITICAL REGION AT CHROMOSOMAL BAND 13Q14.3 THAT IS RECURRENTLY DELETED IN SOLID TUMORS AND HEMATOPOIETIC MALIGNANCIES LIKE CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). WHILE NO POINT MUTATIONS HAVE BEEN FOUND IN THE PROTEIN CODING CANDIDATE GENES AT 13Q14.3, THEY ARE DEREGULATED IN MALIGNANT CELLS, SUGGESTING AN EPIGENETIC TUMOR SUPPRESSOR MECHANISM. WE THEREFORE CHARACTERIZED THE EPIGENETIC MAKEUP OF 13Q14.3 IN CLL CELLS AND FOUND HISTONE MODIFICATIONS BY CHROMATIN-IMMUNOPRECIPITATION (CHIP) THAT ARE ASSOCIATED WITH ACTIVATED TRANSCRIPTION AND SIGNIFICANT DNA-DEMETHYLATION AT THE TRANSCRIPTIONAL START SITES OF DLEU1 AND DLEU2 USING 5 DIFFERENT SEMI-QUANTITATIVE AND QUANTITATIVE METHODS (APRIMES, BIOCOBRA, MCIP, MASSARRAY, AND BISULFITE SEQUENCING). THESE EPIGENETIC ABERRATIONS WERE CORRELATED WITH TRANSCRIPTIONAL DEREGULATION OF THE NEIGHBORING CANDIDATE TUMOR SUPPRESSOR GENES, SUGGESTING A COREGULATION IN CIS OF THIS GENE CLUSTER. WE FOUND THAT THE 13Q14.3 GENES IN ADDITION TO THEIR PREVIOUSLY KNOWN FUNCTIONS REGULATE NF-KB ACTIVITY, WHICH WE COULD SHOW AFTER OVEREXPRESSION, SIRNA-MEDIATED KNOCKDOWN, AND DOMINANT-NEGATIVE MUTANT GENES BY USING WESTERN BLOTS WITH PREVIOUSLY UNDESCRIBED ANTIBODIES, BY A CUSTOMIZED ELISA AS WELL AS BY REPORTER ASSAYS. IN ADDITION, WE PERFORMED AN UNBIASED SCREEN OF 810 HUMAN MIRNAS AND IDENTIFIED THE MIR-15/16 FAMILY OF GENES AT 13Q14.3 AS THE STRONGEST INDUCERS OF NF-KB ACTIVITY. IN SUMMARY, THE TUMOR SUPPRESSOR MECHANISM AT 13Q14.3 IS A CLUSTER OF GENES CONTROLLED BY TWO LNCRNA GENES THAT ARE REGULATED BY DNA-METHYLATION AND HISTONE MODIFICATIONS AND WHOSE MEMBERS ALL REGULATE NF-KB. THEREFORE, THE TUMOR SUPPRESSOR MECHANISM IN 13Q14.3 UNDERLINES THE ROLE BOTH OF EPIGENETIC ABERRATIONS AND OF LNCRNA GENES IN HUMAN TUMORIGENESIS AND IS AN EXAMPLE OF COLOCALIZATION OF A FUNCTIONALLY RELATED GENE CLUSTER. 2013 10 2678 27 EVALUATION OF A PROGNOSTIC EPIGENETIC CLASSIFICATION SYSTEM IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS. BACKGROUND: METHYLATION AT 5 CPG SITES WAS PREVIOUSLY SHOWN TO CLASSIFY CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) INTO 3 PROGNOSTIC SUBGROUPS. HERE, WE AIMED TO VALIDATE THE MARKER SET IN AN ADDITIONAL COHORT AND TO EVALUATE ITS CLINICAL UTILITY FOR CLL PATIENT STRATIFICATION. METHODS: WE EVALUATED THIS EPIGENETIC MARKER SET IN 79 GERMAN PATIENTS USING BISULFITE TREATMENT FOLLOWED BY PYROSEQUENCING AND CLASSIFICATION USING A SUPPORT VECTOR MACHINE-LEARNING TOOL. RESULTS: THE N-CLL, I-CLL, AND M-CLL CLASSIFICATION WAS DETECTED IN 28 (35%), 10 (13%), AND 41 (51%) PATIENTS, RESPECTIVELY. EPIGENETIC GROUPING WAS ASSOCIATED WITH IGHV MUTATIONAL STATUS (P = 2 X 10(-12)), ISOLATED DEL13Q (P = 9 X 10(-6)), DEL17P (P = .015), COMPLEX KARYOTYPE (P = .005), VH-USAGE, AND CLINICAL OUTCOME AS TIME TO FIRST TREATMENT (P = 1.4 X 10(-12)) AND OVERALL SURVIVAL (P = .003). MULTIVARIATE COX REGRESSION ANALYSIS IDENTIFIED N-CLL AS A FACTOR FOR EARLIER TREATMENT HAZARD RATIO (HR), 6.3 (95% CONFIDENCE INTERVAL [CI] 2.4-16.4; P = .0002) COMPARED TO IGHV MUTATIONAL STATUS (HR 4.6, 95% CI 1.9-11.3, P = .0008). IN ADDITION, WHEN COMPARING THE PROGNOSTIC VALUE OF THE EPIGENETIC CLASSIFICATION SYSTEM WITH THE IGHV CLASSIFICATION, EPIGENETIC GROUPING PERFORMED BETTER COMPARED TO IGHV MUTATIONAL STATUS USING KAPLAN-MEIER ESTIMATION AND ALLOWED THE IDENTIFICATION OF A THIRD, INTERMEDIATE (I-CLL) GROUP. THUS, OUR STUDY CONFIRMED THE PROGNOSTIC VALUE OF THE EPIGENETIC MARKER SET FOR PATIENT STRATIFICATION IN ROUTINE CLINICAL DIAGNOSTICS. 2022 11 2440 27 EPIGENETIC SILENCING OF TUMOR SUPPRESSOR LONG NON-CODING RNA BM742401 IN CHRONIC LYMPHOCYTIC LEUKEMIA. BM742401 IS A TUMOR SUPPRESSOR LNCRNA DOWNREGULATED IN GASTRIC CANCER. AS THE PROMOTER REGION AND THE ENTIRE TRANSCRIPT ARE EMBEDDED IN A CPG ISLAND, WE POSTULATED THAT BM742401 IS A TUMOR SUPPRESSOR LNCRNA INACTIVATED BY DNA METHYLATION IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). THE PROMOTER OF BM742401 WAS UNMETHYLATED IN NORMAL CONTROLS INCLUDING THREE EACH OF NORMAL BONE MARROW, PERIPHERAL BLOOD BUFFY COATS, AND CD19-SORTED PERIPHERAL B-CELLS, BUT METHYLATED IN FOUR (57.1%) CLL CELL LINES. METHYLATION OF BM742401 CORRELATED INVERSELY WITH EXPRESSION. IN THE COMPLETELY METHYLATED WAC3CD5+ CLL CELLS, 5-AZA-2'-DEOXYCYTIDINE TREATMENT LED TO PROMOTER DEMETHYLATION AND RE-EXPRESSION OF BM742401 TRANSCRIPT. FUNCTIONALLY, STABLE OVEREXPRESSION OF BM742401 RESULTED IN INHIBITION OF CELLULAR PROLIFERATION AND ENHANCED APOPTOSIS THROUGH CASPASE-9-DEPENDENT INTRINSIC BUT NOT CASPASE-8-DEPENDENT EXTRINSIC APOPTOSIS PATHWAY, SUGGESTING A TUMOR SUPPRESSOR ROLE OF BM742401 IN CLL. IN PRIMARY CLL SAMPLES, METHYLATION OF BM742401 WAS DETECTED IN 43/98 (43.9%) OF PATIENTS. MOREOVER, AMONG CLL PATIENTS WITH STANDARD-RISK CYTOGENETIC ABERRATIONS, METHYLATION OF BM742401 CORRELATED WITH ADVANCED RAI STAGE (>/= STAGE 2)(P = 0.002). FURTHERMORE, BM742401 METHYLATION WAS ASSOCIATED WITH MIR-129-2 METHYLATION (P = 0.05). BM742401 IS A TUMOR SUPPRESSOR LNCRNA FREQUENTLY METHYLATED IN CLL. THE MECHANISM OF BM742401 AS A TUMOR SUPPRESSOR WARRANTS FURTHER STUDIES. 2016 12 3627 35 INACTIVATION OF LARS2, LOCATED AT THE COMMONLY DELETED REGION 3P21.3, BY BOTH EPIGENETIC AND GENETIC MECHANISMS IN NASOPHARYNGEAL CARCINOMA. ALLELIC LOSS OF CHROMOSOME 3P, INCLUDING THE 3P21.3 REGION, IS FOUND IN 95-100% OF PRIMARY NASOPHARYNGEAL CARCINOMA (NPC) BIOPSIES, SUGGESTING THAT THIS REGION SHOULD HARBOR SOME TUMOR SUPPRESSOR GENES (TSGS) CLOSELY RELATED TO NPC DEVELOPMENT. SEVERAL TSGS LOCATED AT 3P21.3, SUCH AS RASSF1A, LTF AND BLU, HAVE BEEN DEMONSTRATED TO BE INVOLVED IN NPC DEVELOPMENT. LARS2 (LEUCYL-TRNA SYNTHETASE 2, MITOCHONDRIAL) IS ANOTHER GENE LOCATED IN THE CHROMOSOME 3 COMMON ELIMINATED REGION-1 (C3CER1) AT 3P21.3. IN THIS STUDY, WE FOCUSSED ON THE EPIGENETIC AND GENETIC ALTERATIONS OF LARS2 IN NPC. THE MRNA EXPRESSION OF LARS2 WAS DETECTED IN 36 NPC AND 8 CHRONIC NASOPHARYNGITIS (NP) TISSUES BY SEMI-QUANTITATIVE REVERSE TRANSCRIPTION-POLYMERASE CHAIN REACTION (RT-PCR) AND REAL-TIME RT-PCR. SUBSEQUENTLY, THE MUTATION, ALLELIC LOSS, AND METHYLATION STATUS OF LARS2 WERE ANALYSED BY POLYMERASE CHAIN REACTION-SINGLE-STRAND CONFORMATION POLYMORPHISM (PCR-SSCP), HOMOZYGOUS DELETION (HD) ANALYSIS AND METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION IN PRIMARY NPC TISSUES. NO EXPRESSION OR DOWNREGULATION OF LARS2 WAS OBSERVED IN 78% OF PRIMARY NPC TISSUES. NO MUTATIONS, ASSESSED BY PCR-SSCP AND DNA SEQUENCING, WERE FOUND IN THE PROMOTER REGION AND EXON 1 OF LARS2 IN NPC TISSUES, WHEREAS HD WAS DETECTED IN 28% OF NPC SPECIMENS AT THE LARS2 LOCUS. IN ADDITION, HYPERMETHYLATION OF LARS2 WAS FOUND IN 64% OF NPC SAMPLES BUT ONLY IN 12.5% OF NP BIOPSIES. OUR DATA INDICATE THAT INACTIVATION OF LARS2 BY BOTH GENETIC AND EPIGENETIC MECHANISMS MAY BE A COMMON AND IMPORTANT EVENT IN THE CARCINOGENESIS OF NPC. 2009 13 4246 35 METHYLATION STATUS OF THE T-CADHERIN GENE PROMOTOR IN PERIPHERAL BLOOD MONONUCLEAR CELLS IS ASSOCIATED WITH HBV-RELATED HEPATOCELLULAR CARCINOMA PROGRESSION. DNA METHYLATION IS ONE OF THE EPIGENETIC MECHANISMS TO REGULATE GENE EXPRESSION AND FREQUENTLY OCCURS IN HUMAN CANCER CELLS. T-CADHERIN (CDH13) IS A NEW MEMBER OF THE CADHERIN SUPERFAMILY AND POSSESSES MULTIPLE FUNCTIONS. OUR STUDY INCLUDED 26 NORMAL CONTROLS (NCS), 65 CHRONIC HEPATITIS B PATIENTS (CHB), 14 LIVER CIRRHOSIS PATIENTS (LC) AND 157 HEPATOCELLULAR CARCINOMA PATIENTS (HCC). WE MAINLY FOCUSED ON THE MRNA EXPRESSION AND METHYLATION STATUS OF CDH13 IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS), WHICH WERE DETECTED BY SEMI-QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION (RT-QPCR) AND METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (MSP) RESPECTIVELY. THE CDH13 MRNA LEVEL WAS LOWER IN HCC, ESPECIALLY IN EARLY-STAGE OF HCC THAN IN NCS AND CHB GROUPS (P < 0.05). METHYLATION FREQUENCY OF THE CDH13 PROMOTER WAS SIGNIFICANTLY HIGHER IN HCC PATIENTS THAN IN THE NCS AND CHB GROUPS (67.52 % VS 0.00 %, P < 0.001, 67.52 % VS 52.31 %, P < 0.05, RESPECTIVELY). CDH13 MRNA LEVEL WAS SIGNIFICANTLY AND RELATIVELY LOWER IN METHYLATED GROUPS THAN IN UNMETHYLATED GROUPS AMONG THE WHOLE PARTICIPANTS. THE METHYLATION LEVEL OF CDH13 PROMOTER IN HCC MIGHT BE INFLUENCED OR PARTLY INFLUENCED BY SOME CRITICAL FACTORS SUCH AS TBIL, ALB AND AFP (P < 0.05). AS AN IMPORTANT FACTOR IN SIGNALING PATHWAY REGULATING BY CDH13 TO PROMOTE CARCINOGENESIS, JNK LEVEL WAS SIGNIFICANTLY HIGHER IN HCC WHICH HAD A HIGHER METHYLATION FREQUENCY THAN IN NCS, CHB AND LC (P < 0.05). FURTHERMORE, THE COMBINATION OF THE METHYLATED CDH13 LEVEL AND AFP LEVEL SHOWED A BETTER SCORE: AUC = 0.796 (SE = 0.031, 95 %CI 0.735-0.857; P < 0.001) IN MALE AND AUC = 0.832 (SE = 0.057, 95 %CI 0.721-0.944; P < 0.001) IN FEMALE COMPARED TO AFP ALONE FOR DIAGNOSING HCC FROM NCS, CHB AND LC. THE METHYLATION OF CDH13 PROMOTER WAS AN INDEPENDENT PREDICTOR FOR ASSESSING THE PROGNOSIS OF HCC PATIENTS (R=-1.378 P < 0.05). IN CONCLUSION, HYPERMETHYLATION OF CDH13 IN PBMCS WAS ASSOCIATED WITH THE UNDEREXPRESSION OF MRNA AND THE HIGH RISK OF HCC. THE METHYLATION STATUS OF THE CDH13 PROMOTER IN PBMCS WAS A POTENTIAL NONINVASIVE BIOMARKER TO PREDICT THE PROGNOSIS OF HCC PATIENTS. 2020 14 5274 15 PROMOTER METHYLATION OF P16 AND EDNRB GENE IN LEUKEMIA PATIENTS IN TAIWAN. BOTH EPIGENETIC AND GENETIC ALTERNATIONS ARE INVOLVED IN CANCER FORMATION. IN THIS STUDY, WE HAVE IDENTIFIED THE METHYLATION FREQUENCY OF P16 AND ENDOTHELIN RECEPTOR TYPE B (EDNRB) OF 26 LEUKEMIA PATIENTS AND 8 RANDOMLY SELECTED NORMAL BLOOD DONORS IN TAIWAN. PROMOTER METHYLATION OF P16 WAS DETECTED IN 85% OF ACUTE LYMPHOCYTIC LEUKEMIA (ALL), 83% IN ACUTE MYELOID LEUKEMIA (AML) WHEREAS NO METHYLATION WAS DETECTED IN CHRONIC MYELOID LEUKEMIA (CML) IN BLAST CRISIS. HYPERMETHYLATION OF EDNRB WAS OBSERVED IN 92% OF ALL, 75% AML AND 100% IN CML IN BLAST CRISIS. NO ABERRANT METHYLATION OF P16 AND EDNRB WAS FOUND IN 8 NORMAL BLOOD DONORS. TAKEN TOGETHER, ABERRANT METHYLATION OF P16 AND EDNRB WAS HIGHLY PREVALENT IN LEUKEMIA PATIENTS IN TAIWAN. 2008 15 939 24 CHRONIC LYMPHOCYTIC LEUKEMIA AND 13Q14: MIRS AND MORE. LOSS OF A CRITICAL REGION IN 13Q14.3 [DEL(13Q)] IS THE MOST COMMON GENOMIC ABERRATION IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), OCCURRING IN MORE THAN 50% OF PATIENTS (STILGENBAUER ET AL., ONCOGENE 1998;16:1891 - 1897, DOHNER ET AL., N ENGL J MED 2000;343:1910 - 1916). DESPITE EXTENSIVE INVESTIGATIONS, NO POINT MUTATIONS HAVE BEEN FOUND IN THE REMAINING ALLELE THAT WOULD INACTIVATE ONE OF THE CANDIDATE TUMOR SUPPRESSOR GENES AND EXPLAIN THE PATHOMECHANISM POSTULATED FOR THIS REGION. HOWEVER, THE GENES IN THE REGION ARE SIGNIFICANTLY DOWN-REGULATED IN CLL CELLS, MORE THAN WOULD BE EXPECTED BY GENE DOSAGE, AND RECENTLY A COMPLEX EPIGENETIC REGULATORY MECHANISM WAS IDENTIFIED FOR 13Q14.3 IN NON-MALIGNANT CELLS THAT INVOLVES ASYNCHRONOUS REPLICATION TIMING AND MONOALLELIC EXPRESSION OF CANDIDATE TUMOR SUPPRESSOR GENES. HERE, WE PROPOSE A MODEL OF A MULTIGENIC PATHOMECHANISM IN 13Q14.3, WHERE SEVERAL TUMOR SUPPRESSOR GENES, INCLUDING THE MIRNA GENES MIR-16-1 AND MIR-15A, ARE CO-REGULATED BY THE TWO LONG NON-CODING RNA GENES DLEU1 AND DLEU2 THAT SPAN THE CRITICAL REGION. FURTHERMORE, WE PROPOSE THESE CO-REGULATED GENES TO BE INVOLVED IN THE SAME MOLECULAR PATHWAYS, THEREBY ALSO FORMING A FUNCTIONAL GENE CLUSTER. ELUCIDATING THE MOLECULAR AND CELLULAR FUNCTION OF THE 13Q14.3 CANDIDATE GENES WILL SHED LIGHT ON THE UNDERLYING PATHOMECHANISM OF CLL. 2009 16 4229 31 METHYLATION OF INK4 AND CIP/KIP FAMILIES OF CYCLIN-DEPENDENT KINASE INHIBITOR IN CHRONIC LYMPHOCYTIC LEUKAEMIA IN CHINESE PATIENTS. BACKGROUND: INK4 (P15, P16, P18 AND P19) AND CIP/KIP (P21, P27 AND P57) ARE TWO FAMILIES OF CYCLIN-DEPENDENT KINASE INHIBITORS (CKI) TARGETING CDK4/6 AND CDK2, RESPECTIVELY. AIM: TO STUDY THE ROLE OF METHYLATION IN THE INACTIVATION OF CKI IN CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL). MATERIALS AND METHODS: METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION WAS CARRIED OUT ON DNA OBTAINED FROM THE BONE MARROW OF 56 NEWLY DIAGNOSED PATIENTS WITH CLL. RESULTS: SIMILAR DEMOGRAPHIC FEATURES AND CLINICAL OUTCOME WERE OBSERVED IN OUR PATIENTS WHEN COMPARED WITH CAUCASIAN PATIENTS, INCLUDING AN INDOLENT CLINICAL COURSE (10-YEAR OVERALL SURVIVAL 51%) AND ADVANCED RAI STAGE (P = 0.006), AND A HIGH-RISK KARYOTYPE SUCH AS TRISOMY 12 AND COMPLEX ABERRATIONS (P = 0.03). IN THE INK4 FAMILY, METHYLATION IN P15 AND P16 OCCURRED IN 20 (35.7%) AND 8 (14.3%) PATIENTS, RESPECTIVELY. IN ALL, 5 (8.9%) CLL SAMPLES HARBOURED CONCURRENT METHYLATION OF BOTH P15 AND P16. APART FROM AN ASSOCIATION OF P16 METHYLATION WITH HIGHER PRESENTING LEUCOCYTE COUNT (64.5 X 10(9)/L IN METHYLATED P16 AND 16.0 X 10(9)/L IN UNMETHYLATED P16 PATIENTS; P = 0.016), THERE WAS NO ASSOCIATION BETWEEN P15 AND P16 METHYLATION AND AGE, SEX AND RAI STAGE. NO DIFFERENCE WAS OBSERVED IN THE OVERALL SURVIVAL FOR PATIENTS WITH AND WITHOUT P15 AND P16 METHYLATION. BY CONTRAST, P18 AND RB WERE UNMETHYLATED IN ALL SAMPLES. IN THE CIP/KIP FAMILY, APART FROM INFREQUENT METHYLATION OF P57 IN 4 (7.1%) PATIENTS, METHYLATION OF P21 AND P27 WAS UNIFORMLY ABSENT. CONCLUSION: P15 AND, LESS FREQUENTLY, P16 OF THE INK4 FAMILY OF CKI, INSTEAD OF THE CIP OR KIP FAMILY, WERE TARGETED BY METHYLATION IN CLL. P16 METHYLATION WAS ASSOCIATED WITH A HIGHER LYMPHOCYTE COUNT AT PRESENTATION. THIS IS THE FIRST COMPREHENSIVE STUDY OF THE EPIGENETIC DYSREGULATION OF THE INK4 AND CIP/KIP FAMILIES OF CKI IN CHINESE PATIENTS WITH CLL. 2006 17 494 29 ASSESSMENT OF PROMOTER METHYLATION IDENTIFIES PTCH AS A PUTATIVE TUMOR-SUPPRESSOR GENE IN HUMAN CLL. BACKGROUND: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS CHARACTERIZED BY A CLONAL ACCUMULATION OF NEOPLASTIC LYMPHOCYTES, INDICATING DISRUPTION OF APOPTOSIS. PATIENTS AND METHODS: DIFFERENTIAL METHYLATION HYBRIDIZATION ANALYSIS WAS PERFORMED TO IDENTIFY NOVEL TARGET GENES SILENCED BY CPG ISLAND METHYLATION IN PATIENTS WITH CLL. RESULTS: PATCHED (PTCH), A TUMOR-SUPPRESSOR GENE, WAS FOUND TO BE FREQUENTLY METHYLATED IN CLL SAMPLES COMPARED TO SAMPLES DERIVED FROM HEALTHY INDIVIDUALS. DE NOVO METHYLATION OF A CPG ISLAND REGION LOCATED UPSTREAM OF PTCH EXON 1 WAS CONFIRMED BY PYROSEQUENCING IN 17/37 (46%) OF PERIPHERAL BLOOD MONONUCLEAR CELLS OF PATIENTS WITH CLL, BUT IN NONE ISOLATED FROM SEVEN HEALTHY INDIVIDUALS. NO ASSOCIATION WAS FOUND BETWEEN PTCH HYPERMETHYLATION AND CURRENTLY USED PROGNOSTIC CLL FACTORS. CONCLUSION: OUR INVESTIGATION SUGGESTS THAT EPIGENETIC SILENCING OF PTCH IS A MECHANISM CONTRIBUTING TO CLL TUMORIGENESIS. 2016 18 2843 37 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 19 156 32 ABERRANT METHYLATION OF THE DEATH-ASSOCIATED PROTEIN KINASE 1 (DAPK1) CPG ISLAND IN CHRONIC MYELOID LEUKEMIA. THE DEATH-ASSOCIATED PROTEIN KINASE 1 (DAPK1) GENE IS A CANDIDATE TUMOR SUPPRESSOR (TSG) AND THE ABNORMAL METHYLATION OF DAPK1 GENE HAS BEEN FOUND IN MANY CARCINOMAS. THE EPIGENETIC CHANGES OF TSGS ARE NOW RECOGNIZED AS A MECHANISM CONTRIBUTING TO THE DEVELOPMENT OF CHRONIC MYELOID LEUKEMIA (CML). TO CLARIFY THE ROLE OF DAPK1 IN CML, WE EXAMINED THE METHYLATION STATUS OF DAPK1 IN 49 PATIENTS WITH CML USING METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION. THE ABERRANT METHYLATION OF THE DAPK1 GENE WAS FOUND IN 25 OF 49 (51.0%) CML CASES, NOT IN ALL CONTROLS. NO CORRELATION WAS FOUND BETWEEN DAPK1 GENE METHYLATION AND THE AGE, HEMATOLOGIC PARAMETERS, CHROMOSOMAL ABNORMALITIES, THE TYPES AND LEVELS OF BCR/ABL TRANSCRIPTS OF CML PATIENTS. HOWEVER, CORRELATION COULD BE OBSERVED BETWEEN THE SEX AND THE STATUS OF DAPK1 METHYLATION IN CML PATIENTS (R = 0.374, P = 0.008). FURTHERMORE, THERE WAS A SIGNIFICANT CORRELATION BETWEEN DAPK1 METHYLATION AND THE STAGES OF CML (R = 0.354, P = 0.013). THE CML PATIENTS IN ACCELERATED PHASE (AP) AND BLAST CRISIS (BC) HAD HIGHER FREQUENCY OF DAPK1 METHYLATION THAN THOSE IN CHRONIC PHASE (CP) (75.0% VS. 34.5%) (CHI(2) = 7.776, P = 0.005). IN ONE PATIENT, THE STATUS OF DAPK1 METHYLATION BECAME POSITIVE ON THE TRANSITION FROM CP TO AP AND BC. THESE RESULTS SUGGESTED THAT DAPK1 PROMOTER METHYLATION MIGHT PLAY A SIGNIFICANT ROLE IN THE PROGRESSION OF CML. 2009 20 1107 33 COMBINING CYTOGENETIC AND EPIGENETIC APPROACHES IN CHRONIC LYMPHOCYTIC LEUKEMIA IMPROVES PROGNOSIS PREDICTION FOR PATIENTS WITH ISOLATED 13Q DELETION. BACKGROUND: BOTH DEFECTIVE DNA METHYLATION AND ACTIVE DNA DEMETHYLATION PROCESSES ARE EMERGING AS IMPORTANT RISK FACTORS IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). HOWEVER, ASSOCIATIONS BETWEEN 5-CYTOSINE EPIGENETIC MARKERS AND THE MOST FREQUENT CHROMOSOMAL ABNORMALITIES DETECTED IN CLL REMAIN TO BE ESTABLISHED. METHODS: CLL PATIENTS WERE RETROSPECTIVELY CLASSIFIED INTO A CYTOGENETIC LOW-RISK GROUP (ISOLATED 13Q DELETION), AN INTERMEDIATE-RISK GROUP (NORMAL KARYOTYPE OR TRISOMY 12), AND A HIGH-RISK GROUP (11Q DELETION, 17P DELETION, OR COMPLEX KARYOTYPE [>/= 3 BREAKPOINTS]). THE TWO 5-CYTOSINE DERIVATIVES, 5-METHYLCYTOSINE (5-MCYT) AND 5-HYDROXYMETHYLCYTOSINE (5-HMCYT), WERE TESTED BY ELISA (N = 60), WHILE REAL-TIME QUANTITATIVE PCR WAS USED FOR DETERMINING TRANSCRIPTIONAL EXPRESSION LEVELS OF DNMT AND TET (N = 24). RESULTS: BY USING GLOBAL DNA METHYLATION/DEMETHYLATION LEVELS, IN THE LOW-RISK DISEASE GROUP, TWO SUBGROUPS WITH SIGNIFICANTLY DIFFERENT CLINICAL OUTCOMES HAVE BEEN IDENTIFIED (MEDIAN TREATMENT-FREE SURVIVAL [TFS] 45 VERSUS > 120 MONTHS FOR 5-MCYT, P = 0.0008, AND 63 VERSUS > 120 MONTHS FOR 5-HMCYT, P = 0.04). A DEFECTIVE 5-MCYT STATUS WAS FURTHER ASSOCIATED WITH A HIGHER PERCENTAGE OF 13Q DELETED NUCLEI (> 80%), THUS SUGGESTING AN ACQUIRED PROCESS. WHEN CONSIDERING THE CYTOGENETIC INTERMEDIATE/HIGH-RISK DISEASE GROUPS, AN ASSOCIATION OF 5-MCYT STATUS WITH LYMPHOCYTOSIS (P = 0.0008) AND THE LYMPHOCYTE DOUBLING TIME (P = 0.04) BUT NOT WITH TFS WAS OBSERVED, AS WELL AS A REDUCTION OF DNMT3A, TET1, AND TET2 TRANSCRIPTS. CONCLUSIONS: COMBINING CYTOGENETIC STUDIES WITH 5-MCYT ASSESSMENT ADDS ACCURACY TO CLL PATIENTS' PROGNOSES AND PARTICULARLY FOR THOSE WITH 13Q DELETION AS A SOLE CYTOGENETIC ABNORMALITY. 2017