1 3294 141 HIGH INCIDENCE OF MGMT AND RARBETA PROMOTER METHYLATION IN PRIMARY GLIOBLASTOMAS: ASSOCIATION WITH HISTOPATHOLOGICAL CHARACTERISTICS, INFLAMMATORY MEDIATORS AND CLINICAL OUTCOME. GLIOBLASTOMAS, THE MOST FREQUENT PRIMARY BRAIN TUMORS IN ADULTS, ARE CHARACTERIZED BY A HIGHLY AGGRESSIVE, INFLAMMATORY AND ANGIOGENIC PHENOTYPE. METHYLATION OF CPG ISLANDS IN CANCER-RELATED GENES MAY SERVE AS AN EPIGENETIC BIOMARKER FOR GLIOBLASTOMA DIAGNOSIS AND PROGNOSIS. THE AIM OF THIS STUDY WAS TO ANALYZE THE METHYLATION STATUS OF FOUR CRITICAL TUMOR-ASSOCIATED GENES (MGMT, RARBETA, RASSF1A, CDH13), AND INVESTIGATE POSSIBLE LINKS WITH INFLAMMATORY (INTERLEUKIN [IL]-6, IL-8) AND ANGIOGENIC MEDIATORS (VASCULAR ENDOTHELIAL GROWTH FACTOR [VEGF], CYCLOOXYGENASE [COX]-2) AND CLINICAL OUTCOME IN 23 GLIOMA SAMPLES (6 GRADE II ASTROCYTOMAS, 17 GRADE IV GLIOBLASTOMAS). RARBETA AND MGMT GENES WERE MORE FREQUENTLY METHYLATED IN 70.58% AND 58.8% OF GLIOBLASTOMAS, RESPECTIVELY. RASSF1A AND CDH13 DISPLAYED A SIMILAR METHYLATION FREQUENCY (23.52%) IN GLIOBLASTOMAS. NO GENE METHYLATION WAS OBSERVED IN GRADE II ASTROCYTOMAS. TUMOR GRADE CORRELATED POSITIVELY WITH MGMT AND RARBETA METHYLATION (P = 0.005 AND P = 0.019, RESPECTIVELY) AND THE EXTENT OF NECROSIS (P = 0.001 AND P = 0.003). INTERESTINGLY, THE MARKER OF CHRONIC INFLAMMATION, IL-6, WAS POSITIVELY ASSOCIATED WITH METHYLATION OF MGMT (P = 0.004), RARBETA (P = 0.002), AND RASSF1A (P = 0.0081) AS WELL AS THE TOTAL NUMBER OF METHYLATED GENES (P < 0.0001), INDICATING THE IMPORTANT ROLE OF IL-6 IN MAINTAINING PROMOTER METHYLATION OF THESE GENES. VEGF EXPRESSION CORRELATED POSITIVELY WITH MGMT AND RARBETA METHYLATION ALTHOUGH THESE RELATIONSHIPS WERE OF MARGINAL SIGNIFICANCE (P = 0.0679 AND P = 0.0757). KAPLAN-MEIER UNIVARIATE SURVIVAL ANALYSIS INDICATED AN UNFAVORABLE SURVIVAL PERIOD IN PATIENTS WITH MGMT METHYLATION COMPARED WITH THOSE WITHOUT METHYLATION (P = 0.0474). OUR STUDY HIGHLIGHTS THE IMPLICATION OF MGMT AND RARBETA METHYLATION IN THE AGGRESSIVE PHENOTYPE OF PRIMARY GLIOBLASTOMAS. THE ASSOCIATION OF MGMT METHYLATION WITH CLINICAL OUTCOME INDICATES ITS POTENTIAL PROGNOSTIC VALUE. 2010 2 2845 34 FREQUENT EPIGENETIC INACTIVATION OF THE SLIT2 GENE IN CHRONIC AND ACUTE LYMPHOCYTIC LEUKEMIA. RECENTLY A MOUSE MODEL OF T/NATURAL KILLER ACUTE LYMPHOBLASTIC LEUKEMIA WAS USED TO ASSESS GLOBAL PROMOTER METHYLATION ACROSS THE MOUSE GENOME USING THE RESTRICTION LANDMARK GENOMIC SCANNING TECHNIQUE. ONE OF THE METHYLATED MOUSE GENES IDENTIFIED IN THIS WAY WAS SLIT2. THERE ARE THREE MAMMALIAN SLIT GENES (SLIT1, SLIT2, SLIT3), THAT BELONG TO A HIGHLY CONSERVED FAMILY OF AXON GUIDANCE MOLECULES. WE HAVE PREVIOUSLY DEMONSTRATED THAT SLIT2 IS FREQUENTLY INACTIVATED IN LUNG, BREAST, COLORECTAL AND GLIOMA TUMORS BY HYPERMETHYLATION OF A CPG ISLAND IN ITS PROMOTER REGION, WHILST INACTIVATING SOMATIC MUTATIONS ARE RARE. FURTHERMORE, WE DEMONSTRATED THAT SLIT2 ACTS AS A TUMOR SUPPRESSOR GENE IN BREAST AND COLORECTAL CANCER CELLS. IN THIS REPORT WE DETERMINED THE METHYLATION STATUS OF THE SLIT2 GENE IN LEUKEMIAS (CLL AND ALL). SLIT2 WAS METHYLATED IN ALL TEN LEUKEMIA CELL LINES ANALYZED (EIGHT COMPLETELY AND TWO PARTIALLY METHYLATED). SLIT2 EXPRESSION WAS RESTORED AFTER TREATING ALL LINES WITH 5-AZA-2DC. IN PRIMARY ALL AND CLL SAMPLES, SLIT2 WAS ALSO FREQUENTLY METHYLATED, 58% (30/52) B-ALL; 83% (10/12) T-ALL AND IN 80% (24/30) CLL. WHILST DNA FROM PERIPHERAL BLOOD AND BONE MARROW FROM HEALTHY CONTROL SAMPLES SHOWED NO SLIT2 METHYLATION. METHYLATION RESULTS IN LEUKEMIA CELL LINES AND ALL AND CLL PRIMARY SAMPLES WERE CONFIRMED BY DIRECT SEQUENCING OF BISULFITE MODIFIED DNA. OUR RESULTS DEMONSTRATE THAT METHYLATION OF THE SLIT2 5' CPG ISLAND IS CONSERVED BETWEEN MICE AND HUMANS, AND THEREFORE IS LIKELY TO BE OF FUNCTIONAL IMPORTANCE. 2009 3 1445 23 DIFFUSE PEDIATRIC-TYPE HIGH-GRADE GLIOMA ARISING IN AN OVARIAN MATURE CYSTIC TERATOMA. IMMATURE NEUROECTODERMAL TISSUE CAN BE FOUND IN THE OVARY AS PART OF AN IMMATURE TERATOMA OR AS PART OF A TERATOMA WITH MALIGNANT NEUROECTODERMAL TRANSFORMATION. SUCH LESIONS MAY CLOSELY RESEMBLE CENTRAL NERVOUS SYSTEM TUMORS, BUT THEIR BIOLOGIC SIMILARITY IS UNCLEAR. WE DESCRIBE AN 18-YR-OLD FEMALE WHO PRESENTED WITH ABDOMINAL PAIN CAUSED BY AN OVARIAN MASS WITH WIDESPREAD METASTASES. HISTOLOGY SHOWED A PRIMITIVE, HIGH-GRADE TUMOR ARISING IN THE BACKGROUND OF A MATURE TERATOMA. THE TUMOR WAS SOX10 POSITIVE, WITH FOCAL EXPRESSION OF GFAP, S100, NSE, AND SYNAPTOPHYSIN. MOLECULAR ANALYSIS DEMONSTRATED CO-AMPLIFICATION OF PDGFRA AND KIT, ALTERATIONS COMMON IN HIGH-GRADE GLIOMAS. BY WHOLE-GENOME METHYLATION PROFILING, IT CLUSTERED INTO THE "DIFFUSE PEDIATRIC-TYPE HIGH-GRADE GLIOMA, RTK1 SUBTYPE, SUBCLASS C" GROUP. DESPITE PROGRESSING THROUGH 2 LINES OF CHEMOTHERAPY WITH WIDESPREAD METASTATIC DISEASE, SHE ACHIEVED AN EXCELLENT RESPONSE TO CHEMOTHERAPY DIRECTED TOWARD AGGRESSIVE GERM CELL TUMORS. THIS CASE EMPHASIZES THE IMPORTANCE OF IMMUNOHISTOCHEMICAL, GENOMIC, AND EPIGENETIC ANALYSES TO ACCURATELY CLASSIFY THESE EXCEEDINGLY RARE TUMORS AND DETERMINE THE OPTIMAL THERAPY. 2023 4 604 30 BEYOND BROODING ON ONCOMETABOLIC HAVOC IN IDH-MUTANT GLIOMAS AND AML: CURRENT AND FUTURE THERAPEUTIC STRATEGIES. ISOCITRATE DEHYDROGENASES 1 AND 2 (IDH1,2), THE KEY KREBS CYCLE ENZYMES THAT GENERATE NADPH REDUCING EQUIVALENTS, UNDERGO HETEROZYGOUS MUTATIONS IN >70% OF LOW- TO MID-GRADE GLIOMAS AND ~20% OF ACUTE MYELOID LEUKEMIAS (AMLS) AND GAIN AN UNUSUAL NEW ACTIVITY OF REDUCING THE ALPHA-KETOGLUTARATE (ALPHA-KG) TO D-2 HYDROXYGLUTARATE (D-2HG) IN A NADPH-CONSUMING REACTION. THE ONCOMETABOLITE D-2HG, WHICH ACCUMULATES >35 MM, IS WIDELY ACCEPTED TO DRIVE A PROGRESSIVE ONCOGENESIS BESIDES EXACERBATING THE ALREADY INCREASED OXIDATIVE STRESS IN THESE CANCERS. MORE IMPORTANTLY, D-2HG COMPETES WITH ALPHA-KG AND INHIBITS A LARGE NUMBER OF ALPHA-KG-DEPENDENT DIOXYGENASES SUCH AS TET (TEN-ELEVEN TRANSLOCATION), JMJC DOMAIN-CONTAINING KDMS (HISTONE LYSINE DEMETHYLASES), AND THE ALKBH DNA REPAIR PROTEINS THAT ULTIMATELY LEAD TO HYPERMETHYLATION OF THE CPG ISLANDS IN THE GENOME. THE RESULTING CPG ISLAND METHYLATOR PHENOTYPE (CIMP) ACCOUNTS FOR MAJOR GENE EXPRESSION CHANGES INCLUDING THE SILENCING OF THE MGMT (O(6)-METHYLGUANINE DNA METHYLTRANSFERASE) REPAIR PROTEIN IN GLIOMAS. GLIOMA PATIENTS WITH IDH1 MUTATIONS ALSO SHOW BETTER THERAPEUTIC RESPONSES AND LONGER SURVIVAL, THE REASONS FOR WHICH ARE YET UNCLEAR. THERE HAS BEEN A GREAT SURGE IN DRUG DISCOVERY FOR CURTAILING THE MUTANT IDH ACTIVITIES, AND ARRESTING TUMOR PROLIFERATION; HOWEVER, GIVEN THE UNIQUE AND CHRONIC METABOLIC EFFECTS OF D-2HG, THE PROMISE OF THESE COMPOUNDS FOR GLIOMA TREATMENT IS UNCERTAIN. THIS COMPREHENSIVE REVIEW DISCUSSES THE BIOLOGY, CURRENT DRUG DESIGN AND OPPORTUNITIES FOR IMPROVED THERAPIES THROUGH EXPLOITABLE SYNTHETIC LETHALITY PATHWAYS, AND AN INTRIGUING ONCOMETABOLITE-INSPIRED STRATEGY FOR PRIMARY GLIOBLASTOMA. 2018 5 6813 30 [EPILEPSY-ASSOCIATED TUMORS OF THE CENTRAL NERVOUS SYSTEM: EPILEPSY SURGERY AND ONCOLOGICAL ASPECTS]. BACKGROUND: AMONG THE TUMORS ASSOCIATED WITH CHRONIC EPILEPSY, DYSEMBRYOPLASTIC NEUROEPITHELIAL TUMOR AND GANGLIOGLIOMA ARE THE MOST COMMON BESIDES ANGIOCENTRIC GLIOMA, PLEOMORPHIC XANTHOASTROCYTOMA AND PILOCYTIC ASTROCYTOMA. THESE TUMORS ARE USUALLY CONSIDERED AS BEING BENIGN. OBJECTIVE: TO DETERMINE THE BEST CONSERVATIVE AND SURGICAL TREATMENT OF TUMORS ASSOCIATED WITH EPILEPSY. MATERIAL AND METHODS: THIS ARTICLE PRESENTS CASE REPORTS OF MALIGNANT TRANSFORMATION OF A DYSEMBRYOPLASTIC NEUROEPITHELIAL TUMOR AND OF A TUMOR INITIALLY DIAGNOSED AS A GANGLIOGLIOMA BASED ON MAGNETIC RESONANCE IMAGING (MRI) CRITERIA. DESCRIPTION OF REFERENCES IN THE LITERATURE ON EPILEPSY SURGERY AND THE NEURO-ONCOLOGY OF EPILEPSY-ASSOCIATED TUMORS. RESULTS: IN THE CASE OF THE INITIALLY HISTOPATHOLOGICALLY DIAGNOSED DYSEMBRYOPLASTIC NEUROEPITHELIAL TUMOR, A MALIGNANT TRANSFORMATION OCCURRED 5 YEARS AFTER INCOMPLETE RESECTION. THE DIFFERENTIATION FROM A GLIOBLASTOMA WAS POSSIBLE THROUGH THE ANALYSIS OF THE METHYLATION PROFILE. IN ANOTHER CASE A TUMOR ASSUMED TO BE A GANGLIOGLIOMA SHOWED AN INCREASE IN SIZE AFTER 6 YEARS. INITIAL HISTOPATHOLOGICAL RESULTS REVEALED A GLIOBLASTOMA. THE ANALYSIS OF THE METHYLATION PROFILE SUGGESTED THE DIAGNOSIS OF AN ANAPLASTIC PLEOMORPHIC XANTHOASTROCYTOMA AND AS A DIFFERENTIAL DIAGNOSIS AN ANAPLASTIC GANGLIOGLIOMA. TUMOR PROGRESS CORRELATED WITH THE WORSENING OF SEIZURES. CONCLUSION: RECENT STUDIES HAVE SHOWN THAT IN THE TREATMENT OF PREDOMINANTLY BENIGN EPILEPSY-ASSOCIATED TUMORS NEURO-ONCOLOGICAL ASPECTS SHOULD ALSO BE TAKEN INTO ACCOUNT IN ADDITION TO THE EPILEPTOLOGICAL CONSIDERATIONS. IN THE CASE OF MALIGNANT TRANSFORMATION EPIGENETIC SCREENING (METHYLATION PROFILES) CAN HELP TO CLASSIFY THE TUMOR ENTITY MORE PRECISELY. 2016 6 5730 35 SLIT2 PROMOTER HYPERMETHYLATION PREDICTS DISEASE PROGRESSION IN CHRONIC MYELOID LEUKEMIA. BACKGROUND: ABERRANT DNA METHYLATION PLAYS A CRUCIAL ROLE IN THE PROGRESSION OF MYELOID NEOPLASMS. PREVIOUSLY, OUR LITERATURE REPORTED THAT SLIT GUIDANCE LIGAND 2 (SLIT2) PROMOTER METHYLATION WAS ASSOCIATED WITH DISEASE PROGRESSION AND INDICATED A POOR PROGNOSIS IN PATIENTS WITH MYELODYSPLASTIC SYNDROME. HEREIN, WE FURTHER INVESTIGATED THE CLINICAL IMPLICATIONS AND ROLE OF SLIT2 PROMOTER METHYLATION IN PATIENTS WITH CHRONIC MYELOID LEUKEMIA (CML). METHODS: THE LEVEL OF SLIT2 PROMOTER METHYLATION WAS DETERMINED IN 104 CML PATIENTS, AND ITS CLINICAL SIGNIFICANCE WAS ANALYZED. MOREOVER, DEMETHYLATION STUDIES WERE PERFORMED IN K562 CELLS TO DETERMINE THE EPIGENETIC MECHANISM BY WHICH SLIT2 PROMOTER METHYLATION IS REGULATED IN CML. RESULTS: THE LEVEL OF SLIT2 PROMOTER METHYLATION WAS SIMILAR BETWEEN CML PATIENTS AND CONTROLS. HOWEVER, DEEPER ANALYSIS REVEALED THAT THE SLIT2 PROMOTER METHYLATION LEVEL IN THE ACCELERATED PHASE (AP) AND BLAST CRISIS (BC) WAS MARKEDLY HIGHER THAN THAT IN THE CHRONIC PHASE (CP) AND CONTROLS. ADDITIONALLY, A MARKED DIFFERENCE WAS IDENTIFIED BETWEEN THE SLIT2 PROMOTER HYPERMETHYLATED AND NON-HYPERMETHYLATED GROUPS AMONG CML PATIENTS GROUPED BY CLINICAL STAGE. THE FREQUENCY OF SLIT2 HYPERMETHYLATION WAS MARKEDLY INCREASED WITH THE PROGRESSION OF CLINICAL STAGE, THAT IS, IT WAS THE LOWEST IN CP SAMPLES (12/80, 15%), HIGHER IN AP SAMPLES (4/8, 50%) AND THE HIGHEST IN BC SAMPLES (11/16, 69%). IMPORTANTLY, THE LEVEL/DENSITY OF SLIT2 PROMOTER METHYLATION WAS SIGNIFICANTLY HIGHER IN THE ADVANCED STAGE THAN IN THE EARLY STAGE AMONG THE 6 TESTED PAIRED CML PATIENTS. EPIGENETICALLY, THE EXPRESSION OF THE SLIT2-EMBEDDED NON-CODING GENES SLIT2-IT1 AND MIR-218 EXPRESSION WAS DECREASED IN PATIENTS WITH CML. SLIT2 PROMOTER HYPERMETHYLATED CASES HAD A MARKEDLY LOWER SLIT2-IT1 EXPRESSION LEVEL THAN SLIT2 PROMOTER NON-HYPERMETHYLATED CASES. MOREOVER, SLIT2-IT1 AND MIR-218 EXPRESSION WAS REMARKABLY UPREGULATED IN A DOSE-DEPENDENT MANNER AFTER DEMETHYLATION TREATMENT OF K562 CELLS. CONCLUSIONS: HYPERMETHYLATION OF THE SLIT2 PROMOTER IS CORRELATED WITH DISEASE PROGRESSION IN CML. FURTHERMORE, SLIT2 PROMOTER METHYLATION MAY FUNCTION BY REGULATING THE EXPRESSION OF THE SLIT2-EMBEDDED NON-CODING GENES SLIT2-IT1 AND MIR-218 DURING CML PROGRESSION. 2022 7 2426 32 EPIGENETIC SILENCING OF LONG NON-CODING RNA BM742401 IN MULTIPLE MYELOMA: IMPACT ON PROGNOSIS AND MYELOMA DISSEMINATION. BACKGROUND: LONG NON-CODING RNA (LNCRNA) BM742401 IS A TUMOR SUPPRESSOR IN GASTRIC CANCER AND CHRONIC LYMPHOCYTIC LEUKEMIA. AS THE PROMOTER AND CODING REGION OF BM742401 ARE FULLY EMBEDDED IN A CPG ISLAND, WE HYPOTHESIZED THAT BM742401 IS A TUMOR SUPPRESSOR LNCRNA EPIGENETICALLY SILENCED BY PROMOTER DNA METHYLATION IN MULTIPLE MYELOMA. METHODS: METHYLATION-SPECIFIC PCR AND QUANTITATIVE BISULFITE PYROSEQUENCING WERE PERFORMED TO DETECT THE METHYLATION OF BM742401 IN NORMAL PLASMA CELLS, MYELOMA CELL LINES AND PRIMARY MYELOMA SAMPLES. THE EXPRESSION OF BM742401 WAS MEASURED BY QRT-PCR. THE FUNCTION OF BM742401 IN MULTIPLE MYELOMA CELLS WAS ANALYZED BY LENTIVIRUS TRANSDUCTION FOLLOWED BY MIGRATION ASSAY. RESULTS: BM742401 METHYLATION WAS DETECTED IN 10 (66.7%) MYELOMA CELL LINES BUT NOT NORMAL PLASMA CELLS, AND INVERSELY CORRELATED WITH EXPRESSION OF BM742401. IN PRIMARY SAMPLES, BM742401 METHYLATION WAS DETECTED IN 3 (12.5%) MONOCLONAL GAMMOPATHY OF UNDETERMINED SIGNIFICANCE, 9 (15.8%) MYELOMA AT DIAGNOSIS AND 8 (17.0%) MYELOMA AT RELAPSE/PROGRESSION. MOREOVER, BM742401 METHYLATION AT DIAGNOSIS WAS ASSOCIATED WITH INFERIOR OVERALL SURVIVAL (MEDIAN OS: 25 VS. 39 MONTHS; P = 0.0496). IN MYELOMA CELL LINE JJN-3, STABLE OVEREXPRESSION OF BM742401 BY LENTIVIRUS TRANSDUCTION RESULTED IN REDUCED CELL MIGRATION (P = 0.0001) BUT NOT IMPACTING CELL DEATH OR PROLIFERATION. CONCLUSIONS: THIS IS THE FIRST REPORT OF TUMOR-SPECIFIC METHYLATION-MEDIATED SILENCING OF BM742401 IN MYELOMA, WHICH IS LIKELY AN EARLY EVENT IN MYELOMAGENESIS WITH ADVERSE IMPACT ON OVERALL SURVIVAL. MOREOVER, BM742401 IS A TUMOR SUPPRESSOR LNCRNA BY INHIBITING MYELOMA CELL MIGRATION, HENCE IMPLICATED IN MYELOMA PLASMA CELL HOMING, METASTASIS AND DISEASE PROGRESSION. 2020 8 1620 29 DNA METHYLTRANSFERASE-MEDIATED TRANSCRIPTIONAL SILENCING IN MALIGNANT GLIOMA: A COMBINED WHOLE-GENOME MICROARRAY AND PROMOTER ARRAY ANALYSIS. EPIGENETIC INACTIVATION OF TUMOR SUPPRESSOR GENES IS A COMMON FEATURE IN HUMAN CANCER. PROMOTER HYPERMETHYLATION AND HISTONE DEACETYLATION ARE REVERSIBLE EPIGENETIC MECHANISMS ASSOCIATED WITH TRANSCRIPTIONAL REGULATION. DNA METHYLTRANSFERASES (DNMT1 AND DNMT3B) REGULATE AND MAINTAIN PROMOTER METHYLATION AND ARE OVEREXPRESSED IN HUMAN CANCER. WE PERFORMED WHOLE-GENOME MICROARRAY ANALYSIS TO IDENTIFY GENES WITH ALTERED EXPRESSION AFTER RNAI-INDUCED SUPPRESSION OF DNMT IN A GLIOBLASTOMA MULTIFORME (GBM) CELL LINE. WE THEN IDENTIFIED GENES WITH BOTH DECREASED EXPRESSION AND EVIDENCE OF PROMOTER CPG ISLAND HYPERMETHYLATION IN GBM TISSUE SAMPLES USING A COMBINED WHOLE-GENOME MICROARRAY TRANSCRIPTOME ANALYSIS IN CONJUNCTION WITH A PROMOTER ARRAY ANALYSIS AFTER DNA IMMUNOPRECIPITATION WITH ANTI-5-METHYLCYTIDINE. DNMT1 AND 3B KNOCKDOWN RESULTED IN THE RESTORED EXPRESSION OF 308 GENES THAT ALSO CONTAINED PROMOTER REGION HYPERMETHYLATION. OF THESE, 43 WERE ALSO FOUND TO BE DOWNREGULATED IN GBM TISSUE SAMPLES. THREE DOWNREGULATED GENES WITH HYPERMETHYLATED PROMOTERS AND RESTORED EXPRESSION IN RESPONSE TO ACUTE DNMT SUPPRESSION WERE ASSAYED FOR METHYLATION CHANGES USING BISULFITE SEQUENCE ANALYSIS OF THE PROMOTER REGION AFTER CHRONIC DNMT SUPPRESSION. RESTORATION OF GENE EXPRESSION WAS NOT ASSOCIATED WITH CHANGES IN PROMOTER REGION METHYLATION, BUT RATHER WITH CHANGES IN HISTONE METHYLATION AND CHROMATIN CONFORMATION. TWO OF THE IDENTIFIED GENES EXHIBITED GROWTH SUPPRESSIVE ACTIVITY IN IN VITRO ASSAYS. COMBINING TARGETED GENETIC MANIPULATIONS WITH COMPREHENSIVE GENOMIC AND EXPRESSION ANALYSES PROVIDES A POTENTIALLY POWERFUL NEW APPROACH FOR IDENTIFYING EPIGENETICALLY REGULATED GENES IN GBM. 2009 9 1484 25 DLEU2: A MEANINGFUL LONG NONCODING RNA IN ONCOGENESIS. BACKGROUND: LONG NON-CODING RNA (LNCRNA) WITH LITTLE OR NO CODING ABILITY HAS SHOWN A VARIETY OF BIOLOGICAL FUNCTIONS IN CANCER, INCLUDING EPIGENETIC REGULATION, DNA DAMAGE, REGULATION OF MICRORNAS, AND PARTICIPATION IN SIGNAL TRANSDUCTION PATHWAYS. LNCRNA CAN BE USED AS AN ONCOGENE AND TUMOR SUPPRESSOR GENE THROUGH TRANSCRIPTIONAL REGULATION IN CANCER. FOR EXAMPLE, THE OVER-EXPRESSED LNCRNA DLEU2 PROMOTES THE OCCURRENCE OF LARYNGEAL CANCER, LUNG CANCER, HEPATOCELLULAR CARCINOMA, ETC., AND INHIBITS THE PROGRESSION OF CHRONIC LYMPHOCYTIC LEUKEMIA. DELETED IN LYMPHOCYTIC LEUKEMIA 2 (DLEU2), AS ONE OF THE LONG NON-CODING RNAS, WAS FIRST FOUND IN CHRONIC LYMPHOBLASTIC LEUKEMIA AND DRAWN INTO THE PROGRESS OF INNUMERABLE CANCERS. THE MOLECULAR MECHANISM OF DLEU2 IN MULTIPLE TUMORS WILL BE REVEALED. METHODS: IN THIS REVIEW, CURRENT STUDIES ON THE BIOLOGICAL FUNCTIONS AND MECHANISMS OF DLEU2 IN TUMORS ARE SUMMARIZED AND ANALYZED; RELATED RESEARCHES ARE SYSTEMATICALLY RETRIEVED AND COLLECTED THROUGH PUBMED. RESULTS: DLEU2, A NOVEL CANCER-RELATED LNCRNA, HAS BEEN DEMONSTRATED TO BE ABNORMALLY EXPRESSED IN VARIOUS MALIGNANT TUMORS, INCLUDING LEUKEMIA, ESOPHAGEAL CANCER, LUNG CANCER, GLIOMA, HEPATOCELLULAR CARCINOMA, MALIGNANT PLEURAL MESOTHELIOMA, BLADDER CANCER, PANCREATIC CANCER, PHARYNX AND THROAT CANCER, RENAL CLEAR CELL CARCINOMA, BREAST CANCER, OSTEOSARCOMA. BESIDES, LNCRNA DLEU2 HAS BEEN SHOWN TO BE INVOLVED IN THE PROCESS OF PROLIFERATION, MIGRATION, INVASION AND INHIBITION OF APOPTOSIS OF CANCER CELLS. CONCLUSION: DUE TO THE BIOLOGICAL FUNCTIONS AND MECHANISMS INVOLVED IN DLEU2, IT MAY REPRESENT AN AVAILABLE BIOMARKER OR POTENTIAL THERAPEUTIC TARGET IN A VARIETY OF MALIGNANT TUMORS. 2021 10 4231 35 METHYLATION OF PROTOCADHERIN 10, A NOVEL TUMOR SUPPRESSOR, IS ASSOCIATED WITH POOR PROGNOSIS IN PATIENTS WITH GASTRIC CANCER. BACKGROUND & AIMS: BY USING METHYLATION-SENSITIVE REPRESENTATIONAL DIFFERENCE ANALYSIS, WE IDENTIFIED PROTOCADHERIN 10 (PCDH10), A GENE THAT ENCODES A PROTOCADHERIN AND IS SILENCED IN A TUMOR-SPECIFIC MANNER. WE ANALYZED ITS EPIGENETIC INACTIVATION, BIOLOGICAL EFFECTS, AND PROGNOSTIC SIGNIFICANCE IN GASTRIC CANCER. METHODS: METHYLATION STATUS WAS EVALUATED BY COMBINED BISULFITE RESTRICTION ANALYSIS AND BISULFITE SEQUENCING. THE EFFECTS OF PCDH10 RE-EXPRESSION WERE DETERMINED IN GROWTH, APOPTOSIS, PROLIFERATION, AND INVASION ASSAYS. PCDH10 TARGET GENES WERE IDENTIFIED BY COMPLEMENTARY DNA MICROARRAY ANALYSIS. RESULTS: PCDH10 WAS SILENCED OR DOWN-REGULATED IN 94% (16 OF 17) OF GASTRIC CANCER CELL LINES; EXPRESSION LEVELS WERE RESTORED BY EXPOSURE TO DEMETHYLATING AGENTS. RE-EXPRESSION OF PCDH10 IN MKN45 GASTRIC CANCER CELLS REDUCED COLONY FORMATION IN VITRO AND TUMOR GROWTH IN MICE; IT ALSO INHIBITED CELL PROLIFERATION (P < .01), INDUCED CELL APOPTOSIS (P < .001), AND REPRESSED CELL INVASION (P < .05), UP-REGULATING THE PRO-APOPTOSIS GENES FAS, CASPASE 8, JUN, AND CDKN1A; THE ANTIPROLIFERATION GENE FGFR; AND THE ANTI-INVASION GENE HTATIP2. PCDH10 METHYLATION WAS DETECTED IN 82% (85 OF 104) OF GASTRIC TUMORS COMPARED WITH 37% (38 OF 104) OF PAIRED NONTUMOR TISSUES (P < .0001). IN THE LATTER, PCDH10 METHYLATION WAS HIGHER IN PRECANCEROUS LESIONS (27 OF 45; 60%) THAN IN CHRONIC GASTRITIS SAMPLES (11 OF 59; 19%) (P < .0001). AFTER A MEDIAN FOLLOW-UP PERIOD OF 16.8 MONTHS, MULTIVARIATE ANALYSIS REVEALED THAT PATIENTS WITH PCDH10 METHYLATION IN ADJACENT NONTUMOR AREAS HAD A SIGNIFICANT DECREASE IN OVERALL SURVIVAL. KAPLAN-MEIER SURVIVAL CURVES SHOWED THAT PCDH10 METHYLATION WAS ASSOCIATED SIGNIFICANTLY WITH SHORTENED SURVIVAL IN STAGE I-III GASTRIC CANCER PATIENTS. CONCLUSIONS: PCDH10 IS A GASTRIC TUMOR SUPPRESSOR; ITS METHYLATION AT EARLY STAGES OF GASTRIC CARCINOGENESIS IS AN INDEPENDENT PROGNOSTIC FACTOR. 2009 11 2440 28 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 2132 24 EPIGENETIC INACTIVATION OF THE MIR-124-1 IN HAEMATOLOGICAL MALIGNANCIES. MIR-124-1 IS A TUMOUR SUPPRESSOR MICRORNA (MIR). EPIGENETIC DEREGULATION OF MIRS IS IMPLICATED IN CARCINOGENESIS. PROMOTER DNA METHYLATION AND HISTONE MODIFICATION OF MIR-124-1 WAS STUDIED IN 5 NORMAL MARROW CONTROLS, 4 LYMPHOMA, 8 MULTIPLE MYELOMA (MM) CELL LINES, 230 DIAGNOSTIC PRIMARY SAMPLES OF ACUTE MYELOID LEUKAEMIA (AML), ACUTE LYMPHOBLASTIC LEUKAEMIA (ALL), CHRONIC MYELOID LEUKAEMIA (CML), CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL), MM, AND NON-HODGKIN'S LYMPHOMA (NHL), AND 53 MM SAMPLES AT STABLE DISEASE OR RELAPSE. PROMOTER OF MIR-124-1 WAS UNMETHYLATED IN NORMAL CONTROLS BUT HOMOZYGOUSLY METHYLATED IN 4 OF 4 LYMPHOMA AND 4 OF 8 MYELOMA CELL LINES. TREATMENT OF 5-AZA-2'-DEOXYCYTIDINE LED TO MIR-124-1 DEMETHYLATION AND RE-EXPRESSION OF MATURE MIR-124, WHICH ALSO ASSOCIATED WITH EMERGENCE OF EUCHROMATIC TRIMETHYL H3K4 AND CONSEQUENT DOWNREGULATION OF CDK6 IN MYELOMA CELLS HARBORING HOMOZYGOUS MIR-124-1 METHYLATION. IN PRIMARY SAMPLES AT DIAGNOSIS, MIR-124-1 METHYLATION WAS ABSENT IN CML BUT DETECTED IN 2% EACH OF MM AT DIAGNOSIS AND RELAPSE/PROGRESSION, 5% ALL, 15% AML, 14% CLL AND 58.1% OF NHL (P<0.001). AMONGST LYMPHOID MALIGNANCIES, MIR-124-1 WAS PREFERENTIALLY METHYLATED IN NHL THAN MM, CLL OR ALL. IN PRIMARY LYMPHOMA SAMPLES, MIR-124-1 WAS PREFERENTIALLY HYPERMETHYLATED IN B- OR NK/T-CELL LYMPHOMAS AND ASSOCIATED WITH REDUCED MIR-124 EXPRESSION. IN CONCLUSION, MIR-124-1 WAS HYPERMETHYLATED IN A TUMOUR-SPECIFIC MANNER, WITH A HETEROCHROMATIC HISTONE CONFIGURATION. HYPOMETHYLATION LED TO PARTIAL RESTORATION OF EUCHROMATIC HISTONE CODE AND MIR RE-EXPRESSION. INFREQUENT MIR-124-1 METHYLATION DETECTED IN DIAGNOSTIC AND RELAPSE MM SAMPLES SHOWED AN UNIMPORTANT ROLE IN MM PATHOGENESIS, DESPITE FREQUENT METHYLATION FOUND IN CELL LINES. AMONGST HAEMATOLOGICAL CANCERS, MIR-124-1 WAS MORE FREQUENTLY HYPERMETHYLATED IN NHL, AND HENCE WARRANTS FURTHER STUDY. 2011 13 2133 22 EPIGENETIC INACTIVATION OF THE MIR-34A IN HEMATOLOGICAL MALIGNANCIES. MIR-34A IS A TRANSCRIPTIONAL TARGET OF P53 AND IMPLICATED IN CARCINOGENESIS. WE STUDIED THE ROLE OF MIR-34A METHYLATION IN A PANEL OF HEMATOLOGICAL MALIGNANCIES INCLUDING ACUTE LEUKEMIA [ACUTE MYELOID LEUKEMIA (AML) AND ACUTE LYMPHOBLASTIC LEUKEMIA (ALL)], CHRONIC LEUKEMIA [CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) AND CHRONIC MYELOID LEUKEMIA (CML)], MULTIPLE MYELOMA (MM) AND NON-HODGKIN'S LYMPHOMA (NHL). THE METHYLATION STATUS OF MIR-34A PROMOTER WAS STUDIED IN 12 CELL LINES AND 188 DIAGNOSTIC SAMPLES BY METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION. MIR-34A PROMOTER WAS UNMETHYLATED IN NORMAL CONTROLS BUT METHYLATED IN 75% LYMPHOMA AND 37% MYELOMA CELL LINES. HYPOMETHYLATING TREATMENT LED TO RE-EXPRESSION OF PRI-MIR-34A TRANSCRIPT IN LYMPHOMA CELLS WITH HOMOZYGOUS MIR-34A METHYLATION. IN PRIMARY SAMPLES AT DIAGNOSIS, MIR-34A METHYLATION WAS DETECTED IN 4% CLL, 5.5% MM SAMPLES AND 18.8% OF NHL AT DIAGNOSIS BUT NONE OF ALL, AML AND CML (P = 0.011). IN MM PATIENTS WITH PAIRED SAMPLES, MIR-34A METHYLATION STATUS REMAINED UNCHANGED AT PROGRESSION. AMONGST LYMPHOID MALIGNANCIES, MIR-34A WAS PREFERENTIALLY METHYLATED IN NHL (P = 0.018), IN PARTICULAR NATURAL KILLER (NK)/T-CELL LYMPHOMA. IN CONCLUSION, AMONGST HEMATOLOGICAL MALIGNANCIES, MIR-34A METHYLATION IS PREFERENTIALLY HYPERMETHYLATED IN NHL, IN PARTICULAR NK/T-CELL LYMPHOMA, IN A TUMOR-SPECIFIC MANNER, THEREFORE THE ROLE OF MIR-34A IN LYMPHOMAGENESIS WARRANTS FURTHER STUDY. 2010 14 2131 28 EPIGENETIC INACTIVATION OF THE HSA-MIR-203 IN HAEMATOLOGICAL MALIGNANCIES. MIR-203 IS A TUMOUR SUPPRESSOR MICRORNA (MIRNA). WE STUDIED THE METHYLATION OF HSA-MIR-203 IN 150 SAMPLES INCLUDING ACUTE MYELOID LEUKAEMIA (AML), ACUTE LYMPHOBLASTIC LEUKAEMIA (ALL), CHRONIC MYELOID LEUKAEMIA (CML), CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) AND NON-HODGKIN'S LYMPHOMA (NHL) BY METHYLATION-SPECIFIC PCR, AND MIRNA EXPRESSION BY STEM-LOOP RT-QPCR. HSA-MIR-203 PROMOTER WAS UNMETHYLATED IN NORMAL CONTROLS BUT HOMOZYGOUSLY METHYLATED IN TWO AML AND FOUR LYMPHOMA CELL LINES, IN WHICH 5-AZA-2'-DEOXYCYTIDINE TREATMENT LED TO PROMOTER DEMETHYLATION AND MIR-203 RE-EXPRESSION. RESTORATION OF MIR-203 EXPRESSION IN LYMPHOMA CELLS INHIBITED CELLULAR PROLIFERATION AND INCREASED CELL DEATH, SUGGESTING AN INHERENT TUMOUR SUPPRESSOR ACTIVITY. IN PRIMARY SAMPLES, HSA-MIR-203 METHYLATION WAS ABSENT IN CML BUT DETECTED IN 5.0% ALL, 10.0% AML, 42.0% CLL AND 38.8% OF NHL (INCLUDING SIX [60.0%] NATURAL KILLER-CELL, NINE [40.9%] B-CELL AND FOUR [23.5%] T CELL NHL). MOREOVER, HSA-MIR-203 METHYLATION WAS ASSOCIATED WITH HYPERMETHYLATION OF HSA-MIR-34A, -124A AND -196B IN NHL BUT NOT CLL. IN CLL, HSA-MIR-203 METHYLATION WAS ASSOCIATED WITH A HIGHER PRESENTING HB LEVEL (P = 0.033). THE PROJECTED 10 YEAR OVERALL SURVIVAL OF THE CLL PATIENTS WAS 58.2%, WHICH WAS IMPACTED BY RAI STAGE AND HIGH-RISK KARYOTYPES BUT NOT HSA-MIR-203 METHYLATION. HSA-MIR-203 WAS MORE FREQUENTLY METHYLATED IN LYMPHOID THAN MYELOID MALIGNANCIES (P = 0.002). IN CONCLUSION, MIR-203, A TUMOUR SUPPRESSOR GENE, WAS HYPERMETHYLATED IN A TUMOUR-SPECIFIC MANNER WITH GENE SILENCING. HSA-MIR-203 WAS MORE FREQUENTLY HYPERMETHYLATED IN LYMPHOID THAN MYELOID MALIGNANCIES. IN NHL, HSA-MIR-203 METHYLATION WAS ASSOCIATED WITH CONCOMITANT METHYLATION OF OTHER TUMOUR SUPPRESSOR MIRNAS. THE FREQUENT HSA-MIR-203 METHYLATION IN LYMPHOID MALIGNANCIES SUGGESTED A PATHOGENETIC ROLE OF HSA-MIR-203 METHYLATION. 2011 15 2379 26 EPIGENETIC REGULATION OF WNT PATHWAY ANTAGONISTS IN HUMAN GLIOBLASTOMA MULTIFORME. EPIGENETIC INACTIVATION OF TUMOR SUPPRESSOR GENES IS COMMON IN HUMAN CANCER. USING A LARGE-SCALE WHOLE-GENOME APPROACH IN AN EARLIER STUDY, THE AUTHORS IDENTIFIED EPIGENETICALLY SILENCED GENES WITH POTENTIAL TUMOR SUPPRESSOR FUNCTION IN GLIOBLASTOMA (GBM). THREE GENES IDENTIFIED IN THIS ANALYSIS-DKK1, SFRP1, AND WIF1-ARE POTENT INHIBITORS OF THE WNT SIGNAL TRANSDUCTION PATHWAY. HERE, THE AUTHORS CONFIRM DECREASED EXPRESSION OF THESE GENES IN GBM TUMOR TISSUE SAMPLES RELATIVE TO NONTUMOR BRAIN TISSUE SAMPLES USING REAL-TIME PCR. THEY THEN SHOW THAT EXPRESSION OF ALL 3 GENES IS RESTORED IN T98 GBM CELLS BY TREATMENT WITH THE HISTONE DEACETYLASE INHIBITOR TRICHOSTATIN A (TSA), BUT ONLY DKK1 EXPRESSION IS RESTORED BY TREATMENT WITH THE DEMETHYLATING AGENT 5-AZACYTIDINE. BISULFITE SEQUENCING DID NOT REVEAL SIGNIFICANT METHYLATION IN THE PROMOTER REGION OF DKK1, WHEREAS HISTONE ACETYLATION AND CHROMATIN ACCESSIBILITY INCREASED SIGNIFICANTLY FOR ALL 3 GENES AFTER TSA TREATMENT. ECTOPIC EXPRESSION OF DKK1 SIGNIFICANTLY REDUCES COLONY FORMATION AND INCREASES CHEMOTHERAPY-INDUCED APOPTOSIS IN T98 CELLS. ECTOPIC EXPRESSION OF THE CANONICAL WNT PATHWAY INHIBITORS WIF1 AND SFRP1 SHOWS A RELATIVE LACK OF RESPONSE. CHRONIC WNT3A STIMULATION ONLY PARTIALLY REVERSES GROWTH SUPPRESSION AFTER DKK1 REEXPRESSION, WHEREAS A SPECIFIC INHIBITOR OF THE JNK PATHWAY SIGNIFICANTLY REVERSES THE EFFECT OF DKK1 REEXPRESSION ON COLONY FORMATION AND APOPTOSIS IN T98 CELLS. THESE RESULTS SUPPORT A POTENTIAL GROWTH-SUPPRESSIVE FUNCTION FOR EPIGENETICALLY SILENCED DKK1 IN GBM AND SUGGEST THAT DKK1 RESTORATION COULD MODULATE WNT SIGNALING THROUGH BOTH CANONICAL AND NONCANONICAL PATHWAYS. 2010 16 4052 30 MALIGNANT TRANSFORMATION OF A DYSEMBRYOPLASTIC NEUROEPITHELIAL TUMOR (DNET) CHARACTERIZED BY GENOME-WIDE METHYLATION ANALYSIS. DYSEMBRYOPLASTIC NEUROEPITHELIAL TUMORS (DNET) ARE CONSIDERED TO BE RARE, BENIGN, AND ASSOCIATED WITH CHRONIC EPILEPSY. WE PRESENT THE CASE OF A 28-YEAR-OLD MAN WITH A HISTORY OF EPILEPSY SINCE AGE 12. SURGERY OF AN OCCIPITAL CORTICAL LESION IN 2009 REVEALED A DNET. FIVE YEARS LATER, A RECURRENT TUMOR AT THE EDGE OF THE RESECTION CAVITY WAS REMOVED, AND THE TISSUE UNDERWENT AN INTENSIVE DIAGNOSTIC WORKUP. THE FIRST TUMOR WAS UNEQUIVOCALLY CHARACTERIZED AS A DNET, BUT NEUROPATHOLOGICAL DIAGNOSTICS OF THE RECURRENT TUMOR REVEALED A GLIOBLASTOMA. AFTER 6 MONTHS, ANOTHER RECURRENT TUMOR WAS DETECTED NEXT TO THE LOCATION OF THE ORIGINAL TUMOR, AND THIS WAS ALSO RESECTED. AN ILLUMINA 450 K BEADCHIP METHYLATION ARRAY WAS PERFORMED TO CHARACTERIZE ALL OF THE TUMORS. THE METHYLATION PROFILE OF THESE TUMORS SIGNIFICANTLY DIFFERED FROM OTHER GLIOBLASTOMA AND EPILEPSY-ASSOCIATED TUMOR PROFILES AND REVEALED A DNET-LIKE METHYLATION PROFILE. THUS, MOLECULAR CHARACTERIZATION OF THESE RECURRENT TUMORS SUGGESTS MALIGNANT TRANSFORMATION OF A PREVIOUSLY BENIGN DNET. WE FOUND INCREASED COPY NUMBER CHANGES IN THE RECURRENT DNET TUMORS AFTER MALIGNANT TRANSFORMATION. MODERN HIGH-THROUGHPUT ANALYSIS ADDS ESSENTIAL MOLECULAR INFORMATION IN ADDITION TO STANDARD HISTOPATHOLOGY FOR PROPER IDENTIFICATION OF RARE BRAIN TUMORS THAT PRESENT WITH AN UNUSUAL CLINICAL COURSE. 2016 17 5667 31 SFRP TUMOUR SUPPRESSOR GENES ARE POTENTIAL PLASMA-BASED EPIGENETIC BIOMARKERS FOR MALIGNANT PLEURAL MESOTHELIOMA. MALIGNANT PLEURAL MESOTHELIOMA (MPM) IS ASSOCIATED WITH ASBESTOS EXPOSURE. ASBESTOS CAN INDUCE CHRONIC INFLAMMATION WHICH IN TURN CAN LEAD TO SILENCING OF TUMOUR SUPPRESSOR GENES. WNT SIGNALING PATHWAY CAN BE AFFECTED BY CHRONIC INFLAMMATION AND IS ABERRANTLY ACTIVATED IN MANY CANCERS INCLUDING COLON AND MPM. SFRP GENES ARE ANTAGONISTS OF WNT PATHWAY, AND SFRPS ARE POTENTIAL TUMOUR SUPPRESSORS IN COLON, GASTRIC, BREAST, OVARIAN, AND LUNG CANCERS AND MESOTHELIOMA. THIS STUDY INVESTIGATED THE EXPRESSION AND DNA METHYLATION OF SFRP GENES IN MPM CELLS LINES WITH AND WITHOUT DEMETHYLATION TREATMENT. SIXTY-SIX PATIENT FFPE SAMPLES WERE ANALYSED AND HAVE SHOWED METHYLATION OF SFRP2 (56%) AND SFRP5 (70%) IN MPM. SFRP2 AND SFRP5 TUMOUR-SUPPRESSIVE ACTIVITY IN ELEVEN MPM LINES WAS CONFIRMED, AND LONG-TERM ASBESTOS EXPOSURE LED TO REDUCED EXPRESSION OF THE SFRP1 AND SFRP2 GENES IN THE MESOTHELIUM (MET-5A) VIA EPIGENETIC ALTERATIONS. FINALLY, DNA METHYLATION OF SFRPS IS DETECTABLE IN MPM PATIENT PLASMA SAMPLES, WITH METHYLATED SFRP2 AND SFRP5 SHOWING A TENDENCY TOWARDS GREATER ABUNDANCE IN PATIENTS. THESE DATA SUGGESTED THAT SFRP GENES HAVE TUMOUR-SUPPRESIVE ACTIVITY IN MPM AND THAT METHYLATED DNA FROM SFRP GENE PROMOTERS HAS THE POTENTIAL TO SERVE AS A BIOMARKER FOR MPM PATIENT PLASMA. 2017 18 3444 29 HYPERMETHYLATION OF E-CADHERIN IN LEUKEMIA. E-CADHERIN GENE IS OFTEN TERMED A "METASTASIS SUPPRESSOR" GENE BECAUSE THE E-CADHERIN PROTEIN CAN SUPPRESS TUMOR CELL INVASION AND METASTASIS. INACTIVATION OF THE E-CADHERIN GENE OCCURS IN UNDIFFERENTIATED SOLID TUMORS BY BOTH GENETIC AND EPIGENETIC MECHANISMS; HOWEVER, THE ROLE OF E-CADHERIN IN HEMATOLOGIC MALIGNANCIES IS ONLY NOW BEING RECOGNIZED. E-CADHERIN EXPRESSION IS ESSENTIAL FOR ERYTHROBLAST AND NORMOBLAST MATURATION, YET EXPRESSION IS REDUCED OR ABSENT IN LEUKEMIC BLAST CELLS. THIS STUDY EXAMINED THE MESSENGER RNA (MRNA) AND PROTEIN EXPRESSION OF THE E-CADHERIN GENE IN BONE MARROW AND BLOOD SAMPLES FROM NORMAL DONORS AND PATIENTS WITH LEUKEMIA. WE FOUND THAT ALL NORMAL DONOR SAMPLES EXPRESSED E-CADHERIN MRNA, WHEREAS BOTH SAMPLES OF ACUTE MYELOGENOUS LEUKEMIA AND CHRONIC LYMPHOCYTIC LEUKEMIA HAD A SIGNIFICANT REDUCTION OR ABSENCE OF EXPRESSION. HOWEVER, NORMAL BLAST COUNTERPARTS EXPRESSED ONLY A LOW LEVEL OF E-CADHERIN SURFACE PROTEIN. SODIUM BISULPHITE GENOMIC SEQUENCING WAS USED TO FULLY CHARACTERIZE THE METHYLATION PATTERNS OF THE CPG ISLAND ASSOCIATED WITH THE E-CADHERIN GENE PROMOTER IN THOSE SAMPLES WITH MATCHED DNA. ALL OF THE NORMAL CONTROL SAMPLES WERE ESSENTIALLY UNMETHYLATED; HOWEVER, 14 OF 18 (78%) OF THE LEUKEMIA SAMPLES HAD ABNORMAL HYPERMETHYLATION OF THE E-CADHERIN CPG ISLAND. IN FACT BOTH ALLELES OF THE E-CADHERIN GENE WERE OFTEN HYPERMETHYLATED. WE CONCLUDE THE E-CADHERIN GENE IS A COMMON TARGET FOR HYPERMETHYLATION IN HEMATOLOGIC MALIGNANCIES. 2000 19 5278 38 PROMOTER METHYLATION-MEDIATED INACTIVATION OF PCDH10 IN ACUTE LYMPHOBLASTIC LEUKEMIA CONTRIBUTES TO CHEMOTHERAPY RESISTANCE. PCDH10 HAS BEEN IMPLICATED AS A TUMOR SUPPRESSOR, SINCE EPIGENETIC ALTERATIONS OF THIS GENE HAVE BEEN NOTED IN MULTIPLE TUMOR TYPES. HOWEVER, TO DATE, STUDIES REGARDING ITS ROLE IN ACUTE AND CHRONIC LEUKEMIAS ARE LACKING. HERE, WE HAVE INVESTIGATED THE PRESENCE OF PROMOTER HYPERMETHYLATION OF TWO CPG ISLANDS OF THE PCDH10 GENE BY METHYLATION-SPECIFIC PCR IN 215 CASES OF VARIOUS SUBSETS OF MYELOID- AND LYMPHOID-LINEAGE LEUKEMIAS. WE FOUND THAT PCDH10 PROMOTER HYPERMETHYLATION WAS FREQUENT IN BOTH B-CELL (81.9%) AND T-CELL (80%) ACUTE LYMPHOBLASTIC LEUKEMIA (ALL), WHILE IT WAS PRESENT IN LOW FREQUENCY IN MOST SUBTYPES OF MYELOID LEUKEMIAS (25.9%) AND RARE IN CHRONIC MYELOID LEUKEMIA (2.2%). PCDH10 EXPRESSION WAS DOWNREGULATED VIA PROMOTER HYPERMETHYLATION IN PRIMARY ALL SAMPLES (N = 4) AND LEUKEMIA CELL LINES (N = 11). THE TRANSCRIPTIONAL REPRESSION CAUSED BY PCDH10 METHYLATION COULD BE RESTORED BY PHARMACOLOGIC INHIBITION OF DNA METHYLTRANSFERASES. ALL CELL LINES HARBORING METHYLATION-MEDIATED INACTIVATION OF PCDH10 WERE LESS SENSITIVE TO COMMONLY USED LEUKEMIA-SPECIFIC DRUGS SUGGESTING THAT PCDH10 METHYLATION MIGHT SERVE AS A BIOMARKER OF CHEMOTHERAPY RESPONSE. OUR RESULTS DEMONSTRATE THAT PCDH10 IS A TARGET OF EPIGENETIC SILENCING IN ALL, A PHENOMENON THAT MAY IMPACT LYMPHOID-LINEAGE LEUKEMOGENESIS, SERVE AS AN INDICATOR OF DRUG RESISTANCE AND MAY ALSO HAVE POTENTIAL IMPLICATIONS FOR TARGETED EPIGENETIC THERAPY. 2011 20 2126 30 EPIGENETIC INACTIVATION OF MIR-34B/C IN ADDITION TO MIR-34A AND DAPK1 IN CHRONIC LYMPHOCYTIC LEUKEMIA. BACKGROUND: TP53 MUTATION/DELETION IS UNCOMMON IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). WE POSTULATED THAT COMPONENTS OF TP53-CENTERED TUMOR SUPPRESSOR NETWORK, MIR-34B/C, IN ADDITION TO DAPK1 AND MIR-34A MIGHT BE INACTIVATED BY DNA HYPERMETHYLATION. MOREOVER, WE TESTED IF MIR-34B/C METHYLATION MIGHT CORRELATE WITH MIR-203 OR MIR-124-1 METHYLATION IN CLL. METHODS: MIR-34B/C, MIR-34A AND DAPK1 METHYLATION WAS STUDIED IN 11 NORMAL CONTROLS, 7 CLL CELL LINES, AND 78 DIAGNOSTIC CLL SAMPLES BY METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION. MEC-1 CELLS WERE TREATED WITH 5-AZA-2'-DEOXYCYTIDINE FOR REVERSAL OF METHYLATION-ASSOCIATED MIRNA SILENCING. TUMOR SUPPRESSOR PROPERTIES OF MIR-34B WERE DEMONSTRATED BY OVER-EXPRESSION OF PRECURSOR MIR-34B IN MEC-1 CELLS. RESULTS: MIR-34B/C PROMOTER WAS UNMETHYLATED IN NORMAL CONTROLS, BUT COMPLETELY METHYLATED IN 4 CLL CELL LINES. MIR-34B/C EXPRESSION WAS INVERSELY CORRELATED WITH MIR-34B/C METHYLATION. DIFFERENT MSP STATUSES OF MIR-34B/C, INCLUDING COMPLETE METHYLATION AND COMPLETE UNMETHYLATION, WERE VERIFIED BY QUANTITATIVE BISULFITE PYROSEQUENCING. 5-AZA-2'-DEOXYCYTIDINE TREATMENT RESULTED IN PROMOTER DEMETHYLATION AND MIR-34B RE-EXPRESSION IN MEC1 CELLS. MOREOVER, OVER-EXPRESSION OF MIR-34B RESULTED IN INHIBITION OF CELLULAR PROLIFERATION AND INCREASED CELL DEATH. IN PRIMARY CLL SAMPLES, MIR-34A, MIR-34B/C AND DAPK1 METHYLATION WAS DETECTED IN 2.6%, 17.9% AND 34.6% OF PATIENTS AT DIAGNOSIS RESPECTIVELY. FURTHERMORE, 39.7%, 3.8% AND 2.6% PATIENTS HAD METHYLATION OF ONE, TWO OR ALL THREE GENES RESPECTIVELY. OVERALL, 46.2% PATIENTS HAD METHYLATION OF AT LEAST ONE OF THESE THREE GENES. BESIDES, MIR-34B/C METHYLATION WAS ASSOCIATED WITH METHYLATION OF MIR-34A (P = 0.03) AND MIR-203 (P = 0.012) IN CLL. CONCLUSIONS: TAKEN TOGETHER, MIR-34B/C IS A TUMOR SUPPRESSOR MIRNA FREQUENTLY METHYLATED, AND HENCE SILENCED IN CLL. TOGETHER WITH DAPK1 METHYLATION, MIR-34B/C METHYLATION IS IMPLICATED IN THE DISRUPTION OF THE TP53-CENTERED TUMOR SUPPRESSOR NETWORK. MOREOVER, THE ASSOCIATION OF MIRNA METHYLATION WARRANTS FURTHER STUDY. 2014