1 2071 125 EPIGENETIC CONTROL OF THE E-CADHERIN GENE (CDH1) BY CPG METHYLATION IN COLECTOMY SAMPLES OF PATIENTS WITH ULCERATIVE COLITIS. E-CADHERIN BELONGS TO THE CADHERIN FAMILY OF CALCIUM-DEPENDENT CELL-ADHESION MOLECULES. THE CADHERINS PLAY AN ESSENTIAL ROLE IN BIOLOGICAL PROCESSES SUCH AS ORDERING OF CELL SORTING, MIGRATION, AND DIFFERENTIATION, AND THEIR MALFUNCTIONING IS CONNECTED WITH NEOPLASIA. NEOPLASTIC PROGRESSION IN PATIENTS WITH CHRONIC ULCERATIVE COLITIS IS CHARACTERIZED BY THE DEVELOPMENT OF EPITHELIAL DYSPLASIA. TRANSCRIPTIONAL SILENCING OF TUMOR-SUPPRESSOR GENES BY PROMOTER METHYLATION HAS BEEN OBSERVED IN DIFFERENT TYPES OF HUMAN CANCERS AND DYSPLASIA. TO EXPLORE THE MODE OF E-CADHERIN REGULATION, 156 BIOPSY SAMPLES FROM 26 PATIENTS WITH LONG-STANDING ULCERATIVE COLITIS WERE SCREENED. TO DETECT THE METHYLATION STATUS OF OUR SAMPLES, A METHYLATION-SPECIFIC PCR WAS APPLIED. METHYLATION OF THE E-CADHERIN (CDH1) PROMOTER WAS DETECTED IN 93% OF THE PATIENTS WITH DYSPLASTIC BIOPSY SAMPLES, IN CONTRAST TO ONLY 6% OF THE PATIENTS WITHOUT DYSPLASIA (P < 0.001). WE ALSO EXAMINED THE LEVEL OF SYNTHESIS OF E-CADHERIN PROTEIN BY IMMUNOHISTOCHEMICAL STAINING IN DIFFERENT PARAFFIN-EMBEDDED SAMPLES OF DYSPLASTIC AND NON-DYSPLASTIC ORIGIN IN A SUBSET OF OUR PATIENTS. SAMPLES WITH DYSPLASIA DISPLAYED REDUCED LEVELS, WHEREAS SAMPLES WITHOUT DYSPLASIA REVEALED NORMAL E-CADHERIN PROTEIN SYNTHESIS. THESE RESULTS SHOW THAT THE E-CADHERIN PROMOTER IS SUBJECTED TO EPIGENETIC CONTROL IN COLORECTAL ULCERATION. OBVIOUSLY, THIS EVENT MAY PLAY AN IMPORTANT ROLE IN THE PROGRESSION FROM CHRONIC INFLAMMATION TO COLORECTAL CANCER. FOR THIS REASON, METHYLATION OF THE CDH1 PROMOTER IS AN ATTRACTIVE NEW BIOMARKER FOR DETECTING ULCERATIVE COLITIS PATIENTS WITH A HIGH RISK FOR DEVELOPING COLORECTAL CANCERS. 2002 2 3444 37 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 3 6820 42 [GASTRIC CARCINOMA AND CHRONIC GASTRITIS: EPIGENETIC REGULATION OF CDH1 (E-CADHERIN), CDKN2A (P16INK4A), PTGS2 (COX-2) AND EGFR GENES THROUGH METHYLATION]. THE GENETIC AND EPIGENETIC ALTERATIONS ARE BEING STUDIED AS ONE OF THE CAUSES OF GASTRIC CANCER (GC) PROGRESSION AND DEVELOPMENT. DNA METHYLATION IS AN EPIGENETIC ALTERATION WHICH LEADS TO SUPPRESSOR GENE SILENCING AND PROTO-ONCOGENE ACTIVATION, PLAYING AN IMPORTANT ROLE IN CARCINOGENESIS. THE HISTOLOGICAL TYPES OF GASTRIC CARCINOMA HAVE DIFFERENT GENETIC PATHS AND THE KNOWLEDGE OF THE MOLECULAR BASES OF TUMORAL PROGRESSION LEADS TO DIAGNOSTIC ACCURACY AND ATTEMPTED THERAPY. CDH1 (E-CADHERIN) AND CDKN2A (P16(INK4A)) GENES ARE THOUGHT TO BE TUMORAL SUPPRESSOR GENES AND PTGS2 (COX-2) AND GENES ARE INVOLVED IN TUMOUR REGULATION AND GROWTH. IN ONE HAND, GENE SILENCING AS AN EPIGENETIC PHENOMENON, AND IN THE OTHER HAND, GENE EXPRESSION ENHANCEMENT DUE TO POSSIBLE DEMETHYLATION, SIMULTANEOUSLY, CAN FACILITATE CARCINOGENESIS AND TUMORAL PROGRESSION. OUR AIM WAS TO RELATE CDH1, P16(INK4A), COX-2 AND EGFR GENES DNA METHYLATION WITH THE SEVERAL HISTOLOGICAL TYPES OF GASTRIC CARCINOMA AND CHRONIC GASTRITIS. WE STUDIED 55 FORMALIN FIXED PARAFFIN EMBEDDED GASTRIC BIOPSIES: 35 WERE GC SPECIMENS (12 DIFFUSE TYPE, 15 INTESTINAL TYPE AND 8 INDETERMINATE TYPE, ACCORDING TO LAUREN'S CLASSIFICATION) AND 20 SAMPLES HAD CHRONIC GASTRITIS (CG). THE DNA WAS TREATED WITH SODIUM BISULFITE AFTER EXTRACTION AND THEN PERFORMED METHYLATION SPECIFIC PCR (MSP). STATISTICAL ANALYSIS WAS BASED ON CHI-SQUARE TEST AND EXACT FISHER'S TEST. CPG ISLAND METHYLATION WAS DETECTED IN 94% OF THE GC SAMPLES FOR CDH1, 91% FOR COX-2, 80% FOR P16(INK4A) AND NO METHYLATION WAS DETECTED IN EGFR GENE (0%). IN CG, CPG ISLAND METHYLATION WAS FOUND IN 100% FOR CDH1 AND COX-2 GENES, 90% FOR P16(INK4A) AND 20% FOR EGFR. THESE RESULTS REVEAL SIGNIFICANT DIFFERENCES IN EGFR GENE METHYLATION DISTINGUISHING GC FROM CG (P < 0, 01), SUGGESTING THAT GENE DEMETHYLATION LEADS TO MALIGNANT TRANSFORMATION AND FAVOURS THE USE OF TYROSINE-KINASE INHIBITORS IN ITS TREATMENT. GENES COX2 E P16INK4A LOWER METHYLATION IN INTESTINAL AND DIFFUSE TYPES OF GC, FAVOURS THEIR DIFFERENT ROLE IN RESPECTIVE HISTOGENESIS. 2010 4 2019 40 EPIGENETIC CHANGE IN E-CADHERIN AND COX-2 TO PREDICT CHRONIC PERIODONTITIS. BACKGROUND: DNA METHYLATION OF CERTAIN GENES FREQUENTLY OCCURS IN NEOPLASTIC CELLS. ALTHOUGH THE CAUSE REMAINS UNKNOWN, MANY GENES HAVE BEEN IDENTIFIED WITH SUCH ATYPICAL METHYLATION IN NEOPLASTIC CELLS. THE HYPERMETHYLATION OF E-CADHERIN AND CYCLOOXYGENASE 2 (COX-2) IN CHRONIC INFLAMMATION SUCH AS CHRONIC PERIODONTITIS MAY DEMONSTRATE MILD LESION/MUTATION EPIGENETIC LEVEL. THIS STUDY COMPARES THE HYPERMETHYLATION STATUS OF E-CADHERIN AND COX-2 GENES WHICH ARE OFTEN FOUND IN BREAST CANCER PATIENTS WITH THAT IN CHRONIC PERIODONTITIS. METHODS: TOTAL DNA WAS EXTRACTED FROM THE BLOOD SAMPLES OF 108 SYSTEMICALLY HEALTHY NON-PERIODONTITIS SUBJECTS, AND THE GINGIVAL TISSUES AND BLOOD SAMPLES OF 110 CHRONIC PERIODONTITIS PATIENT AS WELL AS NEOPLASTIC TISSUES OF 106 BREAST CANCER PATIENTS. METHYLATION-SPECIFIC PCR FOR E-CADHERIN AND COX-2 WAS PERFORMED ON THESE SAMPLES AND THE PCR PRODUCTS WERE ANALYZED ON 2% AGAROSE GEL. RESULTS: HYPERMETHYLATION OF E-CADHERIN AND COX-2 WAS OBSERVED IN 38% AND 35% OF THE BREAST CANCER SAMPLES, RESPECTIVELY. IN CHRONIC PERIODONTITIS PATIENTS THE DETECTION RATE WAS 25% AND 19% RESPECTIVELY, AND NONE WAS FOUND IN THE SYSTEMICALLY HEALTHY NON-PERIODONTITIS CONTROL SUBJECTS. THE HYPERMETHYLATION STATUS WAS SHOWN TO BE CORRELATED AMONG THE THREE GROUPS WITH STATISTICAL SIGNIFICANCE (P < 0.0001). THE METHYLATION OF CPG ISLANDS IN E-CADHERIN AND COX-2 GENES IN PERIODONTITIS PATIENTS OCCURS MORE FREQUENTLY IN PERIODONTITIS PATIENTS THAN IN THE CONTROL SUBJECTS, BUT OCCURS LESS FREQUENTLY THAN IN THE BREAST CANCER PATIENTS. CONCLUSIONS: THIS SET OF DATA SHOWS THAT THE EPIGENETIC CHANGE IN E-CADHERIN AND CYCLOOXYGENASE-2 IS ASSOCIATED WITH CHRONIC PERIODONTITIS. THE EPIGENETIC CHANGES PRESENTED IN CHRONIC INFLAMMATION PATIENTS MIGHT DEMONSTRATE AN IRREVERSIBLE DESTRUCTION IN THE TISSUES OR ORGANS SIMILAR TO THE EFFECTS OF CANCER. CHRONIC PERIODONTITIS TO SOME EXTENT MIGHT BE ASSOCIATED WITH DNA HYPERMETHYLATION WHICH IS RELATED TO CANCER RISK FACTORS. 2010 5 59 33 A GENOME-WIDE SCREEN IDENTIFIES FREQUENTLY METHYLATED GENES IN HAEMATOLOGICAL AND EPITHELIAL CANCERS. BACKGROUND: GENETIC AS WELL AS EPIGENETIC ALTERATIONS ARE A HALLMARK OF BOTH EPITHELIAL AND HAEMATOLOGICAL MALIGNANCIES. HIGH THROUGHPUT SCREENS ARE REQUIRED TO IDENTIFY EPIGENETIC MARKERS THAT CAN BE USEFUL FOR DIAGNOSTIC AND PROGNOSTIC PURPOSES ACROSS MALIGNANCIES. RESULTS: HERE WE REPORT FOR THE FIRST TIME THE USE OF THE MIRA ASSAY (METHYLATED CPG ISLAND RECOVERY ASSAY) IN COMBINATION WITH GENOME-WIDE CPG ISLAND ARRAYS TO IDENTIFY EPIGENETIC MOLECULAR MARKERS IN CHILDHOOD ACUTE LYMPHOBLASTIC LEUKEMIA (ALL) ON A GENOME-WIDE SCALE. WE IDENTIFIED 30 GENES DEMONSTRATING METHYLATION FREQUENCIES OF > OR =25% IN CHILDHOOD ALL, NINE GENES SHOWED SIGNIFICANTLY DIFFERENT METHYLATION FREQUENCIES IN B VS T-ALL. FOR MAJORITY OF THE GENES EXPRESSION COULD BE RESTORED IN METHYLATED LEUKEMIA LINES AFTER TREATMENT WITH 5-AZADC. FORTY-FOUR PERCENT OF THE GENES REPRESENT TARGETS OF THE POLYCOMB COMPLEX. IN CHRONIC MYELOID LEUKEMIA (CML) TWO OF THE GENES, (TFAP2A AND EBF2), DEMONSTRATED INCREASED METHYLATION IN BLAST CRISIS COMPARED TO CHRONIC PHASE (P < 0.05). FURTHERMORE HYPERMETHYLATION OF AN AUTOPHAGY RELATED GENE ATG16L2 WAS ASSOCIATED WITH POORER PROGNOSIS IN TERMS OF MOLECULAR RESPONSE TO IMATINIB TREATMENT. LASTLY WE DEMONSTRATED THAT TEN OF THESE GENES WERE ALSO FREQUENTLY METHYLATED IN COMMON EPITHELIAL CANCERS. CONCLUSION: IN SUMMARY WE HAVE IDENTIFIED A LARGE NUMBER OF GENES SHOWING FREQUENT METHYLATION IN CHILDHOOD ALL, METHYLATION STATUS OF TWO OF THESE GENES IS ASSOCIATED WITH ADVANCED DISEASE IN CML AND METHYLATION STATUS OF ANOTHER GENE IS ASSOCIATED WITH PROGNOSIS. IN ADDITION A SUBSET OF THESE GENES MAY ACT AS EPIGENETIC MARKERS ACROSS HEMATOLOGICAL MALIGNANCIES AS WELL AS COMMON EPITHELIAL CANCERS. 2010 6 5276 37 PROMOTER METHYLATION OF TUMOR-RELATED GENES IN GASTRIC CARCINOGENESIS. ABERRANT PROMOTER METHYLATION AND SUBSEQUENT SILENCING OF CANCER-RELATED GENES HAS BEEN RECOGNIZED AS AN IMPORTANT PATHWAY INVOLVED IN GASTRIC CARCINOGENESIS. IN FACT, SEVERAL FACTORS ARE BELIEVED TO CONTRIBUTE TO ITS INDUCTION IN GASTRIC EPITHELIA, INCLUDING AGING, DIET, CHRONIC INFLAMMATION AND INFECTION OF HELICOBACTER PYLORI (H. PYLORI) AND EPSTEIN-BARR VIRUS (EBV). HOWEVER, THE UNDERLING MECHANISMS ARE NOT COMPLETELY IDENTIFIED, DESPITE THE BELIEF THAT INCREASED EXPRESSION OR ACTIVITY OF DNA METHYLTRANSFERASES (DNMTS), OR DECREASED DEMETHYLATION ACTIVITY MAY CONTRIBUTE TO THE EXCESSIVE METHYLATION. A GREAT NUMBER OF GENES WITH PROMOTER METHYLATION HAVE BEEN OBSERVED IN GASTRIC CANCER (GC), AMONG WHICH P16INK4A (P16), MUT L HOMOLOGUE 1 (MLH1), EPITHELIAL-CADHERIN (E-CADHERIN), RUNT-RELATED TRANSCRIPTION FACTOR 3 (RUNX3), ADENOMATOUS POLYPOSIS COLI (APC), O(6)-METHYLGUANINE-DNA METHYLTRANSFERASE (MGMT), RAS ASSOCIATION DOMAIN FAMILY 1A (RASSF1A) AND DEATH-ASSOCIATED PROTEIN KINASE (DAPK) HAVE BEEN EXTENSIVELY STUDIED. UNLIKE THE DISTINCT METHYLATION CHARACTERIZATION IN SINGLE GENES, METHYLATION ANALYSIS OF MULTIPLE GENES MAY PROVIDE MORE INFORMATION IN RISK PREDICTION, EARLY DETECTION, PROGNOSIS ASSESSMENT AND CHEMOTHERAPY CHOICE FOR GC. SPECIFICALLY, PARTICULAR MONITORING AND SCREENING SHOULD BE PERFORMED ON THOSE OVER 45 YEARS OLD, WITH PRECANCEROUS GASTRIC DISEASE OR INFECTION OF H. PYLORI OR EBV. AS AN ALTERNATIVE TO TUMOR TISSUES, METHYLATION DETECTION IN PATIENT SERA OR GASTRIC WASHES MAY ALSO BE USED IN RISK PREDICTION AND EARLY DETECTION. HOWEVER, WHAT STILL POSES A GREAT CHALLENGE AS WELL AS A PUZZLE IS THE DETERMINATION OF THE VERY GENES THAT SHOULD BE USED IN METHYLATION ANALYSIS. BECAUSE EPIGENETIC ALTERATIONS ARE NORMALLY REVERSIBLE, DRUGS OR CHEMICAL COMPOUNDS WITH DEMETHYLATING ACTIVITY, SUCH AS 5-AZA-2'-DEOXYCYTIDINE (5-AZA-DC) COULD BE USED IN THE TREATMENT OF PATIENTS WITH MULTIPLE GENE METHYLATION. IN VIEW OF THE ADVERSE EFFECTS OF 5-AZA-DC, DNMT-TARGETED STRATEGY HAS BEEN PROPOSED AND MAY PROVE TO BE MORE EFFECTIVE THAN DEMETHYLATING AGENTS. 2012 7 2771 32 EXTENSIVE PROMOTER DNA HYPERMETHYLATION AND HYPOMETHYLATION IS ASSOCIATED WITH ABERRANT MICRORNA EXPRESSION IN CHRONIC LYMPHOCYTIC LEUKEMIA. DYSREGULATED MICRORNA (MIRNA) EXPRESSION CONTRIBUTES TO THE PATHOGENESIS OF HEMATOPOIETIC MALIGNANCIES, INCLUDING CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). HOWEVER, AN UNDERSTANDING OF THE MECHANISMS THAT CAUSE ABERRANT MIRNA TRANSCRIPTIONAL CONTROL IS LACKING. IN THIS STUDY, WE COMPREHENSIVELY INVESTIGATED THE ROLE AND EXTENT OF MIRNA EPIGENETIC REGULATION IN CLL. GENOME-WIDE PROFILING CONDUCTED ON 24 CLL AND 10 HEALTHY B CELL SAMPLES REVEALED GLOBAL DNA METHYLATION PATTERNS UPSTREAM OF MIRNA SEQUENCES THAT DISTINGUISHED MALIGNANT FROM HEALTHY CELLS AND IDENTIFIED PUTATIVE MIRNA PROMOTERS. INTEGRATION OF DNA METHYLATION AND MIRNA PROMOTER DATA LED TO THE IDENTIFICATION OF 128 RECURRENT MIRNA TARGETS FOR ABERRANT PROMOTER DNA METHYLATION. DNA HYPOMETHYLATION ACCOUNTED FOR MORE THAN 60% OF ALL ABERRANT PROMOTER-ASSOCIATED DNA METHYLATION IN CLL, AND PROMOTER DNA HYPOMETHYLATION WAS RESTRICTED TO WELL-DEFINED REGIONS. INDIVIDUAL HYPER- AND HYPOMETHYLATED PROMOTERS ALLOWED DISCRIMINATION OF CLL SAMPLES FROM HEALTHY CONTROLS. PROMOTER DNA METHYLATION PATTERNS WERE CONFIRMED IN AN INDEPENDENT PATIENT COHORT, WITH 11 MIRNAS CONSISTENTLY SHOWING AN INVERSE CORRELATION BETWEEN DNA METHYLATION STATUS AND EXPRESSION LEVEL. TOGETHER, OUR FINDINGS CHARACTERIZE THE ROLE OF EPIGENETIC CHANGES IN THE REGULATION OF MIRNA TRANSCRIPTION AND CREATE A REPOSITORY OF DISEASE-SPECIFIC PROMOTER REGIONS THAT MAY PROVIDE ADDITIONAL INSIGHTS INTO THE PATHOGENESIS OF CLL. 2012 8 5435 39 RELATIVE ROLE OF METHYLATOR AND TUMOR SUPPRESSOR PATHWAYS IN ULCERATIVE COLITIS-ASSOCIATED COLON CANCER. BACKGROUND: CHRONIC ULCERATIVE COLITIS (UC) IS ASSOCIATED WITH AN INCREASED COLORECTAL CANCER RISK WHICH MAY BE SECONDARY TO REPETITIVE MUCOSAL INJURY. BOTH EPIGENETIC METHYLATION AND THE CLASSIC ADENOMA-TO-CARCINOMA SEQUENCE HAVE BEEN IMPLICATED IN THIS MALIGNANT TRANSFORMATION, BUT THE UNDERLYING MOLECULAR MECHANISMS REMAIN POORLY DEFINED. THIS STUDY COMPARES THE MOLECULAR CHARACTERISTICS OF COLITIS-ASSOCIATED AND COMMON COLORECTAL CANCERS. METHODS: NINETEEN PATIENTS WITH COLORECTAL ADENOCARCINOMAS ARISING WITHIN UC WERE MATCHED FOR AGE AND CANCER SITE WITH 54 PATIENTS WITH SPORADIC ADENOCARCINOMAS. TUMOR TISSUE WAS EXAMINED FOR BRAF MUTATIONS, CPG ISLAND METHYLATOR PHENOTYPE (CIMP), AND MLH1 PROMOTER METHYLATION. MUTATIONS OF KRAS AND P53 WERE ASSESSED BY SEQUENCING. RESULTS: PATIENT DEMOGRAPHICS WERE SIMILAR FOR THE TWO GROUPS. CIMP WAS OBSERVED IN 22% OF SPORADIC COLORECTAL CANCERS AND IN 5% OF UC CANCERS (P = 0.162). RATES OF BRAF MUTATION (4% VS 5%, P = 1.0), MLH1 METHYLATION (9% VERSUS 5%, P = 0.682), AND KRAS MUTATIONS (24% VERSUS 32%, P = 0.552) WERE SIMILAR BETWEEN THE GROUPS. HOWEVER, COLITIS-ASSOCIATED COLORECTAL CANCERS WERE MORE LIKELY TO HAVE A P53 MUTATION COMPARED TO SPORADIC ADENOCARCINOMAS (95% VERSUS 53%, P = 0.001). THE DOMINANT MUTATION FOR COLITIS-ASSOCIATED CANCERS WAS A MUTATION IN CODON 4, REPRESENTING HALF OF THE MUTATIONS. FURTHERMORE, COLITIS-ASSOCIATED CANCERS HAD A HIGHER RATE OF MUTATION IN CODON 8 (48% VERSUS 6%, P < 0.001) THAN SPORADIC COUNTERPARTS. CONCLUSIONS: UNLIKE OTHER INFLAMMATORY GASTROINTESTINAL CANCERS, COLITIS-ASSOCIATED COLORECTAL CANCERS DO NOT PREFERENTIALLY ARISE VIA A METHYLATOR PATHWAY WHEN COMPARED TO SPORADIC COLORECTAL CANCERS. CHROMOSOMAL INSTABILITY REMAINS AN IMPORTANT ETIOLOGY, BUT WITH A UNIQUE P53 FREQUENCY AND MUTATION PATTERN. 2011 9 3686 37 INFLAMMATION-RELATED ABERRANT PATTERNS OF DNA METHYLATION: DETECTION AND ROLE IN EPIGENETIC DEREGULATION OF CANCER CELL TRANSCRIPTOME. IT IS NOW APPARENT THAT EPIGENETIC ABNORMALITIES, IN PARTICULAR ALTERED DNA METHYLATION, PLAY A CRUCIAL ROLE IN THE DEVELOPMENT AND PROGRESSION OF HUMAN CANCERS. DNA HYPERMETHYLATION AT PROMOTER CPG ISLANDS IS NOW RECOGNIZED AS A THIRD MECHANISM BY WHICH INACTIVATION OF TUMOR SUPPRESSOR GENES OCCURS. ABERRANT CPG ISLAND HYPERMETHYLATION IS ALSO FREQUENTLY OBSERVED IN CHRONIC INFLAMMATION AND PRECANCEROUS LESIONS, WHICH SUGGESTS THAT IT IS AN EARLY EVENT IN TUMORIGENESIS THAT COULD SERVE AS A USEFUL TUMOR MARKER. A VARIETY OF SCREENING TECHNIQUES HAVE BEEN DEVELOPED FOR GENOME-WIDE SCREENING OF METHYLATION STATUS. OF THOSE, TRANSCRIPTOME ANALYSIS COUPLED WITH PHARMACOLOGICAL UNMASKING HAS EMERGED AS A POWERFUL TOOL FOR REVEALING DNA METHYLATION PATTERNS IN CANCER CELLS AND IDENTIFYING NEW TUMOR MARKER CANDIDATES. 2009 10 342 35 ALTERATIONS OF DNA METHYLATION ASSOCIATED WITH ABNORMALITIES OF DNA METHYLTRANSFERASES IN HUMAN CANCERS DURING TRANSITION FROM A PRECANCEROUS TO A MALIGNANT STATE. ALTERATIONS OF DNA METHYLATION ARE ONE OF THE MOST CONSISTENT EPIGENETIC CHANGES IN HUMAN CANCERS. HUMAN CANCERS GENERALLY SHOW GLOBAL DNA HYPOMETHYLATION ACCOMPANIED BY REGION-SPECIFIC HYPERMETHYLATION. ALTERATIONS OF DNA METHYLATION MAY RESULT IN CHROMOSOMAL INSTABILITY AS A RESULT OF CHANGES IN CHROMATIN STRUCTURE. DNA HYPERMETHYLATION OF CPG ISLANDS SILENCES VARIOUS TUMOR-RELATED GENES. ALTERATIONS OF DNA METHYLATION ARE FREQUENTLY OBSERVED IN CANCERS ASSOCIATED WITH CHRONIC INFLAMMATION AND/OR PERSISTENT INFECTION WITH VIRUSES OR OTHER PATHOGENIC MICROORGANISMS, SUCH AS HEPATITIS B OR C VIRUSES, EPSTEIN-BARR VIRUS, HUMAN PAPILLOMAVIRUS AND HELICOBACTER PYLORI, OR WITH CIGARETTE SMOKING. ACCUMULATING EVIDENCE SUGGESTS THAT ALTERATIONS OF DNA METHYLATION ARE INVOLVED EVEN IN THE EARLY AND PRECANCEROUS STAGES. ON THE OTHER HAND, IN PATIENTS WITH CANCERS, ABERRANT DNA METHYLATION IS SIGNIFICANTLY ASSOCIATED WITH POORER TUMOR DIFFERENTIATION, TUMOR AGGRESSIVENESS AND POOR PROGNOSIS. PRECANCEROUS CONDITIONS SHOWING ALTERATIONS OF DNA METHYLATION MAY PROGRESS RAPIDLY AND GENERATE MORE MALIGNANT CANCERS. DNA METHYLTRANSFERASE (DNMT) 1 OVER-EXPRESSION IS NOT A SECONDARY RESULT OF INCREASED CELL PROLIFERATIVE ACTIVITY BUT IS SIGNIFICANTLY CORRELATED WITH THE CPG ISLAND METHYLATOR PHENOTYPE, WHICH IS DEFINED AS FREQUENT DNA HYPERMETHYLATION OF C-TYPE CPG ISLANDS THAT ARE USUALLY METHYLATED IN A CANCER-SPECIFIC (NOT AGE-DEPENDENT) MANNER. SPLICING ALTERATION OF DNMT3B MAY RESULT IN CHROMOSOMAL INSTABILITY THROUGH DNA HYPOMETHYLATION OF PERICENTROMERIC SATELLITE REGIONS. ALTERATION OF DNA METHYLATION MAY BECOME AN INDICATOR FOR CARCINOGENETIC RISK ESTIMATION AND EARLY DIAGNOSIS OF CANCERS AND A BIOLOGICAL PREDICTOR OF POOR PROGNOSIS IN PATIENTS WITH CANCERS. CORRECTION OF DNA METHYLATION STATUS MAY OFFER A NEW STRATEGY FOR PREVENTION AND THERAPY OF CANCERS. 2007 11 1500 39 DNA METHYLATION ANALYSIS OF CD4+ T CELLS IN PATIENTS WITH PSORIASIS. PSORIASIS IS A CHRONIC INFLAMMATORY SKIN DISEASE THAT IS CHARACTERIZED BY ABERRANT CROSS-TALK BETWEEN KERATINOCYTES AND IMMUNE CELLS SUCH AS CD4+ T CELLS, RESULTING IN KERATINOCYTE HYPERPROLIFERATION IN THE EPIDERMIS. DNA METHYLATION, ONE OF SEVERAL EPIGENETIC MECHANISMS, PLAYS AN IMPORTANT ROLE IN GENE EXPRESSION WITHOUT CHANGING THE DNA SEQUENCE. SEVERAL STUDIES HAVE SUGGESTED THE INVOLVEMENT OF EPIGENETIC REGULATION IN SKIN LESIONS FROM PATIENTS WITH PSORIASIS. IN THIS STUDY, WE INVESTIGATED THE GENOME-WIDE DNA METHYLATION STATUS OF CD4+ T CELLS IN PATIENTS WITH PSORIASIS COMPARED WITH HEALTHY SUBJECTS USING METHYLATED DNA IMMUNOPRECIPITATION SEQUENCING (MEDIP-SEQ). THE RESULTS OF MEDIP-SEQ SHOWED THAT THE GLOBAL METHYLATION VALUES OF CD4+ T CELLS ARE HIGHER IN PATIENTS WITH PSORIASIS THAN IN HEALTHY CONTROLS, PARTICULARLY IN THE PROMOTER REGIONS. AMONG THE MOST HYPERMETHYLATED GENES IN THE PROMOTER REGIONS, WE SELECTED THE GENES WHOSE EXPRESSION IS SIGNIFICANTLY REDUCED IN THE CD4+ T CELLS OF PSORIASIS PATIENTS. STUDIES USING THE METHYLATION INHIBITOR 5-AZACYTIDINE IN VITRO METHYLATION ASSAYS HAVE SHOWN THAT THE DIFFERENTIAL EXPRESSION LEVELS WERE ASSOCIATED WITH THE METHYLATION STATUS OF EACH GENE. BISULFITE SEQUENCING OF THE TRANSCRIPTION START REGION OF PHOSPHATIDIC ACID PHOSPHATASE TYPE 2 DOMAIN CONTAINING 3 (PPAPDC3), ONE OF THE SELECTED GENES, SHOWED HYPERMETHYLATION IN THE CD4+ T CELLS OF PSORIASIS PATIENTS. THESE RESULTS SUGGESTED THAT THE METHYLATION STATUS, WHICH IS IDENTIFIED BY MEDIP-SEQ OF THE GENES, WAS CORRELATED WITH THE MRNA EXPRESSION LEVEL OF THE GENES. COLLECTIVELY, THE DNA METHYLATION STATUS IN CD4+ T CELLS MIGHT BE ASSOCIATED WITH THE PATHOGENESIS OF PSORIASIS. 2014 12 2682 30 EVALUATION OF SERUM LINE-1 HYPOMETHYLATION AS A PROGNOSTIC MARKER FOR HEPATOCELLULAR CARCINOMA. BACKGROUND AND STUDY AIMS: GLOBAL HYPOMETHYLATION IS ONE OF THE MOST CONSISTENT EPIGENETIC CHANGES IN CANCER. DEVELOPMENT OF HEPATOCELLULAR CARCINOMA (HCC) MUST BE UNDERSTOOD AS A MULTISTEP PROCESS WITH ACCUMULATION OF GENETIC AND EPIGENETIC ALTERATIONS. IN THE LAST DECADES, IN ADDITION TO GENETIC ALTERATIONS, EPIGENETIC CHANGES HAVE BEEN RECOGNIZED AS AN IMPORTANT AND ALTERNATIVE MECHANISM IN TUMOURIGENESIS. WE INVESTIGATED THE CLINICAL IMPLICATIONS OF GLOBAL HYPOMETHYLATION IN THE SERA OF PATIENTS WITH HEPATOCELLULAR CARCINOMA (HCC). PATIENTS AND METHODS: PCR WAS USED TO ASSESS THE METHYLATION STATUS OF LONG INTERSPERSED NUCLEAR ELEMENT TYPE 1 (LINE-1) REPETITIVE SEQUENCES IN GENOMIC DNA DERIVED FROM SERA OF 50 PATIENTS WITH HCC, 20 PATIENTS WITH CIRRHOSIS, 20 PATIENTS WITH CHRONIC HEPATITIS C AND 10 HEALTHY SUBJECTS. RESULTS: SERUM GENOME HYPOMETHYLATION WAS SIGNIFICANTLY INCREASED IN PATIENTS WITH HCC (P<0.001). THE LEVELS OF SERUM LINE-1 HYPOMETHYLATION AT INITIAL PRESENTATION CORRELATED SIGNIFICANTLY WITH TUMOUR SIZE, TUMOUR NUMBER AND ALPHA-FOETOPROTEIN LEVEL. MOREOVER HIGH SERUM LINE-1 HYPOMETHYLATION CORRELATES SIGNIFICANTLY WITH POOR SURVIVAL. CONCLUSION: SERUM LINE-1 HYPOMETHYLATION MAY SERVE AS A PROGNOSTIC MARKER FOR PATIENTS WITH HCC. 2011 13 1805 25 EFFECT OF SMOKING ON THE DNA METHYLATION PATTERN OF THE SOCS1 PROMOTER IN EPITHELIAL CELLS FROM THE SALIVA OF PATIENTS WITH CHRONIC PERIODONTITIS. BACKGROUND: THE AIM OF THE PRESENT STUDY WAS TO EVALUATE THE METHYLATION PATTERN IN THE SUPPRESSOR OF CYTOKINE SIGNALING 1 (SOCS1) GENE IN SMOKERS AND NON-SMOKERS WITH CHRONIC PERIODONTITIS (CP). METHODS: METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (PCR) WAS PERFORMED TO DETERMINE THE METHYLATION STATUS OF THE SOCS1 PROMOTER IN 45 SALIVA SAMPLES FROM SMOKERS AND NON-SMOKERS WITH CP. RESULTS: CELLS FROM THE SALIVA OF CP PATIENTS WHO SMOKED WERE 7.08 TIMES MORE LIKELY TO HAVE A METHYLATED SOCS1 PROMOTER THAN CELLS FROM THE SALIVA OF NON-SMOKING PATIENTS. CONCLUSIONS: SOCS1 GENE PROMOTER METHYLATION, WITH ITS POTENTIAL EFFECTS ON THE EXPRESSION OF THIS GENE, SEEMS TO BE A CONSEQUENCE OF EXPOSURE TO TOBACCO AND NOT TO PERIODONTAL DISEASE. FURTHER STUDIES ARE NEEDED TO ELUCIDATE THE RELATIONSHIP BETWEEN THE EPIGENETIC CONTROL OF IMMUNE RESPONSE GENE EXPRESSION, EXPOSURE TO ENVIRONMENTAL FACTORS, AND THE DEVELOPMENT, PROGRESSION, AND PROGNOSIS OF CP. 2019 14 1577 29 DNA METHYLATION PROFILE IN CHRONIC MYELOMONOCYTIC LEUKEMIA ASSOCIATES WITH DISTINCT CLINICAL, BIOLOGICAL AND GENETIC FEATURES. CHROMOSOMAL ABNORMALITIES ARE DETECTED IN 20-30% OF PATIENTS WITH CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML) AND CORRELATE WITH PROGNOSIS. ON THE MUTATION LEVEL, DISRUPTIVE ALTERATIONS ARE PARTICULARLY FREQUENT IN CHROMATIN REGULATORY GENES. HOWEVER, LITTLE IS KNOWN ABOUT THE CONSEQUENTIAL ALTERATIONS IN THE EPIGENETIC MARKING OF THE GENOME. HERE, WE REPORT THE ANALYSIS OF GENOMIC DNA METHYLATION PATTERNS OF 64 CMML PATIENTS AND 10 HEALTHY CONTROLS, USING A DNA METHYLATION MICROARRAY FOCUSED ON PROMOTER REGIONS. DIFFERENTIAL METHYLATION ANALYSIS BETWEEN PATIENTS AND CONTROLS ALLOWED US TO IDENTIFY ABNORMALITIES IN DNA METHYLATION, INCLUDING HYPERMETHYLATION OF SPECIFIC GENES AND LARGE GENOME REGIONS WITH ABERRANT DNA METHYLATION. UNSUPERVISED HIERARCHICAL CLUSTER ANALYSIS IDENTIFIED TWO MAIN CLUSTERS THAT ASSOCIATED WITH THE CLINICAL, BIOLOGICAL, AND GENETIC FEATURES OF PATIENTS. GROUP 1 WAS ENRICHED IN PATIENTS WITH ADVERSE CLINICAL AND BIOLOGICAL CHARACTERISTICS AND POORER OVERALL AND PROGRESSION-FREE SURVIVAL. IN ADDITION, SIGNIFICANT DIFFERENCES IN DNA METHYLATION WERE OBSERVED BETWEEN PATIENTS WITH LOW RISK AND INTERMEDIATE/HIGH RISK KARYOTYPES AND BETWEEN TET2 MUTANT AND WILD TYPE PATIENTS. TAKEN TOGETHER, OUR RESULTS DEMONSTRATE THAT ALTERED DNA METHYLATION PATTERNS REFLECT THE CMML DISEASE STATE AND ALLOW TO IDENTIFY PATIENT GROUPS WITH DISTINCT CLINICAL FEATURES. 2018 15 3765 41 INTEGRATIVE ANALYSIS OF TRANSCRIPTOMIC AND PROTEOMIC PROFILING IN INFLAMMATORY BOWEL DISEASE COLON BIOPSIES. BACKGROUND: CROHN'S DISEASE (CD) AND ULCERATIVE COLITIS (UC) ARE INTESTINAL CHRONIC INFLAMMATORY CONDITIONS CHARACTERIZED BY ALTERED EPITHELIAL BARRIER FUNCTION AND TISSUE DAMAGE. DESPITE SIGNIFICANT EFFORTS TO UNDERSTANDING THE BIOLOGICAL MECHANISMS RESPONSIBLE FOR GUT INFLAMMATION, THE PATHOPHYSIOLOGY OF CD AND UC REMAINS POORLY UNDERSTOOD. METHODS: TO HELP ELUCIDATE THE POTENTIAL MECHANISMS RESPONSIBLE FOR GUT INFLAMMATION IN CD AND UC, TRANSCRIPTOMIC AND PROTEOMIC PROFILING OF HUMAN COLON BIOPSY SPECIMENS WAS PERFORMED. DYSREGULATED GENES AND PROTEINS IN DISEASE TISSUES COMPARED WITH NORMAL TISSUES WERE CHARACTERIZED FROM THE EXPRESSION PROFILES AND FURTHER SUBJECTED TO PATHWAY ANALYSIS TO IDENTIFY ALTERED BIOLOGICAL PROCESSES AND SIGNALING PATHWAYS. RESULTS: SAMPLE ANALYSIS SHOWED 4250 GENES WITH MATCHED PROTEIN EXPRESSION AND A WIDE RANGE OF CORRELATION OF RNA-PROTEIN ABUNDANCE ACROSS SAMPLES. PATHWAY ANALYSIS OF DYSREGULATED GENES AND PROTEINS IN CD AND UC SHOWED ALTERATIONS IN IMMUNE AND INFLAMMATORY RESPONSES, COMPLEMENT CASCADE, AND THE SUPPRESSION OF METABOLIC PROCESSES AND PPAR SIGNALING. IN CD, INCREASED T-HELPER CELL DIFFERENTIATION AND ELEVATED TOLL-LIKE RECEPTOR AND JAK/STAT SIGNALING WERE OBSERVED. INTERESTINGLY, INCREASED MAPK SIGNALING WAS ONLY OBSERVED IN UC. WEIGHTED GENE CO-EXPRESSION NETWORK ANALYSIS SUGGESTED A POSSIBLE ROLE OF EPIGENETIC REGULATION IN UC. OF NOTE, A LARGE DISCREPANCY BETWEEN REGULATION OF RNA AND PROTEIN LEVELS IN INFLAMED COLON SAMPLES WAS DETECTED FOR PREVIOUSLY IDENTIFIED BIOMARKERS INCLUDING MMP14 AND LAMP1. CONCLUSIONS: WITH THE ANALYSIS OF DYSREGULATED GENES AND PATHWAYS, THE PRESENT STUDY UNRAVELS KEY MECHANISMS CONTRIBUTING TO CD AND UC PATHOGENESIS AND EMPHASIZES THAT INTEGRATIVE ANALYSIS OF MULTI-OMICS DATA SETS CAN PROVIDE MORE INSIGHT INTO UNDERSTANDING COMPLEX DISEASE MECHANISMS. 2019 16 3646 35 INCREASED PROTEIN EXPRESSION OF DNA METHYLTRANSFERASE (DNMT) 1 IS SIGNIFICANTLY CORRELATED WITH THE MALIGNANT POTENTIAL AND POOR PROGNOSIS OF HUMAN HEPATOCELLULAR CARCINOMAS. ALTERATION OF DNA METHYLATION IS ONE OF THE MOST CONSISTENT EPIGENETIC CHANGES IN HUMAN CANCERS. DNA METHYLTRANSFERASE (DNMT) 1 IS A MAJOR ENZYME INVOLVED IN ESTABLISHING GENOMIC METHYLATION PATTERNS. MOST OF THE STUDIES CONCERNING DNMT1 EXPRESSION IN HUMAN CANCERS HAVE BEEN PERFORMED ONLY AT THE MRNA LEVEL. TO DIRECTLY EXAMINE DNMT1 PROTEIN EXPRESSION LEVELS DURING HUMAN HEPATOCARCINOGENESIS, 16 HISTOLOGICALLY NORMAL LIVER TISSUES, 51 NONCANCEROUS LIVER TISSUES EXHIBITING CHRONIC HEPATITIS OR CIRRHOSIS, WHICH ARE CONSIDERED TO BE PRECANCEROUS CONDITIONS, AND 53 HEPATOCELLULAR CARCINOMAS (HCCS) WERE SUBJECTED TO IMMUNOHISTOCHEMIC EXAMINATION. IF MORE THAN 20% OF THE CELLS EXHIBITED NUCLEAR DNMT1 STAINING, THE TISSUE SAMPLE WAS CONSIDERED TO BE DNMT1-POSITIVE. DNMT1 IMMUNOREACTIVITY WAS OBSERVED IN 23 (43%) OF THE HCCS, BUT IN NONE (0%) OF THE HISTOLOGICALLY NORMAL LIVER OR NONCANCEROUS LIVER TISSUES EXHIBITING CHRONIC HEPATITIS OR CIRRHOSIS. THE INCIDENCE OF INCREASED DNMT1 PROTEIN EXPRESSION IN HCCS CORRELATED SIGNIFICANTLY WITH POOR TUMOR DIFFERENTIATION (P = 0.0006) AND PORTAL VEIN INVOLVEMENT (P = 0.0002). MOREOVER, THE RECURRENCE-FREE (P = 0.0001) AND OVERALL (P < 0.0001) SURVIVAL RATES OF PATIENTS WITH HCCS EXHIBITING INCREASED DNMT1 PROTEIN EXPRESSION WERE SIGNIFICANTLY LOWER THAN THOSE OF PATIENTS WITH HCCS THAT DID NOT EXHIBIT INCREASED EXPRESSION. INCREASED DNMT1 PROTEIN EXPRESSION MAY PLAY A CRITICAL ROLE IN THE MALIGNANT PROGRESSION OF HCCS AND BE A BIOLOGIC PREDICTOR OF BOTH HCC RECURRENCE AND A POOR PROGNOSIS IN HCC PATIENTS. 2003 17 507 38 ASSOCIATION OF INCREASED DNA METHYLTRANSFERASE EXPRESSION WITH CARCINOGENESIS AND POOR PROGNOSIS IN PANCREATIC DUCTAL ADENOCARCINOMA. INTRODUCTION: EPIGENETIC MODIFICATIONS PLAY AN IMPORTANT ROLE IN MULTISTAGE CARCINOGENESIS. THE ROLE OF THE THREE FUNCTIONAL DNA METHYLTRANSFERASES (DNMTS) IN PANCREATIC CARCINOGENESIS HAS NOT BEEN FULLY UNDERSTOOD. THE MAIN GOAL OF THIS STUDY WAS TO EXAMINE DNMT EXPRESSION IN DIFFERENT STAGES OF PANCREATIC DUCTAL ADENOCARCINOMA (PDAC), AND EVALUATE THEIR PROGNOSTIC SIGNIFICANCE IN PDAC. MATERIALS AND METHODS: A LARGE NUMBER OF PREMALIGNANT AND MALIGNANT PANCREATIC LESIONS WERE OBTAINED BY MANUAL MICRODISSECTION. QUANTITATIVE REAL-TIME RT-PCR WAS USED TO DETECT DNMTS MRNA EXPRESSION. NONPARAMETRIC TEST, LOGRANK TEST AND COX REGRESSION ANALYSIS WERE USED TO EVALUATE THE CLINICAL SIGNIFICANCE OF DNMT EXPRESSION. RESULTS: THE MRNA EXPRESSION OF THE THREE DNMTS INCREASED WITH THE DEVELOPMENT OF PANCREATIC CANCER FROM NORMAL DUCT TO PANCREATIC INTRADUCTAL NEOPLASIA AND FURTHER TO PDAC, AND WERE STATISTICALLY CORRELATED WITH EACH OTHER. EXPRESSION OF THE THREE DNMTS WAS STATISTICALLY CORRELATED WITH TNM STAGING AND HISTORY OF CHRONIC PANCREATITIS. DNMT3A AND DNMT3B, BUT NOT DNMT1 EXPRESSION, WAS STATISTICALLY CORRELATED WITH TUMOUR SIZE. PATIENTS WITH HIGHER LEVELS OF DNMT1, DNMT3A AND/OR DNMT3B EXPRESSION HAD AN OVERALL LOWER SURVIVAL THAN THOSE WITH LOWER LEVELS OF EXPRESSION. UNIVARIATE ANALYSIS SHOWED THAT HIGH EXPRESSION LEVELS OF DNMTS, ALCOHOL CONSUMPTION, TUMOUR DIFFERENTIATION AND TNM STAGING WERE STATISTICALLY SIGNIFICANT RISK FACTORS. MULTIVARIATE ANALYSIS SHOWED THAT HIGH LEVEL OF DNMT3B EXPRESSION AND TUMOUR DIFFERENTIATION WERE STATISTICALLY SIGNIFICANT INDEPENDENT POOR PROGNOSTIC FACTORS. CONCLUSIONS: THESE RESULTS SUGGESTED THAT PANCREATIC CARCINOGENESIS INVOLVES AN INCREASED MRNA EXPRESSION OF THREE DNMTS, AND THEY MAY BECOME VALUABLE DIAGNOSTIC AND PROGNOSTIC MARKERS AS WELL AS POTENTIAL THERAPEUTIC TARGETS FOR PANCREATIC CANCER. 2012 18 3067 34 GENOME-WIDE DNA METHYLATION PROFILES IN PRECANCEROUS CONDITIONS AND CANCERS. ALTERATIONS OF DNA METHYLATION, WHICH RESULT IN CHROMOSOMAL INSTABILITY AND SILENCING OF TUMOR-RELATED GENES, ARE AMONG THE MOST CONSISTENT EPIGENETIC CHANGES OBSERVED IN HUMAN CANCERS. ANALYSIS OF TISSUE SPECIMENS HAS REVEALED THAT DNA METHYLATION ALTERATIONS PARTICIPATE IN MULTISTAGE CARCINOGENESIS, EVEN FROM THE EARLY AND PRECANCEROUS STAGES, ESPECIALLY IN ASSOCIATION WITH CHRONIC INFLAMMATION AND/OR PERSISTENT VIRAL INFECTION, SUCH AS CHRONIC HEPATITIS OR LIVER CIRRHOSIS RESULTING FROM INFECTION WITH HEPATITIS B OR C VIRUS. DNA METHYLATION ALTERATIONS CAN ACCOUNT FOR THE HISTOLOGICAL HETEROGENEITY AND CLINICOPATHOLOGICAL DIVERSITY OF HUMAN CANCERS. OVEREXPRESSION OF DNA METHYLTRANSFERASE 1 IS NOT A SECONDARY RESULT OF INCREASED CELL PROLIFERATIVE ACTIVITY, BUT IS SIGNIFICANTLY CORRELATED WITH ACCUMULATION OF DNA HYPERMETHYLATION IN CPG ISLANDS OF TUMOR-RELATED GENES. ALTERATION OF DNA METHYLTRANSFERASE 3B SPLICING MAY RESULT IN CHROMOSOMAL INSTABILITY THROUGH DNA HYPOMETHYLATION IN PERICENTROMERIC SATELLITE REGIONS. GENOME-WIDE ANALYSIS OF DNA METHYLATION STATUS HAS REVEALED THAT THE DNA METHYLATION PROFILE AT THE PRECANCEROUS STAGE IS BASICALLY INHERITED BY THE CORRESPONDING CANCERS DEVELOPING IN INDIVIDUAL PATIENTS. DNA METHYLATION STATUS IS NOT SIMPLY ALTERED AT THE PRECANCEROUS STAGE; RATHER, DNA METHYLATION ALTERATIONS AT THE PRECANCEROUS STAGE MAY CONFER VULNERABILITY TO FURTHER GENETIC AND EPIGENETIC ALTERATIONS, GENERATE MORE MALIGNANT CANCERS, AND THUS DETERMINE PATIENT OUTCOME. THEREFORE, GENOME-WIDE DNA METHYLATION PROFILING MAY PROVIDE OPTIMAL INDICATORS FOR CARCINOGENETIC RISK ESTIMATION AND PROGNOSTICATION, AND THUS PROVIDE AN AVENUE FOR CANCER PREVENTION AND THERAPY ON AN INDIVIDUAL BASIS. 2010 19 3588 38 IMPACT OF TP53 GENE PROMOTER METHYLATION ON CHRONIC LYMPHOCYTIC LEUKEMIA PATHOGENESIS AND PROGRESSION. BACKGROUND: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS A MALIGNANT LYMPHOID DISORDER THAT RESULTS FROM THE OVERGROWTH OF MATURE-LOOKING LYMPHOID CELLS IN THE BLOOD AND LYMPHATIC TISSUE. VARIOUS CLINICAL PRESENTATIONS HAVE BEEN ATTRIBUTED TO THE DISEASE AS A RESULT OF THE DIFFERENT UNDERLYING GENETIC AND EPIGENETIC ALTERATIONS. THE CURRENT STUDY HAS BEEN INITIATED TO STUDY THE ROLE OF AN EPIGENETIC ALTERATION AFFECTING THE PROMOTER OF THE TP53GENE ON CLL PATHOGENESIS AND PROGRESSION. METHODS: THE CURRENT STUDY INVOLVED 54 NEWLY DIAGNOSED PATIENTS PRESENTING WITH CLL AS WELL AS 30 NORMAL INDIVIDUALS AS CONTROLS. AFTER OBTAINING VERBAL CONSENT, DATA COLLECTION WAS DONE AND THE BLOOD COLLECTED FROM ALL ENROLLED INDIVIDUALS FOR HEMATOLOGICAL INVESTIGATIONS AS WELL AS FOR MOLECULAR CATEGORIZATION OF TP53 METHYLATION STATUS. METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (MS-PCR) TECHNIQUE WAS USED TO DEFINE THE METHYLATION STATUS OF THE TP53 GENE PROMOTER THAT ENCOMPASSES DNA EXTRACTION, BISULFITE CONVERSION, CONVENTIONAL PCR AMPLIFICATION, RUNNING ON AGAROSE GEL AND DOCUMENTATION. FINALLY, STATISTICAL ANALYSIS WAS DONE TO ASSESS ANY CORRELATION OF THE TP53 EPIGENETIC ALTERATION TO THE DISEASE ETIOLOGY AND THE PROGRESSION. RESULTS: IN THE CURRENT STUDY, ALL CONTROLS AND 42 OF 54 PATIENTS SHOW UNMETHYLATED TP53 GENE PROMOTER; ON THE OTHER HAND, THE METHYLATED PROMOTER WAS DETECTED AMONG 12 PATIENTS WITH A P-VALUE OF 0.001. TP53 GENE PROMOTER METHYLATION SIGNIFICANTLY LINKED TO REDUCED PLATELET COUNT (P-VALUE OF 0.047) AND ADVANCED STAGE AT PRESENTATION (P-VALUE OF 0.076). NO SIGNIFICANT DIFFERENCES WERE SEEN AMONG BOTH METHYLATED AND UNMETHYLATED TP53 PROMOTERS IN RELATION TO THE AGE OF THE AFFECTED INDIVIDUALS, TOTAL WHITE BLOOD CELL COUNTS AND HEMOGLOBIN LEVEL OF THE AFFECTED INDIVIDUALS. CONCLUSION: THE CURRENT STUDY REVEALED A SIGNIFICANT CORRELATION OF TP53 GENE PROMOTER METHYLATION TO CHRONIC LYMPHOCYTIC LEUKEMIA PATHOGENESIS AND LOWER PLATELET COUNTS. 2019 20 2494 29 EPIGENETICS AND CHRONIC LYMPHOCYTIC LEUKEMIA. THE DNA METHYLATION LEVEL IN PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA IS GENERALLY LOWER THAN HEALTHY INDIVIDUALS. ALTHOUGH DNA METHYLATION IS GLOBALLY DECREASED, REGIONAL HYPERMETHYLATION OF GENE PROMOTERS LEADS TO GENE SILENCING. MANY OF THESE GENES HAVE TUMOR SUPPRESSOR PHENOTYPES. UNLIKE MUTATIONS OR DELETIONS, HYPERMETHYLATION IS POTENTIALLY REVERSIBLE AFTER INHIBITION WITH DNA METHYLATION MODULATORS. MYELODYSPLASTIC SYNDROME HAS BEEN A MODEL DISEASE IN WHICH TREATMENT OF PATIENTS RESULTS IN DEMETHYLATION OF SPECIFIC GENES. THE STORY IN PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA IS SLOWLY UNRAVELING AS EPIGENETIC MODIFICATIONS LIKELY ALSO PLAY AN IMPORTANT ROLE. ONGOING CLINICAL TRIALS CORRELATING CLINICAL RESPONSE TO GENE EXPRESSION AFTER TREATMENT WITH DNA METHYLATION INHIBITORS WILL ULTIMATELY ALLOW US TO BETTER RISK STRATIFY AND PREDICT THE SUBGROUP OF PATIENTS WHO WILL BENEFIT FROM TREATMENT WITH THIS CLASS OF DRUGS. 2006