1 3071 157 GENOME-WIDE DNA METHYLATION PROFILING INTEGRATED WITH GENE EXPRESSION PROFILING IDENTIFIES PAX9 AS A NOVEL PROGNOSTIC MARKER IN CHRONIC LYMPHOCYTIC LEUKEMIA. BACKGROUND: IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), EPIGENOMIC AND GENOMIC STUDIES HAVE EXPANDED THE EXISTING KNOWLEDGE ABOUT THE DISEASE BIOLOGY AND LED TO THE IDENTIFICATION OF POTENTIAL BIOMARKERS RELEVANT FOR IMPLEMENTATION OF PERSONALIZED MEDICINE. IN THIS STUDY, AN ATTEMPT HAS BEEN MADE TO EXAMINE AND INTEGRATE THE GLOBAL DNA METHYLATION CHANGES WITH GENE EXPRESSION PROFILE AND THEIR IMPACT ON CLINICAL OUTCOME IN EARLY STAGE CLL PATIENTS. RESULTS: THE INTEGRATION OF DNA METHYLATION PROFILE (N = 14) WITH THE GENE EXPRESSION PROFILE (N = 21) REVEALED 142 GENES AS HYPERMETHYLATED-DOWNREGULATED AND; 62 GENES AS HYPOMETHYLATED-UPREGULATED IN EARLY STAGE CLL PATIENTS COMPARED TO CD19+ B-CELLS FROM HEALTHY INDIVIDUALS. THE MRNA EXPRESSION LEVELS OF 17 GENES IDENTIFIED TO BE DIFFERENTIALLY METHYLATED AND/OR DIFFERENTIALLY EXPRESSED WAS FURTHER EXAMINED IN EARLY STAGE CLL PATIENTS (N = 93) BY QUANTITATIVE REAL TIME PCR (RQ-PCR). SIGNIFICANT DIFFERENCES WERE OBSERVED IN THE MRNA EXPRESSION OF MEIS1, PMEPA1, SOX7, SPRY1, CDK6, TBX2, AND SPRY2 GENES IN CLL CELLS AS COMPARED TO B-CELLS FROM HEALTHY INDIVIDUALS. THE ANALYSIS IN THE IGHV MUTATION BASED CATEGORIES (UNMUTATED = 39, MUTATED = 54) REVEALED SIGNIFICANTLY HIGHER MRNA EXPRESSION OF CRY1 AND PAX9 GENES IN THE IGHV UNMUTATED SUBGROUP (P < 0.001). THE RELATIVE RISK OF TREATMENT INITIATION WAS SIGNIFICANTLY HIGHER AMONG PATIENTS WITH HIGH EXPRESSION OF CRY1 (RR = 1.91, P = 0.005) OR PAX9 (RR = 1.87, P = 0.001). HIGH EXPRESSION OF CRY1 (HR: 3.53, P < 0.001) OR PAX9 (HR: 3.14, P < 0.001) GENE WAS SIGNIFICANTLY ASSOCIATED WITH SHORTER TIME TO FIRST TREATMENT. THE HIGH EXPRESSION OF PAX9 GENE (HR: 3.29, 95% CI 1.172-9.272, P = 0.016) WAS ALSO PREDICTIVE OF SHORTER OVERALL SURVIVAL IN CLL. CONCLUSIONS: THE DNA METHYLATION CHANGES ASSOCIATED WITH MRNA EXPRESSION OF CRY1 AND PAX9 GENES ALLOW RISK STRATIFICATION OF EARLY STAGE CLL PATIENTS. THIS COMPREHENSIVE ANALYSIS SUPPORTS THE CONCEPT THAT THE EPIGENETIC CHANGES ALONG WITH THE ALTERED EXPRESSION OF GENES HAVE THE POTENTIAL TO PREDICT CLINICAL OUTCOME IN EARLY STAGE CLL PATIENTS.	2017	

2 5270  41 PROMOTER DNA METHYLATION FREQUENCY AND CLINICOPATHOLOGICAL ROLE OF MIR-129-2 GENE IN PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA. OBJECTIVES: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS CHARACTERIZED BY THE ACCUMULATION OF APPARENTLY MATURE B-TYPE LYMPHOCYTES IN THE LYMPHOHEMATOPOIETIC ORGANS. METHYLATION IN PROMOTERS OF TUMOR SUPPRESSOR GENES IS ONE OF THE MECHANISMS THAT CAUSES BLOOD MALIGNANCY. IN THIS STUDY, WE EVALUATED THE PROMOTER DNA METHYLATION STATUS OF MIR-129-2 TUMOR SUPPRESSOR GENE AND ITS ASSOCIATION WITH CLINICAL AND LABORATORY PARAMETERS OF PATIENTS WITH CLL. METHODS: WE STUDIED THE PROMOTER DNA METHYLATION FREQUENCY OF THE MIR-129-2 GENE IN 50 PATIENTS WITH CLL AND 50 HEALTHY CONTROLS USING METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION METHODS. STATISTICAL ANALYSIS WAS PERFORMED USING SPSS-18 SOFTWARE, AND A P-VALUE < 0.050 WAS CONSIDERED STATISTICALLY SIGNIFICANT. RESULTS: THE FREQUENCY OF PROMOTER DNA METHYLATION OF THE MIR-129-2 GENE WAS SIGNIFICANTLY HIGHER IN THE CLL GROUP COMPARED WITH CONTROL GROUP (38.0% VS. 0.0%, P < 0.001; CHI(2) = 23.457). THE PROMOTER DNA METHYLATION FREQUENCY OF MIR-129-2 GENE WAS NOT SIGNIFICANTLY DIFFERENT BETWEEN THE TWO SEXES (P = 0.236). A SIGNIFICANT BUT WEAK CORRELATION WAS SEEN BETWEEN THE METHYLATED STATE OF THE MIR-129-2 GENE AND ORGANOMEGALY (P = 0.019, R = 0.330) AS WELL AS HEMOGLOBIN LEVELS (P = 0.020, R = -0.233). HOWEVER, BINARY LOGISTIC REGRESSION ANALYSIS INDICATED ORGANOMEGALY AS THE ONLY CLINICAL BIOMARKER WITH A STATISTICALLY SIGNIFICANT ASSOCIATION WITH THE HYPERMETHYLATED MIR-129-2 GENE STATE (P = 0.046). CONCLUSIONS: THE HIGH FREQUENCY OF PROMOTER DNA METHYLATION OF THE MIR-129-2 GENE IN THE CLL GROUP COMPARED TO THE CONTROL GROUP, AS WELL AS ITS SIGNIFICANT ASSOCIATION WITH ORGANOMEGALY, SUGGESTS THE IMPORTANCE OF THIS EPIGENETIC BIOMARKER IN THE PATHOGENESIS AND PROGNOSIS OF CLL DISEASE.	2020	
                                                                                                                                                                                                                                                                                                                                                                                             
3  494  35 ASSESSMENT OF PROMOTER METHYLATION IDENTIFIES PTCH AS A PUTATIVE TUMOR-SUPPRESSOR GENE IN HUMAN CLL. BACKGROUND: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS CHARACTERIZED BY A CLONAL ACCUMULATION OF NEOPLASTIC LYMPHOCYTES, INDICATING DISRUPTION OF APOPTOSIS. PATIENTS AND METHODS: DIFFERENTIAL METHYLATION HYBRIDIZATION ANALYSIS WAS PERFORMED TO IDENTIFY NOVEL TARGET GENES SILENCED BY CPG ISLAND METHYLATION IN PATIENTS WITH CLL. RESULTS: PATCHED (PTCH), A TUMOR-SUPPRESSOR GENE, WAS FOUND TO BE FREQUENTLY METHYLATED IN CLL SAMPLES COMPARED TO SAMPLES DERIVED FROM HEALTHY INDIVIDUALS. DE NOVO METHYLATION OF A CPG ISLAND REGION LOCATED UPSTREAM OF PTCH EXON 1 WAS CONFIRMED BY PYROSEQUENCING IN 17/37 (46%) OF PERIPHERAL BLOOD MONONUCLEAR CELLS OF PATIENTS WITH CLL, BUT IN NONE ISOLATED FROM SEVEN HEALTHY INDIVIDUALS. NO ASSOCIATION WAS FOUND BETWEEN PTCH HYPERMETHYLATION AND CURRENTLY USED PROGNOSTIC CLL FACTORS. CONCLUSION: OUR INVESTIGATION SUGGESTS THAT EPIGENETIC SILENCING OF PTCH IS A MECHANISM CONTRIBUTING TO CLL TUMORIGENESIS.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
4   27  45 A B-CELL EPIGENETIC SIGNATURE DEFINES THREE BIOLOGIC SUBGROUPS OF CHRONIC LYMPHOCYTIC LEUKEMIA WITH CLINICAL IMPACT. PROSPECTIVE IDENTIFICATION OF PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) DESTINED TO PROGRESS WOULD GREATLY FACILITATE THEIR CLINICAL MANAGEMENT. RECENTLY, WHOLE-GENOME DNA METHYLATION ANALYSES IDENTIFIED THREE CLINICOBIOLOGIC CLL SUBGROUPS WITH AN EPIGENETIC SIGNATURE RELATED TO DIFFERENT NORMAL B-CELL COUNTERPARTS. HERE, WE DEVELOPED A CLINICALLY APPLICABLE METHOD TO IDENTIFY THESE SUBGROUPS AND TO STUDY THEIR CLINICAL RELEVANCE. USING A SUPPORT VECTOR MACHINE APPROACH, WE BUILT A PREDICTION MODEL USING FIVE EPIGENETIC BIOMARKERS THAT WAS ABLE TO CLASSIFY CLL PATIENTS ACCURATELY INTO THE THREE SUBGROUPS, NAMELY NAIVE B-CELL-LIKE, INTERMEDIATE AND MEMORY B-CELL-LIKE CLL. DNA METHYLATION WAS QUANTIFIED BY HIGHLY REPRODUCIBLE BISULFITE PYROSEQUENCING ASSAYS IN TWO INDEPENDENT CLL SERIES. IN THE INITIAL SERIES (N=211), THE THREE SUBGROUPS SHOWED DIFFERENTIAL LEVELS OF IGHV (IMMUNOGLOBULIN HEAVY-CHAIN LOCUS) MUTATION (P<0.001) AND VH USAGE (P<0.03), AS WELL AS DIFFERENT CLINICAL FEATURES AND OUTCOME IN TERMS OF TIME TO FIRST TREATMENT (TTT) AND OVERALL SURVIVAL (P<0.001). A MULTIVARIATE COX MODEL SHOWED THAT EPIGENETIC CLASSIFICATION WAS THE STRONGEST PREDICTOR OF TTT (P<0.001) ALONG WITH BINET STAGE (P<0.001). THESE FINDINGS WERE CORROBORATED IN A VALIDATION SERIES (N=97). IN THIS STUDY, WE DEVELOPED A SIMPLE AND ROBUST METHOD USING EPIGENETIC BIOMARKERS TO CATEGORIZE CLLS INTO THREE SUBGROUPS WITH DIFFERENT CLINICOBIOLOGIC FEATURES AND OUTCOME.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
5 2262  45 EPIGENETIC PROFILING IN CHRONIC LYMPHOCYTIC LEUKEMIA REVEALS NOVEL METHYLATION TARGETS. CPG ISLAND METHYLATION IS AN EPIGENETIC ALTERATION THAT CONTRIBUTES TO TUMORIGENESIS BY TRANSCRIPTIONAL INACTIVATION OF GENES. LITTLE IS KNOWN ABOUT THE OVERALL LEVELS OF CPG ISLAND METHYLATION IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). TO PROVIDE A BASELINE ESTIMATE OF GLOBAL ABERRANT METHYLATION AND IDENTIFY TARGET SEQUENCES FOR ADDITIONAL INVESTIGATION, WE PERFORMED RESTRICTION LANDMARK GENOMIC SCANNING ON 10 CLL SAMPLES. TWO METHYLATION-SENSITIVE LANDMARK ENZYMES WERE USED (NOTI AND ASCI), ALLOWING ASSESSMENT OF OVER 3000 CPG ISLANDS IN EACH SAMPLE. TUMOR-DERIVED RESTRICTION LANDMARK GENOMIC SCANNING PROFILES WERE COMPARED WITH PROFILES FROM CD19-SELECTED B CELLS FROM NORMAL VOLUNTEERS AND MATCHED NORMAL NEUTROPHILS FROM 4 CLL PATIENTS. WE FOUND 2.5-8.1% (MEAN 4.8%) OF THE CPG ISLANDS IN CLL SAMPLES WERE ABERRANTLY METHYLATED COMPARED WITH CONTROLS, AND THE METHYLATION EVENTS HAD A NONRANDOM DISTRIBUTION (P < 0.0001). FURTHERMORE, WE IDENTIFIED 193 ABERRANTLY METHYLATED SEQUENCES, OF WHICH 93% HAVE CPG ISLAND CHARACTERISTICS AND 90% HAVE HOMOLOGY TO GENES OR EXPRESSED SEQUENCES. ONE SUCH GENE, THE G PROTEIN-COUPLED METABOTROPIC GLUTAMATE RECEPTOR 7 (GRM7), POSSIBLY INHIBITS CYCLIC AMP SIGNALING IN THE INDUCTION OF APOPTOSIS. BISULFITE SEQUENCING OF GRM7 CONFIRMED EXTENSIVE CPG ISLAND METHYLATION, AND TREATMENT WITH 5-AZA-2'-DEOXYCYTIDINE (DECITABINE) RESULTED IN UP-REGULATED EXPRESSION OF SEVERAL GENES IN VITRO WITH CONCURRENT CELLULAR DEPLETION OF DNMT1 PROTEIN. OUR DUAL-ENZYME GLOBAL METHYLATION STUDY SHOWS THAT CLL IS CHARACTERIZED BY WIDESPREAD NONRANDOM CPG ISLAND METHYLATION SIMILAR TO OTHER TUMORS AND PROVIDES A PANEL OF NOVEL METHYLATION TARGETS THAT CAN BE USED IN LARGER STUDIES DESIGNED TO ASSESS IMPACT ON DISEASE PROGRESSION AND SURVIVAL.	2004	
                                                                                                                                                                                                                                                                                                                                                                                                              
6  831  50 CHARACTERIZATION OF TET AND IDH GENE EXPRESSION IN CHRONIC LYMPHOCYTIC LEUKEMIA: COMPARISON WITH NORMAL B CELLS AND PROGNOSTIC SIGNIFICANCE. BACKGROUND: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS THE MOST COMMON HEMATOLOGICAL MALIGNANCY IN WESTERN COUNTRIES, CHARACTERIZED BY A HETEROGENEOUS CLINICAL COURSE. ALTHOUGH GENETIC STUDIES HAVE IDENTIFIED CHROMOSOMAL ABERRATIONS OR SPECIFIC MUTATIONS, EPIGENETIC CHANGES HAVE BEEN POORLY CHARACTERIZED IN CLL. METHODS: WE ASSESSED TEN-ELEVEN TRANSLOCATIONS (TET) 1, 2, AND 3, ISOCITRATE DEHYDROGENASE (IDH) 1, AND 2 MESSENGER RNA (MRNA) EXPRESSION USING REAL-TIME PCR ON PURIFIED LEUKEMIC B CELLS FROM 214 CLL PATIENTS (MEDIAN FOLLOW-UP = 75 MONTHS, RANGE 1-380), NORMAL PERIPHERAL BLOOD B CELLS (N = 20), AND UMBILICAL CORD BLOOD B CELLS (N = 21). THE MICROENVIRONMENT INFLUENCE WAS ASSESSED AFTER 24 H CO-CULTURE OF CLL CELLS WITH BONE MARROW MESENCHYMAL STROMAL CELLS (BMSC). FINALLY, 5-HYDROXYMETHYLCYTOSINE LEVEL (%5-HMC) WAS ASSESSED BY ELISA IN CLL CELLS ALONE OR WITH MICROENVIRONMENT STIMULI. RESULTS: TET 1 AND 3 AND IDH2 WERE DECREASED IN CLL CELLS COMPARED WITH HEALTHY B CELLS (P = 0.0221, 0.0013, <0.0001, RESPECTIVELY), WHILE IDH1 WAS OVEREXPRESSED (P = 0.0037). TET2 AND IDH1 WERE SIGNIFICANTLY CORRELATED WITH TREATMENT-FREE SURVIVAL (TFS); PATIENTS WITH HIGH TET2/IDH1 EXPRESSION HAD A HIGHER MEDIAN TFS (111 MONTHS) THAN PATIENTS WITH LOW EXPRESSION (78 MONTHS, P = 0.0071/0.0123). MOREOVER, TET1 EXPRESSION DECREASED (P = 0.0371), WHILE TET3 AND IDH2 EXPRESSION INCREASED (P = 0.0273/0.0039) IN CO-CULTURES. HOWEVER, %5-HMC WAS NOT CORRELATED WITH CLINICAL DATA AND WAS UNCHANGED FOLLOWING MICROENVIRONMENT STIMULI. CONCLUSIONS: DESPITE A SLIGHT DEREGULATION IN CLL CELLS COMPARED WITH NORMAL B CELLS, WE IDENTIFIED A SIGNIFICANT ASSOCIATION BETWEEN TET/IDH GENE EXPRESSION AND PROGNOSIS, SUGGESTING THAT EPIGENETIC CHANGES COULD POTENTIALLY BE ASSOCIATED WITH DISEASE PROGRESSION. MOREOVER, DESPITE AN IDENTICAL %5-HMC, TET GENE EXPRESSION WAS INFLUENCED BY CONTACT WITH BMSC CONFIRMING THE CRUCIAL ROLE OF THE MICROENVIRONMENT IN CLL PATHOGENESIS.	2016	
                                                                                                                                                            
7 3125  30 GHSR DNA HYPERMETHYLATION IS A COMMON EPIGENETIC ALTERATION OF HIGH DIAGNOSTIC VALUE IN A BROAD SPECTRUM OF CANCERS. IDENTIFICATION OF A SINGLE MOLECULAR TRAIT THAT IS DETERMINANT OF COMMON MALIGNANCIES MAY SERVE AS A POWERFUL DIAGNOSTIC SUPPLEMENT TO CANCER TYPE-SPECIFIC MARKERS. HERE, WE REPORT A DNA METHYLATION MARK THAT IS CHARACTERISTIC OF SEVEN STUDIED MALIGNANCIES, NAMELY CANCERS OF LUNG, BREAST, PROSTATE, PANCREAS, COLORECTUM, GLIOBLASTOMA AND B CELL CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) (N = 137). THIS MARK WAS DEFINED BY SUBSTANTIAL HYPERMETHYLATION AT THE PROMOTER AND FIRST EXON OF GROWTH HORMONE SECRETAGOUGE RECEPTOR (GHSR) THROUGH BISULFITE PYROSEQUENCING. THE DEGREE OF ABERRANT METHYLATION WAS CAPABLE OF ACCURATE DISCRIMINATION BETWEEN CANCER AND CONTROL SAMPLES. THE HIGHEST SENSITIVITY AND SPECIFICITY OF CANCER DETECTION WAS ACHIEVED FOR CANCERS OF PANCREAS, LUNG, BREAST AND CLL YIELDING THE AREA UNDER THE CURVE (AUC) VALUES OF 1.0000, 0.9952, 0.9800 AND 0.9400, RESPECTIVELY. NARROWING TO A SINGLE CPG SITE WITHIN THE GENE'S PROMOTER OR FOUR CONSECUTIVE CPG UNITS OF THE HIGHEST METHYLATION LEVELS WITHIN THE FIRST EXON IMPROVED THE DETECTION POWER. GHSR HYPERMETHYLATION WAS DETECTED ALREADY AT THE EARLY STAGE TUMORS. THE ACCURATE PERFORMANCE OF THIS MARKER WAS FURTHER REPLICATED IN AN INDEPENDENT SET OF PANCREATIC CANCER AND CONTROL SAMPLES (N = 78). THESE FINDINGS SUPPORT THE CANDIDATURE OF GHSR METHYLATION AS A HIGHLY ACCURATE PAN-CANCER MARKER.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
8 4221  45 METHYLATION AND SILENCING OF PROTEIN TYROSINE PHOSPHATASE RECEPTOR TYPE O IN CHRONIC LYMPHOCYTIC LEUKEMIA. PURPOSE: PREVIOUS STUDIES IN OUR LABORATORY HAVE SHOWN THE PROGRESSIVE METHYLATION AND SUPPRESSION OF THE GENE ENCODING PROTEIN TYROSINE PHOSPHATASE, PTPRO, IN THE LIVERS OF RATS FED A METHYL-DEFICIENT DIET THAT INDUCES HEPATOCARCINOGENESIS. SUBSEQUENTLY, WE OBSERVED THE METHYLATION OF PTPRO IN PRIMARY HUMAN LUNG TUMORS AND ALSO SHOWED ITS POTENTIAL TUMOR SUPPRESSOR CHARACTERISTICS. THE PRESENT STUDY WAS UNDERTAKEN TO INVESTIGATE WHETHER THE TRUNCATED FORM OF PTPRO (PTPROT), SPECIFICALLY EXPRESSED IN NAIVE B LYMPHOCYTES, WAS ALSO METHYLATED AND SUPPRESSED IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), A DISEASE GENERALLY AFFECTING B LYMPHOCYTES. EXPERIMENTAL DESIGN AND RESULTS: INITIAL SCREENING SHOWED THAT 60% OF THE 52 CLL SAMPLES ANALYZED USING METHYLATION-SPECIFIC PCR ASSAY WERE METHYLATED COMPARED WITH B LYMPHOCYTES FROM NORMAL INDIVIDUALS, WHICH WERE NOT METHYLATED. THE EXPRESSION OF PTPROT, AS MEASURED BY SEMIQUANTITATIVE REVERSE TRANSCRIPTION-PCR, INVERSELY CORRELATED WITH METHYLATION IN THE FEW SAMPLES TESTED. ANALYSIS OF ADDITIONAL SAMPLES (N = 50) BY COMBINED BISULFITE RESTRICTION ANALYSIS SHOWED THAT THE PTPRO CPG ISLAND WAS METHYLATED IN 82% OF PATIENTS WITH CLL COMPARED WITH B LYMPHOCYTES FROM NORMAL INDIVIDUALS. FURTHERMORE, OVERALL EXPRESSION OF PTPRO WAS REDUCED IN CLL RELATIVE TO NORMAL LYMPHOCYTES. THE PTPRO GENE WAS ALSO SUPPRESSED BY METHYLATION IN THE CLL CELL LINE WAC3CD5, WHERE IT COULD BE REACTIVATED UPON TREATMENT WITH THE DNA HYPOMETHYLATING AGENT 5-AZAC. ECTOPIC EXPRESSION OF PTPROT IN A NONEXPRESSING CELL LINE INCREASED GROWTH INHIBITION WITH FLUDARABINE TREATMENT, A THERAPY COMMONLY USED FOR CLL. CONCLUSION: THIS STUDY REVEALS THE POTENTIAL ROLE OF PTPRO METHYLATION AND SILENCING IN CLL TUMORIGENESIS AND ALSO PROVIDES A NOVEL MOLECULAR TARGET IN THE EPIGENETIC THERAPY.	2007	
                                                                                                                                                                                                                                                                                                                                                 
9 2753  41 EXPRESSION OF BCL2L12 IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS: ASSOCIATION WITH CLINICAL AND MOLECULAR PROGNOSTIC MARKERS. DYSREGULATION OF APOPTOSIS IS A DISTINCTIVE FEATURE OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), ALTHOUGH A UNIQUE MECHANISM UNDERLYING APOPTOSIS RESISTANCE OF CLL B LYMPHOCYTES HAS NOT BEEN IDENTIFIED YET. ABERRANT EXPRESSION AS WELL AS GENETIC AND EPIGENETIC ALTERATIONS OF NUMEROUS GENES INVOLVED IN DIFFERENT PATHWAYS OF APOPTOSIS REGULATION HAS BEEN DESCRIBED IN CLL. HERE, WE REPORT THE EXPRESSION ANALYSIS OF BCL2L12 (BCL2-LIKE 12), A NOVEL APOPTOTIC GENE BELONGING TO BCL2 FAMILY, IN 58 SERBIAN CLL PATIENTS. QUANTITATIVE REVERSE-TRANSCRIPTASE POLYMERASE CHAIN REACTION (QRT-PCR) ANALYSIS REVEALED A SIGNIFICANT OVEREXPRESSION OF BCL2L12 MRNA IN CLL SAMPLES COMPARED TO NON-LEUKEMIC SAMPLES, IMPLYING ITS ROLE IN THE PATHOGENESIS OF THE DISEASE. RECEIVER OPERATING CHARACTERISTIC (ROC) ANALYSIS SHOWED THAT BCL2L12 EXPRESSION EFFICIENTLY DISCRIMINATES CLL CASES FROM HEALTHY CONTROLS. HOWEVER, RELATIVELY HOMOGENOUS BCL2L12 MRNA EXPRESSION AMONG PATIENTS DID NOT REFLECT THEIR CLINICAL CHARACTERISTICS (WITH THE EXCEPTION OF LACTATE DEHYDROGENASE STATUS AND TIME FROM DIAGNOSIS TO TREATMENT) AND FAILED TO SHOW ASSOCIATION WITH THE MOST INFORMATIVE PROGNOSTIC MARKERS, NAMELY THE MUTATIONAL STATUS OF REARRANGED IMMUNOGLOBULIN HEAVY CHAIN VARIABLE REGION GENES, CD38 AND LIPOPROTEIN LIPASE GENE (LPL) EXPRESSION.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
10 1473  52 DISTINCT PATTERNS OF GLOBAL PROMOTER METHYLATION IN EARLY STAGE CHRONIC LYMPHOCYTIC LEUKEMIA. GENOMIC AND EPIGENOMIC STUDIES OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) ARE RESHAPING OUR UNDERSTANDING OF THE DISEASE AND HAVE PROVIDED NEW PERSPECTIVES FOR A MORE INDIVIDUALIZED DIAGNOSIS AND NEW POTENTIAL THERAPEUTIC TARGETS. IN THIS STUDY, THE GLOBAL PROMOTER METHYLATION PROFILE WAS DETERMINED IN HIGHLY PURIFIED B-CELLS FROM 37 (BINET STAGE A) CLL PATIENTS, USING HIGH-RESOLUTION METHYLATION MICROARRAYS (27,578 CPG). OVERALL, THE METHYLATION PATTERN CORRELATED WITH THE MAJOR BIOLOGICAL (ZAP-70 AND CD38), AND MOLECULAR (IGHV MUTATION) MARKERS, DISTINGUISHING CLL CASES ACCORDING TO IGHV MUTATIONAL STATUS. CELL ADHESION MOLECULES WERE ENRICHED IN THE SIGNATURE OF UNMUTATED (UM) VERSUS MUTATED (M-) CLL. MOREOVER, IN M-CLL CPG HYPER-METHYLATION IN THREE GENES, INCLUDING SPG20, WAS SIGNIFICANTLY ANTI-CORRELATED WITH THE CORRESPONDING GENE EXPRESSION LEVEL. FINALLY, THE CORRELATION BETWEEN THE METHYLATION PATTERN AND CLINICAL PARAMETERS WAS INVESTIGATED. NOTABLY, OUT OF 42 METHYL-PROBES THAT WERE SIGNIFICANTLY ASSOCIATED WITH PROGRESSION FREE SURVIVAL (PFS), HYPER-METHYLATION OF SPG20 WAS ALSO POSITIVELY ASSOCIATED WITH PFS. THESE DATA SUPPORT THE NOTION THAT EPIGENETIC CHANGES HAVE CLINICAL IMPACT IN CLL AND MAY CONTRIBUTE TO THE IDENTIFICATION OF NOVEL CANDIDATE DISEASE-ASSOCIATED GENES POTENTIALLY USEFUL TO PREDICT THE CLINICAL OUTCOME OF EARLY STAGE CLL PATIENTS.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
11   15  44 450K-ARRAY ANALYSIS OF CHRONIC LYMPHOCYTIC LEUKEMIA CELLS REVEALS GLOBAL DNA METHYLATION TO BE RELATIVELY STABLE OVER TIME AND SIMILAR IN RESTING AND PROLIFERATIVE COMPARTMENTS. IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), THE MICROENVIRONMENT INFLUENCES GENE EXPRESSION PATTERNS; HOWEVER, KNOWLEDGE IS LIMITED REGARDING THE EXTENT TO WHICH METHYLATION CHANGES WITH TIME AND EXPOSURE TO SPECIFIC MICROENVIRONMENTS. USING HIGH-RESOLUTION 450K ARRAYS, WE PROVIDE THE MOST COMPREHENSIVE DNA METHYLATION STUDY OF CLL TO DATE, ANALYZING PAIRED DIAGNOSTIC/FOLLOW-UP SAMPLES FROM IGHV-MUTATED/UNTREATED AND IGHV-UNMUTATED/TREATED PATIENTS (N=36) AND PATIENT-MATCHED PERIPHERAL BLOOD AND LYMPH NODE SAMPLES (N=20). ON AN UNPRECEDENTED SCALE, WE REVEALED 2239 DIFFERENTIALLY METHYLATED CPG SITES BETWEEN IGHV-MUTATED AND UNMUTATED PATIENTS, WITH THE MAJORITY OF SITES POSITIONED OUTSIDE ANNOTATED CPG ISLANDS. INTRIGUINGLY, CLL PROGNOSTIC GENES (FOR EXAMPLE, CLLU1, LPL, ZAP70 AND NOTCH1), EPIGENETIC REGULATOR (FOR EXAMPLE, HDAC9, HDAC4 AND DNMT3B), B-CELL SIGNALING (FOR EXAMPLE, IBTK) AND NUMEROUS TGF-BETA AND NF-KAPPAB/TNF PATHWAY GENES WERE ALTERNATIVELY METHYLATED BETWEEN SUBGROUPS. CONTRARY, DNA METHYLATION OVER TIME WAS DEEMED RATHER STABLE WITH FEW RECURRENT CHANGES NOTED WITHIN SUBGROUPS. ALTHOUGH A LARGER NUMBER OF NON-RECURRENT CHANGES WERE IDENTIFIED AMONG IGHV-UNMUTATED RELATIVE TO MUTATED CASES OVER TIME, THESE EQUATED TO A LOW GLOBAL CHANGE. SIMILARLY, FEW CHANGES WERE IDENTIFIED BETWEEN COMPARTMENT CASES. ALTOGETHER, WE REVEAL CLL SUBGROUPS TO DISPLAY UNIQUE METHYLATION PROFILES AND UNVEIL METHYLATION AS RELATIVELY STABLE OVER TIME AND SIMILAR WITHIN DIFFERENT CLL COMPARTMENTS, IMPLYING ABERRANT METHYLATION AS AN EARLY LEUKEMOGENIC EVENT.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
12 4907  41 P53 ABERRATIONS DO NOT PREDICT INDIVIDUAL RESPONSE TO FLUDARABINE IN PATIENTS WITH B-CELL CHRONIC LYMPHOCYTIC LEUKAEMIA IN ADVANCED STAGES RAI III/IV. ABNORMALITIES OF P53 HAVE BEEN ASSOCIATED WITH SHORT SURVIVAL AND NON-RESPONSE TO THERAPY IN CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL). WE HAVE EVALUATED THE RATE OF RESPONSE TO FLUDARABINE AS FIRST-LINE THERAPY IN 54 PATIENTS WITH ADVANCED STAGE CLL, ANALYSING THE CYTOGENETIC PROFILE, ABERRATIONS IN P53, INCLUDING THE METHYLATION STATUS OF ITS PROMOTER, AND THE IMMUNOGLOBULIN HEAVY-CHAIN VARIABLE-REGION (IGVH) MUTATION STATUS. ACCORDING TO THE ADVANCED STAGE OF THE DISEASE IN THIS SERIES, 75% OF PATIENTS PRESENTED GENETIC ABERRATIONS ASSOCIATED WITH POOR PROGNOSIS: DEL(17P) AND/OR DEL(11Q), AND NO-MUTATED IGVH GENES. TEN PATIENTS (18.5%) HAD METHYLATION IN THE PROMOTER REGION OF P53. EIGHTY-THREE PER CENT OF PATIENTS TREATED ACHIEVED A RESPONSE, WITH A HIGH RATE OF COMPLETE REMISSION (47.6%). ALTHOUGH WE FOUND A SIGNIFICANT CORRELATION BETWEEN FAILURES AND THE PRESENCE OF P53 ABERRATIONS (P = 0.0065), EITHER WITH METHYLATION (P = 0.018) OR DELETION (P = 0.015), 64% OF THE PATIENTS WITH ABERRATIONS IN THIS GENE RESPONDED TO TREATMENT (11/17), SUGGESTING THAT FLUDARABINE INDUCES HIGH REMISSION RATES, EVEN IN THESE PATIENTS. THIS IS THE FIRST TIME THAT THE SIGNIFICANCE OF P53 PROMOTER METHYLATION STATUS IS DESCRIBED IN THIS PATHOLOGY, AND OUR DATA SUPPORT THAT THIS EPIGENETIC PHENOMENON COULD BE INVOLVED IN THE PATHOGENESIS AND CLINICAL EVOLUTION OF CLL.	2005	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
13 3062  45 GENOME-WIDE DNA METHYLATION ANALYSIS REVEALS NOVEL EPIGENETIC CHANGES IN CHRONIC LYMPHOCYTIC LEUKEMIA. WE CONDUCTED A GENOME-WIDE DNA METHYLATION ANALYSIS IN CD19 (+) B-CELLS FROM CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) PATIENTS AND NORMAL CONTROL SAMPLES USING REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS). THE METHYLATION STATUS OF 1.8-2.3 MILLION CPGS IN THE CLL GENOME WAS DETERMINED; ABOUT 45% OF THESE CPGS WERE LOCATED IN MORE THAN 23,000 CPG ISLANDS (CGIS). WHILE GLOBAL CPG METHYLATION WAS SIMILAR BETWEEN CLL AND NORMAL B-CELLS, 1764 GENE PROMOTERS WERE IDENTIFIED AS BEING DIFFERENTIALLY METHYLATED IN AT LEAST ONE CLL SAMPLE WHEN COMPARED WITH NORMAL B-CELL SAMPLES. NINETEEN PERCENT OF THE DIFFERENTIALLY METHYLATED GENES WERE INVOLVED IN TRANSCRIPTIONAL REGULATION. ABERRANT HYPERMETHYLATION WAS FOUND IN ALL HOX GENE CLUSTERS AND A SIGNIFICANT NUMBER OF WNT SIGNALING PATHWAY GENES. HYPOMETHYLATION OCCURRED MORE FREQUENTLY IN THE GENE BODY INCLUDING INTRONS, EXONS, AND 3'-UTRS IN CLL. THE NFATC1 P2 PROMOTER AND FIRST INTRON WAS FOUND TO BE HYPOMETHYLATED AND CORRELATED WITH UPREGULATION OF BOTH NFATC1 RNA AND PROTEIN EXPRESSION LEVELS IN CLL SUGGESTING THAT AN EPIGENETIC MECHANISM IS INVOLVED IN THE CONSTITUTIVE ACTIVATION OF NFAT ACTIVITY IN CLL CELLS. THIS COMPREHENSIVE DNA METHYLATION ANALYSIS WILL FURTHER OUR UNDERSTANDING OF THE EPIGENETIC CONTRIBUTION TO CELLULAR DYSFUNCTION IN CLL.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
14 4694  35 NEXT-GENERATION SEQUENCING IDENTIFIES MAJOR DNA METHYLATION CHANGES DURING PROGRESSION OF PH+ CHRONIC MYELOID LEUKEMIA. LITTLE IS KNOWN ABOUT THE IMPACT OF DNA METHYLATION ON THE EVOLUTION/PROGRESSION OF PH+ CHRONIC MYELOID LEUKEMIA (CML). WE INVESTIGATED THE METHYLOME OF CML PATIENTS IN CHRONIC PHASE (CP-CML), ACCELERATED PHASE (AP-CML) AND BLAST CRISIS (BC-CML) AS WELL AS IN CONTROLS BY REDUCED REPRESENTATION BISULFITE SEQUENCING. ALTHOUGH ONLY ~600 DIFFERENTIALLY METHYLATED CPG SITES WERE IDENTIFIED IN SAMPLES OBTAINED FROM CP-CML PATIENTS COMPARED WITH CONTROLS, ~6500 DIFFERENTIALLY METHYLATED CPG SITES WERE FOUND IN SAMPLES FROM BC-CML PATIENTS. IN THE MAJORITY OF AFFECTED CPG SITES, METHYLATION WAS INCREASED. IN CP-CML PATIENTS WHO PROGRESSED TO AP-CML/BC-CML, WE IDENTIFIED UP TO 897 GENES THAT WERE METHYLATED AT THE TIME OF PROGRESSION BUT NOT AT THE TIME OF DIAGNOSIS. USING RNA-SEQUENCING, WE OBSERVED DOWNREGULATED EXPRESSION OF MANY OF THESE GENES IN BC-CML COMPARED WITH CP-CML SAMPLES. SEVERAL OF THEM ARE WELL-KNOWN TUMOR-SUPPRESSOR GENES OR REGULATORS OF CELL PROLIFERATION, AND GENE RE-EXPRESSION WAS OBSERVED BY THE USE OF EPIGENETIC ACTIVE DRUGS. TOGETHER, OUR RESULTS DEMONSTRATE THAT CPG SITE METHYLATION CLEARLY INCREASES DURING CML PROGRESSION AND THAT IT MAY PROVIDE A USEFUL BASIS FOR REVEALING NEW TARGETS OF THERAPY IN ADVANCED CML.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
15 1424  31 DIFFERENTIAL DNA METHYLATION OF GENE PROMOTERS IN SMALL B-CELL LYMPHOMAS. IMPROVED CARE OF PATIENTS WITH SMALL B-CELL LYMPHOMAS (SBCLS) IS LIKELY TO RESULT FROM THE ONGOING DISCOVERY OF MOLECULAR MARKERS THAT BETTER DEFINE THESE MALIGNANT NEOPLASMS. WE IDENTIFIED MULTIPLE GENE LOCI WHOSE DNA METHYLATION PATTERNS DIFFERED BETWEEN 3 TYPES OF SBCL: B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA/SMALL LYMPHOCYTIC LYMPHOMA, MANTLE CELL LYMPHOMA, AND GRADES I AND II FOLLICULAR LYMPHOMA. THIS ANALYSIS WAS PERFORMED USING AN OLIGONUCLEOTIDE MICROARRAY THAT ALLOWED DETERMINATION OF THE DNA METHYLATION STATUS OF 156 LOCI IN 38 GENES. COMBINED BISULFITE RESTRICTION ANALYSIS AND METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION WERE USED TO VALIDATE THE DIFFERENTIAL METHYLATION OF 6 OF THESE GENES. BY USING NON-HODGKIN LYMPHOMA CELL LINES AS MODELS, THESE GENES WERE EXAMINED FURTHER FOR METHYLATION AND GENE EXPRESSION RELATIONSHIPS. THIS STUDY ILLUSTRATES NONRANDOM EPIGENETIC ALTERATIONS IN SBCLS THAT SEEM TO PREFERENTIALLY INVOLVE LYMPHOMAS OF GERMINAL CENTER DERIVATION.	2005	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
16 4242  34 METHYLATION STATUS OF ALU AND LINE-1 INTERSPERSED REPETITIVE SEQUENCES IN BEHCET'S DISEASE PATIENTS. BEHCET'S DISEASE (BD) IS A MULTISYSTEM CHRONIC INFLAMMATORY DISEASE. THE PATHOLOGY IS BELIEVED TO INVOLVE BOTH GENETIC SUSCEPTIBILITY AND ENVIRONMENTAL FACTORS. HYPOMETHYLATION LEADING TO ACTIVATION OF INTERSPERSED REPETITIVE SEQUENCES (IRSS) SUCH AS LINE-1 AND ALU CONTRIBUTES TO THE PATHOLOGIES OF AUTOIMMUNE DISEASES AND CANCER. HEREIN, THE EPIGENETIC CHANGES OF IRSS IN BD WERE EVALUATED USING COMBINED BISULFITE RESTRICTION ANALYSIS-INTERSPERSED REPETITIVE SEQUENCES (COBRA-IRS). DNA FROM NEUTROPHILS AND PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) OF BD PATIENTS WITH OCULAR INVOLVEMENT THAT WERE IN ACTIVE OR INACTIVE STATES AND HEALTHY CONTROLS WERE USED TO ANALYZE LINE-1 AND ALU METHYLATION LEVELS. FOR ALU SEQUENCES, SIGNIFICANT DIFFERENCES WERE OBSERVED IN THE FREQUENCY OF (U)C(U)C ALLELES BETWEEN PBMCS OF PATIENTS AND CONTROLS (P = 0.03), AND BETWEEN INACTIVE PATIENTS AND CONTROLS (P = 0.03). FOR NEUTROPHILS, THE FREQUENCY OF (U)C(U)C WAS SIGNIFICANTLY HIGHER BETWEEN PATIENTS AND CONTROLS (P = 0.006) AND BETWEEN INACTIVE PATIENTS AND CONTROLS (P = 0.002). THE PARTIAL METHYLATION ((U)C(M)C + (M)C(U)C) FREQUENCIES OF ALU BETWEEN INACTIVE PATIENTS AND CONTROL SAMPLES ALSO DIFFERED (P = 0.02). NO STATISTICALLY SIGNIFICANT DIFFERENCES FOR LINE-1 WERE DETECTED. THUS, CHANGES IN THE METHYLATION LEVEL OF IRS ELEMENTS MIGHT CONTRIBUTE TO THE PATHOGENESIS OF BD. THE ROLE OF ALU TRANSCRIPTS IN BD SHOULD BE INVESTIGATED FURTHER.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
17 5275  38 PROMOTER METHYLATION OF THE BONE MORPHOGENETIC PROTEIN-6 GENE IN ASSOCIATION WITH ADULT T-CELL LEUKEMIA. BONE MORPHOGENETIC PROTEINS (BMP), BELONGING TO THE TRANSFORMING GROWTH FACTOR-BETA SUPERFAMILY, ARE MULTIFUNCTIONAL REGULATORS OF CELL PROLIFERATION, DIFFERENTIATION AND APOPTOSIS IN VARIOUS TYPES OF MALIGNANT CELLS. IN THIS STUDY, WE INVESTIGATED BMP-6 PROMOTER METHYLATION IN PATIENTS WITH VARIOUS TYPES OF LEUKEMIAS. THE BMP-6 METHYLATION WAS FOUND PREFERENTIALLY IN ADULT T-CELL LEUKEMIA (ATL) (49 OF 60, 82%) COMPARED WITH OTHER TYPES OF LEUKEMIAS STUDIED INCLUDING ACUTE MYELOID LEUKEMIA (3 OF 67, 5%), ACUTE LYMPHOBLASTIC LEUKEMIA (6 OF 38, 16%) AND CHRONIC LYMPHOCYTIC LEUKEMIA (1 OF 21, 5%). AMONG SUBTYPES OF ATL, THE BMP-6 GENE WAS MORE FREQUENTLY METHYLATED IN AGGRESSIVE ATL FORMS OF ACUTE (96%) AND LYMPHOMA (94%) TYPES THAN LESS MALIGNANT CHRONIC ATL (44%) AND SMOLDERING ATL (20%). WE ALSO ANALYZED THE METHYLATION STATUS OF PERIPHERAL BLOOD MONONUCLEAR CELLS FROM HEALTHY DONORS AND NONMALIGNANT LYMPH NODES WITH REACTIVE LYMPHADENOPATHY, NONE OF WHICH SHOWED DETECTABLE BMP-6 METHYLATION IN THIS STUDY. THE BMP-6 METHYALTION WAS CORRELATED WITH DECREASED MRNA TRANSCRIPT AND PROTEIN EXPRESSION. EXPRESSION OF BMP-6 WAS RESTORED BY THE DEMETHYLATING AGENT 5-AZA-2'-DEOXYCYTIDINE, SUGGESTING THAT METHYLATION WAS ASSOCIATED WITH THE TRANSCRIPTIONAL SILENCING. SERIAL ANALYSIS DEMONSTRATED AN INCREASING METHYLATION OF CPG SITES IN THE BMP-6 PROMOTER AND THE RESULTANT SUPPRESSION OF BMP-6 EXPRESSION AS ATL PROGRESSED. THESE FINDINGS SUGGESTED THAT BMP-6 PROMOTER METHYLATION IS LIKELY TO BE A COMMON EPIGENETIC EVENT AT LATER STAGES OF ATL AND THAT THE METHYLATION PROFILES MAY BE USEFUL FOR THE STAGING OF ATL AS WELL AS FOR EVALUATION OF THE INDIVIDUAL RISK OF DEVELOPING THE DISEASE.	2008	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
18 2048  36 EPIGENETIC CLUSTERING OF LUNG ADENOCARCINOMAS BASED ON DNA METHYLATION PROFILES IN ADJACENT LUNG TISSUE: ITS CORRELATION WITH SMOKING HISTORY AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE. THE AIM OF THIS STUDY WAS TO CLARIFY THE SIGNIFICANCE OF DNA METHYLATION ALTERATIONS DURING LUNG CARCINOGENESIS. INFINIUM ASSAY WAS PERFORMED USING 139 PAIRED SAMPLES OF NON-CANCEROUS LUNG TISSUE (N) AND TUMOROUS TISSUE (T) FROM A LEARNING COHORT OF PATIENTS WITH LUNG ADENOCARCINOMAS (LADCS). FIFTY PAIRED N AND T SAMPLES FROM A VALIDATION COHORT WERE ALSO ANALYZED. DNA METHYLATION ALTERATIONS ON 1,928 PROBES OCCURRED IN N SAMPLES RELATIVE TO NORMAL LUNG TISSUE FROM PATIENTS WITHOUT PRIMARY LUNG TUMORS, AND WERE INHERITED BY, OR STRENGTHENED IN, T SAMPLES. UNSUPERVISED HIERARCHICAL CLUSTERING USING DNA METHYLATION LEVELS IN N SAMPLES ON ALL 26,447 PROBES SUBCLUSTERED PATIENTS INTO CLUSTER I (N = 32), CLUSTER II (N = 35) AND CLUSTER III (N = 72). LADCS IN CLUSTER I DEVELOPED FROM THE INFLAMMATORY BACKGROUND IN CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IN HEAVY SMOKERS AND WERE LOCALLY INVASIVE. MOST PATIENTS IN CLUSTER II WERE NON-SMOKERS AND HAD A FAVORABLE OUTCOME. LADCS IN CLUSTER III DEVELOPED IN LIGHT SMOKERS WERE MOST AGGRESSIVE (FREQUENTLY SHOWING LYMPHATIC AND BLOOD VESSEL INVASION, LYMPH NODE METASTASIS AND AN ADVANCED PATHOLOGICAL STAGE), AND HAD A POOR OUTCOME. DNA METHYLATION LEVELS OF HALLMARK GENES FOR EACH CLUSTER, SUCH AS IRX2, HOXD8, SPARCL1, RGS5 AND EI24, WERE AGAIN CORRELATED WITH CLINICOPATHOLOGICAL CHARACTERISTICS IN THE VALIDATION COHORT. DNA METHYLATION PROFILES REFLECTING CARCINOGENETIC FACTORS SUCH AS SMOKING AND COPD APPEAR TO BE ESTABLISHED IN NON-CANCEROUS LUNG TISSUE FROM PATIENTS WITH LADCS AND MAY DETERMINE THE AGGRESSIVENESS OF TUMORS DEVELOPING IN INDIVIDUAL PATIENTS, AND THUS PATIENT OUTCOME.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                        
19 1433  40 DIFFERENTIAL GENOME-WIDE ARRAY-BASED METHYLATION PROFILES IN PROGNOSTIC SUBSETS OF CHRONIC LYMPHOCYTIC LEUKEMIA. GLOBAL HYPOMETHYLATION AND REGIONAL HYPERMETHYLATION ARE WELL-KNOWN EPIGENETIC FEATURES OF CANCER; HOWEVER, IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), STUDIES ON GENOME-WIDE EPIGENETIC MODIFICATIONS ARE LIMITED. HERE, WE ANALYZED THE GLOBAL METHYLATION PROFILES IN CLL, BY APPLYING HIGH-RESOLUTION METHYLATION MICROARRAYS (27,578 CPG SITES) TO 23 CLL SAMPLES, BELONGING TO THE IMMUNOGLOBULIN HEAVY-CHAIN VARIABLE (IGHV) MUTATED (FAVORABLE) AND IGHV UNMUTATED/IGHV3-21 (POOR-PROGNOSTIC) SUBSETS. OVERALL, RESULTS DEMONSTRATED SIGNIFICANT DIFFERENCES IN METHYLATION PATTERNS BETWEEN THESE SUBGROUPS. SPECIFICALLY, IN IGHV UNMUTATED CLL, WE IDENTIFIED METHYLATION OF 7 KNOWN OR CANDIDATE TUMOR SUPPRESSOR GENES (EG, VHL, ABI3, AND IGSF4) AS WELL AS 8 UNMETHYLATED GENES INVOLVED IN CELL PROLIFERATION AND TUMOR PROGRESSION (EG, ADORA3 AND PRF1 ENHANCING THE NUCLEAR FACTOR-KAPPAB AND MITOGEN-ACTIVATED PROTEIN KINASE PATHWAYS, RESPECTIVELY). IN CONTRAST, THESE LATTER GENES WERE SILENCED BY METHYLATION IN IGHV MUTATED PATIENTS. THE ARRAY DATA WERE VALIDATED FOR SELECTED GENES USING METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION, QUANTITATIVE REVERSE TRANSCRIPTASE-POLYMERASE CHAIN REACTION, AND BISULFITE SEQUENCING. FINALLY, THE SIGNIFICANCE OF DNA METHYLATION IN REGULATING GENE PROMOTERS WAS SHOWN BY REINDUCING 4 METHYLATED TUMOR SUPPRESSOR GENES (EG, VHL AND ABI3) IN IGHV UNMUTATED SAMPLES USING THE METHYL-INHIBITOR 5-AZA-2'-DEOXYCYTIDINE. TAKEN TOGETHER, OUR DATA FOR THE FIRST TIME REVEAL DIFFERENCES IN GLOBAL METHYLATION PROFILES BETWEEN PROGNOSTIC SUBSETS OF CLL, WHICH MAY UNFOLD EPIGENETIC SILENCING MECHANISMS INVOLVED IN CLL PATHOGENESIS.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
20 2327  42 EPIGENETIC REGULATION OF HUMAN CANCER/TESTIS ANTIGEN GENE, HAGE, IN CHRONIC MYELOID LEUKEMIA. BACKGROUND AND OBJECTIVES: CANCER TESTIS ANTIGENS (CTA) PROVIDE ATTRACTIVE TARGETS FOR CANCER-SPECIFIC IMMUNOTHERAPY. ALTHOUGH CTA GENES ARE EXPRESSED IN SOME NORMAL TISSUES, SUCH AS THE TESTIS, THIS IMMUNOLOGICALLY PROTECTED SITE LACKS MHC I EXPRESSION AND AS SUCH, DOES NOT PRESENT SELF ANTIGENS TO T CELLS. TO DATE, CTA GENES HAVE BEEN SHOWN TO BE EXPRESSED IN A RANGE OF SOLID TUMORS VIA DEMETHYLATION OF THEIR PROMOTER CPG ISLANDS, BUT RARELY IN CHRONIC MYELOID LEUKEMIA (CML) OR OTHER HEMATOLOGIC MALIGNANCIES. DESIGN AND METHODS: IN THIS STUDY, THE METHYLATION STATUS OF THE HAGE CTA GENE PROMOTER WAS ANALYZED BY QUANTITATIVE METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (MSP) AND SEQUENCING IN FOUR PHILADELPHIA-POSITIVE CELL LINES (TCC-S, K562, KU812 AND KYO-1) AND IN CML SAMPLES TAKEN FROM PATIENTS IN CHRONIC PHASE (CP N=215) OR BLAST CRISIS (BC N=47). HAGE EXPRESSION WAS ASSESSED BY QUANTITATIVE REVERSE TRANSCRIPTASE-POLYMERASE CHAIN REACTION. RESULTS: THE TCC-S CELL LINE SHOWED DEMETHYLATION OF HAGE THAT WAS ASSOCIATED WITH OVER-EXPRESSION OF THIS GENE. HAGE HYPOMETHYLATION WAS SIGNIFICANTLY MORE FREQUENT IN BC (46%) THAN IN CP (22%) (P=0.01) AND WAS CORRELATED WITH HIGH EXPRESSION LEVELS OF HAGE TRANSCRIPTS (P<0.0001). OF NOTE, IN CP-CML, EXTENSIVE HAGE HYPOMETHYLATION WAS ASSOCIATED WITH POORER PROGNOSIS IN TERMS OF CYTOGENETIC RESPONSE TO INTERFERON (P=0.01) OR IMATINIB (P=0.01), MOLECULAR RESPONSE TO IMATINIB (P=0.003) AND PROGRESSION-FREE SURVIVAL (P=0.05). INTERPRETATIONS AND CONCLUSION: THE METHYLATION STATUS OF THE HAGE PROMOTER DIRECTLY CORRELATES WITH ITS EXPRESSION IN BOTH CML CELL LINES AND PATIENTS AND IS ASSOCIATED WITH ADVANCED DISEASE AND POOR OUTCOME.	2007