1 2845 140 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
2 5730  40 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	
                                                       
3 3444  43 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
4 1211  43 CPG ISLAND METHYLATION AND EXPRESSION OF THE SECRETED FRIZZLED-RELATED PROTEIN GENE FAMILY IN CHRONIC LYMPHOCYTIC LEUKEMIA. B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS CHARACTERIZED BY A CLONAL ACCUMULATION OF MATURE NEOPLASTIC B CELLS INDICATING DISRUPTION OF APOPTOSIS. RESTRICTION LANDMARK GENOME SCANNING WAS DONE TO IDENTIFY NOVEL TARGET GENES SILENCED BY CPG ISLAND METHYLATION IN CLL. SECRETED FRIZZLED-RELATED PROTEIN 4 (SFRP4), A NEGATIVE REGULATOR OF THE WNT SIGNALING PATHWAY, WAS FOUND TO BE FREQUENTLY METHYLATED IN CLL SAMPLES. WNT SIGNALING HAS BEEN SHOWN TO CONTROL NORMAL APOPTOTIC BEHAVIOR AND IS REQUIRED FOR NORMAL B-CELL DEVELOPMENT WHEREAS ABERRANT ACTIVATION OF THIS PATHWAY HAS BEEN OBSERVED IN CLL. WE SHOW ABERRANT DNA METHYLATION AND SILENCING OF SFRP4, AS WELL AS OF ADDITIONAL SFRP FAMILY MEMBERS, IN PRIMARY CLL SAMPLES. INDUCTION OF THEIR EXPRESSION IN A DOSE-DEPENDENT MANNER FOLLOWING TREATMENT WITH A DEMETHYLATING AGENT, 5-AZA-2'-DEOXYCYTIDINE, WAS SHOWN. OF THE FIVE SFRP FAMILY MEMBERS STUDIED IN DETAIL, SFRP1 WAS HYPERMETHYLATED AND DOWN-REGULATED IN ALL CLL PATIENT SAMPLES STUDIED, SUGGESTING THAT THIS EPIGENETIC EVENT IS A CRITICAL STEP DURING LEUKEMOGENESIS. OUR RESULTS SUGGEST THAT SILENCING OF SFRPS BY CPG ISLAND METHYLATION IS ONE POSSIBLE MECHANISM CONTRIBUTING TO ABERRANT ACTIVATION OF WNT SIGNALING PATHWAY IN CLL.	2006	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
5   59  47 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   18  35 5-AZACYTIDINE MODULATES CPG METHYLATION LEVELS OF EZH2 AND NOTCH1 IN MYELODYSPLASTIC SYNDROMES. PURPOSE: MOLECULAR MECHANISMS OF RESPONSE TO HYPOMETHYLATING AGENTS IN PATIENTS WITH MYELODYSPLASTIC SYNDROMES (MDS) AND CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML) STILL REMAIN LARGELY UNKNOWN. THEREFORE, THE EFFECTS OF 5-AZACYTIDINE (AZA) ON CLONAL ARCHITECTURE AND DNA METHYLATION WERE INVESTIGATED IN THIS STUDY. METHODS: USING NEXT-GENERATION SEQUENCING (NGS), 30 MYELOID LEUKEMIA-ASSOCIATED GENES WERE ANALYZED IN 15 MDS/CMML PATIENTS WITH EXCELLENT RESPONSE TO AZA. EFFECTS ON METHYLATION LEVELS WERE ANALYZED BY QUANTITATIVE METHYLATION ANALYSIS USING PYROSEQUENCING FOR THE GLOBAL METHYLATION MARKER LINE-1 IN PATIENTS AND MYELOID CELL LINES. VARIOUS MYELOID CELL LINES AND A HEALTHY COHORT WERE SCREENED FOR METHYLATION LEVELS IN 23 GENES. SELECTED TARGETS WERE VERIFIED ON THE MDS/CMML COHORT. RESULTS: THE STUDY PRESENTED HERE SHOWED A STABLE VARIANT ALLELE FREQUENCY AND STABLE GLOBAL METHYLATION LEVELS IN RESPONDING PATIENTS. A SIGNIFICANT DEMETHYLATION OF EZH2 AND NOTCH1 WAS REVEALED IN PATIENTS WITH AZA RESPONSE. CONCLUSIONS: A RESPONSE TO AZA IS NOT ASSOCIATED WITH ERADICATION OF MALIGNANT CLONES, BUT RATHER WITH A STABILIZATION OF THE CLONAL ARCHITECTURE. WE SUGGEST CHANGES IN CPG METHYLATION LEVELS OF EZH2 AND NOTCH1 AS POTENTIAL TARGETS OF EPIGENETIC RESPONSE TO AZA TREATMENT WHICH MAY ALSO SERVE AS USEFUL BIOMARKERS AFTER CLINICAL EVALUATION.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
7 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
8 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
9 2090  36 EPIGENETIC DYSREGULATION OF THE WNT SIGNALLING PATHWAY IN CHRONIC LYMPHOCYTIC LEUKAEMIA. BACKGROUND: WNT SIGNALLING HAS RECENTLY BEEN IMPLICATED IN THE PATHOGENESIS OF CANCER. METHODS: THIS STUDY INVESTIGATED THE ACTIVITY OF WNT SIGNALLING IN PERIPHERAL BLOOD CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) LYMPHOCYTES, AND THE METHYLATION STATUS OF SEVEN SOLUBLE WNT ANTAGONIST GENES, INCLUDING WIF1, DKK3, APC, SFRP1, SFRP2, SFRP4 AND SFRP5, BY USING METHYLATION-SPECIFIC PCR IN THE PERIPHERAL BLOOD CLL LYMPHOCYTES AND BONE MARROW SAMPLES OF PATIENTS WITH CLL AT DIAGNOSIS. RESULTS: IN THE PERIPHERAL BLOOD CLL LYMPHOCYTES, CONSTITUTIVE ACTIVATION OF WNT SIGNALLING WAS DETECTED, ASSOCIATED WITH HYPERMETHYLATION OF THE SOLUBLE WNT INHIBITOR GENES. IN THE DIAGNOSTIC CLL MARROW SAMPLES, METHYLATION OF THE SEVEN GENES WAS DETECTED IN UP TO 36.4% OF SAMPLES. MOREOVER, 23 (52.3%) PATIENTS HAD METHYLATION OF AT LEAST ONE OF THE SEVEN GENES, OF WHOM 14 (60.8%) HAD METHYLATION OF TWO OR MORE WNT INHIBITOR GENES. APART FROM AN ASSOCIATION OF ADVANCED AGE WITH DKK3 METHYLATION, THERE WAS NO ASSOCIATION OF GENE HYPERMETHYLATION WITH EITHER CLINICAL CHARACTERISTICS (INCLUDING AGE, GENDER, LYMPHOCYTE COUNT AT DIAGNOSIS, RAI STAGE AND POOR-RISK KARYOTYPE) OR SURVIVAL. CONCLUSION: WNT SIGNALLING IS CONSTITUTIVELY ACTIVATED IN CLL B LYMPHOCYTES IN ASSOCIATION WITH METHYLATION OF MULTIPLE SOLUBLE WNT ANTAGONIST GENES. METHYLATION OF THESE SOLUBLE WNT ANTAGONIST GENES, OCCASIONALLY MULTIPLE GENES, IN PRIMARY CLL MARROW SAMPLES SUGGESTS AN IMPORTANT ROLE IN CLL PATHOGENESIS. MOREOVER, THIS STUDY UNDERSCORED THE IMPORTANCE OF STUDYING METHYLATION OF A PANEL OF, BUT NOT INDIVIDUAL, GENES REGULATING A CELLULAR PATHWAY.	2008	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
10 2771  38 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
11 3588  37 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	
                                                                                                                                                                                                                                                                                                                                                         
12 1968  34 EPIGENETIC ALTERATION OF THE SOCS1 GENE IN CHRONIC MYELOID LEUKAEMIA. THE EXPRESSION OF THE SUPPRESSOR OF CYTOKINE SIGNALLING-1 (SOCS1) PROTEIN IS INDUCED IN RESPONSE TO STIMULATION BY SEVERAL CYTOKINES. THE INDUCED SOCS1 INHIBITS THE SIGNALLING PATHWAY THROUGH THE ASSOCIATION WITH A VARIETY OF TYROSINE KINASE PROTEINS. IN THIS STUDY, THE MUTATION ANALYSES, CPG ISLAND METHYLATION STATUS, AND THE EXPRESSION OF THE SOCS1 GENE IN 112 CHRONIC MYELOID LEUKAEMIA (CML) SAMPLES, FIVE LEUKAEMIA CELL LINES, AND 30 NORMAL CONTROLS WERE ANALYSED. NO GENETIC MUTATIONS OF SOCS1 GENE WERE NOTED IN THE CML SAMPLES. THE SOCS1 GENE WAS HYPERMETHYLATED IN 67% AND 46% OF THE BLASTIC AND CHRONIC PHASE CML SAMPLES RESPECTIVELY (P < 0.0001). HOWEVER, THERE WAS NO METHYLATION OF THE SOCS1 GENE IN NORMAL CONTROLS OR CML IN MOLECULAR REMISSION. THE METHYLATION STATUS OF THE SOCS1 GENE IS CONSISTENT WITH THE RESULTS OF THE REAL-TIME QUANTITATIVE REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION AND IMMUNOCYTOCHEMISTRY STAINING. OUR RESULTS DEMONSTRATE THAT THE SOCS1 GENE SILENCING IS CAUSED BY THE METHYLATION OF CPG ISLANDS IN CML AND IS REVERSED TO AN UNMETHYLATED STATUS IN MOLECULAR REMISSION. AS SOCS1 HAS UNIVERSAL ACTIVITY TO NEGATIVELY REGULATE SEVERAL CYTOKINE SIGNALLING PATHWAYS, THE LOSS OF THE NEGATIVE REGULATION OF CYTOKINE SIGNALLING BY THE SOCS1 MAY PLAY A ROLE IN THE PATHOGENESIS OF CML PROGRESSION.	2003	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
13 4243  36 METHYLATION STATUS OF CEBPA GENE PROMOTER IN CHRONIC MYELOID LEUKEMIA. CCAAT/ENHANCER BINDING PROTEIN ALPHA IS ONE OF THE CRUCIAL TRANSCRIPTION FACTORS FOR MYELOID CELL DEVELOPMENT THAT HAS BEEN FOUND TO BE INVOLVED IN HEMATOPOIETIC DIFFERENTIATION AND LEUKEMIOGENESIS. RECENTLY, EPIGENETIC REGULATION OF CEBPA EXPRESSION THROUGH DNA METHYLATION HAS BEEN DEMONSTRATED IN LEUKEMIA. THE AIM OF THIS STUDY WAS TO INVESTIGATE THE METHYLATION STATUS OF CEBPA GENE IN CHRONIC MYELOID LEUKEMIA (CML) PATIENTS. THE METHYLATION STATUS OF CEBPA PROMOTER WAS STUDIED IN 100 PATIENTS WITH CML AND 98 NORMAL HEALTHY INDIVIDUALS FROM HYDERABAD, INDIA, USING METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION. THE ABERRANT METHYLATION OF CEBPA GENE PROMOTER WAS FOUND IN 32 OF THE 100 CML CASES. A HIGHLY SIGNIFICANT ASSOCIATION WAS FOUND BETWEEN THE FREQUENCY OF CEBPA GENE PROMOTER HYPERMETHYLATION AND THE CML STAGES (P = 0.017), BUT ASSOCIATION WITH RESPECT TO AGE AND GENDER OF THE PATIENT WAS NOT FOUND. THE RESULTS SUGGEST THAT ABERRANT METHYLATION IN THE CPG ISLAND OF THE PROMOTER REGION OF THIS GENE MIGHT BE A COMMON EVENT IN CML, AND SYSTEMIC EXPRESSION STUDIES WILL BE NEEDED TO UNFOLD THE ROLE OF CEBPA PROMOTER METHYLATION IN THE DEVELOPMENT, PROGRESSION, AND PROGNOSIS OF CML.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
14  149  39 ABERRANT HYDROXYMETHYLATION IN PROMOTER CPG REGIONS OF GENES RELATED TO THE CELL CYCLE AND APOPTOSIS CHARACTERIZES ADVANCED CHRONIC MYELOID LEUKEMIA DISEASE, POOR IMATINIB RESPONDENTS AND POOR SURVIVAL. BACKGROUND: THERE IS STRONG EVIDENCE THAT DISEASE PROGRESSION, DRUG RESPONSE AND OVERALL CLINICAL OUTCOMES OF CML DISEASE ARE NOT ONLY DECIDED BY BCR/ABL1 ONCOPROTEIN BUT DEPEND ON ACCUMULATION OF ADDITIONAL GENETIC AND EPIGENETIC ABERRATIONS. DNA HYDROXYMETHYLATION IS IMPLICATED IN THE DEVELOPMENT OF VARIETY OF DISEASES. DNA HYDROXYMETHYLATION IN GENE PROMOTERS PLAYS IMPORTANT ROLES IN DISEASE PROGRESSION, DRUG RESPONSE AND CLINICAL OUTCOME OF VARIOUS DISEASES. THEREFORE IN THIS STUDY, WE AIMED TO EXPLORE THE ROLE OF ABERRANT HYDROXYMETHYLATION IN PROMOTER REGIONS OF DIFFERENT TUMOR SUPPRESSOR GENES IN RELATION TO CML DISEASE PROGRESSION, RESPONSE TO IMATINIB THERAPY AND CLINICAL OUTCOME. METHODS: WE RECRUITED 150 CML PATIENTS AT DIFFERENT CLINICAL STAGES OF THE DISEASE. PATIENTS WERE FOLLOWED UP FOR 48 MONTHS AND HAEMATOLOGICAL/MOLECULAR RESPONSES WERE ANALYSED. HAEMATOLOGICAL RESPONSE WAS ANALYSED BY PERIPHERAL BLOOD SMEAR. BCR/ABL1 SPECIFIC TAQMAN PROBE BASED QRT-PCR WAS USED FOR ASSESSING THE MOLECULAR RESPONSE OF CML PATIENTS ON IMATINIB THERAPY. PROMOTER HYDROXYMETHYLATION OF THE GENES WAS CHARACTERIZED USING MS-PCR. RESULTS: WE OBSERVED THAT PROMOTER HYDROXYMETHYLATION OF DAPK1, RIZ1, P16INK4A, RASSF1A AND P14ARF(ARF) GENES CHARACTERIZE ADVANCED CML DISEASE AND POOR IMATINIB RESPONDENTS. ALTHOUGH, CYTOKINE SIGNALLING (SOCS1) GENE WAS HYPERMETHYLATED IN ADVANCED STAGES OF CML AND ACCUMULATED IN PATIENTS WITH POOR IMATINIB RESPONSE, BUT THE DIFFERENCES WERE NOT STATISTICALLY SIGNIFICANT. MOREOVER, WE FOUND HYPERMETHYLATION OF P14(ARF), RASSF1 AND P16(INK4A) GENES AND CYTOKINE SIGNALLING GENE (SOCS1) SIGNIFICANTLY ASSOCIATED WITH POOR OVERALL SURVIVAL OF CML PATIENTS ON IMATINIB THERAPY. THE RESULTS OF THIS STUDY ARE IN AGREEMENT OF THE ROLE OF ABERRANT DNA METHYLATION OF DIFFERENT TUMOR SUPPRESSOR GENES AS POTENTIAL BIOMARKERS OF CML DISEASE PROGRESSION, POOR IMATINIB RESPONSE AND OVERALL CLINICAL OUTCOME. CONCLUSION: IN THIS STUDY, WE REPORT THAT PROMOTER HYDROXYMETHYLATION OF DAPK1, RIZ1, P16INK4A, RASSF1A AND P14ARF(ARF) GENES IS A CHARACTERISTIC FEATURE OF CML DISEASE PROGRESSIONS, DEFINES POOR IMATINIB RESPONDENTS AND POOR OVERALL SURVIVAL OF CML PATIENTS TO IMATINIB THERAPY.	2022	

15 3896  39 LARGE-SCALE ANALYSIS OF DNA METHYLATION IN CHRONIC LYMPHOCYTIC LEUKEMIA. AIMS: B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS A HETEROGENEOUS MALIGNANCY THAT CLINICALLY RANGES FROM INDOLENT TO RAPIDLY PROGRESSIVE. CLL, LIKE OTHER CANCERS, CAN BE AFFECTED BY EPIGENETIC ALTERATIONS. MATERIALS & METHODS: A MICROARRAY DISCOVERY-BASED STUDY WAS INITIATED TO DETERMINE DNA METHYLATION IN CLL CASES WITH A RANGE OF CD38 EXPRESSION (1-92%). RESULTS: MANY LOCI WERE EITHER METHYLATED OR UNMETHYLATED ACROSS ALL CD38 LEVELS, BUT DIFFERENTIAL METHYLATION WAS ALSO OBSERVED FOR SOME GENES. GENOMIC SEQUENCING OF DLEU7 CONFIRMED EXTENSIVE CYTOSINE METHYLATION PREFERENTIALLY IN PATIENT SAMPLES WITH LOW CD38 EXPRESSION, WHEREAS NRP2, SFRP2 AND ADAM12 WERE MORE COMMONLY METHYLATED IN THOSE WITH HIGH CD38 EXPRESSION. CONCLUSION: THIS STUDY DEMONSTRATES THAT CLL IS AFFECTED BY CPG ISLAND METHYLATION IN SOME GENES THAT SEGREGATE WITH CD38 EXPRESSION LEVELS, WHILE MOST OTHERS SHOW SIMILAR METHYLATION PATTERNS ACROSS ALL LEVELS. THE CPG ISLAND METHYLATION IN CERTAIN FUNCTIONAL GENE GROUPS AND PATHWAY-ASSOCIATED GENES THAT ARE KNOWN TO BE DEREGULATED IN CLL PROVIDES ADDITIONAL INSIGHTS INTO THE CLL METHYLOME AND EPIGENETIC CONTRIBUTION TO CELLULAR DYSFUNCTION. IT WILL NOW BE USEFUL TO INVESTIGATE THE EFFECTIVENESS OF EPIGENETIC THERAPEUTIC REVERSAL OF THESE ALTERATIONS TO DEVELOP EFFECTIVE TREATMENTS FOR THE DISEASE.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
16 1662  32 DOWNREGULATION OF DEATH-ASSOCIATED PROTEIN KINASE 1 (DAPK1) IN CHRONIC LYMPHOCYTIC LEUKEMIA. THE HERITABILITY OF B CELL CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS RELATIVELY HIGH; HOWEVER, NO PREDISPOSING MUTATION HAS BEEN CONVINCINGLY IDENTIFIED. WE SHOW THAT LOSS OR REDUCED EXPRESSION OF DEATH-ASSOCIATED PROTEIN KINASE 1 (DAPK1) UNDERLIES CASES OF HERITABLE PREDISPOSITION TO CLL AND THE MAJORITY OF SPORADIC CLL. EPIGENETIC SILENCING OF DAPK1 BY PROMOTER METHYLATION OCCURS IN ALMOST ALL SPORADIC CLL CASES. FURTHERMORE, WE DEFINED A DISEASE HAPLOTYPE, WHICH SEGREGATES WITH THE CLL PHENOTYPE IN A LARGE FAMILY. DAPK1 EXPRESSION OF THE CLL ALLELE IS DOWNREGULATED BY 75% IN GERMLINE CELLS DUE TO INCREASED HOXB7 BINDING. IN THE BLOOD CELLS FROM AFFECTED FAMILY MEMBERS, PROMOTER METHYLATION RESULTS IN ADDITIONAL LOSS OF DAPK1 EXPRESSION. THUS, REDUCED EXPRESSION OF DAPK1 CAN RESULT FROM GERMLINE PREDISPOSITION, AS WELL AS EPIGENETIC OR SOMATIC EVENTS CAUSING OR CONTRIBUTING TO THE CLL PHENOTYPE.	2007	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
17 1424  37 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
18 2639  33 EPIGENOMIC ANALYSIS DETECTS WIDESPREAD GENE-BODY DNA HYPOMETHYLATION IN CHRONIC LYMPHOCYTIC LEUKEMIA. WE HAVE EXTENSIVELY CHARACTERIZED THE DNA METHYLOMES OF 139 PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) WITH MUTATED OR UNMUTATED IGHV AND OF SEVERAL MATURE B-CELL SUBPOPULATIONS THROUGH THE USE OF WHOLE-GENOME BISULFITE SEQUENCING AND HIGH-DENSITY MICROARRAYS. THE TWO MOLECULAR SUBTYPES OF CLL HAVE DIFFERING DNA METHYLOMES THAT SEEM TO REPRESENT EPIGENETIC IMPRINTS FROM DISTINCT NORMAL B-CELL SUBPOPULATIONS. DNA HYPOMETHYLATION IN THE GENE BODY, TARGETING MOSTLY ENHANCER SITES, WAS THE MOST FREQUENT DIFFERENCE BETWEEN NAIVE AND MEMORY B CELLS AND BETWEEN THE TWO MOLECULAR SUBTYPES OF CLL AND NORMAL B CELLS. ALTHOUGH DNA METHYLATION AND GENE EXPRESSION WERE POORLY CORRELATED, WE IDENTIFIED GENE-BODY CPG DINUCLEOTIDES WHOSE METHYLATION WAS POSITIVELY OR NEGATIVELY ASSOCIATED WITH EXPRESSION. WE HAVE ALSO RECOGNIZED A DNA METHYLATION SIGNATURE THAT DISTINGUISHES NEW CLINICO-BIOLOGICAL SUBTYPES OF CLL. WE PROPOSE AN EPIGENOMIC SCENARIO IN WHICH DIFFERENTIAL METHYLATION IN THE GENE BODY MAY HAVE FUNCTIONAL AND CLINICAL IMPLICATIONS IN LEUKEMOGENESIS.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
19 1473  39 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
20  139  34 ABERRANT DNA METHYLATION IS ASSOCIATED WITH DISEASE PROGRESSION, RESISTANCE TO IMATINIB AND SHORTENED SURVIVAL IN CHRONIC MYELOGENOUS LEUKEMIA. THE EPIGENETIC IMPACT OF DNA METHYLATION IN CHRONIC MYELOGENOUS LEUKEMIA (CML) IS NOT COMPLETELY UNDERSTOOD. TO ELUCIDATE ITS ROLE WE ANALYZED 120 PATIENTS WITH CML FOR METHYLATION OF PROMOTER-ASSOCIATED CPG ISLANDS OF 10 GENES. FIVE GENES WERE IDENTIFIED BY DNA METHYLATION SCREENING IN THE K562 CELL LINE AND 3 GENES IN PATIENTS WITH MYELOPROLIFERATIVE NEOPLASMS. THE CDKN2B GENE WAS SELECTED FOR ITS FREQUENT METHYLATION IN MYELOID MALIGNANCIES AND ABL1 AS THE TARGET OF BCR-ABL TRANSLOCATION. THIRTY PATIENTS WERE IMATINIB-NAIVE (MOSTLY TREATED BY INTERFERON-ALPHA BEFORE THE IMATINIB ERA), 30 WERE IMATINIB-RESPONSIVE, 50 WERE IMATINIB-RESISTANT, AND 10 WERE IMATINIB-INTOLERANT. WE QUANTIFIED DNA METHYLATION BY BISULFITE PYROSEQUENCING. THE AVERAGE NUMBER OF METHYLATED GENES WAS 4.5 PER PATIENT IN THE CHRONIC PHASE, INCREASING SIGNIFICANTLY TO 6.2 IN THE ACCELERATED AND 6.4 IN THE BLASTIC PHASE. HIGHER NUMBERS OF METHYLATED GENES WERE ALSO OBSERVED IN PATIENTS RESISTANT OR INTOLERANT TO IMATINIB. THESE PATIENTS ALSO SHOWED ALMOST EXCLUSIVE METHYLATION OF A PUTATIVE TRANSPORTER OSCP1. ABNORMAL METHYLATION OF A SRC SUPPRESSOR GENE PDLIM4 WAS ASSOCIATED WITH SHORTENED SURVIVAL INDEPENDENTLY OF CML STAGE AND IMATINIB RESPONSIVENESS. WE CONCLUDE THAT ABERRANT DNA METHYLATION IS ASSOCIATED WITH CML PROGRESSION AND THAT DNA METHYLATION COULD BE A MARKER ASSOCIATED WITH IMATINIB RESISTANCE. FINALLY, DNA METHYLATION OF PDLIM4 MAY HELP IDENTIFY A SUBSET OF CML PATIENTS THAT WOULD BENEFIT FROM TREATMENT WITH SRC/ABL INHIBITORS.	2011