1   861 110 CHROMATIN REMODELING FACTOR, INO80, INHIBITS PMAIP1 IN RENAL TUBULAR CELLS VIA EXCHANGE OF HISTONE VARIANT H2A.Z. FOR H2A. EPIGENETIC MODIFICATIONS SUCH AS DNA METHYLATION, HISTONE MODIFICATIONS, AND CHROMATIN STRUCTURES IN THE KIDNEY CONTRIBUTE TOWARDS THE PROGRESSION OF CHRONIC KIDNEY DISEASE (CKD). IN THIS STUDY, THE ROLE OF CHROMATIN REMODELING FACTOR INOSITOL REQUIRING 80 (INO80) WAS INVESTIGATED. ALTHOUGH INO80 REGULATES TRANSCRIPTION BY ALTERING THE CHROMATIN STRUCTURE AT THE NUCLEOSOME LEVEL, ITS ROLE IN THE KIDNEY REMAINS UNKNOWN. WE DEMONSTRATED THAT THE EXPRESSION OF INO80 IN IMPAIRED KIDNEYS DECREASED IN RATS WITH UNILATERAL URETHRAL OBSTRUCTION. WE INVESTIGATED INO80 EXPRESSION IN A PROXIMAL TUBULAR CELL LINE AND OBSERVED THAT ITS EXPRESSION DECREASED UNDER HYPOXIC CONDITION. ADDITIONALLY, INO80 KNOCKDOWN PROMOTED APOPTOSIS, SUGGESTING THAT INO80 PLAYS A ROLE IN INHIBITING TUBULAR CELL APOPTOSIS. WE IDENTIFIED DOWNSTREAM TARGET GENES OF INO80 VIA GENOME-WIDE ANALYSIS USING RNA-SEQUENCES AND FOUND THAT THE EXPRESSION OF APOPTOSIS-RELATED GENES, SUCH AS TP53 AND E2F1, AND PRO-APOPTOTIC GENES, SUCH AS PMAIP1, INCREASED UPON INO80 KNOCKDOWN. CHIP-QPCR OF THE LOCI OF PMAIP1 SHOWED THAT THE AMOUNT OF H2A.Z. INCREASED INSTEAD OF DECREASING THE AMOUNT OF H2A WHEN INO80 WAS KNOCKED DOWN. THESE RESULTS INDICATED THAT INO80 PLAYS A ROLE IN THE EXCHANGE OF H2A.Z. FOR H2A IN THE PROMOTER REGION OF PMAIP1 IN TUBULAR CELLS TO INHIBIT APOPTOSIS DURING CKD PROGRESSION.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
2  5714  28 SIRT3 OVEREXPRESSION AND EPIGENETIC SILENCING OF CATALASE REGULATE ROS ACCUMULATION IN CLL CELLS ACTIVATING AXL SIGNALING AXIS. MITOCHONDRIAL METABOLISM IS THE KEY SOURCE FOR ABUNDANT ROS IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) CELLS. HERE, WE DETECTED SIGNIFICANTLY LOWER SUPEROXIDE ANION (O(2)(-)) LEVELS WITH INCREASED ACCUMULATION OF HYDROGEN PEROXIDE (H(2)O(2)) IN CLL CELLS VS. NORMAL B-CELLS. FURTHER ANALYSIS INDICATED THAT MITOCHONDRIAL SUPEROXIDE DISMUTASE (SOD)2, WHICH CONVERTS O(2)(-) INTO H(2)O(2) REMAINED DEACETYLATED IN CLL CELLS DUE TO SIRT3 OVEREXPRESSION RESULTING ITS CONSTITUTIVE ACTIVATION. IN ADDITION, CATALASE EXPRESSION WAS ALSO REDUCED IN CLL CELLS SUGGESTING IMPAIRMENT OF H(2)O(2)-CONVERSION INTO WATER AND O(2) WHICH MAY CAUSE H(2)O(2)-ACCUMULATION. IMPORTANTLY, WE IDENTIFIED TWO CPG-ISLANDS IN THE CATALASE PROMOTER AND DISCOVERED THAT WHILE THE DISTAL CPG-ISLAND (-3619 TO -3765) REMAINED METHYLATED IN BOTH NORMAL B-CELLS AND CLL CELLS, VARIABLE DEGREES OF METHYLATION WERE DISCERNIBLE IN THE PROXIMAL CPG-ISLAND (-174 TO -332) ONLY IN CLL CELLS. FINALLY, TREATMENT OF CLL CELLS WITH A DEMETHYLATING AGENT INCREASED CATALASE MRNA LEVELS. FUNCTIONALLY, ROS ACCUMULATION IN CLL CELLS ACTIVATED THE AXL SURVIVAL AXIS WHILE UPREGULATED SIRT3, SUGGESTING THAT CLL CELLS RAPIDLY REMOVE HIGHLY REACTIVE O(2)(-) TO AVOID ITS CYTOTOXIC EFFECT BUT MAINTAIN INCREASED H(2)O(2)-LEVEL TO PROMOTE CELL SURVIVAL. THEREFORE, ABROGATION OF ABERRANTLY ACTIVATED CELL SURVIVAL PATHWAYS USING ANTIOXIDANTS CAN BE AN EFFECTIVE INTERVENTION IN CLL THERAPY IN COMBINATION WITH CONVENTIONAL AGENTS.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
3   826  32 CHARACTERIZATION OF K562 CELLS: UNCOVERING NOVEL CHROMOSOMES, ASSESSING TRANSFERRIN RECEPTOR EXPRESSION, AND PROBING PHARMACOLOGICAL THERAPIES. HUMAN ERYTHROLEUKEMIC K562 CELLS REPRESENT THE PROTOTYPICAL CELL CULTURE MODEL OF CHRONIC MYELOID LEUKEMIA (CML). THE CELLS ARE PSEUDO-TRIPLOID AND POSITIVE FOR THE PHILADELPHIA CHROMOSOME. THEREFORE, K562 CELLS HAVE BEEN WIDELY USED FOR INVESTIGATING THE BCR/ABL1 ONCOGENE AND THE TYROSINE KINASE INHIBITOR, IMATINIB-MESYLATE. FURTHER, K562 CELLS OVEREXPRESS TRANSFERRIN RECEPTORS (TFR) AND HAVE BEEN USED AS A MODEL FOR TARGETING CYTOTOXIC THERAPIES, VIA RECEPTOR-MEDIATED ENDOCYTOSIS. HERE, WE HAVE CHARACTERIZED K562 CELLS FOCUSING ON THE KARYOTYPE OF CELLS IN PROLONGED CULTURE, REGULATION OF EXPRESSION OF TFR IN WILDTYPE (WT) AND DOXORUBICIN-RESISTANT CELLS, AND RESPONSES TO HISTONE DEACETYLASE INHIBITION (HDACI). KARYOTYPE ANALYSIS INDICATES NOVEL CHROMOSOMES AND GENE EXPRESSION ANALYSIS SUGGESTS A SHIFT OF CULTURED K562 CELLS AWAY FROM PATIENT-DERIVED LEUKEMIC CELLS. WE CONFIRM THE HIGH EXPRESSION OF TFR ON K562 CELLS USING IMMUNOFLUORESCENCE AND CELL-SURFACE RECEPTOR BINDING RADIOASSAYS. IMPORTANTLY, HIGH TFR EXPRESSION IS OBSERVED IN PATIENT-DERIVED CELLS, AND WE HIGHLIGHT THE PERSISTENT EXPRESSION OF TFR FOLLOWING DOXORUBICIN ACQUIRED RESISTANCE. EPIGENETIC ANALYSIS INDICATES THAT PERMISSIVE HISTONE ACETYLATION AND METHYLATION AT THE PROMOTER REGION REGULATES THE TRANSCRIPTION OF TFR IN K562 CELLS. FINALLY, WE SHOW RELATIVELY HIGH EXPRESSION OF HDAC ENZYMES IN K562 CELLS AND DEMONSTRATE THE CHEMOTOXIC EFFECTS OF HDACI, USING THE FDA-APPROVED HYDROXAMIC ACID, VORINOSTAT. TOGETHER WITH A DESCRIPTION OF MORPHOLOGY, INFRARED SPECTRAL ANALYSIS, AND EXAMINATION OF METABOLIC PROPERTIES, WE PROVIDE A COMPREHENSIVE CHARACTERIZATION OF K562 CELLS. OVERALL, K562 CELL CULTURE SYSTEMS REMAIN WIDELY USED FOR THE INVESTIGATION OF NOVEL THERAPEUTICS FOR CML, WHICH IS PARTICULARLY IMPORTANT IN CASES OF IMATINIB-MESYLATE RESISTANCE.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
4  1620  32 DNA METHYLTRANSFERASE-MEDIATED TRANSCRIPTIONAL SILENCING IN MALIGNANT GLIOMA: A COMBINED WHOLE-GENOME MICROARRAY AND PROMOTER ARRAY ANALYSIS. EPIGENETIC INACTIVATION OF TUMOR SUPPRESSOR GENES IS A COMMON FEATURE IN HUMAN CANCER. PROMOTER HYPERMETHYLATION AND HISTONE DEACETYLATION ARE REVERSIBLE EPIGENETIC MECHANISMS ASSOCIATED WITH TRANSCRIPTIONAL REGULATION. DNA METHYLTRANSFERASES (DNMT1 AND DNMT3B) REGULATE AND MAINTAIN PROMOTER METHYLATION AND ARE OVEREXPRESSED IN HUMAN CANCER. WE PERFORMED WHOLE-GENOME MICROARRAY ANALYSIS TO IDENTIFY GENES WITH ALTERED EXPRESSION AFTER RNAI-INDUCED SUPPRESSION OF DNMT IN A GLIOBLASTOMA MULTIFORME (GBM) CELL LINE. WE THEN IDENTIFIED GENES WITH BOTH DECREASED EXPRESSION AND EVIDENCE OF PROMOTER CPG ISLAND HYPERMETHYLATION IN GBM TISSUE SAMPLES USING A COMBINED WHOLE-GENOME MICROARRAY TRANSCRIPTOME ANALYSIS IN CONJUNCTION WITH A PROMOTER ARRAY ANALYSIS AFTER DNA IMMUNOPRECIPITATION WITH ANTI-5-METHYLCYTIDINE. DNMT1 AND 3B KNOCKDOWN RESULTED IN THE RESTORED EXPRESSION OF 308 GENES THAT ALSO CONTAINED PROMOTER REGION HYPERMETHYLATION. OF THESE, 43 WERE ALSO FOUND TO BE DOWNREGULATED IN GBM TISSUE SAMPLES. THREE DOWNREGULATED GENES WITH HYPERMETHYLATED PROMOTERS AND RESTORED EXPRESSION IN RESPONSE TO ACUTE DNMT SUPPRESSION WERE ASSAYED FOR METHYLATION CHANGES USING BISULFITE SEQUENCE ANALYSIS OF THE PROMOTER REGION AFTER CHRONIC DNMT SUPPRESSION. RESTORATION OF GENE EXPRESSION WAS NOT ASSOCIATED WITH CHANGES IN PROMOTER REGION METHYLATION, BUT RATHER WITH CHANGES IN HISTONE METHYLATION AND CHROMATIN CONFORMATION. TWO OF THE IDENTIFIED GENES EXHIBITED GROWTH SUPPRESSIVE ACTIVITY IN IN VITRO ASSAYS. COMBINING TARGETED GENETIC MANIPULATIONS WITH COMPREHENSIVE GENOMIC AND EXPRESSION ANALYSES PROVIDES A POTENTIALLY POWERFUL NEW APPROACH FOR IDENTIFYING EPIGENETICALLY REGULATED GENES IN GBM.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
5   766  37 CCL5 SUPPRESSES KLOTHO EXPRESSION VIA P-STAT3/DNA METHYLTRANSFERASE1-MEDIATED PROMOTER HYPERMETHYLATION. BACKGROUND: ENHANCED INFLAMMATION AND REDUCED KLOTHO ARE COMMON FEATURES IN CHRONIC KIDNEY DISEASE (CKD). INFLAMMATION INDUCES DNA HYPERMETHYLATION. THIS STUDY ASSESSED THE PERFORMANCE OF INFLAMMATORY MARKER C-C MOTIF CHEMOKINE 5 (CCL5) IN EPIGENETIC REGULATION OF KLOTHO EXPRESSION. METHODS: FIFTY CKD PATIENTS AND 25 MATCHED CONTROLS WERE ENROLLED, AND SERUM CCL5 LEVEL, SKLOTHO LEVEL, AND DNA METHYLATION WERE EVALUATED IN THESE SUBJECTS. A RENAL INTERSTITIAL FIBROSIS (RIF) MODEL WITH CKD WAS INDUCED IN MICE VIA UNILATERAL URETERAL OBSTRUCTION (UUO) IN VIVO AND HUMAN PROXIMAL TUBULAR EPITHELIAL (HK-2) CELLS TREATED WITH CCL5 IN VITRO. 5-AZA-2'-DEOXYCYTIDINE (5-AZA), A DNA METHYLTRANSFERASE INHIBITOR WAS GIVEN TO UUO MICE. HEMATOXYLIN AND EOSIN (HE) AND MASSON TRICHROME STAINING WERE ADOPTED TO EVALUATE RENAL PATHOLOGICAL CHANGES. METHYLATION-SPECIFIC PCR WAS PERFORMED TO ASSESS DNA METHYLATION OF KLOTHO PROMOTER IN THE PERIPHERAL BLOOD LEUCOCYTES (PBLS) FROM CKD PATIENTS AND OBSTRUCTIVE KIDNEY FROM UUO MICE. CCL5, KLOTHO, AND DNA METHYLTRANSFERASES (DNMTS) WERE DETERMINED BY ELISAS, IMMUNOFLUORESCENCE, OR WESTERN BLOTTING. HK-2 CELLS WERE EXPOSED TO CCL5 WITH OR WITHOUT 5-AZA AND STATTIC, A P-SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 3 (STAT3) INHIBITOR, AND EXPRESSIONS OF P-STAT3, DNMT1, AND KLOTHO WERE DETERMINED BY WESTERN BLOTTING. RESULTS: CCL5 UPREGULATION CONCOMITANT WITH KLOTHO DOWNREGULATION IN SERUM AND GLOBAL DNA METHYLATION IN PBLS WERE OBSERVED IN CKD SAMPLES. UUO CONTRIBUTED TO SEVERE RENAL INTERSTITIAL FIBROSIS AND ENHANCED EXPRESSIONS OF FIBROTIC MARKERS. MOREOVER, UUO INCREASED THE CCL5 LEVEL, INDUCED KLOTHO PROMOTER METHYLATION, SUPPRESSED KLOTHO LEVEL, ACTIVATED P-STAT3 SIGNALING, AND UPREGULATED DNMT1 LEVEL. A SIMILAR OBSERVATION WAS MADE IN HK-2 CELLS TREATED WITH CCL5. MORE IMPORTANTLY, 5-AZA INHIBITED UUO-INDUCED KLOTHO HYPERMETHYLATION, REVERSED KLOTHO, DOWNREGULATED P-STAT3 EXPRESSIONS, AND AMELIORATED RIF IN VIVO. THE CONSISTENT FINDINGS IN VITRO WERE ALSO OBTAINED IN HK-2 CELLS EXPOSED TO 5-AZA AND STATTIC. CONCLUSION: THE CCL5/P-STAT3/DNMT1 AXIS IS IMPLICATED IN EPIGENETIC REGULATION OF KLOTHO EXPRESSION IN CKD. THIS STUDY PROVIDES NOVEL THERAPEUTIC POSSIBILITIES FOR REVERSAL OF KLOTHO SUPPRESSION BY CKD.	2022	
                                                                                                                                                                                                                                                                                                                                                     
6  5403  31 REGENERATION AFTER ACUTE KIDNEY INJURY REQUIRES PTIP-MEDIATED EPIGENETIC MODIFICATIONS. A TERMINALLY DIFFERENTIATED CELLULAR PHENOTYPE IS THOUGHT TO BE MAINTAINED, AT LEAST IN PART, BY BOTH ACTIVE AND REPRESSIVE HISTONE MARKS. HOWEVER, IT IS UNCLEAR WHETHER REGENERATING CELLS AFTER INJURY NEED TO REPLICATE SUCH EPIGENETIC MARKS TO RECOVER. TO TEST WHETHER RENAL EPITHELIAL CELL REGENERATION IS DEPENDENT ON HISTONE H3K4 METHYLATION, WE GENERATED A MOUSE MODEL THAT DELETED THE PAXIP1 GENE IN MATURE RENAL PROXIMAL TUBULES. PAXIP1 ENCODES PTIP, AN ESSENTIAL PROTEIN IN THE MLL3/4 HISTONE H3K4 METHYLTRANSFERASE COMPLEX. MICE WITH PTIP DELETIONS IN THE ADULT KIDNEY PROXIMAL TUBULES WERE VIABLE AND FERTILE. UPON ACUTE KIDNEY INJURY, SUCH MICE FAILED TO REGENERATE DAMAGED TUBULES, LEADING TO SCARRING AND INTERSTITIAL FIBROSIS. THE INABILITY TO REPAIR DAMAGE WAS LIKELY DUE TO A FAILURE TO REENTER MITOSIS AND REACTIVATE REGULATORY GENES SUCH AS SOX9. PTIP DELETION REDUCED HISTONE H3K4 METHYLATION IN UNINJURED ADULT KIDNEYS BUT DID NOT SIGNIFICANTLY AFFECT FUNCTION OR THE EXPRESSION OF EPITHELIAL SPECIFIC MARKERS. STRIKINGLY, CELL LINEAGE TRACING REVEALED THAT SURVIVING PTIP MUTANT CELLS COULD ALTER THEIR PHENOTYPE AND LOSE EPITHELIAL MARKERS. THESE DATA DEMONSTRATE THAT PTIP AND ASSOCIATED MLL3/4-MEDIATED HISTONE METHYLATION ARE NEEDED FOR REGENERATING PROXIMAL TUBULES AND TO MAINTAIN OR REESTABLISH THE CELLULAR EPITHELIAL PHENOTYPE.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
7   163  30 ABL1 METHYLATION IS A DISTINCT MOLECULAR EVENT ASSOCIATED WITH CLONAL EVOLUTION OF CHRONIC MYELOID LEUKEMIA. METHYLATION OF THE PROXIMAL PROMOTER OF THE ABL1 ONCOGENE IS A COMMON EPIGENETIC ALTERATION ASSOCIATED WITH CLINICAL PROGRESSION OF CHRONIC MYELOID LEUKEMIA (CML). IN THIS STUDY WE QUERIED WHETHER BOTH THE PH'-ASSOCIATED AND NORMAL ABL1 ALLELES UNDERGO METHYLATION; WHAT MAY BE THE PROPORTION OF HEMATOPOIETIC PROGENITORS BEARING METHYLATED ABL1 PROMOTERS IN CHRONIC VERSUS ACUTE PHASE DISEASE; WHETHER METHYLATION AFFECTS THE PROMOTER UNIFORMLY OR IN PATCHES WITH DISCRETE CLINICAL RELEVANCE; AND, FINALLY, WHETHER METHYLATION OF ABL1 REFLECTS A GENERALIZED PROCESS OR IS GENE-SPECIFIC. TO ADDRESS THESE ISSUES, WE ADAPTED THE TECHNIQUES OF METHYLATION-SPECIFIC PCR AND BISULFITE-SEQUENCING TO STUDY THE REGULATORY REGIONS OF ABL1 AND OTHER GENES WITH A ROLE IN DNA REPAIR OR GENOTOXIC STRESS RESPONSE. IN CELL LINES ESTABLISHED FROM CML BLAST CRISIS, WHICH ONLY CARRY A SINGLE ABL1 ALLELE NESTED WITHIN THE BCR-ABL FUSION GENE, ABL1 PROMOTERS WERE UNIVERSALLY METHYLATED. BY CONTRAST, IN CLINICAL SAMPLES FROM PATIENTS AT ADVANCED STAGES OF DISEASE, BOTH METHYLATED AND UNMETHYLATED PROMOTER ALLELES WERE DETECTABLE. TO DISTINGUISH BETWEEN ALLELE-SPECIFIC METHYLATION AND A MIXED CELL POPULATION PATTERN, WE STUDIED THE METHYLATION STATUS OF ABL1 IN COLONIES DERIVED FROM SINGLE HEMATOPOIETIC PROGENITORS. OUR RESULTS SHOWED THAT BOTH METHYLATED AND UNMETHYLATED PROMOTER ALLELES COEXISTED IN THE SAME COLONY. FURTHERMORE, ABL1 METHYLATION WAS NOTED IN THE VAST MAJORITY OF COLONIES FROM BLAST CRISIS, BUT NOT CHRONIC-PHASE CML. BOTH CELL LINES AND CLINICAL SAMPLES FROM ACUTE-PHASE CML SHOWED NEARLY UNIFORM HYPERMETHYLATION ALONG THE PROMOTER REGION. FINALLY, WE SHOWED THAT ABL1 METHYLATION DOES NOT REFLECT A GENERALIZED PROCESS AND MAY BE UNIQUE AMONG DNA REPAIR/GENOTOXIC STRESS RESPONSE GENES. OUR DATA SUGGEST THAT SPECIFIC METHYLATION OF THE PH'-ASSOCIATED ABL1 ALLELE ACCOMPANIES CLONAL EVOLUTION IN CML.	1999	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
8  6366  26 THE ROLE OF METHYLATION IN CML. METHYLATION OF THE PROXIMAL PROMOTER OF THE ABL1 ONCOGENE IS COMMON EPIGENETIC ALTERATION ASSOCIATED WITH CLINICAL PROGRESSION OF CHRONIC MYELOID LEUKEMIA (CML). IN PRESENTED STUDY WE QUERIED WHETHER BOTH THE PH'-ASSOCIATED AND NORMAL ABL1 ALLELES UNDERGO METHYLATION; WHAT MAY BE THE PROPORTION OF HEMATOPOIETIC PROGENITORS BEARING METHYLATED ABL1 PROMOTERS IN CHRONIC VERSUS ACUTE PHASE DISEASE; WHETHER METHYLATION AFFECTS THE PROMOTER UNIFORMLY OR IN PATCHES WITH DISCRETE CLINICAL RELEVANCE; AND, FINALLY WHETHER METHYLATION OF ABL1 REFLECTS A GENERALIZED PROCESS OR IS GENE-SPECIFIC. TO ADDRESS THESE ISSUES, THE TECHNIQUE OF METHYLATION-SPECIFIC PCR AND BISULFITE-SEQUENCING WAS ADAPTED TO STUDY THE REGULATORY REGIONS OF ABL1 AND OTHER GENES. IN CELL LINES ESTABLISHED FROM CML BLAST CRISIS, WHICH ONLY CARRY A SINGLE ABL1 ALLELE NESTED WITHIN THE BCR-ABL FUSION GENE, ABL1 PROMOTERS WERE UNIVERSALLY METHYLATED. IN CLINICAL SAMPLES FROM PATIENTS AT ADVANCED STAGES OF THE DISEASE, BOTH METHYLATED AND UNMETHYLATED PROMOTER ALLELES WERE DETECTABLE. IN COLONIES DERIVED FROM SINGLE HEMATOPOIETIC PROGENITORS METHYLATED AND UNMETHYLATED PROMOTER ALLELES WERE REVEALED AS WELL. ABL1 METHYLATION WAS WAS NOTED IN THE VAST MAJORITY OF COLONIES FROM BLAST CRISIS, BUT NOT CHRONIC-PHASE CML. IT WAS SHOWN FINALLY THAT ABL1 METHYLATION DOES NOT REFLECT A GENERALIZED PROCESS AND MAY BE UNIQUE AMONG DNA REPAIR/GENOTOXIC STRESS RESPONSE GENES. THESE DATA SUGGEST THAT SPECIFIC METHYLATION OF THE PH'-ASSOCIATED ABL1 ALLELE ACCOMPANIES CLONAL EVOLUTION IN CML.	2000	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
9  3460  32 HYPOMETHYLATION OF THE IL8 PROMOTER IN NASAL EPITHELIAL CELLS OF PATIENTS WITH CHRONIC RHINOSINUSITIS WITH NASAL POLYPS. BACKGROUND: IL-8 IS AN IMPORTANT CHEMOKINE IMPLICATED IN THE PATHOGENESIS OF CHRONIC RHINOSINUSITIS (CRS), BUT LITTLE IS KNOWN ABOUT EPIGENETIC REGULATION OF IL8 IN THE PATHOGENESIS OF CRS. OBJECTIVE: WE SOUGHT TO INVESTIGATE THE RELATIONSHIP BETWEEN THE DNA METHYLATION LEVEL IN THE IL8 PROXIMAL PROMOTER AND CRS IN HAN CHINESE SUBJECTS. METHODS: PATIENTS WITH CHRONIC RHINOSINUSITIS WITH NASAL POLYPS (CRSWNP; N = 187), PATIENTS WITH CHRONIC RHINOSINUSITIS WITHOUT NASAL POLYPS (CRSSNP; N = 89), AND CONTROL SUBJECTS (N = 57) WERE ENROLLED IN 2 INDEPENDENT COHORTS. PURIFIED HUMAN NASAL EPITHELIAL CELLS FROM EACH PARTICIPANT WERE ASSESSED FOR PERCENTAGE DNA METHYLATION OF CPG SITES IN THE IL8 PROXIMAL PROMOTER BY USING BISULFITE PYROSEQUENCING AND FOR FUNCTIONAL ASPECTS OF METHYLATION STATUS BY USING IN VITRO ASSAYS. RESULTS: DNA METHYLATION OF CPG SITES 1, 2, AND 3, RESPECTIVELY, IN THE IL8 PROXIMAL PROMOTER WAS SIGNIFICANTLY DECREASED IN HUMAN NASAL EPITHELIAL CELLS OF PATIENTS WITH CRSWNP COMPARED WITH THAT IN PATIENTS WITH CRSSNP (P < .001) AND CONTROL SUBJECTS (P < .001). PERCENTAGE OF DNA METHYLATION OF THE CPG3 SITE WAS CORRELATED NEGATIVELY WITH BOTH TISSUE EOSINOPHILIC CATIONIC PROTEIN (P < .01) AND MYELOPEROXIDASE (P < .05) LEVELS. IL-1BETA (P < .001) AND TNF-ALPHA (P < .01) SIGNIFICANTLY INCREASED IL8 EXPRESSION ACCOMPANIED BY A REDUCTION IN METHYLATION AT THE CPG3 SITE (P < .001). ELECTROPHORETIC MOBILITY SHIFT ASSAYS DEMONSTRATED THAT METHYLATION STATUS OF CPG3 CHANGED THE BINDING OF OCTAMER-BINDING TRANSCRIPTION FACTOR 1 AND NUCLEAR FACTOR KAPPAB. CONCLUSION: DECREASED DNA METHYLATION OF PARTICULARLY CPG SITES IN THE IL8 PROXIMAL PROMOTER MIGHT PLAY A ROLE IN THE PATHOGENESIS OF CRSWNP.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
10  2081  32 EPIGENETIC DOWN-REGULATION OF BIM EXPRESSION IS ASSOCIATED WITH REDUCED OPTIMAL RESPONSES TO IMATINIB TREATMENT IN CHRONIC MYELOID LEUKAEMIA. BACKGROUND: EXPRESSION OF THE PRO-APOPTOTIC BCL-2-INTERACTING MEDIATOR (BIM) HAS RECENTLY BEEN IMPLICATED IN IMATINIB-INDUCED APOPTOSIS OF BCR-ABL1(+) CELLS. HOWEVER, THE MECHANISMS INVOLVED IN THE REGULATION OF BIM IN CML AND ITS ROLE IN THE CLINICAL SETTING HAVE NOT BEEN ESTABLISHED. DESIGN AND METHODS: WE ANALYSED THE MRNA EXPRESSION OF BIM IN 100 NEWLY DIAGNOSED PATIENTS WITH CML IN CHRONIC PHASE BY Q-RT-PCR AND THE PROTEIN LEVELS BY WESTERN BLOT ANALYSIS. METHYLATION STATUS WAS ANALYSED BY BISULPHITE GENOMIC SEQUENCING AND MSP. CML CELL LINES WERE TREATED WITH IMATINIB AND 5-AZA-2'-DEOXYCYTIDINE, AND WERE TRANSFECTED WITH TWO DIFFERENT SIRNAS AGAINST BIM AND CELL PROLIFERATION AND APOPTOSIS WERE ANALYSED. RESULTS: WE DEMONSTRATED THAT DOWN-REGULATION OF BIM EXPRESSION WAS PRESENT IN 36% OF THE PATIENTS AND WAS SIGNIFICANTLY ASSOCIATED WITH A LACK OF OPTIMAL RESPONSE TO IMATINIB AS INDICATED BY THE DECREASE IN CYTOGENETIC AND MOLECULAR RESPONSES AT 6, 12 AND 18 MONTHS IN COMPARISON WITH PATIENTS WITH NORMAL BIM EXPRESSION (P<0.05). EXPRESSION OF BIM WAS MEDIATED BY PROMOTER HYPERMETHYLATION AS DEMONSTRATED BY RESTORATION OF BIM EXPRESSION AFTER TREATMENT OF CML CELLS WITH 5-AZA-2'-DEOXYCYTIDINE. USING CML CELL LINES WITH LOW AND NORMAL EXPRESSION OF BIM WE FURTHER DEMONSTRATED THAT THE EXPRESSION OF BIM IS REQUIRED FOR IMATINIB-INDUCED CML APOPTOSIS. CONCLUSION: OUR DATA INDICATE THAT DOWN-REGULATION OF BIM IS EPIGENETICALLY CONTROLLED BY METHYLATION IN A PERCENTAGE OF CML PATIENTS AND HAS AN UNFAVOURABLE PROGNOSTIC IMPACT, AND THAT THE COMBINATION OF IMATINIB WITH A DE-METHYLATING AGENT MAY RESULT IN IMPROVED RESPONSES IN PATIENTS WITH DECREASED EXPRESSION OF BIM.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
11  6069  37 THE DIOXIN RECEPTOR IS SILENCED BY PROMOTER HYPERMETHYLATION IN HUMAN ACUTE LYMPHOBLASTIC LEUKEMIA THROUGH INHIBITION OF SP1 BINDING. THE TRANSCRIPTION FACTOR ARYL HYDROCARBON RECEPTOR (AHR) HAS RELEVANT FUNCTIONS IN CELL PROLIFERATION. INTERESTINGLY, THE AHR CAN EITHER PROMOTE OR INHIBIT PROLIFERATION DEPENDING ON THE CELL PHENOTYPE. ALTHOUGH RECENT DATA REVEAL POTENTIAL PATHWAYS FOR AHR SIGNALING IN CELL PROLIFERATION, THE MECHANISMS THAT REGULATE ITS ACTIVITY IN TUMOR CELLS REMAIN UNKNOWN. HERE, WE HAVE ANALYZED PROMOTER HYPERMETHYLATION AS A POTENTIAL MECHANISM CONTROLLING AHR EXPRESSION IN HUMAN TUMOR CELLS. AHR PROMOTER CPG METHYLATION WAS SPORADIC IN A PANEL OF 19 TUMOR CELL LINES EXCEPT FOR THE CHRONIC MYELOID LEUKEMIA (CML) K562 AND THE ACUTE LYMPHOBLASTIC LEUKEMIA (ALL) REH. WHEN COMPARED WITH NORMAL LYMPHOCYTES, REH HAD VERY LOW CONSTITUTIVE AHR EXPRESSION THAT COULD BE ATTRIBUTED TO PROMOTER HYPERMETHYLATION SINCE TREATMENT WITH THE DNA DEMETHYLATING AGENT 5-AZA-2'-DEOXYCITIDINE (AZA) SIGNIFICANTLY INCREASED AHR MRNA AND PROTEIN. THESE RESULTS IN LEUKEMIA-DERIVED CELL LINES WERE FURTHER CONFIRMED IN PRIMARY ALL, WHERE 33% OF THE PATIENTS (7/21) HAD AHR PROMOTER HYPERMETHYLATION. CHROMATIN IMMUNOPRECIPITATION (CHIP) SHOWED THAT METHYLATION IMPAIRED BINDING OF THE TRANSCRIPTION FACTOR SP1 TO THE AHR PROMOTER, THUS PROVIDING A MECHANISM FOR AHR DOWNREGULATION IN REH CELLS. THEREFORE, PROMOTER HYPERMETHYLATION REPRESENTS A NOVEL EPIGENETIC MECHANISM DOWNREGULATING AHR ACTIVITY IN HEMATOLOGICAL MALIGNANCIES SUCH AS ALL.	2006	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
12  1613  25 DNA METHYLTRANSFERASE 1 MEDIATED ABERRANT METHYLATION AND SILENCING OF SHP-1 GENE IN CHRONIC MYELOGENOUS LEUKEMIA CELLS. INTRODUCTION: EXTENSIVE STUDIES ON SHP-1 PROTEIN AND SHP-1 MRNA REVEALED THAT THE DIMINISHMENT OR ABOLISHMENT OF THE EXPRESSION OF SHP-1 IN LEUKEMIAS/LYMPHOMAS WAS DUE TO ABERRANT PROMOTER METHYLATION. THUS FAR, THE MECHANISM OF EPIGENETIC SILENCING OF THE SHP-1 TYROSINE PHOSPHATASE GENE THAT OCCURS IN CHRONIC MYELOGENOUS LEUKEMIA CELLS REMAINS POORLY UNDERSTOOD. METHODS: THE EXPRESSIONS OF THE TARGET MOLECULES WERE DETERMINED BY QUANTITATIVE REAL TIME PCR AND WESTERN BLOT, RESPECTIVELY. BISULFITE SEQUENCING PCR WAS USED TO DETECT METHYLATION STATUS OF DNA CPG. THE LENTIVIRAL VECTORS WERE APPLIED TO MODIFY GENE EXPRESSION. RESULTS: IN THE PRESENT STUDY, WE FOUND THAT THE PROMOTER 2 OF SHP-1 GENE IS LOCATED BETWEEN POSITIONS FROM -577BP TO +300BP, AND 22 CPG SITES CONTAINED IN POSITIONS -353BP APPROXIMATELY +182BP ARE ABERRANTLY METHYLATED IN K562 CELLS. IN VITRO, WE DEMONSTRATED THAT DNMT1 SILENCING INDUCED DEMETHYLATION OF THE 22 CPG SITES LOCATED IN THE SHP-1 PROMOTER AND RE-EXPRESSION OF SHP-1 GENE IN K562 CELLS. MOREOVER, WE PROVED THAT THE EXPRESSION LEVELS OF DNMT1 AND SHP-1 MRNA AND PROTEIN WERE NEGATIVELY CORRELATED IN K562 CELLS AND BM ASPIRATES MONONUCLEAR CELLS FROM CML PATIENTS. CONCLUSION: COLLECTIVELY, THESE RESULTS INDICATE THAT DNMT1 MEDIATES ABERRANT METHYLATION AND SILENCING OF SHP-1 GENE IN CHRONIC MYELOGENOUS LEUKEMIA CELLS, AND PROVIDE A NOVEL THERAPEUTIC TARGET FOR CML.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
13  3175  36 H2AX PHOSPHORYLATION REGULATED BY P38 IS INVOLVED IN BIM EXPRESSION AND APOPTOSIS IN CHRONIC MYELOGENOUS LEUKEMIA CELLS INDUCED BY IMATINIB. INCREASING EVIDENCE SUGGESTS THAT HISTONE H2AX PLAYS A CRITICAL ROLE IN REGULATION OF TUMOR CELL APOPTOSIS AND ACTS AS A NOVEL HUMAN TUMOR SUPPRESSOR PROTEIN. HOWEVER, THE ACTION OF H2AX IN CHRONIC MYELOGENOUS LEUKEMIA (CML) CELLS IS UNKNOWN. THE DETAILED MECHANISM AND EPIGENETIC REGULATION BY H2AX REMAIN ELUSIVE IN CANCER CELLS. HERE, WE REPORT THAT H2AX WAS INVOLVED IN APOPTOSIS OF CML CELLS. OVEREXPRESSION OF H2AX INCREASED APOPTOTIC SENSITIVITY OF CML CELLS (K562) INDUCED BY IMATINIB. HOWEVER, OVEREXPRESSION OF SER139-MUTATED H2AX (BLOCKING PHOSPHORYLATION) DECREASED SENSITIVITY OF K562 CELLS TO APOPTOSIS. SIMILARLY, KNOCKDOWN OF H2AX MADE K562 CELLS RESISTANT TO APOPTOTIC INDUCTION. THESE RESULTS REVEALED THAT THE FUNCTION OF H2AX INVOLVED IN APOPTOSIS IS STRICTLY RELATED TO ITS PHOSPHORYLATION (SER139). OUR DATA FURTHER INDICATED THAT IMATINIB MAY STIMULATE MITOGEN-ACTIVATED PROTEIN KINASE (MAPK) FAMILY MEMBER P38, AND H2AX PHOSPHORYLATION FOLLOWED A SIMILAR TIME COURSE, SUGGESTING A PARALLEL RESPONSE. H2AX PHOSPHORYLATION CAN BE BLOCKED BY P38 SIRNA OR ITS INHIBITOR. THESE DATA DEMONSTRATED THAT H2AX PHOSPHORYLATION WAS REGULATED BY P38 MAPK PATHWAY IN K562 CELLS. HOWEVER, THE P38 MAPK DOWNSTREAM, MITOGEN- AND STRESS-ACTIVATED PROTEIN KINASE-1 AND -2, WHICH PHOSPHORYLATED HISTONE H3, WERE NOT REQUIRED FOR H2AX PHOSPHORYLATION DURING APOPTOSIS. FINALLY, WE PROVIDED EPIGENETIC EVIDENCE THAT H2AX PHOSPHORYLATION REGULATED APOPTOSIS-RELATED GENE BIM EXPRESSION. BLOCKING OF H2AX PHOSPHORYLATION INHIBITED BIM GENE EXPRESSION. TAKEN TOGETHER, THESE DATA DEMONSTRATED THAT H2AX PHOSPHORYLATION REGULATED BY P38 IS INVOLVED IN BIM EXPRESSION AND APOPTOSIS IN CML CELLS INDUCED BY IMATINIB.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
14  5459  33 RESEARCH ON THE EPIGENETIC REGULATION MECHANISM OF THE PTPN6 GENE IN ADVANCED CHRONIC MYELOID LEUKAEMIA. PTPN6, A TYROSINE PHOSPHATASE PROTEIN, PLAYS A NEGATIVE ROLE IN CELL SIGNAL TRANSDUCTION AND IS NEGATIVELY CORRELATED WITH TUMOUR FORMATION AND GROWTH. HOWEVER, EPIGENETIC REGULATION MECHANISM OF THE PTPN6 GENE IN ADVANCED CHRONIC MYELOID LEUKAEMIA (CML) REMAINS UNCLEAR. THIS STUDY INVESTIGATED BONE MARROW OR BLOOD SAMPLES FROM 44 CML PATIENTS AND 10 HEALTHY VOLUNTEERS. KCL22 AND K562 CELLS WERE CULTURED AND TREATED WITH DEMETHYLATION DRUGS AND HISTONE DEACETYLASE INHIBITORS. REAL TIME QUANTITATIVE POLYMERASE CHAIN REACTION (QPCR), METHYLATION-SPECIFIC PCR, BISULFITE SEQUENCING PCR, WESTERN BLOTTING, CO-IMMUNOPRECIPITATION AND CHROMATIN IMMUNOPRECIPITATION (CHIP) WAS PERFORMED. PTPN6 WAS DOWN-REGULATED IN CELL LINES AND PATIENTS WITH ADVANCED PHASE CML, WHEREAS DNMT1, DNMT3A, MECP2, MBD2 AND HDAC1 WERE UP-REGULATED. TREATMENT WITH 5-AZACYTIDINE, DECITABINE, SODIUM VALPROATE AND LBH589 INCREASED PTPN6 EXPRESSION, BUT DECREASED THAT OF DNMT1, DNMT3A, MECP2, MBD2 AND HDAC1. IMMUNOPRECIPITATION AND MASS SPECTROMETRY SHOWED THAT HDAC1 COMBINED DIRECTLY WITH PTPN6. CHIP-SEQ SHOWED THAT HDAC1 DID NOT COMBINE WITH THE PROMOTER REGION OF PTPN6, WHILE MAPK, AKT, STAT5, JAK2 AND MYC PROMOTER REGIONS ALL COMBINED WITH HDAC1. PTPN6 IS ASSOCIATED WITH PROGRESSION OF CML. LOW EXPRESSION LEVEL OF PTPN6 WAS ASSOCIATED WITH DNA METHYLATION AND REGULATED BY HISTONE ACETYLATION. HDAC1 PARTICIPATES IN THE REGULATION OF PTPN6.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
15  1632  31 DNMTS ARE INVOLVED IN TGF-BETA1-INDUCED EPITHELIAL-MESENCHYMAL TRANSITIONS IN AIRWAY EPITHELIAL CELLS. CHRONIC RHINOSINUSITIS (CRS) PATHOGENESIS IS CLOSELY RELATED TO TISSUE REMODELING, INCLUDING EPITHELIAL-MESENCHYMAL TRANSITION (EMT). EPIGENETIC MECHANISMS PLAY KEY ROLES IN EMT. DNA METHYLATION, MEDIATED BY DNA METHYLTRANSFERASES (DNMTS), IS AN EPIGENETIC MARKER THAT IS CRITICAL TO EMT. THE GOAL OF THIS STUDY WAS TO DETERMINE WHETHER DNMTS WERE INVOLVED IN TGF-BETA1-INDUCED EMT AND ELUCIDATE THE UNDERLYING MECHANISMS IN NASAL EPITHELIAL CELLS AND AIR-LIQUID INTERFACE CULTURES. GLOBAL DNA METHYLATION AND DNMT ACTIVITY WERE QUANTIFIED. DNMT EXPRESSION WAS MEASURED USING REAL-TIME PCR (QRT-PCR) IN HUMAN CRS TISSUES. MRNA AND PROTEIN LEVELS OF DNMTS, E-CADHERIN, VIMENTIN, ALPHA-SMA, AND FIBRONECTIN WERE DETERMINED USING RT-PCR AND WESTERN BLOTTING, RESPECTIVELY. DNMT1, DNMT3A, AND DNMT3B GENE EXPRESSION WERE KNOCKED DOWN USING SIRNA TRANSFECTION. MAPK PHOSPHORYLATION AND EMT-RELATED TRANSCRIPTION FACTOR LEVELS WERE DETERMINED USING WESTERN BLOTTING. SIGNALING PATHWAYS WERE ANALYZED USING SPECIFIC INHIBITORS OF MAPK. WE DEMONSTRATED THESE DATA IN PRIMARY NASAL EPITHELIAL CELLS AND AIR-LIQUID INTERFACE CULTURES. GLOBAL DNA METHYLATION, DNMT ACTIVITY, AND DNMT EXPRESSION INCREASED IN CRS TISSUES. DNMT EXPRESSION WAS POSITIVELY CORRELATED WITH LUND-MCKAY CT SCORES. TGF-BETA1 DOSE-DEPENDENTLY INDUCED DNMT EXPRESSION. FURTHER, 5-AZA INHIBITED TGF-BETA1-INDUCED DNMT, SNAIL, AND SLUG EXPRESSION RELATED TO EMT, AS WELL AS P38 AND JNK PHOSPHORYLATION IN A549 CELLS AND TGF-BETA1-INDUCED DNMT EXPRESSION AND EMT IN PRIMARY NASAL EPITHELIAL CELLS AND AIR-LIQUID INTERFACE CULTURES. TGF-BETA1-INDUCED DNMT EXPRESSION LEADS TO DNA METHYLATION AND EMT VIA P38, JNK, SNAIL, AND SLUG SIGNALING PATHWAYS. INHIBITION OF DNMT SUPPRESSED THE EMT PROCESS AND THEREFORE IS POTENTIALLY A CRS THERAPEUTIC STRATEGY.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
16  3087  36 GENOME?WIDE EXPRESSION AND METHYLATION ANALYSES REVEAL ABERRANT CELL ADHESION SIGNALING IN TYROSINE KINASE INHIBITOR?RESISTANT CML CELLS. ALTHOUGH CHRONIC MYELOID LEUKEMIA (CML) CAN BE EFFECTIVELY TREATED USING BCR?ABL1 KINASE INHIBITORS, RESISTANCE DUE TO KINASE ALTERATIONS OR TO BCR?ABL1 INDEPENDENT MECHANISMS REMAIN A THERAPEUTIC CHALLENGE. FOR THE LATTER, THE UNDERLYING MECHANISMS ARE WIDELY DISCUSSED; FOR INSTANCE, GENE EXPRESSION CHANGES, EPIGENETIC FACTORS AND ALTERNATIVE SIGNALING PATHWAY ACTIVATION. IN THE PRESENT STUDY, IN VITRO?CML CELL MODELS OF RESISTANCE AGAINST THE TYROSINE KINASE INHIBITORS (TKIS) IMATINIB (0.5 AND 2 MICROM) AND NILOTINIB (0.1 MICROM) WITH BIOLOGICAL REPLICATES WERE GENERATED TO IDENTIFY NOVEL MECHANISMS OF RESISTANCE. SUBSEQUENTLY, GENOME?WIDE MRNA EXPRESSION AND DNA METHYLATION WERE ANALYZED. WHILE MRNA EXPRESSION PATTERNS DIFFERED LARGELY BETWEEN BIOLOGICAL REPLICATES, THERE WAS AN OVERLAP OF 71 GENES DIFFERENTIALLY EXPRESSED BETWEEN CELLS RESISTANT AGAINST IMATINIB OR NILOTINIB. MOREOVER, ALL TKI RESISTANT CELL LINES DEMONSTRATED A SLIGHT HYPERMETHYLATION COMPARED WITH NATIVE CELLS. IN A COMBINED ANALYSIS OF 151 GENES DIFFERENTIALLY EXPRESSED IN THE BIOLOGICAL REPLICATES OF IMATINIB RESISTANCE, CELL ADHESION SIGNALING, IN PARTICULAR THE CELLULAR MATRIX PROTEIN FIBRONECTIN 1 (FN1), WAS SIGNIFICANTLY DYSREGULATED. THIS GENE WAS ALSO DOWNREGULATED IN NILOTINIB RESISTANCE. FURTHER ANALYSES SHOWED SIGNIFICANT FN1?DOWNREGULATION IN IMATINIB RESISTANCE ON MRNA (P<0.001) AND PROTEIN LEVEL (P<0.001). SIRNA?MEDIATED FN1?KNOCKDOWN IN NATIVE CELLS REDUCED CELL ADHESION (P=0.02), DECREASED IMATINIB SUSCEPTIBILITY VISIBLE BY HIGHER KI?67 EXPRESSION (1.5?FOLD, P=0.04) AND INCREASED CELL NUMBER (1.5?FOLD, P=0.03). VICE VERSA, RECOVERY OF FN1?EXPRESSION IN IMATINIB RESISTANT CELLS WAS SUFFICIENT TO PARTIALLY RESTORE THE RESPONSE TO IMATINIB. OVERALL, THESE RESULTS SUGGESTED A ROLE OF CELL ADHESION SIGNALING AND FIBRONECTIN 1 IN TKI RESISTANT CML AND A POTENTIAL TARGET FOR NOVEL STRATEGIES IN TREATMENT OF RESISTANT CML.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
17  1211  32 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
18  3444  26 HYPERMETHYLATION OF E-CADHERIN IN LEUKEMIA. E-CADHERIN GENE IS OFTEN TERMED A "METASTASIS SUPPRESSOR" GENE BECAUSE THE E-CADHERIN PROTEIN CAN SUPPRESS TUMOR CELL INVASION AND METASTASIS. INACTIVATION OF THE E-CADHERIN GENE OCCURS IN UNDIFFERENTIATED SOLID TUMORS BY BOTH GENETIC AND EPIGENETIC MECHANISMS; HOWEVER, THE ROLE OF E-CADHERIN IN HEMATOLOGIC MALIGNANCIES IS ONLY NOW BEING RECOGNIZED. E-CADHERIN EXPRESSION IS ESSENTIAL FOR ERYTHROBLAST AND NORMOBLAST MATURATION, YET EXPRESSION IS REDUCED OR ABSENT IN LEUKEMIC BLAST CELLS. THIS STUDY EXAMINED THE MESSENGER RNA (MRNA) AND PROTEIN EXPRESSION OF THE E-CADHERIN GENE IN BONE MARROW AND BLOOD SAMPLES FROM NORMAL DONORS AND PATIENTS WITH LEUKEMIA. WE FOUND THAT ALL NORMAL DONOR SAMPLES EXPRESSED E-CADHERIN MRNA, WHEREAS BOTH SAMPLES OF ACUTE MYELOGENOUS LEUKEMIA AND CHRONIC LYMPHOCYTIC LEUKEMIA HAD A SIGNIFICANT REDUCTION OR ABSENCE OF EXPRESSION. HOWEVER, NORMAL BLAST COUNTERPARTS EXPRESSED ONLY A LOW LEVEL OF E-CADHERIN SURFACE PROTEIN. SODIUM BISULPHITE GENOMIC SEQUENCING WAS USED TO FULLY CHARACTERIZE THE METHYLATION PATTERNS OF THE CPG ISLAND ASSOCIATED WITH THE E-CADHERIN GENE PROMOTER IN THOSE SAMPLES WITH MATCHED DNA. ALL OF THE NORMAL CONTROL SAMPLES WERE ESSENTIALLY UNMETHYLATED; HOWEVER, 14 OF 18 (78%) OF THE LEUKEMIA SAMPLES HAD ABNORMAL HYPERMETHYLATION OF THE E-CADHERIN CPG ISLAND. IN FACT BOTH ALLELES OF THE E-CADHERIN GENE WERE OFTEN HYPERMETHYLATED. WE CONCLUDE THE E-CADHERIN GENE IS A COMMON TARGET FOR HYPERMETHYLATION IN HEMATOLOGIC MALIGNANCIES.	2000	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
19  3624  37 IN VIVO FUNCTION OF FLOW-RESPONSIVE CIS-DNA ELEMENTS OF ENOS GENE: A ROLE FOR CHROMATIN-BASED MECHANISMS. BACKGROUND: ENOS (ENDOTHELIAL NITRIC OXIDE SYNTHASE) IS AN ENDOTHELIAL CELL (EC)-SPECIFIC GENE PREDOMINANTLY EXPRESSED IN MEDIUM- TO LARGE-SIZED ARTERIES WHERE ECS EXPERIENCE ATHEROPROTECTIVE LAMINAR FLOW WITH HIGH SHEAR STRESS. DISTURBED FLOW WITH LOWER AVERAGE SHEAR STRESS DECREASES ENOS TRANSCRIPTION, WHICH LEADS TO THE DEVELOPMENT OF ATHEROSCLEROSIS, ESPECIALLY AT BIFURCATIONS AND CURVATURES OF ARTERIES. THIS PROTOTYPIC ARTERIAL EC GENE CONTAINS 2 DISTINCT FLOW-RESPONSIVE CIS-DNA ELEMENTS IN THE PROMOTER, THE SHEAR STRESS RESPONSE ELEMENT (SSRE) AND THE KLF (KRUPPEL-LIKE FACTOR) ELEMENT. PREVIOUS IN VITRO STUDIES SUGGESTED THEIR POSITIVE REGULATORY FUNCTIONS ON FLOW-INDUCED TRANSCRIPTION OF EC GENES INCLUDING ENOS. HOWEVER, THE IN VIVO FUNCTION OF THESE CIS-DNA ELEMENTS REMAINS UNKNOWN. METHODS: INSERTIONAL TRANSGENIC MICE WITH A MUTATION AT EACH FLOW-RESPONSIVE CIS-DNA ELEMENT WERE GENERATED USING A MURINE ENOS PROMOTER-BETA-GALACTOSIDASE REPORTER BY LINKER-SCANNING MUTAGENESIS AND COMPARED WITH EPISOMAL-BASED MUTATIONS IN VITRO. DNA METHYLATION AT THE ENOS PROXIMAL PROMOTER IN MOUSE ECS WAS ASSESSED BY BISULFITE SEQUENCING OR PYROSEQUENCING. RESULTS: WILD TYPE MICE WITH A FUNCTIONAL ENOS PROMOTER-REPORTER TRANSGENE EXHIBITED REDUCED ENDOTHELIAL REPORTER EXPRESSION IN THE ATHEROPRONE REGIONS OF DISTURBED FLOW (N=5). IT IS SURPRISING THAT THE SSRE MUTATION ABROGATED REPORTER EXPRESSION IN ECS AND WAS ASSOCIATED WITH ABERRANT HYPERMETHYLATION AT THE ENOS PROXIMAL PROMOTER (N=7). REPORTER GENE SILENCING WAS INDEPENDENT OF TRANSGENE COPY NUMBER AND INTEGRATION POSITION, INDICATING THAT THE SSRE IS A CRITICAL CIS-ELEMENT NECESSARY FOR ENOS TRANSCRIPTION IN VIVO. THE KLF MUTATION DEMONSTRATED AN INTEGRATION SITE-SPECIFIC DECREASE IN ENOS TRANSCRIPTION, AGAIN WITH MARKED PROMOTER METHYLATION (N=8), SUGGESTING THAT THE SSRE ALONE IS NOT SUFFICIENT FOR ENOS TRANSCRIPTION IN VIVO. IN WILD TYPE MICE, THE NATIVE ENOS PROMOTER WAS SIGNIFICANTLY HYPERMETHYLATED IN ECS FROM THE ATHEROPRONE REGIONS WHERE ENOS EXPRESSION WAS MARKEDLY REPRESSED BY CHRONIC DISTURBED FLOW, DEMONSTRATING THAT ENOS EXPRESSION IS REGULATED BY FLOW-DEPENDENT DNA METHYLATION THAT IS REGION-SPECIFIC IN THE ARTERIAL ENDOTHELIUM IN VIVO. CONCLUSIONS: WE REPORT, FOR THE FIRST TIME, THAT THE SSRE AND KLF ELEMENTS ARE CRITICAL FLOW SENSORS NECESSARY FOR A TRANSCRIPTIONALLY PERMISSIVE, HYPOMETHYLATED ENOS PROMOTER IN ECS UNDER CHRONIC SHEAR STRESS IN VIVO. MOREOVER, ENOS EXPRESSION IS REGULATED BY FLOW-DEPENDENT EPIGENETIC MECHANISMS, WHICH OFFERS NOVEL MECHANISTIC INSIGHT ON ENOS GENE REGULATION IN ATHEROGENESIS.	2021	

20  6793  33 [DOWN-REGULATION OF TRANSCRIPTION FACTOR PU.1 VIA ABNORMAL EPIGENETIC MODIFICATION IN CHRONIC MYELOID LEUKEMIA]. OBJECTIVE: TO INVESTIGATE THE UNDERLYING MECHANISM AND CLINICAL SIGNIFICANCE OF PU.1 DOWN-EXPRESSION IN CHRONIC MYELOID LEUKEMIA (CML) PATIENTS. METHODS: DIFFERENT METHYLATION STATUS OF PU.1 PROMOTER REGION CONTAINING 20 CPG ISLANDS IN NORMAL INDIVIDUALS, CML CHRONIC PHASE AND BLAST CRISIS PATIENTS, COMPLETE CYTOGENETIC REMISSION PATIENTS AFTER IMATINIB TREATMENT, AND BLAST CRISIS BONE MARROW K562 CML CELLS WAS DETECTED BY BISULFITE SEQUENCING. SEMI-QUANTITATIVE PCR WAS USED TO DETECT THE PU.1 MRNA EXPRESSION IN NORMAL CONTROLS, CML CHRONIC PHASE AND BLAST CRISIS PATIENTS, AND BLAST CRISIS BONE MARROW K562 CML CELLS. INDIRECT IMMUNE FLUORESCENCE AND WESTERN BLOT WERE USED TO ANALYZE THE EXPRTESSION OF PU.1 PROTEIN IN NORMAL INDIVIDUALS, CML CHRONIC PHASE AND BLAST CRISIS PATIENTS, AND BLAST CRISIS BONE MARROW K562 CML CELLS. RESULTS: ABERRANT METHYLATION IN THE PROMOTER REGION OF TRANSCRIPTION FACTOR PU.1 WAS FOUND IN BOTH CML CHRONIC PHASE AND BLAST CRISIS PHASE BONE MARROW CELLS, AS WELL AS IN CML BLAST K562 CELLS. DOWN-EXPRESSION OF PU.1 MRNA AND PROTEIN LEVELS WAS FOUND IN ABOVE CELLS. NO METHYLATION IN THE PROMOTER REGION OF PU.1 WAS OBSERVED IN NORMAL INDIVIDUALS, AND THE PU.1 MRNA AND PROTEIN EXPRESSIONS WERE NOT REDUCED AT ALL. FURTHERMORE, HIGH METHYLATION STATUS OF BONE MARROW CELLS WAS EVEN OBSERVED IN THE CML PATIENTS WHO ACQUIRED COMPLETE CYTOGENETIC REMISSION. CONCLUSIONS: THE RESULTS OF OUR STUDY INDICATE THAT THE EPIGENETIC MODIFICATION OF PU.1 IN CML PATIENTS AND K562 CELL LINE MIGHT BE RESPONSIBLE FOR THE DOWN-EXPRESSION OF PU.1. THE DATA SUGGEST THAT ABERRANT METHYLATION OF PU.1 PLAYS A ROLE IN CML PATHOGENESIS, THEREFORE, IT MIGHT SERVE AS A USEFUL BIOMARKER AND POTENTIAL TARGET IN THERAPY FOR CHRONIC MYELOID LEUKEMIA.	2012