1  4237 105 METHYLATION PATTERN OF THBS1, GATA-4, AND HIC1 IN PEDIATRIC AND ADULT PATIENTS INFECTED WITH HELICOBACTER PYLORI. BACKGROUND: HELICOBACTER PYLORI INFECTION IS USUALLY ACQUIRED IN CHILDHOOD AND PERSISTS INTO ADULTHOOD IF UNTREATED. THE BACTERIUM INDUCES A CHRONIC INFLAMMATORY RESPONSE, WHICH IS ASSOCIATED WITH EPIGENETIC ALTERATIONS IN ONCOGENES, TUMOR-SUPPRESSOR GENES, CELL-CYCLE REGULATORS, AND CELL-ADHESION MOLECULES. AIM: THE AIM OF THIS STUDY WAS TO ANALYZE THE EFFECT OF H. PYLORI INFECTION ON THE METHYLATION STATUS OF THROMBOSPONDIN-1 (THBS1), HYPERMETHYLATED IN CANCER 1 (HIC1) AND GATA BINDING PROTEIN-4 (GATA-4) IN GASTRIC BIOPSY SAMPLES FROM CHILDREN AND ADULTS INFECTED OR UNINFECTED WITH THE BACTERIUM AND IN SAMPLES OBTAINED FROM GASTRIC CANCER PATIENTS. METHODS: THE METHYLATION PATTERN WAS ANALYZED WITH METHYLATION-SPECIFIC PCR. RESULTS: OUR RESULTS SHOWED THAT H. PYLORI INFECTION WAS ASSOCIATED WITH METHYLATION OF THE PROMOTER REGIONS OF THE THBS1 AND GATA-4 GENES IN PEDIATRIC AND ADULT SAMPLES (P < 0.01). HIC1 SHOWED THE LOWEST LEVEL OF METHYLATION, WHICH WAS NOT AN EARLY EVENT DURING GASTRIC CARCINOGENESIS. CONCLUSIONS: THE RESULTS FROM THIS STUDY INDICATE THAT METHYLATION OF THBS1 AND GATA-4 OCCURS IN THE EARLY STAGES OF CHRONIC GASTRITIS AND GASTRIC CANCER IN ASSOCIATION WITH H. PYLORI INFECTION; HOWEVER, IN GASTRIC CANCER SAMPLES, OTHER MECHANISMS COOPERATE WITH THE DOWN-REGULATION OF THESE GENES. METHYLATION OF HIC1 MAY NOT BE THE PRINCIPAL MECHANISM IMPLICATED IN ITS DOWN-REGULATION IN GASTRIC CANCER SAMPLES.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
2  3061  28 GENOME-WIDE DNA METHYLATION ANALYSIS PREDICTS AN EPIGENETIC SWITCH FOR GATA FACTOR EXPRESSION IN ENDOMETRIOSIS. ENDOMETRIOSIS IS A GYNECOLOGICAL DISEASE DEFINED BY THE EXTRAUTERINE GROWTH OF ENDOMETRIAL-LIKE CELLS THAT CAUSE CHRONIC PAIN AND INFERTILITY. THE DISEASE IS LIMITED TO PRIMATES THAT EXHIBIT SPONTANEOUS DECIDUALIZATION, AND DISEASED CELLS ARE CHARACTERIZED BY SIGNIFICANT DEFECTS IN THE STEROID-DEPENDENT GENETIC PATHWAYS THAT TYPIFY THIS PROCESS. ALTERED DNA METHYLATION MAY UNDERLIE THESE DEFECTS, BUT FEW REGIONS WITH DIFFERENTIAL METHYLATION HAVE BEEN IMPLICATED IN THE DISEASE. WE MAPPED GENOME-WIDE DIFFERENCES IN DNA METHYLATION BETWEEN HEALTHY HUMAN ENDOMETRIAL AND ENDOMETRIOTIC STROMAL CELLS AND CORRELATED THIS WITH GENE EXPRESSION USING AN INTERACTION ANALYSIS STRATEGY. WE IDENTIFIED 42,248 DIFFERENTIALLY METHYLATED CPGS IN ENDOMETRIOSIS COMPARED TO HEALTHY CELLS. THESE EXTENSIVE DIFFERENCES WERE NOT UNIDIRECTIONAL, BUT WERE FOCUSED INTRAGENICALLY AND AT SITES DISTAL TO CLASSIC CPG ISLANDS WHERE METHYLATION STATUS WAS TYPICALLY NEGATIVELY CORRELATED WITH GENE EXPRESSION. SIGNIFICANT DIFFERENCES IN METHYLATION WERE MAPPED TO 403 GENES, WHICH INCLUDED A DISPROPORTIONALLY LARGE NUMBER OF TRANSCRIPTION FACTORS. FURTHERMORE, MANY OF THESE GENES ARE IMPLICATED IN THE PATHOLOGY OF ENDOMETRIOSIS AND DECIDUALIZATION. OUR RESULTS TREMENDOUSLY IMPROVE THE SCOPE AND RESOLUTION OF DIFFERENTIAL METHYLATION AFFECTING THE HOX GENE CLUSTERS, NUCLEAR RECEPTOR GENES, AND INTRIGUINGLY THE GATA FAMILY OF TRANSCRIPTION FACTORS. FUNCTIONAL ANALYSIS OF THE GATA FAMILY REVEALED THAT GATA2 REGULATES KEY GENES NECESSARY FOR THE HORMONE-DRIVEN DIFFERENTIATION OF HEALTHY STROMAL CELLS, BUT IS HYPERMETHYLATED AND REPRESSED IN ENDOMETRIOTIC CELLS. GATA6, WHICH IS HYPOMETHYLATED AND ABUNDANT IN ENDOMETRIOTIC CELLS, POTENTLY BLOCKED HORMONE SENSITIVITY, REPRESSED GATA2, AND INDUCED MARKERS OF ENDOMETRIOSIS WHEN EXPRESSED IN HEALTHY ENDOMETRIAL CELLS. THE UNIQUE EPIGENETIC FINGERPRINT IN ENDOMETRIOSIS SUGGESTS DNA METHYLATION IS AN INTEGRAL COMPONENT OF THE DISEASE, AND IDENTIFIES A NOVEL ROLE FOR THE GATA FAMILY AS KEY REGULATORS OF UTERINE PHYSIOLOGY-ABERRANT DNA METHYLATION IN ENDOMETRIOTIC CELLS CORRELATES WITH A SHIFT IN GATA ISOFORM EXPRESSION THAT FACILITATES PROGESTERONE RESISTANCE AND DISEASE PROGRESSION.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
3  5935  33 TARGETING GATA1 AND P2X7R LOCUS BINDING IN SPINAL ASTROCYTES SUPPRESSES CHRONIC VISCERAL PAIN BY PROMOTING DNA DEMETHYLATION. IRRITABLE BOWEL SYNDROME IS A GASTROINTESTINAL DISORDER OF UNKNOWN ETIOLOGY CHARACTERIZED BY WIDESPREAD, CHRONIC ABDOMINAL PAIN ASSOCIATED WITH ALTERED BOWEL MOVEMENTS. INCREASING AMOUNTS OF EVIDENCE INDICATE THAT INJURY AND INFLAMMATION DURING THE NEONATAL PERIOD HAVE LONG-TERM EFFECTS ON TISSUE STRUCTURE AND FUNCTION IN THE ADULT THAT MAY PREDISPOSE TO GASTROINTESTINAL DISEASES. IN THIS STUDY WE AIMED TO INVESTIGATE HOW THE EPIGENETIC REGULATION OF DNA DEMETHYLATION OF THE P2X7R LOCUS GUIDED BY THE TRANSCRIPTION FACTOR GATA BINDING PROTEIN 1 (GATA1) IN SPINAL ASTROCYTES AFFECTS CHRONIC VISCERAL PAIN IN ADULT RATS WITH NEONATAL COLONIC INFLAMMATION (NCI). THE SPINAL GATA1 TARGETING TO DNA DEMETHYLATION OF P2X7R LOCUS IN THESE RATS WAS ASSESSED BY ASSESSING GATA1 FUNCTION WITH LUCIFERASE ASSAY, CHROMATIN IMMUNOPRECIPITATION, PATCH CLAMP, AND INTERFERENCE IN VITRO AND IN VIVO. IN ADDITION, A DECOY OLIGODEOXYNUCLEOTIDE WAS DESIGNED AND APPLIED TO DETERMINE THE INFLUENCE OF GATA1 ON THE DNA METHYLATION OF A P2X7R CPG ISLAND. WE SHOWED THAT NCI CAUSED THE INDUCTION OF GATA1, TEN-ELEVEN TRANSLOCATION 3 (TET3), AND PURINERGIC RECEPTORS (P2X7RS) IN ASTROCYTES OF THE SPINAL DORSAL HORN, AND DEMONSTRATED THAT INHIBITING THESE MOLECULES MARKEDLY INCREASED THE PAIN THRESHOLD, INHIBITED THE ACTIVATION OF ASTROCYTES, AND DECREASED THE SPINAL SEPSC FREQUENCY. NCI ALSO MARKEDLY DEMETHYLATED THE P2X7R LOCUS IN A MANNER DEPENDENT ON THE ENHANCEMENT OF BOTH A GATA1-TET3 PHYSICAL INTERACTION AND GATA1 BINDING AT THE P2X7R PROMOTER. IMPORTANTLY, WE SHOWED THAT DEMETHYLATION OF THE P2X7R LOCUS (AND THE ATTENDANT INCREASE IN P2X7R EXPRESSION) WAS REVERSED UPON KNOCKDOWN OF GATA1 OR TET3 EXPRESSION, AND DEMONSTRATED THAT A DECOY OLIGODEOXYNUCLEOTIDE THAT SELECTIVELY BLOCKED THE GATA1 BINDING SITE INCREASED THE METHYLATION OF A CPG ISLAND IN THE P2X7R PROMOTER. THESE RESULTS DEMONSTRATE THAT CHRONIC VISCERAL PAIN IS MEDIATED SYNERGISTICALLY BY GATA1 AND TET3 VIA A DNA-DEMETHYLATION MECHANISM THAT CONTROLS P2X7R TRANSCRIPTION IN SPINAL DORSAL HORN ASTROCYTES, AND PROVIDE A POTENTIAL THERAPEUTIC STRATEGY BY TARGETING GATA1 AND P2X7R LOCUS BINDING.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
4  3362  27 HISTONE LYSINE DEMETHYLASE KDM5B MAINTAINS CHRONIC MYELOID LEUKEMIA VIA MULTIPLE EPIGENETIC ACTIONS. THE HISTONE LYSINE DEMETHYLASE KDM5 FAMILY IS IMPLICATED IN NORMAL DEVELOPMENT AND STEM CELL MAINTENANCE BY EPIGENETIC MODULATION OF HISTONE METHYLATION STATUS. DEREGULATION OF THE KDM5 FAMILY HAS BEEN REPORTED IN VARIOUS TYPES OF CANCERS, INCLUDING HEMATOLOGICAL MALIGNANCIES. HOWEVER, THEIR TRANSCRIPTIONAL REGULATORY ROLES IN THE CONTEXT OF LEUKEMIA REMAIN UNCLEAR. HERE, WE FIND THAT KDM5B IS STRONGLY EXPRESSED IN NORMAL CD34(+) HEMATOPOIETIC STEM/PROGENITOR CELLS AND CHRONIC MYELOID LEUKEMIA (CML) CELLS. KNOCKDOWN OF KDM5B IN K562 CML CELLS REDUCED LEUKEMIA COLONY-FORMING POTENTIAL. TRANSCRIPTOME PROFILING OF KDM5B KNOCKDOWN K562 CELLS REVEALED THE DEREGULATION OF GENES INVOLVED IN MYELOID DIFFERENTIATION AND TOLL-LIKE RECEPTOR SIGNALING. THROUGH THE INTEGRATION OF TRANSCRIPTOME AND CHIP-SEQ PROFILING DATA, WE SHOW THAT KDM5B IS ENRICHED AT THE BINDING SITES OF THE GATA AND AP-1 TRANSCRIPTION FACTOR FAMILIES, SUGGESTING THEIR COLLABORATIONS IN THE REGULATION OF TRANSCRIPTION. EVEN THOUGH THE BINDING OF KDM5B SUBSTANTIALLY OVERLAPPED WITH H3K4ME1 OR H3K4ME3 MARK AT GENE PROMOTERS, ONLY A SMALL SUBSET OF THE KDM5B TARGETS SHOWED DIFFERENTIAL EXPRESSION IN ASSOCIATION WITH THE HISTONE DEMETHYLATION ACTIVITY. BY CHARACTERIZING THE INTERACTING PROTEINS IN K562 CELLS, WE DISCOVERED THAT KDM5B RECRUITS PROTEIN COMPLEXES INVOLVED IN THE MRNA PROCESSING MACHINERY, IMPLYING AN ALTERNATIVE EPIGENETIC ACTION MEDIATED BY KDM5B IN GENE REGULATION. OUR STUDY HIGHLIGHTS THE ONCOGENIC FUNCTIONS OF KDM5B IN CML CELLS AND SUGGESTS THAT KDM5B IS VITAL TO THE TRANSCRIPTIONAL REGULATION VIA MULTIPLE EPIGENETIC MECHANISMS.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
5  1798  54 EFFECT OF HELICOBACTER PYLORI INFECTION ON GATA-5 AND TFF1 REGULATION, COMPARISON BETWEEN PEDIATRIC AND ADULT PATIENTS. BACKGROUND: GATA FACTORS, WHICH CONSTITUTE A FAMILY OF TRANSCRIPTION REGULATORY PROTEINS, PARTICIPATE IN GASTROINTESTINAL DEVELOPMENT. TREFOIL FACTOR 1 (TFF1) PLAYS A CRUCIAL ROLE IN MUCOSAL DEFENSE AND HEALING, AND EVIDENCE SUGGESTS THAT GATA-5 MEDIATED ITS REGULATION. GASTRIC CANCER IS A MULTIPLE-STEP PROCESS TRIGGERED BY HELICOBACTER PYLORI AND IS CHARACTERIZED BY ACCUMULATION OF MOLECULAR AND EPIGENETIC ALTERATION. THE AIM OF THIS STUDY WAS TO EVALUATE THE EFFECT OF H. PYLORI INFECTION ON THE REGULATION OF GATA-5 AND TFF1 IN VITRO AND IN VIVO. RESULTS: INFECTED CELLS EXHIBITED UPREGULATION OF GATA-5 AND TFF1 AFTER 48 H. AN INCREASE IN GATA-5 AND TFF1 MRNA LEVELS WAS ALSO FOUND IN MICE SAMPLES AFTER 6 AND 12 MONTHS OF INFECTION, RESPECTIVELY. IN HUMAN SAMPLES, WE FOUND AN ASSOCIATION BETWEEN H. PYLORI INFECTION AND GATA-5 UPREGULATION. IN FACT, AMONG H. PYLORI-INFECTED PATIENTS, HYPERMETHYLATION WAS OBSERVED IN 45.5% OF PEDIATRIC SAMPLES, IN 62.6% OF CHRONIC GASTRITIS SAMPLES, AND IN 63% OF GASTRIC CANCER SAMPLES. REGARDING TFF1, THE EXPRESSION LEVELS WERE SIMILAR IN PEDIATRICS AND ADULTS PATIENTS, AND WERE INDEPENDENT OF H. PYLORI INFECTION, AND THE EXPRESSION OF THESE FACTORS WAS DOWNREGULATED IN GASTRIC CANCER SAMPLES. GATA-5 PROMOTER METHYLATION WAS ASSOCIATED WITH A DECREASE IN TFF1 MRNA LEVELS. CONCLUSIONS: OUR RESULTS SUGGEST THAT THE UPREGULATION OF GATA-5 AND TFF1 OBSERVED IN VITRO AND IN VIVO MAY BE CORRELATED WITH A PROTECTIVE EFFECT OF THE MUCOSA IN RESPONSE TO INFECTION. THE EPIGENETIC INACTIVATION OF GATA-5 OBSERVED IN HUMAN BIOPSIES FROM INFECTED PATIENTS MAY SUGGEST THAT THIS ALTERATION IS AN EARLY EVENT OCCURRING IN ASSOCIATION WITH H. PYLORI INFECTION.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
6  3231  34 HELICOBACTER PYLORI-INDUCED MODULATION OF THE PROMOTER METHYLATION OF WNT ANTAGONIST GENES IN GASTRIC CARCINOGENESIS. BACKGROUND: THIS STUDY AIMED TO INVESTIGATE THE CHANGES IN THE PROMOTER METHYLATION AND GENE EXPRESSION OF MULTIPLE WNT ANTAGONISTS BETWEEN THE CHRONIC INFECTION AND ERADICATION OF HELICOBACTER PYLORI (H. PYLORI) IN GASTRIC CARCINOGENESIS. METHODS: THE LEVELS OF METHYLATION AND CORRESPONDING MRNA EXPRESSION OF SEVEN WNT ANTAGONIST GENES (SFRP1, -2, -5, DKK1, -2, -3, WIF1) WERE COMPARED AMONG THE PATIENTS WITH H. PYLORI-POSITIVE GASTRIC CANCERS (GCS), AND H. PYLORI-POSITIVE AND H. PYLORI-NEGATIVE CONTROLS, BY QUANTITATIVE METHYLIGHT ASSAY AND REAL-TIME REVERSE TRANSCRIPTION (RT)-POLYMERASE CHAIN REACTION (PCR), RESPECTIVELY. THE CHANGES OF THE METHYLATION AND EXPRESSION LEVELS OF THE GENES WERE ALSO COMPARED BETWEEN THE H. PYLORI ERADICATION AND H. PYLORI-PERSISTENT GROUPS 1 YEAR AFTER ENDOSCOPIC RESECTION OF GCS. RESULTS: THE METHYLATION LEVELS OF SFRP AND DKK FAMILY GENES WERE SIGNIFICANTLY INCREASED IN THE PATIENTS WITH H. PYLORI-POSITIVE GCS AND FOLLOWED BY H. PYLORI-POSITIVE CONTROLS COMPARED WITH H. PYLORI-NEGATIVE CONTROLS (P < 0.001). SFRP1, -2, AND DKK3 GENE EXPRESSION WAS STEPWISE DOWNREGULATED FROM H. PYLORI-NEGATIVE CONTROLS, H. PYLORI-POSITIVE CONTROLS, AND TO H. PYLORI-POSITIVE GCS (P < 0.05). AMONG THE WNT ANTAGONISTS, ONLY THE DEGREES OF METHYLATION AND DOWNREGULATION OF DKK3 WERE SIGNIFICANTLY REDUCED AFTER H. PYLORI ERADICATION (P < 0.05). CONCLUSION: EPIGENETIC SILENCING OF SFRP AND DKK FAMILY GENES MAY FACILITATE THE FORMATION OF AN EPIGENETIC FIELD DURING H. PYLORI-ASSOCIATED GASTRIC CARCINOGENESIS. THE EPIGENETIC FIELD MAY NOT BE REVERSED EVEN AFTER H. PYLORI ERADICATION EXCEPT BY DKK3 METHYLATION.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
7  3877  21 KDM6A PROMOTES IMATINIB RESISTANCE THROUGH YY1-MEDIATED TRANSCRIPTIONAL UPREGULATION OF TRKA INDEPENDENTLY OF ITS DEMETHYLASE ACTIVITY IN CHRONIC MYELOGENOUS LEUKEMIA. RATIONALE: DESPITE LANDMARK THERAPY OF CHRONIC MYELOGENOUS LEUKEMIA (CML) WITH TYROSINE KINASE INHIBITORS (TKIS), DRUG RESISTANCE REMAINS PROBLEMATIC. CANCER PATHOGENESIS INVOLVES EPIGENETIC DYSREGULATION AND IN PARTICULAR, HISTONE LYSINE DEMETHYLASES (KDMS) HAVE BEEN IMPLICATED IN TKI RESISTANCE. WE SOUGHT TO IDENTIFY KDMS WITH ALTERED EXPRESSION IN CML AND DEFINE THEIR CONTRIBUTION TO IMATINIB RESISTANCE. METHODS: BIOINFORMATICS SCREENING COMPARED KDM EXPRESSION IN CML VERSUS NORMAL BONE MARROW WITH SHRNA KNOCKDOWN AND FLOW CYTOMETRY USED TO MEASURE EFFECTS ON IMATINIB-INDUCED APOPTOSIS IN K562 CELLS. TRANSCRIPTOMIC ANALYSES WERE PERFORMED AGAINST KDM6A CRISPR KNOCKOUT/SHRNA KNOCKDOWN K562 CELLS ALONG WITH GENE RESCUE EXPERIMENTS USING WILDTYPE AND MUTANT DEMETHYLASE-DEAD KDM6A CONSTRUCTS. CO-IMMUNOPRECIPITATION, LUCIFERASE REPORTER AND CHIP WERE EMPLOYED TO ELUCIDATE MECHANISMS OF KDM6A-DEPENDENT RESISTANCE. RESULTS: AMONGST FIVE KDMS UPREGULATED IN CML, ONLY KDM6A DEPLETION SENSITIZED CML CELLS TO IMATINIB-INDUCED APOPTOSIS. RE-INTRODUCTION OF DEMETHYLASE-DEAD KDM6A AS WELL AS WILD-TYPE KDM6A RESTORED IMATINIB RESISTANCE. RNA-SEQ IDENTIFIED NTRK1 GENE DOWNREGULATION AFTER DEPLETION OF KDM6A. MOREOVER, NTRK1 EXPRESSION POSITIVELY CORRELATED WITH KDM6A IN A SUBSET OF CLINICAL CML SAMPLES AND KDM6A KNOCKDOWN IN FRESH CML ISOLATES DECREASED NTRK1 ENCODED PROTEIN (TRKA) EXPRESSION. MECHANISTICALLY, KDM6A WAS RECRUITED TO THE NTRK1 PROMOTER BY THE TRANSCRIPTION FACTOR YY1 WITH SUBSEQUENT TRKA UPREGULATION ACTIVATING DOWN-STREAM SURVIVAL PATHWAYS TO INVOKE IMATINIB RESISTANCE. CONCLUSION: CONTRARY TO ITS REPORTED ROLE AS A TUMOR SUPPRESSOR AND INDEPENDENT OF ITS DEMETHYLASE FUNCTION, KDM6A PROMOTES IMATINIB-RESISTANCE IN CML CELLS. THE IDENTIFICATION OF THE KDM6A/YY1/TRKA AXIS AS A NOVEL IMATINIB-RESISTANCE MECHANISM REPRESENTS AN UNEXPLORED AVENUE TO OVERCOME TKI RESISTANCE IN CML.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
8  6069  27 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
9  5459  30 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
10  1483  25 DKK1 IS EPIGENETICALLY DOWNREGULATED BY PROMOTER METHYLATION AND INHIBITS BILE ACID-INDUCED GASTRIC INTESTINAL METAPLASIA. DICKKOPF-RELATED PROTEIN 1 (DKK1) IS ESSENTIAL TO GASTRIC CANCER AS AN INHIBITOR OF WNT SIGNALING. GASTRIC INTESTINAL METAPLASIA (GIM) IS AN IMPORTANT PRECANCEROUS LESION OF GASTRIC CANCER THAT CAN BE ACTIVATED BY BILE ACID REFLUX AND CHRONIC INFLAMMATION. HOWEVER, THE EXACT MECHANISM OF DKK1 IN BILE ACID-INDUCED GIM HAS NOT BEEN COMPLETELY ELUCIDATED. WE AIMED TO EXPLORE THE EPIGENETIC ALTERATIONS AND BIOLOGICAL FUNCTIONS OF DKK1 IN THE DEVELOPMENT OF GIM. IN THE PRESENT STUDY, BILE ACID WAS FOUND TO INDUCE THE EXPRESSION OF INTESTINAL MARKERS IN GASTRIC EPITHELIAL CELLS, WHEREAS DKK1 WAS DOWNREGULATED IN RESPONSE TO BILE ACID STIMULATION. THE MRNA AND PROTEIN EXPRESSION LEVELS OF DKK1 WERE DECREASED IN GIM TISSUES AS EVIDENCED BY QRT-PCR AND IMMUNOHISTOCHEMICAL STAINING. SURPRISINGLY, THE METHYLATION OF THE DKK1 PROMOTER INCREASED IN GIM TISSUES, AND WE DISCOVERED 28 DIFFERENTIAL METHYLATION SITES OF THE DKK1 PROMOTER IN GIM TISSUES. BILE ACID WAS ABLE TO INDUCE THE PARTIAL METHYLATION OF THE DKK1 PROMOTER, WHILE 5-AZA COULD INCREASE DKK1 EXPRESSION AS WELL AS DECREASE INTESTINAL MARKERS EXPRESSION IN GASTRIC EPITHELIAL CELLS. IN CONCLUSION, THE PROMOTER METHYLATION AND DOWNREGULATION OF DKK1 MIGHT PLAY IMPORTANT ROLES IN THE DEVELOPMENT OF GIM, ESPECIALLY BILE ACID-INDUCED GIM.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
11  6660  32 UPREGULATION OF CXCR4 THROUGH PROMOTER DEMETHYLATION CONTRIBUTES TO INFLAMMATORY HYPERALGESIA IN RATS. AIM AND METHODS: CHRONIC PAIN ASSOCIATED WITH INFLAMMATION IS A COMMON CLINICAL PROBLEM, AND THE UNDERLYING MECHANISMS YET ARE INCOMPLETELY DEFINED. DNA METHYLATION HAS BEEN IMPLICATED IN THE PATHOGENESIS OF CHRONIC PAIN. HOWEVER, THE SPECIFIC GENES REGULATED BY DNA METHYLATION UNDER INFLAMMATORY PAIN CONDITION REMAIN LARGELY UNKNOWN. HERE, WE INVESTIGATED HOW CHEMOKINE RECEPTOR CXCR4 EXPRESSION IS REGULATED BY DNA METHYLATION AND HOW IT CONTRIBUTES TO INFLAMMATORY PAIN INDUCED BY COMPLETE FREUND'S ADJUVANT (CFA) IN RATS. RESULTS: INTRAPLANTAR INJECTION OF CFA COULD NOT ONLY INDUCE SIGNIFICANT HYPERALGESIA IN RATS, BUT ALSO SIGNIFICANTLY INCREASE THE EXPRESSION OF CXCR4 MRNA AND PROTEIN IN THE DORSAL ROOT GANGLION (DRG). INTRATHECAL INJECTION OF CXCR4 ANTAGONIST AMD3100 SIGNIFICANTLY RELIEVED HYPERALGESIA IN INFLAMMATORY RATS IN A TIME- AND DOSE-DEPENDENT MANNER. BISULFITE SEQUENCING AND METHYLATION-SPECIFIC PCR DEMONSTRATE THAT CFA INJECTION LED TO A SIGNIFICANT DEMETHYLATION OF CPG ISLAND AT CXCR4 GENE PROMOTER. CONSISTENTLY, THE EXPRESSION OF DNMT3B WAS SIGNIFICANTLY DOWNREGULATED AFTER CFA INJECTION. ONLINE SOFTWARE PREDICTION REVEALS THREE BINDING SITES OF P65 IN THE CPG ISLAND OF CXCR4 GENE PROMOTER, WHICH HAS CONFIRMED BY THE CHROMATIN IMMUNOPRECIPITATION ASSAY, CFA TREATMENT SIGNIFICANTLY INCREASES THE RECRUITMENT OF P65 TO CXCR4 GENE PROMOTER. INHIBITION OF NF-KB SIGNALING USING P65 INHIBITOR PYRROLIDINE DITHIOCARBAMATE SIGNIFICANTLY PREVENTED THE INCREASES OF THE CXCR4 EXPRESSION. CONCLUSION: UPREGULATION OF CXCR4 EXPRESSION DUE TO PROMOTER DEMETHYLATION FOLLOWED BY INCREASED RECRUITMENT OF P65 TO PROMOTER OF CXCR4 GENE CONTRIBUTES TO INFLAMMATORY HYPERALGESIA. THESE FINDINGS PROVIDE A THEORETICAL BASIS FOR THE TREATMENT OF CHRONIC PAIN FROM AN EPIGENETIC PERSPECTIVE.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
12  3227  39 HELICOBACTER PYLORI INFECTION-INDUCED H3SER10 PHOSPHORYLATION IN STEPWISE GASTRIC CARCINOGENESIS AND ITS CLINICAL IMPLICATIONS. BACKGROUND: OUR PREVIOUS WORKS HAVE DEMONSTRATED THAT HELICOBACTER PYLORI (HP) INFECTION CAN ALTER HISTONE H3 SERINE 10 PHOSPHORYLATION STATUS IN GASTRIC EPITHELIAL CELLS. HOWEVER, WHETHER HELICOBACTER PYLORI-INDUCED HISTONE H3 SERINE 10 PHOSPHORYLATION PARTICIPATES IN GASTRIC CARCINOGENESIS IS UNKNOWN. WE INVESTIGATE THE EXPRESSION OF HISTONE H3 SERINE 10 PHOSPHORYLATION IN VARIOUS STAGES OF GASTRIC DISEASE AND EXPLORE ITS CLINICAL IMPLICATION. MATERIALS AND METHODS: STOMACH BIOPSY SAMPLES FROM 129 PATIENTS WERE COLLECTED AND STAINED WITH HISTONE H3 SERINE 10 PHOSPHORYLATION, KI67, AND HELICOBACTER PYLORI BY IMMUNOHISTOCHEMISTRY STAINING, EXPRESSED AS LABELING INDEX. THEY WERE CATEGORIZED INTO NONATROPHIC GASTRITIS, CHRONIC ATROPHIC GASTRITIS, INTESTINAL METAPLASIA, LOW-GRADE INTRAEPITHELIAL NEOPLASIA, HIGH-GRADE INTRAEPITHELIAL NEOPLASIA, AND INTESTINAL-TYPE GASTRIC CANCER GROUPS. HELICOBACTER PYLORI INFECTION WAS DETERMINED BY EITHER (13) C-UREA BREATH TEST OR IMMUNOHISTOCHEMISTRY STAINING. RESULTS: IN HELICOBACTER PYLORI-NEGATIVE PATIENTS, LABELING INDEX OF HISTONE H3 SERINE 10 PHOSPHORYLATION WAS GRADUALLY INCREASED IN NONATROPHIC GASTRITIS, CHRONIC ATROPHIC GASTRITIS, INTESTINAL METAPLASIA GROUPS, PEAKED AT LOW-GRADE INTRAEPITHELIAL NEOPLASIA, AND DECLINED IN HIGH-GRADE INTRAEPITHELIAL NEOPLASIA AND GASTRIC CANCER GROUPS. IN HELICOBACTER PYLORI-INFECTED PATIENTS, LABELING INDEX OF HISTONE H3 SERINE 10 PHOSPHORYLATION FOLLOWED THE SIMILAR PATTERN AS ABOVE, WITH INCREASED EXPRESSION OVER THE CORRESPONDING HELICOBACTER PYLORI-NEGATIVE CONTROLS EXCEPT IN NONATROPHIC GASTRITIS PATIENT WHOSE LABELING INDEX WAS DECREASED WHEN COMPARED WITH HELICOBACTER PYLORI-NEGATIVE CONTROL. LABELING INDEX OF KI67 IN HELICOBACTER PYLORI-NEGATIVE GROUPS WAS HIGHER IN GASTRIC CANCER THAN CHRONIC ATROPHIC GASTRITIS AND LOW-GRADE INTRAEPITHELIAL NEOPLASIA GROUPS, AND HIGHER IN INTESTINAL METAPLASIA GROUP COMPARED WITH CHRONIC ATROPHIC GASTRITIS GROUP. IN HELICOBACTER PYLORI-POSITIVE GROUPS, KI67 LABELING INDEX WAS INCREASED STEPWISE FROM NONATROPHIC GASTRITIS TO GASTRIC CANCER EXCEPT SLIGHTLY DECREASE IN CHRONIC ATROPHIC GASTRITIS GROUP. IN ADDITION, WE NOTED THAT HISTONE H3 SERINE 10 PHOSPHORYLATION STAINING IS ACCOMPANIED WITH ITS LOCATION CHANGES FROM GASTRIC GLAND BOTTOM EXPANDED TO WHOLE GLAND AS DISEASE STAGE PROGRESS. CONCLUSIONS: THESE RESULTS INDICATE THAT STEPWISE GASTRIC CARCINOGENESIS IS ASSOCIATED WITH ALTERED HISTONE H3 SERINE 10 PHOSPHORYLATION, HELICOBACTER PYLORI INFECTION ENHANCES HISTONE H3 SERINE 10 PHOSPHORYLATION EXPRESSION IN THESE PROCESSES; IT IS ALSO ACCOMPANIED WITH HISTONE H3 SERINE 10 PHOSPHORYLATION LOCATION CHANGE FROM GLAND BOTTOM STAINING EXPAND TO WHOLE GLAND EXPRESSION. THE RESULTS SUGGEST THAT EPIGENETIC DYSREGULATION MAY PLAY IMPORTANT ROLES IN HELICOBACTER PYLORI-INDUCED GASTRIC CANCER.	2018	

13  6756  27 WNT ANTAGONIST, SFRP1, IS HEDGEHOG SIGNALING TARGET. HEDGEHOG AND WNT SIGNALING PATHWAYS NETWORK TOGETHER DURING EMBRYOGENESIS AND CARCINOGENESIS. HEDGEHOG SIGNALING IN INTESTINAL EPITHELIUM REPRESSES CANONICAL WNT SIGNALING TO RESTRICT EXPRESSION OF WNT TARGET GENES TO STEM OR PROGENITOR CELLS; HOWEVER, THE MECHANISM REMAINS UNCLEAR. THE HEDGEHOG SIGNAL IS TRANSDUCED TO GLI FAMILY TRANSCRIPTION FACTORS THOUGH PATCHED RECEPTOR, SMOOTHENED SIGNAL TRANSDUCER, AND OTHER SIGNALING COMPONENTS, SUCH AS KIF27, KIF7, STK36, SUFU, AND DZIP1. HERE, WE SEARCHED FOR THE GLI-BINDING SITE WITHIN THE PROMOTER REGION OF GENES ENCODING SECRETED-TYPE WNT SIGNAL INHIBITORS, INCLUDING SFRP1, SFRP2, SFRP3, SFRP4, SFRP5, DKK1, DKK2, DKK3, DKK4, AND WIF1. THE GLI-BINDING SITE WAS IDENTIFIED WITHIN THE HUMAN SFRP1 PROMOTER BASED ON BIOINFORMATICS AND HUMAN INTELLIGENCE. THE CHIMPANZEE SFRP1 GENE WAS IDENTIFIED WITHIN THE NW_110515.1 GENOME SEQUENCE. THE GLI-BINDING SITE OF THE HUMAN SFRP1 PROMOTER WAS CONSERVED IN CHIMPANZEE SFRP1, MOUSE SFRP1, AND RAT SFRP1 PROMOTERS. SFRP1 IS THE EVOLUTIONARILY CONSERVED TARGET OF THE HEDGEHOG-GLI SIGNALING PATHWAY. EXPRESSION DOMAIN ANALYSES BASED ON TEXT MINING REVEALED THAT INDIAN HEDGEHOG (IHH), SFRP1, AND WNT6 ARE EXPRESSED IN DIFFERENTIATED INTESTINAL EPITHELIAL CELLS, MESENCHYMAL CELLS, AND STEM/PROGENITOR CELLS, RESPECTIVELY. HEDGEHOG IS SECRETED FROM DIFFERENTIATED EPITHELIAL CELLS TO INDUCE SFRP1 EXPRESSION IN MESENCHYMAL CELLS, WHICH KEEPS DIFFERENTIATED EPITHELIAL CELLS AWAY FROM THE EFFECTS OF CANONICAL WNT SIGNALING. THESE FACTS INDICATE THAT SFRP1 IS THE HEDGEHOG TARGET TO CONFINE CANONICAL WNT SIGNALING WITHIN STEM OR PROGENITOR CELLS. THEREFORE, EPIGENETIC CPG HYPERMETHYLATION OF THE SFRP1 PROMOTER DURING CHRONIC PERSISTENT INFLAMMATION AND AGING LEADS TO THE OCCURRENCE OF GASTROINTESTINAL CANCERS, SUCH AS COLORECTAL CANCER AND GASTRIC CANCER, THROUGH THE BREAKDOWN OF HEDGEHOG-DEPENDENT WNT SIGNAL INHIBITION.	2006	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
14  2366  31 EPIGENETIC REGULATION OF STEROIDOGENIC ENZYMES EXPRESSED IN PERIPHERAL BLOOD MONONUCLEAR CELLS FROM HEALTHY INDIVIDUALS AND FROM PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA. SEX HORMONE SYNTHESIS OCCURS IN VARIOUS ORGANS AND TISSUES BESIDES THE GONADS, SUCH AS ADRENAL GLANDS, BRAIN, INTESTINES, SKIN, FAT, BONE, AND CELLS OF THE IMMUNE SYSTEM. REGARDING THE LATTER, IT IS STILL NOT CLEAR WHICH PATHWAYS ARE ACTIVE, AND IF THEY ARE MODIFIED IN CASE OF ILLNESS OF THE IMMUNE SYSTEM. OUR GOAL IN THIS STUDY WAS TO DETERMINE MRNA EXPRESSION OF DIFFERENT STEROIDOGENIC ENZYMES IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) FROM HEALTHY INDIVIDUALS OF BOTH SEXES AND OF DIFFERENT AGES, AND THEN TO COMPARE THEIR EXPRESSION BETWEEN HEALTHY INDIVIDUALS AND PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). FURTHERMORE, TO ELUCIDATE POSSIBLE MECHANISMS THAT REGULATE ENZYME EXPRESSION, WE ANALYZED EPIGENETIC EVENTS LIKE PROMOTER METHYLATION. WE DETERMINED THAT NORMAL CELLS OF THE IMMUNE SYSTEM, REGARDLESS OF SEX AND AGE, EXPRESSED P450 SIDE CHAIN CLEAVAGE (P450SCC), CYTOCHROME P450 17ALPHA-HYDROXYLASE/C17,20-LYASE (P45017ALPHA), 3BETA-HYDROXYSTEROID DEHYDROGENASE/DELTA5-DELTA4-ISOMERASE (3BETA-HSD), STEROID 5 ALPHA REDUCTASE (5ALPHA-R) TYPES 1, 2 AND 3, 3ALPHA-HYDROXYSTEROID DEHYDROGENASE (3ALPHA-HSD) TYPE 3, AND 17BETA-HYDROXYSTEROID DEHYDROGENASE (17BETA-HSD) TYPES 1, 3 AND 5. WE ALSO ESTABLISHED THAT 5ALPHA-R 1, 5ALPHA-R 3, 3ALPHA-HSD 3, 17BETA-HSD 1 AND 17BETA-HSD 5 EXPRESSION WAS ALTERED IN CLL PATIENTS, AND THAT PROMOTER REGIONS OF 5ALPHA-R 1, 17BETA-HSD 1 AND 17BETA-HSD 5 WERE DIFERENTIALLY METHYLATED. THESE RESULTS SUGGEST THAT STEROIDOGENIC PATHWAYS MAY BE AFFECTED IN CLL CELLS, AND THIS COULD BE RELATED TO DISEASE PATHOGENESIS.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
15  1620  25 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
16  5458  26 RESEARCH ON EPIGENETIC MECHANISM OF SFRP2 IN ADVANCED CHRONIC MYELOID LEUKEMIA. SECRETED FRIZZLED-RELATED PROTEIN 2 (SFRP2) HAS BEEN REPORTED TO ACT AS A TUMOR SUPPRESSORS. THIS STUDY AIMS TO DETECT THE BIOLOGICAL ROLE OF SFRP2 IN ADVANCED CHRONIC MYELOID LEUKEMIA (CML). IN THIS STUDY WE EXAMINED BONE MARROW SAMPLES FROM 45 CML PATIENTS AND 10 HEALTHY DONORS. K562 AND KCL22 CELLS WERE CULTURED AND TREATED WITH DEMETHYLATION DRUG AND HISTONE DEACETYLASE INHIBITOR (HDACI). KCL22 AND K562 CELLS WERE TRANSFECTED WITH LENTIVIRAL VECTOR (LV)-SFRP2, LV-CONTROL. THE CELLS WERE THEN SUBJECTED TO PROLIFERATION AND APOPTOSIS ASSAYS, REAL TIME POLYMERASE CHAIN REACTION (PCR), METHYLATION-SPECIFIC PCR (MSP), WESTERN BLOTTING, CO-IMMUNOPRECIPITATION (COIP) AND CHROMATIN IMMUNOPRECIPITATION (CHIP), WE FOUND THAT SFRP2 WAS DOWN-REGULATED IN THE ACCELERATED AND BLAST PHASE OF CML, WHEREAS, THE LEVELS OF WNT1, WNT3 AND WNT5A WERE UP-REGULATED IN THE ACCELERATED AND BLAST PHASE OF CML. OVEREXPRESSION SFRP2 INHIBITED PROLIFERATION, PROMOTED APOPTOSIS AND ACTIVATED THE WNT PATHWAY. COIP-MS RESULTS SHOWED THAT SFRP2 INTERACTED WITH WNT1 AND WNT5A. CHIP-SEQ RESULT INDICATED THAT THE PROMOTER OF H3K4ME3 AND H3K27ME3 WERE ABLE TO INTERACT WITH SFRP2. IN CONCLUSION, OUR FINDINGS DEMONSTRATED THE SFRP2 ACT AS A POTENTIAL THERAPEUTIC TARGET FOR ADVANCED CML. FURTHERMORE, OUR RESULTS SUPPORT THE USE OF DEMETHYLATION DRUGS AND HDACI AS A POTENTIAL CML TREATMENT STRATEGY.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
17  2374  43 EPIGENETIC REGULATION OF TNFA EXPRESSION IN PERIODONTAL DISEASE. BACKGROUND: TUMOR NECROSIS FACTOR-ALPHA (TNF-ALPHA) PLAYS A CENTRAL ROLE IN THE MOLECULAR PATHOGENESIS OF PERIODONTAL DISEASE. HOWEVER, THE EPIGENETIC REGULATION ATTRIBUTABLE TO MICROBIAL AND INFLAMMATORY SIGNALS AT THE BIOFILM-GINGIVAL INTERFACE ARE POORLY UNDERSTOOD. IN THIS STUDY, THE DNA METHYLATION ALTERATION WITHIN THE TNFA PROMOTER IN HUMAN GINGIVAL BIOPSIES FROM DIFFERENT STAGES OF PERIODONTAL DISEASE IS INVESTIGATED AND THE REGULATORY MECHANISM OF TNFA TRANSCRIPTION BY DNA METHYLATION IS EXPLORED. METHODS: GINGIVAL BIOPSIES WERE OBTAINED FROM 17 PATIENTS WITH CHRONIC PERIODONTITIS (CP) AND 18 PERIODONTALLY HEALTHY INDIVIDUALS. ANOTHER 11 INDIVIDUALS PARTICIPATED IN AN EXPERIMENTALLY INDUCED GINGIVITIS STUDY, AND GINGIVAL BIOPSIES WERE COLLECTED AT THE BASELINE, INDUCTION, AND RESOLUTION PHASE. TO CONFIRM THAT TNFA PROMOTER METHYLATION MODULATED TNFA TRANSCRIPTION, THP.1 CELLS WERE TREATED WITH A DNA METHYLTRANSFERASE INHIBITOR, 5-AZA-2-DEOXYCYTIDINE (5-AZA-2DC), AND AN RAW294.7 CELL LINE TRANSFECTED WITH A TNFA PROMOTER-SPECIFIC LUCIFERASE REPORTER SYSTEM WITH OR WITHOUT METHYLATION WAS USED. RESULTS: IN GINGIVAL BIOPSIES FROM INDIVIDUALS WITH SEVERE CP, TWO INDIVIDUAL CYTOSINE-GUANINE DINUCLEOTIDES (CPG SITES) WITHIN THE TNFA PROMOTER (AT -163 AND -161 BP) DISPLAYED INCREASED METHYLATION IN CP SAMPLES COMPARED TO THOSE WITH GINGIVAL HEALTH (16.1% +/- 5.1% VERSUS 11.0% +/- 4.6%, P = 0.02 AND 19.8% +/- 4.1% VERSUS 15.4% +/- 3.6%, P = 0.04, RESPECTIVELY). THE METHYLATION LEVEL AT -163 BP WAS INVERSELY ASSOCIATED WITH THE TRANSCRIPTION LEVEL OF TNFA (P = 0.018). HOWEVER, NO SIGNIFICANT DIFFERENCE IN THE TNFA PROMOTER METHYLATION PATTERN WAS OBSERVED IN SAMPLES BIOPSIED DURING THE INDUCTION OR RESOLUTION PHASE OF EXPERIMENTALLY INDUCED GINGIVITIS, WHICH REPRESENTED A REVERSIBLE PERIODONTAL LESION. THP.1 CELLS TREATED WITH 5-AZA-2DC DEMONSTRATED A TIME-DEPENDENT INCREASE IN TNFA MESSENGER LEVEL. IT WAS ALSO FOUND THAT THE LUCIFERASE ACTIVITY DECREASED 2.6-FOLD IN A CONSTRUCT CONTAINING AN IN VITRO METHYLATED TNFA PROMOTER WHEN COMPARED TO THE UNMETHYLATED INSERT (P = 0.03). CONCLUSION: ALTHOUGH THE BIOPSY SAMPLES REPRESENTED A MIXED CELL POPULATION, THE CHANGE IN PROMOTER METHYLATION STATUS IN CHRONIC PERIODONTAL DISEASE SUGGESTED THAT DNA METHYLATION MAY BE AN IMPORTANT REGULATORY MECHANISM IN CONTROLLING TNFA TRANSCRIPTIONAL EXPRESSION IN PERIODONTAL DISEASE.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
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  2326  24 EPIGENETIC REGULATION OF HOTAIR IN ADVANCED CHRONIC MYELOID LEUKEMIA. PURPOSE: CHRONIC MYELOID LEUKEMIA (CML) ACCOUNTS FOR ~10% OF LEUKEMIA CASES, AND ITS PROGRESSION INVOLVES EPIGENETIC GENE REGULATION. THIS STUDY INVESTIGATED EPIGENETIC REGULATION OF HOTAIR AND ITS TARGET MICRORNA, MIR-143, IN ADVANCED CML. PATIENTS AND METHODS: WE FIRST ISOLATED BONE MARROW MONONUCLEAR CELLS FROM 70 PATIENTS WITH DIFFERENT PHASES OF CML AND FROM HEALTHY DONORS AS NORMAL CONTROL; WE ALSO CULTURED K562 AND KCL22 CELLS, TREATED WITH DEMETHYLATION DRUG; MTT ASSAY, FLOW CYTOMETRY, QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION (QPCR), METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (MSP), WESTERN BLOT, LUCIFERASE ASSAY, RNA PULL-DOWN ASSAY AND RNA-BINDING PROTEIN IMMUNOPRECIPITATION (RIP) ASSAY WERE PERFORMED. RESULT: AS MEASURED BY QPCR, HOTAIR EXPRESSION IN K562 CELLS, KCL22 CELLS, AND SAMPLES FROM CASES OF ADVANCED-STAGE CML INCREASED WITH LEVELS OF SEVERAL DNA METHYLTRANSFERASES AND HISTONE DEACETYLATES, INCLUDING DNMT1, DNMT3A, HDAC1, EZH2, AND LSD1, AND MIR-143 LEVELS WERE DECREASED AND HOTAIR LEVELS WERE INCREASED. TREATMENT WITH 5-AZACYTIDINE, A DNA METHYLATION INHIBITOR, DECREASED DNMT1, DNMT3A, HDAC1, EZH2, LSD1 MRNA, PROTEIN LEVELS, AND HOTAIR MRNA LEVELS BUT INCREASED MIR-143 LEVELS. HOTAIR KNOCKDOWN AND MIR-143 OVEREXPRESSION BOTH INHIBITED PROLIFERATION AND PROMOTED APOPTOSIS IN KCL22 AND K562 CELLS THROUGH THE PI3K/AKT PATHWAY. RNA PULL-DOWN, MASS SPECTROMETRY, AND RIP ASSAYS SHOWED THAT HOTAIR INTERACTED WITH EZH2 AND LSD1. A DUAL-LUCIFERASE ASSAY DEMONSTRATED THAT HOTAIR INTERACTED WITH MIR-143. CONCLUSION: OUR FINDINGS DEMONSTRATE THE KEY EPIGENETIC INTERACTIONS OF HOTAIR RELATED TO CML PROGRESSION AND SUGGEST HOTAIR AS A POTENTIAL THERAPEUTIC TARGET FOR ADVANCED CML. FURTHERMORE, OUR RESULTS SUPPORT THE USE OF DEMETHYLATION DRUGS AS A CML TREATMENT STRATEGY.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
20  2379  27 EPIGENETIC REGULATION OF WNT PATHWAY ANTAGONISTS IN HUMAN GLIOBLASTOMA MULTIFORME. EPIGENETIC INACTIVATION OF TUMOR SUPPRESSOR GENES IS COMMON IN HUMAN CANCER. USING A LARGE-SCALE WHOLE-GENOME APPROACH IN AN EARLIER STUDY, THE AUTHORS IDENTIFIED EPIGENETICALLY SILENCED GENES WITH POTENTIAL TUMOR SUPPRESSOR FUNCTION IN GLIOBLASTOMA (GBM). THREE GENES IDENTIFIED IN THIS ANALYSIS-DKK1, SFRP1, AND WIF1-ARE POTENT INHIBITORS OF THE WNT SIGNAL TRANSDUCTION PATHWAY. HERE, THE AUTHORS CONFIRM DECREASED EXPRESSION OF THESE GENES IN GBM TUMOR TISSUE SAMPLES RELATIVE TO NONTUMOR BRAIN TISSUE SAMPLES USING REAL-TIME PCR. THEY THEN SHOW THAT EXPRESSION OF ALL 3 GENES IS RESTORED IN T98 GBM CELLS BY TREATMENT WITH THE HISTONE DEACETYLASE INHIBITOR TRICHOSTATIN A (TSA), BUT ONLY DKK1 EXPRESSION IS RESTORED BY TREATMENT WITH THE DEMETHYLATING AGENT 5-AZACYTIDINE. BISULFITE SEQUENCING DID NOT REVEAL SIGNIFICANT METHYLATION IN THE PROMOTER REGION OF DKK1, WHEREAS HISTONE ACETYLATION AND CHROMATIN ACCESSIBILITY INCREASED SIGNIFICANTLY FOR ALL 3 GENES AFTER TSA TREATMENT. ECTOPIC EXPRESSION OF DKK1 SIGNIFICANTLY REDUCES COLONY FORMATION AND INCREASES CHEMOTHERAPY-INDUCED APOPTOSIS IN T98 CELLS. ECTOPIC EXPRESSION OF THE CANONICAL WNT PATHWAY INHIBITORS WIF1 AND SFRP1 SHOWS A RELATIVE LACK OF RESPONSE. CHRONIC WNT3A STIMULATION ONLY PARTIALLY REVERSES GROWTH SUPPRESSION AFTER DKK1 REEXPRESSION, WHEREAS A SPECIFIC INHIBITOR OF THE JNK PATHWAY SIGNIFICANTLY REVERSES THE EFFECT OF DKK1 REEXPRESSION ON COLONY FORMATION AND APOPTOSIS IN T98 CELLS. THESE RESULTS SUPPORT A POTENTIAL GROWTH-SUPPRESSIVE FUNCTION FOR EPIGENETICALLY SILENCED DKK1 IN GBM AND SUGGEST THAT DKK1 RESTORATION COULD MODULATE WNT SIGNALING THROUGH BOTH CANONICAL AND NONCANONICAL PATHWAYS.	2010