1 2973 155 GENETIC AND EPIGENETIC STUDIES OF ATOPIC DERMATITIS. BACKGROUND: ATOPIC DERMATITIS (AD) IS A CHRONIC INFLAMMATORY DISEASE CAUSED BY THE COMPLEX INTERACTION OF GENETIC, IMMUNE AND ENVIRONMENTAL FACTORS. THERE HAVE MANY RECENT DISCOVERIES INVOLVING THE GENETIC AND EPIGENETIC STUDIES OF AD. METHODS: A RETROSPECTIVE PUBMED SEARCH WAS CARRIED OUT FROM JUNE 2009 TO JUNE 2016 USING THE TERMS "ATOPIC DERMATITIS", "ASSOCIATION", "ECZEMA", "GENE", "POLYMORPHISM", "MUTATION", "VARIANT", "GENOME WIDE ASSOCIATION STUDY", "MICROARRAY" "GENE PROFILING", "RNA SEQUENCING", "EPIGENETICS" AND "MICRORNA". A TOTAL OF 132 PUBLICATIONS IN ENGLISH WERE IDENTIFIED. RESULTS: TO ELUCIDATE THE GENETIC FACTORS FOR AD PATHOGENESIS, CANDIDATE GENE ASSOCIATION STUDIES, GENOME-WIDE ASSOCIATION STUDIES (GWAS) AND TRANSCRIPTOMIC PROFILING ASSAYS HAVE BEEN PERFORMED IN THIS PERIOD. EPIGENETIC MECHANISMS FOR AD DEVELOPMENT, INCLUDING GENOMIC DNA MODIFICATION AND MICRORNA POSTTRANSCRIPTIONAL REGULATION, HAVE BEEN EXPLORED. TO DATE, CANDIDATE GENE ASSOCIATION STUDIES INDICATE THAT FILAGGRIN (FLG) NULL GENE MUTATIONS ARE THE MOST SIGNIFICANT KNOWN RISK FACTOR FOR AD, AND GENES IN THE TYPE 2 T HELPER LYMPHOCYTE (TH2) SIGNALING PATHWAYS ARE THE SECOND REPLICATED GENETIC RISK FACTOR FOR AD. GWAS STUDIES IDENTIFIED 34 RISK LOCI FOR AD, THESE LOCI ALSO SUGGEST THAT GENES IN IMMUNE RESPONSES AND EPIDERMAL SKIN BARRIER FUNCTIONS ARE ASSOCIATED WITH AD. ADDITIONALLY, GENE PROFILING ASSAYS DEMONSTRATED AD IS ASSOCIATED WITH DECREASED GENE EXPRESSION OF EPIDERMAL DIFFERENTIATION COMPLEX GENES AND ELEVATED TH2 AND TH17 GENES. HYPOMETHYLATION OF TSLP AND FCER1G IN AD WERE REPORTED; AND MIR-155, WHICH TARGET THE IMMUNE SUPPRESSOR CTLA-4, WAS FOUND TO BE SIGNIFICANTLY OVER-EXPRESSED IN INFILTRATING T CELLS IN AD SKIN LESIONS. CONCLUSIONS: THE RESULTS SUGGEST THAT TWO MAJOR BIOLOGIC PATHWAYS ARE RESPONSIBLE FOR AD ETIOLOGY: SKIN EPITHELIAL FUNCTION AND INNATE/ADAPTIVE IMMUNE RESPONSES. THE DYSFUNCTIONAL EPIDERMAL BARRIER AND IMMUNE RESPONSES RECIPROCALLY AFFECT EACH OTHER, AND THEREBY DRIVE DEVELOPMENT OF AD. 2016 2 6158 66 THE GENETICS AND EPIGENETICS OF ATOPIC DERMATITIS-FILAGGRIN AND OTHER POLYMORPHISMS. ATOPIC DERMATITIS (AD) IS A CHRONIC INFLAMMATORY SKIN DISEASE CAUSED BY A COMBINATION OF GENETIC AND ENVIRONMENTAL FACTORS. GENETIC EVIDENCES DEPICT A COMPLEX NETWORK COMPRISING BY EPIDERMAL BARRIER DYSFUNCTIONS AND DYSREGULATION OF INNATE AND ADAPTIVE IMMUNITY IN THE PATHOGENESIS OF AD. MUTATIONS IN THE HUMAN FILAGGRIN GENE (FLG) ARE THE MOST SIGNIFICANT AND WELL-REPLICATED GENETIC MUTATION ASSOCIATED WITH AD, AND OTHER MUTATIONS ASSOCIATED WITH EPIDERMAL BARRIERS SUCH AS SPINK5, FLG-2, SPRR3, AND CLDN1 HAVE ALL BEEN LINKED TO AD. GENE VARIANTS MAY ALSO CONTRIBUTE TO THE ABNORMAL INNATE AND ADAPTIVE RESPONSES FOUND IN AD, INCLUDING MUTATIONS IN PRRS AND AMPS, TSLP AND TSLPR, IL-1 FAMILY CYTOKINES AND RECEPTORS GENES, VITAMIN D PATHWAY GENES, FCER1A, AND TH2 AND OTHER CYTOKINES GENES. GWAS AND IMMUNOCHIP ANALYSIS HAVE IDENTIFIED A TOTAL OF 19 SUSCEPTIBILITY LOCI FOR AD. CANDIDATE GENES AT THESE SUSCEPTIBILITY LOCI IDENTIFIED BY GWAS AND IMMUNOCHIP ANALYSIS ALSO SUGGEST ROLES FOR EPIDERMAL BARRIER FUNCTIONS, INNATE AND ADAPTIVE IMMUNITY, INTERLEUKIN-1 FAMILY SIGNALING, REGULATORY T CELLS, THE VITAMIN D PATHWAY, AND THE NERVE GROWTH FACTOR PATHWAY IN THE PATHOGENESIS OF AD. INCREASING EVIDENCES SHOW THE MODERN LIFESTYLE (I.E., THE HYGIENE HYPOTHESIS, WESTERN DIET) AND OTHER ENVIRONMENTAL FACTORS SUCH AS POLLUTION AND ENVIRONMENTAL TOBACCO SMOKE (ETS) LEAD TO THE INCREASING PREVALENCE OF AD WITH THE DEVELOPMENT OF INDUSTRIALIZATION. EPIGENETIC ALTERATIONS IN RESPONSE TO THESE ENVIRONMENTAL FACTORS, INCLUDING DNA METHYLATION AND MICRORNA RELATED TO IMMUNE SYSTEM AND SKIN BARRIERS, HAVE BEEN FOUND TO CONTRIBUTE TO THE PATHOGENESIS OF AD. GENETIC VARIANTS AND EPIGENETIC ALTERATION MIGHT BE THE KEY TOOLS FOR THE MOLECULAR TAXONOMY OF AD AND PROVIDE THE BACKGROUND FOR THE PERSONALIZED MANAGEMENT. 2016 3 2797 31 FCER1G GENE HYPOMETHYLATION IN PATIENTS WITH RHEUMATOID ARTHRITIS. RHEUMATOID ARTHRITIS (RA) IS A CHRONIC AUTOIMMUNE DISEASE THAT, WHEN IMPROPERLY TREATED, LEADS TO DISABILITY IN PATIENTS. VARIOUS FACTORS THAT MAY CAUSE THE DEVELOPMENT AND ACTIVITY OF RA ARE BEING CONSIDERED. EPIGENETIC FACTORS ARE ALSO RECEIVING INCREASING ATTENTION. IN OUR STUDY, WE ANALYZED THE ASSOCIATION BETWEEN FCER1G GENE METHYLATION AND RA ACTIVITY. WE CONDUCTED OUR STUDY IN 50 RA PATIENTS AND 24 CONTROLS. THE PATIENTS WERE DIVIDED INTO TWO GROUPS IN TERMS OF HIGH DISEASE ACTIVITY AND REMISSION. QUANTITATIVE REAL-TIME METHYLATION-SPECIFIC PCR WAS USED TO ANALYZE THE METHYLATION STATUS OF THE INVESTIGATED GENES. WE OBSERVED THAT RA PATIENTS HAVE LOWER LEVELS OF METHYLATION OF THE FCER1G GENE COMPARED TO CONTROLS, BUT WE DID NOT FIND ANY DIFFERENCE IN THE METHYLATION STATUS OF THIS GENE BETWEEN PATIENTS WITH HIGH DISEASE ACTIVITY AND REMISSION. THE RESULTS OF THIS STUDY SUGGEST THAT FCER1G GENE METHYLATION MAY BE A NEW POTENTIAL EPIGENETIC MARKER OF RA THAT IS INDEPENDENT OF DISEASE ACTIVITY. 2022 4 5116 21 POSITIVE REGULATION OF HUMAN TELOMERASE REVERSE TRANSCRIPTASE GENE EXPRESSION AND TELOMERASE ACTIVITY BY DNA METHYLATION IN PANCREATIC CANCER. AIM: WE SOUGHT TO DETERMINE THE ROLE OF TELOMERASE AND ITS CATALYTIC SUBUNIT HTERT IN PANCREATIC CANCER AND EVALUATE THE EPIGENETIC REGULATION OF HTERT BY PROMOTER METHYLATION. METHODS: THIRTY PAIRED SAMPLES OF PANCREATIC DUCTAL ADENOCARCINOMAS AND ADJACENT NORMAL TISSUE AND 12 CHRONIC PANCREATITIS SAMPLES WERE STUDIED. REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION, TELOMERIC REPEAT AMPLIFICATION PROTOCOL ASSAY, AND METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION WERE PERFORMED TO ANALYZE HTERT EXPRESSION, TELOMERASE ACTIVITY, AND METHYLATION STATUS OF GENE PROMOTERS, RESPECTIVELY. RESULT: HTERT AND TELOMERASE ACTIVITY WERE UPREGULATED IN PANCREATIC CANCER COMPARED WITH PAIRED NORMAL TISSUES AND SAMPLES OF PANCREATITIS. HTERT EXPRESSION CORRELATED WITH TELOMERASE ACTIVITY (P \ .05) AND IN TURN CORRELATED POSITIVELY WITH HTERT PROMOTER METHYLATION (P \ .001) AND P16 PROMOTER METHYLATION. HTERT TRANSCRIPT EXPRESSION AND TELOMERASE ACTIVITY BOTH CONFERRED A WORSE OUTCOME BY UNIVARIATE AND MULTIVARIATE ANALYSIS (P \ .05). CONCLUSION: HTERT EXPRESSION AND TELOMERASE ACTIVITY ARE PREDICTORS OF POOR OUTCOME IN PANCREATIC CANCER. HTERT GENE EXPRESSION IS POSITIVELY REGULATED BY PROMOTER METHYLATION. 2009 5 1225 37 CRITICAL ROLE OF EPIGENETIC MODIFICATION IN THE PATHOGENESIS OF ATOPIC DERMATITIS. ATOPIC DERMATITIS IS A CHRONIC INFLAMMATORY SKIN DISEASE CHARACTERISED BY RECURRENT ECZEMA-LIKE LESIONS AND SEVERE PRURITUS, ALONG WITH DRYING AND DECRUSTATION OF SKIN. CURRENT RESEARCH RELATES THE PATHOGENESIS OF ATOPIC DERMATITIS MAINLY TO GENETIC SUSCEPTIBILITY, ABNORMAL SKIN BARRIER FUNCTION, IMMUNE DISORDERS, STAPHYLOCOCCUS AUREUS COLONISATION, MICROBIOLOGICAL DYSFUNCTION AND VITAMIN D INSUFFICIENCY. EPIGENETIC MODIFICATIONS ARE DISTINCT GENETIC PHENOTYPES RESULTING FROM ENVIRONMENT-DRIVEN CHANGES IN CHROMOSOME FUNCTIONS IN THE ABSENCE OF NUCLEAR DNA SEQUENCE VARIATION. CLASSIC EPIGENETIC EVENTS INCLUDE DNA METHYLATION, HISTONE PROTEIN MODIFICATIONS AND NON-CODING RNA REGULATION. INCREASING EVIDENCE HAS INDICATED THAT EPIGENETIC EVENTS ARE INVOLVED IN THE PATHOGENESIS OF ATOPIC DERMATITIS BY THEIR EFFECTS ON MULTIPLE SIGNALLING PATHWAYS WHICH IN TURN INFLUENCE THE ABOVE FACTORS. THIS REVIEW PRIMARILY ANALYSES THE FUNCTION OF EPIGENETIC REGULATION IN THE PATHOGENESIS OF ATOPIC DERMATITIS. IN ADDITION, IT TRIES TO MAKE RECOMMENDATIONS FOR PERSONALISED EPIGENETIC TREATMENT STRATEGIES FOR ATOPIC DERMATITIS IN THE FUTURE. 2023 6 5269 46 PROMOTER DNA METHYLATION CONTRIBUTES TO HUMAN BETA-DEFENSIN-1 DEFICIENCY IN ATOPIC DERMATITIS. ATOPIC DERMATITIS (AD) IS A CHRONIC INFLAMMATORY SKIN DISEASE CAUSED BY EPIDERMAL BARRIER DYSFUNCTION AND DYSREGULATION OF INNATE AND ADAPTIVE IMMUNITY. EPIGENETIC REGULATION OF HUMAN BETA-DEFENSIN-1 (HBD-1) MIGHT BE ASSOCIATED WITH A VARIETY OF DEFECTS IN THE INNATE IMMUNE SYSTEM DURING AD PATHOGENESIS. WE INVESTIGATED THE POSSIBLE MECHANISM OF DECREASED HBD-1 GENE EXPRESSION IN AD AND DEMONSTRATED THE RESTORATION OF HBD-1 TRANSCRIPTION IN UNDIFFERENTIATED NORMAL HUMAN EPIDERMAL KERATINOCYTE CELLS AFTER TREATMENT WITH A DNA METHYLTRANSFERASE INHIBITOR. WE ALSO CONDUCTED AN IN VITRO METHYLATED REPORTER ASSAY USING A REPORTER CONTAINING 14 CPG SITES. METHYLATION OF THE 14 CPG SITES WITHIN THE HBD-1 5' REGION RESULTED IN AN APPROXIMATELY 86% REDUCTION IN PROMOTER ACTIVITY AND AFFECTED HBD-1 TRANSCRIPTIONAL REGULATION. WE THEN COMPARED METHYLATION FREQUENCIES AT CPG 3 AND CPG 4 BETWEEN NON-LESIONAL AND LESIONAL EPIDERMIS SAMPLES OF PATIENTS WITH SEVERE AD AND BETWEEN THESE PAIRED TISSUES AND HEALTHY CONTROL EPIDERMIS FROM NORMAL VOLUNTEERS WITHOUT AD HISTORY. BISULFITE PYROSEQUENCING DATA SHOWED SIGNIFICANTLY HIGHER METHYLATION FREQUENCIES AT THE CPG 3 AND 4 SITES IN AD LESIONAL SAMPLES THAN IN NON-LESIONAL AD SKIN AND NORMAL SKIN SAMPLES (P < 0.05). THESE RESULTS SUGGEST THAT THE DNA METHYLATION SIGNATURE OF HBD-1 IS A NOVEL DIAGNOSTIC/PROGNOSTIC MARKER AND A PROMISING THERAPEUTIC TARGET FOR THE COMPROMISED STRATUM CORNEUM BARRIER ATTRIBUTED TO HBD-1 DEFICIENCY. 2018 7 3161 41 GRAINYHEAD-LIKE 2 (GRHL2) INHIBITS KERATINOCYTE DIFFERENTIATION THROUGH EPIGENETIC MECHANISM. WE RECENTLY IDENTIFIED GRAINYHEAD-LIKE 2 (GRHL2), A MAMMALIAN HOMOLOG OF GRAINYHEAD IN DROSOPHILA, TO BE A NOVEL TRANSCRIPTION FACTOR THAT REGULATES HTERT GENE EXPRESSION AND ENHANCES PROLIFERATION OF NORMAL HUMAN EPIDERMAL KERATINOCYTES (NHEK). IN THE CURRENT STUDY, WE SHOW THAT GRHL2 IMPAIRS KERATINOCYTE DIFFERENTIATION THROUGH TRANSCRIPTIONAL INHIBITION OF THE GENES CLUSTERED AT THE EPIDERMAL DIFFERENTIATION COMPLEX (EDC), LOCATED AT CHROMOSOME 1Q21. GENE EXPRESSION PROFILING AND SUBSEQUENT IN VITRO ASSAYS REVEALED CONSISTENT DOWNREGULATION OF EDC GENES, FOR EXAMPLE, IVL, KRT1, FLG, LCES, AND SPRRS, IN NHEK EXPRESSING EXOGENOUS GRHL2. IN VIVO BINDING ASSAY BY CHROMATIN IMMUNOPRECIPITATION REVEALED GRHL2 ASSOCIATION AT THE PROMOTER REGIONS OF ITS TARGET GENES, MANY OF WHICH BELONG TO EDC. EXOGENOUS GRHL2 EXPRESSION ALSO INHIBITED RECRUITMENT OF HISTONE DEMETHYLASE JMJD3 TO THE EDC GENE PROMOTERS AND ENHANCED THE LEVEL OF HISTONE 3 LYS 27 TRIMETHYLATION ENRICHMENT AT THESE PROMOTERS. SURVEY OF GRHL2 EXPRESSION IN HUMAN SKIN TISSUES DEMONSTRATED ENHANCED PROTEIN AND MRNA LEVELS IN CHRONIC SKIN LESIONS WITH IMPAIRED KERATINOCYTE DIFFERENTIATION, FOR EXAMPLE, ATOPIC DERMATITIS AND PSORIASIS, COMPARED WITH NORMAL EPIDERMIS. THESE DATA INDICATE THAT GRHL2 IMPAIRS EPIDERMAL DIFFERENTIATION BY INHIBITING EDC GENE EXPRESSION THROUGH EPIGENETIC MECHANISMS AND SUPPORT ITS ROLE IN THE HYPERPROLIFERATIVE SKIN DISEASES. 2012 8 3104 44 GENOMIC, EPIGENOMIC, TRANSCRIPTOMIC, PROTEOMIC AND METABOLOMIC APPROACHES IN ATOPIC DERMATITIS. ATOPIC DERMATITIS (AD) IS A CHRONIC INFLAMMATORY SKIN DISEASE WITH A HIGH PREVALENCE IN THE DEVELOPED COUNTRIES. IT IS ASSOCIATED WITH ATOPIC AND NON-ATOPIC DISEASES, AND ITS CLOSE CORRELATION WITH ATOPIC COMORBIDITIES HAS BEEN GENETICALLY DEMONSTRATED. ONE OF THE MAIN ROLES OF GENETIC STUDIES IS TO COMPREHEND THE DEFECTS OF THE CUTANEOUS BARRIER DUE TO FILAGGRIN DEFICIT AND EPIDERMAL SPONGIOSIS. RECENTLY, EPIGENETIC STUDIES STARTED TO ANALYZE THE INFLUENCE OF THE ENVIRONMENTAL FACTORS ON GENE EXPRESSION. THE EPIGENOME IS CONSIDERED TO BE A SUPERIOR SECOND CODE THAT CONTROLS THE GENOME, WHICH INCLUDES ALTERATIONS OF THE CHROMATIN. THE EPIGENETIC CHANGES DO NOT ALTER THE GENETIC CODE, HOWEVER, CHANGES IN THE CHROMATIN STRUCTURE COULD ACTIVATE OR INHIBIT THE TRANSCRIPTION PROCESS OF CERTAIN GENES AND CONSEQUENTLY, THE TRANSLATION PROCESS OF THE NEW MRNA INTO A POLYPEPTIDE CHAIN. IN-DEPTH ANALYSIS OF THE TRANSCRIPTOMIC, METABOLOMIC AND PROTEOMIC STUDIES ALLOW TO UNRAVEL DETAILED MECHANISMS THAT CAUSE AD. THE EXTRACELLULAR SPACE AND LIPID METABOLISM ARE ASSOCIATED WITH AD THAT IS INDEPENDENT OF THE FILAGGRIN EXPRESSION. ON THE OTHER HAND, AROUND 45 PROTEINS ARE CONSIDERED AS THE PRINCIPAL COMPONENTS IN THE ATOPIC SKIN. MOREOVER, GENETIC STUDIES BASED ON THE DISRUPTED CUTANEOUS BARRIER CAN LEAD TO THE DEVELOPMENT OF NEW TREATMENTS TARGETING THE CUTANEOUS BARRIER OR CUTANEOUS INFLAMMATION. UNFORTUNATELY, AT PRESENT, THERE ARE NO TARGET THERAPIES THAT FOCUS ON THE EPIGENETIC PROCESS OF AD. HOWEVER, IN THE FUTURE, MIR-143 COULD BE AN IMPORTANT OBJECTIVE FOR NEW THERAPIES, AS IT TARGETS THE MIR-335:SOX AXIS, THEREBY RESTORING THE MIR-335 EXPRESSION, AND REPAIRING THE CUTANEOUS BARRIER DEFECTS. 2023 9 4231 38 METHYLATION OF PROTOCADHERIN 10, A NOVEL TUMOR SUPPRESSOR, IS ASSOCIATED WITH POOR PROGNOSIS IN PATIENTS WITH GASTRIC CANCER. BACKGROUND & AIMS: BY USING METHYLATION-SENSITIVE REPRESENTATIONAL DIFFERENCE ANALYSIS, WE IDENTIFIED PROTOCADHERIN 10 (PCDH10), A GENE THAT ENCODES A PROTOCADHERIN AND IS SILENCED IN A TUMOR-SPECIFIC MANNER. WE ANALYZED ITS EPIGENETIC INACTIVATION, BIOLOGICAL EFFECTS, AND PROGNOSTIC SIGNIFICANCE IN GASTRIC CANCER. METHODS: METHYLATION STATUS WAS EVALUATED BY COMBINED BISULFITE RESTRICTION ANALYSIS AND BISULFITE SEQUENCING. THE EFFECTS OF PCDH10 RE-EXPRESSION WERE DETERMINED IN GROWTH, APOPTOSIS, PROLIFERATION, AND INVASION ASSAYS. PCDH10 TARGET GENES WERE IDENTIFIED BY COMPLEMENTARY DNA MICROARRAY ANALYSIS. RESULTS: PCDH10 WAS SILENCED OR DOWN-REGULATED IN 94% (16 OF 17) OF GASTRIC CANCER CELL LINES; EXPRESSION LEVELS WERE RESTORED BY EXPOSURE TO DEMETHYLATING AGENTS. RE-EXPRESSION OF PCDH10 IN MKN45 GASTRIC CANCER CELLS REDUCED COLONY FORMATION IN VITRO AND TUMOR GROWTH IN MICE; IT ALSO INHIBITED CELL PROLIFERATION (P < .01), INDUCED CELL APOPTOSIS (P < .001), AND REPRESSED CELL INVASION (P < .05), UP-REGULATING THE PRO-APOPTOSIS GENES FAS, CASPASE 8, JUN, AND CDKN1A; THE ANTIPROLIFERATION GENE FGFR; AND THE ANTI-INVASION GENE HTATIP2. PCDH10 METHYLATION WAS DETECTED IN 82% (85 OF 104) OF GASTRIC TUMORS COMPARED WITH 37% (38 OF 104) OF PAIRED NONTUMOR TISSUES (P < .0001). IN THE LATTER, PCDH10 METHYLATION WAS HIGHER IN PRECANCEROUS LESIONS (27 OF 45; 60%) THAN IN CHRONIC GASTRITIS SAMPLES (11 OF 59; 19%) (P < .0001). AFTER A MEDIAN FOLLOW-UP PERIOD OF 16.8 MONTHS, MULTIVARIATE ANALYSIS REVEALED THAT PATIENTS WITH PCDH10 METHYLATION IN ADJACENT NONTUMOR AREAS HAD A SIGNIFICANT DECREASE IN OVERALL SURVIVAL. KAPLAN-MEIER SURVIVAL CURVES SHOWED THAT PCDH10 METHYLATION WAS ASSOCIATED SIGNIFICANTLY WITH SHORTENED SURVIVAL IN STAGE I-III GASTRIC CANCER PATIENTS. CONCLUSIONS: PCDH10 IS A GASTRIC TUMOR SUPPRESSOR; ITS METHYLATION AT EARLY STAGES OF GASTRIC CARCINOGENESIS IS AN INDEPENDENT PROGNOSTIC FACTOR. 2009 10 2326 36 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 11 1212 38 CPG ISLAND METHYLATION OF THE HTERT PROMOTER IS ASSOCIATED WITH LOWER TELOMERASE ACTIVITY IN B-CELL LYMPHOCYTIC LEUKEMIA. OBJECTIVE: EXPRESSION OF THE CATALYTIC SUBUNIT OF THE TELOMERASE ENZYME HTERT IS ESSENTIAL FOR PROLONGING THE REPLICATIVE LIFESPAN AND IS THE RATE-LIMITING STEP IN CELLULAR IMMORTALIZATION AND CARCINOGENESIS. BECAUSE HTERT EXPRESSION IS POSITIVELY CORRELATED WITH TELOMERASE ACTIVITY, ITS REGULATION IS SUGGESTED AS THE MAJOR DETERMINANT OF ENZYMATIC ACTIVITY. THE HTERT PROMOTER REGION CONTAINS TWO CPG ISLANDS, WHICH ARE KNOWN TO BE TARGET SITES FOR DE NOVO DNA METHYLATION. TO ELUCIDATE THE IMPACT OF THIS EPIGENETIC MECHANISM ON TELOMERASE ACTIVITY, WE ANALYZED THE DEGREE OF HTERT PROMOTER METHYLATION IN 30 PATIENTS WITH B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA. MATERIALS AND METHODS: HTERT PROMOTER METHYLATION WAS ASSESSED USING A METHYLATION-SPECIFIC COMPETITIVE POLYMERASE CHAIN REACTION ASSAY. THE ASSAY IS BASED ON DIGESTION OF GENOMIC DNA WITH A METHYLATION-SENSITIVE RESTRICTION ENZYME BEFORE AMPLIFICATION WITH AN INTERNAL STANDARD. RESULTS: PATIENTS EXHIBITING HIGH TELOMERASE ACTIVITY SHOWED SIGNIFICANTLY LESS METHYLATION OF THE HTERT PROMOTER CORE DOMAIN THAN PATIENTS WITH LOW ENZYME ACTIVITY. IN ADDITION, TELOMERASE ACTIVITY WAS SIGNIFICANTLY ASSOCIATED WITH TELOMERE LENGTH AND OVERALL SURVIVAL. CONCLUSIONS: OUR DATA SHOW THAT THE DEGREE OF CPG ISLAND METHYLATION OF THE HTERT PROMOTER EXHIBITS AN IMPACT ON TELOMERASE ACTIVITY IN A SUBGROUP OF PATIENTS WITH B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA AND THEREFORE IS ASSUMED TO PLAY A ROLE IN REGULATING HTERT GENE EXPRESSION IN THESE PATIENTS. 2002 12 2064 36 EPIGENETIC CONTROL OF INFLAMMATION IN ATOPIC DERMATITIS. ATOPIC DERMATITIS (AD), ALSO KNOWN AS ATOPIC ECZEMA, IS A COMMON BUT ALSO COMPLEX CHRONIC, ITCHY SKIN CONDITION WITH UNDERLYING INFLAMMATION OF THE SKIN. THIS SKIN AILMENT IS PREVALENT WORLDWIDE AND AFFECTS PEOPLE OF ALL AGES, PARTICULARLY CHILDREN BELOW FIVE YEARS OF AGE. THE ITCHING AND RESULTING RASHES IN AD PATIENTS ARE OFTEN THE RESULT OF INFLAMMATORY SIGNALS, THUS NECESSITATING A CLOSER LOOK AT THE INFLAMMATION-REGULATING MECHANISMS FOR PUTATIVE RELIEF, CARE AND THERAPY. SEVERAL CHEMICAL- AS WELL AS GENETICALLY-INDUCED ANIMAL MODELS HAVE ESTABLISHED THE IMPORTANCE OF TARGETING PRO-INFLAMMATORY AD MICROENVIRONMENT. EPIGENETIC MECHANISMS ARE GAINING ATTENTION TOWARDS A BETTER UNDERSTANDING OF THE ONSET AS WELL AS THE PROGRESSION OF INFLAMMATION. SEVERAL PHYSIOLOGICAL PROCESSES WITH IMPLICATIONS IN PATHOPHYSIOLOGY OF AD, SUCH AS, BARRIER DYSFUNCTION EITHER DUE TO REDUCED FILAGGRIN / HUMAN BETA-DEFENSINS OR ALTERED MICROBIOME, REPROGRAMING OF FC RECEPTORS WITH RESULTING OVEREXPRESSION OF HIGH AFFINITY IGE RECEPTORS, ELEVATED EOSINOPHIL NUMBERS OR THE ELEVATED IL-22 PRODUCTION BY CD4 + T CELLS HAVE UNDERLYING EPIGENETIC MECHANISMS THAT INCLUDE DIFFERENTIAL PROMOTER METHYLATION AND/OR REGULATION BY NON-CODING RNAS. REVERSING THESE EPIGENETIC CHANGES HAS BEEN VERIFIED TO REDUCE INFLAMMATORY BURDEN THROUGH ALTERED SECRETION OF CYTOKINES IL-6, IL-4, IL-13, IL-17, IL-22 ETC, WITH BENEFIT AGAINST AD PROGRESSION IN EXPERIMENTAL MODELS. A THOROUGH UNDERSTANDING OF EPIGENETIC REMODELING OF INFLAMMATION IN AD HAS THE POTENTIAL OF OPENING AVENUES FOR NOVEL DIAGNOSTIC, PROGNOSTIC AND THERAPEUTIC OPTIONS. 2023 13 3070 48 GENOME-WIDE DNA METHYLATION PROFILING IN CD8 T-CELLS AND GAMMA DELTA T-CELLS OF ASIAN INDIAN PATIENTS WITH TAKAYASU ARTERITIS. BACKGROUND: TAKAYASU'S ARTERITIS (TA) IS A CHRONIC INFLAMMATORY DISEASE THAT AFFECTS AORTA AND ITS MAIN BRANCHES AT THEIR ORIGIN. GENETIC, PATHOLOGICAL AND FUNCTIONAL STUDIES HAVE SHOWN THAT CD8 AND GAMMA DELTA (GAMMA/DELTA) T-LYMPHOCYTES ARE INVOLVED IN INFLAMMATORY PROCESSES IN AFFECTED REGIONS OF ARTERIES CAUSING VASCULAR DAMAGE. THE MOLECULAR FUNCTION OF THESE LYMPHOCYTES REMAINS UNCLEAR AND CURRENTLY NO EPIGENETIC STUDIES ARE AVAILABLE IN TA. WE PRIMARILY PERFORMED GENOME WIDE METHYLATION ANALYSIS IN CD8 T CELLS AND GAMMADELTA T CELLS OF PATIENTS WITH TA AND COMPARED WITH HEALTHY CONTROLS. METHODS: WE RECRUITED 12 SUBJECTS IN EACH GROUP NAMELY TA PATIENT AND HEALTHY CONTROLS. BLOOD SAMPLES WERE COLLECTED AFTER OBTAINING INFORMED WRITTEN CONSENT. CD8 T CELLS AND GAMMADELTA T CELLS WERE SEPARATED FROM WHOLE BLOOD. DNA EXTRACTED FROM THESE CELLS AND WERE SUBJECTED TO BISULFITE TREATMENT. FINALLY, BISULFITE TREATED DNA WAS LOADED IN INFINIUM METHYLATION EPIC ARRAY. BIOINFORMATICS ANALYSIS WAS USED TO IDENTIFY DIFFERENTIAL METHYLATION REGIONS WHICH WERE THEN MAPPED TO GENES. RESULTS: INTERLEUKIN (IL)-32 AND LYMPHOTOXIN-A WERE GENES SIGNIFICANTLY HYPOMETHYLATED IN CD8 T-CELLS. ANTI-INFLAMMATORY CYTOKINE GENES, IL-10, IL-1RN AND IL-27 WERE HYPOMETHYLATED IN GAMMADELTA T CELLS OF TA PATIENTS AS COMPARED TO HEALTHY CONTROLS. GENE ENRICHMENT ANALYSIS USING GENE ONTOLOGY (GO) DATABASE AND KYOTO ENCYCLOPAEDIA OF GENES AND GENOMES (KEGG) IDENTIFIED THAT GENES INVOLVED IN T-CELL RECEPTOR SIGNALLING PATHWAYS WERE HYPOMETHYLATED IN CD8 T-CELLS AND HYPERMETHYLATED IN GAMMADELTA T CELLS OF TA PATIENTS. CONCLUSION: CD8 T-CELLS MIGHT PLAY A MAJOR ROLE IN IMMUNOPATHOGENESIS OF INFLAMMATION IN TA, WHEREAS GAMMADELTA T CELLS MAY PLAY A REGULATORY ROLE. 2022 14 6643 58 UNRAVELLING THE COMPLEX GENETIC BACKGROUND OF ATOPIC DERMATITIS: FROM GENETIC ASSOCIATION RESULTS TOWARDS NOVEL THERAPEUTIC STRATEGIES. ATOPIC DERMATITIS (AD) IS A CHRONIC INFLAMMATORY SKIN DISEASE ARISING FROM COMPLEX INTERACTION BETWEEN GENETIC AND ENVIRONMENTAL FACTORS. AS THE STARTING POINT OF THE SO-CALLED "ATOPIC MARCH", E.G. THE PROGRESSION TOWARDS ALLERGIC ASTHMA IN SOME BUT NOT ALL AFFECTED CHILDREN, AD HAS COME INTO FOCUS FOR POTENTIAL DISEASE-MODIFYING STRATEGIES. TO ELUCIDATE THE GENETIC FACTORS INFLUENCING AD DEVELOPMENT, LINKAGE, ASSOCIATION AS WELL AS GENOME-WIDE ASSOCIATION STUDIES HAVE BEEN PERFORMED OVER THE LAST TWO DECADES. THE RESULTS SUGGEST THAT BESIDES VARIATION IN IMMUNE-MEDIATED PATHWAYS, AN INTACT SKIN BARRIER FUNCTION PLAYS A KEY ROLE IN AD DEVELOPMENT. MUTATIONS IN THE GENE ENCODING FILAGGRIN, A MAJOR STRUCTURAL PROTEIN IN THE EPIDERMIS, HAVE BEEN CONSISTENTLY ASSOCIATED WITH AD, ESPECIALLY THE EARLY-ONSET PERSISTENT FORM OF DISEASE, AND ARE REGARDED AS THE MOST SIGNIFICANT KNOWN RISK FACTOR FOR AD DEVELOPMENT TO DATE. ADDITIONALLY, VARIATION IN SOME OTHER GENES INVOLVED IN SKIN INTEGRITY AND BARRIER FUNCTION HAVE SHOWN ASSOCIATION WITH AD. HOWEVER, THE KNOWN GENETIC RISK FACTORS CAN ONLY EXPLAIN A SMALL PART OF THE HERITABILITY AT THE MOMENT. WHOLE-EXOME OR WHOLE-GENOME SEQUENCING STUDIES HAVE NOT BEEN REPORTED YET, BUT WILL PROBABLY SOON EVALUATE THE INFLUENCE OF RARE VARIATIONS FOR AD DEVELOPMENT. ADDITIONALLY, LARGE MULTI-CENTRE STUDIES COMPREHENSIVELY INCORPORATING GENE-GENE AND GENE-ENVIRONMENT INTERACTIONS AS WELL AS EPIGENETIC MECHANISMS MIGHT FURTHER ELUCIDATE THE GENETIC FACTORS UNDERLYING AD PATHOGENESIS AND, THUS, OPEN THE WAY FOR A MORE INDIVIDUALIZED TREATMENT IN THE FUTURE. 2015 15 6231 30 THE LONG NONCODING RNA MEG3 AND ITS TARGET MIR-147 REGULATE JAK/STAT PATHWAY IN ADVANCED CHRONIC MYELOID LEUKEMIA. BACKGROUND: LONG NON-CODING (LNC) RNAS PLAYS AN IMPORTANT ROLE IN CHRONIC MYELOID LEUKEMIA (CML). IN THIS STUDY, WE AIMED TO UNCOVER THE MECHANISM OF THE LNCRNA MATERNALLY EXPRESSED 3 (MEG3) AND ITS TARGET MICRORNA-147 (MIR-147) IN CML. METHODS: SIXTY CML PATIENTS AND 10 HEALTHY DONORS WERE INCLUDED IN THE STUDY. THE METHYLATION OF MEG3 AND MIR-147 PROMOTER WAS DETERMINED BY METHYLATION-SPECIFIC PCR. THE RELATIONSHIP OF MEG3 AND MIR-147 WAS EXPLORED BY LUCIFERASE ASSAY. THE INTERACTIONS OF PROTEINS WERE STUDIED BY RNA PULL-DOWN ASSAY, RNA IMMUNOPRECIPITATION AND CO-IMMUNOPRECIPITATION. FINDINGS: PATIENTS IN ACCELERATED PHASE CML (CML-AP) AND BLAST PHASE CML (CML-BP) SHOWED LOWER EXPRESSIONS OF MEG3 AND MIR-147 AND HIGHER EXPRESSIONS OF DNMT1, DNMT3B, MBD2, MECP2 AND HDAC1 COMPARED TO THE CONTROLS. THESE PATIENTS ALSO SHOWED A HIGHER DEGREE OF METHYLATION OF MEG3 AND MIR-147 WHILE THERE WAS A REDUCTION AFTER CHIDAMIDE TREATMENT. FURTHERMORE, THE OVEREXPRESSION OF MEG3 AND MIR-147 INHIBITED CELL PROLIFERATION BOTH IN VIVO AND IN VITRO, PROMOTED APOPTOSIS AND DECREASED THE EXPRESSIONS OF DNMT1, DNMT3A, DNMT3B, MBD2, HDAC1 AND MECP2. WE ALSO FOUND MEG3 INTERACTED WITH DNMT1, JAK2, STAT3, HDAC1, AND TYK2, AND JAK2 WAS BOUND TO STAT3, STAT5 AND MYC. MORE INTERESTINGLY, JAK2 WAS BOUND TO TYK2 BY THE BRIDGE OF MEG3. INTERPRETATION: LNCRNA MEG3 AND ITS TARGET MIR-147 MAY SERVE AS A NOVEL THERAPEUTIC TARGET FOR CML BLAST CRISIS, AND CHIDAMIDE MIGHT HAVE A POTENTIAL CLINICAL APPLICATION IN TREATING CML BLAST CRISIS. 2018 16 4364 36 MIRNA DEREGULATION BY EPIGENETIC SILENCING DISRUPTS SUPPRESSION OF THE ONCOGENE PLAG1 IN CHRONIC LYMPHOCYTIC LEUKEMIA. MICRORNAS (MIRNA) PLAY A KEY ROLE IN CELLULAR REGULATION AND, IF DEREGULATED, IN THE DEVELOPMENT OF NEOPLASTIC DISORDERS INCLUDING CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). RNAS FROM PRIMARY CELLS OF 50 TREATMENT-NAIVE CLL PATIENTS AND PERIPHERAL B CELLS OF 14 HEALTHY DONORS WERE APPLIED TO MIRNA EXPRESSION PROFILING USING BEAD CHIP TECHNOLOGY. IN CLL CELLS, A SET OF 7 UP- AND 19 DOWN-REGULATED MIRNAS WAS IDENTIFIED. AMONG THE MIRNAS DOWN-REGULATED IN CLL CELLS, 6 OF 10 MIRNA PROMOTERS EXAMINED SHOWED GAIN OF METHYLATION COMPARED WITH NORMAL B-CELL CONTROLS. SUBSEQUENT TARGET PREDICTION OF DEREGULATED MIRNAS REVEALED A HIGHLY SIGNIFICANT BINDING PREDICTION AT THE 3' UNTRANSLATED REGION OF THE PLEOMORPHIC ADENOMA GENE 1 (PLAG1) ONCOGENE. LUCIFERASE REPORTER ASSAYS INCLUDING SITE-DIRECTED MUTAGENESIS OF BINDING SITES REVEALED A SIGNIFICANT REGULATION OF PLAG1 BY MIR-181A, MIR-181B, MIR-107, AND MIR-424. ALTHOUGH EXPRESSION OF PLAG1 MRNA WAS NOT AFFECTED, PLAG1 PROTEIN EXPRESSION WAS SHOWN TO BE SIGNIFICANTLY ELEVATED IN CLL CELLS COMPARED WITH THE LEVELS IN HEALTHY DONOR B CELLS. IN SUMMARY, WE COULD DEMONSTRATE DISRUPTION OF MIRNA-MEDIATED TRANSLATIONAL CONTROL, PARTLY DUE TO EPIGENETIC TRANSCRIPTIONAL SILENCING OF MIRNAS, WITH SUBSEQUENT OVEREXPRESSION OF THE ONCOGENIC TRANSCRIPTION FACTOR PLAG1 AS A PUTATIVE NOVEL MECHANISM OF CLL PATHOGENESIS. 2009 17 5417 38 REGULATION OF DNA METHYLATION IN RHEUMATOID ARTHRITIS SYNOVIOCYTES. RHEUMATOID ARTHRITIS (RA) IS A CHRONIC INFLAMMATORY DISEASE IN WHICH FIBROBLAST-LIKE SYNOVIOCYTES (FLS) EXHIBIT AN AGGRESSIVE PHENOTYPE. ALTHOUGH THE MECHANISMS RESPONSIBLE ARE NOT WELL DEFINED, EPIGENETIC DETERMINANTS SUCH AS DNA METHYLATION MIGHT CONTRIBUTE. DNA METHYLTRANSFERASES (DNMTS) ARE CRITICAL ENZYMES THAT ESTABLISH AND MAINTAIN DNA METHYLATION. WE EVALUATED WHETHER PROINFLAMMATORY CYTOKINES MIGHT CONTRIBUTE TO DIFFERENTIAL DNA METHYLATION PREVIOUSLY DESCRIBED IN RA FLS THROUGH ALTERED DNMT EXPRESSION. FLS WERE OBTAINED FROM RA AND OSTEOARTHRITIS (OA) SYNOVIUM AT THE TIME OF TOTAL JOINT REPLACEMENT. GENE EXPRESSION WAS DETERMINED BY QUANTITATIVE REAL-TIME PCR AND PROTEIN EXPRESSION BY WESTERN BLOT ANALYSIS. DNMT ACTIVITY WAS MEASURED WITH A FUNCTIONAL ASSAY, AND GLOBAL METHYLATION WAS DETERMINED BY AN IMMUNOASSAY THAT DETECTS METHYLCYTOSINE. RESTING EXPRESSION OF DNMT1, -3A, AND -3B MRNA WERE SIMILAR IN RA AND OA FLS. WESTERN BLOT SHOWED ABUNDANT DNMT1 AND DNMT3A PROTEIN. EXPOSURE TO IL-1 DECREASED DNMT1 AND DNMT3A MRNA EXPRESSION IN FLS. DOSE RESPONSES DEMONSTRATED DECREASED DNMT EXPRESSION AT CONCENTRATIONS AS LOW AS 1 PG/ML OF IL-1. DNMT MRNA LEVELS DECREASED RAPIDLY, WITH SIGNIFICANT SUPPRESSION AFTER 2-8 H OF IL-1 STIMULATION. IL-1 STIMULATION OF OA FLS DID NOT AFFECT METHYLATION OF LINE1 SITES BUT LED TO DEMETHYLATION OF A CHI3L1 LOCUS THAT IS HYPOMETHYLATED IN RA FLS. CHRONIC IL-1 STIMULATION ALSO MIMICKED THE EFFECT OF A DNMT INHIBITOR ON FLS GENE EXPRESSION. EXPOSURE TO PROINFLAMMATORY MEDIATORS REVERSIBLY ALTERS DNA METHYLATION IN FLS BY DECREASING DNMT EXPRESSION AND FUNCTION. THESE DATA SUGGEST THAT IL-1 CAN POTENTIALLY IMPRINT CELLS IN CHRONIC INFLAMMATORY DISEASES. 2013 18 1500 51 DNA METHYLATION ANALYSIS OF CD4+ T CELLS IN PATIENTS WITH PSORIASIS. PSORIASIS IS A CHRONIC INFLAMMATORY SKIN DISEASE THAT IS CHARACTERIZED BY ABERRANT CROSS-TALK BETWEEN KERATINOCYTES AND IMMUNE CELLS SUCH AS CD4+ T CELLS, RESULTING IN KERATINOCYTE HYPERPROLIFERATION IN THE EPIDERMIS. DNA METHYLATION, ONE OF SEVERAL EPIGENETIC MECHANISMS, PLAYS AN IMPORTANT ROLE IN GENE EXPRESSION WITHOUT CHANGING THE DNA SEQUENCE. SEVERAL STUDIES HAVE SUGGESTED THE INVOLVEMENT OF EPIGENETIC REGULATION IN SKIN LESIONS FROM PATIENTS WITH PSORIASIS. IN THIS STUDY, WE INVESTIGATED THE GENOME-WIDE DNA METHYLATION STATUS OF CD4+ T CELLS IN PATIENTS WITH PSORIASIS COMPARED WITH HEALTHY SUBJECTS USING METHYLATED DNA IMMUNOPRECIPITATION SEQUENCING (MEDIP-SEQ). THE RESULTS OF MEDIP-SEQ SHOWED THAT THE GLOBAL METHYLATION VALUES OF CD4+ T CELLS ARE HIGHER IN PATIENTS WITH PSORIASIS THAN IN HEALTHY CONTROLS, PARTICULARLY IN THE PROMOTER REGIONS. AMONG THE MOST HYPERMETHYLATED GENES IN THE PROMOTER REGIONS, WE SELECTED THE GENES WHOSE EXPRESSION IS SIGNIFICANTLY REDUCED IN THE CD4+ T CELLS OF PSORIASIS PATIENTS. STUDIES USING THE METHYLATION INHIBITOR 5-AZACYTIDINE IN VITRO METHYLATION ASSAYS HAVE SHOWN THAT THE DIFFERENTIAL EXPRESSION LEVELS WERE ASSOCIATED WITH THE METHYLATION STATUS OF EACH GENE. BISULFITE SEQUENCING OF THE TRANSCRIPTION START REGION OF PHOSPHATIDIC ACID PHOSPHATASE TYPE 2 DOMAIN CONTAINING 3 (PPAPDC3), ONE OF THE SELECTED GENES, SHOWED HYPERMETHYLATION IN THE CD4+ T CELLS OF PSORIASIS PATIENTS. THESE RESULTS SUGGESTED THAT THE METHYLATION STATUS, WHICH IS IDENTIFIED BY MEDIP-SEQ OF THE GENES, WAS CORRELATED WITH THE MRNA EXPRESSION LEVEL OF THE GENES. COLLECTIVELY, THE DNA METHYLATION STATUS IN CD4+ T CELLS MIGHT BE ASSOCIATED WITH THE PATHOGENESIS OF PSORIASIS. 2014 19 1620 38 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 20 3068 43 GENOME-WIDE DNA METHYLATION PROFILING IDENTIFIES DIFFERENTIAL METHYLATION IN UNINVOLVED PSORIATIC EPIDERMIS. PSORIASIS IS A CHRONIC INFLAMMATORY SKIN DISEASE WITH BOTH LOCAL AND SYSTEMIC COMPONENTS. GENOME-WIDE APPROACHES HAVE IDENTIFIED MORE THAN 60 PSORIASIS-SUSCEPTIBILITY LOCI, BUT GENES ARE ESTIMATED TO EXPLAIN ONLY ONE-THIRD OF THE HERITABILITY IN PSORIASIS, SUGGESTING ADDITIONAL, YET UNIDENTIFIED, SOURCES OF HERITABILITY. EPIGENETIC MODIFICATIONS HAVE BEEN LINKED TO PSORIASIS AND ALTERED DNA METHYLATION PATTERNS IN PSORIATIC VERSUS HEALTHY SKIN HAVE BEEN REPORTED IN WHOLE-SKIN BIOPSIES. IN THIS STUDY, FOCUSING ON EPIGENETIC MODIFICATIONS IN THE PSORIATIC UNINVOLVED SKIN, WE COMPARED THE LESIONAL AND NON-LESIONAL EPIDERMIS FROM PSORIASIS PATIENTS WITH EPIDERMIS FROM HEALTHY CONTROLS. WE PERFORMED AN EXHAUSTIVE GENOME-WIDE DNA METHYLATION PROFILING USING REDUCED REPRESENTATION BISULFITE SEQUENCING, WHICH INTERROGATES THE METHYLATION STATUS OF APPROXIMATELY 3-4 MILLION CPG SITES. MORE THAN 2,000 STRONGLY DIFFERENTIALLY METHYLATED SITES WERE IDENTIFIED AND A STRIKING OVERREPRESENTATION OF THE WNT AND CADHERIN PATHWAYS AMONG THE DIFFERENTIALLY METHYLATED SITES WAS FOUND. IN PARTICULAR, WE OBSERVE A STRONG DIFFERENTIAL METHYLATION IN SEVERAL PSORIASIS CANDIDATE GENES. A SUBSTANTIAL NUMBER OF DIFFERENTIALLY METHYLATED SITES PRESENT IN THE UNINVOLVED VERSUS HEALTHY EPIDERMIS SUGGESTS THE PRESENCE OF A PRE-PSORIATIC STATE IN THE CLINICALLY HEALTHY SKIN TYPE. OUR EXPLORATORY STUDY REPRESENTS A STARTING POINT FOR IDENTIFYING BIOMARKERS FOR PSORIASIS-PRONE SKIN BEFORE DISEASE ONSET. 2018