1 3794 156 INTERLEUKIN-33 MEDIATES BOTH IMMUNE-RELATED AND NON-IMMUNE-RELATED INHIBITORY EFFECTS AGAINST HEPATITIS B VIRUS. CHRONIC INFECTION BY HEPATITIS B VIRUS (HBV) IS ASSOCIATED WITH HIGH RISKS OF LIVER FIBROSIS, CIRRHOSIS AND HEPATOCELLULAR CARCINOMA. HBV COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) IN THE NUCLEUS OF INFECTED HEPATOCYTE SERVES AS TRANSCRIPTION TEMPLATE. NEITHER NATURAL RESOLUTION OF ACUTE INFECTION NOR CURRENT TREATMENT OPTIONS FOR CHRONIC INFECTION ARE BELIEVED TO CAUSE CCCDNA CLEARANCE. WE PREVIOUSLY SHOWED THAT INJECTION OF IL-33-EXPRESSING PLASMID FACILITATED CLEARANCE OF INTRAHEPATIC HBV DNA IN A MOUSE MODEL OF HBV PERSISTENCE. IN THIS WORK, HBV-TARGETING THERAPEUTIC EFFECTS OF IL-33 WERE FURTHER EXPLORED. MURINE IL-33 DELIVERED BY RECOMBINANT ADENO-ASSOCIATED VIRUS (AAV-MIL-33) INDUCED CLEARANCE OF BOTH SERUM HBV MARKERS AND INTRAHEPATIC HBV DNA IN TWO MOUSE MODELS OF HBV PERSISTENCE BASED ON REPLICON PLASMID AND RECOMBINANT CCCDNA (RCCCDNA) RESPECTIVELY. CLEARANCE WAS ASSOCIATED WITH SERUM ALT ELEVATIONS AND LIVER INFILTRATIONS BY CD4(+) AND CD8(+) T CELLS, INDICATING IL-33-INDUCED CELLULAR IMMUNE RESPONSES AGAINST HBV-HARBORING CELLS. ADOPTIVE TRANSFER OF SPLENOCYTES FROM AAV-MIL-33-CURED MICE WAS INDEED SUFFICIENT TO ENGENDER SIMILAR CLEARANCE IN RECIPIENT MICE. IN VITRO, INTRACELLULAR, INSTEAD OF EXTRACELLULAR, IL-33 WAS MAINLY RESPONSIBLE FOR REPRESSING VIRAL TRANSCRIPTION, PROTEIN PRODUCTION AND GENOME REPLICATION IN HUH7 CELLS TRANSFECTED WITH HBV REPLICON OR RCCCDNA. IL-33 WAS SHOWN TO BE RECRUITED ONTO RCCCDNA MINICHROMOSOME ACCOMPANIED BY LOSS OF TRANSCRIPTIONAL ACTIVATION EPIGENETIC MARKS. FINALLY, TRANSFECTION OF IL-33 INTO HBV-INFECTED HEPG2/NTCP CELLS RESULTED IN REDUCED TRANSCRIPTION, ANTIGEN EXPRESSION AND GENOME REPLICATION, SUGGESTING REPRESSION OF CANONICAL CCCDNA. THESE DATA DEMONSTRATED DIVERSE INHIBITORY EFFECTS ON HBV AND HBV-INFECTED CELLS MEDIATED BY IL-33, AND SUGGEST IL-33 AS AN INTERESTING THERAPEUTIC CANDIDATE. 2022 2 3246 36 HEPATITIS B VIRUS (HBV) INDUCES THE EXPRESSION OF INTERLEUKIN-8 THAT IN TURN REDUCES HBV SENSITIVITY TO INTERFERON-ALPHA. HIGH LEVELS OF SERUM INTERLEUKIN-8 (IL-8) HAVE BEEN DETECTED IN CHRONIC HEPATITIS B (CHB) PATIENTS DURING EPISODES OF HEPATITIS FLARES. WE INVESTIGATED WHETHER HEPATITIS B VIRUS (HBV) MAY DIRECTLY INDUCE IL-8 PRODUCTION AND WHETHER IL-8 MAY ANTAGONIZE INTERFERON-ALPHA (IFN-ALPHA) ANTIVIRAL ACTIVITY AGAINST HBV. WE SHOWED THAT CHB PATIENTS HAD SIGNIFICANTLY HIGHER IL-8 LEVELS BOTH IN SERUM AND IN LIVER TISSUE THAN CONTROLS. IN HBV-REPLICATING HEPG2 CELLS, IL-8 TRANSCRIPTION WAS SIGNIFICANTLY ACTIVATED. AP-1, C/EBP AND NF-KB TRANSCRIPTION FACTORS WERE CONCURRENTLY NECESSARY FOR MAXIMUM IL-8 INDUCTION. MOREOVER, HBX VIRAL PROTEIN WAS RECRUITED ONTO THE IL-8 PROMOTER AND THIS WAS PARALLELED BY IL8-BOUND HISTONE HYPERACETYLATION AND BY ACTIVE RECRUITMENT OF TRANSCRIPTIONAL COACTIVATORS. INHIBITION OF IL-8 INCREASES THE ANTIVIRAL ACTIVITY OF IFN-ALPHA AGAINST HBV. OUR RESULTS INDICATE THAT HBV ACTIVATES IL-8 GENE EXPRESSION BY TARGETING THE EPIGENETIC REGULATION OF THE IL-8 PROMOTER AND THAT IL-8 MAY CONTRIBUTE TO REDUCE HBV SENSITIVITY TO IFN-ALPHA. 2013 3 4546 29 MUTANT P53 REGULATES ENHANCER-ASSOCIATED H3K4 MONOMETHYLATION THROUGH INTERACTIONS WITH THE METHYLTRANSFERASE MLL4. MONOMETHYLATION OF HISTONE H3 LYSINE 4 (H3K4ME1) IS ENRICHED AT ENHANCERS THAT ARE PRIMED FOR ACTIVATION AND THE LEVELS OF THIS HISTONE MARK ARE FREQUENTLY ALTERED IN VARIOUS HUMAN CANCERS. YET, HOW ALTERATIONS IN H3K4ME1 ARE ESTABLISHED AND THE CONSEQUENCES OF THESE EPIGENETIC CHANGES IN TUMORIGENESIS ARE NOT WELL UNDERSTOOD. USING CHIP-SEQ IN HUMAN COLON CANCER CELLS, WE DEMONSTRATE THAT MUTANT P53 DEPLETION RESULTS IN DECREASED H3K4ME1 LEVELS AT ACTIVE ENHANCERS THAT REVEAL A STRIKING COLOCALIZATION OF MUTANT P53 AND THE H3K4 MONOMETHYLTRANSFERASE MLL4 FOLLOWING CHRONIC TUMOR NECROSIS FACTOR ALPHA (TNFALPHA) SIGNALING. WE FURTHER REVEAL THAT MUTANT P53 FORMS PHYSIOLOGICAL ASSOCIATIONS AND DIRECT INTERACTIONS WITH MLL4 AND PROMOTES THE ENHANCER BINDING OF MLL4, WHICH IS REQUIRED FOR TNFALPHA-INDUCIBLE H3K4ME1 AND HISTONE H3 LYSINE 27 ACETYLATION (H3K27AC) LEVELS, ENHANCER-DERIVED TRANSCRIPT (ERNA) SYNTHESIS, AND MUTANT P53-DEPENDENT TARGET GENE ACTIVATION. COMPLEMENTARY IN VITRO STUDIES WITH RECOMBINANT CHROMATIN AND PURIFIED PROTEINS DEMONSTRATE THAT BINDING OF THE MLL3/4 COMPLEX AND H3K4ME1 DEPOSITION IS ENHANCED BY MUTANT P53 AND P300-MEDIATED ACETYLATION, WHICH IN TURN REFLECTS A MLL3/4-DEPENDENT ENHANCEMENT OF MUTANT P53 AND P300-DEPENDENT TRANSCRIPTIONAL ACTIVATION. COLLECTIVELY, OUR FINDINGS ESTABLISH A MECHANISM IN WHICH MUTANT P53 COOPERATES WITH MLL4 TO REGULATE ABERRANT ENHANCER ACTIVITY AND TUMOR-PROMOTING GENE EXPRESSION IN RESPONSE TO CHRONIC IMMUNE SIGNALING. 2018 4 3633 29 INCREASE IN HDAC9 SUPPRESSES MYOBLAST DIFFERENTIATION VIA EPIGENETIC REGULATION OF AUTOPHAGY IN HYPOXIA. EXTREMELY REDUCED OXYGEN (O(2)) LEVELS ARE DETRIMENTAL TO MYOGENIC DIFFERENTIATION AND MULTINUCLEATED MYOTUBE FORMATION, AND CHRONIC EXPOSURE TO HIGH-ALTITUDE HYPOXIA HAS BEEN REPORTED TO BE AN IMPORTANT FACTOR IN SKELETAL MUSCLE ATROPHY. HOWEVER, HOW CHRONIC HYPOXIA CAUSES MUSCLE DYSFUNCTION REMAINS UNKNOWN. IN THE PRESENT STUDY, WE FOUND THAT SEVERE HYPOXIA (1% O(2)) SIGNIFICANTLY INHIBITED THE FUNCTION OF C2C12 CELLS (FROM A MYOBLAST CELL LINE). IMPORTANTLY, THE IMPAIRMENT WAS CONTINUOUSLY MANIFESTED EVEN DURING CULTURE UNDER NORMOXIC CONDITIONS FOR SEVERAL PASSAGES. MECHANISTICALLY, WE REVEALED THAT HISTONE DEACETYLASES 9 (HDAC9), A MEMBER OF THE HISTONE DEACETYLASE FAMILY, WAS SIGNIFICANTLY INCREASED IN C2C12 CELLS UNDER HYPOXIC CONDITIONS, THEREBY INHIBITING INTRACELLULAR AUTOPHAGY LEVELS BY DIRECTLY BINDING TO THE PROMOTER REGIONS OF ATG7, BECLIN1, AND LC3. THIS PHENOMENON RESULTED IN THE SEQUENTIAL DEPHOSPHORYLATION OF GSK3BETA AND INACTIVATION OF THE CANONICAL WNT PATHWAY, IMPAIRING THE FUNCTION OF THE C2C12 CELLS. TAKEN TOGETHER, OUR RESULTS SUGGEST THAT HYPOXIA-INDUCED MYOBLAST DYSFUNCTION IS DUE TO ABERRANT EPIGENETIC REGULATION OF AUTOPHAGY, AND OUR EXPERIMENTAL EVIDENCE REVEALS THE POSSIBLE MOLECULAR PATHOGENESIS RESPONSIBLE FOR SOME MUSCLE DISEASES CAUSED BY CHRONIC HYPOXIA AND SUGGESTS A POTENTIAL THERAPEUTIC OPTION. 2019 5 923 31 CHRONIC INFECTION DRIVES DNMT3A-LOSS-OF-FUNCTION CLONAL HEMATOPOIESIS VIA IFNGAMMA SIGNALING. AGE-RELATED CLONAL HEMATOPOIESIS (CH) IS A RISK FACTOR FOR MALIGNANCY, CARDIOVASCULAR DISEASE, AND ALL-CAUSE MORTALITY. SOMATIC MUTATIONS IN DNMT3A ARE DRIVERS OF CH, BUT DECADES MAY ELAPSE BETWEEN THE ACQUISITION OF A MUTATION AND CH, SUGGESTING THAT ENVIRONMENTAL FACTORS CONTRIBUTE TO CLONAL EXPANSION. WE TESTED WHETHER INFECTION PROVIDES SELECTIVE PRESSURE FAVORING THE EXPANSION OF DNMT3A MUTANT HEMATOPOIETIC STEM CELLS (HSCS) IN MOUSE CHIMERAS. WE CREATED DNMT3A-MOSAIC MICE BY TRANSPLANTING DNMT3A(-/-) AND WT HSCS INTO WT MICE AND OBSERVED THE SUBSTANTIAL EXPANSION OF DNMT3A(-/-) HSCS DURING CHRONIC MYCOBACTERIAL INFECTION. INJECTION OF RECOMBINANT IFNGAMMA ALONE WAS SUFFICIENT TO PHENOCOPY CH BY DNMT3A(-/-) HSCS UPON INFECTION. TRANSCRIPTIONAL AND EPIGENETIC PROFILING AND FUNCTIONAL STUDIES INDICATE REDUCED DIFFERENTIATION ASSOCIATED WITH WIDESPREAD METHYLATION ALTERATIONS, AND REDUCED SECONDARY STRESS-INDUCED APOPTOSIS ACCOUNTS FOR DNMT3A(-/-) CLONAL EXPANSION DURING INFECTION. DNMT3A MUTANT HUMAN HSCS SIMILARLY EXHIBIT DEFECTIVE IFNGAMMA-INDUCED DIFFERENTIATION. WE THUS DEMONSTRATE THAT IFNGAMMA SIGNALING INDUCED DURING CHRONIC INFECTION CAN DRIVE DNMT3A-LOSS-OF-FUNCTION CH. 2021 6 3186 45 HBV COVALENTLY CLOSED CIRCULAR DNA MINICHROMOSOMES IN DISTINCT EPIGENETIC TRANSCRIPTIONAL STATES DIFFER IN THEIR VULNERABILITY TO DAMAGE. BACKGROUND AND AIMS: HBV COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) IS A MAJOR OBSTACLE FOR A CURE OF CHRONIC HEPATITIS B. ACCUMULATING EVIDENCE SUGGESTS THAT EPIGENETIC MODIFICATIONS REGULATE THE TRANSCRIPTIONAL ACTIVITY OF CCCDNA MINICHROMOSOMES. HOWEVER, IT REMAINS UNCLEAR HOW THE EPIGENETIC STATE OF CCCDNA AFFECTS ITS STABILITY. APPROACHES AND RESULTS: BY USING HBV INFECTION CELL MODELS AND IN VITRO AND IN VIVO RECOMBINANT CCCDNA (RCCCDNA) AND HBVCIRCLE MODELS, THE REDUCTION RATE OF HBV CCCDNA AND THE EFFICACY OF APOLIPOPROTEIN B MRNA EDITING ENZYME CATALYTIC SUBUNIT 3A (APOBEC3A)-MEDIATED AND CRISPR/CRISPR-ASSOCIATED 9 (CAS9)-MEDIATED CCCDNA TARGETING WERE COMPARED BETWEEN CCCDNAS WITH DISTINCT TRANSCRIPTIONAL ACTIVITIES. INTERFERON-ALPHA TREATMENT AND HEPATITIS B X PROTEIN (HBX) DELETION WERE APPLIED AS TWO STRATEGIES FOR CCCDNA REPRESSION. CHROMATIN IMMUNOPRECIPITATION AND MICROCOCCAL NUCLEASE ASSAYS WERE PERFORMED TO DETERMINE THE EPIGENETIC PATTERN OF CCCDNA. HBV CCCDNA LEVELS REMAINED STABLE IN NONDIVIDING HEPATOCYTES; HOWEVER, THEY WERE SIGNIFICANTLY REDUCED DURING CELL DIVISION, AND THE REDUCTION RATE WAS SIMILAR BETWEEN CCCDNAS IN TRANSCRIPTIONALLY ACTIVE AND TRANSCRIPTIONALLY REPRESSED STATES. STRIKINGLY, HBV RCCCDNA WITHOUT HBX EXPRESSION EXHIBITED A SIGNIFICANTLY LONGER PERSISTENCE IN MICE. THE CCCDNA WITH LOW TRANSCRIPTIONAL ACTIVITY EXHIBITED AN EPIGENETICALLY INACTIVE PATTERN AND WAS MORE DIFFICULT TO ACCESS BY APOBEC3A AND ENGINEERED CRISPR-CAS9. THE EPIGENETIC REGULATOR ACTIVATING CCCDNA INCREASED ITS VULNERABILITY TO APOBEC3A. CONCLUSIONS: HBV CCCDNA MINICHROMOSOMES IN DISTINCT EPIGENETIC TRANSCRIPTIONAL STATES SHOWED A SIMILAR REDUCTION RATE DURING CELL DIVISION BUT SIGNIFICANTLY DIFFERED IN THEIR ACCESSIBILITY AND VULNERABILITY TO TARGETED NUCLEASES AND ANTIVIRAL AGENTS. EPIGENETIC SENSITIZATION OF CCCDNA MAKES IT MORE SUSCEPTIBLE TO DAMAGE AND MAY POTENTIALLY CONTRIBUTE TO AN HBV CURE. 2022 7 5803 39 STING SIGNALING ACTIVATION INHIBITS HBV REPLICATION AND ATTENUATES THE SEVERITY OF LIVER INJURY AND HBV-INDUCED FIBROSIS. THE COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) OF HBV PLAYS A CRUCIAL ROLE IN VIRAL PERSISTENCE AND IS ALSO A RISK FACTOR FOR DEVELOPING HBV-INDUCED DISEASES, INCLUDING LIVER FIBROSIS. STIMULATOR OF INTERFERON GENES (STING), A MASTER REGULATOR OF DNA-MEDIATED INNATE IMMUNE ACTIVATION, IS A POTENTIAL THERAPEUTIC TARGET FOR VIRAL INFECTION AND VIRUS-RELATED DISEASES. IN THIS STUDY, AGONIST-INDUCED STING SIGNALING ACTIVATION IN MACROPHAGES WAS REVEALED TO INHIBIT CCCDNA-MEDIATED TRANSCRIPTION AND HBV REPLICATION VIA EPIGENETIC MODIFICATION IN HEPATOCYTES. NOTABLY, STING ACTIVATION COULD EFFICIENTLY ATTENUATE THE SEVERITY OF LIVER INJURY AND FIBROSIS IN A CHRONIC RECOMBINANT CCCDNA (RCCCDNA) MOUSE MODEL, WHICH IS A PROVEN SUITABLE RESEARCH PLATFORM FOR HBV-INDUCED FIBROSIS. MECHANISTICALLY, STING-ACTIVATED AUTOPHAGIC FLUX COULD SUPPRESS MACROPHAGE INFLAMMASOME ACTIVATION, LEADING TO THE AMELIORATION OF LIVER INJURY AND HBV-INDUCED FIBROSIS. OVERALL, THE ACTIVATION OF STING SIGNALING COULD INHIBIT HBV REPLICATION THROUGH EPIGENETIC SUPPRESSION OF CCCDNA AND ALLEVIATE HBV-INDUCED LIVER FIBROSIS THROUGH THE SUPPRESSION OF MACROPHAGE INFLAMMASOME ACTIVATION BY ACTIVATING AUTOPHAGIC FLUX IN A CHRONIC HBV MOUSE MODEL. THIS STUDY SUGGESTS THAT TARGETING THE STING SIGNALING PATHWAY MAY BE AN IMPORTANT THERAPEUTIC STRATEGY TO PROTECT AGAINST PERSISTENT HBV REPLICATION AND HBV-INDUCED FIBROSIS. 2022 8 1667 46 DOWNREGULATION OF PCAF BY MIR-181A/B PROVIDES FEEDBACK REGULATION TO TNF-ALPHA-INDUCED TRANSCRIPTION OF PROINFLAMMATORY GENES IN LIVER EPITHELIAL CELLS. ABERRANT CELLULAR RESPONSES TO PROINFLAMMATORY CYTOKINES, SUCH AS TNF-ALPHA, ARE PATHOGENIC FEATURES IN MOST CHRONIC INFLAMMATORY DISEASES. A VARIETY OF EXTRACELLULAR AND INTRACELLULAR FEEDBACK PATHWAYS HAS EVOLVED TO PREVENT AN INAPPROPRIATE CELLULAR REACTION TO THESE PROINFLAMMATORY CYTOKINES. IN THIS STUDY, WE REPORT THAT TNF-ALPHA TREATMENT OF HUMAN AND MOUSE CHOLANGIOCYTES AND HEPATOCYTES DOWNREGULATED EXPRESSION OF P300/CBP-ASSOCIATED FACTOR (PCAF), A COACTIVATOR AND AN ACETYLTRANSFERASE THAT PROMOTES HISTONE ACETYLATION AND GENE TRANSCRIPTION. OF THESE UPREGULATED MICRORNAS IN TNF-ALPHA-TREATED CELLS, MIR-181A/B (MIR-181A AND MIR-181B) SUPPRESSED TRANSLATION OF PCAF MRNA. FUNCTIONAL MANIPULATION OF MIR-181A/B CAUSED RECIPROCAL ALTERATIONS IN PCAF PROTEIN EXPRESSION IN CULTURED CHOLANGIOCYTES AND HEPATOCYTES. INHIBITION OF MIR-181A/B FUNCTION WITH ANTI-MIRS BLOCKED TNF-ALPHA-INDUCED SUPPRESSION OF PCAF EXPRESSION. PROMOTER RECRUITMENT OF PCAF WAS SHOWN TO BE ASSOCIATED WITH TNF-ALPHA-INDUCED TRANSCRIPTION OF INFLAMMATORY GENES. INTRIGUINGLY, PRETREATMENT OF CELLS WITH TNF-ALPHA INHIBITED TRANSCRIPTION OF INFLAMMATORY GENES IN RESPONSE TO SUBSEQUENT TNF-ALPHA STIMULATION. OVEREXPRESSION OF PCAF OR INHIBITION OF MIR-181A/B FUNCTION WITH ANTI-MIRS ATTENUATED THE INHIBITORY EFFECTS OF TNF-ALPHA PRETREATMENT ON EPITHELIAL INFLAMMATORY RESPONSE TO SUBSEQUENT TNF-ALPHA STIMULATION. DOWNREGULATION OF PCAF AND THE INHIBITORY EFFECTS OF TNF-ALPHA PRETREATMENT ON LIVER EPITHELIAL INFLAMMATORY RESPONSE WERE FURTHER CONFIRMED IN A MOUSE MODEL OF TNF-ALPHA I.P. INJECTION. THESE DATA SUGGEST THAT PCAF IS A TARGET FOR MIR-181A/B, AND DOWNREGULATION OF PCAF BY TNF-ALPHA PROVIDES NEGATIVE FEEDBACK REGULATION TO INFLAMMATORY REACTIONS IN LIVER EPITHELIAL CELLS, A PROCESS THAT MAY BE RELEVANT TO THE EPIGENETIC FINE-TUNING OF EPITHELIAL INFLAMMATORY PROCESSES IN GENERAL. 2012 9 5301 23 PROTEIN PHOSPHATASE 2A CATALYTIC SUBUNIT ALPHA PLAYS A MYD88-DEPENDENT, CENTRAL ROLE IN THE GENE-SPECIFIC REGULATION OF ENDOTOXIN TOLERANCE. MYD88, THE INTRACELLULAR ADAPTOR OF MOST TLRS, MEDIATES EITHER PROINFLAMMATORY OR IMMUNOSUPPRESSIVE SIGNALING THAT CONTRIBUTES TO CHRONIC INFLAMMATION-ASSOCIATED DISEASES. ALTHOUGH GENE-SPECIFIC CHROMATIN MODIFICATIONS REGULATE INFLAMMATION, THE ROLE OF MYD88 SIGNALING IN ESTABLISHING SUCH EPIGENETIC LANDSCAPES UNDER DIFFERENT INFLAMMATORY STATES REMAINS ELUSIVE. USING QUANTITATIVE PROTEOMICS TO ENUMERATE THE INFLAMMATION-PHENOTYPIC CONSTITUENTS OF THE MYD88 INTERACTOME, WE FOUND THAT IN ENDOTOXIN-TOLERANT MACROPHAGES, PROTEIN PHOSPHATASE 2A CATALYTIC SUBUNIT ALPHA (PP2AC) ENHANCES ITS ASSOCIATION WITH MYD88 AND IS CONSTITUTIVELY ACTIVATED. KNOCKDOWN OF PP2AC PREVENTS SUPPRESSION OF PROINFLAMMATORY GENES AND RESISTANCE TO APOPTOSIS. THROUGH SITE-SPECIFIC DEPHOSPHORYLATION, CONSTITUTIVELY ACTIVE PP2AC DISRUPTS THE SIGNAL-PROMOTING TLR4-MYD88 COMPLEX AND BROADLY SUPPRESSES THE ACTIVITIES OF MULTIPLE PROINFLAMMATORY/PROAPOPTOTIC PATHWAYS AS WELL, SHIFTING PROINFLAMMATORY MYD88 SIGNALING TO A PROSURVIVAL MODE. CONSTITUTIVELY ACTIVE PP2AC TRANSLOCATED WITH MYD88 INTO THE NUCLEI OF TOLERANT MACROPHAGES ESTABLISHES THE IMMUNOSUPPRESSIVE PATTERN OF CHROMATIN MODIFICATIONS AND REPRESSES CHROMATIN REMODELING TO SELECTIVELY SILENCE PROINFLAMMATORY GENES, COORDINATING THE MYD88-DEPENDENT INFLAMMATION CONTROL AT BOTH SIGNALING AND EPIGENETIC LEVELS UNDER ENDOTOXIN-TOLERANT CONDITIONS. 2013 10 5592 30 ROLE OF TUMOR NECROSIS FACTOR-ALPHA IN THE HUMAN SYSTEMIC ENDOTOXIN-INDUCED TRANSCRIPTOME. TNFALPHA HAS BEEN IMPLICATED IN THE PATHOGENESIS OF VARIOUS INFLAMMATORY DISEASES. DIFFERENT STRATEGIES TO INHIBIT TNFALPHA IN PATIENTS WITH SEPSIS AND CHRONIC INFLAMMATORY CONDITIONS HAVE SHOWN CONTRASTING OUTCOMES. ALTHOUGH TNFALPHA INHIBITORS ARE WIDELY USED IN CLINICAL PRACTICE, THE IMPACT OF TNFALPHA ANTAGONISM ON WHITE BLOOD CELL GENE EXPRESSION PROFILES DURING ACUTE INFLAMMATION IN HUMANS IN VIVO HAS NOT BEEN ASSESSED. WE HERE LEVERAGED THE ESTABLISHED MODEL OF HUMAN ENDOTOXEMIA TO EXAMINE THE EFFECT OF THE TNFALPHA ANTAGONIST, ETANERCEPT, ON THE GENOME-WIDE TRANSCRIPTIONAL RESPONSES IN CIRCULATING LEUKOCYTES INDUCED BY INTRAVENOUS LPS ADMINISTRATION IN MALE SUBJECTS. ETANERCEPT PRE-TREATMENT RESULTED IN A MARKEDLY DAMPENED TRANSCRIPTIONAL RESPONSE TO LPS. GENE CO-EXPRESSION NETWORK ANALYSIS REVEALED THIS LPS-INDUCED TRANSCRIPTOME CAN BE CATEGORIZED AS TNFALPHA RESPONSIVE AND NON-RESPONSIVE MODULES. HIGHLY SIGNIFICANT TNFALPHA RESPONSIVE MODULES INCLUDE NF-KB SIGNALING, ANTIVIRAL RESPONSES AND T-CELL MEDIATED RESPONSES. WITHIN THESE TNFALPHA RESPONSIVE MODULES WE DELINEATE FUNDAMENTAL GENES INVOLVED IN EPIGENETIC MODIFICATIONS, TRANSCRIPTIONAL INITIATION AND ELONGATION. THUS, WE PROVIDE COMPREHENSIVE INFORMATION ABOUT MOLECULAR PATHWAYS THAT MIGHT BE TARGETED BY THERAPEUTIC INTERVENTIONS THAT SEEK TO INHIBIT TNFALPHA ACTIVITY DURING HUMAN INFLAMMATORY DISEASES. 2013 11 4239 39 METHYLATION PROFILE OF HEPATITIS B VIRUS IS NOT INFLUENCED BY INTERFERON ALPHA IN HUMAN LIVER CANCER CELLS. INTERFERON (IFN) ALPHA IS USED FOR THE TREATMENT OF CHRONIC HEPATITIS B VIRUS (HBV) INFECTION, BUT THE MOLECULAR MECHANISMS UNDERLYING ITS ANTIVIRAL EFFECT HAVE NOT BEEN FULLY ELUCIDATED. EPIGENETIC MODIFICATIONS REGULATE THE TRANSCRIPTIONAL ACTIVITY OF COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) IN CELLS WITH CHRONIC HBV INFECTION. IFN?ALPHA HAS BEEN SHOWN TO MODIFY CCCDNA?BOUND HISTONES, BUT IT IS NOT KNOWN WHETHER THE ANTI?HBV EFFECT OF IFN?ALPHA INVOLVES METHYLATION OF CCCDNA. THE PRESENT STUDY AIMED TO DETERMINE WHETHER IFN?ALPHA INDUCED METHYLATION OF HBV CCCDNA IN A CELL?BASED MODEL IN WHICH HEPG2 CELLS WERE DIRECTLY INFECTED WITH WILD?TYPE HBV VIRIONS. METHYLATION STATUS OF HBV CCCDNA WAS ASSESSED USING GLOBAL DNA METHYLATION ELISA ASSAY, METHYLATION?SPECIFIC PCR AND BISULFITE SEQUENCING. IFN?ALPHA SUPPRESSED HBV DNA AND RNA TRANSCRIPTS, BUT METHYLATION PROFILES WERE SIMILAR BETWEEN THE CONTROL AND IFN?ALPHA TREATED GROUPS. CHROMATIN IMMUNOPRECIPITATION RESULTS REVEALED BINDING OF DNA METHYLTRANSFERASES (DNMT) 3A AND DNMT3B TO HBV CCCDNA AND TREATMENT WITH IFN?ALPHA SUPPRESSED THE RECRUITMENT OF DNMT3B TO CCCDNA. TAKEN TOGETHER, THESE RESULTS SUGGEST THAT IFN?ALPHA DOES NOT INDUCE METHYLATION OF HBV CCCDNA. THEREFORE, IT WAS CONCLUDED THAT METHYLATION IS UNLIKELY TO CONTRIBUTE TO THE ANTI?HBV EFFECT OF IFN?ALPHA IN HEPG2 CELLS, AND THAT ALTERNATIVE MECHANISMS NEED TO BE SOUGHT TO ENHANCE CCCDNA METHYLATION AS A NOVEL THERAPY AGAINST HBV. 2021 12 3529 42 ILLUMINATING THE LIVE-CELL DYNAMICS OF HEPATITIS B VIRUS COVALENTLY CLOSED CIRCULAR DNA USING THE CRISPR-TAG SYSTEM. THE COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) OF HEPATITIS B VIRUS (HBV) IS THE MAJOR OBSTACLE TO CURING CHRONIC HEPATITIS B (CHB). CURRENT CCCDNA DETECTION METHODS ARE MOSTLY BASED ON BIOCHEMICAL EXTRACTION AND BULK MEASUREMENTS. THEY NEVERTHELESS GENERATED A GENERAL SKETCH OF ITS BIOLOGICAL FEATURES. HOWEVER, AN UNDERSTANDING OF THE SPATIOTEMPORAL FEATURES OF CCCDNA IS STILL LACKING. TO ACHIEVE THIS, WE ESTABLISHED A SYSTEM COMBINING CRISPR-TAG AND RECOMBINANT HBV MINICIRCLE TECHNOLOGY TO VISUALIZE CCCDNA AT SINGLE-CELL LEVEL IN REAL TIME. USING THIS SYSTEM, WE FOUND THAT THE OBSERVED RECOMBINANT CCCDNA (RCCCDNA) CORRELATED QUANTITATIVELY WITH ITS ACTIVE TRANSCRIPTS WHEN A LOW TO MEDIUM NUMBER OF FOCI (<20) ARE PRESENT, BUT THIS CORRELATION WAS LOST IN CELLS HARBORING HIGH COPY NUMBERS (>/=20) OF RCCCDNA. THE DISRUPTION OF HBX EXPRESSION SEEMS TO DISPLACE CCCDNA FROM THE DCAS9-ACCESSIBLE REGION, WHILE HBX COMPLEMENTATION RESTORED THE NUMBER OF OBSERVABLE CCCDNA FOCI. THIS INDICATED REGULATION OF CCCDNA ACCESSIBILITY BY HBX. SECOND, OBSERVABLE HBV AND DUCK HBV (DHBV) CCCDNA MOLECULES ARE SUBSTANTIALLY LOST DURING CELL DIVISION, AND THE REMAINING ONES WERE DISTRIBUTED RANDOMLY TO DAUGHTER CELLS. IN CONTRAST, KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS (KSHV)-DERIVED EPISOMES CAN BE RETAINED IN A LANA (LATENCY-ASSOCIATED NUCLEAR ANTIGEN)-DEPENDENT MANNER. LAST, THE DYNAMICS OF RCCCDNA EPISOMES IN NUCLEI DISPLAYED CONFINED DIFFUSION AT SHORT TIME SCALES, WITH DIRECTIONAL TRANSPORT OVER LONGER TIME SCALES. IN CONCLUSION, THIS SYSTEM ENABLES THE STUDY OF PHYSIOLOGICAL KINETICS OF CCCDNA AT THE SINGLE-CELL LEVEL. THE DIFFERENTIAL ACCESSIBILITY OF RCCCDNA TO DCAS9 UNDER VARIOUS PHYSIOLOGICAL CONDITIONS MAY BE EXPLOITED TO ELUCIDATE THE COMPLEX TRANSCRIPTIONAL AND EPIGENETIC REGULATION OF THE HBV MINICHROMOSOME. IMPORTANCE UNDERSTANDING THE FORMATION AND MAINTENANCE OF HBV CCCDNA HAS ALWAYS BEEN A CENTRAL ISSUE IN THE STUDY OF HBV PATHOBIOLOGY. HOWEVER, LITTLE PROGRESS HAS BEEN MADE DUE TO THE LACK OF ROBUST ASSAY SYSTEMS AND ITS RESISTANCE TO GENETIC MODIFICATION. HERE, A LIVE-CELL IMAGING SYSTEM BY GRAFTING CRISPR-TAG INTO THE RECOMBINANT CCCDNA WAS ESTABLISHED TO VISUALIZE ITS MOLECULAR BEHAVIOR IN REAL TIME. WE FOUND THAT THE ACCESSIBILITY OF RCCCDNA TO DCAS9-BASED IMAGING IS RELATED TO HBX-REGULATED MECHANISMS. WE ALSO CONFIRMED THE SUBSTANTIAL LOSS OF OBSERVABLE RCCCDNA IN ONE-ROUND CELL DIVISION AND RANDOM DISTRIBUTION OF THE REMAINING MOLECULES. MOLECULAR DYNAMICS ANALYSIS REVEALED THE CONFINED MOVEMENT OF THE RCCCDNA EPISOME, SUGGESTING ITS JUXTAPOSITION TO CHROMATIN DOMAINS. OVERALL, THIS NOVEL SYSTEM OFFERS A UNIQUE PLATFORM TO INVESTIGATE THE INTRANUCLEAR DYNAMICS OF CCCDNA WITHIN LIVE CELLS. 2023 13 3642 28 INCREASED H3K4ME3 METHYLATION AND DECREASED MIR-7113-5P EXPRESSION LEAD TO ENHANCED WNT/BETA-CATENIN SIGNALING IN IMMUNE CELLS FROM PTSD PATIENTS LEADING TO INFLAMMATORY PHENOTYPE. BACKGROUND: POSTTRAUMATIC STRESS DISORDER (PTSD) IS A PSYCHIATRIC DISORDER ACCOMPANIED BY CHRONIC PERIPHERAL INFLAMMATION. WHAT TRIGGERS INFLAMMATION IN PTSD IS CURRENTLY UNCLEAR. IN THE PRESENT STUDY, WE IDENTIFIED POTENTIAL DEFECTS IN SIGNALING PATHWAYS IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) FROM INDIVIDUALS WITH PTSD. METHODS: RNASEQ (5 SAMPLES EACH FOR CONTROLS AND PTSD), CHIPSEQ (5 SAMPLES EACH) AND MIRNA ARRAY (6 SAMPLES EACH) WERE USED IN COMBINATION WITH BIOINFORMATICS TOOLS TO IDENTIFY DYSREGULATED GENES IN PBMCS. REAL TIME QRT-PCR (24 SAMPLES EACH) AND IN VITRO ASSAYS WERE EMPLOYED TO VALIDATE OUR PRIMARY FINDINGS AND HYPOTHESIS. RESULTS: BY RNA-SEQ ANALYSIS OF PBMCS, WE FOUND THAT WNT SIGNALING PATHWAY WAS UPREGULATED IN PTSD WHEN COMPARED TO NORMAL CONTROLS. SPECIFICALLY, WE FOUND INCREASED EXPRESSION OF WNT10B IN THE PTSD GROUP WHEN COMPARED TO CONTROLS. OUR FINDINGS WERE CONFIRMED USING NCBI'S GEO DATABASE INVOLVING A LARGER SAMPLE SIZE. ADDITIONALLY, IN VITRO ACTIVATION STUDIES REVEALED THAT ACTIVATED BUT NOT NAIVE PBMCS FROM CONTROL INDIVIDUALS EXPRESSED MORE IFNGAMMA IN THE PRESENCE OF RECOMBINANT WNT10B SUGGESTING THAT WNT SIGNALING PLAYED A CRUCIAL ROLE IN EXACERBATING INFLAMMATION. NEXT, WE INVESTIGATED THE MECHANISM OF INDUCTION OF WNT10B AND FOUND THAT INCREASED EXPRESSION OF WNT10B MAY RESULT FROM EPIGENETIC MODULATION INVOLVING DOWNREGULATION OF HSA-MIR-7113-5P WHICH TARGETED WNT10B. FURTHERMORE, WE ALSO OBSERVED THAT WNT10B OVEREXPRESSION WAS LINKED TO HIGHER EXPRESSION OF H3K4ME3 HISTONE MODIFICATION AROUND THE PROMOTOR OF WNT10B. ADDITIONALLY, KNOCKDOWN OF HISTONE DEMETHYLASE SPECIFIC TO H3K4ME3, USING SIRNA, LED TO INCREASED EXPRESSION OF WNT10B PROVIDING CONCLUSIVE EVIDENCE THAT H3K4ME3 INDEED CONTROLLED WNT10B EXPRESSION. CONCLUSIONS: IN SUMMARY, OUR DATA DEMONSTRATE FOR THE FIRST TIME THAT WNT SIGNALING PATHWAY IS UPREGULATED IN PBMCS OF PTSD PATIENTS RESULTING FROM EPIGENETIC CHANGES INVOLVING MICRORNA DYSREGULATION AND HISTONE MODIFICATIONS, WHICH IN TURN MAY PROMOTE THE INFLAMMATORY PHENOTYPE IN SUCH CELLS. 2020 14 3781 30 INTERFERON SIGNATURE IN PATIENTS WITH STAT1 GAIN-OF-FUNCTION MUTATION IS EPIGENETICALLY DETERMINED. STAT1 GAIN-OF-FUNCTION (GOF) VARIANTS LEAD TO DEFECTIVE TH17 CELL DEVELOPMENT AND CHRONIC MUCOCUTANEOUS CANDIDIASIS (CMC), BUT FREQUENTLY ALSO TO AUTOIMMUNITY. STIMULATION OF CELLS WITH STAT1 INDUCING CYTOKINES LIKE INTERFERONS (IFN) RESULT IN HYPERPHOSPHORYLATION AND DELAYED DEPHOSPHORYLATION OF GOF STAT1. HOWEVER, THE MECHANISM HOW THE DELAYED DEPHOSPHORYLATION EXACTLY CAUSES THE INCREASED EXPRESSION OF STAT1-DEPENDENT GENES, AND HOW THE INTRACELLULAR SIGNAL TRANSDUCTION FROM CYTOKINE RECEPTORS IS AFFECTED, REMAINS UNKNOWN. IN THIS STUDY WE SHOW THAT THE CIRCULATING LEVELS OF IFN-ALPHA WERE NOT PERSISTENTLY ELEVATED IN STAT1 GOF PATIENTS. NEVERTHELESS, THE EXPRESSION OF INTERFERON SIGNATURE GENES WAS EVIDENT EVEN IN THE PATIENT WITH LOW OR UNDETECTABLE SERUM IFN-ALPHA LEVELS. CHROMATIN IMMUNOPRECIPITATION (CHIP) EXPERIMENTS REVEALED THAT THE ACTIVE CHROMATIN MARK TRIMETHYLATION OF LYSINE 4 OF HISTONE 3 (H3K4ME3), WAS SIGNIFICANTLY ENRICHED IN AREAS ASSOCIATED WITH INTERFERON-STIMULATED GENES IN STAT1 GOF CELLS IN COMPARISON TO CELLS FROM HEALTHY DONORS. THIS SUGGESTS THAT THE CHROMATIN BINDING OF GOF STAT1 VARIANT PROMOTES EPIGENETIC CHANGES COMPATIBLE WITH HIGHER GENE EXPRESSION AND ELEVATED REACTIVITY TO TYPE I INTERFERONS, AND POSSIBLY PREDISPOSES FOR INTERFERON-RELATED AUTOIMMUNITY. THE RESULTS ALSO SUGGEST THAT EPIGENETIC REWIRING MAY BE RESPONSIBLE FOR TREATMENT FAILURE OF JANUS KINASE 1/2 (JAK1/2) INHIBITORS IN CERTAIN PATIENTS. 2019 15 1906 39 ENHANCER OF ZESTE HOMOLOG 2-CATALYSED H3K27 TRIMETHYLATION PLAYS A KEY ROLE IN ACUTE-ON-CHRONIC LIVER FAILURE VIA TNF-MEDIATED PATHWAY. ACUTE-ON-CHRONIC LIVER FAILURE IS MAINLY DUE TO HOST IMMUNITY SELF-DESTRUCTION. THE HISTONE H3 LYSINE 27 (H3K27) TRIMETHYLATING ENZYME, ENHANCER OF ZESTE HOMOLOG 2 (EZH2) MEDIATES EPIGENETIC SILENCING OF GENE EXPRESSION AND REGULATES IMMUNITY, ALSO INVOLVES PATHOGENESIS OF SEVERAL LIVER DISEASES. THE CURRENT STUDY WAS TO DETERMINE THE ROLE OF METHYLTRANSFERASE EZH2 AND ITS CATALYSED H3K27 TRIMETHYLATION (H3K27ME3) IN LIVER FAILURE, AND TO FURTHER INVESTIGATE THE POTENTIAL TARGET FOR LIVER FAILURE TREATMENT. EZH2 AND ITS CATALYSED H3K27ME3 WERE DETERMINED IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMC) FROM LIVER FAILURE PATIENTS AND KUPFFER CELLS FROM EXPERIMENTAL MICE. FURTHERMORE, GSK126 (AN INHIBITOR FOR EZH2 TRIMETHYLATION FUNCTION) WAS APPLIED IN LIVER FAILURE MICE IN VIVO, AND LIPOPOLYSACCHARIDE-STIMULATED MONONUCLEAR CELLS IN VITRO. EZH2 AND H3K27ME3 WERE SIGNIFICANTLY UPREGULATED IN HUMAN PBMC FROM LIVER FAILURE PATIENTS OR MURINE KUPFFER CELLS FROM THE LIVER FAILURE ANIMALS, RESPECTIVELY. GSK126 AMELIORATED DISEASE SEVERITY IN LIVER FAILURE MICE, WHICH MAYBE ATTRIBUTE TO DOWN-REGULATE CIRCULATING AND HEPATIC PROINFLAMMATORY CYTOKINES, ESPECIALLY TNF VIA REDUCING H3K27ME3. IN-DEPTH CHROMATIN IMMUNOPRECIPITATION ANALYSIS UNRAVELLED THAT DECREASED ENRICHMENT OF H3K27ME3 ON TNF PROMOTOR, RESULTING IN TNF ELEVATION IN KUPFFER CELLS FROM LIVER FAILURE MICE. NUCLEAR FACTOR KAPPA B (NF-KAPPAB) AND PROTEIN KINASE B (AKT) SIGNALLING PATHWAYS WERE ACTIVATED UPON LIPOPOLYSACCHARIDE STIMULATION, BUT ATTENUATED BY USING GSK126, ACCOMPANIED WITH DECREASED TNF IN VITRO. IN CONCLUSION, EZH2 AND H3K27ME3 CONTRIBUTED TO THE PATHOGENESIS OF LIVER FAILURE VIA TRIGGERING TNF AND OTHER INDISPENSABLE PROINFLAMMATORY CYTOKINES. EZH2 WAS TO MODIFY H3K27ME3 ENRICHMENT, AS WELL AS, ACTIVATION OF THE DOWNSTREAM NF-KAPPAB AND AKT SIGNALLING PATHWAYS. 2018 16 245 31 ADRENERGIC REPRESSION OF THE EPIGENETIC READER MECP2 FACILITATES CARDIAC ADAPTATION IN CHRONIC HEART FAILURE. RATIONALE: IN CHRONIC HEART FAILURE, INCREASED ADRENERGIC ACTIVATION CONTRIBUTES TO STRUCTURAL REMODELING AND ALTERED GENE EXPRESSION. ALTHOUGH ADRENERGIC SIGNALING ALTERS HISTONE MODIFICATIONS, IT IS UNKNOWN, WHETHER IT ALSO AFFECTS OTHER EPIGENETIC PROCESSES, INCLUDING DNA METHYLATION AND ITS RECOGNITION. OBJECTIVE: THE AIM OF THIS STUDY WAS TO IDENTIFY THE MECHANISM OF REGULATION OF THE METHYL-CPG-BINDING PROTEIN 2 (MECP2) AND ITS FUNCTIONAL SIGNIFICANCE DURING CARDIAC PRESSURE OVERLOAD AND UNLOADING. METHODS AND RESULTS: MECP2 WAS IDENTIFIED AS A REVERSIBLY REPRESSED GENE IN MOUSE HEARTS AFTER TRANSVERSE AORTIC CONSTRICTION AND WAS NORMALIZED AFTER REMOVAL OF THE CONSTRICTION. SIMILARLY, MECP2 REPRESSION IN HUMAN FAILING HEARTS RESOLVED AFTER UNLOADING BY A LEFT VENTRICULAR ASSIST DEVICE. THE CLUSTER MIR-212/132 WAS UPREGULATED AFTER TRANSVERSE AORTIC CONSTRICTION OR ON ACTIVATION OF ALPHA1- AND BETA1-ADRENOCEPTORS AND MIR-212/132 LED TO REPRESSION OF MECP2. PREVENTION OF MECP2 REPRESSION BY A CARDIOMYOCYTE-SPECIFIC, DOXYCYCLINE-REGULATABLE TRANSGENIC MOUSE MODEL AGGRAVATED CARDIAC HYPERTROPHY, FIBROSIS, AND CONTRACTILE DYSFUNCTION AFTER TRANSVERSE AORTIC CONSTRICTION. ABLATION OF MECP2 IN CARDIOMYOCYTES FACILITATED RECOVERY OF FAILING HEARTS AFTER REVERSIBLE TRANSVERSE AORTIC CONSTRICTION. GENOME-WIDE EXPRESSION ANALYSIS, CHROMATIN IMMUNOPRECIPITATION EXPERIMENTS, AND DNA METHYLATION ANALYSIS IDENTIFIED MITOCHONDRIAL GENES AND THEIR TRANSCRIPTIONAL REGULATORS AS MECP2 TARGET GENES. COINCIDENT WITH ITS REPRESSION, MECP2 WAS REMOVED FROM ITS TARGET GENES, WHEREAS DNA METHYLATION OF MECP2 TARGET GENES REMAINED STABLE DURING PRESSURE OVERLOAD. CONCLUSIONS: THESE DATA CONNECT ADRENERGIC ACTIVATION WITH A MICRORNA-MECP2 EPIGENETIC PATHWAY THAT IS IMPORTANT FOR CARDIAC ADAPTATION DURING THE DEVELOPMENT AND RECOVERY FROM HEART FAILURE. 2015 17 6599 27 TWIST1 AND TWIST2 INDUCE HUMAN MACROPHAGE MEMORY UPON CHRONIC INNATE RECEPTOR TREATMENT BY HDAC-MEDIATED DEACETYLATION OF CYTOKINE PROMOTERS. INTESTINAL TISSUES ARE CONTINUOUSLY EXPOSED TO MICROBIAL PRODUCTS THAT STIMULATE PATTERN-RECOGNITION RECEPTORS (PRRS). ONGOING PRR STIMULATION CAN CONFER EPIGENETIC CHANGES IN MACROPHAGES, WHICH CAN THEN REGULATE SUBSEQUENT IMMUNE OUTCOMES AND ADAPTATION TO THE LOCAL ENVIRONMENT. MECHANISMS LEADING TO THESE CHANGES ARE INCOMPLETELY UNDERSTOOD. WE FOUND THAT SHORT-TERM STIMULATION OF THE PRR NOD2 IN PRIMARY HUMAN MONOCYTE-DERIVED MACROPHAGES RESULTED IN INCREASED H3 AND H4 ACETYLATION OF CYTOKINE PROMOTERS, CONSISTENT WITH THE INCREASED CYTOKINE SECRETION OBSERVED. HOWEVER, WITH PROLONGED NOD2 STIMULATION, BOTH THE ACETYLATION AND CYTOKINE SECRETION WERE DRAMATICALLY DECREASED. CHRONIC NOD2 STIMULATION UPREGULATED THE TRANSCRIPTION FACTORS TWIST1 AND TWIST2, WHICH BOUND TO THE PROMOTERS OF THE HISTONE DEACETYLASES HDAC1 AND HDAC3 AND INDUCED HDAC1 AND HDAC3 EXPRESSION. HDAC1 AND HDAC3 THEN MEDIATED HISTONE DEACETYLATION AT CYTOKINE PROMOTERS AND, IN TURN, CYTOKINE DOWNREGULATION UNDER THESE CONDITIONS. SIMILAR REGULATION WAS OBSERVED UPON CHRONIC STIMULATION OF MULTIPLE PRRS. CONSISTENT WITH THE CHRONIC MICROBIAL EXPOSURE IN THE INTESTINAL ENVIRONMENT, TWIST1, TWIST2, HDAC1, AND HDAC3 WERE UPREGULATED IN HUMAN INTESTINAL RELATIVE TO PERIPHERAL MACROPHAGES. IMPORTANTLY, COMPLEMENTING HDAC1 AND HDAC3 IN TWIST1/TWIST2-DEFICIENT MONOCYTE-DERIVED MACROPHAGES RESTORED THE REDUCED HISTONE ACETYLATION ON CYTOKINE PROMOTERS AND THE DECREASED CYTOKINE SECRETION WITH CHRONIC NOD2 STIMULATION. TAKEN TOGETHER, WE IDENTIFY MECHANISMS WHEREIN TWIST1 AND TWIST2 PROMOTE CHROMATIN MODIFICATIONS, RESULTING IN MACROPHAGE INSTRUCTION AND ADAPTATION TO CONDITIONS IN THE INTESTINAL MICROENVIRONMENT. 2019 18 6074 35 THE DYNAMIC CHROMATIN ARCHITECTURE OF THE REGENERATING LIVER. BACKGROUND & AIMS: THE ADULT LIVER IS THE MAIN DETOXIFICATION ORGAN AND ROUTINELY IS EXPOSED TO ENVIRONMENTAL INSULTS BUT RETAINS THE ABILITY TO RESTORE ITS MASS AND FUNCTION UPON TISSUE DAMAGE. HOWEVER, EXTENSIVE INJURY CAN LEAD TO LIVER FAILURE, AND CHRONIC INJURY CAUSES FIBROSIS, CIRRHOSIS, AND HEPATOCELLULAR CARCINOMA. CURRENTLY, THE TRANSCRIPTIONAL REGULATION OF ORGAN REPAIR IN THE ADULT LIVER IS INCOMPLETELY UNDERSTOOD. METHODS: WE ISOLATED NUCLEI FROM QUIESCENT AS WELL AS REPOPULATING HEPATOCYTES IN A MOUSE MODEL OF HEREDITARY TYROSINEMIA, WHICH RECAPITULATES THE INJURY AND REPOPULATION SEEN IN TOXIC LIVER INJURY IN HUMAN BEINGS. WE THEN PERFORMED THE ASSAY FOR TRANSPOSASE ACCESSIBLE CHROMATIN WITH HIGH-THROUGHPUT SEQUENCING SPECIFICALLY IN REPOPULATING HEPATOCYTES TO IDENTIFY DIFFERENTIALLY ACCESSIBLE CHROMATIN REGIONS AND NUCLEOSOME POSITIONING. IN ADDITION, WE USED MOTIF ANALYSIS TO PREDICT DIFFERENTIAL TRANSCRIPTION FACTOR OCCUPANCY AND VALIDATED THE IN SILICO RESULTS WITH CHROMATIN IMMUNOPRECIPITATION FOLLOWED BY SEQUENCING FOR HEPATOCYTE NUCLEAR FACTOR 4ALPHA (HNF4ALPHA) AND CCCTC-BINDING FACTOR (CTCF). RESULTS: CHROMATIN ACCESSIBILITY IN REPOPULATING HEPATOCYTES WAS INCREASED IN THE REGULATORY REGIONS OF GENES PROMOTING PROLIFERATION AND DECREASED IN THE REGULATORY REGIONS OF GENES INVOLVED IN METABOLISM. THE EPIGENETIC CHANGES AT PROMOTERS AND LIVER ENHANCERS CORRESPOND WITH THE REGULATION OF GENE EXPRESSION, WITH ENHANCERS OF MANY LIVER FUNCTION GENES SHOWING A LESS ACCESSIBLE STATE DURING THE REGENERATIVE PROCESS. MOREOVER, INCREASED CTCF OCCUPANCY AT PROMOTERS AND DECREASED HNF4ALPHA BINDING AT ENHANCERS IMPLICATE THESE FACTORS AS KEY DRIVERS OF THE TRANSCRIPTOMIC CHANGES IN REPLICATING HEPATOCYTES THAT ENABLE LIVER REPOPULATION. CONCLUSIONS: OUR ANALYSIS OF HEPATOCYTE-SPECIFIC EPIGENOMIC CHANGES DURING LIVER REPOPULATION IDENTIFIED CTCF AND HNF4ALPHA AS KEY REGULATORS OF HEPATOCYTE PROLIFERATION AND REGULATION OF METABOLIC PROGRAMS. THUS, LIVER REPOPULATION IN THE SETTING OF TOXIC INJURY MAKES USE OF BOTH GENERAL TRANSCRIPTION FACTORS (CTCF) FOR PROMOTER ACTIVATION, AND REDUCED BINDING BY A HEPATOCYTE-ENRICHED FACTOR (HNF4ALPHA) TO TEMPORARILY LIMIT ENHANCER ACTIVITY. ALL SEQUENCING DATA IN THIS STUDY WERE DEPOSITED TO THE GENE EXPRESSION OMNIBUS DATABASE AND CAN BE DOWNLOADED WITH ACCESSION NUMBER GSE109466. 2020 19 5715 53 SIRT3 RESTRICTS HEPATITIS B VIRUS TRANSCRIPTION AND REPLICATION THROUGH EPIGENETIC REGULATION OF COVALENTLY CLOSED CIRCULAR DNA INVOLVING SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 1 AND SET DOMAIN CONTAINING 1A HISTONE METHYLTRANSFERASES. HEPATITIS B VIRUS (HBV) INFECTION REMAINS A MAJOR HEALTH PROBLEM WORLDWIDE. MAINTENANCE OF THE COVALENTLY CLOSED CIRCULAR DNA (CCCDNA), WHICH SERVES AS A TEMPLATE FOR HBV RNA TRANSCRIPTION, IS RESPONSIBLE FOR THE FAILURE OF ERADICATING CHRONIC HBV DURING CURRENT ANTIVIRAL THERAPY. CCCDNA IS ASSEMBLED WITH CELLULAR HISTONE PROTEINS INTO CHROMATIN, BUT LITTLE IS KNOWN ABOUT THE REGULATION OF HBV CHROMATIN BY HISTONE POSTTRANSLATIONAL MODIFICATIONS. IN THIS STUDY, WE IDENTIFIED SILENT MATING TYPE INFORMATION REGULATION 2 HOMOLOG 3 (SIRT3) AS A HOST FACTOR RESTRICTING HBV TRANSCRIPTION AND REPLICATION BY SCREENING SEVEN MEMBERS OF THE SIRTUIN FAMILY, WHICH IS THE CLASS III HISTONE DEACETYLASE. ECTOPIC SIRT3 EXPRESSION SIGNIFICANTLY REDUCED TOTAL HBV RNAS, 3.5-KB RNA, AS WELL AS REPLICATIVE INTERMEDIATE DNA IN HBV-INFECTED HEPG2-NA(+) /TAUROCHOLATE COTRANSPORTING POLYPEPTIDE CELLS AND PRIMARY HUMAN HEPATOCYTES. IN CONTRAST, GENE SILENCING OF SIRT3 PROMOTED HBV TRANSCRIPTION AND REPLICATION. A MECHANISTIC STUDY FOUND THAT NUCLEAR SIRT3 WAS RECRUITED TO THE HBV CCCDNA, WHERE IT DEACETYLATED HISTONE 3 LYSINE 9. IMPORTANTLY, OCCUPANCY OF SIRT3 ON CCCDNA COULD INCREASE THE RECRUITMENT OF HISTONE METHYLTRANSFERASE SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 1 TO CCCDNA AND DECREASE RECRUITMENT OF SET DOMAIN CONTAINING 1A, LEADING TO A MARKED INCREASE OF TRIMETHYL-HISTONE H3 (LYS9) AND A DECREASE OF TRIMETHYL-HISTONE H3 (LYS4) ON CCCDNA. MOREOVER, SIRT3-MEDIATED HBV CCCDNA TRANSCRIPTIONAL REPRESSION INVOLVED DECREASED BINDING OF HOST RNA POLYMERASE II AND TRANSCRIPTION FACTOR YIN YANG 1 TO CCCDNA. FINALLY, HEPATITIS B VIRAL X PROTEIN COULD RELIEVE SIRT3-MEDIATED CCCDNA TRANSCRIPTIONAL REPRESSION BY INHIBITING BOTH SIRT3 EXPRESSION AND ITS RECRUITMENT TO CCCDNA. CONCLUSION: SIRT3 IS A HOST FACTOR EPIGENETICALLY RESTRICTING HBV CCCDNA TRANSCRIPTION BY ACTING COOPERATIVELY WITH HISTONE METHYLTRANSFERASE; THESE DATA PROVIDE A RATIONALE FOR THE USE OF SIRT3 ACTIVATORS IN THE PREVENTION OR TREATMENT OF HBV INFECTION. (HEPATOLOGY 2018). 2018 20 1826 35 EFFECTS OF HISTONE DEACETYLASE INHIBITOR ON EXTRACELLULAR MATRIX PRODUCTION IN HUMAN NASAL POLYP ORGAN CULTURES. BACKGROUND: NASAL POLYPOSIS IS ASSOCIATED WITH A CHRONIC INFLAMMATORY CONDITION OF THE SINONASAL MUCOSA AND INVOLVES MYOFIBROBLAST DIFFERENTIATION AND EXTRACELLULAR MATRIX (ECM) ACCUMULATION. EPIGENETIC MODULATION BY HISTONE DEACETYLASE (HDAC) INHIBITORS INCLUDING TRICHOSTATIN A (TSA) HAS BEEN REPORTED TO HAVE INHIBITORY EFFECTS ON MYOFIBROBLAST DIFFERENTIATION IN LUNG AND RENAL FIBROBLASTS. THE PURPOSE OF THIS STUDY WAS TO INVESTIGATE THE INHIBITORY EFFECT OF TSA ON MYOFIBROBLAST DIFFERENTIATION AND ECM PRODUCTION IN NASAL POLYP ORGAN CULTURES. METHODS: NASAL POLYP TISSUES FROM 18 PATIENTS WERE ACQUIRED DURING ENDOSCOPIC SINUS SURGERY. AFTER ORGAN CULTURE, NASAL POLYPS WERE STIMULATED WITH TGF-BETA1 AND THEN TREATED WITH TSA. ALPHA-SMOOTH MUSCLE ACTIN (ALPHA-SMA), FIBRONECTIN, AND COLLAGEN TYPE I EXPRESSION LEVELS WERE EXAMINED BY REVERSE TRANSCRIPTION-POLYMERASE CHAIN REACTION (PCR), REAL-TIME PCR, WESTERN BLOT, AND IMMUNOFLUORESCENT STAINING. HDAC2, HDAC4, AND ACETYLATED H4 EXPRESSION LEVELS WERE ASSAYED BY WESTERN BLOT. CYTOTOXICITY WAS ANALYZED BY THE TERMINAL DEOXYNUCLEOTIDYL TRANSFERASE BIOTIN-DUTP NICK END LABELING ASSAY. RESULTS: THE EXPRESSION LEVELS OF ALPHA-SMA, FIBRONECTIN, AND COLLAGEN TYPE 1 WERE INCREASED IN NASAL POLYP AFTER TRANSFORMING GROWTH FACTOR (TGF) BETA1 TREATMENT. TSA-INHIBITED TGF-BETA1 INDUCED THESE GENE AND PROTEIN EXPRESSION LEVELS. FURTHERMORE, TSA SUPPRESSED PROTEIN EXPRESSION LEVELS OF HDAC2 AND HDAC4. HOWEVER, TSA INDUCED HYPERACETYLATION OF HISTONES H4. TREATMENT WITH TGF-BETA1 WITH OR WITHOUT TSA DID NOT HAVE CYTOTOXIC EFFECT. CONCLUSION: THESE FINDINGS PROVIDE NOVEL INSIGHTS INTO THE EPIGENETIC REGULATION IN MYOFIBROBLAST DIFFERENTIATION AND ECM PRODUCTION OF NASAL POLYP. TSA COULD BE A CANDIDATE OF A THERAPEUTIC AGENT FOR REVERSING THE TGF-BETA1-INDUCED ECM SYNTHESIS THAT LEADS TO NASAL POLYP DEVELOPMENT. 2013