1 5610 141 S100A4/TCF COMPLEX TRANSCRIPTION REGULATION DRIVES EPITHELIAL-MESENCHYMAL TRANSITION IN CHRONIC SINUSITIS THROUGH WNT/GSK-3BETA/BETA-CATENIN SIGNALING. EPITHELIAL-MESENCHYMAL TRANSITION (EMT) IS THOUGHT TO BE INVOLVED IN THE TISSUE REMODELING AND LONG-TERM INFLAMMATORY PROCESS OF CHRONIC SINUSITIS (CRS), BUT THE DRIVING MECHANISM IS STILL UNCLEAR. USING HIGH-RESOLUTION MASS SPECTROMETRY, WE PERFORMED A PROTEOMIC SCREEN OF CRS NASAL MUCOSAL TISSUE TO IDENTIFY DIFFERENTIALLY EXPRESSED PROTEINS. DATA ARE AVAILABLE VIA PROTEOMEXCHANGE WITH IDENTIFIER PXD030884. SPECIFICALLY, WE IDENTIFIED S100 CALCIUM BINDING PROTEIN A4 (S100A4), AN EFFECTIVE FACTOR IN INFLAMMATION-RELATED DISEASES, AND ITS DOWNSTREAM PROTEIN CLOSELY RELATED TO TISSUE FIBROSIS COLLAGEN TYPE I ALPHA 1 CHAIN (COL1A1), WHICH SUGGESTED ITS INVOLVEMENT IN NASAL MUCOSAL TISSUE REMODELING. IN ADDITION, STIMULATION OF HUMAN NASAL EPITHELIAL CELLS (HNEPCS) WITH LIPOPOLYSACCHARIDE (LPS) MIMICKED THE INFLAMMATORY ENVIRONMENT OF CRS AND SHOWED THAT S100A4 IS INVOLVED IN REGULATING EMT AND THUS ACCELERATING TISSUE REMODELING IN THE NASAL MUCOSA, BOTH IN TERMS OF INCREASED CELL MOTILITY AND OVEREXPRESSION OF MESENCHYMAL-TYPE PROTEINS. ADDITIONALLY, WE FURTHER INVESTIGATED THE REGULATION MECHANISM OF S100A4 INVOLVED IN EMT IN CRS. OUR RESEARCH RESULTS SHOW THAT IN THE INFLAMMATORY ENVIRONMENT OF CRS NASAL MUCOSAL EPITHELIAL CELLS, TCF-4 WILL TARGET TO BIND TO S100A4 AND REGULATE ITS TRANSCRIPTION. THE TRANSCRIPTION OF S100A4 IN TURN AFFECTS THE EXECUTION OF THE IMPORTANT SIGNALING PATHWAY IN EMT, THE WNT/GSK-3BETA/BETA-CATENIN PATHWAY, THROUGH THE TCF-4/BETA-CATENIN COMPLEX. IN CONCLUSION, THIS STUDY CONFIRMED THAT THE EXPRESSION OF S100A4 WAS SIGNIFICANTLY INCREASED DURING THE PROGRESSIVE EMT PROCESS OF CRS MUCOSAL EPITHELIAL CELLS, AND REVEALED THAT THE TRANSCRIPTIONAL REGULATION OF S100A4 PLAYS AN IMPORTANT ROLE IN THE OCCURRENCE AND DEVELOPMENT OF EMT. THIS FINDING WILL HELP US TO BETTER UNDERSTAND THE PATHOGENESIS BEHIND THE REMODELING IN CRS PATIENTS, AND IDENTIFY TARGET MOLECULES FOR THE TREATMENT OF CRS. 2022 2 5889 39 SYSTEMS APPROACHES TO MODELING CHRONIC MUCOSAL INFLAMMATION. THE RESPIRATORY MUCOSA IS A MAJOR COORDINATOR OF THE INFLAMMATORY RESPONSE IN CHRONIC AIRWAY DISEASES, INCLUDING ASTHMA AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD). SIGNALS PRODUCED BY THE CHRONIC INFLAMMATORY PROCESS INDUCE EPITHELIAL MESENCHYMAL TRANSITION (EMT) THAT DRAMATICALLY ALTERS THE EPITHELIAL CELL PHENOTYPE. THE EFFECTS OF EMT ON EPIGENETIC REPROGRAMMING AND THE ACTIVATION OF TRANSCRIPTIONAL NETWORKS ARE KNOWN, ITS EFFECTS ON THE INNATE INFLAMMATORY RESPONSE ARE UNDEREXPLORED. WE USED A MULTIPLEX GENE EXPRESSION PROFILING PLATFORM TO INVESTIGATE THE PERTURBATIONS OF THE INNATE PATHWAYS INDUCED BY TGF BETA IN A PRIMARY AIRWAY EPITHELIAL CELL MODEL OF EMT. EMT HAD DRAMATIC EFFECTS ON THE INDUCTION OF THE INNATE PATHWAY AND THE COUPLING INTERVAL OF THE CANONICAL AND NONCANONICAL NF- KAPPA B PATHWAYS. SIMULATION EXPERIMENTS DEMONSTRATE THAT RAPID, COORDINATED CAP-INDEPENDENT TRANSLATION OF TRAF-1 AND NF- KAPPA B2 IS REQUIRED TO REDUCE THE NONCANONICAL PATHWAY COUPLING INTERVAL. EXPERIMENTS USING AMANTADINE CONFIRMED THE PREDICTION THAT TRAF-1 AND NF- KAPPA B2/P100 PRODUCTION IS MEDIATED BY AN IRES-DEPENDENT MECHANISM. THESE DATA INDICATE THAT THE EPIGENETIC CHANGES PRODUCED BY EMT INDUCE DYNAMIC STATE CHANGES OF THE INNATE SIGNALING PATHWAY. FURTHER APPLICATIONS OF SYSTEMS APPROACHES WILL PROVIDE UNDERSTANDING OF THIS COMPLEX PHENOTYPE THROUGH DETERMINISTIC MODELING AND MULTIDIMENSIONAL (GENOMIC AND PROTEOMIC) PROFILING. 2013 3 5114 39 PORPHYROMONAS GINGIVALIS LIPOPOLYSACCHARIDE STIMULATION IN HUMAN PERIODONTAL LIGAMENT STEM CELLS: ROLE OF EPIGENETIC MODIFICATIONS TO THE INFLAMMATION. PERIODONTITIS IS A CHRONIC ORAL INFLAMMATORY DISEASE PRODUCED BY BACTERIA. GINGIVAL RETRACTION AND BONE AND CONNECTIVE TISSUES RESORPTION ARE THE HALLMARKS OF THIS DISEASE. CHRONIC PERIODONTITIS MAY CONTRIBUTE TO THE RISK OF ONSET OR PROGRESSION OF NEUROINFLAMMATORY PATHOLOGICAL CONDITIONS, SUCH AS ALZHEIMER'S DISEASE. THE MAIN GOAL OF THE PRESENT STUDY WAS TO INVESTIGATE IF THE ROLE OF EPIGENETIC MODULATIONS IS INVOLVED IN PERIODONTITIS USING HUMAN PERIODONTAL LIGAMENT STEM CELLS (HPDLSCS) AS AN IN VITRO MODEL SYSTEM. HPDLSCS WERE TREATED WITH LIPOPOLYSACCHARIDE OF PORPHYROMONAS GINGIVALIS AND THE EXPRESSION OF PROTEINS ASSOCIATED WITH DNA METHYLATION AND HISTONE ACETYLATION, SUCH AS DNMT1 AND P300, RESPECTIVELY, AND INFLAMMATORY TRANSCRIPTION FACTOR NF-KB, WERE EXAMINED. IMMUNOFLUORESCENCE, WESTERN BLOT AND NEXT GENERATION SEQUENCING RESULTS DEMONSTRATED THAT P. GINGIVALIS LIPOPOLYSACCHARIDE SIGNIFICANTLY REDUCED DNA METHYLASE DNMT1, WHILE IT MARKEDLY UPREGULATED THE LEVEL OF HISTONE ACETYLTRANSFERASE P300 AND NF-KB IN HPDLSCS. OUR RESULTS SHOWED THAT P. GINGIVALIS LIPOPOLYSACCHARIDE MARKEDLY REGULATE THE GENES INVOLVED IN EPIGENETIC MECHANISM, WHICH MAY RESULT IN INFLAMMATION INDUCTION. WE PROPOSE THAT P. GINGIVALIS LIPOPOLYSACCHARIDE-TREATED HPDLSCS COULD BE A POTENTIAL IN VITRO MODEL SYSTEM TO STUDY EPIGENETICS MODULATIONS ASSOCIATED WITH PERIODONTITIS, WHICH MIGHT BE HELPFUL TO IDENTIFY NOVEL BIOMARKERS LINKED TO THIS ORAL INFLAMMATORY DISEASE. 2017 4 194 32 ACETYLSHIKONIN SUPPRESSES INVASION OF PORPHYROMONAS GINGIVALIS?INFECTED YD10B ORAL CANCER CELLS BY MODULATING THE INTERLEUKIN-8/MATRIX METALLOPROTEINASE AXIS. THE DEVELOPMENT OF PHARMACEUTICAL AGENTS POSSESSING ANTI?INVASIVE AND ANTI?METASTATIC ABILITIES, AS WELL AS APOPTOTIC ACTIVITY, IS IMPORTANT IN DECREASING THE INCIDENCE AND RECURRENCE OF ORAL CANCER. CANCER CELLS ARE KNOWN TO ACQUIRE INVASIVENESS NOT ONLY THROUGH EPIGENETIC CHANGES, BUT ALSO FROM INFLAMMATORY STIMULI WITHIN THE TUMOR MICROENVIRONMENT. ACCORDINGLY, THE IDENTIFICATION OF AGENTS THAT CAN SUPPRESS THE INFLAMMATION?PROMOTED INVASIVENESS OF CANCER CELLS MAY BE IMPORTANT IN TREATING CANCER AND IMPROVING THE PROGNOSIS OF PATIENTS WITH CANCER. ACETYLSHIKONIN, A FLAVONOID WITH ANTI?INFLAMMATORY ACTIVITY, INHIBITS PROLIFERATION AND INDUCES APOPTOSIS OF ORAL CANCER CELLS. IN THE PRESENT STUDY, THE ANTI?INVASIVE EFFECT OF ACETYLSHIKONIN ON YD10B ORAL CANCER CELLS INFECTED WITH PORPHYROMONAS GINGIVALIS, A MAJOR PATHOGEN OF CHRONIC PERIODONTITIS, AND THE MECHANISMS INVOLVED WERE INVESTIGATED. FIRSTLY, WE EXAMINED WHETHER P. GINGIVALIS INFECTION INCREASED THE INVASIVENESS OF YD10B CELLS. RESULTS SUGGESTED THAT YD10B ORAL CANCER CELLS BECOME MORE AGGRESSIVE WHEN THEY ARE INFECTED WITH P. GINGIVALIS. SECONDLY, ACETYLSHIKONIN SIGNIFICANTLY INHIBITED THE INVASION OF P. GINGIVALIS?INFECTED YD10B CELLS BY SUPPRESSING IL?8 RELEASE AND IL?8?DEPENDENT MMP RELEASE. THESE DATA SUGGEST THAT ACETYLSHIKONIN MAY BE A USEFUL PREVENTIVE AND THERAPEUTIC CANDIDATE FOR ORAL CANCER THAT IS CHRONICALLY INFECTED WITH PERIODONTAL PATHOGENS. 2018 5 4362 42 MIR?152 REGULATES TGF?BETA1?INDUCED EPITHELIAL?MESENCHYMAL TRANSITION BY TARGETING HPIP IN TUBULAR EPITHELIAL CELLS. RENAL FIBROSIS IS A COMMON PATHOLOGICAL FEATURE OF CHRONIC KIDNEY DISEASES, AND THEIR DEVELOPMENT AND PROGRESSION ARE INFLUENCED BY EPIGENETIC MODIFICATIONS INCLUDING ABERRANT MICRORNA (MIRNA OR MIR) EXPRESSION. MIRNAS HAVE BEEN DEMONSTRATED TO MODULATE THE AGGRESSIVENESS OF VARIOUS CANCERS AND HAVE EMERGED AS POSSIBLE THERAPEUTIC AGENTS FOR THE MANAGEMENT OF RENAL FIBROSIS. TRANSFORMING GROWTH FACTOR BETA1 (TGF?BETA1)?INDUCED EPITHELIAL?MESENCHYMAL TRANSITION (EMT) OF TUBULAR EPITHELIAL CELLS SERVES A ROLE IN THE INITIATION AND PROGRESSION OF RENAL FIBROSIS. FURTHERMORE, RECENT RESULTS INDICATED THAT THE PROGRESSION OF EMT IS REVERSIBLE. THE PRESENT STUDY AIMED TO CLARIFY THE ROLE OF MIR?152 IN EMT OF THE TUBULAR EPITHELIAL CELL LINE HK?2, STIMULATED BY TGF?BETA1, USING IN VITRO TRANSFECTION WITH A MIR?152 MIMIC AND TO FURTHER INVESTIGATE THE UNDERLYING MECHANISM OF MIR?152 ACTIVITY. IN THE PRESENT STUDY, MIR?152 EXPRESSION WAS SIGNIFICANTLY REDUCED IN TGF?BETA1?TREATED HK?2 CELLS, ACCOMPANIED BY AN INCREASED EXPRESSION OF HEMATOPOIETIC PRE?B?CELL LEUKEMIA TRANSCRIPTION FACTOR (PBX)?INTERACTING PROTEIN (HPIP). ADDITIONALLY, MIR?152 OVEREXPRESSION INHIBITED TGF?BETA1?INDUCED EMT AND SUPPRESSED HPIP EXPRESSION BY DIRECTLY TARGETING THE 3' UNTRANSLATED REGION OF HPIP IN HK?2 CELLS. FURTHERMORE, UPREGULATION OF HPIP REVERSED MIR?152?MEDIATED INHIBITORY EFFECTS ON THE EMT. COLLECTIVELY, THE RESULTS SUGGEST THAT DOWNREGULATION OF MIR?152 INITIATES THE DEDIFFERENTIATION OF RENAL TUBULES AND PROGRESSION OF RENAL FIBROSIS, WHICH MAY PROVIDE IMPORTANT TARGETS FOR PREVENTION STRATEGIES OF RENAL FIBROSIS. 2018 6 3525 29 IL-1BETA, IL-8, AND MATRIX METALLOPROTEINASES-1, -2, AND -10 ARE ENRICHED UPON MONOCYTE-BREAST CANCER CELL COCULTIVATION IN A MATRIGEL-BASED THREE-DIMENSIONAL SYSTEM. BREAST CANCER REMAINS THE FIRST CANCER-RELATED CAUSE OF DEATH IN WOMEN WORLDWIDE, PARTICULARLY IN DEVELOPING COUNTRIES IN WHICH MOST CASES ARE DIAGNOSED IN LATE STAGES. ALTHOUGH MOST CANCER STUDIES ARE BASED IN THE GENETIC OR EPIGENETIC CHANGES OF THE TUMOR CELLS, IMMUNE CELLS WITHIN THE TUMOR STROMA OFTEN COOPERATE WITH CANCER PROGRESSION. PARTICULARLY, MONOCYTES ARE ATTRACTED TO THE TUMOR PRIMARY SITE IN WHICH THEY ARE DIFFERENTIATED INTO TUMOR-ASSOCIATED MACROPHAGES THAT FACILITATE TUMOR CELL INVASION AND METASTASIS. IN THIS STUDY, WE USED THREE-DIMENSIONAL CULTURES TO FORM ACINI-LIKE STRUCTURES TO ANALYZE THE INFLAMMATORY SECRETION PROFILE OF TUMOR CELLS INDIVIDUALLY OR IN CO-CULTURE WITH MONOCYTES. BREAST CANCER CELL LINES AND PRIMARY ISOLATES FROM EIGHT MEXICAN PATIENTS WITH BREAST CANCER WERE USED. WE FOUND HIGH LEVELS OF RANTES/CCL5, MCP-1/CCL2, AND G-CSF IN THE BREAST CANCER INDIVIDUAL CULTURES, SUPPORTING AN IMPORTANT RECRUITMENT CAPACITY OF MONOCYTES, BUT ALSO OF NEUTROPHILS. THE CO-CULTURES OF THE TUMOR CELLS AND MONOCYTES WERE SIGNIFICANTLY ENRICHED WITH THE POTENT PRO-INFLAMMATORY CYTOKINES INTERLEUKIN (IL)-1BETA AND IL-8, KNOWN TO SUPPORT MALIGNANT PROGRESSION. WE ALSO FOUND THAT THE INTERACTION OF TUMOR CELLS WITH MONOCYTES PROMOTED HIGH LEVELS OF MATRIX METALLOPROTEINASES (MMP)-1, MMP-2, AND MMP-10. OUR STUDY SUPPORTS THAT A KEY EVENT FOR MALIGNANT PROGRESSION IS THE RECRUITMENT OF DIFFERENT IMMUNE CELL POPULATIONS, WHICH HELP TO SUSTAIN AND ENHANCE A CHRONIC INFLAMMATORY MICROENVIRONMENT THAT HIGHLY FAVORS TUMOR MALIGNANCY. 2017 7 164 40 ABNORMAL HISTONE METHYLATION IS RESPONSIBLE FOR INCREASED VASCULAR ENDOTHELIAL GROWTH FACTOR 165A SECRETION FROM AIRWAY SMOOTH MUSCLE CELLS IN ASTHMA. VASCULAR ENDOTHELIAL GROWTH FACTOR (VEGF), A KEY ANGIOGENIC MOLECULE, IS ABERRANTLY EXPRESSED IN SEVERAL DISEASES INCLUDING ASTHMA WHERE IT CONTRIBUTES TO BRONCHIAL VASCULAR REMODELING AND CHRONIC INFLAMMATION. ASTHMATIC HUMAN AIRWAY SMOOTH MUSCLE CELLS HYPERSECRETE VEGF, BUT THE MECHANISM IS UNCLEAR. IN THIS STUDY, WE DEFINED THE MECHANISM IN HUMAN AIRWAY SMOOTH MUSCLE CELLS FROM NONASTHMATIC AND ASTHMATIC PATIENTS. WE FOUND THAT ASTHMATIC CELLS LACKED A REPRESSION COMPLEX AT THE VEGF PROMOTER, WHICH WAS PRESENT IN NONASTHMATIC CELLS. RECRUITMENT OF G9A, TRIMETHYLATION OF HISTONE H3 AT LYSINE 9 (H3K9ME3), AND A RESULTANT DECREASE IN RNA POLYMERASE II AT THE VEGF PROMOTER WAS CRITICAL TO REPRESSION OF VEGF SECRETION IN NONASTHMATIC CELLS. AT THE ASTHMATIC PROMOTER, H3K9ME3 WAS ABSENT BECAUSE OF FAILED RECRUITMENT OF G9A; RNA POLYMERASE II BINDING, IN ASSOCIATION WITH TATA-BINDING PROTEIN-ASSOCIATED FACTOR 1, WAS INCREASED; H3K4ME3 WAS PRESENT; AND SP1 BINDING WAS EXAGGERATED AND SUSTAINED. IN CONTRAST, DNA METHYLATION AND HISTONE ACETYLATION WERE SIMILAR IN ASTHMATIC AND NONASTHMATIC CELLS. THIS IS THE FIRST STUDY, TO OUR KNOWLEDGE, TO SHOW THAT AIRWAY CELLS IN ASTHMA HAVE ALTERED EPIGENETIC REGULATION OF REMODELING GENE(S). HISTONE METHYLATION AT GENES SUCH AS VEGF MAY BE AN IMPORTANT NEW THERAPEUTIC TARGET. 2012 8 2926 29 GENERATION OF AN EPIGENETIC SIGNATURE BY CHRONIC HYPOXIA IN PROSTATE CELLS. INCREASING LEVELS OF TISSUE HYPOXIA HAVE BEEN REPORTED AS A NATURAL FEATURE OF THE AGING PROSTATE GLAND AND MAY BE A RISK FACTOR FOR THE DEVELOPMENT OF PROSTATE CANCER. IN THIS STUDY, WE HAVE USED PWR-1E BENIGN PROSTATE EPITHELIAL CELLS AND AN EQUIVALENTLY AGED HYPOXIA-ADAPTED PWR-1E SUB-LINE TO IDENTIFY PHENOTYPIC AND EPIGENETIC CONSEQUENCES OF CHRONIC HYPOXIA IN PROSTATE CELLS. WE HAVE IDENTIFIED A SIGNIFICANTLY ALTERED CELLULAR PHENOTYPE IN RESPONSE TO CHRONIC HYPOXIA AS CHARACTERIZED BY INCREASED RECEPTOR-MEDIATED APOPTOTIC RESISTANCE, THE INDUCTION OF CELLULAR SENESCENCE, INCREASED INVASION AND THE INCREASED SECRETION OF IL-1 BETA, IL6, IL8 AND TNFALPHA CYTOKINES. IN ASSOCIATION WITH THESE PHENOTYPIC CHANGES AND THE ABSENCE OF HIF-1 ALPHA PROTEIN EXPRESSION, WE HAVE DEMONSTRATED SIGNIFICANT INCREASES IN GLOBAL LEVELS OF DNA METHYLATION AND H3K9 HISTONE ACETYLATION IN THESE CELLS, CONCOMITANT WITH THE INCREASED EXPRESSION OF DNA METHYLTRANSFERASE DMNT3B AND GENE-SPECIFIC CHANGES IN DNA METHYLATION AT KEY IMPRINTING LOCI. IN CONCLUSION, WE HAVE DEMONSTRATED A GENOME-WIDE ADJUSTMENT OF DNA METHYLATION AND HISTONE ACETYLATION UNDER CHRONIC HYPOXIC CONDITIONS IN THE PROSTATE. THESE EPIGENETIC SIGNATURES MAY REPRESENT AN ADDITIONAL MECHANISM TO PROMOTE AND MAINTAIN A HYPOXIC-ADAPTED CELLULAR PHENOTYPE WITH A POTENTIAL ROLE IN TUMOUR DEVELOPMENT. 2009 9 3764 38 INTEGRATIVE ANALYSIS OF DNA METHYLATION AND GENE EXPRESSION DATA IDENTIFIES EPAS1 AS A KEY REGULATOR OF COPD. CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS A COMPLEX DISEASE. GENETIC, EPIGENETIC, AND ENVIRONMENTAL FACTORS ARE KNOWN TO CONTRIBUTE TO COPD RISK AND DISEASE PROGRESSION. THEREFORE WE DEVELOPED A SYSTEMATIC APPROACH TO IDENTIFY KEY REGULATORS OF COPD THAT INTEGRATES GENOME-WIDE DNA METHYLATION, GENE EXPRESSION, AND PHENOTYPE DATA IN LUNG TISSUE FROM COPD AND CONTROL SAMPLES. OUR INTEGRATIVE ANALYSIS IDENTIFIED 126 KEY REGULATORS OF COPD. WE IDENTIFIED EPAS1 AS THE ONLY KEY REGULATOR WHOSE DOWNSTREAM GENES SIGNIFICANTLY OVERLAPPED WITH MULTIPLE GENES SETS ASSOCIATED WITH COPD DISEASE SEVERITY. EPAS1 IS DISTINCT IN COMPARISON WITH OTHER KEY REGULATORS IN TERMS OF METHYLATION PROFILE AND DOWNSTREAM TARGET GENES. GENES PREDICTED TO BE REGULATED BY EPAS1 WERE ENRICHED FOR BIOLOGICAL PROCESSES INCLUDING SIGNALING, CELL COMMUNICATIONS, AND SYSTEM DEVELOPMENT. WE CONFIRMED THAT EPAS1 PROTEIN LEVELS ARE LOWER IN HUMAN COPD LUNG TISSUE COMPARED TO NON-DISEASE CONTROLS AND THAT EPAS1 GENE EXPRESSION IS REDUCED IN MICE CHRONICALLY EXPOSED TO CIGARETTE SMOKE. AS EPAS1 DOWNSTREAM GENES WERE SIGNIFICANTLY ENRICHED FOR HYPOXIA RESPONSIVE GENES IN ENDOTHELIAL CELLS, WE TESTED EPAS1 FUNCTION IN HUMAN ENDOTHELIAL CELLS. EPAS1 KNOCKDOWN BY SIRNA IN ENDOTHELIAL CELLS IMPACTED GENES THAT SIGNIFICANTLY OVERLAPPED WITH EPAS1 DOWNSTREAM GENES IN LUNG TISSUE INCLUDING HYPOXIA RESPONSIVE GENES, AND GENES ASSOCIATED WITH EMPHYSEMA SEVERITY. OUR FIRST INTEGRATIVE ANALYSIS OF GENOME-WIDE DNA METHYLATION AND GENE EXPRESSION PROFILES ILLUSTRATES THAT NOT ONLY DOES DNA METHYLATION PLAY A 'CAUSAL' ROLE IN THE MOLECULAR PATHOPHYSIOLOGY OF COPD, BUT IT CAN BE LEVERAGED TO DIRECTLY IDENTIFY NOVEL KEY MEDIATORS OF THIS PATHOPHYSIOLOGY. 2015 10 4210 28 METFORMIN AND VITAMIN D MODULATE INFLAMMATION AND AUTOPHAGY DURING ADIPOSE-DERIVED STEM CELL DIFFERENTIATION. ADIPOSE-DERIVED STEM CELLS (ADSCS) CAME OUT FROM THE REGENERATIVE MEDICINE LANDSCAPE FOR THEIR ABILITY TO DIFFERENTIATE INTO SEVERAL PHENOTYPES, CONTRIBUTING TO TISSUE REGENERATION BOTH IN VITRO AND IN VIVO. DYSREGULATION IN STEM CELL RECRUITMENT AND DIFFERENTIATION DURING ADIPOGENESIS IS LINKED TO A CHRONIC LOW-GRADE INFLAMMATION AND MACROPHAGE INFILTRATION INSIDE THE ADIPOSE TISSUE, INSULIN RESISTANCE, CARDIOVASCULAR DISEASE AND OBESITY. IN THE PRESENT PAPER WE AIMED TO EVALUATE THE ROLE OF METFORMIN AND VITAMIN D, ALONE OR IN COMBINATION, IN MODULATING INFLAMMATION AND AUTOPHAGY IN ADSCS DURING ADIPOGENIC COMMITMENT. ADSCS WERE CULTURED FOR 21 DAYS IN THE PRESENCE OF A SPECIFIC ADIPOGENIC DIFFERENTIATION MEDIUM, TOGETHER WITH METFORMIN, OR VITAMIN D, OR BOTH. WE THEN ANALYZED THE EXPRESSION OF FOXO1 AND HEAT SHOCK PROTEINS (HSP) AND THE SECRETION OF PROINFLAMMATORY CYTOKINES IL-6 AND TNF-ALPHA BY ELISA. AUTOPHAGY WAS ALSO ASSESSED BY SPECIFIC WESTERN BLOT ANALYSIS OF ATG12, LC3B I, AND LC3B II EXPRESSION. OUR RESULTS SHOWED THE ABILITY OF THE CONDITIONED MEDIA TO MODULATE ADIPOGENIC DIFFERENTIATION, FINELY TUNING THE INFLAMMATORY RESPONSE AND AUTOPHAGY. WE OBSERVED A MODULATION IN HSP MRNA LEVELS, AND A SIGNIFICANT DOWNREGULATION IN CYTOKINE SECRETION. TAKEN TOGETHER, OUR FINDINGS SUGGEST THE POSSIBLE APPLICATION OF THESE MOLECULES IN CLINICAL PRACTICE TO COUNTERACT UNCONTROLLED LIPOGENESIS AND PREVENT OBESITY AND OBESITY-RELATED METABOLIC DISORDERS. 2021 11 3468 46 HYPOXIA-INDUCED DNA HYPERMETHYLATION IN HUMAN PULMONARY FIBROBLASTS IS ASSOCIATED WITH THY-1 PROMOTER METHYLATION AND THE DEVELOPMENT OF A PRO-FIBROTIC PHENOTYPE. BACKGROUND: PULMONARY FIBROSIS IS A DEBILITATING AND LETHAL DISEASE WITH NO EFFECTIVE TREATMENT OPTIONS. UNDERSTANDING THE PATHOLOGICAL PROCESSES AT PLAY WILL DIRECT THE APPLICATION OF NOVEL THERAPEUTIC AVENUES. HYPOXIA HAS BEEN IMPLICATED IN THE PATHOGENESIS OF PULMONARY FIBROSIS YET THE PRECISE MECHANISM BY WHICH IT CONTRIBUTES TO DISEASE PROGRESSION REMAINS TO BE FULLY ELUCIDATED. IT HAS BEEN SHOWN THAT CHRONIC HYPOXIA CAN ALTER DNA METHYLATION PATTERNS IN TUMOUR-DERIVED CELL LINES. THIS EPIGENETIC ALTERATION CAN INDUCE CHANGES IN CELLULAR PHENOTYPE WITH PROMOTER METHYLATION BEING ASSOCIATED WITH GENE SILENCING. OF PARTICULAR RELEVANCE TO IDIOPATHIC PULMONARY FIBROSIS (IPF) IS THE OBSERVATION THAT THY-1 PROMOTER METHYLATION IS ASSOCIATED WITH A MYOFIBROBLAST PHENOTYPE WHERE LOSS OF THY-1 OCCURS ALONGSIDE INCREASED ALPHA SMOOTH MUSCLE ACTIN (ALPHA-SMA) EXPRESSION. THE INITIAL AIM OF THIS STUDY WAS TO DETERMINE WHETHER HYPOXIA REGULATES DNA METHYLATION IN NORMAL HUMAN LUNG FIBROBLASTS (CCD19LU). AS IT HAS BEEN REPORTED THAT HYPOXIA SUPPRESSES THY-1 EXPRESSION DURING LUNG DEVELOPMENT WE ALSO STUDIED THE EFFECT OF HYPOXIA ON THY-1 PROMOTER METHYLATION AND GENE EXPRESSION. METHODS: CCD19LU WERE GROWN FOR UP TO 8 DAYS IN HYPOXIA AND ASSESSED FOR GLOBAL CHANGES IN DNA METHYLATION USING FLOW CYTOMETRY. REAL-TIME PCR WAS USED TO QUANTIFY EXPRESSION OF THY-1, ALPHA-SMA, COLLAGEN I AND III. GENOMIC DNA WAS BISULPHITE TREATED AND METHYLATION SPECIFIC PCR (MSPCR) WAS USED TO EXAMINE THE METHYLATION STATUS OF THE THY-1 PROMOTER. RESULTS: SIGNIFICANT GLOBAL HYPERMETHYLATION WAS DETECTED IN HYPOXIC FIBROBLASTS RELATIVE TO NORMOXIC CONTROLS AND WAS ACCOMPANIED BY INCREASED EXPRESSION OF MYOFIBROBLAST MARKERS. THY-1 MRNA EXPRESSION WAS SUPPRESSED IN HYPOXIC CELLS, WHICH WAS RESTORED WITH THE DEMETHYLATING AGENT 5-AZA-2'-DEOXYCYTIDINE. MSPCR REVEALED THAT THY-1 BECAME METHYLATED FOLLOWING FIBROBLAST EXPOSURE TO 1% O2. CONCLUSION: THESE DATA SUGGEST THAT GLOBAL AND GENE-SPECIFIC CHANGES IN DNA METHYLATION MAY PLAY AN IMPORTANT ROLE IN FIBROBLAST FUNCTION IN HYPOXIA. 2012 12 51 40 A DISTINCT EPIGENETIC PROFILE DISTINGUISHES STENOTIC FROM NON-INFLAMED FIBROBLASTS IN THE ILEAL MUCOSA OF CROHN'S DISEASE PATIENTS. BACKGROUND: THE CHRONIC REMITTING AND RELAPSING INTESTINAL INFLAMMATION CHARACTERISTIC OF CROHN'S DISEASE FREQUENTLY LEADS TO FIBROSIS AND SUBSEQUENT STENOSIS OF THE INFLAMED REGION. APPROXIMATELY A THIRD OF ALL CROHN'S DISEASE PATIENTS REQUIRE RESECTION AT SOME STAGE IN THEIR DISEASE COURSE. AS THE PATHOGENESIS OF CROHN'S DISEASE ASSOCIATED FIBROSIS IS LARGELY UNKNOWN, A STRONG NECESSITY EXISTS TO BETTER UNDERSTAND THE PATHOPHYSIOLOGY THEREOF. METHODS: IN THIS STUDY, WE INVESTIGATED CHANGES OF THE DNA METHYLOME AND TRANSCRIPTOME OF ILEUM-DERIVED FIBROBLASTS ASSOCIATED TO THE OCCURRENCE OF CROHN'S DISEASE ASSOCIATED FIBROSIS. EIGHTEEN SAMPLES WERE INCLUDED IN A DNA METHYLATION ARRAY AND TWENTY-ONE SAMPLES WERE USED FOR RNA SEQUENCING. RESULTS: MOST DIFFERENTIALLY METHYLATED REGIONS AND DIFFERENTIALLY EXPRESSED GENES WERE OBSERVED WHEN COMPARING STENOTIC WITH NON-INFLAMED SAMPLES. BY CONTRAST, FEW DIFFERENCES WERE OBSERVED WHEN COMPARING CROHN'S DISEASE WITH NON-CROHN'S DISEASE, OR INFLAMED WITH NON-INFLAMED TISSUE. INTEGRATIVE METHYLATION AND GENE EXPRESSION ANALYSES REVEALED DYSREGULATION OF GENES ASSOCIATED TO THE PRKACA AND E2F1 NETWORK, WHICH IS INVOLVED IN CELL CYCLE PROGRESSION, ANGIOGENESIS, EPITHELIAL TO MESENCHYMAL TRANSITION, AND BILE METABOLISM. CONCLUSION: OUR RESEARCH PROVIDES EVIDENCE THAT THE METHYLOME AND THE TRANSCRIPTOME ARE SYSTEMATICALLY DYSREGULATED IN STENOSIS-ASSOCIATED FIBROBLASTS. 2018 13 3524 47 IL-13 REGULATES HUMAN NASAL EPITHELIAL CELL DIFFERENTIATION VIA H3K4ME3 MODIFICATION. INTRODUCTION: EPIGENETIC REGULATION HAS BEEN SHOWN TO PLAY AN IMPORTANT ROLE IN THE DEVELOPMENT OF INFLAMMATORY DISEASES, INCLUDING CHRONIC RHINOSINUSITIS AND NASAL POLYPS. THE LATTER ARE CHARACTERIZED BY EPITHELIAL MIS-DIFFERENTIATION AND INFILTRATION OF INFLAMMATORY CYTOKINES. H3K4ME3 HAS BEEN SHOWN TO BE INVOLVED IN REGULATING LINEAGE COMMITMENT. HOWEVER, THE UNDERLYING MECHANISMS, ESPECIALLY IN HUMAN NASAL EPITHELIAL CELLS (HNEPC), REMAIN UNDEREXPLORED. THE OBJECTIVE OF THIS STUDY WAS TO INVESTIGATE THE ROLE OF H3K4ME3 IN HNEPC DIFFERENTIATION TREATED WITH THE TH2 CYTOKINE IL-13. PATIENTS AND METHODS: THE EXPRESSION LEVELS OF MRNA AND PROTEINS WERE INVESTIGATED USING REVERSE TRANSCRIPTION-POLYMERASE CHAIN REACTION (RT-PCR) ASSAYS AND WESTERN BLOT IN NASAL POLYP TISSUES AND HUMAN NASAL EPITHELIAL CELLS RESPECTIVELY. WE MEASURED THESE LEVELS OF H3K4ME3, MLL1 AND TARGETED GENES COMPARED WITH CONTROL SUBJECTS. RESULTS: WE DEMONSTRATE THAT EXPRESSION OF H3K4ME3 AND ITS METHYLTRANSFERASE MLL1 WAS SIGNIFICANTLY UPREGULATED IN IL-13-TREATED HNEPC. THIS ELEVATION WAS ALSO OBSERVED IN NASAL POLYPS. EXPRESSION OF CILIA-RELATED TRANSCRIPTION FACTORS FOXJ1 AND DNAI2 DECREASED, WHILE GOBLET CELL-DERIVED GENES CLCA1 AND MUC5A INCREASED UPON IL-13 TREATMENT. MECHANISTICALLY, KNOCKDOWN OF MLL1 RESTORED EXPRESSION OF THESE FOUR GENES INDUCED BY IL-13. CONCLUSION: THESE FINDINGS SUGGEST THAT H3K4ME3 IS A CRITICAL REGULATOR IN CONTROL OF NASAL EPITHELIAL CELL DIFFERENTIATION. MLL1 MAY BE A POTENTIAL THERAPEUTIC TARGET FOR NASAL INFLAMMATORY DISEASES. 2017 14 1618 35 DNA METHYLTRANSFERASE INHIBITORS INCREASE NOD-LIKE RECEPTOR ACTIVITY AND EXPRESSION IN A MONOCYTIC CELL LINE. BACKGROUND: THE INTRACELLULAR NOD-LIKE RECEPTOR (NLR) FAMILY OF PATHOGEN RECOGNITION RECEPTORS (PRRA) IS INVOLVED IN INITIATING THE INNATE IMMUNE RESPONSE OF WHICH NOD1 AND NOD2 ARE THE BEST-CHARACTERIZED MEMBERS. ABERRANT EXPRESSION OF NOD1 AND NOD2 HAS BEEN UNCOVERED IN A NUMBER OF CHRONIC INFLAMMATORY DISEASES, SUCH AS INFLAMMATORY BOWEL DISEASE AND RHEUMATOID ARTHRITIS. HOWEVER, THE MECHANISM UNDERLYING NOD1/NOD2 GENE EXPRESSION REGULATION IS STILL IN ITS INFANCY. EPIGENETIC MODIFICATIONS SUCH AS DNA METHYLATION AND HISTONE ACETYLATION REGULATE THE EXPRESSION OF GENES AND ALTERATIONS IN THEIR PATTERNS HAVE BEEN LINKED TO MANY INFLAMMATORY DISEASES. THIS STUDY INVESTIGATED WHETHER EPIGENETIC MODIFYING DRUGS AFFECT THE REGULATION OF NOD1/NOD2 ACTIVITY AND EXPRESSION. DNA METHYLTRANSFERASE INHIBITORS HAVE RECENTLY BEEN USED IN THE TREATMENT OF MYELODYSPLASTIC SYNDROME AND AS COMBINATION THERAPY IN CANCER BUT THE FULL EXTENT OF THEIR EFFECTS HAS NOT BEEN QUANTIFIED.METHODS: PHARMACOLOGICAL INHIBITION OF EPIGENETIC ENZYMES IN A HUMAN MONOCYTIC THP-1 CELL LINE WAS CARRIED OUT AND NOD1/NOD2 EXPRESSION AND PRO-INFLAMMATORY RESPONSES WERE QUANTIFIED.RESULTS: CELLS PRIMED WITH A DNA METHYLTRANSFERASE INHIBITOR (BUT NOT A HISTONE DEACETYLASE [HDAC] INHIBITOR) WERE FOUND TO BE CONSISTENTLY MORE RESPONSIVE TO NOD1/NOD2 STIMULATION AND HAD INCREASED BASAL EXPRESSION.CONCLUSION: THE NOVEL EXPERIMENTATION CARRIED OUT HERE SUGGESTS FOR THE FIRST TIME THAT NOD1/NOD2 RECEPTOR ACTIVITY AND EXPRESSION IN MONOCYTES ARE POSSIBLY REGULATED DIRECTLY BY DNA METHYLATION. 2022 15 3693 34 INFLAMMATORY CELLS CAN ALTER THE LEVELS OF H3K9AC AND GAMMAH2AX IN DYSPLASTIC CELLS AND FAVOR TUMOR PHENOTYPE. ORAL POTENTIALLY MALIGNANT DISORDERS (OPMD) ARE CLINICAL PRESENTATIONS THAT CARRY AN INCREASED RISK OF CANCER DEVELOPMENT. CURRENTLY, EPITHELIAL DYSPLASIA GRADE IS BASED ON ARCHITECTURAL AND CYTOLOGICAL EPITHELIAL CHANGES AND IS USED TO PREDICT THE MALIGNANT TRANSFORMATION OF THESE LESIONS. HOWEVER, PREDICTING WHICH OPMD WILL PROGRESS TO A MALIGNANT TUMOR IS VERY CHALLENGING. INFLAMMATORY INFILTRATES CAN FAVOR CANCER DEVELOPMENT, AND RECENT STUDIES SUGGEST THAT THIS ASSOCIATION WITH OPMD LESIONS MAY BE RELATED TO THE ETIOLOGY AND/OR AGGRESSIVE CLINICAL BEHAVIOR OF THESE LESIONS. EPIGENETIC CHANGES SUCH AS HISTONE MODIFICATIONS MAY MEDIATE CHRONIC INFLAMMATION AND ALSO FAVOR TUMOR CELLS IN IMMUNE RESISTANCE AND EVASION. THIS STUDY AIMED TO EVALUATE THE RELATIONSHIP BETWEEN HISTONE ACETYLATION (H3K9AC) AND DNA DAMAGE IN THE CONTEXT OF DYSPLASTIC LESIONS WITH PROMINENT CHRONIC INFLAMMATION. IMMUNOFLUORESCENCE OF "LOW-RISK" AND "HIGH-RISK" OPMD LESIONS (N = 24) AND INFLAMMATORY FIBROUS HYPERPLASIA (N = 10) AS THE CONTROL GROUP WAS PERFORMED TO ASSESS HISTONE ACETYLATION LEVELS AND DNA DAMAGE THROUGH THE PHOSPHORYLATION OF H2AX (GAMMAH2AX). CELL CO-CULTURE ASSAYS WITH PBMCS AND ORAL KERATINOCYTE CELL LINES (NOK-SI, DOK, AND SCC-25) WERE PERFORMED TO ASSESS PROLIFERATION, ADHESION, MIGRATION, AND EPITHELIAL-MESENCHYMAL TRANSITION (EMT). ORAL DYSPLASTIC LESIONS SHOWED A HYPOACETYLATION OF H3K9 AND LOW LEVELS OF GAMMAH2AX COMPARED TO CONTROL. THE CONTACT OF DYSPLASTIC ORAL KERATINOCYTES WITH PBMCS FAVORED EMT AND THE LOSS OF CELL-CELL ADHESION. ON THE OTHER HAND, P27 LEVELS INCREASED AND CYCLIN E DECREASED IN DOK, INDICATING CELL CYCLE ARREST. WE CONCLUDE THAT THE PRESENCE OF CHRONIC INFLAMMATION ASSOCIATED TO DYSPLASTIC LESIONS IS CAPABLE OF PROMOTING EPIGENETIC ALTERATIONS, WHICH IN TURN CAN FAVOR THE PROCESS OF MALIGNANT TRANSFORMATION. 2023 16 3963 37 LONG NONCODING RNA UC.98 STABILIZES ATHEROSCLEROTIC PLAQUES BY PROMOTING THE PROLIFERATION AND ADHESIVE CAPACITY IN MURINE AORTIC ENDOTHELIAL CELLS. PATHOLOGICAL STUDIES HAVE SHOWN THAT THE VULNERABILITY OF PLAQUES AFFECTS OUTCOMES IN PATIENTS WITH ATHEROSCLEROSIS (AS), A CHRONIC INFLAMMATORY DISEASE AND COMMON CAUSE OF MORBIDITY AND MORTALITY WORLDWIDE. ALTHOUGH EMERGING TECHNOLOGIES HAVE ENABLED EARLY DIAGNOSIS OF AS WITH HIGH-RISK VULNERABLE PLAQUES, MORE ACCURATE AND NONINVASIVE DIAGNOSTIC METHODS ARE URGENTLY REQUIRED. TO THIS END, MOLECULES INVOLVED IN GENETIC OR EPIGENETIC REGULATION OF THE VULNERABILITY OF ATHEROSCLEROTIC PLAQUES HAVE BEEN EXTENSIVELY STUDIED. HERE, WE EVALUATED LONG NONCODING RNA (LNCRNA) VARIABILITY BY MICROARRAY ASSAY IN MURINE AORTIC ENDOTHELIAL CELLS (MAECS) BEARING VULNERABLE PLAQUES AND IDENTIFIED THE NOVEL FUNCTIONAL LNCRNA UC.98, WHOSE EXPRESSION PATTERN WAS ASSOCIATED WITH THE VULNERABILITY OF ATHEROSCLEROTIC PLAQUES. CONSISTENT WITH THIS, CLINICAL STATISTICS COMPARING THE PERIPHERAL BLOOD SPECIMENS FROM SETS OF PATIENTS WITH AS WITH OR WITHOUT VULNERABLE PLAQUES CONFIRMED THE LINEAR RELATIONSHIP BETWEEN THE EXPRESSION PATTERN OF UC.98 AND PLAQUE INSTABILITY. MOREOVER, MTT ASSAYS AND WESTERN BLOT ANALYSIS SHOWED THAT SILENCING OF INTRINSIC UC.98 IN MAECS NOT ONLY SUPPRESSED CELL PROLIFERATION BUT ALSO DECREASED THE EXPRESSIONS OF VASCULAR CELL ADHESION MOLECULE-1 AND INTERCELLULAR ADHESION MOLECULE-1, THEREBY INACTIVATING THE NUCLEAR FACTOR-KAPPAB PATHWAY. IN CONCLUSION, OUR RESULTS HIGHLIGHTED THE PIVOTAL ROLE OF UC.98 IN REGULATING THE VULNERABILITY OF PLAQUES DURING AS PROGRESSION AND SUGGESTED THAT UC.98 MAY BE A BIOMARKER OF THE EARLY DIAGNOSIS AND PROGNOSIS OF AS WITH VULNERABLE PLAQUES AND A POTENTIAL THERAPEUTIC TARGET FOR SLOWING AS PROGRESSION. 2020 17 5491 36 REVIEW ARTICLE: INFLAMMATION-RELATED PROMOTION OF GASTROINTESTINAL CARCINOGENESIS--A PERIGENETIC PATHWAY. CHRONIC INFLAMMATION HAS BEEN REPORTED TO ACCELERATE NEOPLASMAS IN GASTROINTESTINAL TRACT. CERTAIN BACTERIA INCLUDING HELICOBACTER PYLORI DIRECTLY INTERACT WITH HOST CELLS, INDUCE PROINFLAMMATORY CYTOKINES AND STIMULATE PRODUCTION OF FREE RADICALS. FREE RADICALS CAUSE MUTATIONS IN TARGET CELLS SO THAT NEOPLASTIC CLONES ARE ESTABLISHED. ACCUMULATION OF SUCH GENETIC ALTERATIONS MAY CAUSE MALIGNANT TRANSFORMATION OF SOME ESTABLISHED CLONES. IN ADDITION, INFLAMMATORY ALTERATIONS MAY PROMOTE GROWTH, EXPANSION AND INVASION OF GASTROINTESTINAL EPITHELIAL CELLS. THE LATTER CHANGES CAUSED BY INFLAMMATION MAY OCCUR EVEN WITHOUT FURTHER GENETIC MUTATIONS OR EPIGENETIC ALTERATIONS, AND THEREFORE MAY BE CATEGORIZED AS 'PERIGENETIC ALTERATIONS' OF NEOPLASTIC CELLS. FOR AN EXAMPLE, TUMOUR NECROSIS FACTOR ALPHA (TNF-ALPHA) PLAYS PIVOTAL ROLES NOT ONLY IN THE REDUCTION BUT ALSO IN THE GROWTH, INVASION AND METASTASES OF CERTAIN NEOPLASMAS. OUR STUDIES SHOW THAT TNF-ALPHA INCREASES INTRACELLULAR RADICAL PRODUCTION, DEGRADATES E-CADHERIN / BETA-CATENIN COMPLEX AND PROMOTES DISPERSION AND MIGRATION IN EPITHELIAL CELLS TRANSFORMED WITH AN ACTIVATED SRC ONCOGENE (V-SRC). THESE DATA INDICATE THAT AN INFLAMMATORY CYTOKINE INDUCES THE MALIGNANT POTENTIAL OF SRC-ACTIVATED NEOPLASTIC CELLS. INTERESTINGLY, TNF-ALPHA ALSO INDUCED THESE PHENOTYPIC CHANGES IN NONMUTATED CELLS WHOSE C-SRC WAS ACTIVATED BY TGF-ALPHA, SUGGESTING THAT THE INVASIVE PROPERTIES OF THE CELL WERE NOT NECESSARILY RELATED TO GENE MUTATION. FURTHERMORE, CERTAIN RADICAL SCAVENGERS SUPPRESSED THE INVASIVE PHENOTYPE OF THE CELLS. THESE RESULTS INDICATE THAT PERIGENETIC ALTERATIONS ARE AN IMPORTANT TARGET OF PHARMACOLOGICAL INTERVENTION OF CARCINOGENESIS. 2003 18 1117 33 COMPARATIVE AND EXPERIMENTAL STUDIES ON THE GENES ALTERED BY CHRONIC HYPOXIA IN HUMAN BRAIN MICROENDOTHELIAL CELLS. BACKGROUND : HYPOXIA INDUCIBLE FACTOR 1 ALPHA (HIF1A) IS A MASTER REGULATOR OF ACUTE HYPOXIA; HOWEVER, WITH CHRONIC HYPOXIA, HIF1A LEVELS RETURN TO THE NORMOXIC LEVELS. IMPORTANTLY, THE GENES THAT ARE INVOLVED IN THE CELL SURVIVAL AND VIABILITY UNDER CHRONIC HYPOXIA ARE NOT KNOWN. THEREFORE, WE TESTED THE HYPOTHESIS THAT CHRONIC HYPOXIA LEADS TO THE UPREGULATION OF A CORE GROUP OF GENES WITH ASSOCIATED CHANGES IN THE PROMOTER DNA METHYLATION THAT MEDIATES THE CELL SURVIVAL UNDER HYPOXIA. RESULTS : WE EXAMINED THE EFFECT OF CHRONIC HYPOXIA (3 DAYS; 0.5% OXYGEN) ON HUMAN BRAIN MICRO ENDOTHELIAL CELLS (HBMEC) VIABILITY AND APOPTOSIS. HYPOXIA CAUSED A SIGNIFICANT REDUCTION IN CELL VIABILITY AND AN INCREASE IN APOPTOSIS. NEXT, WE EXAMINED CHRONIC HYPOXIA ASSOCIATED CHANGES IN TRANSCRIPTOME AND GENOME-WIDE PROMOTER METHYLATION. THE DATA OBTAINED WAS COMPARED WITH 16 OTHER MICROARRAY STUDIES ON CHRONIC HYPOXIA. NINE GENES WERE ALTERED IN RESPONSE TO CHRONIC HYPOXIA IN ALL 17 STUDIES. INTERESTINGLY, HIF1A WAS NOT ALTERED WITH CHRONIC HYPOXIA IN ANY OF THE STUDIES. FURTHERMORE, WE COMPARED OUR DATA TO THREE OTHER STUDIES THAT IDENTIFIED HIF-RESPONSIVE GENES BY VARIOUS APPROACHES. ONLY TWO GENES WERE FOUND TO BE HIF DEPENDENT. WE SILENCED EACH OF THESE 9 GENES USING CRISPR/CAS9 SYSTEM. DOWNREGULATION OF EGLN3 SIGNIFICANTLY INCREASED THE CELL DEATH UNDER CHRONIC HYPOXIA, WHEREAS DOWNREGULATION OF ERO1L, ENO2, ADRENOMEDULLIN, AND SPAG4 REDUCED THE CELL DEATH UNDER HYPOXIA. CONCLUSIONS : WE PROVIDE A CORE GROUP OF GENES THAT REGULATES CELLULAR ACCLIMATIZATION UNDER CHRONIC HYPOXIC STRESS, AND MOST OF THEM ARE HIF INDEPENDENT. 2017 19 1615 35 DNA METHYLTRANSFERASE 3B PLAYS A PROTECTIVE ROLE AGAINST HEPATOCARCINOGENESIS CAUSED BY CHRONIC INFLAMMATION VIA MAINTAINING MITOCHONDRIAL HOMEOSTASIS. MOST HEPATOCELLULAR CARCINOMAS (HCCS) DEVELOP ON THE BASIS OF CHRONIC HEPATITIS, BUT THE MECHANISM OF EPIGENETIC REGULATION IN INFLAMMATORY HEPATOCARCINOGENESIS HAS YET TO BE ELUCIDATED. AMONG DE NOVO DNA METHYLTRANSFERASES (DNMTS), DNMT3B HAS LATELY BEEN REPORTED TO ACT SPECIFICALLY ON ACTIVELY TRANSCRIBED GENES, SUGGESTING THE POSSIBILITY THAT IT PLAYS A ROLE IN THE PATHOGENESIS OF CANCER. WE CONFIRMED THAT DNMT3B ISOFORMS LACKING ITS CATALYTIC DOMAIN WERE HIGHLY EXPRESSED IN HCCS COMPARED WITH NON-TUMOROUS LIVER TISSUE. TO ELUCIDATE THE ROLE OF DNMT3B IN HEPATOCARCINOGENESIS, WE GENERATED A GENETICALLY ENGINEERED MOUSE MODEL WITH HEPATOCYTE-SPECIFIC DNMT3B DELETION. THE LIVER OF THE DNMT3B-DEFICIENT MICE EXHIBITED AN EXACERBATION OF THIOACETAMIDE-INDUCED HEPATITIS, PROGRESSION OF LIVER FIBROSIS AND A HIGHER INCIDENCE OF HCC COMPARED WITH THE LIVER OF THE CONTROL MICE. WHOLE-GENOME BISULFITE SEQUENCING VERIFIED A LOWER CG METHYLATION LEVEL IN THE DNMT3B-DEFICIENT LIVER, DEMONSTRATING DIFFERENTIALLY METHYLATED REGIONS THROUGHOUT THE GENOME. TRANSCRIPTOME ANALYSIS REVEALED DECREASED EXPRESSION OF GENES RELATED TO OXIDATIVE PHOSPHORYLATION IN THE DNMT3B-DEFICIENT LIVER. MOREOVER, PRIMARY HEPATOCYTES ISOLATED FROM THE DNMT3B-DEFICIENT MICE SHOWED REDUCED MITOCHONDRIAL RESPIRATORY CAPACITY, LEADING TO THE ENHANCEMENT OF OXIDATIVE STRESS IN THE LIVER TISSUE. OUR FINDINGS SUGGEST THE PROTECTIVE ROLE OF DNMT3B AGAINST CHRONIC INFLAMMATION AND HCC DEVELOPMENT VIA MAINTAINING MITOCHONDRIAL HOMEOSTASIS. 2020 20 3473 29 IDENTIFICATION OF A NOVEL, METHYLATION-DEPENDENT, RUNX2 REGULATORY REGION ASSOCIATED WITH OSTEOARTHRITIS RISK. OSTEOARTHRITIS (OA) IS A COMMON, MULTIFACTORIAL AND POLYGENIC SKELETAL DISEASE THAT, IN ITS SEVEREST FORM, REQUIRES JOINT REPLACEMENT SURGERY TO RESTORE MOBILITY AND TO RELIEVE CHRONIC PAIN. USING TISSUES FROM THE ARTICULATING JOINTS OF 260 PATIENTS WITH OA AND A RANGE OF IN VITRO EXPERIMENTS, INCLUDING CRISPR-CAS9, WE HAVE CHARACTERIZED AN INTERGENIC REGULATORY ELEMENT. HERE, GENOTYPE AT AN OA RISK LOCUS CORRELATES WITH DIFFERENTIAL DNA METHYLATION, WITH ALTERED GENE EXPRESSION OF BOTH A TRANSCRIPTIONAL REGULATOR (RUNX2), AND A CHROMATIN REMODELLING PROTEIN (SUPT3H). RUNX2 IS A STRONG CANDIDATE FOR OA SUSCEPTIBILITY, WITH ITS ENCODED PROTEIN BEING ESSENTIAL FOR SKELETOGENESIS AND HEALTHY JOINT FUNCTION. THE OA RISK LOCUS INCLUDES SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) LOCATED WITHIN AND FLANKING THE DIFFERENTIALLY METHYLATED REGION (DMR). THE OA ASSOCIATION SNP, RS10948172, DEMONSTRATES PARTICULARLY STRONG CORRELATION WITH METHYLATION, AND TWO INTERGENIC SNPS FALLING WITHIN THE DMR (RS62435998 AND RS62435999) DEMONSTRATE GENETIC AND EPIGENETIC EFFECTS ON THE REGULATORY ACTIVITY OF THIS REGION. WE THEREFORE POSIT THAT THE OA SIGNAL MEDIATES ITS EFFECT BY MODULATING THE METHYLATION OF THE REGULATORY ELEMENT, WHICH THEN IMPACTS ON GENE EXPRESSION, WITH RUNX2 BEING THE PRINCIPAL TARGET. OUR STUDY HIGHLIGHTS THE INTERPLAY BETWEEN DNA METHYLATION, OA GENETIC RISK AND THE DOWNSTREAM REGULATION OF GENES CRITICAL TO NORMAL JOINT FUNCTION. 2018