1 5388 131 REDOX REGULATION OF MICRORNAS IN ENDOMETRIOSIS-ASSOCIATED PAIN. ENDOMETRIOSIS IS A CHRONIC, PAINFUL CONDITION WITH UNKNOWN ETIOLOGY. A DIFFERENTIAL EXPRESSION OF MICRORNAS IN THE ENDOMETRIOTIC TISSUES FROM WOMEN WITH ENDOMETRIOSIS WITH PAIN COMPARED TO THOSE WITHOUT SUGGESTED A PLAUSIBLE ROLE FOR MIRNA OR EPIGENETIC MECHANISMS IN THE ETIOLOGY OF ENDOMETRIOTIC PAIN. THE PERITONEAL MILIEU IS INVOLVED IN MAINTENANCE OF ENDOMETRIOTIC LESION AND NOCICEPTION. WE RECENTLY SHOWED THE MECHANISTIC ROLE FOR OXIDIZED-LIPOPROTEINS (OX-LDLS) PRESENT IN PERITONEAL FLUID (PF) IN ENDOMETRIOSIS AND PAIN. WE EXPLORED THE POSSIBILITY OF OX-LDLS MODULATING THE EXPRESSION OF MIRNAS IN A MANNER SIMILAR TO PF FROM WOMEN WITH ENDOMETRIOSIS. EXPRESSION LEVELS OF MIRNAS AND THEIR PREDICTED NOCICEPTIVE AND INFLAMMATORY TARGETS WERE DETERMINED IN PF AND OX-LDL TREATED HUMAN ENDOMETRIAL CELL-LINES. SAMPLES FROM IRB-APPROVED AND CONSENTED PATIENTS WITH AND WITHOUT ENDOMETRIOSIS OR PAIN WERE USED. THESE WERE COMPARED TO ENDOMETRIAL CELL-LINES TREATED WITH VARIOUS FORMS OF OXIDIZED-LIPOPROTEINS. RNA (INCLUDING MIRNAS) WERE ISOLATED FROM TREATED ENDOMETRIAL CELLS AND EXPRESSION LEVELS WERE DETERMINED USING COMMERCIAL MIRNOME ARRAYS. CELL LYSATES WERE USED IN IMMUNOBLOTTING FOR INFLAMMATORY PROTEINS USING A PROTEIN ARRAY. TWENTY MIRNAS INCLUDING ISOFORMS OF MIR-29, MIR-181 AND LET-7 WERE MUTUALLY DIFFERENTIALLY EXPRESSED IN CELLS TREATED WITH PF FROM ENDOMETRIOSIS PATIENTS WITH PAIN AND THOSE TREATED WITH OX-LDL COMPONENTS. THE OX-LDLS AND ENDO-PF TREATMENT ALSO PRODUCED SIGNIFICANT OVEREXPRESSION OF MICRORNA PREDICTED TARGET GENES NERVE GROWTH FACTOR, INTERLEUKIN-6 AND PROSTAGLANDIN E SYNTHASE AND OVEREXPRESSION OF THEIR DOWNSTREAM PROTEIN TARGETS MIP1ALPHA AND MCP1. THIS STUDY SHOWED SIMILARITIES BETWEEN MIRNA REGULATION IN PF FROM ENDOMETRIOTIC WOMEN AND OX-LDLS PRESENT IN ABUNDANCE IN THE PF OF THESE WOMEN. KEY MIRNAS RESPONSIBLE FOR TARGETING NOCICEPTIVE AND INFLAMMATORY MOLECULES WERE DOWNREGULATED IN THE PRESENCE OF OX-LDLS AND ENDO-PF, THUS PLAYING A ROLE IN THE ETIOLOGY OF ENDOMETRIOTIC PAIN. THESE REDOX-SENSITIVE MIRNAS CAN BE OF POTENTIAL USE AS TARGETS IN THE TREATMENT OF ENDOMETRIOSIS-ASSOCIATED PAIN. 2017 2 3667 31 INFILTRATING MACROPHAGES INDUCE ERALPHA EXPRESSION THROUGH AN IL17A-MEDIATED EPIGENETIC MECHANISM TO SENSITIZE ENDOMETRIAL CANCER CELLS TO ESTROGEN. PERSISTENT UNOPPOSED ESTROGEN STIMULATION IS A CENTRAL ONCOGENIC MECHANISM DRIVING THE FORMATION OF TYPE I ENDOMETRIAL CANCER. RECENT EPIDEMIOLOGIC AND CLINICAL STUDIES OF ENDOMETRIAL CANCER HAVE ALSO REVEALED A ROLE FOR INSULIN RESISTANCE, CLINICALLY MANIFESTED BY CHRONIC INFLAMMATION. HOWEVER, THE ROLE OF INFLAMMATION IN ESTROGEN-DRIVEN ENDOMETRIAL CANCER IS NOT WELL CHARACTERIZED. IN THIS STUDY, WE INVESTIGATED THE ASSOCIATION BETWEEN INFILTRATING MACROPHAGES AND ESTROGEN SENSITIVITY IN ENDOMETRIAL CANCER. EVALUATING TISSUE SAMPLES AND SERUM FROM PATIENTS WITH PRECANCEROUS LESIONS OR ENDOMETRIAL CANCER, WE FOUND THAT TISSUE MACROPHAGE INFILTRATION, BUT NOT SERUM ESTRADIOL LEVELS, CORRELATED POSITIVELY WITH ENDOMETRIAL CANCER DEVELOPMENT. FURTHERMORE, IL4/IL13-INDUCED CD68(+)CD163(+) MACROPHAGES ENHANCED THE PROLIFERATIVE EFFECTS OF ESTRADIOL IN ENDOMETRIAL CANCER CELLS BY UPREGULATING ESTROGEN RECEPTOR ALPHA (ERALPHA), BUT NOT ERBETA. MECHANISTIC INVESTIGATIONS REVEALED THAT CD68(+)CD163(+) MACROPHAGES SECRETED CYTOKINES, SUCH AS IL17A, THAT UPREGULATED ERALPHA EXPRESSION THROUGH TET1-MEDIATED EPIGENETIC MODULATION OF THE ERALPHA GENE. OVERALL, OUR FINDINGS SHOW HOW CYTOKINES PRODUCED BY INFILTRATING MACROPHAGES IN THE ENDOMETRIAL MICROENVIRONMENT CAN INDUCE EPIGENETIC UPREGULATION OF ERALPHA EXPRESSION, WHICH IN TURN SENSITIZES ENDOMETRIAL CELLS TO ESTROGEN STIMULATION. THE CONCEPT THAT INFLAMMATION-INDUCED ESTROGEN SENSITIVITY IN THE ENDOMETRIUM ACTS AS A DRIVER OF TYPE I ENDOMETRIAL CANCER HAS IMPLICATIONS FOR INFILTRATING MACROPHAGES AS A PROGNOSTIC BIOMARKER OF PROGRESSION IN THIS DISEASE SETTING. 2016 3 468 35 ARGININE METHYLTRANSFERASES MEDIATE AN EPIGENETIC OVARIAN RESPONSE TO ENDOMETRIOSIS. ENDOMETRIOSIS IS ASSOCIATED WITH INFERTILITY AND DEBILITATING CHRONIC PAIN. ABNORMAL EPIGENETIC MODIFICATIONS IN THE HUMAN ENDOMETRIUM HAVE RECENTLY BEEN IMPLICATED IN THE PATHOGENESIS OF THIS CONDITION. HOWEVER, WHETHER AN ALTERED EPIGENETIC LANDSCAPE CONTRIBUTES TO PATHOLOGICAL CHANGES IN THE OVARY IS UNKNOWN. USING AN ESTABLISHED BABOON ENDOMETRIOSIS MODEL, EARLY-, AND LATE-STAGE EPIGENETIC CHANGES IN THE OVARY WERE INVESTIGATED. TRANSCRIPT PROFILING OF KEY CHROMATIN-MODIFYING ENZYMES USING PATHWAY-FOCUSED PCR ARRAYS ON OVARIAN TISSUE FROM HEALTHY CONTROL ANIMALS AND AT 3 AND 15 MONTHS OF ENDOMETRIOSIS REVEALED DRAMATIC CHANGES IN GENE EXPRESSION IN A DISEASE DURATION-DEPENDENT MANNER. INGENUITY PATHWAY ANALYSIS INDICATED THAT TRANSCRIPTS FOR CHROMATIN-REMODELING ENZYMES ASSOCIATED WITH REPRODUCTIVE SYSTEM DISEASE AND CANCER DEVELOPMENT WERE ABNORMALLY REGULATED, MOST PROMINENTLY THE ARGININE METHYLTRANSFERASES CARM1, PRMT2, AND PRMT8. DOWNREGULATION OF CARM1 PROTEIN EXPRESSION WAS ALSO DETECTED IN THE OVARY, FULLY-GROWN OOCYTES AND EUTOPIC ENDOMETRIUM FOLLOWING 15 MONTHS OF ENDOMETRIOSIS. SODIUM BISULFITE SEQUENCING REVEALED DNA HYPERMETHYLATION WITHIN THE PRMT8 PROMOTER, SUGGESTING THAT DEREGULATED CPG METHYLATION MAY PLAY A ROLE IN TRANSCRIPTIONAL REPRESSION OF THIS GENE. THESE RESULTS DEMONSTRATE THAT ENDOMETRIOSIS IS ASSOCIATED WITH CHANGES OF EPIGENETIC PROFILES IN THE PRIMATE OVARY AND SUGGEST THAT ARGININE METHYLTRANSFERASES PLAY A PROMINENT ROLE IN MEDIATING THE OVARIAN RESPONSE TO ENDOMETRIOSIS. OWING TO THE CRITICAL ROLE OF CARM1 IN NUCLEAR RECEPTOR-MEDIATED TRANSCRIPTION AND MAINTENANCE OF PLURIPOTENCY IN THE CLEAVAGE STAGE EMBRYO, OUR RESULTS SUGGEST THAT EPIGENETIC ALTERATIONS IN THE OVARY MAY HAVE FUNCTIONAL CONSEQUENCES FOR OOCYTE QUALITY AND THE ETIOLOGY OF INFERTILITY ASSOCIATED WITH ENDOMETRIOSIS. 2015 4 1584 23 DNA METHYLATION PROFILES OF SELECTED PRO-INFLAMMATORY CYTOKINES IN ALZHEIMER DISEASE. BY MEANS OF FUNCTIONAL GENOMICS ANALYSIS, WE RECENTLY DESCRIBED THE MRNA EXPRESSION PROFILES OF VARIOUS GENES INVOLVED IN THE NEUROINFLAMMATORY RESPONSE IN THE BRAINS OF SUBJECTS WITH LATE-ONSET ALZHEIMER DISEASE (LOAD). SOME OF THESE GENES, NAMELY INTERLEUKIN (IL)-1BETA AND IL-6, SHOWED DISTINCT EXPRESSION PROFILES WITH PEAK EXPRESSION DURING THE FIRST STAGES OF THE DISEASE AND CONTROL-LIKE LEVELS AT LATER STAGES. IL-1BETA AND IL-6 GENES ARE MODULATED BY DNA METHYLATION IN DIFFERENT CHRONIC AND DEGENERATIVE DISEASES; IT IS ALSO WELL KNOWN THAT LOAD MAY HAVE AN EPIGENETIC BASIS. INDEED, WE AND OTHERS HAVE PREVIOUSLY REPORTED GENE-SPECIFIC DNA METHYLATION ALTERATIONS IN LOAD AND IN RELATED ANIMAL MODELS. BASED ON THESE DATA, WE STUDIED THE DNA METHYLATION PROFILES, AT SINGLE CYTOSINE RESOLUTION, OF IL-1BETA AND IL-6 5'-FLANKING REGION BY BISULPHITE MODIFICATION IN THE CORTEX OF HEALTHY CONTROLS AND LOAD PATIENTS AT 2 DIFFERENT DISEASE STAGES: BRAAK I-II/A AND BRAAK V-VI/C. OUR ANALYSIS PROVIDES EVIDENCE THAT NEUROINFLAMMATION IN LOAD IS ASSOCIATED WITH (AND POSSIBLY MEDIATED BY) EPIGENETIC MODIFICATIONS. 2017 5 1840 34 EFFECTS OF SELECTIVE INHIBITION OF PROSTAGLANDIN E2 RECEPTORS EP2 AND EP4 ON THE MIRNA PROFILE IN ENDOMETRIOSIS. ENDOMETRIOSIS IS AN ESTROGEN-DEPENDENT, PROGESTERONE-RESISTANT, CHRONIC INFLAMMATORY GYNECOLOGICAL DISEASE OF REPRODUCTIVE-AGE WOMEN. TWO MAJOR CLINICAL SYMPTOMS OF ENDOMETRIOSIS ARE CHRONIC PELVIC PAIN AND INFERTILITY, WHICH PROFOUNDLY AFFECT THE QUALITY OF LIFE IN WOMEN. CURRENT HORMONAL THERAPIES TO INDUCE A HYPOESTROGENIC STATE ARE UNSUCCESSFUL BECAUSE OF UNDESIRABLE SIDE EFFECTS, REPRODUCTIVE HEALTH CONCERNS, AND FAILURE TO PREVENT DISEASE RECURRENCE. PROSTAGLANDIN E(2) (PGE(2)) PLAYS AN IMPORTANT ROLE IN THE SURVIVAL AND GROWTH OF ENDOMETRIOTIC LESIONS. MICRORNAS (MIRNAS) ARE SMALL, NONCODING RNAS THAT CONTROL GENE EXPRESSIONS THROUGH MULTIPLE MECHANISMS AND HAVE IMPORTANT ROLES IN THE PATHOGENESIS OF ENDOMETRIOSIS. THE OBJECTIVE OF THE PRESENT STUDY IS TO DETERMINE THE EFFECTS OF PHARMACOLOGICAL INHIBITION OF PGE(2) RECEPTORS, EP2 AND EP4, ON MIRNA PROFILE IN ENDOMETRIOSIS. THE NOVEL RESULTS COLLECTIVELY INDICATE THAT INHIBITION OF PGE(2)-EP2/EP4 SIGNALING REGULATED SEVERAL MIRNA CLUSTERS ASSOCIATED WITH CELL ADHESION, MIGRATION, INVASION, SURVIVAL AND GROWTH IN CELL-SPECIFIC AND THE CHROMOSOME-SPECIFIC MANNER AND REVERSES THE EPIGENETIC SILENCING OF PROAPOPTOTIC MIRNAS 15A AND 34C IN THE HUMAN ENDOMETRIOTIC EPITHELIAL AND STROMAL CELLS AND EXPERIMENTAL ENDOMETRIOTIC LESIONS. THUS, SELECTIVE INHIBITION OF EP2/EP4 RECEPTORS COULD EMERGE AS A POTENTIAL NONSTEROIDAL THERAPY FOR ENDOMETRIOSIS. 2022 6 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 7 146 27 ABERRANT ENDOMETRIAL DNA METHYLOME AND ASSOCIATED GENE EXPRESSION IN WOMEN WITH ENDOMETRIOSIS. ENDOMETRIOSIS IS AN ESTROGEN-DEPENDENT, PROGESTERONE-RESISTANT DISORDER LARGELY DERIVED FROM RETROGRADE TRANSPLANTATION OF MENSTRUAL TISSUE/CELLS INTO THE PELVIS, ELICITING AN INFLAMMATORY RESPONSE, PELVIC PAIN, AND INFERTILITY. EUTOPIC ENDOMETRIUM (WITHIN THE UTERUS), GIVING RISE TO PELVIC DISEASE, DISPLAYS CYCLE-DEPENDENT TRANSCRIPTOMIC, PROTEOMIC, AND SIGNALING ABNORMALITIES, AND ALTHOUGH ITS DNA METHYLATION PROFILES DYNAMICALLY CHANGE ACROSS THE CYCLE IN HEALTHY WOMEN, STUDIES IN ENDOMETRIOSIS ARE LIMITED. HEREIN, WE INVESTIGATED THE DNA METHYLOME AND ASSOCIATED GENE EXPRESSION IN THREE PHASES OF THE CYCLE IN EUTOPIC ENDOMETRIUM OF WOMEN WITH SEVERE ENDOMETRIOSIS VERSUS CONTROLS, MATCHED FOR ETHNICITY, MEDICATIONS, SMOKING, AND NO RECENT CONTRACEPTIVE STEROID USE. GENOME-WIDE DNA METHYLATION AND GENE EXPRESSION WERE COASSESSED IN EACH SAMPLE. CYCLE PHASE WAS DETERMINED BY HISTOLOGY, SERUM HORMONE LEVELS, AND UNSUPERVISED PRINCIPAL COMPONENT AND HIERARCHICAL CLUSTER ANALYSES OF MICROARRAY DATA. ALTERED ENDOMETRIAL DNA METHYLATION IN ENDOMETRIOSIS WAS MOST PROMINENT IN THE MIDSECRETORY PHASE (PEAK PROGESTERONE), WITH DISRUPTION OF THE NORMAL PATTERN OF CYCLE-DEPENDENT DNA METHYLATION CHANGES, INCLUDING A BIAS TOWARD METHYLATION OF CPG ISLANDS, SUGGESTING WIDE-RANGE ABNORMALITIES OF THE CHROMATIN REMODELING MACHINERY IN ENDOMETRIOSIS. DNA METHYLATION CHANGES WERE ASSOCIATED WITH ALTERED GENE EXPRESSION RELEVANT TO ENDOMETRIAL FUNCTION/DYSFUNCTION, INCLUDING CELL PROLIFERATION, INFLAMMATION/IMMUNE RESPONSE, ANGIOGENESIS, AND STEROID HORMONE RESPONSE. THE DATA PROVIDE INSIGHT INTO EPIGENETIC REPROGRAMMING AND STEROID HORMONE ACTIONS IN ENDOMETRIUM CONTRIBUTING TO THE PATHOGENESIS AND PATHOPHYSIOLOGY OF ENDOMETRIOSIS. 2016 8 1545 30 DNA METHYLATION IN LIVER TUMORIGENESIS IN FISH FROM THE ENVIRONMENT. THE LINK BETWEEN ENVIRONMENT, ALTERATION IN DNA METHYLATION AND CANCER HAS BEEN WELL ESTABLISHED IN HUMANS; YET, IT IS UNDER-STUDIED IN UNSEQUENCED NON-MODEL ORGANISMS. THE OCCURRENCE OF LIVER TUMORS IN THE FLATFISH DAB COLLECTED AT CERTAIN UK SAMPLING SITES EXCEEDS 20%, YET THE CAUSATIVE AGENTS AND THE MOLECULAR MECHANISMS OF TUMOR FORMATION ARE NOT KNOWN, ESPECIALLY REGARDING THE BALANCE BETWEEN EPIGENETIC AND GENETIC FACTORS. METHYLATED DNA IMMUNOPRECIPITATION (MEDIP) COMBINED WITH DE NOVO HIGH-THROUGHPUT DNA SEQUENCING WERE USED TO INVESTIGATE DNA METHYLATION CHANGES IN DAB HEPATOCELLULAR ADENOMA TUMORS FOR THE FIRST TIME IN AN UNSEQUENCED SPECIES. NOVEL CUSTOM-MADE DAB GENE EXPRESSION ARRAYS WERE DESIGNED AND USED TO DETERMINE THE RELATIONSHIP BETWEEN DNA METHYLATION AND GENE EXPRESSION. IN ADDITION, THE CONFIRMATORY TECHNIQUES OF BISULFITE SEQUENCING PCR (BSP) AND RT-PCR WERE APPLIED. GENES INVOLVED IN PATHWAYS RELATED TO CANCER, INCLUDING APOPTOSIS, WNT/BETA-CATENIN SIGNALING AND GENOMIC AND NON-GENOMIC ESTROGEN RESPONSES, WERE ALTERED BOTH IN METHYLATION AND TRANSCRIPTION. GLOBAL METHYLATION WAS STATISTICALLY SIGNIFICANTLY 1.8-FOLD REDUCED IN HEPATOCELLULAR ADENOMA AND NON-CANCEROUS SURROUNDING TISSUES COMPARED WITH LIVER FROM NON-CANCER BEARING DAB. BASED ON THE IDENTIFIED CHANGES AND CHEMICAL EXPOSURE DATA, OUR STUDY SUPPORTS THE EPIGENETIC MODEL OF CANCER. WE HYPOTHESIZE THAT CHRONIC EXPOSURE TO A MIXTURE OF ENVIRONMENTAL CONTAMINANTS CONTRIBUTES TO A GLOBAL HYPOMETHYLATION FOLLOWED BY FURTHER EPIGENETIC AND GENOMIC CHANGES. THE FINDINGS SUGGEST A LINK BETWEEN ENVIRONMENT, EPIGENETICS AND CANCER IN FISH TUMORS IN THE WILD AND SHOW THE UTILITY OF THIS METHODOLOGY FOR STUDIES IN NON-MODEL ORGANISMS. 2011 9 6226 19 THE LINK BETWEEN EPIGENETICS, PAIN SENSITIVITY AND CHRONIC PAIN. INCREASING EVIDENCE SUGGESTS AN ASSOCIATION BETWEEN GENE EXPRESSION AND CLINICAL PAIN. EPIGENETIC MODIFICATIONS ARE THE MAIN MODULATORS OF GENE EXPRESSION OR PROTEIN TRANSLATION IN RESPONSE TO ENVIRONMENTAL STIMULI AND PATHOPHYSIOLOGICAL CONDITIONS. PRECLINICAL AND CLINICAL STUDIES INDICATE THAT EPIGENETIC MODIFICATIONS COULD ALSO IMPACT THE DEVELOPMENT OF PAIN, THE TRANSITION FROM ACUTE TO CHRONIC PAIN, AND THE MAINTENANCE HEREOF. 2022 10 6794 32 [EFFECT OF BENZO(A)PYRENE ON THE EXPRESSION OF AHR-REGULATED MICRORNA IN FEMALE AND MALE RAT LUNGS]. SMOKING IS THE MAIN RISK FACTOR FOR LUNG CANCER, MAINLY DUE TO PRESENCE OF NITROSAMINES AND POLYCYCLIC AROMATIC HYDROCARBONS, INCLUDING BENZO[A]PYRENE (BP) IN TOBACCO SMOKE COMPOSITION. THE GENOTOXIC EFFECT OF BP IS BASED ON THE HIGH DNA-BINDING ABILITY OF ITS METABOLITES, WHILE THE EPIGENETIC EFFECTS ARE MEDIATED BY A CHANGE IN THE EXPRESSION OF CANCER RELATED GENES OR REGULATORY RNAS. IT HAS BEEN SHOWN THAT WOMEN HAVE A HIGHER RISK TO DEVELOP LUNG CANCER UPON SMOKING RATHER THAN MEN. WE HYPOTHESIZED THAT CROSSTALK BETWEEN SIGNALING PATHWAYS ACTIVATED BY BP AND ESTROGENS COULD UNDERLIE THE SEX-DEPENDENT DIFFERENCES IN MIRNAS EXPRESSION. TO TEST THIS HYPOTHESIS, MALE AND FEMALE RATS WERE SUBJECTED TO SHORT-TERM OR LONG-TERM BP EXPOSURE. USING IN SILICO ANALYSIS, MIRNAS CONTAINING THE ER- AND AHR-BINDING SITES IN THE PROMOTERS OF THE GENES (OR HOST GENES) WERE SELECTED. DURING CHRONIC EXPOSURE OF BP THE EXPRESSION OF MIR-22-3P, -29A-3P, -126A-3P, -193B-5P IN THE LUNGS OF MALE RATS WERE SIGNIFICANTLY INCREASED, WHILE THE LEVEL OF MIRNA-483-3P WERE DECREASED. EXPRESSION OF MIRNA-483-3P WAS UP-REGULATED DURING CHRONIC BP EXPOSURE IN THE LUNGS OF FEMALE RATS AND THE LEVELS OF OTHER STUDIED MIRNAS WERE UNCHANGED. IN TURN, CHANGES IN THE EXPRESSION OF MIRNAS WERE FOLLOWED BY CHANGES IN THE EXPRESSION OF THEIR TARGET GENES, INCLUDING PTEN, EMP2, IGF1, ITGA6, SLC34A2, AND THE OBSERVED CHANGES IN FEMALE AND MALE RAT LUNGS WERE VARIED. THUS, OUR RESULTS SUGGEST THAT SEX-DEPENDENT EPIGENETIC EFFECTS OF BP MAY BE BASED ON DIFFERENT EXPRESSION OF AHR- AND ER- REGULATED MIRNAS. 2020 11 3076 34 GENOME-WIDE EPIGENOMIC ANALYSES IN PATIENTS WITH NOCICEPTIVE AND NEUROPATHIC CHRONIC PAIN SUBTYPES REVEALS ALTERATIONS IN METHYLATION OF GENES INVOLVED IN THE NEURO-MUSCULOSKELETAL SYSTEM. NOCICEPTIVE PAIN INVOLVES THE ACTIVATION OF NOCICEPTORS WITHOUT DAMAGE TO THE NERVOUS SYSTEM, WHEREAS NEUROPATHIC PAIN IS RELATED TO AN ALTERATION IN THE CENTRAL OR PERIPHERAL NERVOUS SYSTEM. CHRONIC PAIN ITSELF AND THE TRANSITION FROM ACUTE TO CHRONIC PAIN MAY BE EPIGENETICALLY CONTROLLED. IN THIS CROSS-SECTIONAL STUDY, A GENOME-WIDE DNA METHYLATION ANALYSIS WAS PERFORMED USING THE BLOOD DNA REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS) TECHNIQUE. THREE PROSPECTIVE COHORTS INCLUDING 20 HEALTHY CONTROLS (CTL), 18 PATIENTS WITH CHRONIC NOCICEPTIVE PAIN (NOCI), AND 19 PATIENTS WITH CHRONIC NEUROPATHIC PAIN (NEURO) WERE COMPARED AT BOTH THE SINGLE CPG AND DIFFERENTIALLY METHYLATED REGION (DMR) LEVELS. GENES WITH DMRS WERE SEEN IN THE NOCI AND NEURO GROUPS BELONGED TO THE NEURO-MUSCULOSKELETAL SYSTEM AND DIFFERED BETWEEN NOCI AND NEURO PATIENTS. OUR RESULTS DEMONSTRATE THAT THE EPIGENETIC DISTURBANCES ACCOMPANYING NOCICEPTIVE PAIN ARE VERY DIFFERENT FROM THOSE ACCOMPANYING NEUROPATHIC PAIN. IN THE FORMER, AMONG OTHERS, THE EPIGENETIC DISTURBANCE OBSERVED WOULD AFFECT THE FUNCTION OF THE OPIOID ANALGESIC SYSTEM, WHEREAS IN THE LATTER IT WOULD AFFECT THAT OF THE GABAERGIC REWARD SYSTEM. THIS STUDY PRESENTS BIOLOGICAL FINDINGS THAT HELP TO CHARACTERIZE NOCI- AND NEURO-AFFECTED PATHWAYS AND OPENS THE POSSIBILITY OF DEVELOPING EPIGENETIC DIAGNOSTIC ASSAYS. PERSPECTIVE: OUR RESULTS HELP TO EXPLAIN THE VARIOUS BIOLOGICAL PATHWAYS MODIFICATIONS UNDERLYING THE DIFFERENT CLINICAL MANIFESTATIONS OF NOCICEPTIVE AND NEUROPATHIC PAINS. FURTHERMORE, THE NEW TARGETS IDENTIFIED IN OUR STUDY MIGHT HELP TO DISCOVER MORE SPECIFIC TREATMENTS FOR NOCICEPTIVE OR NEUROPATHIC PAINS. 2022 12 3764 37 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 13 3963 33 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 14 3165 32 GRIK1-AS1 DEFICIENCY ACCELERATES ENDOMETRIOSIS PROGRESSION BY BOOSTING DNMT1-DEPENDENT SFRP1 PROMOTER METHYLATION IN ENDOMETRIAL STROMAL CELLS. BACKGROUND: ENDOMETRIOSIS, A GYNECOLOGICAL DISEASE THAT AFFECTS UP TO 10% OF WOMEN, IS A MAJOR CAUSE OF PAIN AND INFERTILITY. DEREGULATION OF THE EPIGENOME IS ACCOUNTABLE FOR THE ONSET AND PROGRESSION OF ENDOMETRIOSIS, ALTHOUGH ITS EXACT MECHANISM IS UNKNOWN. THE PURPOSE OF THE CURRENT STUDY IS TO EXAMINE THE ROLE OF THE LONG NON-CODING RNA (LNCRNA) GRIK1-AS1 IN THE EPIGENETIC REGULATION OF ENDOMETRIAL STROMAL CELL PROLIFERATION AND THE DEVELOPMENT OF ENDOMETRIOSIS. METHODS: ENDOMETRIOSIS DATASETS WERE SCREENED TO IDENTIFY GRIKI-AS1 AS DRAMATICALLY DECLINING IN ENDOMETRIOSIS. GAIN OR LOSS OF FUNCTION ENDOMETRIAL STROMAL CELL (ESC) MODELS WERE ESTABLISHED. THE ANTI-PROLIFERATION PHENOTYPE WAS INVESTIGATED USING IN VITRO AND IN VIVO EXPERIMENTS. EPIGENETIC REGULATORY NETWORK ANALYSES WERE CONDUCTED TO SUGGEST THE INTRINSIC MOLECULAR MECHANISM. RESULTS: WITH BIOINFORMATIC AND CLINICAL DATA, WE OBSERVED THAT GRIK1-AS1 AND SFRP1 WERE EXPRESSED AT LOW LEVELS IN ENDOMETRIOSIS. OVEREXPRESSED GRIK1-AS1 INHIBITED ESC PROLIFERATION, WHILE SFRP1 KNOCKDOWN RESCUED THE ANTIPROLIFERATIVE ABILITY OF GRIK1-AS1. SPECIFICALLY, METHYLATION-DEPENDENT EXPRESSION INHIBITION OF SFRP1 WAS REVEALED IN ESCS. MECHANISTICALLY, GRIK1-AS1 HAMPERS THE OCCUPANCY OF DNMT1 IN SRFP1 PROMOTER, LEADING TO HYPOMETHYLATION OF SFRP1 AND UPREGULATED SFRP1 EXPRESSION, THEREBY POTENTIALLY SUPPRESSING WNT SIGNALING AND ITS ADVERSE PROLIFERATIVE EFFECT. THERAPEUTICALLY, LENTIVIRUS-MEDIATED UPREGULATION OF GRIK1-AS1 INHIBITED ENDOMETRIOSIS DISEASE PROGRESSION IN VIVO. CONCLUSIONS: OUR STUDY IS A PROOF-OF-CONCEPT DEMONSTRATION FOR GRIKI-AS1-ASSOCIATED ENDOMETRIOSIS PATHOGENESIS AND HIGHLIGHTS A POTENTIAL INTERVENTION TARGET. 2023 15 194 30 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 16 3468 33 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 17 5347 30 RARBETA AGONIST DRUG (C286) DEMONSTRATES EFFICACY IN A PRE-CLINICAL NEUROPATHIC PAIN MODEL RESTORING MULTIPLE PATHWAYS VIA DNA REPAIR MECHANISMS. NEUROPATHIC PAIN (NP) IS ASSOCIATED WITH PROFOUND GENE EXPRESSION ALTERATIONS WITHIN THE NOCICEPTIVE SYSTEM. DNA MECHANISMS, SUCH AS EPIGENETIC REMODELING AND REPAIR PATHWAYS HAVE BEEN IMPLICATED IN NP. HERE WE HAVE USED A RAT MODEL OF PERIPHERAL NERVE INJURY TO STUDY THE EFFECT OF A RECENTLY DEVELOPED RARBETA AGONIST, C286, CURRENTLY UNDER CLINICAL RESEARCH, IN NP. A 4-WEEK TREATMENT INITIATED 2 DAYS AFTER THE INJURY NORMALIZED PAIN SENSATION. GENOME-WIDE AND PATHWAY ENRICHMENT ANALYSIS SHOWED THAT MULTIPLE MECHANISMS PERSISTENTLY ALTERED IN THE SPINAL CORD WERE RESTORED TO PREINJURY LEVELS BY THE AGONIST. CONCOMITANT UPREGULATION OF DNA REPAIR PROTEINS, ATM AND BRCA1, THE LATTER BEING REQUIRED FOR C286-MEDIATED PAIN MODULATION, SUGGESTS THAT EARLY DNA REPAIR MAY BE IMPORTANT TO PREVENT PHENOTYPIC EPIGENETIC IMPRINTS IN NP. THUS, C286 IS A PROMISING DRUG CANDIDATE FOR NEUROPATHIC PAIN AND DNA REPAIR MECHANISMS MAY BE USEFUL THERAPEUTIC TARGETS TO EXPLORE. 2019 18 1117 27 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 1567 32 DNA METHYLATION OF THE KLF14 GENE REGION IN WHOLE BLOOD CELLS PROVIDES PREDICTION FOR THE CHRONIC INFLAMMATION IN THE ADIPOSE TISSUE. KRUPPEL-LIKE FACTOR 14 (KLF14) GENE, WHICH APPEARS TO BE A MASTER REGULATOR OF GENE EXPRESSION IN THE ADIPOSE TISSUE AND HAVE PREVIOUSLY BEEN ASSOCIATED WITH BMI AND TYPE 2 DIABETES (T2D) BY LARGE GENOME-WIDE ASSOCIATION STUDIES. IN ORDER TO FIND PREDICTIVE BIOMARKERS FOR THE DEVELOPMENT OF T2D, IT IS NECESSARY TO TAKE EPIGENOMIC CHANGES AFFECTED BY ENVIRONMENTAL FACTORS INTO ACCOUNT. THIS STUDY FOCUSES ON AGEING AND OBESITY, WHICH ARE T2D RISK FACTORS, AND EXAMINES EPIGENETIC CHANGES AND INFLAMMATORY CHANGES. WE INVESTIGATED DNA METHYLATION CHANGES IN THE KLF14 PROMOTER REGION IN DIFFERENT ORGANS OF MICE FOR COMPARING AGING AND WEIGHT. WE FOUND THAT METHYLATION LEVELS OF THESE SITES WERE INCREASED WITH AGING AND WEIGHT IN THE SPLEEN, THE ADIPOSE TISSUE, THE KIDNEY, THE LUNG, THE COLON AND THE WHOLE BLOOD CELLS. IN ADDITION, IN THE SPLEEN, THE ADIPOSE TISSUE AND THE WHOLE BLOOD, THESE EPIGENETIC CHANGES WERE ALSO SIGNIFICANTLY ASSOCIATED WITH INFLAMMATORY LEVELS. MOREOVER, NOT ONLY KLF14, BUT ALSO EXPRESSION LEVELS OF SOME DOWNSTREAM GENES WERE DECREASED WITH METHYLATION IN THE SPLEEN, THE ADIPOSE TISSUE AND THE WHOLE BLOOD CELLS. TAKEN TOGETHER, OUR RESULTS SUGGEST THAT METHYLATION CHANGES OF KLF14 IN THOSE TISSUES MAY BE ASSOCIATED WITH CHANGES IN GENE EXPRESSION AND INFLAMMATION ON THE ADIPOSE TISSUE OF OBESITY AND T2D. IN ADDITION, THE METHYLATION CHANGES IN THE WHOLE BLOOD CELLS MAY SERVE AS A PREDICTIVE EPIGENETIC BIOMARKER FOR THE DEVELOPMENT OF T2D. 2018 20 3959 39 LONG NON-CODING RNAS TARGET PATHOGENETICALLY RELEVANT GENES AND PATHWAYS IN RHEUMATOID ARTHRITIS. RHEUMATOID ARTHRITIS (RA) IS A CHRONIC INFLAMMATORY AUTOIMMUNE DISEASE DRIVEN BY GENETIC, ENVIRONMENTAL AND EPIGENETIC FACTORS. LONG NON-CODING RNAS (LNCRNAS) ARE A KEY COMPONENT OF THE EPIGENETIC MECHANISMS AND ARE KNOWN TO BE INVOLVED IN THE DEVELOPMENT OF AUTOIMMUNE DISEASES. IN THIS WORK WE AIMED TO IDENTIFY SIGNIFICANTLY DIFFERENTIALLY EXPRESSED LNCRNAS (DE-LNCRNAS) THAT ARE FUNCTIONALLY CONNECTED TO MODULATED GENES STRICTLY ASSOCIATED WITH RA. IN TOTAL, 542,500 TRANSCRIPTS HAVE BEEN PROFILED IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) FROM FOUR PATIENTS WITH EARLY ONSET RA PRIOR ANY TREATMENT AND FOUR HEALTHY DONORS USING CLARIOM D ARRAYS. RESULTS WERE CONFIRMED BY REAL-TIME PCR IN 20 PATIENTS AND 20 CONTROLS. SIX DE-LNCRNAS TARGET EXPERIMENTALLY VALIDATED MIRNAS ABLE TO REGULATE DIFFERENTIALLY EXPRESSED GENES (DEGS) IN RA; AMONG THEM, ONLY FTX, HNRNPU-AS1 AND RP11-498C9.15 TARGETED A LARGE NUMBER OF DEGS. MOST IMPORTANTLY, RP11-498C9.15 TARGETED THE LARGEST NUMBER OF SIGNALLING PATHWAYS THAT WERE FOUND TO BE ENRICHED BY THE GLOBAL AMOUNT OF RA-DEGS AND THAT HAVE ALREADY BEEN ASSOCIATED WITH RA AND RA-SYNOVIOCYTES. MOREOVER, RP11-498C9.15 TARGETED THE MOST HIGHLY CONNECTED GENES IN THE RA INTERACTOME, THUS SUGGESTING ITS INVOLVEMENT IN CRUCIAL GENE REGULATION. THESE RESULTS INDICATE THAT, BY MODULATING BOTH MICRORNAS AND GENE EXPRESSION, RP11-498C9.15 MAY PLAY A PIVOTAL ROLE IN RA PATHOGENESIS. 2019