1 2941 115 GENETIC AND EPIGENETIC ALTERATIONS IN TOLL LIKE RECEPTOR 2 AND WOUND HEALING IMPAIRMENT IN TYPE 2 DIABETES PATIENTS. AIM: PERSISTENT HYPERGLYCEMIC MICROENVIRONMENT IN TYPE 2 DIABETES MELLITUS (T2DM) LEADS TO THE DEVELOPMENT OF SECONDARY COMPLICATIONS LIKE WOUND HEALING IMPAIRMENT. PROPER CO-ORDINATION OF INNATE IMMUNE SYSTEM PLAYS AN INTEGRAL ROLE IN WOUND HEALING. TOLL LIKE RECEPTORS (TLRS) ARE PROMINENT CONTRIBUTORS FOR THE INDUCTION OF THE INNATE IMMUNE AND INFLAMMATION RESPONSE. TLR2 IS AN IMPORTANT EXTRACELLULAR MEMBER IN MAMMALIAN TLR FAMILY AND HAS BEEN SHOWN TO BE A POTENT PLAYER IN THE WOUND HEALING MECHANISM. METHODS: EXPRESSIONAL STATUS OF TLR2 WAS SEEN IN WOUNDS OF T2DM CASES WITH RESPECT TO THE SEVERITY OF WOUNDS IN 110 HUMAN LOWER EXTREMITY WOUNDS. THE METHYLATION STATUS OF TLR2 PROMOTER WAS ALSO EXAMINED. RESULTS: ALTHOUGH TLR2 TRANSCRIPTS WERE DOWNREGULATED IN T2DM WOUNDS COMPARED TO CONTROL, THEIR LEVELS TEND TO INCREASE WITH THE SEVERITY OF T2DM WOUNDS. THE METHYLATION STATUS OF TLR2 GENE PROMOTER WAS NOT SIGNIFICANTLY DIFFERENT AMONG DIFFERENT GRADES OF WOUNDS IN T2DM SUBJECTS. THE CPG SITES INVESTIGATED WERE TOTALLY OR PARTIALLY METHYLATED IN MAJORITY OF DFU CASES. CONCLUSION: TLR2 DOWN REGULATION IN WOUNDS OF T2DM PATIENTS COMPARED TO NON DIABETIC PATIENTS MAY LEAD TO DEVELOPMENT OF NON HEALING CHRONIC ULCERS IN THEM. 2015 2 3440 34 HYPERMETHYLATION AND LOW TRANSCRIPTION OF TLR2 GENE IN CHRONIC PERIODONTITIS. PERIODONTITIS IS AN INFLAMMATORY DISORDER CHARACTERIZED BY INTERACTIONS BETWEEN PERIODONTAL PATHOGENS AND HOST'S IMMUNE RESPONSE. EPIGENETIC MAY CONTRIBUTE TO DISEASE DEVELOPMENT AND OUTCOME BY INFLUENCING THE EXPRESSION OF GENES INVOLVED IN THE IMMUNE RESPONSE. IT HAS BEEN SHOWN THAT TOLL-LIKE RECEPTORS (TLR) PLAY AN IMPORTANT ROLE IN THE RESPONSE TO PERIODONTOPATHIC BACTERIA. THE AIM OF STUDY WAS TO EVALUATE THE METHYLATION STATUS AND THE EXPRESSION OF TLR2 GENE IN GINGIVAL SAMPLES FROM INDIVIDUALS WITH AND WITHOUT PERIODONTITIS. DNA WAS ANALYZED USING THE METHYL PROFILER DNA METHYLATION QPCR ASSAY. DNA METHYLATION AND TRANSCRIPT LEVELS WERE EVALUATED BY REAL-TIME POLYMERASE CHAIN REACTION. THE PERIODONTITIS GROUP SHOWED A HYPERMETHYLATED PROFILE AND A LOW EXPRESSION OF GENE. POSITIVE CORRELATION BETWEEN THE TLR2 METHYLATION FREQUENCY AND PROBING DEPTH WAS OBSERVED. THIS STUDY GIVES THE FIRST EVIDENCE OF METHYLATION FREQUENCY IN INFLAMED PERIODONTAL TISSUES AND OF THE POSSIBLE PARTICIPATION OF METHYLATION IN THE DEVELOPMENT OF PERIODONTITIS. 2013 3 1794 35 EFFECT OF DIABETES STATUS AND HYPERGLYCEMIA ON GLOBAL DNA METHYLATION AND HYDROXYMETHYLATION. TYPE 2 DIABETES MELLITUS (T2DM) IS CHARACTERIZED BY OXIDATIVE STRESS THAT COULD LEAD TO CHRONIC MICRO- AND MACROVASCULAR COMPLICATIONS. WE HYPOTHESIZED THAT SOME OF THE TARGET ORGAN DAMAGE IS MEDIATED BY OXIDATIVE ALTERATIONS IN EPIGENETIC MECHANISMS INVOLVING DNA METHYLATION (5MC) AND DNA HYDROXYMETHYLATION (5HMC). WE ANALYZED GLOBAL DNA METHYLATION AND HYDROXYMETHYLATION IN PERIPHERAL BLOOD CELLS IN WELL-CONTROLLED AND POORLY CONTROLLED PATIENTS WITH T2DM AND COMPARED THEM WITH HEALTHY CONTROLS. WE ALSO ANALYZED MICROARRAYS OF DNA METHYLATION AND GENE EXPRESSION OF OTHER IMPORTANT TISSUES IN THE CONTEXT OF DIABETES FROM THE GEO DATABASE REPOSITORY AND THEN COMPARED THESE RESULTS WITH OUR EXPERIMENTAL GENE EXPRESSION DATA. DNA METHYLATION AND, MORE IMPORTANTLY, DNA HYDROXYMETHYLATION LEVELS WERE INCREASED IN POORLY CONTROLLED PATIENTS COMPARED TO WELL-CONTROLLED AND HEALTHY INDIVIDUALS. BOTH 5MC AND 5HMC MEASUREMENTS WERE CORRELATED WITH THE PERCENTAGE OF GLYCATED HEMOGLOBIN, INDICATING A DIRECT IMPACT OF HYPERGLYCEMIA ON CHANGES OVER THE EPIGENOME. THE ANALYSIS OF METHYLATION MICROARRAYS WAS CONCORDANT, AND 5MC LEVELS WERE INCREASED IN THE PERIPHERAL BLOOD OF T2DM PATIENTS. HOWEVER, THE DNA METHYLATION LEVELS WERE THE OPPOSITE OF THOSE IN OTHER TISSUES, SUCH AS THE PANCREAS, ADIPOSE TISSUE AND SKELETAL MUSCLE. WE HYPOTHESIZE THAT A PROCESS OF DNA OXIDATION ASSOCIATED WITH HYPERGLYCEMIA MAY EXPLAIN THE DNA DEMETHYLATION IN WHICH THE ACTIVITY OF TEN-ELEVEN TRANSLOCATION (TET) PROTEINS IS NOT SUFFICIENT TO COMPLETE THE PROCESS. HIGH LEVELS OF GLUCOSE LEAD TO CELLULAR OXIDATION, WHICH TRIGGERS THE PROCESS OF DNA DEMETHYLATION AIDED BY TET ENZYMES, RESULTING IN EPIGENETIC DYSREGULATION OF THE DAMAGED TISSUES. 2017 4 776 34 CELL- AND TISSUE-SPECIFIC EPIGENETIC CHANGES ASSOCIATED WITH CHRONIC INFLAMMATION IN INSULIN RESISTANCE AND TYPE 2 DIABETES MELLITUS. TYPE 2 DIABETES MELLITUS (T2DM) IS A CHRONIC METABOLIC DISORDER CHARACTERIZED BY HYPERGLYCAEMIA, WHICH CAN CAUSE MICRO- AND MACROVASCULAR COMPLICATIONS. CHRONIC INFLAMMATION MAY BE THE CAUSE AND RESULT OF T2DM, AND ITS RELATED COMPLICATIONS AS AN IMBALANCE BETWEEN PRO- AND ANTI-INFLAMMATORY CYTOKINES CAN AFFECT IMMUNE FUNCTIONS. APART FROM GENETIC CHANGES OCCURRING WITHIN THE BODY RESULTING IN INFLAMMATION IN T2DM, EPIGENETIC MODIFICATIONS CAN MODIFY GENE EXPRESSION IN RESPONSE TO ENVIRONMENTAL CUES SUCH AS AN UNHEALTHY DIET, LACK OF EXERCISE AND OBESITY. THE MOST WIDELY STUDIED EPIGENETIC MODIFICATION, DNA METHYLATION (DNAM), REGULATES GENE EXPRESSION AND MAY MANIPULATE INFLAMMATORY GENES TO INCREASE OR DECREASE INFLAMMATION ASSOCIATED WITH T2DM. THIS REVIEW EXPLORES THE STUDIES RELATED TO EPIGENETIC CHANGES, MORE SPECIFICALLY DNAM, ASSOCIATED WITH CHRONIC INFLAMMATION IN T2DM, AT BOTH THE CELL AND TISSUE LEVELS. STUDYING EPIGENETIC ALTERATIONS DURING INFLAMMATORY RESPONSE, AS A RESULT OF GENETIC AND ENVIRONMENTAL SIGNALS, CREATES OPPORTUNITIES FOR THE DEVELOPMENT OF "EARLY DETECTION/RELATIVE RISK" TESTS TO AID IN PREVENTION OF T2DM. UNDERSTANDING INFLAMMATION IN T2DM AT THE GENE LEVEL IN INFLAMMATION-ASSOCIATED CELLS AND TISSUES MAY PROVIDE FURTHER INSIGHT FOR THE DEVELOPMENT OF SPECIFIC THERAPEUTIC TARGETS FOR THE DISORDER. 2018 5 5922 32 TARGETING DNA METHYLATION AND DEMETHYLATION IN DIABETIC FOOT ULCERS. BACKGROUND: POOR WOUND HEALING IS A SIGNIFICANT COMPLICATION OF DIABETES, WHICH IS COMMONLY CAUSED BY NEUROPATHY, TRAUMA, DEFORMITIES, PLANTAR HYPERTENSION AND PERIPHERAL ARTERIAL DISEASE. DIABETIC FOOT ULCERS (DFU) ARE DIFFICULT TO HEAL, WHICH MAKES PATIENTS SUSCEPTIBLE TO INFECTIONS AND CAN ULTIMATELY CONDUCE TO LIMB AMPUTATION OR EVEN DEATH IN SEVERE CASES. AN INCREASING NUMBER OF STUDIES HAVE FOUND THAT EPIGENETIC ALTERATIONS ARE STRONGLY ASSOCIATED WITH POOR WOUND HEALING IN DIABETES. AIM OF REVIEW: THIS WORK PROVIDES SIGNIFICANT INSIGHTS INTO THE DEVELOPMENT OF THERAPEUTICS FOR IMPROVING CHRONIC DIABETIC WOUND HEALING, PARTICULARLY BY TARGETING AND REGULATING DNA METHYLATION AND DEMETHYLATION IN DFU. KEY SCIENTIFIC CONCEPTS OF REVIEW: DNA METHYLATION AND DEMETHYLATION PLAY AN IMPORTANT PART IN DIABETIC WOUND HEALING, VIA REGULATING CORRESPONDING SIGNALING PATHWAYS IN DIFFERENT BREEDS OF CELLS, INCLUDING MACROPHAGES, VASCULAR ENDOTHELIAL CELLS AND KERATINOCYTES. IN THIS REVIEW, WE DESCRIBE THE FOUR MAIN PHASES OF WOUND HEALING AND THEIR ABNORMALITY IN DIABETIC PATIENTS. FURTHERMORE, WE PROVIDED AN IN-DEPTH SUMMARY AND DISCUSSION ON HOW DNA METHYLATION AND DEMETHYLATION REGULATE DIABETIC WOUND HEALING IN DIFFERENT TYPES OF CELLS; AND GAVE A BRIEF SUMMARY ON RECENT ADVANCES IN APPLYING CELLULAR REPROGRAMMING TECHNIQUES FOR IMPROVING DIABETIC WOUND HEALING. 2023 6 3436 29 HYPERGLYCEMIC MEMORY OF INNATE IMMUNE CELLS PROMOTES IN VITRO PROINFLAMMATORY RESPONSES OF HUMAN MONOCYTES AND MURINE MACROPHAGES. IT HAS BEEN WELL ESTABLISHED THAT THE PRESENCE OF DIABETES IS ACCOMPANIED BY A CHRONIC INFLAMMATORY STATE PROMOTING VARIOUS DIABETES-ASSOCIATED COMPLICATIONS. ONE POTENTIAL DRIVER OF THIS ENHANCED INFLAMMATORY STATE IN PATIENTS WITH DIABETES IS HYPERGLYCEMIA. EVEN AFTER BLOOD GLUCOSE CONTROL IS ACHIEVED, DIABETES-ASSOCIATED COMPLICATIONS PERSIST, SUGGESTING THE PRESENCE OF A "HYPERGLYCEMIC MEMORY." INNATE IMMUNE CELLS, CRITICALLY INVOLVED IN VARIOUS COMPLICATIONS ASSOCIATED WITH DIABETES, CAN BUILD NONSPECIFIC, IMMUNOLOGICAL MEMORY (TRAINED IMMUNITY) VIA EPIGENETIC REGULATION. WE EXAMINE THE POTENTIAL INVOLVEMENT OF HYPERGLYCEMIA-INDUCED TRAINED IMMUNITY IN PROMOTING INFLAMMATION. OUR RESULTS SHOW THAT HYPERGLYCEMIA INDUCES A TRAINED PHENOTYPE IN VIVO IN MICE AND IN VITRO IN HUMAN MONOCYTES, REPRESENTATIVE BY AN INCREASED TNF-ALPHA SECRETION AFTER EX VIVO STIMULATION WITH LPS. THESE EFFECTS WERE LARGELY MEDIATED BY EPIGENETIC CHANGES CONTROLLED BY THE MIXED LINEAGE LEUKEMIA (MLL) FAMILY BECAUSE TREATMENT WITH THE MLL INHIBITOR MENIN-MLL DURING THE PROCESS OF TRAINED IMMUNITY ACQUISITION REPRESSED THE PROINFLAMMATORY PHENOTYPE. COLLECTIVELY, OUR RESULTS IDENTIFY A NOVEL LINK BETWEEN HYPERGLYCEMIA AND INFLAMMATION IN INNATE IMMUNE CELLS THAT MIGHT EXPLAIN THE INCREASED PROINFLAMMATORY STATE DURING DIABETES POTENTIALLY CONTRIBUTING TO THE DEVELOPMENT OF VARIOUS DIABETES-ASSOCIATED COMPLICATIONS. 2021 7 2248 27 EPIGENETIC MODULATION OF MACROPHAGE POLARIZATION- PERSPECTIVES IN DIABETIC WOUNDS. DIABETES IS A CHRONIC METABOLIC DISORDER THAT POSES A GLOBAL BURDEN TO HEALTHCARE. INCREASING INCIDENCE OF DIABETES-RELATED COMPLICATIONS IN THE AFFECTED POPULATION INCLUDES A DELAY IN WOUND HEALING THAT OFTEN RESULTS IN NON-TRAUMATIC LIMB AMPUTATIONS. OWING TO THE INTRICACIES OF THE HEALING PROCESS AND CROSSTALK BETWEEN THE MULTITUDE OF PARTICIPATING CELLS, THE IDENTIFICATION OF HYPERGLYCAEMIA-INDUCED CHANGES AT BOTH CELLULAR AND MOLECULAR LEVELS POSES A CHALLENGE. MACROPHAGES ARE ONE OF THE KEY PARTICIPANTS IN WOUND HEALING AND CONTINUE TO EXERT FUNCTIONAL CHANGES AT THE WOUND SITE SINCE THE TIME OF INJURY. IN THE PRESENT REVIEW, WE DISCUSS THE ROLE OF THESE CELLS AND THEIR ABERRANT FUNCTIONS IN DIABETIC WOUNDS. WE HAVE EXTENSIVELY STUDIED THE PROCESS OF MACROPHAGE POLARIZATION (MP) AND ITS MODULATION THROUGH EPIGENETIC MODIFICATIONS. DATA FROM BOTH PRE-CLINICAL AND CLINICAL STUDIES ON DIABETES HAVE CO-RELATED HYPERGLYCAEMIA INDUCED CHANGES IN GENE EXPRESSION TO AN INCREASED INCIDENCE OF DIABETIC COMPLICATIONS. HYPERGLYCAEMIA AND OXIDATIVE STRESS, CREATE AN ENVIRONMENT PRONE TO CHANGES IN THE EPIGENETIC CODE, THAT IS MANIFESTED AS AN ALTERED INFLAMMATORY GENE EXPRESSION. HERE, WE HAVE ATTEMPTED TO UNDERSTAND THE DIFFERENT EPIGENETIC MODULATIONS THAT POSSIBLY CONTRIBUTE TOWARDS DYSREGULATED MP, RESULTING IN DELAYED WOUND HEALING. 2018 8 271 33 AGE-ASSOCIATED EPIGENETIC MODIFICATIONS IN HUMAN DNA INCREASE ITS IMMUNOGENICITY. CHRONIC INFLAMMATION, INCREASED REACTIVITY TO SELF-ANTIGENS AND INCIDENCES OF CANCER ARE HALLMARKS OF AGING. HOWEVER, THE UNDERLYING MECHANISMS ARE NOT WELL UNDERSTOOD. AGE-ASSOCIATED ALTERATIONS IN THE DNA EITHER DUE TO OXIDATIVE DAMAGE, DEFECTS IN DNA REPAIR OR EPIGENETIC MODIFICATIONS SUCH AS METHYLATION THAT LEAD TO MUTATIONS AND CHANGES IN THE EXPRESSION OF GENES ARE THOUGHT TO BE PARTIALLY RESPONSIBLE. HERE WE REPORT THAT EPIGENETIC MODIFICATIONS IN AGED DNA ALSO INCREASE ITS IMMUNOGENICITY RENDERING IT MORE REACTIVE TO INNATE IMMUNE SYSTEM CELLS SUCH AS THE DENDRITIC CELLS. WE OBSERVED INCREASED UPREGULATION OF COSTIMULATORY MOLECULES AS WELL AS ENHANCED SECRETION OF IFN-ALPHA FROM DENDRITIC CELLS IN RESPONSE TO DNA FROM AGED DONORS AS COMPARED TO DNA FROM YOUNG DONORS WHEN IT WAS DELIVERED INTRACELLULARLY VIA LIPOFECTAMINE. INVESTIGATIONS INTO THE MECHANISMS REVEALED THAT DNA FROM AGED SUBJECTS IS NOT DEGRADED, NEITHER IS IT MORE DAMAGED COMPARED TO DNA FROM YOUNG SUBJECTS. HOWEVER, THERE IS SIGNIFICANTLY DECREASED GLOBAL LEVEL OF METHYLATION SUGGESTING THAT AGE-ASSOCIATED HYPOMETHYLATION OF THE DNA MAY BE THE CAUSE OF ITS INCREASED IMMUNOGENICITY. INCREASED IMMUNOGENICITY OF SELF DNA MAY THUS BE ANOTHER MECHANISM THAT MAY CONTRIBUTE TO THE INCREASE IN AGE-ASSOCIATED CHRONIC INFLAMMATION, AUTOIMMUNITY AND CANCER. 2010 9 2026 31 EPIGENETIC CHANGES IN BONE MARROW PROGENITOR CELLS INFLUENCE THE INFLAMMATORY PHENOTYPE AND ALTER WOUND HEALING IN TYPE 2 DIABETES. CLASSICALLY ACTIVATED (M1) MACROPHAGES ARE KNOWN TO PLAY A ROLE IN THE DEVELOPMENT OF CHRONIC INFLAMMATION ASSOCIATED WITH IMPAIRED WOUND HEALING IN TYPE 2 DIABETES (T2D); HOWEVER, THE MECHANISM RESPONSIBLE FOR THE DOMINANT PROINFLAMMATORY (M1) MACROPHAGE PHENOTYPE IN T2D WOUNDS IS UNKNOWN. SINCE EPIGENETIC ENZYMES CAN DIRECT MACROPHAGE PHENOTYPES, WE ASSESSED THE ROLE OF HISTONE METHYLATION IN BONE MARROW (BM) STEM/PROGENITOR CELLS IN THE PROGRAMMING OF MACROPHAGES TOWARD A PROINFLAMMATORY PHENOTYPE. WE HAVE FOUND THAT A REPRESSIVE HISTONE METHYLATION MARK, H3K27ME3, IS DECREASED AT THE PROMOTER OF THE IL-12 GENE IN BM PROGENITORS AND THIS EPIGENETIC SIGNATURE IS PASSED DOWN TO WOUND MACROPHAGES IN A MURINE MODEL OF GLUCOSE INTOLERANCE (DIET-INDUCED OBESE). THESE EPIGENETICALLY "PREPROGRAMMED" MACROPHAGES RESULT IN POISED MACROPHAGES IN PERIPHERAL TISSUE AND NEGATIVELY IMPACT WOUND REPAIR. WE FOUND THAT IN DIABETIC CONDITIONS THE H3K27 DEMETHYLASE JMJD3 DRIVES IL-12 PRODUCTION IN MACROPHAGES AND THAT IL-12 PRODUCTION CAN BE MODULATED BY INHIBITING JMJD3. USING HUMAN T2D TISSUE AND MURINE MODELS, WE HAVE IDENTIFIED A PREVIOUSLY UNRECOGNIZED MECHANISM BY WHICH MACROPHAGES ARE PROGRAMMED TOWARD A PROINFLAMMATORY PHENOTYPE, ESTABLISHING A PATTERN OF UNRESTRAINED INFLAMMATION ASSOCIATED WITH NONHEALING WOUNDS. HENCE, HISTONE DEMETHYLASE INHIBITOR-BASED THERAPY MAY REPRESENT A NOVEL TREATMENT OPTION FOR DIABETIC WOUNDS. 2015 10 2909 32 GENE EXPRESSION PROFILING IN FIBROMYALGIA INDICATES AN AUTOIMMUNE ORIGIN OF THE DISEASE AND OPENS NEW AVENUES FOR TARGETED THERAPY. FIBROMYALGIA IS A CHRONIC DISORDER CHARACTERIZED BY WIDESPREAD PAIN AND BY SEVERAL NON-PAIN SYMPTOMS. AUTOIMMUNITY, SMALL FIBER NEUROPATHY AND NEUROINFLAMMATION HAVE BEEN SUGGESTED TO BE INVOLVED IN THE PATHOGENESIS OF THE DISEASE. WE HAVE INVESTIGATED THE GENE EXPRESSION PROFILE IN PERIPHERAL BLOOD MONONUCLEAR CELLS OBTAINED FROM TEN PATIENTS AND TEN HEALTHY SUBJECTS. OF THE 545,500 TRANSCRIPTS ANALYZED, 1673 RESULTED MODULATED IN FIBROMYALGIC PATIENTS. THE MAJORITY OF THESE GENES ARE INVOLVED IN BIOLOGICAL PROCESSES AND PATHWAYS LINKED TO THE CLINICAL MANIFESTATIONS OF THE DISEASE. MOREOVER, GENES INVOLVED IN IMMUNOLOGICAL PATHWAYS CONNECTED TO INTERLEUKIN-17 AND TO TYPE I INTERFERON SIGNATURES WERE ALSO MODULATED, SUGGESTING THAT AUTOIMMUNITY PLAYS A ROLE IN THE DISEASE. WE THEN AIMED AT IDENTIFYING DIFFERENTIALLY EXPRESSED LONG NON-CODING RNAS (LNCRNAS) FUNCTIONALLY CONNECTED TO MODULATED GENES BOTH DIRECTLY AND VIA MICRORNA TARGETING. ONLY TWO LNCRNAS OF THE 298 FOUND MODULATED IN PATIENTS, WERE ABLE TO TARGET THE MOST HIGHLY CONNECTED GENES IN THE FIBROMYALGIA INTERACTOME, SUGGESTING THEIR INVOLVEMENT IN CRUCIAL GENE REGULATION. OUR GENE EXPRESSION DATA WERE CONFIRMED BY REAL TIME PCR, BY AUTOANTIBODY TESTING, DETECTION OF SOLUBLE MEDIATORS AND TH-17 POLARIZATION IN A VALIDATION COHORT OF 50 PATIENTS. OUR RESULTS INDICATE THAT GENETIC AND EPIGENETIC MECHANISMS AS WELL AS AUTOIMMUNITY PLAY A PIVOTAL ROLE IN THE PATHOGENESIS OF FIBROMYALGIA. 2020 11 1307 24 DEFINING A METHYLATION SIGNATURE ASSOCIATED WITH OPERATIONAL TOLERANCE IN KIDNEY TRANSPLANT RECIPIENTS. OPERATIONAL TOLERANCE AFTER KIDNEY TRANSPLANTATION IS DEFINED AS STABLE GRAFT ACCEPTANCE WITHOUT THE NEED FOR IMMUNOSUPPRESSION THERAPY. HOWEVER, IT IS NOT CLEAR WHICH CELLULAR AND MOLECULAR PATHWAYS ARE DRIVING TOLERANCE IN THESE PATIENTS. WE PERFORMED GENOME-WIDE ANALYSIS OF DNA METHYLATION IN PERIPHERAL BLOOD MONONUCLEAR CELLS FROM KIDNEY TRANSPLANT RECIPIENTS WITH CHRONIC REJECTION AND OPERATIONAL TOLERANCE FROM THE GENETIC ANALYSIS OF MOLECULAR BIOMARKERS OF IMMUNOLOGICAL TOLERANCE (GAMBIT) STUDY. OUR RESULTS SHOWED THAT BOTH CLINICAL STAGES DIVERGE IN 2737 GENES, INDICATING THAT EACH ONE HAS A SPECIFIC METHYLATION SIGNATURE ASSOCIATED WITH TRANSPLANT OUTCOME. WE ALSO OBSERVED THAT TOLERANCE IS ASSOCIATED WITH DEMETHYLATION IN GENES INVOLVED IN IMMUNE FUNCTION, INCLUDING B AND T CELL ACTIVATION AND TH17 DIFFERENTIATION, WHILE IN CHRONIC REJECTION IT IS ASSOCIATED WITH INTRACELLULAR SIGNALING AND UBIQUITINATION PATHWAYS. USING CO-EXPRESSION NETWORK ANALYSIS, WE SELECTED 12 GENOMIC REGIONS THAT ARE SPECIFICALLY HYPOMETHYLATED OR HYPERMETHYLATED IN TOLERANT PATIENTS. ANALYSIS OF THESE GENES IN TRANSPLANTED PATIENTS WITH LOW DOSE OF STEROIDS SHOWED THAT THESE HAVE A SIMILAR METHYLATION SIGNATURE TO THAT OF TOLERANT RECIPIENTS. OVERALL, THESE RESULTS DEMONSTRATE THAT METHYLATION ANALYSIS CAN MIRROR THE IMMUNE STATUS ASSOCIATED WITH TRANSPLANT OUTCOME AND PROVIDES A STARTING POINT FOR UNDERSTANDING THE EPIGENETIC MECHANISMS ASSOCIATED WITH TOLERANCE. 2021 12 5305 39 PROTEOMICS ANALYSIS OF HUMAN OBESITY REVEALS THE EPIGENETIC FACTOR HDAC4 AS A POTENTIAL TARGET FOR OBESITY. SEDENTARY LIFESTYLE AND EXCESSIVE ENERGY INTAKE ARE PROMINENT CONTRIBUTORS TO OBESITY; A MAJOR RISK FACTORS FOR THE DEVELOPMENT OF INSULIN RESISTANCE, TYPE 2 DIABETES AND CARDIOVASCULAR DISEASES. ELUCIDATING THE MOLECULAR MECHANISMS UNDERLYING THESE CHRONIC CONDITIONS IS OF RELEVANT IMPORTANCE AS IT MIGHT LEAD TO THE IDENTIFICATION OF NOVEL ANTI-OBESITY TARGETS. THE PURPOSE OF THE CURRENT STUDY IS TO INVESTIGATE DIFFERENTIALLY EXPRESSED PROTEINS BETWEEN LEAN AND OBESE SUBJECTS THROUGH A SHOT-GUN QUANTITATIVE PROTEOMICS APPROACH USING PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) EXTRACTS AS WELL AS POTENTIAL MODULATION OF THOSE PROTEINS BY PHYSICAL EXERCISE. USING THIS APPROACH, A TOTAL OF 47 PROTEINS SHOWED AT LEAST 1.5 FOLD CHANGE BETWEEN LEAN AND OBESE SUBJECTS. IN OBESE, THE PROTEOMIC PROFILING BEFORE AND AFTER 3 MONTHS OF PHYSICAL EXERCISE SHOWED DIFFERENTIAL EXPRESSION OF 38 PROTEINS. THROMBOSPONDIN 1 (TSP1) WAS AMONG THE PROTEINS THAT WERE UPREGULATED IN OBESE SUBJECTS AND THEN DECREASED BY PHYSICAL EXERCISE. CONVERSELY, THE HISTONE DEACETYLASE 4 (HDAC4) WAS DOWNREGULATED IN OBESE SUBJECTS AND THEN INDUCED BY PHYSICAL EXERCISE. THE PROTEOMIC DATA WAS FURTHER VALIDATED BY QRT-PCR, WESTERN BLOT AND IMMUNOHISTOCHEMISTRY IN BOTH PBMCS AND ADIPOSE TISSUE. WE ALSO SHOWED THAT HDAC4 LEVELS CORRELATED POSITIVELY WITH MAXIMUM OXYGEN CONSUMPTION (VO2 MAX) BUT NEGATIVELY WITH BODY MASS INDEX, PERCENT BODY FAT, AND THE INFLAMMATORY CHEMOKINE RANTES. IN FUNCTIONAL ASSAYS, OUR DATA INDICATED THAT ECTOPIC EXPRESSION OF HDAC4 SIGNIFICANTLY IMPAIRED TNF-ALPHA-DEPENDENT ACTIVATION OF NF-KAPPAB, ESTABLISHING THUS A LINK BETWEEN HDAC4 AND REGULATION OF THE IMMUNE SYSTEM. TOGETHER, THE EXPRESSION PATTERN OF HDAC4 IN OBESE SUBJECTS BEFORE AND AFTER PHYSICAL EXERCISE, ITS CORRELATION WITH VARIOUS PHYSICAL, CLINICAL AND METABOLIC PARAMETERS ALONG WITH ITS INHIBITORY EFFECT ON NF-KAPPAB ARE SUGGESTIVE OF A PROTECTIVE ROLE OF HDAC4 AGAINST OBESITY. HDAC4 COULD THEREFORE REPRESENT A POTENTIAL THERAPEUTIC TARGET FOR THE CONTROL AND MANAGEMENT OF OBESITY AND PRESUMABLY INSULIN RESISTANCE. 2013 13 2036 24 EPIGENETIC CHANGES OF THE IMMUNE SYSTEM WITH ROLE IN TUMOR DEVELOPMENT. TUMOR DEVELOPMENT IS CLOSELY RELATED TO CHRONIC INFLAMMATION AND TO EVASION OF IMMUNE DEFENSE MECHANISMS BY NEOPLASTIC CELLS. THE MEDIATORS OF THE INFLAMMATORY PROCESS AS WELL AS PROTEINS INVOLVED IN IMMUNE RESPONSE OR IMMUNE RESPONSE EVASION CAN BE SUBJECT TO VARIOUS EPIGENETIC CHANGES SUCH AS METHYLATION, ACETYLATION, OR PHOSPHORYLATION. SOME OF THESE, SUCH AS CYTOKINE SUPPRESSORS, ARE UNDERGOING REPRESSION THROUGH EPIGENETIC CHANGES, AND OTHERS SUCH AS CYTOKINES OR CHEMOKINES ARE UNDERGOING ACTIVATION THROUGH EPIGENETIC CHANGES, BOTH MODIFICATIONS HAVING AS A RESULT TUMOR PROGRESSION. THE ACTIVATING CHANGES CAN AFFECT THE RECEPTOR MOLECULES INVOLVED IN IMMUNE RESPONSE AND THESE PROMOTE INFLAMMATION AND SUBSEQUENTLY TUMOR DEVELOPMENT WHILE THE INACTIVATING CHANGES SEEM TO BE RELATED TO THE TUMOR REGRESSION PROCESS. THE PROTEINS INVOLVED IN ANTIGEN PRESENTATION, AND, THEREFORE IN IMMUNE RESPONSE ESCAPE, SUCH AS CLASSICAL HLA PROTEINS AND RELATED APM (ANTIGEN PRESENTATION MACHINERY) WITH THEIR EPIGENETIC CHANGES CONTRIBUTE TO THE TUMOR DEVELOPMENT PROCESS, EITHER TO TUMOR PROGRESSION OR REGRESSION, DEPENDING ON THE IMMUNE EFFECTOR CELLS THAT ARE IN PLAY. 2018 14 2228 22 EPIGENETIC MODIFICATIONS OF HISTONES IN PERIODONTAL DISEASE. PERIODONTITIS IS A CHRONIC INFECTIOUS DISEASE DRIVEN BY DYSBIOSIS, AN IMBALANCE BETWEEN COMMENSAL BACTERIA AND THE HOST ORGANISM. PERIODONTITIS IS A LEADING CAUSE OF TOOTH LOSS IN ADULTS AND OCCURS IN ABOUT 50% OF THE US POPULATION. IN ADDITION TO THE CLINICAL CHALLENGES ASSOCIATED WITH TREATING PERIODONTITIS, THE PROGRESSION AND CHRONIC NATURE OF THIS DISEASE SERIOUSLY AFFECT HUMAN HEALTH. EMERGING EVIDENCE SUGGESTS THAT PERIODONTITIS IS ASSOCIATED WITH MECHANISMS BEYOND BACTERIA-INDUCED PROTEIN AND TISSUE DEGRADATION. HERE, WE HYPOTHESIZE THAT BACTERIA ARE ABLE TO INDUCE EPIGENETIC MODIFICATIONS IN ORAL EPITHELIAL CELLS MEDIATED BY HISTONE MODIFICATIONS. IN THIS STUDY, WE FOUND THAT DYSBIOSIS IN VIVO LED TO EPIGENETIC MODIFICATIONS, INCLUDING ACETYLATION OF HISTONES AND DOWNREGULATION OF DNA METHYLTRANSFERASE 1. IN ADDITION, IN VITRO EXPOSURE OF ORAL EPITHELIAL CELLS TO LIPOPOLYSACCHARIDES RESULTED IN HISTONE MODIFICATIONS, ACTIVATION OF TRANSCRIPTIONAL COACTIVATORS, SUCH AS P300/CBP, AND ACCUMULATION OF NUCLEAR FACTOR-KAPPAB (NF-KAPPAB). GIVEN THAT ORAL EPITHELIAL CELLS ARE THE FIRST LINE OF DEFENSE FOR THE PERIODONTIUM AGAINST BACTERIA, WE ALSO EVALUATED WHETHER ACTIVATION OF PATHOGEN RECOGNITION RECEPTORS INDUCED HISTONE MODIFICATIONS. WE FOUND THAT ACTIVATION OF THE TOLL-LIKE RECEPTORS 1, 2, AND 4 AND THE NUCLEOTIDE-BINDING OLIGOMERIZATION DOMAIN PROTEIN 1 INDUCED HISTONE ACETYLATION IN ORAL EPITHELIAL CELLS. OUR FINDINGS CORROBORATE THE EMERGING CONCEPT THAT EPIGENETIC MODIFICATIONS PLAY A ROLE IN THE DEVELOPMENT OF PERIODONTITIS. 2016 15 4228 23 METHYLATION OF INFLAMMATORY CELLS IN LUNG DISEASES. THIS CHAPTER OVERVIEWS ROLES OF DNA METHYLATION IN INFLAMMATORY CELL BIOLOGY WITH THE FOCUSES ON LYMPHOCYTES AND MACROPHAGES/MONOCYTES IN LUNG DISEASES, ALTHOUGH THE MOLECULAR MECHANISMS BY WHICH TARGET GENES ARE METHYLATED AND REGULATED IN LUNG DISEASES REMAIN UNCLEAR. MOST OF EPIGENETIC STUDIES ON DNA METHYLATION OF TARGET GENES IN LUNG DISEASES MAINLY DEMONSTRATED THE CORRELATION OF DNA METHYLATION OF TARGET GENES WITH THE LEVELS OF OTHER CORRESPONDING FACTORS, WITH THE SPECIFICITY OF CLINICAL PHENOMES, AND WITH THE SEVERITY OF LUNG DISEASES. THERE IS AN URGENT NEED TO IDENTIFY AND VALIDATE THE SPECIFICITY AND REGULATORY MECHANISMS OF INFLAMMATORY CELL EPIGENETICS IN DEPTH. THE EPIGENETIC HETEROGENEITY AMONG DIFFERENT SUBSETS OF T CELLS AND AMONG PROMOTERS OR NON-PROMOTERS OF TARGET GENES SHOULD BE FURTHERMORE CLARIFIED IN ACUTE OR CHRONIC LUNG DISEASES AND CANCERS. THE HYPER/HYPO-METHYLATION AND MODIFICATIONS OF CHROMOSOL AND EXTRACHROMOSOMAL DNA MAY RESULT IN ALTERNATIONS IN PROTEINS WITHIN INFLAMMATORY CELLS, WHICH CAN BE IDENTIFIED AS DISEASE-SPECIFIC BIOMARKERS AND THERAPEUTIC TARGETS. 2020 16 6284 26 THE POTENTIAL OF HUMAN INDUCED PLURIPOTENT STEM CELLS FOR MODELLING DIABETIC WOUND HEALING IN VITRO. IMPAIRED WOUND HEALING AND ULCERATION CAUSED BY DIABETES MELLITUS, IS A SIGNIFICANT HEALTHCARE BURDEN, MARKEDLY IMPAIRS QUALITY OF LIFE FOR PATIENTS, AND IS THE MAJOR CAUSE OF AMPUTATION WORLDWIDE. CURRENT EXPERIMENTAL APPROACHES USED TO INVESTIGATE THE COMPLEX WOUND HEALING PROCESS OFTEN INVOLVE CULTURES OF FIBROBLASTS AND/OR KERATINOCYTES IN VITRO, WHICH CAN BE LIMITED IN TERMS OF COMPLEXITY AND CAPACITY, OR UTILISATION OF RODENT MODELS IN WHICH THE MECHANISMS OF WOUND REPAIR DIFFER SUBSTANTIVELY FROM THAT IN HUMANS. HOWEVER, ADVANCES IN TISSUE ENGINEERING, AND THE DISCOVERY OF STRATEGIES TO REPROGRAMME ADULT SOMATIC CELLS TO PLURIPOTENCY, HAS LED TO THE POSSIBILITY OF DEVELOPING MODELS OF HUMAN SKIN ON A LARGE SCALE. GENERATION OF INDUCED PLURIPOTENT STEM CELLS (IPSCS) FROM TISSUES DONATED BY DIABETIC PATIENTS ALLOWS THE (EPI)GENETIC BACKGROUND OF THIS DISEASE TO BE STUDIED, AND THE ABILITY TO DIFFERENTIATE IPSCS TO MULTIPLE CELL TYPES FOUND WITHIN SKIN MAY FACILITATE THE DEVELOPMENT OF MORE COMPLEX SKIN MODELS; THESE ADVANCES OFFER KEY OPPORTUNITIES FOR IMPROVING MODELLING OF WOUND HEALING IN DIABETES, AND THE DEVELOPMENT OF EFFECTIVE THERAPEUTICS FOR TREATMENT OF CHRONIC WOUNDS. 2018 17 523 33 ASSOCIATIONS BETWEEN PERIODONTITIS AND SYSTEMIC INFLAMMATORY DISEASES: RESPONSE TO TREATMENT. THERE IS A SIGNIFICANT PREVALENCE OF SUBJECTS WITH PERIODONTITIS PRESENTING WITH OTHER INFLAMMATORY CONDITIONS SUCH AS CORONARY HEART DISEASE, INSULIN RESISTANCE AND ARTHRITIS. THIS PATTERN OF DISEASE PRESENTATION UNDERSCORES THE IMPORTANCE OF INFLAMMATORY LOADING FROM CHRONIC DISEASES, IN DRIVING THEIR PATHOGENESES IN A MULTIDIRECTIONAL MANNER. PRO-INFLAMMATORY CYTOKINES AND OTHER AGENTS PLAY AN IMPORTANT ROLE IN THIS PROCESS; FOR EXAMPLE, A SINGLE NUCLEOTIDE POLYMORPHISM OF THE TNF-ALPHA GENE IS ASSOCIATED WITH SIGNIFICANT PERIODONTAL ATTACHMENT LOSS IN PATIENTS WITH CORONARY HEART DISEASE. CHANGES IN GENE EXPRESSION ASSOCIATED WITH INFLAMMATION AND LIPID METABOLISM IN RESPONSE TO ORAL INFECTION WITH THE PERIODONTAL PATHOGEN PORPHYROMONAS GINGIVALIS (PG) HAVE BEEN DEMONSTRATED IN MOUSE MODELS, INDEPENDENT OF THE DEMONSTRATION OF ATHEROSCLEROTIC LESIONS. INSULIN RESISTANCE IS CONSIDERED TO BE A CHRONIC LOW-GRADE INFLAMMATORY CONDITION, ASSOCIATED WITH ALTERED GLUCOSE TOLERANCE, HYPERTRIGLYCERIDEMIA, CENTRAL OBESITY AND CORONARY HEART DISEASE. IT IS ACCOMPANIED BY ELEVATED LEVELS OF IL-1, IL-6 AND TNF-ALPHA ALSO RELEVANT TO THE PROGRESSION OF PERIODONTITIS. THERE IS EVIDENCE THAT UNCONTROLLED PERIODONTAL DISEASE CONTRIBUTES TO MAINTENANCE OF SYSTEMIC DISEASES, INCLUDING RHEUMATOID ARTHRITIS (RA), WITH INCREASED RISK OF PERIODONTITIS IN SUBJECTS WITH RA. THE PERIODONTAL PATHOGEN PG IS SIGNIFICANT IN CONTRIBUTING TO CITRULLINATION OF PROTEINS RESULTING IN IMMUNE DYSREGULATION AND AUTOIMMUNE RESPONSES, SEEN IN RA. HOWEVER, THEY ARE BOTH MULTIFACTORIAL CHRONIC DISEASES WITH COMPLEX ETIOPATHOGENESES THAT AFFECT THEIR PRESENTATION. CONSISTENT BUT WEAK ASSOCIATIONS ARE SEEN FOR SURROGATE MARKERS OF PERIODONTITIS SUCH AS TOOTH LOSS, WITH MULTIPLE SYSTEMIC CONDITIONS. EFFECTIVE TREATMENT OF PERIODONTITIS WOULD BE IMPORTANT IN REDUCING SYSTEMIC INFLAMMATORY LOADING FROM CHRONIC LOCAL INFLAMMATION AND IN ACHIEVING SYSTEMIC HEALTH. LACK OF A CONSISTENT CAUSE AND EFFECT RELATIONSHIP IN ALL SUBJECTS WOULD BE INFLUENCED BY GENETIC, EPIGENETIC AND OTHER SUBJECT VARIABLES, ALTHOUGH THERE ARE CLEAR MECHANISMS THAT LINK THE ASSOCIATIONS. THIS ARTICLE INCLUDES AN APPRAISAL OF PATENTS AND THEIR APPLICATIONS. 2013 18 551 31 AUTOIMMUNITY AS AN ETIOLOGICAL FACTOR OF CANCER: THE TRANSFORMATIVE POTENTIAL OF CHRONIC TYPE 2 INFLAMMATION. RECENT EPIDEMIOLOGICAL STUDIES HAVE FOUND AN ALARMING TREND OF INCREASED CANCER INCIDENCE IN ADULTS YOUNGER THAN 50 YEARS OF AGE AND PROJECTED A SUBSTANTIAL RISE IN CANCER INCIDENCE OVER THE NEXT 10 YEARS IN THIS AGE GROUP. THIS TREND WAS EXEMPLIFIED IN THE INCIDENCE OF NON-CARDIA GASTRIC CANCER AND ITS DISPROPORTIONATE IMPACT ON NON-HISPANIC WHITE FEMALES UNDER THE AGE OF 50. THE TREND IS CONCURRENT WITH THE INCREASING INCIDENCE OF AUTOIMMUNE DISEASES IN INDUSTRIALIZED COUNTRIES, SUGGESTING A CAUSAL LINK BETWEEN THE TWO. WHILE AUTOIMMUNITY HAS BEEN SUSPECTED TO BE A RISK FACTOR FOR SOME CANCERS, THE EXACT MECHANISMS UNDERLYING THE CONNECTION BETWEEN AUTOIMMUNITY AND CANCER REMAIN UNCLEAR AND ARE OFTEN CONTROVERSIAL. THE LINK HAS BEEN ATTRIBUTED TO SEVERAL MEDIATORS SUCH AS IMMUNE SUPPRESSION, INFECTION, DIET, ENVIRONMENT, OR, PERHAPS MOST PLAUSIBLY, CHRONIC INFLAMMATION BECAUSE OF ITS WELL-RECOGNIZED ROLE IN TUMORIGENESIS. IN THAT REGARD, AUTOIMMUNE CONDITIONS ARE COMMON CAUSES OF CHRONIC INFLAMMATION AND MAY TRIGGER REPETITIVE CYCLES OF ANTIGEN-SPECIFIC CELL DAMAGE, TISSUE REGENERATION, AND WOUND HEALING. ILLUSTRATING THE CONNECTION BETWEEN AUTOIMMUNE DISEASES AND CANCER ARE PATIENTS WHO HAVE AN INCREASED RISK OF CANCER DEVELOPMENT ASSOCIATED WITH GENETICALLY PREDISPOSED INSUFFICIENCY OF CYTOTOXIC T LYMPHOCYTE-ASSOCIATED PROTEIN 4 (CTLA4), A PROTOTYPICAL IMMUNE CHECKPOINT AGAINST AUTOIMMUNITY AND ONE OF THE MAIN TARGETS OF CANCER IMMUNE THERAPY. THE TUMORIGENIC PROCESS TRIGGERED BY CTLA4 INSUFFICIENCY HAS BEEN SHOWN IN A MOUSE MODEL TO BE DEPENDENT ON THE TYPE 2 CYTOKINES INTERLEUKIN-4 (IL4) AND INTERLEUKIN-13 (IL13). IN THIS TYPE 2 INFLAMMATORY MILIEU, CROSSTALK WITH TYPE 2 IMMUNE CELLS MAY INITIATE EPIGENETIC REPROGRAMMING OF EPITHELIAL CELLS, LEADING TO A METAPLASTIC DIFFERENTIATION AND EVENTUALLY MALIGNANT TRANSFORMATION EVEN IN THE ABSENCE OF CLASSICAL ONCOGENIC MUTATIONS. THOSE FINDINGS COMPLEMENT A LARGE BODY OF EVIDENCE FOR TYPE 1, TYPE 3, OR OTHER INFLAMMATORY MEDIATORS IN INFLAMMATORY TUMORIGENESIS. THIS REVIEW ADDRESSES THE POTENTIAL OF AUTOIMMUNITY AS A CAUSAL FACTOR FOR TUMORIGENESIS, THE UNDERLYING INFLAMMATORY MECHANISMS THAT MAY VARY DEPENDING ON HOST-ENVIRONMENT VARIATIONS, AND IMPLICATIONS TO CANCER PREVENTION AND IMMUNOTHERAPY. 2021 19 6902 30 [THE IMPACT OF CHROMATIN MODIFICATION ON THE DEVELOPMENT OF CHRONIC COMPLICATIONS IN PATIENTS WITH DIABETES]. DIABETES IS A CHRONIC, METABOLIC DISEASE. OVER 347 MILLION PEOPLE WORLDWIDE HAVE DIABETES. CHRONIC COMPLICATIONS (RETINOPATHY, NEPHROPATHY OR NEUROPATHY) ARE THE MAJOR DANGEROUS OUTCOME OF THIS DISEASE. RECENT STUDIES INDICATE A SIGNIFICANT ROLE OF EPIGENETIC REGULATION IN THE DEVELOPMENT OF CHRONIC COMPLICATIONS IN PATIENTS WITH DIABETES. HYPERGLYCEMIA COULD CAUSE ABNORMAL REGULATION OF THE ACTIVITY OF ENZYMES PARTICIPATING IN THE POST-TRANSLATIONAL HISTONE MODIFICATIONS (PTHMS) AND INITIATION OF CHANGES IN PATTERNS OF DNA METHYLATION. IT LEADS TO MODIFICATION OF CHROMATIN STRUCTURE. THESE EPIGENETIC ABNORMALITIES RESULT IN CHANGES IN THE EXPRESSION OF GENES INVOLVED IN DEVELOPMENT OF CHRONIC INFLAMMATION, SUCH AS NF-KAPPAB (NUCLEAR FACTOR KAPPAB GENE), TNFALPHA (TUMOR NECROSIS FACTOR A GENE), IL6 (INTERLEUKIN 6 GENE) OR MCP1 (MONOCYTE CHEMOATTRACTANT PROTEIN 1 GENE). IT ENHANCES ENDOTHELIAL CELL DYSFUNCTION, WHICH PLAYS AN IMPORTANT ROLE IN DEVELOPMENT OF CHRONIC, DIABETIC COMPLICATIONS. IN ADDITION, CAUSED BY HYPERGLYCEMIA EPIGENETIC MODIFICATIONS CHANGES IN STRUCTURE OF CHROMATIN EXPLAINS "METABOLIC MEMORY", A PHENOMENON OF PRESENCE OF PATHOLOGICAL PATHWAYS RELATED TO THE PROLONGED HYPERGLYCEMIA IN THE PAST, DESPITE MAINTAINING GOOD METABOLIC CONTROL LATER ON. 2015 20 1269 29 CYTOSINE METHYLATION CHANGES IN ENHANCER REGIONS OF CORE PRO-FIBROTIC GENES CHARACTERIZE KIDNEY FIBROSIS DEVELOPMENT. BACKGROUND: ONE IN ELEVEN PEOPLE IS AFFECTED BY CHRONIC KIDNEY DISEASE, A CONDITION CHARACTERIZED BY KIDNEY FIBROSIS AND PROGRESSIVE LOSS OF KIDNEY FUNCTION. EPIDEMIOLOGICAL STUDIES INDICATE THAT ADVERSE INTRAUTERINE AND POSTNATAL ENVIRONMENTS HAVE A LONG-LASTING ROLE IN CHRONIC KIDNEY DISEASE DEVELOPMENT. EPIGENETIC INFORMATION REPRESENTS A PLAUSIBLE CARRIER FOR MEDIATING THIS PROGRAMMING EFFECT. HERE WE DEMONSTRATE THAT GENOME-WIDE CYTOSINE METHYLATION PATTERNS OF HEALTHY AND CHRONIC KIDNEY DISEASE TUBULE SAMPLES OBTAINED FROM PATIENTS SHOW SIGNIFICANT DIFFERENCES. RESULTS: WE IDENTIFY DIFFERENTIALLY METHYLATED REGIONS AND VALIDATE THESE IN A LARGE REPLICATION DATASET. THE DIFFERENTIALLY METHYLATED REGIONS ARE RARELY OBSERVED ON PROMOTERS, BUT MOSTLY OVERLAP WITH PUTATIVE ENHANCER REGIONS, AND THEY ARE ENRICHED IN CONSENSUS BINDING SEQUENCES FOR IMPORTANT RENAL TRANSCRIPTION FACTORS. THIS INDICATES THEIR IMPORTANCE IN GENE EXPRESSION REGULATION. A CORE SET OF GENES THAT ARE KNOWN TO BE RELATED TO KIDNEY FIBROSIS, INCLUDING GENES ENCODING COLLAGENS, SHOW CYTOSINE METHYLATION CHANGES CORRELATING WITH DOWNSTREAM TRANSCRIPT LEVELS. CONCLUSIONS: OUR REPORT RAISES THE POSSIBILITY THAT EPIGENETIC DYSREGULATION PLAYS A ROLE IN CHRONIC KIDNEY DISEASE DEVELOPMENT VIA INFLUENCING CORE PRO-FIBROTIC PATHWAYS AND CAN AID THE DEVELOPMENT OF NOVEL BIOMARKERS AND FUTURE THERAPEUTICS. 2013