1 6544 125 TRANSCRIPTOMIC AND EPIGENETIC ALTERATIONS IN DENDRITIC CELLS CORRESPOND WITH CHRONIC KIDNEY DISEASE IN LUPUS NEPHRITIS. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A SERIOUS AUTOIMMUNE DISEASE WITH VARIETY OF ORGAN MANIFESTATIONS. THE MOST DREADFUL ONE, AFFECTING THE MAJORITY OF SLE PATIENTS, IS KIDNEY MANIFESTATION-LUPUS NEPHRITIS (LN). DENDRITIC CELLS (DC) ARE BELIEVED TO BE ONE OF THE CULPRITS OF IMMUNE DYSREGULATION IN LN. FLOW CYTOMETRY ANALYSIS WAS APPLIED TO IDENTIFY THE FREQUENCY AND ACTIVITY OF PERIPHERAL BLOOD DCS SUBPOPULATIONS: MYELOID AND PLASMACYTOID, IN LN PATIENTS. MAGNETICALLY ISOLATED MDCS AND PDCS WERE SUBJECTED TO MOLECULAR ANALYSIS OF GENES EXPRESSION, EVALUATION OF GLOBAL DNA METHYLATION AND HISTONE H3 METHYLATION. WE OBSERVED DISTINCTIVE FEATURES OF DCS ASSOCIATED WITH THE STAGES OF NEPHRITIS IN LN PATIENTS. LOWER NUMBERS OF PDCS WERE OBSERVED IN PATIENTS WITH SEVERE LN, WHILE INCREASED CO-STIMULATORY POTENTIAL OF MDCS WAS CONNECTED WITH THE EARLY, MILD STAGE OF THIS DISEASE. IRF1 TRANSCRIPT UPREGULATION WAS SPECIFIC FOR MDCS FROM TOTAL LN PATIENTS, WHILE EXCEPTIONAL AMOUNT OF IRF1 MRNA WAS DETECTED IN MDCS FROM SEVERE LN PATIENTS. DCS DNA HYPERMETHYLATION SEEMED CHARACTERISTIC FOR SEVERE LN, WHEREAS A DECREASE IN H3K4ME3 AND H3K27ME3 MARKS WAS SIGNIFICANT FOR THE EARLY STAGES OF LN. THESE FINDINGS PRESENT DENDRITIC CELL ALTERATIONS THAT MAY REFLECT RENAL INVOLVEMENT IN SLE, LAYING FOUNDATIONS FOR NEW STRATEGY OF DIAGNOSIS AND MONITORING OF LN PATIENTS, OMITTING INVASIVE KIDNEY BIOPSIES. 2019 2 1508 42 DNA METHYLATION AND MRNA AND MICRORNA EXPRESSION OF SLE CD4+ T CELLS CORRELATE WITH DISEASE PHENOTYPE. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS AN AUTOIMMUNE DISEASE WELL KNOWN FOR ITS CLINICAL HETEROGENEITY, AND ITS ETIOLOGY SECONDARY TO A CROSS-TALK INVOLVING GENETIC PREDISPOSITION AND ENVIRONMENTAL STIMULI. ALTHOUGH GENOME-WIDE ANALYSIS HAS CONTRIBUTED GREATLY TO OUR UNDERSTANDING OF THE GENETIC BASIS OF SLE, THERE IS INCREASING EVIDENCE FOR A ROLE OF EPIGENETICS. INDEED, RECENT DATA HAVE DEMONSTRATED THAT IN PATIENTS WITH SLE, THERE ARE STRIKING ALTERATIONS OF DNA METHYLATION, HISTONE MODIFICATIONS, AND DEREGULATED MICRORNA EXPRESSION, THE SUM OF WHICH CONTRIBUTE TO OVER-EXPRESSION OF SELECT AUTOIMMUNE-RELATED GENES AND LOSS OF TOLERANCE. TO ADDRESS THIS ISSUE AT THE LEVEL OF CLINICAL PHENOTYPE, WE PERFORMED DNA METHYLATION, MRNA AND MICRORNA EXPRESSION SCREENING USING HIGH-THROUGHPUT SEQUENCING OF PURIFIED CD4+ T CELLS FROM PATIENTS WITH SLE, COMPARED TO AGE AND SEX MATCHED CONTROLS. IN PARTICULAR, WE STUDIED 42 PATIENTS WITH SLE AND DIVIDED THIS GROUP INTO THREE CLINICAL PHENOTYPES: A) THE PRESENCE OF SKIN LESIONS WITHOUT SIGNS OF SYSTEMIC PATHOLOGY; B) SKIN LESIONS BUT ALSO CHRONIC RENAL PATHOLOGY; AND C) SKIN LESIONS, CHRONIC RENAL PATHOLOGY AND POLYARTICULAR DISEASE. INTERESTINGLY, AND AS EXPECTED, SEQUENCING DATA REVEALED CHANGES IN DNA METHYLATION IN SLE COMPARED TO CONTROLS. HOWEVER, AND MORE IMPORTANTLY, ALTHOUGH THERE WERE COMMON METHYLATION CHANGES FOUND IN ALL GROUPS OF SLE COMPARED TO CONTROLS, THERE WAS SPECIFIC DNA METHYLATION CHANGES THAT CORRELATED WITH CLINICAL PHENOTYPE. THESE INCLUDED CHANGES IN THE NOVEL KEY TARGET GENES NLRP2, CD300LB AND S1PR3, AS WELL AS CHANGES IN THE CRITICAL PATHWAYS, INCLUDING THE ADHERENS JUNCTION AND LEUKOCYTE TRANSENDOTHELIAL MIGRATION. WE ALSO NOTED THAT A SIGNIFICANT PROPORTION OF GENES UNDERGOING DNA METHYLATION CHANGES WERE INVERSELY CORRELATED WITH GENE EXPRESSION AND THAT MIRNA SCREENING REVEALED THE EXISTENCE OF SUBSETS WITH CHANGES IN EXPRESSION. INTEGRATED ANALYSIS OF THIS DATA HIGHLIGHTS SPECIFIC SETS OF MIRNAS CONTROLLED BY DNA METHYLATION, AND GENES THAT ARE ALTERED BY METHYLATION AND TARGETED BY MIRNAS. IN CONCLUSION, OUR FINDINGS SUGGEST SELECT EPIGENETIC MECHANISMS THAT CONTRIBUTE TO CLINICAL PHENOTYPES AND FURTHER SHED LIGHT ON A NEW VENUE FOR BASIC SLE RESEARCH. 2014 3 1307 36 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 4 1500 40 DNA METHYLATION ANALYSIS OF CD4+ T CELLS IN PATIENTS WITH PSORIASIS. PSORIASIS IS A CHRONIC INFLAMMATORY SKIN DISEASE THAT IS CHARACTERIZED BY ABERRANT CROSS-TALK BETWEEN KERATINOCYTES AND IMMUNE CELLS SUCH AS CD4+ T CELLS, RESULTING IN KERATINOCYTE HYPERPROLIFERATION IN THE EPIDERMIS. DNA METHYLATION, ONE OF SEVERAL EPIGENETIC MECHANISMS, PLAYS AN IMPORTANT ROLE IN GENE EXPRESSION WITHOUT CHANGING THE DNA SEQUENCE. SEVERAL STUDIES HAVE SUGGESTED THE INVOLVEMENT OF EPIGENETIC REGULATION IN SKIN LESIONS FROM PATIENTS WITH PSORIASIS. IN THIS STUDY, WE INVESTIGATED THE GENOME-WIDE DNA METHYLATION STATUS OF CD4+ T CELLS IN PATIENTS WITH PSORIASIS COMPARED WITH HEALTHY SUBJECTS USING METHYLATED DNA IMMUNOPRECIPITATION SEQUENCING (MEDIP-SEQ). THE RESULTS OF MEDIP-SEQ SHOWED THAT THE GLOBAL METHYLATION VALUES OF CD4+ T CELLS ARE HIGHER IN PATIENTS WITH PSORIASIS THAN IN HEALTHY CONTROLS, PARTICULARLY IN THE PROMOTER REGIONS. AMONG THE MOST HYPERMETHYLATED GENES IN THE PROMOTER REGIONS, WE SELECTED THE GENES WHOSE EXPRESSION IS SIGNIFICANTLY REDUCED IN THE CD4+ T CELLS OF PSORIASIS PATIENTS. STUDIES USING THE METHYLATION INHIBITOR 5-AZACYTIDINE IN VITRO METHYLATION ASSAYS HAVE SHOWN THAT THE DIFFERENTIAL EXPRESSION LEVELS WERE ASSOCIATED WITH THE METHYLATION STATUS OF EACH GENE. BISULFITE SEQUENCING OF THE TRANSCRIPTION START REGION OF PHOSPHATIDIC ACID PHOSPHATASE TYPE 2 DOMAIN CONTAINING 3 (PPAPDC3), ONE OF THE SELECTED GENES, SHOWED HYPERMETHYLATION IN THE CD4+ T CELLS OF PSORIASIS PATIENTS. THESE RESULTS SUGGESTED THAT THE METHYLATION STATUS, WHICH IS IDENTIFIED BY MEDIP-SEQ OF THE GENES, WAS CORRELATED WITH THE MRNA EXPRESSION LEVEL OF THE GENES. COLLECTIVELY, THE DNA METHYLATION STATUS IN CD4+ T CELLS MIGHT BE ASSOCIATED WITH THE PATHOGENESIS OF PSORIASIS. 2014 5 3822 24 INVESTIGATING EPIGENETIC EFFECTS OF ACTIVATION-INDUCED DEAMINASE IN CHRONIC LYMPHOCYTIC LEUKEMIA. ACTIVATION INDUCED DEAMINASE (AID) HAS TWO DISTINCT AND WELL DEFINED ROLES, BOTH RELYING ON ITS DEOXYCYTIDINE (DC) DEAMINATING FUNCTION: ONE AS A DNA MUTATOR AND ANOTHER IN DNA DEMETHYLATION. IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), AID WAS PREVIOUSLY SHOWN TO BE AN INDEPENDENT NEGATIVE PROGNOSTIC FACTOR. WHILE THERE IS SUBSTANTIAL IMPACT ON DNA MUTATIONS, EFFECTS OF AID ON GENE EXPRESSION BY PROMOTER DEMETHYLATION OF DISEASE RELATED TARGET GENES IN LEUKEMIA HAS NOT BEEN ADDRESSED. TO SHED LIGHT ON THIS QUESTION, WE AIMED AT DETERMINING GENOME WIDE METHYLATION CHANGES AS WELL AS GENE EXPRESSION CHANGES IN RESPONSE TO AID EXPRESSION IN CLL. ALTHOUGH WE FOUND MINOR DIFFERENCES IN INDIVIDUAL METHYLATION VARIABLE POSITIONS FOLLOWING AID EXPRESSION, WE COULD NOT FIND RECURRENT METHYLATION CHANGES OF SPECIFIC TARGET SITES OR CHANGES IN GLOBAL METHYLATION. 2018 6 271 32 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 7 3069 38 GENOME-WIDE DNA METHYLATION PROFILING IDENTIFIES EPIGENETIC CHANGES IN CD4+ AND CD14+ CELLS OF MULTIPLE SCLEROSIS PATIENTS. MULTIPLE SCLEROSIS (MS) IS A CHRONIC AUTOIMMUNE AND DEGENERATIVE DISEASE OF THE CENTRAL NERVOUS SYSTEM, WHICH DEVELOPS IN GENETICALLY PREDISPOSED INDIVIDUALS UPON EXPOSURE TO ENVIRONMENTAL INFLUENCES. ENVIRONMENTAL TRIGGERS OF MS, SUCH AS VIRAL INFECTIONS OR SMOKING, WERE DEMONSTRATED TO AFFECT DNA METHYLATION, AND THUS TO INVOLVE THIS IMPORTANT EPIGENETIC MECHANISM IN THE DEVELOPMENT OF PATHOLOGICAL PROCESS. TO IDENTIFY MS-ASSOCIATED DNA METHYLATION HALLMARKS, WE PERFORMED GENOME-WIDE DNA METHYLATION PROFILING OF TWO CELL POPULATIONS (CD4+ T-LYMPHOCYTES AND CD14+ MONOCYTES), COLLECTED FROM THE SAME TREATMENT-NAIVE RELAPSING-REMITTING MS PATIENTS AND HEALTHY SUBJECTS, USING ILLUMINA 450 K METHYLATION ARRAYS. WE REVEALED SIGNIFICANT CHANGES IN DNA METHYLATION FOR BOTH CELL POPULATIONS IN MS. IN CD4+ CELLS OF MS PATIENTS THE MAJORITY OF DIFFERENTIALLY METHYLATED POSITIONS (DMPS) WERE SHOWN TO BE HYPOMETHYLATED, WHILE IN CD14+ CELLS - HYPERMETHYLATED. DIFFERENTIAL METHYLATION OF HLA-DRB1 GENE IN CD4+ AND CD14+ CELLS WAS ASSOCIATED WITH CARRIAGE OF DRB1*15 ALLELE INDEPENDENTLY FROM THE DISEASE STATUS. BESIDES, ABOUT 20% OF IDENTIFIED DMPS WERE SHARED BETWEEN TWO CELL POPULATIONS AND HAD THE SAME DIRECTION OF METHYLATION CHANGES; THEY MAY BE INVOLVED IN BASIC EPIGENETIC PROCESSES OCCURING IN MS. THESE FINDINGS SUGGEST THAT THE EPIGENETIC MECHANISM OF DNA METHYLATION IN IMMUNE CELLS CONTRIBUTES TO MS; FURTHER STUDIES ARE NOW REQUIRED TO VALIDATE THESE RESULTS AND UNDERSTAND THEIR FUNCTIONAL SIGNIFICANCE. 2022 8 2494 25 EPIGENETICS AND CHRONIC LYMPHOCYTIC LEUKEMIA. THE DNA METHYLATION LEVEL IN PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA IS GENERALLY LOWER THAN HEALTHY INDIVIDUALS. ALTHOUGH DNA METHYLATION IS GLOBALLY DECREASED, REGIONAL HYPERMETHYLATION OF GENE PROMOTERS LEADS TO GENE SILENCING. MANY OF THESE GENES HAVE TUMOR SUPPRESSOR PHENOTYPES. UNLIKE MUTATIONS OR DELETIONS, HYPERMETHYLATION IS POTENTIALLY REVERSIBLE AFTER INHIBITION WITH DNA METHYLATION MODULATORS. MYELODYSPLASTIC SYNDROME HAS BEEN A MODEL DISEASE IN WHICH TREATMENT OF PATIENTS RESULTS IN DEMETHYLATION OF SPECIFIC GENES. THE STORY IN PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA IS SLOWLY UNRAVELING AS EPIGENETIC MODIFICATIONS LIKELY ALSO PLAY AN IMPORTANT ROLE. ONGOING CLINICAL TRIALS CORRELATING CLINICAL RESPONSE TO GENE EXPRESSION AFTER TREATMENT WITH DNA METHYLATION INHIBITORS WILL ULTIMATELY ALLOW US TO BETTER RISK STRATIFY AND PREDICT THE SUBGROUP OF PATIENTS WHO WILL BENEFIT FROM TREATMENT WITH THIS CLASS OF DRUGS. 2006 9 1577 33 DNA METHYLATION PROFILE IN CHRONIC MYELOMONOCYTIC LEUKEMIA ASSOCIATES WITH DISTINCT CLINICAL, BIOLOGICAL AND GENETIC FEATURES. CHROMOSOMAL ABNORMALITIES ARE DETECTED IN 20-30% OF PATIENTS WITH CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML) AND CORRELATE WITH PROGNOSIS. ON THE MUTATION LEVEL, DISRUPTIVE ALTERATIONS ARE PARTICULARLY FREQUENT IN CHROMATIN REGULATORY GENES. HOWEVER, LITTLE IS KNOWN ABOUT THE CONSEQUENTIAL ALTERATIONS IN THE EPIGENETIC MARKING OF THE GENOME. HERE, WE REPORT THE ANALYSIS OF GENOMIC DNA METHYLATION PATTERNS OF 64 CMML PATIENTS AND 10 HEALTHY CONTROLS, USING A DNA METHYLATION MICROARRAY FOCUSED ON PROMOTER REGIONS. DIFFERENTIAL METHYLATION ANALYSIS BETWEEN PATIENTS AND CONTROLS ALLOWED US TO IDENTIFY ABNORMALITIES IN DNA METHYLATION, INCLUDING HYPERMETHYLATION OF SPECIFIC GENES AND LARGE GENOME REGIONS WITH ABERRANT DNA METHYLATION. UNSUPERVISED HIERARCHICAL CLUSTER ANALYSIS IDENTIFIED TWO MAIN CLUSTERS THAT ASSOCIATED WITH THE CLINICAL, BIOLOGICAL, AND GENETIC FEATURES OF PATIENTS. GROUP 1 WAS ENRICHED IN PATIENTS WITH ADVERSE CLINICAL AND BIOLOGICAL CHARACTERISTICS AND POORER OVERALL AND PROGRESSION-FREE SURVIVAL. IN ADDITION, SIGNIFICANT DIFFERENCES IN DNA METHYLATION WERE OBSERVED BETWEEN PATIENTS WITH LOW RISK AND INTERMEDIATE/HIGH RISK KARYOTYPES AND BETWEEN TET2 MUTANT AND WILD TYPE PATIENTS. TAKEN TOGETHER, OUR RESULTS DEMONSTRATE THAT ALTERED DNA METHYLATION PATTERNS REFLECT THE CMML DISEASE STATE AND ALLOW TO IDENTIFY PATIENT GROUPS WITH DISTINCT CLINICAL FEATURES. 2018 10 2909 35 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 4004 31 LOSS OF THE POLYCOMB MARK FROM BIVALENT PROMOTERS LEADS TO ACTIVATION OF CANCER-PROMOTING GENES IN COLORECTAL TUMORS. IN COLON TUMORS, THE TRANSCRIPTION OF MANY GENES BECOMES DEREGULATED BY POORLY DEFINED EPIGENETIC MECHANISMS THAT HAVE BEEN STUDIED MAINLY IN ESTABLISHED CELL LINES. IN THIS STUDY, WE USED FROZEN HUMAN COLON TISSUES TO ANALYZE PATTERNS OF HISTONE MODIFICATION AND DNA CYTOSINE METHYLATION IN CANCER AND MATCHED NORMAL MUCOSA SPECIMENS. DNA METHYLATION IS STRONGLY TARGETED TO BIVALENT H3K4ME3- AND H3K27ME3-ASSOCIATED PROMOTERS, WHICH LOSE BOTH HISTONE MARKS AND ACQUIRE DNA METHYLATION. HOWEVER, WE FOUND THAT LOSS OF THE POLYCOMB MARK H3K27ME3 FROM BIVALENT PROMOTERS WAS ACCOMPANIED OFTEN BY ACTIVATION OF GENES ASSOCIATED WITH CANCER PROGRESSION, INCLUDING NUMEROUS STEM CELL REGULATORS, ONCOGENES, AND PROLIFERATION-ASSOCIATED GENES. INDEED, WE FOUND MANY OF THESE SAME GENES WERE ALSO ACTIVATED IN PATIENTS WITH ULCERATIVE COLITIS WHERE CHRONIC INFLAMMATION PREDISPOSES THEM TO COLON CANCER. BASED ON OUR FINDINGS, WE PROPOSE THAT A LOSS OF POLYCOMB REPRESSION AT BIVALENT GENES COMBINED WITH AN ENSUING SELECTION FOR TUMOR-DRIVING EVENTS PLAYS A MAJOR ROLE IN CANCER PROGRESSION. 2014 12 3422 30 HUMAN MONOCYTE-TO-MACROPHAGE DIFFERENTIATION INVOLVES HIGHLY LOCALIZED GAIN AND LOSS OF DNA METHYLATION AT TRANSCRIPTION FACTOR BINDING SITES. BACKGROUND: MACROPHAGES AND THEIR PRECURSORS MONOCYTES PLAY A KEY ROLE IN INFLAMMATION AND CHRONIC INFLAMMATORY DISORDERS. MONOCYTE-TO-MACROPHAGE DIFFERENTIATION AND ACTIVATION PROGRAMS ARE ACCOMPANIED BY SIGNIFICANT EPIGENETIC REMODELING WHERE DNA METHYLATION ASSOCIATES WITH CELL IDENTITY. HERE WE SHOW THAT DNA METHYLATION CHANGES CHARACTERISTIC FOR MONOCYTE-TO-MACROPHAGE DIFFERENTIATION OCCUR AT TRANSCRIPTION FACTOR BINDING SITES, AND, IN CONTRAST TO WHAT WAS PREVIOUSLY DESCRIBED, ARE GENERALLY HIGHLY LOCALIZED AND ENCOMPASS BOTH LOSSES AND GAINS OF DNA METHYLATION. RESULTS: WE COMPARED GENOME-WIDE DNA METHYLATION ACROSS 440,292 CPG SITES BETWEEN HUMAN MONOCYTES, NAIVE MACROPHAGES AND MACROPHAGES FURTHER ACTIVATED TOWARD A PRO-INFLAMMATORY STATE (USING LPS/IFNGAMMA), AN ANTI-INFLAMMATORY STATE (IL-4) OR FOAM CELLS (OXLDL AND ACLDL). MOREOVER, WE INTEGRATED THESE DATA WITH PUBLIC WHOLE-GENOME SEQUENCING DATA ON MONOCYTES AND MACROPHAGES TO DEMARCATE DIFFERENTIALLY METHYLATED REGIONS. OUR ANALYSIS SHOWED THAT DIFFERENTIAL DNA METHYLATION WAS MOST PRONOUNCED DURING MONOCYTE-TO-MACROPHAGE DIFFERENTIATION, WAS TYPICALLY RESTRICTED TO SINGLE CPGS OR VERY SHORT REGIONS, AND CO-LOCALIZED WITH LINEAGE-SPECIFIC ENHANCERS IRRESPECTIVE OF WHETHER IT CONCERNS GAIN OR LOSS OF METHYLATION. FURTHERMORE, DIFFERENTIALLY METHYLATED CPGS WERE LOCATED AT SITES CHARACTERIZED BY INCREASED BINDING OF TRANSCRIPTION FACTORS KNOWN TO BE INVOLVED IN MONOCYTE-TO-MACROPHAGE DIFFERENTIATION INCLUDING C/EBP AND ETS FOR GAIN AND AP-1 FOR LOSS OF METHYLATION. CONCLUSION: OUR STUDY HIGHLIGHTS THE INVOLVEMENT OF SUBTLE, YET HIGHLY LOCALIZED REMODELING OF DNA METHYLATION AT REGULATORY REGIONS IN CELL DIFFERENTIATION. 2019 13 2008 37 EPIGENETIC BASIS FOR MONOCYTE DYSFUNCTION IN PATIENTS WITH SEVERE ALCOHOLIC HEPATITIS. BACKGROUND & AIMS: SEVERE FORMS OF ALCOHOL-RELATED LIVER DISEASE ARE ASSOCIATED WITH INCREASED SUSCEPTIBILITY TO INFECTIONS WHICH ARE ASSOCIATED WITH POOR PROGNOSIS. THE CELLULAR AND MOLECULAR MECHANISMS RESPONSIBLE FOR THIS ALTERED HOST DEFENSE ARE INCOMPLETELY UNDERSTOOD. METHODS: WE PERFORMED WHOLE BLOOD PHENOTYPIC ANALYSIS AND EX VIVO STIMULATION WITH VARIOUS PATHOGEN-ASSOCIATED MOLECULAR PATTERNS (PAMPS). WE INCLUDED 34 PATIENTS WITH ALCOHOL-RELATED CIRRHOSIS (18 OF WHOM HAD BIOPSY-PROVEN SEVERE ALCOHOLIC HEPATITIS [SAH]), 12 HEALTHY CONTROLS AND 11 PATIENTS WITH CHRONIC ALCOHOL CONSUMPTION WITHOUT SIGNIFICANT LIVER DISEASE. WE ALSO EVALUATED THE TRANSCRIPTOMIC (RNA-SEQ) AND CHROMATIN ACCESSIBILITY (ATAC-SEQ) PROFILES OF CD14(+) MONOCYTES FROM A SUBSET OF PATIENTS. RESULTS: CIRCULATING MONOCYTES AND CONVENTIONAL DENDRITIC CELLS (DCS) FROM PATIENTS WITH SAH DISPLAYED COMPLEX ALTERATIONS CHARACTERIZED BY INCREASED EXPRESSION OF BOTH ACTIVATING AND INHIBITORY SURFACE MARKERS AND AN IMPAIRED PRO-INFLAMMATORY RESPONSE UPON STIMULATION WITH PAMPS REPRESENTATIVE OF GRAM-NEGATIVE BACTERIA (LIPOPOLYSACCHARIDE, PAM3CSK4) OR FUNGAL PATHOGENS (ZYMOSAN). THEIR DECREASED ABILITY TO PRODUCE MORE THAN 1 CYTOKINE (POLYFUNCTIONALITY) UPON PAMP STIMULATION CORRELATED WITH THE RISK OF DEVELOPING INFECTION AT 28 DAYS OR MORTALITY AT 90 DAYS. THE PRESENCE OF ACUTE-ON-CHRONIC LIVER FAILURE IN PATIENTS WITH SAH DID NOT SIGNIFICANTLY MODIFY THE IMMUNE PROFILE OF MONOCYTES AND DCS. MOREOVER, CD14(+) MONOCYTES OF PATIENTS WITH SAH DISPLAYED ALTERED TRANSCRIPTIONAL AND EPIGENOMIC PROFILES CHARACTERIZED BY DOWNREGULATION OF KEY INNATE IMMUNE AND METABOLIC PATHWAYS AND UPREGULATION OF IMPORTANT IMMUNOMODULATORY FACTORS. CONCLUSIONS: IN PATIENTS WITH SAH, THE ALTERED TRANSCRIPTIONAL PROGRAM AND FUNCTIONAL PROPERTIES OF MONOCYTES THAT CONTRIBUTE TO PATIENTS' SUSCEPTIBILITY TO INFECTION HAVE STRONG EPIGENETIC DETERMINANTS. LAY SUMMARY: PATIENTS WITH SEVERE ALCOHOLIC HEPATITIS ARE AT INCREASED RISK OF INFECTIONS, WHICH CONTRIBUTE TO THE POOR PROGNOSIS ASSOCIATED WITH THE DISEASE. HEREIN, WE SHOW THAT EPIGENETIC DETERMINANTS UNDERLY THE IMMUNE CELL DYSFUNCTION AND INAPPROPRIATE RESPONSES TO PATHOGENS THAT ARE ASSOCIATED WITH SEVERE ALCOHOLIC HEPATITIS. 2020 14 4775 46 NUCLEIC ACID-SENSING AND INTERFERON-INDUCIBLE PATHWAYS SHOW DIFFERENTIAL METHYLATION IN MZ TWINS DISCORDANT FOR LUPUS AND OVEREXPRESSION IN INDEPENDENT LUPUS SAMPLES: IMPLICATIONS FOR PATHOGENIC MECHANISM AND DRUG TARGETING. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC, MULTISYSTEM, AUTOIMMUNE INFLAMMATORY DISEASE WITH GENOMIC AND NON-GENOMIC CONTRIBUTIONS TO RISK. WE HYPOTHESIZE THAT EPIGENETIC FACTORS ARE A SIGNIFICANT CONTRIBUTOR TO SLE RISK AND MAY BE INFORMATIVE FOR IDENTIFYING PATHOGENIC MECHANISMS AND THERAPEUTIC TARGETS. TO TEST THIS HYPOTHESIS WHILE CONTROLLING FOR GENETIC BACKGROUND, WE PERFORMED AN EPIGENOME-WIDE ANALYSIS OF DNA METHYLATION IN GENOMIC DNA FROM WHOLE BLOOD IN THREE PAIRS OF FEMALE MONOZYGOTIC (MZ) TWINS OF EUROPEAN ANCESTRY, DISCORDANT FOR SLE. RESULTS WERE REPLICATED ON THE SAME ARRAY IN FOUR CELL TYPES FROM A SET OF FOUR DANISH FEMALE MZ TWIN PAIRS DISCORDANT FOR SLE. GENES IMPLICATED BY THE EPIGENETIC ANALYSES WERE THEN EVALUATED IN 10 INDEPENDENT SLE GENE EXPRESSION DATASETS FROM THE GENE EXPRESSION OMNIBUS (GEO). THERE WERE 59 DIFFERENTIALLY METHYLATED LOCI BETWEEN UNAFFECTED AND AFFECTED MZ TWINS IN WHOLE BLOOD, INCLUDING 11 NOVEL LOCI. ALL BUT TWO OF THESE LOCI WERE HYPOMETHYLATED IN THE SLE TWINS RELATIVE TO THE UNAFFECTED TWINS. THE GENES HARBORING THESE HYPOMETHYLATED LOCI EXHIBITED INCREASED EXPRESSION IN MULTIPLE INDEPENDENT DATASETS OF SLE PATIENTS. THIS PATTERN WAS LARGELY CONSISTENT REGARDLESS OF DISEASE ACTIVITY, CELL TYPE, OR RENAL TISSUE TYPE. THE GENES PROXIMAL TO CPGS EXHIBITING DIFFERENTIAL METHYLATION (DM) IN THE SLE-DISCORDANT MZ TWINS AND EXHIBITING DIFFERENTIAL EXPRESSION (DE) IN INDEPENDENT SLE GEO COHORTS (DM-DE GENES) CLUSTERED INTO TWO PATHWAYS: THE NUCLEIC ACID-SENSING PATHWAY AND THE TYPE I INTERFERON PATHWAY. THE DM-DE GENES WERE ALSO INFORMATICALLY QUERIED FOR POTENTIAL GENE-DRUG INTERACTIONS, YIELDING A LIST OF 41 DRUGS INCLUDING A KNOWN SLE THERAPY. THE DM-DE GENES DELINEATE TWO IMPORTANT BIOLOGIC PATHWAYS THAT ARE NOT ONLY REFLECTIVE OF THE HETEROGENEITY OF SLE BUT MAY ALSO CORRELATE WITH DISTINCT IFN RESPONSES THAT DEPEND ON THE SOURCE, TYPE, AND LOCATION OF NUCLEIC ACID MOLECULES AND THE ACTIVATED RECEPTORS IN INDIVIDUAL PATIENTS. CELL- AND TISSUE-SPECIFIC ANALYSES WILL BE CRITICAL TO THE UNDERSTANDING OF GENETIC FACTORS DYSREGULATING THE NUCLEIC ACID-SENSING AND IFN PATHWAYS AND WHETHER THESE FACTORS COULD BE APPROPRIATE TARGETS FOR THERAPEUTIC INTERVENTION. 2021 15 2873 23 FUNCTIONAL METHYLOME ANALYSIS OF HUMAN DIABETIC KIDNEY DISEASE. IN PATIENTS WITH DIABETES MELLITUS, POOR METABOLIC CONTROL HAS A LONG-LASTING IMPACT ON KIDNEY DISEASE DEVELOPMENT. EPIGENETIC CHANGES, INCLUDING CYTOSINE METHYLATION, HAVE BEEN PROPOSED AS POTENTIAL MEDIATORS OF THE LONG-LASTING EFFECT OF ADVERSE METABOLIC EVENTS. OUR UNDERSTANDING OF THE PRESENCE AND CONTRIBUTION OF METHYLATION CHANGES TO DISEASE DEVELOPMENT IS LIMITED BECAUSE OF THE LACK OF COMPREHENSIVE BASE-RESOLUTION METHYLOME INFORMATION OF HUMAN KIDNEY TISSUE SAMPLES AND SITE-SPECIFIC METHYLATION EDITING. BASE RESOLUTION, WHOLE-GENOME BISULFITE SEQUENCING METHYLOME MAPS OF HUMAN DIABETIC KIDNEY DISEASE (DKD) TUBULE SAMPLES, AND ASSOCIATED GENE EXPRESSION MEASURED BY RNA SEQUENCING HIGHLIGHTED WIDESPREAD METHYLATION CHANGES IN DKD. PATHWAY ANALYSIS HIGHLIGHTED COORDINATED (METHYLATION AND GENE EXPRESSION) CHANGES IN IMMUNE SIGNALING, INCLUDING TUMOR NECROSIS FACTOR ALPHA (TNF). CHANGES IN TNF METHYLATION CORRELATED WITH KIDNEY FUNCTION DECLINE. DCAS9-TET1-BASED LOWERING OF THE CYTOSINE METHYLATION LEVEL OF THE TNF DIFFERENTIALLY METHYLATED REGION RESULTED IN AN INCREASE IN THE TNF TRANSCRIPT LEVEL, INDICATING THAT METHYLATION OF THIS LOCUS PLAYS AN IMPORTANT ROLE IN CONTROLLING TNF EXPRESSION. INCREASING THE TNF LEVEL IN DIABETIC MICE INCREASED DISEASE SEVERITY, SUCH AS ALBUMINURIA. IN SUMMARY, OUR RESULTS INDICATE WIDESPREAD METHYLATION DIFFERENCES IN DKD KIDNEYS AND HIGHLIGHTS EPIGENETIC CHANGES IN THE TNF LOCUS AND ITS CONTRIBUTION TO THE DEVELOPMENT OF NEPHROPATHY IN PATIENTS WITH DIABETES MELLITUS. 2019 16 1269 32 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 17 141 32 ABERRANT DNA METHYLATION OF MTOR PATHWAY GENES PROMOTES INFLAMMATORY ACTIVATION OF IMMUNE CELLS IN DIABETIC KIDNEY DISEASE. DNA METHYLATION HAS BEEN IMPLICATED IN THE PATHOGENESIS OF DIABETIC KIDNEY DISEASE (DKD), BUT THE UNDERLYING MECHANISMS REMAIN UNCLEAR. IN THIS STUDY, WE TESTED THE HYPOTHESIS THAT ABERRANT DNA METHYLATION IN PERIPHERAL IMMUNE CELLS CONTRIBUTES TO DKD PROGRESSION. WE SHOWED THAT LEVELS OF DNA METHYLTRANSFERASE 1 (DNMT1), A KEY ENZYME FOR DNA METHYLATION, WERE INCREASED ALONG WITH INFLAMMATORY ACTIVITY OF PERIPHERAL BLOOD MONONUCLEAR CELLS IN DKD PATIENTS. INHIBITION OF DNMT1 WITH 5-AZA-2'-DEOXYCYTIDINE (5-AZA) MARKEDLY INCREASED THE PROPORTION OF CD4(+)CD25(+) REGULATORY T CELLS IN PERIPHERAL BLOOD MONONUCLEAR CELLS IN CULTURE AND IN DIABETIC ANIMALS. ADOPTIVE TRANSFER OF IMMUNE CELLS FROM 5-AZA-TREATED ANIMALS SHOWED BENEFICIAL EFFECTS ON THE HOST IMMUNE SYSTEM, RESULTING IN A SIGNIFICANT IMPROVEMENT OF DKD. USING GENOME-WIDE DNA METHYLATION ASSAYS, WE IDENTIFIED THE DIFFERENTIALLY METHYLATED CYTOSINES IN THE PROMOTER REGIONS OF MAMMALIAN TARGET OF RAPAMYCIN (MTOR) REGULATORS IN PERIPHERAL BLOOD MONONUCLEAR CELLS OF DIABETIC PATIENTS. FURTHER, MRNA ARRAYS CONFIRMED THE CONSISTENT INDUCTION OF GENES EXPRESSED IN THE MTOR PATHWAY. IMPORTANTLY, DOWN-REGULATION OF DNMT1 EXPRESSION VIA RNA INTERFERENCE RESULTED IN PROMINENT CYTOSINE DEMETHYLATION OF MTOR NEGATIVE REGULATORS AND SUBSEQUENT DECREASE OF MTOR ACTIVITY. LASTLY, MODULATION OF MTOR RESULTED IN CHANGES IN THE EFFECT OF 5-AZA ON DIABETIC IMMUNE CELLS. THUS, UP-REGULATION OF DNMT1 IN DIABETIC IMMUNE CELLS INDUCES ABERRANT CYTOSINE METHYLATION OF THE UPSTREAM REGULATORS OF MTOR, LEADING TO PATHOGENIC ACTIVATION OF THE MTOR PATHWAY AND CONSEQUENT INFLAMMATION IN DIABETIC KIDNEYS. HENCE, THIS STUDY HIGHLIGHTS THERAPEUTIC POTENTIAL OF TARGETING EPIGENETIC EVENTS IN IMMUNE SYSTEM FOR TREATING DKD. 2019 18 1794 33 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 19 6800 38 [EPIGENETIC DISTURBANCES IN SYSTEMIC LUPUS ERYTHEMATOSUS]. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC INFLAMMATORY AUTOIMMUNE DISEASE THAT RESULTS IN UNCONTROLLED IMMUNE SYSTEM ACTIVATION AND OVERPRODUCTION OF AUTOANTIBODIES. THE PATHOGENESIS OF THE DISEASE IS COMPLEX AND NOT FULLY UNDERSTOOD, NEVERTHELESS, GENETIC AND ENVIRONMENTAL FACTORS PLAY AN IMPORTANT ROLE. SO FAR, ABOUT 30 GENES HAVE BEEN IDENTIFIED TO BE INVOLVED IN THE SLE PATHOMECHANISM. HOWEVER, NOT ALL GENETICALLY PREDISPOSED INDIVIDUALS DEVELOP THE DISEASE. THIS PHENOMENON CAN BE ASSOCIATED WITH EPIGENETIC CHANGES THAT OCCUR UNDER THE INFLUENCE OF ENVIRONMENTAL FACTORS. THEY CAN AFFECT GENE EXPRESSION AND ARE POTENTIALLY HEREDITARY, BUT DO NOT LEAD TO CHANGES IN THE NUCLEOTIDE SEQUENCE. EPIGENETIC DYSFUNCTIONS, IDENTIFIED IN THE COURSE OF THE DISEASE, LEAD TO CHANGES IN THE EXPRESSION OF GENES THAT PLAY A KEY ROLE IN MAINTAINING THE BODY'S IMMUNE TOLERANCE. MAJOR MECHANISMS OF EPIGENETIC VARIABILITY ARE: DNA METHYLATION, HISTONE PROTEIN MODIFICATION, NON-CODING RNA EXPRESSION, AS WELL AS GENE IMPRINTING. THE MAJOR EPIGENETIC DYSFUNCTIONS AFFECTING THE PATHOGENESIS OF THE DISEASE ARE GLOBAL HYPOMETHYLATION ON CD4+ T CELLS RESULTING FROM ERK SIGNALING PATHWAY REGULATION, HISTONE HYPOACETYLATION, HISTONE H3 LYSINE METHYLATION, AND REACTIVATION OF INACTIVE CHROMOSOME X. IN LUPUS PATIENTS, VARIOUS EPIGENETIC MECHANISMS INTERACT WITH EACH OTHER, ENHANCING THE EXPRESSION OR SILENCING OF GENES RESPONSIBLE FOR THE PRODUCTION OF PRO-INFLAMMATORY AND ANTI-INFLAMMATORY CYTOKINES AND ACTIVATION OF AUTOREACTIVE B-LYMPHOCYTES. 2018 20 2920 31 GENE-SET ANALYSIS IS SEVERELY BIASED WHEN APPLIED TO GENOME-WIDE METHYLATION DATA. MOTIVATION: DNA METHYLATION IS AN EPIGENETIC MARK THAT CAN STABLY REPRESS GENE EXPRESSION. BECAUSE OF ITS BIOLOGICAL AND CLINICAL SIGNIFICANCE, SEVERAL METHODS HAVE BEEN DEVELOPED TO COMPARE GENOME-WIDE PATTERNS OF METHYLATION BETWEEN GROUPS OF SAMPLES. THE APPLICATION OF GENE SET ANALYSIS TO IDENTIFY RELEVANT GROUPS OF GENES THAT ARE ENRICHED FOR DIFFERENTIALLY METHYLATED GENES IS OFTEN A MAJOR COMPONENT OF THE ANALYSIS OF THESE DATA. THIS CAN BE USED, FOR EXAMPLE, TO IDENTIFY PROCESSES OR PATHWAYS THAT ARE PERTURBED IN DISEASE DEVELOPMENT. WE SHOW THAT GENE-SET ANALYSIS, AS IT IS TYPICALLY APPLIED TO GENOME-WIDE METHYLATION ASSAYS, IS SEVERELY BIASED AS A RESULT OF DIFFERENCES IN THE NUMBERS OF CPG SITES ASSOCIATED WITH DIFFERENT CLASSES OF GENES AND GENE PROMOTERS. RESULTS: WE DEMONSTRATE THIS BIAS USING PUBLISHED DATA FROM A STUDY OF DIFFERENTIAL CPG ISLAND METHYLATION IN LUNG CANCER AND A DATASET WE GENERATED TO STUDY METHYLATION CHANGES IN PATIENTS WITH LONG-STANDING ULCERATIVE COLITIS. WE SHOW THAT SEVERAL OF THE GENE SETS THAT SEEM ENRICHED WOULD ALSO BE IDENTIFIED WITH RANDOMIZED DATA. WE SUGGEST TWO EXISTING APPROACHES THAT CAN BE ADAPTED TO CORRECT THE BIAS. ACCOUNTING FOR THE BIAS IN THE LUNG CANCER AND ULCERATIVE COLITIS DATASETS PROVIDES NOVEL BIOLOGICAL INSIGHTS INTO THE ROLE OF METHYLATION IN CANCER DEVELOPMENT AND CHRONIC INFLAMMATION, RESPECTIVELY. OUR RESULTS HAVE SIGNIFICANT IMPLICATIONS FOR MANY PREVIOUS GENOME-WIDE METHYLATION STUDIES THAT HAVE DRAWN CONCLUSIONS ON THE BASIS OF SUCH STRONGLY BIASED ANALYSIS. CONTACT: CATHAL.SEOIGHE@NUIGALWAY.IE SUPPLEMENTARY INFORMATION: SUPPLEMENTARY DATA ARE AVAILABLE AT BIOINFORMATICS ONLINE. 2013