1 2684 151 EVALUATION OF X CHROMOSOME INACTIVATION WITH RESPECT TO HLA GENETIC SUSCEPTIBILITY IN RHEUMATOID ARTHRITIS AND SYSTEMIC SCLEROSIS. BACKGROUND: AUTOIMMUNE DISEASES, INCLUDING RHEUMATOID ARTHRITIS (RA) AND SYSTEMIC SCLEROSIS (SSC) ARE CHARACTERIZED BY A STRONG GENETIC SUSCEPTIBILITY FROM THE HUMAN LEUCOCYTE ANTIGEN (HLA) LOCUS. ADDITIONALLY, DISORDERS OF EPIGENETIC PROCESSES, IN PARTICULAR NON-RANDOM X CHROMOSOME INACTIVATION (XCI), HAVE BEEN REPORTED IN MANY FEMALE-PREDOMINANT AUTOIMMUNE DISEASES. HERE WE TEST THE HYPOTHESIS THAT WOMEN WITH RA OR SSC WHO ARE STRONGLY GENETICALLY PREDISPOSED ARE LESS SUSCEPTIBLE TO XCI BIAS. METHODS: USING METHYLATION SENSITIVE GENOTYPING OF THE ANDROGEN RECEPTOR (AR) GENE, XCI PROFILES WERE PERFORMED IN PERIPHERAL BLOOD MONONUCLEAR CELLS FROM 161 WOMEN WITH RA, 96 WOMEN WITH SSC AND 100 HEALTHY WOMEN. HLA-DRB1 AND DQB1 WERE GENOTYPED. PRESENCE OF SPECIFIC AUTOANTIBODIES WAS DOCUMENTED FOR PATIENTS. XCI SKEWING WAS DEFINED AS HAVING A RATIO >/= 80:20 OF CELLS INACTIVATING THE SAME X CHROMOSOME. RESULTS: 110 WOMEN WITH RA, 68 WOMEN WITH SSC, AND 69 CONTROLS WERE INFORMATIVE FOR THE AR POLYMORPHISM. AMONG THEM 40.9% OF RA PATIENTS AND 36.8% OF SSC PATIENTS HAD SKEWED XCI COMPARED TO 17.4% OF HEALTHY WOMEN (P = 0.002 AND 0.018, RESPECTIVELY). PRESENCE OF RA-SUSCEPTIBILITY ALLELES CODING FOR THE "SHARED EPITOPE" CORRELATED WITH HIGHER SKEWING AMONG RA PATIENTS (P = 0.002) AND SUCH CORRELATION WAS NOT OBSERVED IN OTHER WOMEN, HEALTHY OR WITH SSC. PRESENCE OF SSC-SUSCEPTIBILITY ALLELES DID NOT CORRELATE WITH XCI PATTERNS AMONG SSC PATIENTS. CONCLUSION: DATA DEMONSTRATE XCI SKEWING IN BOTH RA AND SSC COMPARED TO HEALTHY WOMEN. UNEXPECTEDLY, SKEWED XCI OCCURS MORE OFTEN IN WOMEN WITH RA CARRYING THE SHARED EPITOPE, WHICH USUALLY REFLECTS SEVERE DISEASE. THIS REINFORCES THE VIEW THAT LOSS OF MOSAICISM IN PERIPHERAL BLOOD MAY BE A CONSEQUENCE OF CHRONIC AUTOIMMUNITY. 2016 2 2142 51 EPIGENETIC INVESTIGATION OF VARIABLY X CHROMOSOME INACTIVATED GENES IN MONOZYGOTIC FEMALE TWINS DISCORDANT FOR PRIMARY BILIARY CIRRHOSIS. PRIMARY BILIARY CIRRHOSIS (PBC) IS AN AUTOIMMUNE CHRONIC CHOLESTATIC LIVER DISEASE WITH A STRONG GENETIC SUSCEPTIBILITY DUE TO THE HIGH CONCORDANCE IN MONOZYGOTIC (MZ) TWINS AND A STRIKING FEMALE PREDOMINANCE. WOMEN WITH PBC MANIFEST AN ENHANCED X MONOSOMY RATE IN PERIPHERAL LYMPHOCYTES AND WE THUS HYPOTHESIZED AN X CHROMOSOME EPIGENETIC COMPONENT TO EXPLAIN PBC FEMALE PREVALENCE. WHILE MOST GENES ON THE FEMALE INACTIVE X CHROMOSOME ARE SILENCED BY PROMOTER METHYLATION FOLLOWING X CHROMOSOME INACTIVATION (XCI), APPROXIMATELY 10% OF X- LINKED GENES EXHIBIT VARIABLE ESCAPE FROM XCI IN HEALTHY FEMALES. THIS STUDY WAS DESIGNED TO TEST THE HYPOTHESIS THAT SUSCEPTIBILITY TO PBC IS MODIFIED BY ONE OR MORE X-LINKED GENE WITH VARIABLE XCI STATUS. PERIPHERAL BLOOD MRNA AND DNA SAMPLES WERE OBTAINED FROM A UNIQUE COHORT OF MZ TWIN SETS DISCORDANT AND CONCORDANT FOR PBC. TRANSCRIPT LEVELS OF THE 125 VARIABLE XCI STATUS GENES WAS DETERMINED BY QUANTITATIVE RT-PCR ANALYSIS AND TWO GENES (CLIC2 AND PIN4) WERE IDENTIFIED AS CONSISTENTLY DOWNREGULATED IN THE AFFECTED TWIN OF DISCORDANT PAIRS. BOTH CLIC2 AND PIN4 DEMONSTRATED PARTIAL AND VARIABLE METHYLATION OF CPG SITES WITHIN 300 BP OF THE TRANSCRIPTION START SITE THAT DID NOT PREDICT THE XCI STATUS. PROMOTER METHYLATION OF CLIC2 MANIFESTED NO SIGNIFICANT DIFFERENCE BETWEEN SAMPLES AND NO SIGNIFICANT CORRELATION WITH TRANSCRIPT LEVELS. PIN4 METHYLATION SHOWED A POSITIVE TREND WITH TRANSCRIPTION IN ALL SAMPLES BUT NO DIFFERENTIAL METHYLATION WAS OBSERVED BETWEEN DISCORDANT TWINS. A GENETIC POLYMORPHISM AFFECTING THE NUMBER OF CPG SITES IN THE PIN4 PROMOTER DID NOT IMPACT METHYLATION OR TRANSCRIPT LEVELS IN A HETEROZYGOUS TWIN PAIR AND SHOWED A SIMILAR FREQUENCY IN INDEPENDENT SERIES OF UNRELATED PBC CASES AND CONTROLS. OUR RESULTS SUGGEST THAT EPIGENETIC FACTORS INFLUENCING PBC ONSET ARE MORE COMPLEX THAN METHYLATION DIFFERENCES AT X-LINKED PROMOTERS AND VARIABLY 3 INACTIVATED X-LINKED GENES MAY BE CHARACTERIZED BY PARTIAL PROMOTER METHYLATION AND BIALLELIC TRANSCRIPTION. 2011 3 2205 47 EPIGENETIC MODIFICATION OF THE X CHROMOSOME INFLUENCES SUSCEPTIBILITY TO POLYCYSTIC OVARY SYNDROME. CONTEXT: THE CAUSE OF POLYCYSTIC OVARY SYNDROME (PCOS) IS UNKNOWN, ALTHOUGH GENETIC AND ENVIRONMENTAL INFLUENCES ARE CLEARLY IMPLICATED. SOME GENETIC STUDIES HAVE SUGGESTED THE INVOLVEMENT OF X-LINKED GENES IN PCOS, BUT THE INFLUENCE OF X CHROMOSOME INACTIVATION (XCI) ON MANIFESTATION OF THIS DISORDER HAS NOT PREVIOUSLY BEEN EXAMINED. OBJECTIVE: THE OBJECTIVE OF THE STUDY WAS TO TEST THE NULL HYPOTHESIS THAT XCI HAS NO INFLUENCE ON CLINICAL PRESENTATION OF PCOS. DESIGN: WE EXAMINED PATTERNS OF XCI BETWEEN SISTER PAIRS WITH THE SAME GENOTYPE AT A POLYMORPHIC LOCUS ON THE X CHROMOSOME IN FAMILIES WITH PCOS. SETTING: THE STUDY WAS CONDUCTED AT A PRIVATE PRACTICE. PARTICIPANTS: PCOS WAS DEFINED AS HYPERANDROGENEMIA WITH CHRONIC ANOVULATION. FORTY FAMILIES WERE STUDIED IN WHICH DNA WAS OBTAINED FROM AT LEAST ONE PARENT, THE PROBAND, AND ONE SISTER THAT COULD BE ACCURATELY DIAGNOSED AS BEING AFFECTED OR UNAFFECTED. MAIN OUTCOME MEASURE(S): RELATIVE EXPRESSION OF TWO X-LINKED ALLELES WAS DETERMINED, AND THE RATIO OF ONE TO THE OTHER REPRESENTED THE PATTERN OF XCI. RESULTS: THE STATISTICAL ODDS ON A DIFFERENT CLINICAL PRESENTATION BETWEEN SISTERS WAS APPROXIMATELY 29 TIMES HIGHER IN SISTER PAIRS WITH DIFFERENT PATTERNS OF XCI, COMPARED WITH SISTER PAIRS WITH THE SAME PATTERN OF XCI (ODDS RATIO 28.9; 95% CONFIDENCE INTERVAL 4.0-206; P = 0.0008). CONCLUSIONS: THIS STUDY PROVIDES EVIDENCE TO REFUTE THE NULL HYPOTHESIS AND PROPOSE A CLOSER INSPECTION OF X-LINKED GENES IN PCOS, ONE IN WHICH BOTH GENOTYPE AND EPIGENOTYPE ARE CONSIDERED. ENVIRONMENTAL DETERMINANTS OF PCOS MAY ALTER CLINICAL PRESENTATION VIA EPIGENETIC MODIFICATIONS, WHICH CURRENTLY REMAIN UNDETECTED IN TRADITIONAL GENETIC ANALYSES. 2006 4 3069 43 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 5 1739 39 EARLY DNA METHYLATION CHANGES IN CHILDREN DEVELOPING BETA CELL AUTOIMMUNITY AT A YOUNG AGE. AIMS/HYPOTHESIS: TYPE 1 DIABETES IS A CHRONIC AUTOIMMUNE DISEASE OF COMPLEX AETIOLOGY, INCLUDING A POTENTIAL ROLE FOR EPIGENETIC REGULATION. PREVIOUS EPIGENOMIC STUDIES FOCUSED MAINLY ON CLINICALLY DIAGNOSED INDIVIDUALS. THE AIM OF THE STUDY WAS TO ASSESS EARLY DNA METHYLATION CHANGES ASSOCIATED WITH TYPE 1 DIABETES ALREADY BEFORE THE DIAGNOSIS OR EVEN BEFORE THE APPEARANCE OF AUTOANTIBODIES. METHODS: REDUCED REPRESENTATION BISULPHITE SEQUENCING (RRBS) WAS APPLIED TO STUDY DNA METHYLATION IN PURIFIED CD4(+) T CELL, CD8(+) T CELL AND CD4(-)CD8(-) CELL FRACTIONS OF 226 PERIPHERAL BLOOD MONONUCLEAR CELL SAMPLES LONGITUDINALLY COLLECTED FROM SEVEN TYPE 1 DIABETES-SPECIFIC AUTOANTIBODY-POSITIVE INDIVIDUALS AND CONTROL INDIVIDUALS MATCHED FOR AGE, SEX, HLA RISK AND PLACE OF BIRTH. WE ALSO EXPLORED CORRELATIONS BETWEEN DNA METHYLATION AND GENE EXPRESSION USING RNA SEQUENCING DATA FROM THE SAME SAMPLES. TECHNICAL VALIDATION OF RRBS RESULTS WAS PERFORMED USING PYROSEQUENCING. RESULTS: WE IDENTIFIED 79, 56 AND 45 DIFFERENTIALLY METHYLATED REGIONS IN CD4(+) T CELLS, CD8(+) T CELLS AND CD4(-)CD8(-) CELL FRACTIONS, RESPECTIVELY, BETWEEN TYPE 1 DIABETES-SPECIFIC AUTOANTIBODY-POSITIVE INDIVIDUALS AND CONTROL PARTICIPANTS. THE ANALYSIS OF PRE-SEROCONVERSION SAMPLES IDENTIFIED DNA METHYLATION SIGNATURES AT THE VERY EARLY STAGE OF DISEASE, INCLUDING DIFFERENTIAL METHYLATION AT THE PROMOTER OF IRF5 IN CD4(+) T CELLS. FURTHER, WE VALIDATED RRBS RESULTS USING PYROSEQUENCING AT THE FOLLOWING CPG SITES: CHR19:18118304 IN THE PROMOTER OF ARRDC2; CHR21:47307815 IN THE INTRON OF PCBP3; AND CHR14:81128398 IN THE INTERGENIC REGION NEAR TRAF3 IN CD4(+) T CELLS. CONCLUSIONS/INTERPRETATION: THESE PRELIMINARY RESULTS PROVIDE NOVEL INSIGHTS INTO CELL TYPE-SPECIFIC DIFFERENTIAL EPIGENETIC REGULATION OF GENES, WHICH MAY CONTRIBUTE TO TYPE 1 DIABETES PATHOGENESIS AT THE VERY EARLY STAGE OF DISEASE DEVELOPMENT. SHOULD THESE FINDINGS BE VALIDATED, THEY MAY SERVE AS A POTENTIAL SIGNATURE USEFUL FOR DISEASE PREDICTION AND MANAGEMENT. 2022 6 2797 32 FCER1G GENE HYPOMETHYLATION IN PATIENTS WITH RHEUMATOID ARTHRITIS. RHEUMATOID ARTHRITIS (RA) IS A CHRONIC AUTOIMMUNE DISEASE THAT, WHEN IMPROPERLY TREATED, LEADS TO DISABILITY IN PATIENTS. VARIOUS FACTORS THAT MAY CAUSE THE DEVELOPMENT AND ACTIVITY OF RA ARE BEING CONSIDERED. EPIGENETIC FACTORS ARE ALSO RECEIVING INCREASING ATTENTION. IN OUR STUDY, WE ANALYZED THE ASSOCIATION BETWEEN FCER1G GENE METHYLATION AND RA ACTIVITY. WE CONDUCTED OUR STUDY IN 50 RA PATIENTS AND 24 CONTROLS. THE PATIENTS WERE DIVIDED INTO TWO GROUPS IN TERMS OF HIGH DISEASE ACTIVITY AND REMISSION. QUANTITATIVE REAL-TIME METHYLATION-SPECIFIC PCR WAS USED TO ANALYZE THE METHYLATION STATUS OF THE INVESTIGATED GENES. WE OBSERVED THAT RA PATIENTS HAVE LOWER LEVELS OF METHYLATION OF THE FCER1G GENE COMPARED TO CONTROLS, BUT WE DID NOT FIND ANY DIFFERENCE IN THE METHYLATION STATUS OF THIS GENE BETWEEN PATIENTS WITH HIGH DISEASE ACTIVITY AND REMISSION. THE RESULTS OF THIS STUDY SUGGEST THAT FCER1G GENE METHYLATION MAY BE A NEW POTENTIAL EPIGENETIC MARKER OF RA THAT IS INDEPENDENT OF DISEASE ACTIVITY. 2022 7 1508 44 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 8 1345 33 DETECTION OF DIFFERENTIALLY METHYLATED REGIONS USING BAYES FACTOR FOR ORDINAL GROUP RESPONSES. RESEARCHERS IN GENOMICS ARE INCREASINGLY INTERESTED IN EPIGENETIC FACTORS SUCH AS DNA METHYLATION, BECAUSE THEY PLAY AN IMPORTANT ROLE IN REGULATING GENE EXPRESSION WITHOUT CHANGES IN THE DNA SEQUENCE. THERE HAVE BEEN SIGNIFICANT ADVANCES IN DEVELOPING STATISTICAL METHODS TO DETECT DIFFERENTIALLY METHYLATED REGIONS (DMRS) ASSOCIATED WITH BINARY DISEASE STATUS. MOST OF THESE METHODS ARE BEING DEVELOPED FOR DETECTING DIFFERENTIAL METHYLATION RATES BETWEEN CASES AND CONTROLS. WE CONSIDER MULTIPLE SEVERITY LEVELS OF DISEASE, AND DEVELOP A BAYESIAN STATISTICAL METHOD TO DETECT THE REGION WITH INCREASING (OR DECREASING) METHYLATION RATES AS THE DISEASE SEVERITY INCREASES. PATIENTS ARE CLASSIFIED INTO MORE THAN TWO GROUPS, BASED ON THE DISEASE SEVERITY (E.G., STAGES OF CANCER), AND DMRS ARE DETECTED BY USING MOVING WINDOWS ALONG THE GENOME. WITHIN EACH WINDOW, THE BAYES FACTOR IS CALCULATED TO TEST THE HYPOTHESIS OF MONOTONIC INCREASE IN METHYLATION RATES CORRESPONDING TO SEVERITY OF THE DISEASE VERSUS NO DIFFERENCE. A MIXED-EFFECT MODEL IS USED TO INCORPORATE THE CORRELATION OF METHYLATION RATES OF NEARBY CPG SITES IN THE REGION. RESULTS FROM EXTENSIVE SIMULATION INDICATE THAT OUR PROPOSED METHOD IS STATISTICALLY VALID AND REASONABLY POWERFUL. WE DEMONSTRATE OUR APPROACH ON A BISULFITE SEQUENCING DATASET FROM A CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) STUDY. 2019 9 1519 27 DNA METHYLATION AT ATP11A CG11702988 IS A BIOMARKER OF LUNG DISEASE SEVERITY IN CYSTIC FIBROSIS: A LONGITUDINAL STUDY. CYSTIC FIBROSIS (CF) IS A CHRONIC GENETIC DISEASE THAT MAINLY AFFECTS THE RESPIRATORY AND GASTROINTESTINAL SYSTEMS. NO CURATIVE TREATMENTS ARE AVAILABLE, BUT THE FOLLOW-UP IN SPECIALIZED CENTERS HAS GREATLY IMPROVED THE PATIENT LIFE EXPECTANCY. ROBUST BIOMARKERS ARE REQUIRED TO MONITOR THE DISEASE, GUIDE TREATMENTS, STRATIFY PATIENTS, AND PROVIDE OUTCOME MEASURES IN CLINICAL TRIALS. IN THE PRESENT STUDY, WE OUTLINE A STRATEGY TO SELECT PUTATIVE DNA METHYLATION BIOMARKERS OF LUNG DISEASE SEVERITY IN CYSTIC FIBROSIS PATIENTS. IN THE DISCOVERY STEP, WE SELECTED SEVEN POTENTIAL BIOMARKERS USING A GENOME-WIDE DNA METHYLATION DATASET THAT WE GENERATED IN NASAL EPITHELIAL SAMPLES FROM THE METHYLCF COHORT. IN THE REPLICATION STEP, WE ASSESSED THE SAME BIOMARKERS USING SPUTUM CELL SAMPLES FROM THE METHYLBIOMARK COHORT. OF INTEREST, DNA METHYLATION AT THE CG11702988 SITE (ATP11A GENE) POSITIVELY CORRELATED WITH LUNG FUNCTION AND BMI, AND NEGATIVELY CORRELATED WITH LUNG DISEASE SEVERITY, P. AERUGINOSA CHRONIC INFECTION, AND THE NUMBER OF EXACERBATIONS. THESE RESULTS WERE REPLICATED IN PROSPECTIVE SPUTUM SAMPLES COLLECTED AT FOUR TIME POINTS WITHIN AN 18-MONTH PERIOD AND LONGITUDINALLY. TO CONCLUDE, (I) WE IDENTIFIED A DNA METHYLATION BIOMARKER THAT CORRELATES WITH CF SEVERITY, (II) WE PROVIDED A METHOD TO EASILY ASSESS THIS BIOMARKER, AND (III) WE CARRIED OUT THE FIRST LONGITUDINAL ANALYSIS OF DNA METHYLATION IN CF PATIENTS. THIS NEW EPIGENETIC BIOMARKER COULD BE USED TO STRATIFY CF PATIENTS IN CLINICAL TRIALS. 2021 10 5638 38 SERUM METABOLOMICS REVEALS PATHWAYS AND BIOMARKERS ASSOCIATED WITH ASTHMA PATHOGENESIS. BACKGROUND: ASTHMA IS A CHRONIC INFLAMMATORY DISEASE CAUSED BY COMPLEX INTERACTIONS OF GENETIC, EPIGENETIC, AND ENVIRONMENTAL FACTORS. FOR THIS REASON, NEW APPROACHES ARE REQUIRED TO CLARIFY THE PATHOGENESIS OF ASTHMA BY SYSTEMIC REVIEW. OBJECTIVE: WE APPLIED A (1)H-NMR METABOLOMICS APPROACH TO INVESTIGATE THE ALTERED METABOLIC PATTERN IN SERA FROM PATIENTS WITH ASTHMA AND SOUGHT TO IDENTIFY THE MECHANISM UNDERLYING ASTHMA AND POTENTIAL BIOMARKERS. METHOD: A GLOBAL PROFILE OF SERA FROM PATIENTS WITH ASTHMA (N = 39) AND CONTROLS (N = 26) WAS GENERATED USING (1)H-NMR SPECTROSCOPY COUPLED WITH MULTIVARIATE STATISTICAL ANALYSIS. ENDOGENOUS METABOLITES IN SERUM WERE RAPIDLY MEASURED USING THE TARGET-PROFILING PROCEDURE. RESULTS: MULTIVARIATE STATISTICAL ANALYSIS SHOWED A CLEAR DISTINCTION BETWEEN PATIENTS WITH ASTHMA AND HEALTHY SUBJECTS. SERA OF ASTHMA PATIENTS WERE CHARACTERIZED BY INCREASED LEVELS OF METHIONINE, GLUTAMINE, AND HISTIDINE AND BY DECREASED LEVELS OF FORMATE, METHANOL, ACETATE, CHOLINE, O-PHOSPHOCHOLINE, ARGININE, AND GLUCOSE. THE METABOLITES DETECTED IN THE SERA OF PATIENTS WITH ASTHMA ARE INVOLVED IN HYPERMETHYLATION, RESPONSE TO HYPOXIA, AND IMMUNE REACTION. FURTHERMORE, THE LEVELS OF SERUM METABOLITES FROM PATIENTS WITH ASTHMA CORRELATED WITH ASTHMA SEVERITY; IN PARTICULAR, LIPID METABOLISM WAS ALTERED IN PATIENTS WITH LOWER FORCED EXPIRATORY VOLUME IN 1 S PERCENTAGE (FEV(1)%) PREDICTED VALUES. IN ADDITION, POTENTIAL BIOMARKERS SHOWED STRONG PREDICTIVE POWER IN ROC ANALYSIS, AND THE PRESENCE OF ASTHMA IN EXTERNAL VALIDATION MODELS WAS PREDICTED WITH HIGH ACCURACY (90.9% FOR ASTHMA AND 100% FOR CONTROL SUBJECTS). CONCLUSION & CLINICAL RELEVANCE: THESE DATA SHOWED THAT (1)H-NMR-BASED METABOLITE PROFILING OF SERUM MAY BE USEFUL FOR THE EFFECTIVE DIAGNOSIS OF ASTHMA AND A FURTHER UNDERSTANDING OF ITS PATHOGENESIS. 2013 11 4775 41 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 12 6311 39 THE RELATION BETWEEN DNA METHYLATION PATTERNS AND SERUM CYTOKINE LEVELS IN COMMUNITY-DWELLING ADULTS: A PRELIMINARY STUDY. BACKGROUND: THE LEVELS OF CIRCULATING CYTOKINES FLUCTUATE WITH AGE, ACUTE ILLNESS, AND CHRONIC DISEASE, AND ARE PREDICTIVE OF MORTALITY; THIS IS ALSO TRUE FOR PATTERNS OF DNA (CPG) METHYLATION. GIVEN THAT IMMUNE CELLS ARE PARTICULARLY SENSITIVE TO CHANGES IN THE CONCENTRATION OF CYTOKINES IN THEIR MICROENVIRONMENT, WE HYPOTHESIZED THAT SERUM LEVELS OF TNF, IL-6, IL-8 AND IL-10 WOULD CORRELATE WITH GENOME-WIDE ALTERATIONS IN THE DNA METHYLATION LEVELS OF BLOOD LEUKOCYTES. TO TEST THIS, WE EVALUATED COMMUNITY-DWELLING ADULTS (N = 14; 48-78 YEARS OLD) RECRUITED TO A PILOT STUDY FOR THE CANADIAN LONGITUDINAL STUDY ON AGING (CLSA), EXAMINING DNA METHYLATION PATTERNS IN PERIPHERAL BLOOD MONONUCLEAR CELLS USING THE ILLUMINA HUMANMETHYLATION 450 K BEADCHIP. RESULTS: WE SHOW THAT, APART FROM AGE, SERUM IL-10 LEVELS EXHIBITED THE MOST SUBSTANTIAL ASSOCIATION TO DNA METHYLATION PATTERNS, FOLLOWED BY TNF, IL-6 AND IL-8. FURTHERMORE, WHILE THE LEVELS OF THESE CYTOKINES WERE HIGHER IN ELDERLY ADULTS, NO ASSOCIATIONS WITH EPIGENETIC ACCELERATED AGING, DERIVED USING THE EPIGENETIC CLOCK, WERE OBSERVED. CONCLUSIONS: AS A PRELIMINARY STUDY WITH A SMALL SAMPLE SIZE, THE CONCLUSIONS DRAWN FROM THIS WORK MUST BE VIEWED WITH CAUTION; HOWEVER, OUR OBSERVATIONS ARE ENCOURAGING AND CERTAINLY WARRANT MORE SUITABLY POWERED STUDIES OF THIS RELATIONSHIP. 2017 13 2820 30 FINE-MAPPING INFLAMMATORY BOWEL DISEASE LOCI TO SINGLE-VARIANT RESOLUTION. INFLAMMATORY BOWEL DISEASES ARE CHRONIC GASTROINTESTINAL INFLAMMATORY DISORDERS THAT AFFECT MILLIONS OF PEOPLE WORLDWIDE. GENOME-WIDE ASSOCIATION STUDIES HAVE IDENTIFIED 200 INFLAMMATORY BOWEL DISEASE-ASSOCIATED LOCI, BUT FEW HAVE BEEN CONCLUSIVELY RESOLVED TO SPECIFIC FUNCTIONAL VARIANTS. HERE WE REPORT FINE-MAPPING OF 94 INFLAMMATORY BOWEL DISEASE LOCI USING HIGH-DENSITY GENOTYPING IN 67,852 INDIVIDUALS. WE PINPOINT 18 ASSOCIATIONS TO A SINGLE CAUSAL VARIANT WITH GREATER THAN 95% CERTAINTY, AND AN ADDITIONAL 27 ASSOCIATIONS TO A SINGLE VARIANT WITH GREATER THAN 50% CERTAINTY. THESE 45 VARIANTS ARE SIGNIFICANTLY ENRICHED FOR PROTEIN-CODING CHANGES (N = 13), DIRECT DISRUPTION OF TRANSCRIPTION-FACTOR BINDING SITES (N = 3), AND TISSUE-SPECIFIC EPIGENETIC MARKS (N = 10), WITH THE LAST CATEGORY SHOWING ENRICHMENT IN SPECIFIC IMMUNE CELLS AMONG ASSOCIATIONS STRONGER IN CROHN'S DISEASE AND IN GUT MUCOSA AMONG ASSOCIATIONS STRONGER IN ULCERATIVE COLITIS. THE RESULTS OF THIS STUDY SUGGEST THAT HIGH-RESOLUTION FINE-MAPPING IN LARGE SAMPLES CAN CONVERT MANY DISCOVERIES FROM GENOME-WIDE ASSOCIATION STUDIES INTO STATISTICALLY CONVINCING CAUSAL VARIANTS, PROVIDING A POWERFUL SUBSTRATE FOR EXPERIMENTAL ELUCIDATION OF DISEASE MECHANISMS. 2017 14 2400 36 EPIGENETIC REPROGRAMMING OF IMMUNE CELLS IN WOMEN WITH PCOS IMPACT GENES CONTROLLING REPRODUCTIVE FUNCTION. CONTEXT: POLYCYSTIC OVARY SYNDROME (PCOS) IS A CHRONIC DISEASE AFFECTING REPRODUCTIVE FUNCTION AND WHOLE-BODY METABOLISM. ALTHOUGH THE ETIOLOGY IS UNCLEAR, EMERGING EVIDENCE INDICATES THAT THE EPIGENETICS MAY BE A CONTRIBUTING FACTOR. OBJECTIVE: TO DETERMINE THE ROLE OF GLOBAL AND GENOME-WIDE EPIGENETIC MODIFICATIONS IN SPECIFIC IMMUNE CELLS IN PCOS COMPARED WITH CONTROLS AND WHETHER THESE COULD BE RELATED TO CLINICAL FEATURES OF PCOS. DESIGN: CROSS-SECTIONAL STUDY. PARTICIPANTS: WOMEN WITH (N = 17) OR WITHOUT PCOS (N = 17). SETTING: RECRUITED FROM THE GENERAL COMMUNITY. MAIN OUTCOME MEASURES: ISOLATED PERIPHERAL BLOOD MONONUCLEAR CELLS WERE ANALYZED USING MULTICOLOR FLOW CYTOMETRY METHODS TO DETERMINE GLOBAL DNA METHYLATION LEVELS IN A CELL-SPECIFIC FASHION. TRANSCRIPTOMIC AND GENOME-WIDE DNA METHYLATION ANALYSES WERE PERFORMED ON T HELPER CELLS USING RNA SEQUENCING AND REDUCED REPRESENTATION BISULFITE SEQUENCING. RESULTS: WOMEN WITH PCOS HAD LOWER GLOBAL DNA METHYLATION IN MONOCYTES (P = 0.006) AND IN T HELPER (P = 0.004), T CYTOTOXIC (P = 0.004), AND B CELLS (P = 0.03). SPECIFIC GENOME-WIDE DNA METHYLATION ANALYSIS OF T HELPER CELLS FROM WOMEN WITH PCOS IDENTIFIED 5581 DIFFERENTIALLY METHYLATED CPG SITES. FUNCTIONAL GENE ONTOLOGY ENRICHMENT ANALYSIS SHOWED THAT GENES LOCATED AT THE PROXIMITY OF DIFFERENTIALLY METHYLATED CPG SITES BELONG TO PATHWAYS RELATED TO REPRODUCTIVE FUNCTION AND IMMUNE CELL FUNCTION. HOWEVER, THESE GENES WERE NOT ALTERED AT THE TRANSCRIPTOMIC LEVEL. CONCLUSIONS: IT WAS SHOWN THAT PCOS IS ASSOCIATED WITH GLOBAL AND GENE-SPECIFIC DNA METHYLATION REMODELING IN A CELL TYPE-SPECIFIC MANNER. FURTHER INVESTIGATION IS WARRANTED TO DETERMINE WHETHER EPIGENETIC REPROGRAMMING OF IMMUNE CELLS IS IMPORTANT IN DETERMINING THE DIFFERENT PHENOTYPES OF PCOS. 2019 15 5393 45 REDUCED CHROMATIN ACCESSIBILITY TO CD4 T CELL SUPER-ENHANCERS ENCOMPASSING SUSCEPTIBILITY LOCI OF RHEUMATOID ARTHRITIS. BACKGROUND: RHEUMATOID ARTHRITIS (RA) IS AN INFLAMMATORY DISEASE THAT MANIFESTS AS A PRECLINICAL STAGE OF SYSTEMIC AUTOIMMUNITY FOLLOWED BY CHRONIC PROGRESSIVE SYNOVITIS. DISEASE-ASSOCIATED GENETIC SNP VARIANTS PREDOMINANTLY MAP TO NON-CODING, REGULATORY REGIONS OF FUNCTIONAL IMPORTANCE IN CD4 T CELLS, IMPLICATING THESE CELLS AS KEY REGULATORS. A BETTER UNDERSTANDING OF THE EPIGENOME OF CD4 T CELLS HOLDS THE PROMISE OF PROVIDING INFORMATION ON THE INTERACTION BETWEEN GENETIC SUSCEPTIBILITY AND EXOGENOUS FACTORS. METHODS: WE MAPPED REGIONS OF CHROMATIN ACCESSIBILITY USING ATAC-SEQ IN PERIPHERAL CD4 T CELL SUBSETS OF PATIENTS WITH RA (N=18) AND COMPARED THEM TO T CELLS FROM PATIENTS WITH PSORIATIC ARTHRITIS (N=11) AND AGE-MATCHED HEALTHY CONTROLS (N=10). TRANSCRIPTS OF SELECTED GENES WERE QUANTIFIED USING QPCR. FINDINGS: RA-ASSOCIATED EPIGENETIC SIGNATURES WERE IDENTIFIED THAT IN PART OVERLAPPED BETWEEN CENTRAL AND EFFECTOR MEMORY CD4 T CELLS AND THAT WERE TO A LESSER EXTENT ALREADY PRESENT IN NAIVE CELLS. SITES MORE ACCESSIBLE IN RA WERE HIGHLY ENRICHED FOR THE MOTIF OF THE TRANSCRIPTION FACTOR (TF) CTCF SUGGESTING DIFFERENCES IN THE THREE-DIMENSIONAL CHROMATIN STRUCTURE. UNEXPECTEDLY, SITES WITH REDUCED CHROMATIN ACCESSIBILITY WERE ENRICHED FOR MOTIFS OF TFS PERTINENT FOR T CELL FUNCTION. MOST STRIKINGLY, SUPER-ENHANCERS ENCOMPASSING RA-ASSOCIATED SNPS WERE LESS ACCESSIBLE. ANALYSIS OF SELECTED TRANSCRIPTS AND PUBLISHED DNA METHYLATION PATTERNS WERE CONSISTENT WITH THIS FINDING. THE PREFERENTIAL LOSS IN ACCESSIBILITY AT THESE SUPER-ENHANCERS WAS SEEN IN PATIENTS WITH HIGH AND LOW DISEASE ACTIVITY AND ON A VARIETY OF IMMUNOSUPPRESSIVE TREATMENT MODALITIES. INTERPRETATION: DISEASE-ASSOCIATED GENES ARE EPIGENETICALLY LESS POISED TO RESPOND IN CD4 T CELLS FROM PATIENTS WITH ESTABLISHED RA. FUNDING: THIS WORK WAS SUPPORTED BY I01 BX001669 FROM THE VETERANS ADMINISTRATION. 2022 16 1587 30 DNA METHYLATION PROFILING IDENTIFIES NOVEL MARKERS OF PROGRESSION IN HEPATITIS B-RELATED CHRONIC LIVER DISEASE. BACKGROUND: CHRONIC HEPATITIS B INFECTION IS CHARACTERIZED BY HEPATIC IMMUNE AND INFLAMMATORY RESPONSE WITH CONSIDERABLE VARIATION IN THE RATES OF PROGRESSION TO CIRRHOSIS. GENETIC VARIANTS AND ENVIRONMENTAL CUES INFLUENCE PREDISPOSITION TO THE DEVELOPMENT OF CHRONIC LIVER DISEASE; HOWEVER, IT REMAINS UNKNOWN IF ABERRANT DNA METHYLATION IS ASSOCIATED WITH FIBROSIS PROGRESSION IN CHRONIC HEPATITIS B. RESULTS: TO IDENTIFY EPIGENETIC MARKS ASSOCIATED WITH INFLAMMATORY AND FIBROTIC PROCESSES OF THE HEPATITIS B-INDUCED CHRONIC LIVER DISEASE, WE CARRIED OUT HEPATIC GENOME-WIDE METHYLATION PROFILING USING ILLUMINA INFINIUM BEADARRAYS COMPARING MILD AND SEVERE FIBROTIC DISEASE IN A DISCOVERY COHORT OF 29 PATIENTS. WE OBTAINED 310 DIFFERENTIALLY METHYLATED REGIONS AND SELECTED FOUR LOCI COMPRISING THREE GENES FROM THE TOP DIFFERENTIALLY METHYLATED REGIONS: HYPERMETHYLATION OF HOXA2 AND HDAC4 ALONG WITH HYPOMETHYLATION OF PPP1R18 WERE SIGNIFICANTLY LINKED TO SEVERE FIBROSIS. WE REPLICATED THE PROMINENT METHYLATION MARKS IN AN INDEPENDENT COHORT OF 102 PATIENTS BY BISULFITE MODIFICATION AND PYROSEQUENCING. THE TIMING AND CAUSAL RELATIONSHIP OF EPIGENETIC MODIFICATIONS WITH DISEASE SEVERITY WAS FURTHER INVESTIGATED USING A COHORT OF PATIENTS WITH SERIAL BIOPSIES. CONCLUSIONS: OUR FINDINGS SUGGEST A LINKAGE OF WIDESPREAD EPIGENETIC DYSREGULATION WITH DISEASE PROGRESSION IN CHRONIC HEPATITIS B INFECTION. CPG METHYLATION AT NOVEL GENES SHEDS LIGHT ON NEW MOLECULAR PATHWAYS, WHICH CAN BE POTENTIALLY EXPLOITED AS A BIOMARKER OR TARGETED TO ATTENUATE INFLAMMATION AND FIBROSIS. 2016 17 6083 41 THE EFFECT OF SMOKING ON DNA METHYLATION OF PERIPHERAL BLOOD MONONUCLEAR CELLS FROM AFRICAN AMERICAN WOMEN. BACKGROUND: REGULAR SMOKING IS ASSOCIATED WITH A WIDE VARIETY OF SYNDROMES WITH PROMINENT INFLAMMATORY COMPONENTS SUCH AS CANCER, OBESITY AND TYPE 2 DIABETES. HEAVY REGULAR SMOKING IS ALSO ASSOCIATED WITH CHANGES IN THE DNA METHYLATION OF PERIPHERAL MONONUCLEAR CELLS. HOWEVER, IN YOUNGER SMOKERS, INFLAMMATORY EPIGENETIC FINDINGS ARE LARGELY ABSENT WHICH SUGGESTS THE INFLAMMATORY RESPONSE(S) TO SMOKING MAY BE DOSE DEPENDENT. TO HELP UNDERSTAND WHETHER PERIPHERAL MONONUCLEAR CELLS HAVE A ROLE IN MEDIATING THESE RESPONSES IN OLDER SMOKERS WITH HIGHER CUMULATIVE SMOKE EXPOSURE, WE EXAMINED GENOME-WIDE DNA METHYLATION IN A GROUP OF WELL CHARACTERIZED ADULT AFRICAN AMERICAN SUBJECTS INFORMATIVE FOR SMOKING, AS WELL AS SERUM C-REACTIVE PROTEIN (CRP) AND INTERLEUKIN-6 RECEPTOR (IL6R) LEVELS. IN ADDITION, COMPLEMENTARY BIOINFORMATIC ANALYSES WERE CONDUCTED TO DELINEATE POSSIBLE PATHWAYS AFFECTED BY LONG-TERM SMOKING. RESULTS: GENOME-WIDE DNA METHYLATION ANALYSIS WITH RESPECT TO SMOKING STATUS YIELDED 910 SIGNIFICANT LOCI AFTER BENJAMINI-HOCHBERG CORRECTION. IN PARTICULAR, TWO LOCI FROM THE AHRR GENE (CG05575921 AND CG23576855) AND ONE LOCUS FROM THE GPR15 GENE (CG19859270) WERE IDENTIFIED AS HIGHLY SIGNIFICANTLY DIFFERENTIALLY METHYLATED BETWEEN SMOKERS AND NON-SMOKERS. THE BIOINFORMATIC ANALYSES SHOWED THAT LONG-TERM CHRONIC SMOKING IS ASSOCIATED WITH ALTERED PROMOTER DNA METHYLATION OF GENES CODING FOR PROTEINS MAPPING TO CRITICAL SUB-NETWORKS MODERATING INFLAMMATION, IMMUNE FUNCTION, AND COAGULATION. CONCLUSIONS: WE CONCLUDE THAT CHRONIC REGULAR SMOKING IS ASSOCIATED WITH CHANGES IN PERIPHERAL MONONUCLEAR CELL METHYLATION SIGNATURE WHICH PERTURB INFLAMMATORY AND IMMUNE FUNCTION PATHWAYS AND MAY CONTRIBUTE TO INCREASED VULNERABILITY FOR COMPLEX ILLNESSES WITH INFLAMMATORY COMPONENTS. 2014 18 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 19 3031 43 GENETICS OF RHEUMATOID ARTHRITIS. RHEUMATOID ARTHRITIS (RA) IS AN INFLAMMATORY AUTOIMMUNE DISEASE INVOLVING SYMMETRIC JOINTS AND IS GENERALLY CHARACTERIZED BY PERSISTENT PAIN, TENDERNESS, AND DESTRUCTION OF JOINTS. THE VAST MAJORITY OF RA PATIENTS PRODUCE AUTOANTIBODIES, AND IMMUNE CELL INVOLVEMENT IN DISEASE DEVELOPMENT IS WELL RECOGNIZED, AS IS THE CONTRIBUTION OF OTHER TYPES OF CELLS IN SYNOVIAL TISSUE, LIKE FIBROBLASTS. IT IS KNOWN THAT THERE ARE MAJOR GENETIC ASSOCIATIONS WITH THE HLA LOCUS, WHILE MULTIPLE NON-HLA GENETIC VARIANTS DISPLAY RELATIVELY LOW RISK OF RA. BOTH HLA AND NON-HLA ASSOCIATIONS SUGGEST THAT THE PROFILES OF GENETIC ASSOCIATIONS FOR AUTOANTIBODY-POSITIVE VS. AUTOANTIBODY-NEGATIVE RA ARE DIFFERENT. SEVERAL ALLELES OF HLA-DRB1 ARE ASSOCIATED WITH HIGH RISK FOR AUTOANTIBODY-POSITIVE RA, WITH THE STRONGEST RISK CHARACTERIZED BY VALINE AT POSITION 11 OF THE PROTEIN SEQUENCE (HLA-DRB1*04 AND *10 ALLELES). THERE IS A STRONG PROTECTIVE EFFECT FOR THE RISK OF AUTOANTIBODY-POSITIVE RA ASSOCIATED WITH HLA-DRB1*13 ALLELES. ALTHOUGH MAJOR GENETIC ASSOCIATIONS HAVE BEEN KNOWN FOR SEVERAL YEARS, UNDERSTANDING OF THE SPECIFIC MECHANISMS IN THE DEVELOPMENT OF INCREASED RISK OF RA FOR THESE VARIATIONS IS WORK IN PROGRESS. CURRENT STUDIES FOCUS ON THE BINDING OF IMMUNE RECEPTORS INVOLVED IN RECOGNITION OF PUTATIVE PEPTIDES IN ACTIVATION OF T CELLS, AS WELL AS INVESTIGATION OF CELL SIGNALING MECHANISMS. AT LEAST A PART OF RA RISK COULD BE EXPLAINED BY GENE-GENE AND GENE-ENVIRONMENT INTERACTIONS. THERE ARE CURRENTLY MORE THAN 150 CANDIDATE LOCI WITH POLYMORPHISMS THAT ASSOCIATE WITH RA, MAINLY RELATED TO SEROPOSITIVE DISEASE, AND NEW DISCOVERIES ARE ANTICIPATED IN THE FUTURE FROM INVESTIGATION OF DIVERSE HUMAN POPULATIONS. THIS NEW RESEARCH WILL HELP CREATE A STRONG FOUNDATION FOR THE CONTINUING PROCESS OF INTEGRATING GENETIC, EPIGENETIC, TRANSCRIPTOMIC, AND PROTEOMIC DATA IN STUDIES OF RA. 2022 20 2620 39 EPIGENOME-WIDE ASSOCIATION DATA IMPLICATES DNA METHYLATION-MEDIATED GENETIC RISK IN PSORIASIS. BACKGROUND: PSORIASIS IS A CHRONIC INFLAMMATORY SKIN DISEASE CHARACTERIZED BY EPIDERMAL HYPERPROLIFERATION AND ALTERED KERATINOCYTE DIFFERENTIATION AND INFLAMMATION AND IS CAUSED BY THE INTERPLAY OF GENETIC AND ENVIRONMENTAL FACTORS. PREVIOUS STUDIES HAVE REVEALED THAT DNA METHYLATION (DNAM) AND GENETIC MAKERS ARE CLOSELY ASSOCIATED WITH PSORIASIS, AND STRONG EVIDENCES HAVE SHOWN THAT DNAM CAN BE CONTROLLED BY GENETIC FACTORS, WHICH ATTRACTED US TO EVALUATE THE RELATIONSHIP AMONG DNAM, GENETIC MAKERS, AND DISEASE STATUS. METHODS: WE UTILIZED THE GENOME-WIDE METHYLATION DATA OF PSORIATIC SKIN (PP, N = 114) AND UNAFFECTED CONTROL SKIN (NN, N = 62) TISSUE SAMPLES IN OUR PREVIOUS STUDY, AND WE PERFORMED WHOLE-GENOME GENOTYPING WITH PERIPHERAL BLOOD OF THE SAME SAMPLES TO EVALUATE THE UNDERLYING GENETIC EFFECT ON SKIN DNA METHYLATION. CAUSAL INFERENCE TEST (CIT) WAS USED TO ASSESS WHETHER DNAM REGULATE GENETIC VARIATION AND GAIN A BETTER UNDERSTANDING OF THE EPIGENETIC BASIS OF PSORIASIS SUSCEPTIBILITY. RESULTS: WE IDENTIFIED 129 SNP-CPG PAIRS ACHIEVING THE SIGNIFICANT ASSOCIATION THRESHOLD, WHICH CONSTITUTED 28 UNIQUE METHYLATION QUANTITATIVE TRAIT LOCI (METHQTL) AND 34 UNIQUE CPGS. THERE ARE 18 SNPS WERE ASSOCIATED WITH PSORIASIS AT A BONFERONI-CORRECTED P < 0.05, AND THESE 18 SNPS FORMED 93 SNP-CPG PAIRS WITH 17 UNIQUE CPG SITES. WE FOUND THAT 11 OF 93 SNP-CPG PAIRS, COMPOSED OF 5 UNIQUE SNPS AND 3 CPG SITES, PRESENTED A METHYLATION-MEDIATED RELATIONSHIP BETWEEN SNPS AND PSORIASIS. THE 3 CPG SITES WERE LOCATED ON THE BODY OF C1ORF106, THE TSS1500 PROMOTER REGION OF DMBX1 AND THE BODY OF SIK3. CONCLUSIONS: THIS STUDY REVEALED THAT DNAM OF SOME GENES CAN BE CONTROLLED BY GENETIC FACTORS AND ALSO MEDIATE RISK VARIATION FOR PSORIASIS IN CHINESE HAN POPULATION AND PROVIDED NOVEL MOLECULAR INSIGHTS INTO THE PATHOGENESIS OF PSORIASIS. 2016