1 1527 127 DNA METHYLATION CHANGES IN LUNG IMMUNE CELLS ARE ASSOCIATED WITH GRANULOMATOUS LUNG DISEASE. EPIGENETIC MARKS ARE LIKELY TO EXPLAIN VARIABILITY OF RESPONSE TO ANTIGEN IN GRANULOMATOUS LUNG DISEASE. THE OBJECTIVE OF THIS STUDY WAS TO IDENTIFY DNA METHYLATION AND GENE EXPRESSION CHANGES ASSOCIATED WITH CHRONIC BERYLLIUM DISEASE (CBD) AND SARCOIDOSIS IN LUNG CELLS OBTAINED BY BAL. BAL CELLS FROM CBD (N = 8), BERYLLIUM-SENSITIZED (N = 8), SARCOIDOSIS (N = 8), AND ADDITIONAL PROGRESSIVE SARCOIDOSIS (N = 9) AND REMITTING (N = 15) SARCOIDOSIS WERE PROFILED ON THE ILLUMINA 450K METHYLATION AND AFFYMETRIX/AGILENT GENE EXPRESSION MICROARRAYS. STATISTICAL ANALYSES WERE PERFORMED TO IDENTIFY DNA METHYLATION AND GENE EXPRESSION CHANGES ASSOCIATED WITH CBD, SARCOIDOSIS, AND DISEASE PROGRESSION IN SARCOIDOSIS. DNA METHYLATION ARRAY FINDINGS WERE VALIDATED BY PYROSEQUENCING. WE IDENTIFIED 52,860 SIGNIFICANT (P < 0.005 AND Q < 0.05) CPGS ASSOCIATED WITH CBD; 2,726 CPGS NEAR 1,944 UNIQUE GENES HAVE GREATER THAN 25% METHYLATION CHANGE. A TOTAL OF 69% OF DIFFERENTIALLY METHYLATED GENES ARE SIGNIFICANTLY (Q < 0.05) DIFFERENTIALLY EXPRESSED IN CBD, WITH MANY CANONICAL INVERSE RELATIONSHIPS OF METHYLATION AND EXPRESSION IN GENES CRITICAL TO T-HELPER CELL TYPE 1 DIFFERENTIATION, CHEMOKINES AND THEIR RECEPTORS, AND OTHER GENES INVOLVED IN IMMUNITY. TESTING OF THESE CBD-ASSOCIATED CPGS IN SARCOIDOSIS REVEALS THAT METHYLATION CHANGES ONLY APPROACH SIGNIFICANCE, BUT ARE METHYLATED IN THE SAME DIRECTION, SUGGESTING SIMILARITIES BETWEEN THE TWO DISEASES WITH MORE HETEROGENEITY IN SARCOIDOSIS THAT LIMITS POWER WITH THE CURRENT SAMPLE SIZE. ANALYSIS OF PROGRESSIVE VERSUS REMITTING SARCOIDOSIS IDENTIFIED 15,215 CPGS (P < 0.005 AND Q < 0.05), BUT ONLY 801 OF THEM HAVE GREATER THAN 5% METHYLATION CHANGE, DEMONSTRATING THAT DNA METHYLATION MARKS OF DISEASE PROGRESSION CHANGES ARE MORE SUBTLE. OUR STUDY HIGHLIGHTS THE SIGNIFICANCE OF EPIGENETIC MARKS IN LUNG IMMUNE RESPONSE IN GRANULOMATOUS LUNG DISEASE. 2019 2 1215 45 CPG PROMOTER METHYLATION STATUS IS NOT A PROGNOSTIC INDICATOR OF GENE EXPRESSION IN BERYLLIUM CHALLENGE. INDIVIDUALS EXPOSED TO BERYLLIUM (BE) MAY DEVELOP BE SENSITIZATION (BES) AND PROGRESS TO CHRONIC BERYLLIUM DISEASE (CBD). RECENT STUDIES WITH OTHER METAL ANTIGENS SUGGEST EPIGENETIC MECHANISMS MAY BE INVOLVED IN INFLAMMATORY DISEASE PROCESSES, INCLUDING GRANULOMATOUS LUNG DISORDERS AND THAT A NUMBER OF METAL CATIONS ALTER GENE METHYLATION. THE OBJECTIVE OF THIS STUDY WAS TO DETERMINE IF BE CAN EXERT AN EPIGENETIC EFFECT ON GENE EXPRESSION BY ALTERING METHYLATION IN THE PROMOTER REGION OF SPECIFIC GENES KNOWN TO BE INVOLVED IN BE ANTIGEN-MEDIATED GENE EXPRESSION. TO INVESTIGATE THIS OBJECTIVE, THREE MACROPHAGE TUMOR MOUSE CELL LINES KNOWN TO DIFFERENTIALLY PRODUCE TUMOR NECROSIS FACTOR (TNF)-ALPHA, BUT NOT INTERFERON (IFN)-GAMMA, IN RESPONSE TO BE ANTIGEN WERE CULTURED WITH BE OR CONTROLS. FOLLOWING CHALLENGES, ELISA WERE PERFORMED TO QUANTIFY INDUCED TNFALPHA AND IFNGAMMA EXPRESSION. BISULFATE-CONVERTED DNA WAS EVALUATED BY PYROSEQUENCING TO QUANTIFY CPG METHYLATION WITHIN THE PROMOTERS OF TNFALPHA AND IFNGAMMA. BE-CHALLENGED H36.12J CELLS EXPRESSED HIGHER LEVELS OF TNFALPHA COMPARED TO EITHER H36.12E CELLS OR P388D.1 CELLS. HOWEVER, THERE WERE NO VARIATIONS IN TNFALPHA PROMOTER CPG METHYLATION LEVELS BETWEEN CELL LINES AT THE SIX CPG SITES TESTED. H36.12J CELL TNFALPHA EXPRESSION WAS SHOWN TO BE METAL-SPECIFIC BY THE INDUCTION OF SIGNIFICANTLY MORE TNFALPHA WHEN EXPOSED TO BE THAN WHEN EXPOSED TO ALUMINUM SULFATE, OR NICKEL (II) CHLORIDE, BUT NOT WHEN EXPOSED TO COBALT (II) CHLORIDE. HOWEVER, H36.12J CELL METHYLATION LEVELS AT THE SIX CPG SITES EXAMINED IN THE TNFALPHA PROMOTER DID NOT CORRELATE WITH CYTOKINE EXPRESSION DIFFERENCES. NONETHELESS, ALL THREE CELL LINES HAD SIGNIFICANTLY MORE PROMOTER METHYLATION AT THE SIX CPG SITES INVESTIGATED WITHIN THE IFNGAMMA PROMOTER (A GENE THAT IS NOT EXPRESSED) WHEN COMPARED TO THE SIX CPG SITES INVESTIGATED IN THE TNFALPHA PROMOTER, REGARDLESS OF TREATMENT CONDITION (P < 1.17 X 10(-9)). THESE FINDINGS SUGGEST THAT, IN THIS CELL SYSTEM, PROMOTER HYPO-METHYLATION MAY BE NECESSARY TO ALLOW EXPRESSION OF METAL-INDUCED TNFALPHA AND THAT PROMOTER HYPER-METHYLATION IN THE IFNGAMMA PROMOTER MAY INTERFERE WITH EXPRESSION. ALSO, AT THE DOZEN CPG SITES INVESTIGATED IN THE PROMOTER REGIONS OF BOTH GENES, BERYLLIUM HAD NO IMPACT ON PROMOTER METHYLATION STATUS, DESPITE ITS ABILITY TO INDUCE PRO-INFLAMMATORY CYTOKINE EXPRESSION. 2016 3 184 27 ACCOUNTING FOR TRANSGENERATIONAL EFFECTS OF TOXICANT EXPOSURE IN POPULATION MODELS ALTERS THE PREDICTED LONG-TERM POPULATION STATUS. ACUTE ENVIRONMENTAL STRESSORS SUCH AS SHORT-TERM EXPOSURE TO POLLUTANTS CAN HAVE LASTING EFFECTS ON ORGANISMS, POTENTIALLY IMPACTING FUTURE GENERATIONS. PARENTAL EXPOSURE TO TOXICANTS CAN RESULT IN CHANGES TO THE EPIGENOME (E.G., DNA METHYLATION) THAT ARE PASSED DOWN TO SUBSEQUENT, UNEXPOSED GENERATIONS. HOWEVER, IT IS DIFFICULT TO GAUGE THE CUMULATIVE POPULATION-SCALE IMPACTS OF EPIGENETIC EFFECTS FROM LABORATORY EXPERIMENTS ALONE. HERE, WE DEVELOPED A SIZE- AND AGE-STRUCTURED DELAY-COORDINATE POPULATION MODEL TO EVALUATE THE LONG-TERM CONSEQUENCES OF EPIGENETIC MODIFICATIONS ON POPULATION SUSTAINABILITY. THE MODEL EMULATED CHANGES IN GROWTH, MORTALITY, AND FECUNDITY IN THE F0, F1, AND F2 GENERATIONS OBSERVED IN EXPERIMENTS IN WHICH LARVAL MENIDIA BERYLLINA WERE EXPOSED TO ENVIRONMENTALLY RELEVANT CONCENTRATIONS OF BIFENTHRIN (BIF), ETHINYLESTRADIOL (EE2), LEVONORGESTREL (LV), OR TRENBOLONE (TB) IN THE PARENT GENERATION (F0) AND REARED IN CLEAN WATER UP TO THE F2 GENERATION. OUR ANALYSIS SUGGESTS POTENTIALLY DRAMATIC POPULATION-LEVEL EFFECTS OF REPEATED, CHRONIC EXPOSURES OF EARLY-LIFE STAGE FISH THAT ARE NOT CAPTURED BY MODELS NOT ACCOUNTING FOR THOSE EFFECTS. SIMULATED EXPOSURES LED TO SUBSTANTIAL DECLINES IN POPULATION ABUNDANCE (LV AND BIF) OR NEAR-EXTINCTION (EE2 AND TB) WITH THE EXACT TRAJECTORY AND TIMELINE OF POPULATION DECLINE DEPENDENT ON THE COMBINATION OF F0, F1, AND F2 EFFECTS PRODUCED BY EACH COMPOUND. EVEN ACUTE ONE-TIME EXPOSURES OF EACH COMPOUND LED TO DECLINES AND RECOVERY OVER MULTIPLE YEARS DUE TO LAGGED EPIGENETIC EFFECTS. THESE RESULTS DEMONSTRATE THE POTENTIAL FOR ENVIRONMENTALLY RELEVANT CONCENTRATIONS OF COMMONLY USED COMPOUNDS TO IMPACT THE POPULATION DYNAMICS AND SUSTAINABILITY OF AN ECOLOGICALLY RELEVANT SPECIES AND MODEL ORGANISM. 2022 4 2514 29 EPIGENETICS AND SARCOIDOSIS. EPIGENETIC MODIFICATIONS ARE EMERGING AS IMPORTANT REGULATORY MECHANISMS OF GENE EXPRESSION IN LUNG DISEASE, GIVEN THAT THEY ARE INFLUENCED BY ENVIRONMENTAL EXPOSURES AND GENETIC VARIANTS, AND THAT THEY REGULATE IMMUNE AND FIBROTIC PROCESSES. IN THIS REVIEW, WE INTRODUCE THESE CONCEPTS WITH A FOCUS ON THE STUDY OF DNA METHYLATION AND HISTONE MODIFICATIONS AND DISCUSS HOW THEY HAVE BEEN APPLIED TO LUNG DISEASE, AND HOW THEY CAN BE APPLIED TO SARCOIDOSIS. THIS INFORMATION HAS IMPLICATIONS FOR OTHER EXPOSURE AND IMMUNOLOGICALLY MEDIATED LUNG DISEASES, SUCH AS CHRONIC BERYLLIUM DISEASE, HYPERSENSITIVITY PNEUMONITIS, AND ASBESTOSIS. 2021 5 3301 21 HIGH-FAT OR ETHINYL-OESTRADIOL INTAKE DURING PREGNANCY INCREASES MAMMARY CANCER RISK IN SEVERAL GENERATIONS OF OFFSPRING. MATERNAL EXPOSURES TO ENVIRONMENTAL FACTORS DURING PREGNANCY INFLUENCE THE RISK OF MANY CHRONIC ADULT-ONSET DISEASES IN THE OFFSPRING. HERE WE INVESTIGATE WHETHER FEEDING PREGNANT RATS A HIGH-FAT (HF)- OR ETHINYL-OESTRADIOL (EE2)-SUPPLEMENTED DIET AFFECTS CARCINOGEN-INDUCED MAMMARY CANCER RISK IN DAUGHTERS, GRANDDAUGHTERS AND GREAT-GRANDDAUGHTERS. WE SHOW THAT MAMMARY TUMOURIGENESIS IS HIGHER IN DAUGHTERS AND GRANDDAUGHTERS OF HF RAT DAMS AND IN DAUGHTERS AND GREAT-GRANDDAUGHTERS OF EE2 RAT DAMS. OUTCROSS EXPERIMENTS SUGGEST THAT THE INCREASE IN MAMMARY CANCER RISK IS TRANSMITTED TO HF GRANDDAUGHTERS EQUALLY THROUGH THE FEMALE OR MALE GERM LINES, BUT IT IS ONLY TRANSMITTED TO EE2 GRANDDAUGHTERS THROUGH THE FEMALE GERM LINE. THE EFFECTS OF MATERNAL EE2 EXPOSURE ON OFFSPRING'S MAMMARY CANCER RISK ARE ASSOCIATED WITH CHANGES IN THE DNA METHYLATION MACHINERY AND METHYLATION PATTERNS IN MAMMARY TISSUE OF ALL THREE EE2 GENERATIONS. WE CONCLUDE THAT DIETARY AND OESTROGENIC EXPOSURES IN PREGNANCY INCREASE BREAST CANCER RISK IN MULTIPLE GENERATIONS OF OFFSPRING, POSSIBLY THROUGH EPIGENETIC MEANS. 2012 6 974 28 CHRONIC OCCUPATIONAL EXPOSURE ENDURED BY TOBACCO FARMERS FROM BRAZIL AND ASSOCIATION WITH DNA DAMAGE. TOBACCO FARMING IS AN IMPORTANT ECONOMIC INCOME IN BRAZIL, ALTHOUGH IT HAS BEEN CHALLENGED AS REGARD THE OCCUPATIONAL EXPOSURE TO BOTH PESTICIDES AND NICOTINE ENDURED BY FARMERS. CHRONIC OCCUPATIONAL EXPOSURE TO COMPLEX MIXTURES CAN LEAD TO HEALTH HAZARDOUS. WE EXAMINED GENOMIC INSTABILITY AND EPIGENETIC CHANGES IN TOBACCO FARMERS OCCUPATIONALLY EXPOSED TO PESTICIDE MIXTURES AND NICOTINE AT TOBACCO FIELDS. DNA DAMAGE WAS ASSESSED BY ALKALINE COMET ASSAY IN BLOOD CELLS. GENOMIC DNA WAS ISOLATED, AND TELOMERE LENGTH WAS MEASURED USING QUANTITATIVE POLYMERASE CHAIN REACTION ASSAY. WE MEASURED 5-METHYL-2'-DEOXYCYTIDINE, A MARKER OF GLOBAL DNA METHYLATION, AND P16 PROMOTER METHYLATION. THE OXIDATIVE PROFILE WAS EVALUATED BY TROLOX EQUIVALENT ANTIOXIDANT CAPACITY AND LIPID PEROXIDATION (THIOBARBITURIC ACID REACTIVE SUBSTANCES) IN SERUM. EXPOSURE PARAMETERS, PLASMA COTININE AND INORGANIC ELEMENT LEVELS, WERE ALSO MEASURED. DNA DAMAGE WAS SIGNIFICANTLY ELEVATED FOR FARMERS IN RELATION TO UNEXPOSED GROUP (P < 0.001; MANN-WHITNEY TEST) AND POSITIVELY ASSOCIATED WITH YEARS OF EXPOSURE. INVERSE RELATIONSHIP BETWEEN DNA DAMAGE AND TOTAL EQUIVALENT ANTIOXIDANT ACTIVITY WAS DEMONSTRATED FOR EXPOSED AND UNEXPOSED GROUPS. EXPOSED GROUP SHOWED SIGNIFICANTLY SHORTER TELOMERES (P < 0.001; UNPAIRED T-TEST) AND DNA HYPOMETHYLATION (P < 0.001; UNPAIRED T-TEST), AS WELL AS P16 HYPERMETHYLATION (P = 0.003; MANN-WHITNEY TEST). LIPID PEROXIDATION WAS INCREASED FOR EXPOSED GROUP IN RELATION TO UNEXPOSED ONE (P = 0.02; MANN-WHITNEY TEST) AND PRESENTED A POSITIVE CORRELATION WITH GLOBAL DNA METHYLATION (P = 0.0264). FARMERS HAVE INCREASED PLASMA COTININE LEVELS (P < 0.001) AND INORGANIC ELEMENTS (PHOSPHORUS, SULPHUR AND CHLORINE) IN RELATION TO UNEXPOSED GROUP. ELEVATED OXIDATIVE STRESS LEVELS DUE TO CHRONIC OCCUPATIONAL PESTICIDE MIXTURES AND NICOTINE EXPOSURE IN TOBACCO FARMERS WERE ASSOCIATED WITH HIGHER DNA DAMAGE, SHORTER TELOMERES AND ALTERED DNA METHYLATION. TELOMERE-ACCELERATED ATTRITION DUE TO EXPOSURE MAY BE POTENTIAL INTERMEDIATE STEP BEFORE A DISEASE STATE. 2018 7 1980 32 EPIGENETIC ALTERATIONS IN CYTOCHROME P450 OXIDOREDUCTASE (POR) IN SPERM OF RATS EXPOSED TO TETRAHYDROCANNABINOL (THC). AS MARIJUANA LEGALIZATION IS INCREASING, RESEARCH REGARDING POSSIBLE LONG-TERM RISKS FOR USERS AND THEIR OFFSPRING IS NEEDED. LITTLE DATA EXISTS ON EFFECTS OF PATERNAL TETRAHYDROCANNABINOL (THC) EXPOSURE PRIOR TO REPRODUCTION. THIS STUDY DETERMINED IF CHRONIC THC EXPOSURE ALTERS SPERM DNA METHYLATION (DNAM) AND IF SUCH EFFECTS ARE INTERGENERATIONALLY TRANSMITTED. ADULT MALE RATS UNDERWENT ORAL GAVAGE WITH THC OR VEHICLE CONTROL. DIFFERENTIALLY METHYLATED (DM) LOCI IN MOTILE SPERM WERE IDENTIFIED USING REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS). ANOTHER COHORT WAS INJECTED WITH VEHICLE OR THC, AND SPERM DNAM WAS ANALYZED. FINALLY, THC-EXPOSED AND CONTROL ADULT MALE RATS WERE MATED WITH THC-NAIVE FEMALES. DNAM LEVELS OF TARGET GENES IN BRAIN TISSUES OF THE OFFSPRING WERE DETERMINED BY PYROSEQUENCING. RRBS IDENTIFIED 2,940 DM CPGS MAPPING TO 627 GENES. SIGNIFICANT HYPERMETHYLATION WAS CONFIRMED (P < 0.05) FOLLOWING ORAL THC ADMINISTRATION FOR CYTOCHROME P450 OXIDOREDUCTASE (POR), INVOLVED IN TOXIN PROCESSING AND DISORDERS OF SEXUAL DEVELOPMENT. POR HYPERMETHYLATION WAS NOT OBSERVED AFTER THC INJECTION OR IN THE SUBSEQUENT GENERATION. THESE RESULTS SUPPORT THAT THC ALTERS DNAM IN SPERM AND THAT ROUTE OF EXPOSURE CAN HAVE DIFFERENTIAL EFFECTS. ALTHOUGH WE DID NOT OBSERVE EVIDENCE OF INTERGENERATIONAL TRANSMISSION OF THE DNAM CHANGE, LARGER STUDIES ARE REQUIRED TO DEFINITIVELY EXCLUDE THIS POSSIBILITY. 2020 8 521 40 ASSOCIATIONS BETWEEN MATERNAL PSYCHOSOCIAL STRESS, DNA METHYLATION, AND NEWBORN BIRTH WEIGHT IDENTIFIED BY INVESTIGATING METHYLATION AT INDIVIDUAL, REGIONAL, AND GENOME LEVELS. STRESS IS KNOWN TO AFFECT HEALTH THROUGHOUT LIFE AND INTO FUTURE GENERATIONS, BUT THE UNDERLYING MOLECULAR MECHANISMS ARE UNKNOWN. WE TESTED THE HYPOTHESIS THAT MATERNAL PSYCHOSOCIAL STRESS INFLUENCES DNA METHYLATION (DNAM), WHICH IN TURN IMPACTS NEWBORN HEALTH OUTCOMES. SPECIFICALLY, WE ANALYZED DNAM AT INDIVIDUAL, REGIONAL, AND GENOME-WIDE LEVELS TO TEST FOR ASSOCIATIONS WITH MATERNAL STRESS AND NEWBORN BIRTH WEIGHT. MATERNAL VENOUS BLOOD AND NEWBORN CORD BLOOD (N = 24 AND 22, RESPECTIVELY) WERE ASSAYED FOR METHYLATION AT APPROXIMATELY 450,000 CPG SITES. METHYLATION WAS ANALYZED BY EXAMINING CPG SITES INDIVIDUALLY IN AN EPIGENOME-WIDE ASSOCIATION STUDY (EWAS), AS REGIONAL GROUPS USING VARIABLY METHYLATED REGION (VMR) ANALYSIS IN MATERNAL BLOOD ONLY, AND THROUGH THE EPIGENOME-WIDE MEASURES USING GENOME-WIDE MEAN METHYLATION (GMM), HORVATH'S EPIGENETIC CLOCK, AND MITOTIC AGE. THESE METHYLATION MEASURES WERE TESTED FOR ASSOCIATION WITH THREE MEASURES OF MATERNAL STRESS (MATERNAL WAR TRAUMA, CHRONIC STRESS, AND EXPERIENCE OF SEXUAL VIOLENCE) AND ONE HEALTH OUTCOME (NEWBORN BIRTH WEIGHT). WE OBSERVED THAT MATERNAL EXPERIENCES OF WAR TRAUMA, CHRONIC STRESS, AND SEXUAL ASSAULT WERE EACH ASSOCIATED WITH DECREASED NEWBORN BIRTH WEIGHT (P < 1.95 X 10(-7) IN ALL CASES). TESTING INDIVIDUAL CPG SITES USING EWAS, WE OBSERVED NO ASSOCIATIONS BETWEEN DNAM AND ANY MEASURE OF MATERNAL STRESS OR NEWBORN BIRTH WEIGHT IN EITHER MATERNAL OR CORD BLOOD, AFTER BONFERRONI MULTIPLE TESTING CORRECTION. HOWEVER, THE TOP-RANKED CPG SITE IN MATERNAL BLOOD THAT ASSOCIATED WITH MATERNAL CHRONIC STRESS AND SEXUAL VIOLENCE BEFORE MULTIPLE TESTING CORRECTION IS LOCATED NEAR THE SPON1 GENE. TESTING AT A REGIONAL LEVEL, WE FOUND INCREASED METHYLATION OF A VMR IN MATERNAL BLOOD NEAR SPON1 THAT WAS ASSOCIATED WITH CHRONIC STRESS AND SEXUAL VIOLENCE AFTER BONFERRONI MULTIPLE TESTING CORRECTION (P = 1.95 X 10(-7) AND 8.3 X 10(-6), RESPECTIVELY). AT THE EPIGENOMIC LEVEL, CORD BLOOD GMM WAS ASSOCIATED WITH SIGNIFICANTLY HIGHER LEVELS OF WAR TRAUMA (P = 0.025) AND WAS SUGGESTIVELY ASSOCIATED WITH SEXUAL VIOLENCE (P = 0.053). THE OTHER TWO EPIGENOME-WIDE MEASURES WERE NOT ASSOCIATED WITH MATERNAL STRESS OR NEWBORN BIRTH WEIGHT IN EITHER TISSUE TYPE. DESPITE OUR SMALL SAMPLE SIZE, WE IDENTIFIED ASSOCIATIONS EVEN AFTER CONSERVATIVE MULTIPLE TESTING CORRECTION. SPECIFICALLY, WE FOUND ASSOCIATIONS BETWEEN DNAM AND THE THREE MEASURES OF MATERNAL STRESS ACROSS BOTH TISSUES; SPECIFICALLY, A VMR IN MATERNAL BLOOD AND GMM IN CORD BLOOD WERE BOTH ASSOCIATED WITH DIFFERENT MEASURES OF MATERNAL STRESS. THE ASSOCIATION OF CORD BLOOD GMM, BUT NOT MATERNAL BLOOD GMM, WITH MATERNAL STRESS MAY SUGGEST DIFFERENT RESPONSES TO STRESS IN MOTHER AND NEWBORN. IT IS NOTEWORTHY THAT WE FOUND ASSOCIATIONS ONLY WHEN CPG SITES WERE ANALYZED IN AGGREGATE, EITHER AS VMRS OR AS A BROAD SUMMARY MEASURE OF GMM. 2019 9 4077 21 MATERNAL INFLAMMATION INDUCES SPATIAL LEARNING AND MEMORY IMPAIRMENT IN THE F1 AND F2 GENERATIONS OF MICE VIA SEX-SPECIFIC EPIGENETIC MECHANISMS. MOUNTING EVIDENCE INDICATES THAT HISTONE MODIFICATIONS ARE INVOLVED IN AGING-ASSOCIATED COGNITIVE DECLINE (AACD) AND CAN BE TRANSMITTED TO OFFSPRING OVER MULTIPLE GENERATIONS UNDER CONDITIONS OF STRESS. HERE, WE INVESTIGATED THE EFFECTS OF MATERNAL SUB-CHRONIC INFLAMMATION CAUSED BY LIPOPOLYSACCHARIDE (LPS) ON AACD AND HISTONE MODIFICATIONS IN THE F1 AND F2 GENERATIONS OF EXPERIMENTAL MICE AS WELL AS THE POTENTIAL SEX SPECIFICITY OF INTERGENERATIONAL EFFECTS. IN BRIEF, F0-GENERATION CD-1 DAMS WERE EXPOSED TO LPS (50 MICROG/KG) OR SALINE (CON) DURING LATE PREGNANCY. SUBSEQUENTLY, F1 MALES AND FEMALES (AT 2 MONTHS-OF-AGE) FROM THE LPS TREATMENT GROUP WERE MATED WITH NON-LITTERMATES FROM THE LPS GROUP OR WILD-TYPE MICE TO PRODUCE F2 GENERATIONS OF PARENTAL- (F2-LPS(2)), PATERNAL- (F2M-LPS(1)) AND MATERNAL-ORIGIN (F2F-LPS(1)) MICE. THEN, CON-F1 MALES AND FEMALES WERE MATED WITH WILD-TYPE MICE TO GENERATE F2 GENERATIONS OF PATERNAL- (F2M-CON(1)) AND MATERNAL-ORIGIN (F2F-CON(1)). NEXT, WE EVALUATED THE COGNITIVE ABILITY AND LEVELS OF HIPPOCAMPAL H4K12AC AND H3K9ME3 IN THE F1 AND F2 OFFSPRING AT 3- AND 13 MONTHS-OF-AGE. OVERALL, F1 MALE AND FEMALE LPS GROUPS PRESENTED WITH ELEVATED CORTICOSTERONE (P < 0.001, P = 0.036, P = 0.025, 0.012, RESPECTIVELY) AND CYTOKINE RESPONSES, POORER COGNITIVE PERFORMANCE (ALL P < 0.05) AND H3K9 HYPERMETHYLATION AND H4K12 HYPOACETYLATION IN THE DORSAL HIPPOCAMPUS (ALL P < 0.05); THESE ISSUES WERE CARRIED OVER TO THE F2 GENERATION VIA THE PARENTS, PREDOMINANTLY IN THE PATERNAL LINEAGE. MOREOVER, THE LEVELS OF H3K9ME3 AND H4K12AC WERE SIGNIFICANT CORRELATED WITH COGNITIVE PERFORMANCE (ALL P < 0.05), REGARDLESS OF WHETHER INFLAMMATORY INSULTS HAD BEEN INCURRED DIRECTLY OR INDIRECTLY. THESE FINDINGS INDICATED THAT GESTATIONAL INFLAMMATORY INSULTS IN THE F0 GENERATION ACCELERATED AACD IN THE F2 GENERATION, ALONG WITH H3K9 HYPERMETHYLATION AND H4K12 HYPOACETYLATION IN THE HIPPOCAMPUS, AND THAT THESE ISSUES WERE DERIVED FROM THE F1 PARENTS, ESPECIALLY FROM THE F1 FATHERS. 2022 10 3007 27 GENETIC, IMMUNOLOGIC, AND ENVIRONMENTAL BASIS OF SARCOIDOSIS. SARCOIDOSIS IS A MULTISYSTEM DISEASE WITH TREMENDOUS HETEROGENEITY IN DISEASE MANIFESTATIONS, SEVERITY, AND CLINICAL COURSE THAT VARIES AMONG DIFFERENT ETHNIC AND RACIAL GROUPS. TO BETTER UNDERSTAND THIS DISEASE AND TO IMPROVE THE OUTCOMES OF PATIENTS, A NATIONAL HEART, LUNG, AND BLOOD INSTITUTE WORKSHOP WAS CONVENED TO ASSESS THE CURRENT STATE OF KNOWLEDGE, GAPS, AND RESEARCH NEEDS ACROSS THE CLINICAL, GENETIC, ENVIRONMENTAL, AND IMMUNOLOGIC ARENAS. WE ALSO EXPLORED TO WHAT EXTENT THE INTERPLAY OF THE GENETIC, ENVIRONMENTAL, AND IMMUNOLOGIC FACTORS COULD EXPLAIN THE DIFFERENT PHENOTYPES AND OUTCOMES OF PATIENTS WITH SARCOIDOSIS, INCLUDING THE CHRONIC PHENOTYPES THAT HAVE THE GREATEST HEALTHCARE BURDEN. THE POTENTIAL USE OF CURRENT GENETIC, EPIGENETIC, AND IMMUNOLOGIC TOOLS ALONG WITH STUDY APPROACHES THAT INTEGRATE ENVIRONMENTAL EXPOSURES AND PRECISE CLINICAL PHENOTYPING WERE ALSO EXPLORED. FINALLY, WE MADE EXPERT PANEL-BASED CONSENSUS RECOMMENDATIONS FOR RESEARCH APPROACHES AND PRIORITIES TO IMPROVE OUR UNDERSTANDING OF THE EFFECT OF THESE FACTORS ON THE HEALTH OUTCOMES IN SARCOIDOSIS. 2017 11 308 33 ALCOHOL AND DNA METHYLATION: AN EPIGENOME-WIDE ASSOCIATION STUDY IN BLOOD AND NORMAL BREAST TISSUE. THE BIOLOGICAL MECHANISMS DRIVING ASSOCIATIONS BETWEEN ALCOHOL CONSUMPTION AND CHRONIC DISEASES MIGHT INCLUDE EPIGENETIC MODIFICATION OF DNA METHYLATION. WE EXPLORED THE HYPOTHESIS THAT ALCOHOL CONSUMPTION IS ASSOCIATED WITH METHYLATION IN AN EPIGENOME-WIDE ASSOCIATION STUDY OF BLOOD AND NORMAL BREAST TISSUE DNA. INFINIUM HUMANMETHYLATION450 BEADCHIP (ILLUMINA INC., SAN DIEGO, CALIFORNIA) ARRAY DATA ON BLOOD DNA METHYLATION WAS EXAMINED IN A DISCOVERY SET OF 2,878 NON-HISPANIC WHITE WOMEN FROM THE SISTER STUDY (UNITED STATES, 2004-2015) WHO PROVIDED DETAILED QUESTIONNAIRE INFORMATION ON LIFETIME ALCOHOL USE. ROBUST LINEAR REGRESSION MODELING WAS USED TO IDENTIFY SIGNIFICANT ASSOCIATIONS (FALSE DISCOVERY RATE OF Q < 0.05) BETWEEN THE NUMBER OF ALCOHOLIC DRINKS PER WEEK AND DNA METHYLATION AT 5,458 CYTOSINE-PHOSPHATE-GUANINE (CPG) SITES. ASSOCIATIONS WERE REPLICATED (P < 0.05) FOR 677 CPGS IN AN INDEPENDENT SET OF 187 BLOOD DNA SAMPLES FROM THE SISTER STUDY AND FOR 628 CPGS IN AN INDEPENDENT SET OF 171 NORMAL BREAST DNA SAMPLES; 1,207 CPGS WERE REPLICATED IN EITHER BLOOD OR NORMAL BREAST, WITH 98 CPGS REPLICATED IN BOTH TISSUES. INDIVIDUAL GENE EFFECTS WERE NOTABLE FOR PHOSPHOGLYCERATE DEHYDROGENASE (PGHDH), PEPTIDYL-PROLYL CIS-TRANS ISOMERASE (PPIF), SOLUTE CARRIER 15 (SLC15), SOLUTE CARRIER FAMILY 43 MEMBER 1 (SLC43A1), AND SOLUTE CARRIER FAMILY 7 MEMBER 11 (SLC7A11). WE ALSO FOUND THAT HIGH ALCOHOL CONSUMPTION WAS ASSOCIATED WITH SIGNIFICANTLY LOWER GLOBAL METHYLATION AS MEASURED BY THE AVERAGE OF CPGS ON THE ENTIRE ARRAY. 2019 12 6761 37 X CHROMOSOME-WIDE ANALYSIS IDENTIFIES DNA METHYLATION SITES INFLUENCED BY CIGARETTE SMOKING. BACKGROUND: TOBACCO SMOKING IS A MAJOR CAUSE OF CHRONIC DISEASE WORLDWIDE. SMOKING MAY INDUCE CELLULAR AND MOLECULAR CHANGES INCLUDING EPIGENETIC MODIFICATION, WITH BOTH SHORT-TERM AND LONG-TERM MODIFICATION PATTERNS THAT MAY CONTRIBUTE TO PHENOTYPIC EXPRESSION OF DISEASES. RECENT EPIGENOME-WIDE ASSOCIATION STUDIES (EWAS) HAVE IDENTIFIED DOZENS OF SMOKING-RELATED DNA METHYLATION (DNAM) SITES. HOWEVER, THE X CHROMOSOMAL DNAM SITES HAVE BEEN LARGELY OVERLOOKED DUE TO A LACK OF AN ANALYTICAL FRAMEWORK FOR DEALING WITH THE SEX-DIMORPHIC DISTRIBUTION. TO IDENTIFY NOVEL SMOKING-RELATED DNAM SITES ON THE X CHROMOSOME, WE EXAMINED THE MODALITY OF EACH X CHROMOSOMAL DNAM SITE AND CONDUCTED A SEX-SPECIFIC ASSOCIATION STUDY OF CIGARETTE SMOKING. RESULTS: WE USED A DISCOVERY SAMPLE OF 139 MIDDLE-AGE TWINS, AND THREE REPLICATION SAMPLES OF 78 TWINS, 464 AND 333 UNRELATED INDIVIDUALS INCLUDING 47, 17, 22, AND 89 CURRENT SMOKERS, RESPECTIVELY. AFTER CORRECTION FOR MULTIPLE TESTING, THE TOP SMOKING-RELATED DNAM SITES IN BCOR AND TSC22D3 WERE SIGNIFICANTLY HYPERMETHYLATED AND HYPOMETHYLATED, RESPECTIVELY, AMONG CURRENT SMOKERS. THESE SMOKING-ASSOCIATED SITES WERE REPLICATED WITH META-ANALYSIS P-VALUES OF 9.17 X 10(-12) AND 1.61 X 10(-9). FOR BOTH SITES, THE SMOKING EFFECTS ON METHYLATION LEVELS WERE LARGER IN MALES THAN THAT IN FEMALES. CONCLUSIONS: OUR FINDINGS HIGHLIGHT THE IMPORTANCE OF INVESTIGATING X CHROMOSOME METHYLATION PATTERNS AND THEIR ASSOCIATIONS WITH ENVIRONMENTAL EXPOSURES AND DISEASE PHENOTYPES AND DEMONSTRATE A ROBUST STATISTICAL METHODOLOGY FOR SUCH STUDY. EXISTING EWAS OF HUMAN DISEASES SHOULD INCORPORATE THE X CHROMOSOMAL SITES TO COMPLETE A COMPREHENSIVE EPIGENOME-WIDE SCAN. 2016 13 972 46 CHRONIC OBSTRUCTIVE PULMONARY DISEASE IS ASSOCIATED WITH EPIGENOME-WIDE DIFFERENTIAL METHYLATION IN BAL LUNG CELLS. DNA METHYLATION PATTERNS IN CHRONIC PULMONARY OBSTRUCTIVE DISEASE (COPD) MIGHT OFFER NEW INSIGHTS INTO DISEASE PATHOGENESIS. TO ASSESS METHYLATION PROFILES IN THE MAIN COPD TARGET ORGAN, WE PERFORMED AN EPIGENOME-WIDE ASSOCIATION STUDY ON BAL CELLS. BRONCHOSCOPIES WERE PERFORMED IN 18 SUBJECTS WITH COPD AND 15 CONTROL SUBJECTS (EX- AND CURRENT SMOKERS). DNA METHYLATION WAS MEASURED USING THE ILLUMINA METHYLATIONEPIC BEADCHIP KIT, COVERING MORE THAN 850,000 CPGS. DIFFERENTIALLY METHYLATED POSITIONS (DMPS) WERE EXAMINED FOR 1) ENRICHMENT IN PATHWAYS AND FUNCTIONAL GENE RELATIONSHIPS USING THE KYOTO ENCYCLOPEDIA OF GENES AND GENOMES AND GENE ONTOLOGY, 2) ACCELERATED AGING USING HORVATH'S EPIGENETIC CLOCK, 3) CORRELATION WITH GENE EXPRESSION, AND 4) COLOCALIZATION WITH GENETIC VARIATION. WE FOUND 1,155 BONFERRONI-SIGNIFICANT (P < 6.74 X 10(-8)) DMPS ASSOCIATED WITH COPD, MANY WITH LARGE EFFECT SIZES. FUNCTIONAL ANALYSIS IDENTIFIED BIOLOGICALLY PLAUSIBLE PATHWAYS AND GENE RELATIONSHIPS, INCLUDING ENRICHMENT FOR TRANSCRIPTION FACTOR ACTIVITY. STRONG CORRELATION WAS FOUND BETWEEN DNA METHYLATION AND CHRONOLOGICAL AGE BUT NOT BETWEEN COPD AND ACCELERATED AGING. FOR 79 UNIQUE DMPS, DNA METHYLATION CORRELATED SIGNIFICANTLY WITH GENE EXPRESSION IN BAL CELLS. THIRTY-NINE PERCENT OF DMPS WERE COLOCALIZED WITH COPD-ASSOCIATED SNPS. TO THE BEST OF OUR KNOWLEDGE, THIS IS THE FIRST EPIGENOME-WIDE ASSOCIATION STUDY OF COPD ON BAL CELLS, AND OUR ANALYSES REVEALED MANY DIFFERENTIAL METHYLATION SITES. INTEGRATION WITH MRNA DATA SHOWED A STRONG FUNCTIONAL READOUT FOR RELEVANT GENES, IDENTIFYING SITES WHERE DNA METHYLATION MIGHT DIRECTLY AFFECT EXPRESSION. ALMOST HALF OF DMPS WERE COLOCATED WITH SNPS IDENTIFIED IN PREVIOUS GENOME-WIDE ASSOCIATION STUDIES OF COPD, SUGGESTING JOINT GENETIC AND EPIGENETIC PATHWAYS RELATED TO DISEASE. 2022 14 3995 33 LONGITUDINAL STUDY OF DNA METHYLATION OF INFLAMMATORY GENES AND CANCER RISK. BACKGROUND: CHRONIC INFLAMMATION PLAYS A KEY ROLE IN CANCER ETIOLOGY. DNA METHYLATION MODIFICATION, ONE OF THE EPIGENETIC MECHANISMS REGULATING GENE EXPRESSION, IS CONSIDERED A HALLMARK OF CANCER. HUMAN AND ANIMAL MODELS HAVE IDENTIFIED NUMEROUS LINKS BETWEEN DNA METHYLATION AND INFLAMMATORY BIOMARKERS. OUR OBJECTIVE WAS TO PROSPECTIVELY AND LONGITUDINALLY EXAMINE ASSOCIATIONS BETWEEN METHYLATION OF FOUR INFLAMMATORY GENES AND CANCER RISK. METHODS: WE INCLUDED 795 NORMATIVE AGING STUDY PARTICIPANTS WITH BLOOD DRAWN ONE TO FOUR TIMES FROM 1999 TO 2012 (MEDIAN FOLLOW-UP, 10.6 YEARS). PROMOTER DNA METHYLATION OF IL6, ICAM-1, IFN, AND TLR2 IN BLOOD LEUKOCYTES WAS MEASURED USING PYROSEQUENCING AT MULTIPLE CPG SITES AND AVERAGED BY GENE FOR DATA ANALYSIS. WE USED COX REGRESSION MODELS TO EXAMINE PROSPECTIVE ASSOCIATIONS OF BASELINE AND TIME-DEPENDENT METHYLATION WITH CANCER RISK AND COMPARED MEAN METHYLATION DIFFERENCES OVER TIME BETWEEN CANCER CASES AND CANCER-FREE PARTICIPANTS. RESULTS: BASELINE IFN HYPERMETHYLATION WAS ASSOCIATED WITH ALL-CANCER (HR, 1.49; P = 0.04) AND PROSTATE CANCER INCIDENCE (HR, 1.69; P = 0.02). BASELINE ICAM-1 AND IL6 HYPERMETHYLATION WERE ASSOCIATED WITH PROSTATE CANCER INCIDENCE (HR, 1.43; P = 0.02; HR, 0.70; P = 0.03, RESPECTIVELY). IN OUR TIME-DEPENDENT ANALYSES, IFN HYPERMETHYLATION WAS ASSOCIATED WITH ALL-CANCER (HR, 1.79; P = 0.007) AND PROSTATE CANCER (HR, 1.57; P = 0.03) INCIDENCE; AND ICAM-1 AND IL6 HYPERMETHYLATION WERE ASSOCIATED WITH PROSTATE CANCER INCIDENCE (HR, 1.39; P = 0.02; HR, 0.69; P = 0.03, RESPECTIVELY). WE DETECTED SIGNIFICANT ICAM-1 HYPERMETHYLATION IN CANCER CASES (P = 0.0003) 10 TO 13 YEARS PREDIAGNOSIS. CONCLUSION: HYPERMETHYLATION OF IFN AND ICAM-1 MAY PLAY IMPORTANT ROLES IN EARLY CARCINOGENESIS, PARTICULARLY THAT OF PROSTATE CANCER. IMPACT: THESE METHYLATION CHANGES COULD INFORM THE DEVELOPMENT OF EARLY DETECTION BIOMARKERS AND POTENTIAL TREATMENTS OF INFLAMMATION-RELATED CARCINOGENESIS. 2015 15 6552 29 TRANSGENERATIONAL DNA METHYLATION CHANGES IN DAPHNIA MAGNA EXPOSED TO CHRONIC GAMMA IRRADIATION. OUR AIM WAS TO INVESTIGATE EPIGENETIC CHANGES IN DAPHNIA MAGNA AFTER A 25-DAY CHRONIC EXTERNAL GAMMA IRRADIATION (GENERATION F0 EXPOSED TO 6.5 MUGY.H(-1) OR 41.3 MGY.H(-1)) AND THEIR POTENTIAL INHERITANCE BY SUBSEQUENT RECOVERING GENERATIONS, NAMELY, F2 (EXPOSED AS GERMLINE CELLS IN F1 EMBRYOS) AND F3 (THE FIRST TRULY UNEXPOSED GENERATION). EFFECTS ON SURVIVAL, GROWTH, AND REPRODUCTION WERE OBSERVED AND DNA WAS EXTRACTED FOR WHOLE-GENOME BISULFITE SEQUENCING IN ALL GENERATIONS. RESULTS SHOWED EFFECTS ON REPRODUCTION IN F0 BUT NO EFFECT IN THE SUBSEQUENT GENERATIONS F1, F2, AND F3. IN CONTRAST, WE OBSERVED SIGNIFICANT METHYLATION CHANGES AT SPECIFIC CPG POSITIONS IN EVERY GENERATION INDEPENDENT OF DOSE RATE, WITH A MAJORITY OF HYPOMETHYLATION. SOME OF THESE CHANGES WERE SHARED BETWEEN DOSE RATES AND BETWEEN GENERATIONS. ASSOCIATED GENE FUNCTIONS INCLUDED GENE FAMILIES AND GENES THAT WERE PREVIOUSLY SHOWN TO PLAY ROLES DURING EXPOSURE TO IONIZING RADIATION. COMMON METHYLATION CHANGES DETECTED BETWEEN GENERATIONS F2 AND F3 CLEARLY SHOWED THAT EPIGENETIC MODIFICATIONS CAN BE TRANSMITTED TO UNEXPOSED GENERATIONS, MOST LIKELY THROUGH THE GERMLINE, WITH POTENTIAL IMPLICATIONS FOR ENVIRONMENTAL RISK. 2018 16 2623 32 EPIGENOME-WIDE ASSOCIATION STUDIES OF THE FRACTIONAL EXHALED NITRIC OXIDE AND BRONCHODILATOR DRUG RESPONSE IN MODERATE-TO-SEVERE PEDIATRIC ASTHMA. ASTHMA IS THE MOST PREVALENT PEDIATRIC CHRONIC DISEASE. BRONCHODILATOR DRUG RESPONSE (BDR) AND FRACTIONAL EXHALED NITRIC OXIDE (FENO) ARE CLINICAL BIOMARKERS OF ASTHMA. ALTHOUGH DNA METHYLATION (DNAM) CONTRIBUTES TO ASTHMA PATHOGENESIS, THE INFLUENCE OF DNAM ON BDR AND FENO IS SCARCELY INVESTIGATED. THIS STUDY AIMS TO IDENTIFY DNAM MARKERS IN WHOLE BLOOD ASSOCIATED EITHER WITH BDR OR FENO IN PEDIATRIC ASTHMA. WE ANALYZED 121 SAMPLES FROM CHILDREN WITH MODERATE-TO-SEVERE ASTHMA. THE ASSOCIATION OF GENOME-WIDE DNAM WITH BDR AND FENO HAS BEEN ASSESSED USING REGRESSION MODELS, ADJUSTING FOR AGE, SEX, ANCESTRY, AND TISSUE HETEROGENEITY. CROSS-TISSUE VALIDATION WAS ASSESSED IN 50 NASAL SAMPLES. DIFFERENTIALLY METHYLATED REGIONS (DMRS) AND ENRICHMENT IN TRAITS AND BIOLOGICAL PATHWAYS WERE ASSESSED. A FALSE DISCOVERY RATE (FDR) < 0.1 AND A GENOME-WIDE SIGNIFICANCE THRESHOLD OF P < 9 X 10(-8) WERE USED TO CONTROL FOR FALSE-POSITIVE RESULTS. THE CPG CG12835256 (PLA2G12A) WAS GENOME-WIDE ASSOCIATED WITH FENO IN BLOOD SAMPLES (COEFFICIENT= -0.015, P = 2.53 X 10(-9)) AND NOMINALLY ASSOCIATED IN NASAL SAMPLES (COEFFICIENT = -0.015, P = 0.045). ADDITIONALLY, THREE CPGS WERE SUGGESTIVELY ASSOCIATED WITH BDR (FDR < 0.1). WE IDENTIFIED 12 AND FOUR DMRS ASSOCIATED WITH FENO AND BDR (FDR < 0.05), RESPECTIVELY. AN ENRICHMENT IN ALLERGIC AND INFLAMMATORY PROCESSES, SMOKING, AND AGING WAS OBSERVED. WE REPORTED NOVEL ASSOCIATIONS OF DNAM MARKERS ASSOCIATED WITH BDR AND FENO ENRICHED IN ASTHMA-RELATED PROCESSES. 2023 17 1580 45 DNA METHYLATION PROFILES ARE ASSOCIATED WITH COMPLEX REGIONAL PAIN SYNDROME AFTER TRAUMATIC INJURY. FACTORS CONTRIBUTING TO DEVELOPMENT OF COMPLEX REGIONAL PAIN SYNDROME (CRPS) ARE NOT FULLY UNDERSTOOD. THIS STUDY EXAMINED POSSIBLE EPIGENETIC MECHANISMS THAT MAY CONTRIBUTE TO CRPS AFTER TRAUMATIC INJURY. DNA METHYLATION PROFILES WERE COMPARED BETWEEN INDIVIDUALS DEVELOPING CRPS (N = 9) AND THOSE DEVELOPING NON-CRPS NEUROPATHIC PAIN (N = 38) AFTER UNDERGOING AMPUTATION FOLLOWING MILITARY TRAUMA. LINEAR MODELS FOR MICROARRAY (LIMMA) ANALYSES REVEALED 48 DIFFERENTIALLY METHYLATED CYTOSINE-PHOSPHATE-GUANINE DINUCLEOTIDE (CPG) SITES BETWEEN GROUPS (UNADJUSTED P'S < 0.005), WITH THE TOP GENE COL11A1 MEETING BONFERRONI-ADJUSTED P < 0.05. THE SECOND LARGEST DIFFERENTIAL METHYLATION WAS OBSERVED FOR THE HLA-DRB6 GENE, AN IMMUNE-RELATED GENE LINKED PREVIOUSLY TO CRPS IN A SMALL GENE EXPRESSION STUDY. FOR ALL BUT 7 OF THE SIGNIFICANT CPG SITES, THE CRPS GROUP WAS HYPOMETHYLATED. NUMEROUS FUNCTIONAL GENE ONTOLOGY-BIOLOGICAL PROCESS CATEGORIES WERE SIGNIFICANTLY ENRICHED (FALSE DISCOVERY RATE-ADJUSTED Q VALUE <0.15), INCLUDING MULTIPLE IMMUNE-RELATED CATEGORIES (EG, ACTIVATION OF IMMUNE RESPONSE, IMMUNE SYSTEM DEVELOPMENT, REGULATION OF IMMUNE SYSTEM PROCESSES, AND ANTIGEN PROCESSING AND PRESENTATION). DIFFERENTIALLY METHYLATED GENES WERE MORE HIGHLY CONNECTED IN HUMAN PROTEIN-PROTEIN NETWORKS THAN EXPECTED BY CHANCE (P < 0.05), SUPPORTING THE BIOLOGICAL RELEVANCE OF THE FINDINGS. RESULTS WERE VALIDATED IN AN INDEPENDENT SAMPLE LINKING A DNA BIOBANK WITH ELECTRONIC HEALTH RECORDS (N = 126 CRPS PHENOTYPE, N = 19,768 NON-CRPS CHRONIC PAIN PHENOTYPE). ANALYSES USING PREDIXCAN METHODOLOGY INDICATED DIFFERENCES IN THE GENETICALLY DETERMINED COMPONENT OF GENE EXPRESSION IN 7 OF 48 GENES IDENTIFIED IN METHYLATION ANALYSES (P'S < 0.02). RESULTS SUGGEST THAT IMMUNE- AND INFLAMMATORY-RELATED FACTORS MIGHT CONFER RISK OF DEVELOPING CRPS AFTER TRAUMATIC INJURY. VALIDATION FINDINGS DEMONSTRATE THE POTENTIAL OF USING ELECTRONIC HEALTH RECORDS LINKED TO DNA FOR GENOMIC STUDIES OF CRPS. 2019 18 1521 33 DNA METHYLATION AT IMPRINT REGULATORY REGIONS IN PRETERM BIRTH AND INFECTION. OBJECTIVE: TO AID IN UNDERSTANDING LONG-TERM HEALTH CONSEQUENCES OF INTRAUTERINE INFECTIONS IN PRETERM BIRTH, WE EVALUATED DNA METHYLATION AT 9 DIFFERENTIALLY METHYLATED REGIONS THAT REGULATE IMPRINTED GENES BY TYPE OF PRETERM BIRTH (SPONTANEOUS PRETERM LABOR, PRETERM PREMATURE RUPTURE OF MEMBRANES, OR MEDICALLY INDICATED [FETAL GROWTH RESTRICTION AND PREECLAMPSIA]) AND INFECTION STATUS (CHORIOAMNIONITIS OR FUNISITIS). STUDY DESIGN: DATA ON TYPE OF PRETERM BIRTH AND INFECTION STATUS WERE ABSTRACTED FROM MEDICAL RECORDS AND STANDARDIZED PATHOLOGY REPORTS IN 73 PRETERM INFANTS ENROLLED IN THE NEWBORN EPIGENETICS STUDY, A PROSPECTIVE COHORT STUDY OF MOTHER-INFANT DYADS IN DURHAM, NC. CORD BLOOD WAS COLLECTED AT BIRTH, AND INFANT DNA METHYLATION LEVELS AT THE H19, IGF2, MEG3, MEST, SGCE/PEG10, PEG3, NNAT, AND PLAGL1 DIFFERENTIALLY METHYLATED REGIONS WERE MEASURED USING BISULFITE PYROSEQUENCING. ONE-WAY ANALYSES OF VARIANCE AND LOGISTIC REGRESSION MODELS WERE USED TO COMPARE DNA METHYLATION LEVELS BY TYPE OF PRETERM BIRTH AND INFECTION STATUS. RESULTS: DNA METHYLATION LEVELS DID NOT DIFFER AT ANY OF THE REGIONS (P > .20) BETWEEN INFANTS BORN VIA SPONTANEOUS PRETERM LABOR (AVERAGE N = 29), PRETERM PREMATURE RUPTURE OF MEMBRANES (AVERAGE N = 17), OR MEDICALLY INDICATED PRETERM BIRTH (AVERAGE N = 40). LEVELS WERE SIGNIFICANTLY INCREASED AT PLAGL1 IN INFANTS WITH CHORIOAMNIONITIS (N = 10, 64.4%) COMPARED WITH INFANTS WITHOUT CHORIOAMNIONITIS (N = 63, 57.9%), P < .01. DNA METHYLATION LEVELS WERE ALSO INCREASED AT PLAGL1 FOR INFANTS WITH FUNISITIS (N = 7, 63.3%) COMPARED WITH INFANTS WITHOUT FUNISITIS (N = 66, 58.3%), P < .05. CONCLUSION: DYSREGULATION OF PLAGL1 HAS BEEN ASSOCIATED WITH ABNORMAL DEVELOPMENT AND CANCER. EARLY-LIFE EXPOSURES, INCLUDING INFECTION/INFLAMMATION, MAY AFFECT EPIGENETIC CHANGES THAT INCREASE SUSCEPTIBILITY TO LATER CHRONIC DISEASE. 2013 19 5330 38 PUTATIVE EPIGENETIC BIOMARKERS OF STRESS IN RED BLOOD CELLS OF CHICKENS REARED ACROSS DIFFERENT BIOMES. PRODUCTION ANIMALS ARE CONSTANTLY SUBJECTED TO EARLY ADVERSE ENVIRONMENTAL CONDITIONS THAT INFLUENCE THE ADULT PHENOTYPE AND PRODUCE EPIGENETIC EFFECTS. CPG DINUCLEOTIDE METHYLATION IN RED BLOOD CELLS (RBC) COULD BE A USEFUL EPIGENETIC BIOMARKER TO IDENTIFY ANIMALS SUBJECTED TO CHRONIC STRESS IN THE PRODUCTION ENVIRONMENT. HERE WE COMPARED A REDUCED FRACTION OF THE RBC METHYLOME OF CHICKENS EXPOSED TO SOCIAL ISOLATION TO NON-EXPOSED. THESE EXPERIMENTS WERE PERFORMED IN TWO DIFFERENT LOCATIONS: BRAZIL AND SWEDEN. THE AIM WAS TO IDENTIFY STRESS-ASSOCIATED DNA METHYLATION PROFILES IN RBC ACROSS THESE POPULATIONS, IN SPITE OF THE VARIABLE CONDITIONS TO WHICH BIRDS ARE EXPOSED IN EACH FACILITY AND THEIR DIFFERENT LINEAGES. BIRDS WERE INCREASINGLY EXPOSED TO A SOCIAL ISOLATION TREATMENT, COMBINED WITH FOOD AND WATER DEPRIVATION, AT RANDOM PERIODS OF THE DAY FROM WEEKS 1-4 AFTER HATCHING. WE THEN COLLECTED THE RBC DNA FROM INDIVIDUALS AND COMPARED A REDUCED FRACTION OF THEIR METHYLOME BETWEEN THE EXPERIMENTAL GROUPS USING TWO BIOINFORMATIC APPROACHES TO IDENTIFY DIFFERENTIALLY METHYLATED REGIONS (DMRS): ONE USING FIXED-SIZE WINDOWS AND ANOTHER THAT PRESELECTED DIFFERENTIAL PEAKS WITH MACS2. THREE LEVELS OF SIGNIFICANCE WERE USED (P 50%) OF SPECIFIC TRANSCRIPTION FACTOR BINDING SITES. THREE OVERLAPPING DMRS WERE FOUND BETWEEN THE BR AND SW POPULATION USING THE MOST RELAXED P-VALUE (P