1 3478 128 IDENTIFICATION OF ADPKD-RELATED GENES AND PATHWAYS IN CELLS OVEREXPRESSING PKD2. CONSISTENT WITH THE GENE DOSAGE EFFECT HYPOTHESIS, RENAL CYSTS CAN ARISE IN TRANSGENIC MURINE MODELS OVEREXPRESSING EITHER PKD1 OR PKD2, WHICH ARE CAUSAL GENES FOR AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE (ADPKD). TO DETERMINE WHETHER PKD GENE OVEREXPRESSION IS A UNIVERSAL MECHANISM DRIVING CYSTOGENESIS OR IS MERELY RESTRICTED TO RODENTS, OTHER ANIMAL MODELS ARE REQUIRED. PREVIOUSLY, WE FAILED TO OBSERVE ANY RENAL CYSTS IN A TRANSGENIC PORCINE MODEL OF PKD2 OVEREXPRESSION PARTIALLY DUE TO EPIGENETIC SILENCING OF THE TRANSGENE. THUS, TO EXPLORE THE FEASIBILITY OF PORCINE MODELS AND IDENTIFY POTENTIAL GENES/PATHWAYS AFFECTED IN ADPKD, LLC-PK1 CELLS WITH HIGH PKD2 EXPRESSION WERE GENERATED. MRNA SEQUENCING (RNA-SEQ) WAS PERFORMED, AND MYC, IER3, AND ADM WERE FOUND TO BE UPREGULATED GENES COMMON TO THE DIFFERENT PKD2 OVEREXPRESSION CELL MODELS. MYC IS A WELL-CHARACTERIZED FACTOR CONTRIBUTING TO CYSTOGENESIS, AND ADM IS A BIOMARKER FOR CHRONIC KIDNEY DISEASE. THUS, THESE GENES MIGHT BE INDICATORS OF DISEASE PROGRESSION. ADDITIONALLY, SOME ADPKD-ASSOCIATED PATHWAYS, E.G., THE MITOGEN-ACTIVATED PROTEIN KINASE (MAPK) PATHWAY, WERE ENRICHED IN THE CELLS. MOREOVER, GENE ONTOLOGY (GO) ANALYSIS DEMONSTRATED THAT PROLIFERATION, APOPTOSIS, AND CELL CYCLE REGULATION, WHICH ARE HALLMARKS OF ADPKD, WERE ALTERED. THEREFORE, OUR EXPERIMENT IDENTIFIED SOME BIOMARKERS OR INDICATORS OF ADPKD, INDICATING THAT HIGH PKD2 EXPRESSION WOULD LIKELY DRIVE CYSTOGENESIS IN FUTURE PORCINE MODELS. 2020 2 5173 35 PREDICTING PROGRESSION OF AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE BY CHANGES IN THE TELOMERIC EPIGENOME. AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE (ADPKD) IS THE MOST COMMON INHERITED CAUSE OF CHRONIC KIDNEY DISEASE WITH POLYCYSTIN&NBSP;(PKD) 1 AND 2 GENE MUTATION. HOWEVER, THE INTRA-FAMILIAL VARIABILITY IN SYMPTOMS FURTHER SUGGESTS A NON-MENDELIAN CONTRIBUTION TO THE DISEASE. OUR GOAL WAS TO FIND A MARKER TO TRACK THE EPIGENETIC CHANGES COMMON TO RAPIDLY PROGRESSING FORMS OF THE DISEASE. THE RISK OF ADPKD INCREASES WITH AGE, AND AGING SHORTENS THE TELOMERE LENGTH (TL). TELOMERES ARE A NUCLEOPROTEIN STRUCTURE COMPOSED MAINLY OF THREE COMPLEXES, SHELTERIN, CST AND RNA-CONTAINING TELOMERE REPEAT(TERRA), WHICH PROTECTS THE ENDS OF CHROMOSOMES FROM DEGRADATION AND FUSION, AND PLAYS A ROLE IN MAINTAINING CELLULAR STABILITY AND IN THE REPAIR OF TELOMERIC DAMAGE. TERRAS ARE TRANSCRIBED FROM TELOMERIC REGIONS AND A PART OF THEM IS ENGAGED IN A DNA/RNA HYBRID (R-LOOP) AT EACH CHROMOSOME END. WE TRACKED TL AND TERRA LEVELS IN BLOOD SAMPLES OF 78 PATIENTS AND 20 HEALTHY CONTROL. OUR STUDY DEMONSTRATES THAT TL WAS SHORTENED AND TERRA EXPRESSION LEVELS IN THE DNA-ATTACHED FRACTION INCREASED IN AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY PATIENTS WITH MUTATIONS IN PKD1 AND PKD2 COMPARED TO THE CONTROL GROUP. MOREOVER, IT WAS OBSERVED THAT THE EXPRESSION OF TERRA ENGAGED IN THE R-LOOP WAS HIGHER AND THE LENGTH OF TELOMERES SHORTER IN PATIENTS WITH ADPKD WHO SHOWED RAPID DISEASE PROGRESSION. INTRAFAMILIAL VARIATION IN TL AND TERRA LEVELS WITH THE SAME MUTATION WOULD INDICATE RELIABLE EPIGENETIC POTENTIAL BIOMARKERS IN DISEASE MONITORING. 2022 3 1154 27 CONSERVED DNA METHYLATION PATTERNS IN HEALTHY BLOOD CELLS AND EXTENSIVE CHANGES IN LEUKEMIA MEASURED BY A NEW QUANTITATIVE TECHNIQUE. GENOME WIDE ANALYSIS OF DNA METHYLATION PROVIDES IMPORTANT INFORMATION IN A VARIETY OF DISEASES, INCLUDING CANCER. HERE, WE DESCRIBE A SIMPLE METHOD, DIGITAL RESTRICTION ENZYME ANALYSIS OF METHYLATION (DREAM), BASED ON NEXT GENERATION SEQUENCING ANALYSIS OF METHYLATION-SPECIFIC SIGNATURES CREATED BY SEQUENTIAL DIGESTION OF GENOMIC DNA WITH SMAI AND XMAI ENZYMES. DREAM PROVIDES INFORMATION ON 150,000 UNIQUE CPG SITES, OF WHICH 39,000 ARE IN CPG ISLANDS AND 30,000 ARE AT TRANSCRIPTION START SITES OF 13,000 REFSEQ GENES. WE ANALYZED DNA METHYLATION IN HEALTHY WHITE BLOOD CELLS AND FOUND METHYLATION PATTERNS TO BE REMARKABLY UNIFORM. INTER INDIVIDUAL DIFFERENCES > 30% WERE OBSERVED ONLY AT 227 OF 28,331 (0.8%) OF AUTOSOMAL CPG SITES. SIMILARLY, > 30% DIFFERENCES WERE OBSERVED AT ONLY 59 SITES WHEN WE COMPARING THE CORD AND ADULT BLOOD. THESE CONSERVED METHYLATION PATTERNS CONTRASTED WITH EXTENSIVE CHANGES AFFECTING 18-40% OF CPG SITES IN A PATIENT WITH ACUTE MYELOID LEUKEMIA AND IN TWO LEUKEMIA CELL LINES. THE METHOD IS COST EFFECTIVE, QUANTITATIVE (R ( 2) = 0.93 WHEN COMPARED WITH BISULFITE PYROSEQUENCING) AND REPRODUCIBLE (R ( 2) = 0.997). USING 100-FOLD COVERAGE, DREAM CAN DETECT DIFFERENCES IN METHYLATION GREATER THAN 10% OR 30% WITH A FALSE POSITIVE RATE BELOW 0.05 OR 0.001, RESPECTIVELY. DREAM CAN BE USEFUL IN QUANTIFYING EPIGENETIC EFFECTS OF ENVIRONMENT AND NUTRITION, CORRELATING DEVELOPMENTAL EPIGENETIC VARIATION WITH PHENOTYPES, UNDERSTANDING EPIGENETICS OF CANCER AND CHRONIC DISEASES, MEASURING THE EFFECTS OF DRUGS ON DNA METHYLATION OR DERIVING NEW BIOLOGICAL INSIGHTS INTO MAMMALIAN GENOMES. 2012 4 1477 30 DIVERSE PHENOTYPIC EXPRESSION OF NPHP4 MUTATIONS IN FOUR SIBLINGS. NEPHRONOPHTHISIS (NPHP) IS AN AUTOSOMAL RECESSIVE DISEASE CHARACTERIZED BY RENAL TUBULAR BASEMENT MEMBRANE DISRUPTION, INTERSTITIAL FIBROSIS AND TUBULAR CYSTS THAT PROGRESSES TO END-STAGE KIDNEY DISEASE (ESKD). THERE ARE ALSO CHARACTERISTIC EXTRARENAL MANIFESTATIONS. MUTATIONS OF MORE THAN THIRTEEN GENES THAT CAN CAUSE NPHP HAVE BEEN IDENTIFIED. WE HEREIN REPORT FOUR SIBLINGS FROM A CONSANGUINEOUS FAMILY, WHO CARRIED THE SAME NPHP4 MUTATIONS BUT PRESENTED WITH DIFFERENT DISEASE PHENOTYPES RANGING FROM ENURESIS NOCTURNA TO ESKD. DILUTED URINE AND ECHOGENIC KIDNEYS IN ULTRASOUND EXAMINATION WERE CONSISTENT, WHICH IS TYPICAL FOR 100% OF THE NPHP CASES THAT HAVE BEEN DESCRIBED. CHRONIC KIDNEY DISEASE DEVELOPED IN THE OLDER TWO BROTHERS. THE OBSERVED PHENOTYPIC DIFFERENCES ARE LIKELY TO BE RELATED TO ENVIRONMENTAL AND EPIGENETIC FACTORS, OLIGOGENIC INHERITANCE AND MODIFIER GENES AFFECTING THE AGE OF PRESENTATION OF SIGNS AND SYMPTOMS. NPHP SHOULD BE CONSIDERED AS AN IMPORTANT CAUSE OF CKD IN CHILDREN, WHICH INSIDIOUSLY PROGRESSES TO ESKD, WITH NO SPECIFIC THERAPY AVAILABLE. 2014 5 504 29 ASSOCIATION OF CIGARETTE SMOKING AND CRP LEVELS WITH DNA METHYLATION IN ALPHA-1 ANTITRYPSIN DEFICIENCY. ALPHA-1 ANTITRYPSIN (AAT) DEFICIENCY AND TOBACCO SMOKING ARE CONFIRMED RISK FACTORS FOR CHRONIC OBSTRUCTIVE PULMONARY DISEASE. WE HYPOTHESIZED THAT VARIABLE DNA METHYLATION WOULD BE ASSOCIATED WITH SMOKING AND INFLAMMATION, AS REFLECTED BY THE LEVEL OF C-REACTIVE PROTEIN (CRP) IN AAT-DEFICIENT SUBJECTS. METHYLATION LEVELS OF 1,411 AUTOSOMAL CPG SITES FROM THE ILLUMINA GOLDENGATE METHYLATION CANCER PANEL I WERE ANALYZED IN 316 SUBJECTS. ASSOCIATIONS OF FIVE SMOKING BEHAVIORS AND CRP LEVELS WITH INDIVIDUAL CPG SITES AND AVERAGE METHYLATION LEVELS WERE ASSESSED USING NON-PARAMETRIC TESTING, LINEAR REGRESSION AND LINEAR MIXED EFFECT MODELS, WITH AND WITHOUT ADJUSTMENT FOR AGE AND GENDER. UNIVARIATE LINEAR REGRESSION ANALYSIS REVEALED THAT METHYLATION LEVELS OF 16 CPG SITES SIGNIFICANTLY ASSOCIATED WITH EVER-SMOKING STATUS. A CPG SITE IN THE TGFBI GENE WAS THE ONLY SITE ASSOCIATED WITH EVER-SMOKING AFTER ADJUSTMENT FOR AGE AND GENDER. NO HIGHLY SIGNIFICANT ASSOCIATIONS EXISTED BETWEEN AGE AT SMOKING INITIATION, PACK-YEARS SMOKED, DURATION OF SMOKING, AND TIME SINCE QUITTING SMOKING AS PREDICTORS OF INDIVIDUAL CPG SITE METHYLATION LEVELS. HOWEVER, EVER-SMOKING AND YOUNGER AGE AT SMOKING INITIATION ASSOCIATED WITH LOWER METHYLATION LEVEL AVERAGED ACROSS ALL SITES. DNA METHYLATION AT CPG SITES IN THE RUNX3, JAK3 AND KRT1 GENES ASSOCIATED WITH CRP LEVELS. THE MOST SIGNIFICANTLY ASSOCIATED CPG SITES WITH GENDER AND AGE MAPPED TO THE CASP6 AND FZD9 GENES, RESPECTIVELY. IN SUMMARY, THIS STUDY IDENTIFIED MULTIPLE POTENTIAL CANDIDATE CPG SITES ASSOCIATED WITH EVER-SMOKING AND CRP LEVEL IN AAT-DEFICIENT SUBJECTS. PHENOTYPIC VARIABILITY IN MENDELIAN DISEASES MAY BE DUE TO EPIGENETIC FACTORS. 2012 6 6817 23 [FACIOSCAPULOHUMERAL MUSCULAR DYSTROPHY: REPORT OF SEVEN PATIENTS]. BACKGROUND: FACIOSCAPULOHUMERAL MUSCULAR DYSTROPHY IS THE THIRD MOST COMMON MUSCULAR DYSTROPHY WITH AN ESTIMATED PREVALENCE OF 1 PER 20.000 AND A NORMAL LIFE EXPECTANCY IN THE MAJORITY OF PATIENTS. HOWEVER, APPROXIMATELY 15% OF PATIENTS BECOME WHEELCHAIR BOUND IN THE COURSE OF THEIR LIFE. IT IS A HEREDITARY AUTOSOMAL DOMINANT DISEASE WITH HIGH (95%) PENETRANCE BY THE AGE OF 20, BUT WITH VARIABLE DEGREE OF PHENOTYPIC EXPRESSION EVEN IN THE SAME FAMILY GROUP. SYMPTOMS FREQUENTLY START IN THE SECOND DECADE OF LIFE, WITH FACIAL AND SCAPULAR WEAKNESS. AIM: TO REPORT THE CLINICAL FEATURES OF SEVEN PATIENTS WITH THE DISEASE, SEEN AT A PUBLIC HOSPITAL. MATERIAL AND METHODS: ANALYSIS OF SEVEN PATIENTS WITH GENETIC STUDY SEEN IN A PUBLIC HOSPITAL IN SANTIAGO. RESULTS: THE AGE OF PATIENTS FLUCTUATED FROM 18 TO 61 YEARS AND FOUR WERE FEMALES. THE MEAN AGE AT ONSET OF SYMPTOMS WAS 29 YEARS AND FOUR HAD A FAMILY HISTORY OF THE DISEASE. THE USUAL PRESENTING COMPLAINT WAS ARM OR SHOULDER ASYMMETRIC WEAKNESS. FOUR PATIENTS HAD BONE PAIN. FACIAL INVOLVEMENT WAS PRESENT IN FOUR. A GENETIC STUDY WAS DONE IN FIVE PATIENTS, THE OTHER TWO PATIENTS WERE RELATIVES, CONFIRMING THE CONTRACTION OR LOWER NUMBER OF REPETITIONS IN D4Z4 REGION. AFTER 12 YEARS OF FOLLOW UP ONLY 2 PATIENTS OLDER THAN 60 YEARS CANNOT WORK AND ONE FEMALE PATIENTS IS IN A SEMI DEPENDENT STATE AT THE AGE OF 30. CONCLUSIONS: THE CLINICAL WORKUP IN THE DIAGNOSIS AND THE TIMELY INDICATION OF GENETIC STUDIES ARE HIGHLIGHTED, TO AVOID UNNECESSARY AND INVASIVE PROCEDURES. THE VARIABILITY IN THE PHENOTYPIC EXPRESSION IN A SIMILAR GENETIC DEFECT IS DISCUSSED AND THE GENETIC OR EPIGENETIC MECHANISMS OF THIS MUSCULAR DYSTROPHY ARE DESCRIBED. 2015 7 5463 27 RESIDENTIAL PM(2.5) EXPOSURE AND THE NASAL METHYLOME IN CHILDREN. RATIONALE: PM(2.5-)INDUCED ADVERSE EFFECTS ON RESPIRATORY HEALTH MAY BE DRIVEN BY EPIGENETIC MODIFICATIONS IN AIRWAY CELLS. THE POTENTIAL IMPACT OF EXPOSURE DURATION ON EPIGENETIC ALTERATIONS IN THE AIRWAYS IS NOT YET KNOWN. OBJECTIVES: WE AIMED TO STUDY ASSOCIATIONS OF FINE PARTICULATE MATTER PM(2.5) EXPOSURE WITH DNA METHYLATION IN NASAL CELLS. METHODS: WE CONDUCTED NASAL EPIGENOME-WIDE ASSOCIATION ANALYSES WITHIN 503 CHILDREN FROM PROJECT VIVA (MEAN AGE 12.9 Y), AND EXAMINED VARIOUS EXPOSURE DURATIONS (1-DAY, 1-WEEK, 1-MONTH, 3-MONTHS AND 1-YEAR) PRIOR TO NASAL SAMPLING. WE USED RESIDENTIAL ADDRESSES TO ESTIMATE AVERAGE DAILY PM(2.5) AT 1 KM RESOLUTION. WE COLLECTED NASAL SWABS FROM THE ANTERIOR NARES AND MEASURED DNA METHYLATION (DNAM) USING THE ILLUMINA METHYLATIONEPIC BEADCHIP. WE TESTED 719,075 HIGH QUALITY AUTOSOMAL CPGS USING CPG-BY-CPG AND REGIONAL DNAM ANALYSES CONTROLLING FOR MULTIPLE COMPARISONS, AND ADJUSTED FOR MATERNAL EDUCATION, HOUSEHOLD SMOKERS, CHILD SEX, RACE/ETHNICITY, BMI Z-SCORE, AGE, SEASON AT SAMPLE COLLECTION AND CELL-TYPE HETEROGENEITY. WE FURTHER CORRECTED FOR BIAS AND GENOMIC INFLATION. WE TESTED FOR REPLICATION IN A COHORT FROM THE NETHERLANDS (PIAMA). RESULTS: IN ADJUSTED ANALYSES, WE FOUND 362 CPGS ASSOCIATED WITH 1-YEAR PM(2.5) (FDR < 0.05), 20 CPGS PASSING BONFERRONI CORRECTION (P < 7.0X10(-8)) AND 10 DIFFERENTIALLY METHYLATED REGIONS (DMRS). IN 445 PIAMA PARTICIPANTS (MEAN AGE 16.3 YEARS) 11 OF 203 AVAILABLE CPGS REPLICATED AT P < 0.05. WE OBSERVED DIFFERENTIAL DNAM AT/NEAR GENES IMPLICATED IN CELL CYCLE, IMMUNE AND INFLAMMATORY RESPONSES. THERE WERE NO CPGS OR REGIONS ASSOCIATED WITH PM(2.5) LEVELS AT 1-DAY, 1-WEEK, OR 1-MONTH PRIOR TO SAMPLE COLLECTION, ALTHOUGH 2 CPGS WERE ASSOCIATED WITH PAST 3-MONTH PM(2.5). CONCLUSION: WE OBSERVED WIDE-SPREAD DNAM VARIABILITY ASSOCIATED WITH AVERAGE PAST YEAR PM(2.5) EXPOSURE BUT WE DID NOT DETECT ASSOCIATIONS WITH SHORTER-TERM EXPOSURE. OUR RESULTS SUGGEST THAT NASAL DNAM MARKS REFLECT CHRONIC AIR POLLUTION EXPOSURE. 2021 8 5333 26 PYRUVATE KINASE DEFICIENCY: THE GENOTYPE-PHENOTYPE ASSOCIATION. RED CELL PYRUVATE KINASE (PK) DEFICIENCY IS THE MOST FREQUENT ENZYME ABNORMALITY OF GLYCOLYSIS CAUSING CHRONIC NON-SPHEROCYTIC HAEMOLYTIC ANAEMIA. THE DISEASE IS TRANSMITTED AS AN AUTOSOMAL RECESSIVE TRAIT, CLINICAL SYMPTOMS USUALLY OCCURRING IN COMPOUND HETEROZYGOTES FOR TWO MUTANT ALLELES AND IN HOMOZYGOTES. THE SEVERITY OF HAEMOLYSIS IS HIGHLY VARIABLE, RANGING FROM VERY MILD OR FULLY COMPENSATED FORMS TO LIFE-THREATENING NEONATAL ANAEMIA NECESSITATING EXCHANGE TRANSFUSIONS. ERYTHROCYTE PK IS SYNTHESISED UNDER THE CONTROL OF THE PK-LR GENE LOCATED ON CHROMOSOME 1. ONE HUNDRED EIGHTY DIFFERENT MUTATIONS IN PK-LR GENE, MOSTLY MISSENSE, HAVE BEEN SO FAR REPORTED ASSOCIATED TO PK DEFICIENCY. FIRST ATTEMPTS TO DELINEATE THE GENOTYPE-PHENOTYPE ASSOCIATION WERE MAINLY BASED ON THE ANALYSIS OF THE ENZYME'S THREE-DIMENSIONAL STRUCTURE AND THE OBSERVATION OF THE FEW HOMOZYGOUS PATIENTS. MORE RECENTLY, THE COMPARISON OF THE RECOMBINANT MUTANTS OF HUMAN RED CELL PK WITH THE WILD-TYPE ENZYME HAS ENABLED THE EFFECTS OF AMINO ACID REPLACEMENTS ON THE ENZYME MOLECULAR PROPERTIES TO BE DETERMINED. HOWEVER, THE CLINICAL MANIFESTATIONS OF RED CELL ENZYME DEFECTS ARE NOT MERELY DEPENDENT ON THE MOLECULAR PROPERTIES OF THE MUTANT PROTEIN BUT RATHER REFLECT THE COMPLEX INTERACTIONS OF ADDITIONAL FACTORS, INCLUDING GENETIC BACKGROUND, CONCOMITANT FUNCTIONAL POLYMORPHISMS OF OTHER ENZYMES, POSTTRANSLATIONAL OR EPIGENETIC MODIFICATIONS, INEFFECTIVE ERYTHROPOIESIS AND DIFFERENCES IN SPLENIC FUNCTION. 2007 9 378 37 AN EPIGENETIC MAP OF AGE-ASSOCIATED AUTOSOMAL LOCI IN NORTHERN EUROPEAN FAMILIES AT HIGH RISK FOR THE METABOLIC SYNDROME. BACKGROUND: THE PREVALENCE OF CHRONIC DISEASES SUCH AS CANCER, TYPE 2 DIABETES, METABOLIC SYNDROME (METS), AND CARDIOVASCULAR DISEASE INCREASES WITH AGE IN ALL POPULATIONS. EPIGENETIC FEATURES ARE HYPOTHESIZED TO PLAY IMPORTANT ROLES IN THE PATHOPHYSIOLOGY OF AGE-ASSOCIATED DISEASES, BUT A MAP OF THESE MARKERS IS LACKING. WE SEARCHED FOR GENOME-WIDE AGE-ASSOCIATED METHYLATION SIGNATURES IN PERIPHERAL BLOOD OF INDIVIDUALS AT HIGH RISKS FOR METS BY PROFILING 485,000 CPG SITES IN 192 INDIVIDUALS OF NORTHERN EUROPEAN ANCESTRY USING THE ILLUMINA HM450 ARRAY. SUBJECTS (AGES 6-85 YEARS) WERE PART OF SEVEN EXTENDED FAMILIES, AND 73% OF ADULTS AND 32% OF CHILDREN WERE OVERWEIGHT OR OBESE. RESULTS: WE FOUND 22,122 GENOME-WIDE SIGNIFICANT AGE-ASSOCIATED CPG SITES (P ALPHA=0.05 = 3.65 X 10(-7) AFTER CORRECTION FOR MULTIPLE TESTING) OF WHICH 14,155 ARE POSITIVELY ASSOCIATED WITH AGE WHILE 7,967 ARE NEGATIVELY ASSOCIATED. BY APPLYING A POSITIONAL DENSITY-BASED CLUSTERING ALGORITHM, WE GENERATED A MAP OF EPIGENETIC 'HOT-SPOTS' OF AGE-ASSOCIATED GENOMIC SEGMENTS, WHICH INCLUDE 290 AGE-ASSOCIATED DIFFERENTIALLY METHYLATED CPG CLUSTERS (ADMCS), OF WHICH 207 ARE POSITIVELY ASSOCIATED WITH AGE. GENE/PATHWAY ENRICHMENT ANALYSES WERE PERFORMED ON THESE CLUSTERS USING FATIGO. GENES LOCALIZED TO BOTH THE POSITIVELY (N = 241) AND NEGATIVELY (N = 16) AGE-ASSOCIATED CLUSTERS ARE SIGNIFICANTLY ENRICHED IN SPECIFIC KEGG PATHWAYS AND GO TERMS. THE MOST SIGNIFICANTLY ENRICHED PATHWAYS ARE THE HEDGEHOG SIGNALING PATHWAY (ADJUSTED P = 3.96 X 10(-3)) AND MATURITY-ONSET DIABETES OF THE YOUNG (MODY) (ADJUSTED P = 6.26 X 10(-3)) IN THE POSITIVE ADMCS AND TYPE I DIABETES MELLITUS (ADJUSTED P = 3.69 X 10(-7)) IN THE NEGATIVE ADMCS. WE ALSO IDENTIFIED SEVERAL EPIGENETIC LOCI WHOSE AGE-ASSOCIATED CHANGE RATES DIFFER BETWEEN SUBJECTS DIAGNOSED WITH METS AND THOSE WITHOUT. CONCLUSION: WE CONCLUDE THAT IN A FAMILY COHORT AT HIGH RISK FOR METS, AGE-ASSOCIATED EPIGENETIC FEATURES ENRICH IN BIOLOGICAL PATHWAYS IMPORTANT FOR DETERMINING THE FATE OF FAT CELLS AND FOR INSULIN PRODUCTION. WE ALSO OBSERVE THAT SEVERAL GENES KNOWN TO BE RELATED TO METS SHOW DIFFERENTIAL EPIGENETIC RESPONSE TO AGE IN INDIVIDUALS WITH AND WITHOUT METS. 2015 10 5329 36 PURINERGIC SIGNALING IN THE LUMEN OF A NORMAL NEPHRON AND IN REMODELED PKD ENCAPSULATED CYSTS. THE NEPHRON IS THE FUNCTIONAL UNIT OF THE KIDNEY. BLOOD AND PLASMA ARE CONTINUALLY FILTERED WITHIN THE GLOMERULI THAT BEGIN EACH NEPHRON. ADENOSINE 5' TRIPHOSPHATE (ATP) AND ITS METABOLITES ARE FREELY FILTERED BY EACH GLOMERULUS AND ENTER THE LUMEN OF EACH NEPHRON BEGINNING AT THE PROXIMAL CONVOLUTED TUBULE (PCT). FLOW RATE, OSMOLALITY, AND OTHER MECHANICAL OR CHEMICAL STIMULI FOR ATP SECRETION ARE PRESENT IN EACH NEPHRON SEGMENT. THESE ATP-RELEASE STIMULI ARE ALSO DIFFERENT IN EACH NEPHRON SEGMENT DUE TO WATER OR SALT PERMEABILITY OR IMPERMEABILITY ALONG DIFFERENT LUMINAL MEMBRANES OF THE CELLS THAT LINE EACH NEPHRON SEGMENT. EACH OF THE ABOVE STIMULI CAN TRIGGER ADDITIONAL ATP RELEASE INTO THE LUMEN OF A NEPHRON SEGMENT. EACH NEPHRON-LINING EPITHELIAL CELL IS A POTENTIAL SOURCE OF SECRETED ATP. TOGETHER WITH FILTERED ATP AND ITS METABOLITES DERIVED FROM THE GLOMERULUS, SECRETED ATP AND ADENOSINE DERIVED FROM CELLS ALONG THE NEPHRON ARE LIKELY THE PRINCIPAL TWO OF SEVERAL NUCLEOTIDE AND NUCLEOSIDE CANDIDATES FOR RENAL AUTOCRINE AND PARACRINE LIGANDS WITHIN THE TUBULAR FLUID OF THE NEPHRON. THIS MINIREVIEW DISCUSSES THE FIRST PRINCIPLES OF PURINERGIC SIGNALING AS THEY RELATE TO THE NEPHRON AND THE URINARY BLADDER. THE REVIEW DISCUSSES HOW THE LUMEN OF A RENAL TUBULE PRESENTS AN IDEAL PURINERGIC SIGNALING MICROENVIRONMENT. THE REVIEW ALSO ILLUSTRATES HOW REMODELED AND ENCAPSULATED CYSTS IN AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE (ADPKD) AND REMODELED PSEUDOCYSTS IN AUTOSOMAL RECESSIVE PKD (ARPKD) OF THE RENAL COLLECTING DUCT LIKELY CREATE AN EVEN MORE IDEAL MICROENVIRONMENT FOR PURINERGIC SIGNALING. ONCE TRAPPED IN THESE CLOSED MICROENVIRONMENTS, PURINERGIC SIGNALING BECOMES CHRONIC AND LIKELY PLAYS A SIGNIFICANT EPIGENETIC AND DETRIMENTAL ROLE IN THE SECONDARY PROGRESSION OF PKD, ONCE THE REMODELING OF THE RENAL TISSUE HAS BEGUN. IN PKD CYSTIC MICROENVIRONMENTS, WE ARGUE THAT NORMAL PURINERGIC SIGNALING WITHIN THE LUMEN OF THE NEPHRON PROVIDES DETRIMENTAL ACCELERATION OF ADPKD ONCE REMODELING IS COMPLETE. 2008 11 4825 18 OCULAR FUNDUS ABNORMALITIES IN PATIENTS WITH BALKAN ENDEMIC NEPHROPATHY AND OTHER CHRONIC KIDNEY DISEASES. AIM: THE AIM OF THIS STUDY WAS TO EXAMINE THE OCULAR FUNDUS PATHOLOGY IN PATIENTS WITH BALKAN ENDEMIC NEPHROPATHY (BN) AND CHRONIC KIDNEY DISEASES (CKD). METHODS: THE STUDY INCLUDED 51 PATIENTS WITH BN FROM THE SOUTH MORAVA RIVER REGION IN SERBIA, AND 102 SUBJECTS WITH DIFFERENT STAGES OF CHRONIC RENAL DISEASES, MATCHED ACCORDING TO AGE AND GENDER, OBTAINED FROM A DATABASE USED IN A RECENTLY PUBLISHED STUDY. ALL PATIENTS HAD VISITED OUTPATIENT DEPARTMENT OF THE CLINIC OF NEPHROLOGY, CLINICAL CENTER NIS. ALL PATIENTS UNDERWENT ROUTINE OPHTHALMIC EXAMINATIONS. RESULTS: THERE WERE SIGNIFICANTLY MORE (P < 0.001) PATIENTS WITH AGE-RELATED MACULAR DEGENERATION (AMD) IN THE GROUP WITH BN (31.37 %) THAN IN THOSE WITH CKD (5.88 %). MULTIVARIATE LOGISTIC REGRESSION ANALYSIS CONFIRMED THAT THE SIGNIFICANT FACTORS RELATED TO AMD IN THE GROUP WITH BN WERE ALBUMINURIA (P < 0.05) AND PROTEINURIA (P < 0.05); IN CKD PATIENTS, THE LEVEL OF HDL (P < 0.05), WHILE NEGATIVE CORRELATION WITH THE LEVEL OF TRIGLYCERIDE WAS REGISTERED (P < 0.05). THERE WAS NO ASSOCIATION BETWEEN ESTIMATED GLOMERULAR FILTRATION RATE AND AMD. THE SIGNIFICANT FACTORS RELATED TO RETINOPATHY IN THE GROUP WITH BN ARE AGE (P < 0.05) AND SERUM CREATININE VALUES (P < 0.05), IN PATIENTS WITH CKD INCREASING AGE (P < 0.001) AND DM (P < 0.05). CONCLUSION: OCULAR FUNDUS PATHOLOGY IN PATIENTS WITH BN IS SIMILAR TO THE PATHOLOGY OF OTHER CKD, BUT WITH SIGNIFICANTLY MORE AMD (ABOUT FOUR TIMES), PROBABLY RELATED TO THE GENETIC/EPIGENETIC FACTORS. 2015 12 382 30 AN EPIGENOME-WIDE STUDY OF BODY MASS INDEX AND DNA METHYLATION IN BLOOD USING PARTICIPANTS FROM THE SISTER STUDY COHORT. BACKGROUND/OBJECTIVES: THE RELATIONSHIP BETWEEN OBESITY AND CHRONIC DISEASE RISK IS WELL-ESTABLISHED; THE UNDERLYING BIOLOGICAL MECHANISMS DRIVING THIS RISK INCREASE MAY INCLUDE OBESITY-RELATED EPIGENETIC MODIFICATIONS. TO EXPLORE THIS HYPOTHESIS, WE CONDUCTED A GENOME-WIDE ANALYSIS OF DNA METHYLATION AND BODY MASS INDEX (BMI) USING DATA FROM A SUBSET OF WOMEN IN THE SISTER STUDY. SUBJECTS/METHODS: THE SISTER STUDY IS A COHORT OF 50 884 US WOMEN WHO HAD A SISTER WITH BREAST CANCER BUT WERE FREE OF BREAST CANCER THEMSELVES AT ENROLLMENT. STUDY PARTICIPANTS COMPLETED EXAMINATIONS WHICH INCLUDED MEASUREMENTS OF HEIGHT AND WEIGHT, AND PROVIDED BLOOD SAMPLES. BLOOD DNA METHYLATION DATA GENERATED WITH THE ILLUMINA INFINIUM HUMANMETHYLATION27 BEADCHIP ARRAY COVERING 27,589 CPG SITES WAS AVAILABLE FOR 871 WOMEN FROM A PRIOR STUDY OF BREAST CANCER AND DNA METHYLATION. TO IDENTIFY DIFFERENTIALLY METHYLATED CPG SITES ASSOCIATED WITH BMI, WE ANALYZED THIS METHYLATION DATA USING ROBUST LINEAR REGRESSION WITH ADJUSTMENT FOR AGE AND CASE STATUS. FOR THOSE CPGS PASSING THE FALSE DISCOVERY RATE SIGNIFICANCE LEVEL, WE EXAMINED THE ASSOCIATION IN A REPLICATION SET COMPRISED OF A NON-OVERLAPPING GROUP OF 187 WOMEN FROM THE SISTER STUDY WHO HAD DNA METHYLATION DATA GENERATED USING THE INFINIUM HUMANMETHYLATION450 BEADCHIP ARRAY. ANALYSIS OF THIS EXPANDED 450 K ARRAY IDENTIFIED ADDITIONAL BMI-ASSOCIATED SITES WHICH WERE INVESTIGATED WITH TARGETED PYROSEQUENCING. RESULTS: FOUR CPG SITES REACHED GENOME-WIDE SIGNIFICANCE (FALSE DISCOVERY RATE (FDR) Q<0.05) IN THE DISCOVERY SET AND ASSOCIATIONS FOR ALL FOUR WERE SIGNIFICANT AT STRICT BONFERRONI CORRECTION IN THE REPLICATION SET. AN ADDITIONAL 23 SITES PASSED FDR IN THE REPLICATION SET AND FIVE WERE REPLICATED BY PYROSEQUENCING IN THE DISCOVERY SET. SEVERAL OF THE GENES IDENTIFIED INCLUDING ANGPT4, RORC, SOCS3, FSD2, XYLT1, ABCG1, STK39, ASB2 AND CRHR2 HAVE BEEN LINKED TO OBESITY AND OBESITY-RELATED CHRONIC DISEASES. CONCLUSIONS: OUR FINDINGS SUPPORT THE HYPOTHESIS THAT OBESITY-RELATED EPIGENETIC DIFFERENCES ARE DETECTABLE IN BLOOD AND MAY BE RELATED TO RISK OF CHRONIC DISEASE. 2017 13 517 20 ASSOCIATION STUDY OF FOXO3A SINGLE-NUCLEOTIDE POLYMORPHISM AND BRONCHIAL ASTHMA IN EGYPTIAN CHILDREN. ASTHMA IS THE MOST COMMON CHRONIC ILLNESS IN CHILDREN AND IS A LEADING CAUSE OF CHILDHOOD HOSPITALIZATION AND SCHOOL ABSENTEEISM. ASTHMA PRESENTS WITH DIFFERENT PHENOTYPES DEPENDING ON AGE, GENDER, GENETIC BACKGROUND, ENVIRONMENTAL EXPOSURES AND EPIGENETIC FACTORS. FORKHEAD BOX O3 (FOXO3) IS A TRANSCRIPTION FACTOR INVOLVED IN THE PATHOGENESIS OF A NUMBER OF INFLAMMATORY AND RESPIRATORY DISEASES. THE STUDY AIMS TO INVESTIGATE THE ASSOCIATION BETWEEN THE SNP RS13217795 IN FOXO3 GENE AND PEDIATRIC ONSET ASTHMA IN THE EGYPTIAN POPULATION. NINETY ASTHMATICS AND 160 HEALTHY CONTROLS WERE SUBJECTED TO GENOTYPING OF FOXO3 SNP (RS13217795) USING THE PCR-RFLP METHOD. THE PROPORTION OF HOMOZYGOUS (CC) AND HETEROZYGOUS (CT) GENOTYPES WAS LOWER IN THE ASTHMATIC GROUP COMPARED TO THE CONTROL GROUP BUT STATISTICALLY INSIGNIFICANT; P > 0.05. ON THE OTHER HAND THE PROPORTION OF THE MUTANT HOMOZYGOUS (TT) GENOTYPE IN ASTHMATIC GROUP WAS HIGHER; 30 (33.3%) THAN THE CONTROL GROUP; 28(17.5%), THE DIFFERENCE WAS SIGNIFICANT IN RECESSIVE MODEL OF DISEASE PENETRANCE WITH ODDS RATIO OR (95% CI) OF 2.4(1 - 5.49) AND P=0.039. THIS ASSOCIATION WAS MORE PRONOUNCED IN MALE GENDER; OR AND 95% CI OF 5.3 (1.4- 19.3) AND P=0.01. IN CONCLUSIONS, EGYPTIAN CHILDREN CARRYING THE MUTANT (TT) GENOTYPE WERE AT HIGHER RISK TO DEVELOP ASTHMA WITH A HIGHER RISK IN MALE GENDER. 2020 14 1552 28 DNA METHYLATION IS PREDICTIVE OF MORTALITY IN CURRENT AND FORMER SMOKERS. RATIONALE: SMOKING RESULTS IN AT LEAST A DECADE LOWER LIFE EXPECTANCY. MORTALITY AMONG CURRENT SMOKERS IS TWO TO THREE TIMES AS HIGH AS NEVER SMOKERS. DNA METHYLATION IS AN EPIGENETIC MODIFICATION OF THE HUMAN GENOME THAT HAS BEEN ASSOCIATED WITH BOTH CIGARETTE SMOKING AND MORTALITY.OBJECTIVES: WE SOUGHT TO IDENTIFY DNA METHYLATION MARKS IN BLOOD THAT ARE PREDICTIVE OF MORTALITY IN A SUBSET OF THE COPDGENE (GENETIC EPIDEMIOLOGY OF COPD) STUDY, REPRESENTING 101 DEATHS AMONG 667 CURRENT AND FORMER SMOKERS.METHODS: WE ASSAYED GENOME-WIDE DNA METHYLATION IN NON-HISPANIC WHITE SMOKERS WITH AND WITHOUT CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) USING BLOOD SAMPLES FROM THE COPDGENE ENROLLMENT VISIT. WE TESTED WHETHER DNA METHYLATION WAS ASSOCIATED WITH MORTALITY IN MODELS ADJUSTED FOR COPD STATUS, AGE, SEX, CURRENT SMOKING STATUS, AND PACK-YEARS OF CIGARETTE SMOKING. REPLICATION WAS PERFORMED IN A SUBSET OF 231 INDIVIDUALS FROM THE ECLIPSE (EVALUATION OF COPD LONGITUDINALLY TO IDENTIFY PREDICTIVE SURROGATE ENDPOINTS) STUDY.MEASUREMENTS AND MAIN RESULTS: WE IDENTIFIED SEVEN CPG SITES ASSOCIATED WITH MORTALITY (FALSE DISCOVERY RATE < 20%) THAT REPLICATED IN THE ECLIPSE COHORT (P < 0.05). NONE OF THESE MARKS WERE ASSOCIATED WITH LONGITUDINAL LUNG FUNCTION DECLINE IN SURVIVORS, SMOKING HISTORY, OR CURRENT SMOKING STATUS. HOWEVER, DIFFERENTIAL METHYLATION OF TWO REPLICATED PIK3CD (PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT DELTA) SITES WERE ASSOCIATED WITH LUNG FUNCTION AT ENROLLMENT (P < 0.05). WE ALSO OBSERVED ASSOCIATIONS BETWEEN DNA METHYLATION AND GENE EXPRESSION FOR THE PIK3CD SITES.CONCLUSIONS: THIS STUDY IS THE FIRST TO IDENTIFY VARIABLE DNA METHYLATION ASSOCIATED WITH ALL-CAUSE MORTALITY IN SMOKERS WITH AND WITHOUT COPD. EVALUATING PREDICTIVE EPIGENOMIC MARKS OF SMOKERS IN PERIPHERAL BLOOD MAY ALLOW FOR TARGETED RISK STRATIFICATION AND AID IN DELIVERY OF FUTURE TAILORED THERAPEUTIC INTERVENTIONS. 2020 15 2205 29 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 16 1343 35 DETECTING CORD BLOOD CELL TYPE-SPECIFIC EPIGENETIC ASSOCIATIONS WITH GESTATIONAL DIABETES MELLITUS AND EARLY CHILDHOOD GROWTH. BACKGROUND: EPIGENOME-WIDE ASSOCIATION STUDIES (EWAS) HAVE PROVIDED OPPORTUNITIES TO UNDERSTAND THE ROLE OF EPIGENETIC MECHANISMS IN DEVELOPMENT AND PATHOPHYSIOLOGY OF MANY CHRONIC DISEASES. HOWEVER, AN IMPORTANT LIMITATION OF CONVENTIONAL EWAS IS THAT PROFILES OF EPIGENETIC VARIABILITY ARE OFTEN OBTAINED IN SAMPLES OF MIXED CELL TYPES. HERE, WE AIM TO ASSESS WHETHER CHANGES IN CORD BLOOD DNA METHYLATION (DNAM) ASSOCIATED WITH GESTATIONAL DIABETES MELLITUS (GDM) EXPOSURE AND EARLY CHILDHOOD GROWTH MARKERS OCCUR IN A CELL TYPE-SPECIFIC MANNER. RESULTS: WE ANALYZED 275 CORD BLOOD SAMPLES COLLECTED AT DELIVERY FROM A PROSPECTIVE PRE-BIRTH COHORT WITH GENOME-WIDE DNAM PROFILED BY THE ILLUMINA METHYLATIONEPIC ARRAY. WE ESTIMATED PROPORTIONS OF SEVEN COMMON CELL TYPES IN EACH SAMPLE USING A CORD BLOOD-SPECIFIC DNAM REFERENCE PANEL. LEVERAGING A RECENTLY DEVELOPED APPROACH NAMED CELLDMC, WE PERFORMED CELL TYPE-SPECIFIC EWAS TO IDENTIFY CPG LOCI SIGNIFICANTLY ASSOCIATED WITH GDM, OR 3-YEAR-OLD BODY MASS INDEX (BMI) Z-SCORE. A TOTAL OF 1410 CPG LOCI DISPLAYED SIGNIFICANT CELL TYPE-SPECIFIC DIFFERENCES IN METHYLATION LEVEL BETWEEN 23 GDM CASES AND 252 CONTROLS WITH A FALSE DISCOVERY RATE < 0.05. GENE ONTOLOGY ENRICHMENT ANALYSIS INDICATED THAT LDL TRANSPORTATION EMERGED FROM CPG SPECIFICALLY IDENTIFIED FROM B-CELLS DNAM ANALYSES AND THE MITOGEN-ACTIVATED PROTEIN KINASE PATHWAY EMERGED FROM CPG SPECIFICALLY IDENTIFIED FROM NATURAL KILLER CELLS DNAM ANALYSES. IN ADDITION, WE IDENTIFIED FOUR AND SIX LOCI ASSOCIATED WITH 3-YEAR-OLD BMI Z-SCORE THAT WERE SPECIFIC TO CD8+ T-CELLS AND MONOCYTES, RESPECTIVELY. BY PERFORMING GENOME-WIDE PERMUTATION TESTS, WE VALIDATED THAT MOST OF OUR DETECTED SIGNALS HAD LOW FALSE POSITIVE RATES. CONCLUSION: COMPARED TO CONVENTIONAL EWAS ADJUSTING FOR THE EFFECTS OF CELL TYPE HETEROGENEITY, THE PROPOSED APPROACH BASED ON CELL TYPE-SPECIFIC EWAS COULD PROVIDE ADDITIONAL BIOLOGICALLY MEANINGFUL ASSOCIATIONS BETWEEN CPG METHYLATION, PRENATAL MATERNAL GDM OR 3-YEAR-OLD BMI. WITH CAREFUL VALIDATION, THESE FINDINGS MAY PROVIDE NEW INSIGHTS INTO THE PATHOGENESIS, PROGRAMMING, AND CONSEQUENCES OF RELATED CHILDHOOD METABOLIC DYSREGULATION. THEREFORE, WE PROPOSE THAT CELL TYPE-SPECIFIC ANALYSES ARE WORTH CAUTIOUS EXPLORATIONS. 2021 17 4256 30 METHYLOMIC MARKERS OF PERSISTENT CHILDHOOD ASTHMA: A LONGITUDINAL STUDY OF ASTHMA-DISCORDANT MONOZYGOTIC TWINS. BACKGROUND: ASTHMA IS THE MOST COMMON CHRONIC INFLAMMATORY DISORDER IN CHILDREN. THE AETIOLOGY OF ASTHMA PATHOLOGY IS COMPLEX AND HIGHLY HETEROGENEOUS, INVOLVING THE INTERPLAY BETWEEN GENETIC AND ENVIRONMENTAL RISK FACTORS THAT IS HYPOTHESIZED TO INVOLVE EPIGENETIC PROCESSES. OUR AIM WAS TO EXPLORE WHETHER METHYLOMIC VARIATION IN EARLY CHILDHOOD IS ASSOCIATED WITH DISCORDANCE FOR ASTHMA SYMPTOMS WITHIN MONOZYGOTIC (MZ) TWIN PAIRS RECRUITED FROM THE ENVIRONMENTAL RISK (E-RISK) LONGITUDINAL TWIN STUDY. WE ALSO AIMED TO IDENTIFY DIFFERENCES IN DNA METHYLATION THAT ARE ASSOCIATED WITH ASTHMA THAT DEVELOPS IN CHILDHOOD AND PERSISTS INTO EARLY ADULTHOOD AS THESE MAY REPRESENT USEFUL PROGNOSTIC BIOMARKERS. RESULTS: WE EXAMINED GENOME-WIDE PATTERNS OF DNA METHYLATION IN BUCCAL CELL SAMPLES COLLECTED FROM 37 MZ TWIN PAIRS DISCORDANT FOR ASTHMA AT AGE 10. DNA METHYLATION AT INDIVIDUAL CPG SITES DEMONSTRATED SIGNIFICANT VARIABILITY WITHIN DISCORDANT MZ TWIN PAIRS WITH THE TOP-RANKED NOMINALLY SIGNIFICANT DIFFERENTIALLY METHYLATED POSITION (DMP) LOCATED IN THE HGSNAT GENE. WE STRATIFIED OUR ANALYSIS BY ASSESSING DNA METHYLATION DIFFERENCES IN A SUB-GROUP OF MZ TWIN PAIRS WHO REMAINED PERSISTENTLY DISCORDANT FOR ASTHMA AT AGE 18. THE TOP-RANKED NOMINALLY SIGNIFICANT DMP ASSOCIATED WITH PERSISTING ASTHMA IS LOCATED IN THE VICINITY OF THE HLX GENE, WHICH HAS BEEN PREVIOUSLY IMPLICATED IN CHILDHOOD ASTHMA. CONCLUSIONS: WE IDENTIFIED DNA METHYLATION DIFFERENCES ASSOCIATED WITH CHILDHOOD ASTHMA IN PERIPHERAL DNA SAMPLES FROM DISCORDANT MZ TWIN PAIRS. OUR DATA SUGGEST THAT DIFFERENCES IN DNA METHYLATION ASSOCIATED WITH CHILDHOOD ASTHMA WHICH PERSISTS INTO EARLY ADULTHOOD ARE DISTINCT FROM THOSE ASSOCIATED WITH ASTHMA WHICH REMITS. 2015 18 404 27 ANALYSIS OF EPIGENETIC AGE PREDICTORS IN PAIN-RELATED CONDITIONS. CHRONIC PAIN PREVALENCE IS HIGH WORLDWIDE AND INCREASES AT OLDER AGES. SIGNS OF PREMATURE AGING HAVE BEEN ASSOCIATED WITH CHRONIC PAIN, BUT FEW STUDIES HAVE INVESTIGATED AGING BIOMARKERS IN PAIN-RELATED CONDITIONS. A SET OF DNA METHYLATION (DNAM)-BASED ESTIMATES OF AGE, CALLED "EPIGENETIC CLOCKS," HAS BEEN PROPOSED AS BIOLOGICAL MEASURES OF AGE-RELATED ADVERSE PROCESSES, MORBIDITY, AND MORTALITY. THE AIM OF THIS STUDY IS TO ASSESS IF DIFFERENT PAIN-RELATED PHENOTYPES SHOW ALTERATIONS IN DNAM AGE. IN OUR ANALYSIS, WE CONSIDERED THREE COHORTS FOR WHICH WHOLE-BLOOD DNAM DATA WERE AVAILABLE: HEAT PAIN SENSITIVITY (HPS), INCLUDING 20 MONOZYGOTIC TWIN PAIRS DISCORDANT FOR HEAT PAIN TEMPERATURE THRESHOLD; FIBROMYALGIA (FM), INCLUDING 24 CASES AND 20 CONTROLS; AND HEADACHE, INCLUDING 22 CHRONIC MIGRAINE AND MEDICATION OVERUSE HEADACHE PATIENTS (MOH), 18 EPISODIC MIGRAINEURS (EM), AND 13 HEALTHY SUBJECTS. WE USED THE HORVATH'S EPIGENETIC AGE CALCULATOR TO OBTAIN DNAM-BASED ESTIMATES OF EPIGENETIC AGE, TELOMERE LENGTH, LEVELS OF 7 PROTEINS IN PLASMA, NUMBER OF SMOKED PACKS OF CIGARETTES PER YEAR, AND BLOOD CELL COUNTS. WE DID NOT FIND DIFFERENCES IN EPIGENETIC AGE ACCELERATION, CALCULATED USING FIVE DIFFERENT EPIGENETIC CLOCKS, BETWEEN SUBJECTS DISCORDANT FOR PAIN-RELATED PHENOTYPES. TWINS WITH HIGH HPS HAD INCREASED CD8+ T CELL COUNTS (NOMINAL P = 0.028). HPS THRESHOLDS WERE NEGATIVELY ASSOCIATED WITH ESTIMATED LEVELS OF GDF15 (NOMINAL P = 0.008). FM PATIENTS SHOWED DECREASED NAIVE CD4+ T CELL COUNTS COMPARED WITH CONTROLS (NOMINAL P = 0.015). THE SEVERITY OF FM MANIFESTATIONS EXPRESSED THROUGH VARIOUS EVALUATION TESTS WAS ASSOCIATED WITH DECREASED LEVELS OF LEPTIN, SHORTER LENGTH OF TELOMERES, AND REDUCED CD8+ T AND NATURAL KILLER CELL COUNTS (NOMINAL P < 0.05), WHILE THE DURATION OF PAINFUL SYMPTOMS WAS POSITIVELY ASSOCIATED WITH TELOMERE LENGTH (NOMINAL P = 0.034). NO DIFFERENCES IN DNAM-BASED ESTIMATES WERE DETECTED FOR MOH OR EM COMPARED WITH CONTROLS. IN SUMMARY, OUR STUDY SUGGESTS THAT HPS, FM, AND MOH/EM DO NOT SHOW SIGNS OF EPIGENETIC AGE ACCELERATION IN WHOLE BLOOD, WHILE HPS AND FM ARE ASSOCIATED WITH DNAM-BASED ESTIMATES OF IMMUNOLOGICAL PARAMETERS, PLASMA PROTEINS, AND TELOMERE LENGTH. FUTURE STUDIES SHOULD EXTEND THESE OBSERVATIONS IN LARGER COHORTS. 2020 19 6761 23 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 20 2643 28 EPIGENOMIC ASSOCIATION ANALYSIS IDENTIFIES SMOKING-RELATED DNA METHYLATION SITES IN AFRICAN AMERICANS. CIGARETTE SMOKING IS AN ENVIRONMENTAL RISK FACTOR FOR MANY CHRONIC DISEASES, AND DISEASE RISK CAN OFTEN BE MANAGED BY SMOKING CONTROL. SMOKING CAN INDUCE CELLULAR AND MOLECULAR CHANGES, INCLUDING EPIGENETIC MODIFICATION, BUT THE SHORT- AND LONG-TERM EPIGENETIC MODIFICATIONS CAUSED BY CIGARETTE SMOKING AT THE GENE LEVEL HAVE NOT BEEN WELL UNDERSTOOD. RECENT STUDIES HAVE IDENTIFIED SMOKING-RELATED DNA METHYLATION (DNAM) SITES IN CAUCASIANS. TO DETERMINE WHETHER THE SAME DNAM SITES ASSOCIATE WITH SMOKING IN AFRICAN AMERICANS, AND TO IDENTIFY NOVEL SMOKING-RELATED DNAM SITES, WE CONDUCTED A METHYLOME-WIDE ASSOCIATION STUDY OF CIGARETTE SMOKING USING A DISCOVERY SAMPLE OF 972 AFRICAN AMERICANS, AND A REPLICATION SAMPLE OF 239 AFRICAN AMERICANS WITH TWO ARRAY-BASED METHODS. AMONG 15 DNAM SITES SIGNIFICANTLY ASSOCIATED WITH SMOKING AFTER CORRECTION FOR MULTIPLE TESTING IN OUR DISCOVERY SAMPLE, 5 DNAM SITES ARE REPLICATED IN AN INDEPENDENT COHORT, AND 14 SITES IN THE REPLICATION SAMPLE HAVE EFFECTS IN THE SAME DIRECTION AS IN THE DISCOVERY SAMPLE. THE TOP TWO SMOKING-RELATED DNAM SITES IN F2RL3 (FACTOR II RECEPTOR-LIKE 3) AND GPR15 (G-PROTEIN-COUPLED RECEPTOR 15) OBSERVED IN AFRICAN AMERICANS ARE CONSISTENT WITH PREVIOUS FINDINGS IN CAUCASIANS. THE ASSOCIATIONS BETWEEN THE REPLICATED DNAM SITES AND SMOKING REMAIN SIGNIFICANT AFTER ADJUSTING FOR GENETIC BACKGROUND. DESPITE THE DISTINCT GENETIC BACKGROUND BETWEEN AFRICAN AMERICANS AND CAUCASIANS, THE DNAM FROM THE TWO ETHNIC GROUPS SHARES COMMON ASSOCIATIONS WITH CIGARETTE SMOKING, WHICH SUGGESTS A COMMON MOLECULAR MECHANISM OF EPIGENETIC MODIFICATION INFLUENCED BY ENVIRONMENTAL EXPOSURE. 2013