1 1080 50 CLOSED COMPLETE GENOME SEQUENCES OF TWO NONTYPEABLE HAEMOPHILUS INFLUENZAE STRAINS CONTAINING NOVEL MODA ALLELES FROM THE SPUTUM OF PATIENTS WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE. NONTYPEABLE HAEMOPHILUS INFLUENZAE (NTHI) IS AN IMPORTANT BACTERIAL PATHOGEN THAT CAUSES OTITIS MEDIA AND EXACERBATIONS OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD). HERE, WE REPORT THE COMPLETE GENOME SEQUENCES OF NTHI STRAINS 10P129H1 AND 84P36H1, ISOLATED FROM COPD PATIENTS, WHICH CONTAIN THE PHASE-VARIABLE EPIGENETIC REGULATORS MODA15 AND MODA18, RESPECTIVELY. 2018 2 4718 36 NON-TYPEABLE HAEMOPHILUS INFLUENZAE ISOLATES FROM PATIENTS WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE CONTAIN NEW PHASE-VARIABLE MODA METHYLTRANSFERASE ALLELES CONTROLLING PHASEVARIONS. PHASEVARIONS (PHASE-VARIABLE REGULONS) ARE EMERGING AS AN IMPORTANT AREA OF BACTERIAL GENE REGULATION. MANY BACTERIAL PATHOGENS CONTAIN PHASEVARIONS, WITH GENE EXPRESSION CONTROLLED BY THE PHASE-VARIABLE EXPRESSION OF DNA METHYLTRANSFERASES VIA EPIGENETIC MECHANISMS. NON-TYPEABLE HAEMOPHILUS INFLUENZAE (NTHI) CONTAINS THE PHASE-VARIABLE METHYLTRANSFERASE MODA, OF WHICH MULTIPLE ALLELIC VARIANTS EXIST (MODA1-21). WE HAVE PREVIOUSLY DEMONSTRATED 5 OF 21 THESE MODA ALLELES ARE OVERREPRESENTED IN NTHI STRAINS ISOLATED FROM CHILDREN WITH MIDDLE EAR INFECTIONS. IN THIS STUDY WE INVESTIGATED THE MODA ALLELE DISTRIBUTION IN NTHI STRAINS ISOLATED FROM PATIENTS WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE, COPD. WE DEMONSTRATE THAT THE DISTRIBUTION OF MODA ALLELES IN A LARGE PANEL OF COPD ISOLATES IS DIFFERENT TO THE DISTRIBUTION SEEN IN MIDDLE EAR INFECTIONS, SUGGESTING DIFFERENT MODA ALLELES MAY PROVIDE DISTINCT ADVANTAGES IN THE DIFFERING NICHES OF THE MIDDLE EAR AND COPD AIRWAYS. WE ALSO IDENTIFIED TWO NEW PHASE-VARIABLE MODA ALLELES - MODA15 AND MODA18 - AND DEMONSTRATE THAT THESE ALLELES METHYLATE DISTINCT DNA SEQUENCES AND CONTROL UNIQUE PHASEVARIONS. THE MODA15 AND MODA18 ALLELES HAVE ONLY BEEN OBSERVED IN COPD ISOLATES, INDICATING THAT THESE TWO ALLELES MAY BE MARKERS FOR ISOLATES LIKELY TO CAUSE EXACERBATIONS OF COPD. 2019 3 1124 29 COMPLETE GENOME SEQUENCE OF MORAXELLA CATARRHALIS STRAIN CCRI-195ME, ISOLATED FROM THE MIDDLE EAR. MORAXELLA CATARRHALIS IS AN IMPORTANT BACTERIAL PATHOGEN THAT CAUSES OTITIS MEDIA AND EXACERBATIONS OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE. HERE, WE REPORT THE COMPLETE GENOME SEQUENCE OF M. CATARRHALIS STRAIN CCRI-195ME, WHICH CONTAINS THE PHASE-VARIABLE EPIGENETIC REGULATOR MODM3. 2017 4 2273 25 EPIGENETIC REGULATION ALTERS BIOFILM ARCHITECTURE AND COMPOSITION IN MULTIPLE CLINICAL ISOLATES OF NONTYPEABLE HAEMOPHILUS INFLUENZAE. BIOFILMS PLAY A CRITICAL ROLE IN THE COLONIZATION, PERSISTENCE, AND PATHOGENESIS OF MANY HUMAN PATHOGENS. MULTIPLE MUCOSA-ASSOCIATED PATHOGENS HAVE EVOLVED A MECHANISM OF RAPID ADAPTATION, TERMED THE PHASEVARION, WHICH FACILITATES A COORDINATED REGULATION OF NUMEROUS GENES THROUGHOUT THE BACTERIAL GENOME. THIS EPIGENETIC REGULATION OCCURS VIA PHASE VARIATION OF A DNA METHYLTRANSFERASE, MOD. THE PHASEVARION OF NONTYPEABLE HAEMOPHILUS INFLUENZAE (NTHI) SIGNIFICANTLY AFFECTS THE SEVERITY OF EXPERIMENTAL OTITIS MEDIA AND REGULATES SEVERAL DISEASE-RELATED PROCESSES. HOWEVER, THE ROLE OF THE NTHI PHASEVARION IN BIOFILM FORMATION IS UNCLEAR. THE PRESENT STUDY SHOWS THAT THE PHASEVARIONS OF MULTIPLE NTHI CLINICAL ISOLATES REGULATE IN VITRO BIOFILM FORMATION UNDER DISEASE-SPECIFIC MICROENVIRONMENTAL CONDITIONS. THE IMPACT OF PHASEVARION REGULATION WAS GREATEST UNDER ALKALINE CONDITIONS THAT MIMIC THOSE KNOWN TO OCCUR IN THE MIDDLE EAR DURING DISEASE. UNDER ALKALINE CONDITIONS, NTHI STRAINS THAT EXPRESS THE MODA2 METHYLTRANSFERASE FORMED BIOFILMS WITH SIGNIFICANTLY GREATER BIOMASS AND LESS DISTINCT ARCHITECTURE THAN THOSE FORMED BY A MODA2-DEFICIENT POPULATION. THE BIOFILMS FORMED BY NTHI STRAINS THAT EXPRESS MODA2 ALSO CONTAINED LESS EXTRACELLULAR DNA (EDNA) AND SIGNIFICANTLY LESS EXTRACELLULAR HU, A DNABII DNA-BINDING PROTEIN CRITICAL FOR BIOFILM STRUCTURAL STABILITY. STABLE BIOFILM STRUCTURE IS CRITICAL FOR BACTERIAL PATHOGENESIS AND PERSISTENCE IN MULTIPLE EXPERIMENTAL MODELS OF DISEASE. THESE RESULTS IDENTIFY A ROLE FOR THE PHASEVARION IN REGULATION OF BIOFILM FORMATION, A PROCESS INTEGRAL TO THE CHRONIC NATURE OF MANY INFECTIONS. UNDERSTANDING THE ROLE OF THE PHASEVARION IN BIOFILM FORMATION IS CRITICAL TO THE DEVELOPMENT OF PREVENTION AND TREATMENT STRATEGIES FOR THESE CHRONIC DISEASES.IMPORTANCE UPPER RESPIRATORY TRACT INFECTIONS ARE THE NUMBER ONE REASON FOR A CHILD TO VISIT THE EMERGENCY DEPARTMENT, AND OTITIS MEDIA (MIDDLE EAR INFECTION) RANKS THIRD OVERALL. BIOFILMS CONTRIBUTE SIGNIFICANTLY TO THE CHRONIC NATURE OF BACTERIAL RESPIRATORY TRACT INFECTIONS, INCLUDING OTITIS MEDIA, AND MAKE THESE DISEASES PARTICULARLY DIFFICULT TO TREAT. SEVERAL MUCOSA-ASSOCIATED HUMAN PATHOGENS UTILIZE A MECHANISM OF RAPID ADAPTATION TERMED THE PHASEVARION, OR PHASEVARIABLE REGULON, TO RESIST ENVIRONMENTAL AND HOST IMMUNE PRESSURES. IN THIS STUDY, WE ASSESSED THE ROLE OF THE PHASEVARION IN REGULATION OF BIOFILM FORMATION BY NONTYPEABLE HAEMOPHILUS INFLUENZAE (NTHI), WHICH CAUSES NUMEROUS RESPIRATORY TRACT DISEASES. WE FOUND THAT THE NTHI PHASEVARION REGULATES BIOFILM STRUCTURE AND CRITICAL BIOFILM MATRIX COMPONENTS UNDER DISEASE-SPECIFIC CONDITIONS. THE FINDINGS OF THIS WORK COULD BE SIGNIFICANT IN THE DESIGN OF IMPROVED STRATEGIES AGAINST NTHI INFECTIONS, AS WELL AS DISEASES DUE TO OTHER PATHOGENS THAT UTILIZE A PHASEVARION. 2018 5 4395 27 MODM DNA METHYLTRANSFERASE METHYLOME ANALYSIS REVEALS A POTENTIAL ROLE FOR MORAXELLA CATARRHALIS PHASEVARIONS IN OTITIS MEDIA. MORAXELLA CATARRHALIS IS A SIGNIFICANT CAUSE OF OTITIS MEDIA AND EXACERBATIONS OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE. HERE, WE CHARACTERIZE A PHASE-VARIABLE DNA METHYLTRANSFERASE (MODM), WHICH CONTAINS 5'-CAAC-3' REPEATS IN ITS OPEN READING FRAME THAT MEDIATE HIGH-FREQUENCY MUTATION RESULTING IN REVERSIBLE ON/OFF SWITCHING OF MODM EXPRESSION. THREE MODM ALLELES HAVE BEEN IDENTIFIED (MODM1-3), WITH MODM2 BEING THE MOST COMMONLY FOUND ALLELE. USING SINGLE-MOLECULE, REAL-TIME (SMRT) GENOME SEQUENCING AND METHYLOME ANALYSIS, WE HAVE DETERMINED THAT THE MODM2 METHYLATION TARGET IS 5'-GAR(M6)AC-3', AND 100% OF THESE SITES ARE METHYLATED IN THE GENOME OF THE M. CATARRHALIS 25239 MODM2 ON STRAIN. PROTEOMIC ANALYSIS OF MODM2 ON AND OFF VARIANTS REVEALED THAT MODM2 REGULATES EXPRESSION OF MULTIPLE GENES THAT HAVE POTENTIAL ROLES IN COLONIZATION, INFECTION, AND PROTECTION AGAINST HOST DEFENSES. INVESTIGATION OF THE DISTRIBUTION OF MODM ALLELES IN A PANEL OF M. CATARRHALIS STRAINS, ISOLATED FROM THE NASOPHARYNX OF HEALTHY CHILDREN OR MIDDLE EAR EFFUSIONS FROM PATIENTS WITH OTITIS MEDIA, REVEALED A STATISTICALLY SIGNIFICANT ASSOCIATION OF MODM3 WITH OTITIS MEDIA ISOLATES. THE MODULATION OF GENE EXPRESSION VIA THE MODM PHASE-VARIABLE REGULON (PHASEVARION), AND THE SIGNIFICANT ASSOCIATION OF THE MODM3 ALLELE WITH OTITIS MEDIA, SUGGESTS A KEY ROLE FOR MODM PHASEVARIONS IN THE PATHOGENESIS OF THIS ORGANISM. 2014 6 6261 26 THE MORAXELLA CATARRHALIS PHASE-VARIABLE DNA METHYLTRANSFERASE MODM3 IS AN EPIGENETIC REGULATOR THAT AFFECTS BACTERIAL SURVIVAL IN AN IN VIVO MODEL OF OTITIS MEDIA. BACKGROUND: MORAXELLA CATARRHALIS IS A LEADING CAUSE OF OTITIS MEDIA (OM) AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD). M. CATARRHALIS CONTAINS A TYPE III DNA ADENINE METHYLTRANSFERASE (MODM) THAT IS PHASE-VARIABLY EXPRESSED (I.E., ITS EXPRESSION IS SUBJECT TO RANDOM, REVERSIBLE ON/OFF SWITCHING). MODM HAS SIX TARGET RECOGNITION DOMAIN ALLELES (MODM1-6), AND WE HAVE PREVIOUSLY SHOWN THAT MODM2 IS THE PREDOMINANT ALLELE, WHILE MODM3 IS ASSOCIATED WITH OM. PHASE-VARIABLE DNA METHYLTRANSFERASES MEDIATE EPIGENETIC REGULATION AND MODULATE PATHOGENESIS IN SEVERAL BACTERIA. MODM2 OF M. CATARRHALIS REGULATES THE EXPRESSION OF A PHASEVARION CONTAINING GENES IMPORTANT FOR COLONIZATION AND INFECTION. HERE WE DESCRIBE THE PHASE-VARIABLE EXPRESSION OF MODM3, THE MODM3 METHYLATION SITE AND THE SUITE OF GENES REGULATED WITHIN THE MODM3 PHASEVARION. RESULTS: PHASE-VARIABLE EXPRESSION OF MODM3, MEDIATED BY VARIATION IN LENGTH OF A 5'-(CAAC)(N)-3' TETRANUCLEOTIDE REPEAT TRACT IN THE OPEN READING FRAME WAS DEMONSTRATED IN M. CATARRHALIS STRAIN CCRI-195ME WITH GENESCAN FRAGMENT LENGTH ANALYSIS AND WESTERN IMMUNOBLOT. WE DETERMINED THAT MODM3 IS AN ACTIVE N6-ADENINE METHYLTRANSFERASE THAT METHYLATES THE SEQUENCE 5'-AC(M6)ATC-3'. METHYLATION WAS DETECTED AT ALL 4446 5'-ACATC-3' SITES IN THE GENOME WHEN MODM3 IS EXPRESSED. RNASEQ ANALYSIS IDENTIFIED 31 GENES THAT ARE DIFFERENTIALLY EXPRESSED BETWEEN MODM3 ON AND OFF VARIANTS, INCLUDING FIVE GENES THAT ARE INVOLVED IN THE RESPONSE TO OXIDATIVE AND NITROSATIVE STRESS, WITH POTENTIAL ROLES IN BIOFILM FORMATION AND SURVIVAL IN ANAEROBIC ENVIRONMENTS. AN IN VIVO CHINCHILLA (CHINCHILLA LANIGERA) MODEL OF OTITIS MEDIA DEMONSTRATED THAT TRANSBULLAR CHALLENGE WITH THE MODM3 OFF VARIANT RESULTED IN AN INCREASED MIDDLE EAR BACTERIAL LOAD COMPARED TO A MODM3 ON VARIANT. IN ADDITION, CO-INFECTION EXPERIMENTS WITH NTHI AND M. CATARRHALIS MODM3 ON OR MODM3 OFF VARIANTS REVEALED THAT PHASE VARIATION OF MODM3 ALTERED SURVIVAL OF NTHI IN THE MIDDLE EAR DURING EARLY AND LATE STAGE INFECTION. CONCLUSIONS: PHASE VARIATION OF MODM3 EPIGENETICALLY REGULATES THE EXPRESSION OF A PHASEVARION CONTAINING MULTIPLE GENES THAT ARE POTENTIALLY IMPORTANT IN THE PROGRESSION OF OTITIS MEDIA. 2019 7 4835 15 ON THE RELATIONSHIP BETWEEN THEORETICAL PRESUMPTIONS ASBESTOS GENOTOXICITY AND THE PRACTICAL MONITORING OF EXPOSED WORKERS. FROM THE GENOTOXIC VIEWPOINT, THERE EXISTS A SUFFICIENT EVIDENCE FOR ASBESTOS CARCINOGENICITY TO HUMAN POPULATION AND ANIMALS. ASBESTOS IS A SOLID CANCER PROMOTER (COCARCINOGEN) OF NON-MUTAGENIC CHARACTER HAVING EPIGENETIC EFFECTS (15, 16). NO DATA HAVE BEEN PUBLISHED ON ITS MUTAGENIC ACTIVITY IN "IN VIVO" CONDITIONS IN MAN. THE ONLY RESULTS ARE THOSE OF OUR PILOT STUDY CARRIED OUT IN THE PERIOD OF 1981-1983, WHICH CAST DOUBTS ON THE OFFICIAL VIEW OF NON-MUTAGENIC CHARACTER OF ASBESTOS--AT LEAST UNDER OCCUPATIONAL CONDITIONS OF ITS PROCESSING (34, 36, 37). THE STUDY PRESENTED HERE REPRESENTS TEN YEARS' EFFORTS MADE IN THE BIOLOGICAL (CYTOGENETIC) MONITORING OF PERSONS OCCUPATIONALLY EXPOSED TO ASBESTOS IN A FACTORY FOR ITS PROCESSING (OCCUPATIONAL RISK). SIMULTANEOUSLY, A PRELIMINARY ANSWER IS GIVEN TO THE QUESTION WHETHER THE OSINEK FACTORY (SITUATED IN A HOUSING AREA) IS OR IS NOT DANGEROUS FOR INHABITANTS OF THE TOWN OF KOSTELEC NAD ORLICI, NAMELY FOR THEIR GENETIC APPARATUS (ENVIRONMENTAL RISK). USING THE METHOD OF CHROMOSOME ABERRATIONS ANALYSIS IN PERIPHERAL BLOOD LYMPHOCYTES, A TOTAL OF 431 SUBJECTS (245 MALES AND 186 FEMALES) WERE EXAMINED IN THE PERIOD OF 1981 TO 1988. OF THESE, 111 PERSONS WERE FROM CONTROL WORKPLACES (FROM OSINEK OR--STARTING FROM 1984--FROM OTHER PLANTS IN KOSTELEC NAD ORLICI; IN ADDITION TO THAT 14 PENSIONERS WITHOUT ANY OCCUPATIONAL EXPOSURE WERE EXAMINED). THE AVERAGE AGE OF WORKERS EXPOSED TO ASBESTOS RISK WAS 42.7 YEARS, IN THE CONTROLS IT WAS 43.9 YEARS, IN PENSIONERS EXPOSED TO ASBESTOS EARLIER 63.5 YEARS AND IN THOSE NEVER EXPOSED TO ASBESTOS 66.5 YEARS. THE AVERAGE NUMBER OF YEARS SPENT AT OSINEK FACTORY AMOUNTED TO 21.5 YEARS. ABOUT ONE THIRD OF EMPLOYEES WERE FOUND TO SUFFER FROM ALLERGIES (FIRST OF ALL THOSE OF AIR PASSAGES) AND ONE SIXTH FROM CHRONIC AILMENTS OF THE UPPER AIR PASSAGES (STAPHYLOCOCCUS AUREUS, HAEMOPHILUS INFLUENZAE AND STREPTOCOCCUS BETA-HAEMOLYTICUS WERE DIAGNOSED MOST FREQUENTLY). A THIRD PART OF WORKERS FROM HIGH-RISK WORKSHOPS ARE SMOKERS, ONLY A FOURTH OF THE CONTROLS. ABOUT 40% OF WORKERS REGULARLY CONSUME ALCOHOLIC DRINKS. THE AVERAGE MORBIDITY RATE AT OSINEK IN 1981 TO 1988 WAS 6.3% (IN WORKERS AS HIGH AS 9%), WHICH IS ABOUT 2% HIGHER AS COMPARED WITH MEAN VALUES OBTAINED IN THE DISTRICT OF RYCHNOV NAD KNEZNOU AND EAST-BOHEMIAN REGION. WITHIN THE NINE-YEAR PERIOD (1981-1989), 21 OCCUPATIONAL DISEASES WERE DIAGNOSED, WHILE IN THE PREVIOUS 24 YEARS THERE WERE 24 CASES OF AN OCCUPATIONAL DISEASE. EARLIER THEY WERE MAINLY ASBESTOSES (87%), IN THE LAST PERIOD MAINLY CANCER DISEASES COINCIDING WITH ASBESTOSIS (81%).(ABSTRACT TRUNCATED AT 400 WORDS) 1992 8 4494 25 MORAXELLA CATARRHALIS RESTRICTION-MODIFICATION SYSTEMS ARE ASSOCIATED WITH PHYLOGENETIC LINEAGE AND DISEASE. MORAXELLA CATARRHALIS IS A HUMAN-ADAPTED PATHOGEN, AND A MAJOR CAUSE OF OTITIS MEDIA (OM) AND EXACERBATIONS OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE. THE SPECIES IS COMPRISED OF TWO MAIN PHYLOGENETIC LINEAGES, RB1 AND RB2/3. RESTRICTION-MODIFICATION (R-M) SYSTEMS ARE AMONG THE FEW LINEAGE-ASSOCIATED GENES IDENTIFIED IN OTHER BACTERIAL GENERA AND HAVE MULTIPLE FUNCTIONS INCLUDING DEFENSE AGAINST FOREIGN INVADING DNA, MAINTENANCE OF SPECIATION, AND EPIGENETIC REGULATION OF GENE EXPRESSION. HERE, WE DEFINE THE REPERTOIRE OF R-M SYSTEMS IN 51 PUBLICLY AVAILABLE M. CATARRHALIS GENOMES AND REPORT THEIR DISTRIBUTION AMONG M. CATARRHALIS PHYLOGENETIC LINEAGES. AN ASSOCIATION WITH PHYLOGENETIC LINEAGE (RB1 OR RB2/3) WAS OBSERVED FOR SIX R-M SYSTEMS, WHICH MAY CONTRIBUTE TO THE EVOLUTION OF THE LINEAGES BY RESTRICTING DNA TRANSFORMATION. IN ADDITION, WE OBSERVED A RELATIONSHIP BETWEEN A MUTUALLY EXCLUSIVE TYPE I R-M SYSTEM AND A TYPE III R-M SYSTEM AT A SINGLE LOCUS CONSERVED THROUGHOUT A GEOGRAPHICALLY AND CLINICALLY DIVERSE SET OF M. CATARRHALIS ISOLATES. THE TYPE III R-M SYSTEM AT THIS LOCUS CONTAINS THE PHASE-VARIABLE TYPE III DNA METHYLTRANSFERASE, MODM, WHICH CONTROLS A PHASEVARION (PHASE-VARIABLE REGULON). WE OBSERVED AN ASSOCIATION BETWEEN MODM PRESENCE AND OM-ASSOCIATED MIDDLE EAR ISOLATES, INDICATING A POTENTIAL ROLE FOR MODM-MEDIATED EPIGENETIC REGULATION IN OM PATHOBIOLOGY. 2018 9 4493 17 MORAXELLA CATARRHALIS INDUCES INFLAMMATORY RESPONSE OF BRONCHIAL EPITHELIAL CELLS VIA MAPK AND NF-KAPPAB ACTIVATION AND HISTONE DEACETYLASE ACTIVITY REDUCTION. MORAXELLA CATARRHALIS IS A MAJOR CAUSE OF INFECTIOUS EXACERBATIONS OF CHRONIC OBSTRUCTIVE LUNG DISEASE (COPD) AND MAY ALSO CONTRIBUTE TO THE PATHOGENESIS OF COPD. LITTLE IS KNOWN ABOUT M. CATARRHALIS-BRONCHIAL EPITHELIUM INTERACTION. WE INVESTIGATED ACTIVATION OF M. CATARRHALIS INFECTED BRONCHIAL EPITHELIAL CELLS AND CHARACTERIZED THE SIGNAL TRANSDUCTION PATHWAYS. MOREOVER, WE TESTED THE HYPOTHESIS THAT THE M. CATARRHALIS-INDUCED CYTOKINE EXPRESSION IS REGULATED BY ACETYLATION OF HISTONE RESIDUES AND CONTROLLED BY HISTONE DEACETYLASE ACTIVITY (HDAC). WE DEMONSTRATED THAT M. CATARRHALIS INDUCED A STRONG TIME- AND DOSE-DEPENDENT INFLAMMATORY RESPONSE IN THE BRONCHIAL EPITHELIAL CELL LINE (BEAS-2B), CHARACTERIZED BY THE RELEASE OF IL-8 AND GM-CSF. FOR THIS CYTOKINE LIBERATION ACTIVATION OF THE ERK AND P38 MITOGEN-ACTIVATED PROTEIN (MAP) KINASES AND TRANSCRIPTION FACTOR NF-KAPPAB WAS REQUIRED. FURTHERMORE, M. CATARRHALIS-INFECTED BRONCHIAL EPITHELIAL CELLS SHOWED AN ENHANCED ACETYLATION OF HISTONE H3 AND H4 GLOBALLY AND AT THE PROMOTER OF THE IL8 GENE. PREVENTING HISTONE DEACETYLATION BY THE HISTONE DEACETYLASE INHIBITOR TRICHOSTATIN A AUGMENTED THE M. CATARRHALIS-INDUCED IL-8 RESPONSE. AFTER EXPOSURE TO M. CATARRHALIS, WE FOUND A DECREASE IN GLOBAL HISTONE DEACETYLASE EXPRESSION AND ACTIVITY. OUR FINDINGS SUGGEST THAT M. CATARRHALIS-INDUCED ACTIVATION OF IL8 GENE TRANSCRIPTION WAS CAUSED BY INTERFERENCE WITH EPIGENETIC MECHANISMS REGULATING IL8 GENE ACCESSIBILITY. OUR FINDINGS PROVIDE INSIGHT INTO IMPORTANT MOLECULAR AND CELLULAR MECHANISMS OF M. CATARRHALIS-INDUCED ACTIVATION OF HUMAN BRONCHIAL EPITHELIUM. 2006 10 2147 18 EPIGENETIC MARKER OF TELOMERIC AGE IS ASSOCIATED WITH EXACERBATIONS AND HOSPITALIZATIONS IN CHRONIC OBSTRUCTIVE PULMONARY DISEASE. BACKGROUND: CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS AN AGE-RELATED CONDITION THAT HAS BEEN ASSOCIATED WITH EARLY TELOMERE ATTRITION; THE CLINICAL IMPLICATIONS OF TELOMERE SHORTENING IN COPD ARE NOT WELL KNOWN. IN THIS STUDY WE AIMED TO DETERMINE THE RELATIONSHIP OF THE EPIGENETIC REGULATION OF TELOMERIC LENGTH IN PERIPHERAL BLOOD WITH THE RISK OF EXACERBATIONS AND HOSPITALIZATION IN PATIENTS WITH COPD. METHODS: BLOOD DNA METHYLATION PROFILES WERE OBTAINED FROM 292 PATIENTS WITH COPD ENROLLED IN THE PLACEBO ARM OF THE MACROLIDE AZITHROMYCIN TO PREVENT RAPID WORSENING OF SYMPTOMS ASSOCIATED WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE (MACRO) STUDY AND WHO WERE FOLLOWED FOR 1-YEAR. WE CALCULATED TELOMERE LENGTH BASED ON DNA METHYLATION MARKERS (DNAMTL) AND RELATED THIS BIOMARKER TO THE RISK OF EXACERBATION AND HOSPITALIZATION AND HEALTH STATUS (ST. GEORGE RESPIRATORY QUESTIONNAIRE [SGRQ]) SCORE OVER TIME USING A COX PROPORTIONAL HAZARDS MODEL. WE ALSO USED LINEAR MODELS TO INVESTIGATE THE ASSOCIATIONS OF DNAMTL WITH THE RATES OF EXACERBATION AND HOSPITALIZATION (ADJUSTED FOR CHRONOLOGICAL AGE, LUNG FUNCTION, RACE, SEX, SMOKING, BODY MASS INDEX AND CELL COMPOSITION). RESULTS: PARTICIPANTS WITH SHORT DNAMTL DEMONSTRATED INCREASED RISK OF EXACERBATION (P = 0.02) AND HOSPITALIZATION (P = 0.03) COMPARED TO THOSE WITH LONGER DNAMTL. DNAMTL AGE ACCELERATION WAS ASSOCIATED WITH HIGHER RATES OF EXACERBATION (P = 1.35 X 10(-04)) AND HOSPITALIZATION (P = 5.21 X 10(-03)) AND POOR HEALTH STATUS (LOWER SGRQ SCORES) INDEPENDENT OF CHRONOLOGICAL AGE (P = 0.03). CONCLUSION: TELOMERIC AGE BASED ON BLOOD DNA METHYLATION IS ASSOCIATED WITH COPD EXACERBATION AND HOSPITALIZATION AND THUS A PROMISING BIOMARKER FOR POOR OUTCOMES IN COPD. 2021 11 308 11 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 1552 17 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 13 3625 18 IN VIVO GENOME AND METHYLOME ADAPTATION OF CAG-NEGATIVE HELICOBACTER PYLORI DURING EXPERIMENTAL HUMAN INFECTION. MULTIPLE STUDIES HAVE DEMONSTRATED RAPID BACTERIAL GENOME EVOLUTION DURING CHRONIC INFECTION WITH HELICOBACTER PYLORI IN CONTRAST, LITTLE WAS KNOWN ABOUT GENETIC CHANGES DURING THE FIRST STAGES OF INFECTION, WHEN SELECTIVE PRESSURE IS LIKELY TO BE HIGHEST. USING SINGLE-MOLECULE, REAL-TIME (SMRT) AND ILLUMINA SEQUENCING TECHNOLOGIES, WE ANALYZED GENOME AND METHYLOME EVOLUTION DURING THE FIRST 10 WEEKS OF INFECTION BY COMPARING THE CAG PATHOGENICITY ISLAND (CAGPAI)-NEGATIVE H. PYLORI CHALLENGE STRAIN BCS 100 WITH PAIRS OF H. PYLORI REISOLATES FROM GASTRIC ANTRUM AND CORPUS BIOPSY SPECIMENS OF 10 HUMAN VOLUNTEERS WHO HAD BEEN INFECTED WITH THIS STRAIN AS PART OF A VACCINE TRIAL. MOST GENETIC CHANGES DETECTED IN THE REISOLATES AFFECTED GENES WITH A SURFACE-RELATED ROLE OR A PREDICTED FUNCTION IN PEPTIDE UPTAKE. APART FROM PHENOTYPIC CHANGES OF THE BACTERIAL ENVELOPE, A DUPLICATION OF THE CATALASE GENE WAS OBSERVED IN ONE REISOLATE, WHICH RESULTED IN HIGHER CATALASE ACTIVITY AND IMPROVED SURVIVAL UNDER OXIDATIVE STRESS CONDITIONS. THE METHYLOMES ALSO VARIED IN SOME OF THE REISOLATES, MOSTLY BY ACTIVITY SWITCHING OF PHASE-VARIABLE METHYLTRANSFERASE (MTASE) GENES. THE OBSERVED IN VIVO MUTATION SPECTRUM WAS REMARKABLE FOR A VERY HIGH PROPORTION OF NONSYNONYMOUS MUTATIONS. ALTHOUGH THE DATA SHOWED SUBSTANTIAL WITHIN-STRAIN GENOME DIVERSITY IN THE CHALLENGE STRAIN, MOST ANTRUM AND CORPUS REISOLATES FROM THE SAME VOLUNTEERS WERE HIGHLY SIMILAR TO EACH OTHER, INDICATING THAT THE CHALLENGE INFECTION REPRESENTS A MAJOR SELECTIVE BOTTLENECK SHAPING THE TRANSMITTED POPULATION. OUR FINDINGS SUGGEST RAPID IN VIVO SELECTION OF H. PYLORI DURING EARLY-PHASE INFECTION PROVIDING ADAPTATION TO DIFFERENT INDIVIDUALS BY COMMON MECHANISMS OF GENETIC AND EPIGENETIC ALTERATIONS.IMPORTANCE EXCEPTIONAL GENETIC DIVERSITY AND VARIABILITY ARE HALLMARKS OF HELICOBACTER PYLORI, BUT THE BIOLOGICAL ROLE OF THIS PLASTICITY REMAINS INCOMPLETELY UNDERSTOOD. HERE, WE HAD THE RARE OPPORTUNITY TO INVESTIGATE THE MOLECULAR EVOLUTION DURING THE FIRST WEEKS OF H. PYLORI INFECTION BY COMPARING THE GENOMES AND EPIGENOMES OF H. PYLORI STRAIN BCS 100 USED TO CHALLENGE HUMAN VOLUNTEERS IN A VACCINE TRIAL WITH THOSE OF BACTERIA REISOLATED FROM THE VOLUNTEERS 10 WEEKS AFTER THE CHALLENGE. THE DATA PROVIDE MOLECULAR INSIGHTS INTO THE PROCESS OF ESTABLISHMENT OF THIS HIGHLY VERSATILE PATHOGEN IN 10 DIFFERENT HUMAN INDIVIDUAL HOSTS, SHOWING, FOR EXAMPLE, SELECTION FOR CHANGES IN HOST-INTERACTION MOLECULES AS WELL AS CHANGES IN EPIGENETIC METHYLATION PATTERNS. THE DATA PROVIDE IMPORTANT CLUES TO THE EARLY ADAPTATION OF H. PYLORI TO NEW HOST NICHES AFTER TRANSMISSION, WHICH WE BELIEVE IS VITAL TO UNDERSTAND ITS SUCCESS AS A CHRONIC PATHOGEN AND DEVELOP MORE EFFICIENT TREATMENTS AND VACCINES. 2020 14 2018 16 EPIGENETIC CHANGE (GATA-4 GENE METHYLATION) IS ASSOCIATED WITH HEALTH STATUS IN CHRONIC OBSTRUCTIVE PULMONARY DISEASE. GENE METHYLATION IS AN EPIGENETIC CHANGE THAT INVOLVES A HERITABLE MODIFICATION OF CHROMATIN STRUCTURE THAT ALTERS GENE EXPRESSION WITHOUT A CHANGE IN DNA SEQUENCE. IT HAS PREVIOUSLY BEEN SHOWN THAT METHYLATION OF THE GATA-4 GENE PROMOTER REGION IN SPUTUM DNA IS ASSOCIATED WITH LOW LUNG FUNCTION AND INCREASED ODDS OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) AMONG SMOKERS. GIVEN THESE FINDINGS, WE HYPOTHESIZED THAT GATA-4 GENE METHYLATION IN SPUTUM DNA WOULD BE ASSOCIATED WITH LOW HEALTH STATUS, AS MEASURED BY THE ST. GEORGE'S RESPIRATORY QUESTIONNAIRE (SGRQ), IN SUBJECTS WITH COPD. SELF-REPORTED SGRQ, SPIROMETRY, AND INDUCED SPUTUM SAMPLES WERE OBTAINED FROM 168 COPD SUBJECTS FROM THE LOVELACE SMOKERS COHORT. GATA-4 GENE METHYLATION WAS EVALUATED IN SPUTUM DNA USING NESTED METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (PCR) ASSAYS. USING GENERAL LINEAR MODEL WITH POISSON REGRESSION, WE FOUND THAT GATA-4 GENE METHYLATION WAS SIGNIFICANTLY ASSOCIATED WITH OVERALL LOWER SGRQ HEALTH STATUS (PARAMETER ESTIMATE = .296, P < .001). THIS FINDING REMAINED SIGNIFICANT EVEN AFTER CONTROLLING FOR AGE, LUNG FUNCTION, AND OTHER COVARIATES. IN AN ADDITIONAL ANALYSIS USING LOGISTIC REGRESSION AND COMPARING EXTREME TERTILES OF OVERALL SGRQ SCORE, WE CONFIRMED THAT GATA-4 GENE METHYLATION WAS ASSOCIATED WITH A 3-FOLD INCREASE IN RISK OF POOR HEALTH STATUS (OR 2.95 AND P = .028). THE UNEXPLORED LINKS BETWEEN EPIGENETIC CHANGES AND PSYCHOSOCIAL FACTORS SUCH AS HEALTH STATUS ARE CRITICAL GAPS IN THE LITERATURE. THIS STUDY IS THE FIRST TO SUGGEST THAT AIRWAY GATA-4 GENE METHYLATION STATUS MAY INDEPENDENTLY PREDICT HEALTH STATUS IN INDIVIDUALS WITH COPD. 2015 15 158 14 ABERRANT P16 PROMOTER METHYLATION AMONG GREEK LUNG CANCER PATIENTS AND SMOKERS: CORRELATION WITH SMOKING. GENETIC AND ENVIRONMENTAL FACTORS (DIETARY AND SMOKING) INFLUENCE LUNG CANCER EPIDEMIOLOGY AND INDUCE EPIGENETIC MODIFICATIONS THAT SHOULD BE ASSESSED IN INDIVIDUAL POPULATIONS. WE ANALYZED P16 METHYLATION AMONG GREEK NON-SMALL CELL LUNG CARCINOMA PATIENTS AND SMOKERS USING TWO-STAGE METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION. ONE HUNDRED AND FIFTY SPECIMENS FROM CANCEROUS AND ADJACENT NON-CANCEROUS TISSUE, BRONCHIAL WASHINGS AND SPUTUM FROM PATIENTS AND 48 SPECIMENS, MOSTLY SPUTUM, FROM DISEASE-FREE SMOKERS WERE INCLUDED. P16 METHYLATION WAS VERY FREQUENT IN BIOPSIES (82.85%) AND BRONCHIAL WASHINGS (NON-SMALL CELL LUNG CARCINOMA, 80.35%; SMALL CELL LUNG CARCINOMA, 16.66%) FROM PATIENTS, BUT ALSO IN ADJACENT NON-CANCEROUS TISSUE (45.71%). CONCORDANCE OF P16 METHYLATION AND POSITIVITY BY CYTOLOGICAL EXAMINATION WAS 51.78%. METHYLATION WAS ALSO OBSERVED IN SPUTUM FROM ASYMPTOMATIC CYTOLOGY-NEGATIVE SMOKERS (22.5%) AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE PATIENTS (THREE OF EIGHT). AMONG DISEASE-FREE INDIVIDUALS, METHYLATION CORRELATED ONLY WITH HEAVY SMOKING (>50 PACK-YEARS, P<0.001) AND DIFFERED AMONG MALE AND FEMALE DISEASE-FREE SMOKERS. IN SUMMARY, P16 METHYLATION IS VERY FREQUENT AMONG NON-SMALL CELL LUNG CARCINOMA PATIENTS, AND CORRELATES WITH HEAVY CIGARETTE CONSUMPTION ONLY IN DISEASE-FREE SMOKERS. 2007 16 3037 18 GENOME AND METHYLOME VARIATION IN HELICOBACTER PYLORI WITH A CAG PATHOGENICITY ISLAND DURING EARLY STAGES OF HUMAN INFECTION. BACKGROUND & AIMS: HELICOBACTER PYLORI IS REMARKABLE FOR ITS GENETIC VARIATION; YET, LITTLE IS KNOWN ABOUT ITS GENETIC CHANGES DURING EARLY STAGES OF HUMAN INFECTION, AS THE BACTERIA ADAPT TO THEIR NEW ENVIRONMENT. WE ANALYZED GENOME AND METHYLOME VARIATIONS IN A FULLY VIRULENT STRAIN OF H PYLORI DURING EXPERIMENTAL INFECTION. METHODS: WE PERFORMED A RANDOMIZED PHASE I/II, OBSERVER-BLIND, PLACEBO-CONTROLLED STUDY OF 12 HEALTHY, H PYLORI-NEGATIVE ADULTS IN GERMANY FROM OCTOBER 2008 THROUGH MARCH 2010. THE VOLUNTEERS WERE GIVEN A PROPHYLACTIC VACCINE CANDIDATE (N = 7) OR PLACEBO (N = 5) AND THEN CHALLENGED WITH H PYLORI STRAIN BCM-300. BIOPSY SAMPLES WERE COLLECTED AND H PYLORI WERE ISOLATED. GENOMES OF THE CHALLENGE STRAIN AND 12 REISOLATES, OBTAINED 12 WEEKS AFTER (OR IN 1 CASE, 62 WEEKS AFTER) INFECTION WERE SEQUENCED BY SINGLE-MOLECULE, REAL-TIME TECHNOLOGY, WHICH, IN PARALLEL, PERMITTED DETERMINATION OF GENOME-WIDE METHYLATION PATTERNS FOR ALL STRAINS. FUNCTIONAL EFFECTS OF GENETIC CHANGES OBSERVED IN H PYLORI STRAINS DURING HUMAN INFECTION WERE ASSESSED BY MEASURING RELEASE OF INTERLEUKIN 8 FROM AGS CELLS (TO DETECT CAG PATHOGENICITY ISLAND FUNCTION), NEUTRAL RED UPTAKE (TO DETECT VACUOLATING CYTOTOXIN ACTIVITY), AND ADHESION ASSAYS. RESULTS: THE OBSERVED MUTATION RATE WAS IN AGREEMENT WITH RATES PREVIOUSLY DETERMINED FROM PATIENTS WITH CHRONIC H PYLORI INFECTIONS, WITHOUT EVIDENCE OF A MUTATION BURST. A LOSS OF CAG PATHOGENICITY ISLAND FUNCTION WAS OBSERVED IN 3 REISOLATES. IN ADDITION, 3 REISOLATES FROM THE VACCINE GROUP ACQUIRED MUTATIONS IN THE VACUOLATING CYTOTOXIN GENE VACA, RESULTING IN LOSS OF VACUOLIZATION ACTIVITY. WE OBSERVED INTERSTRAIN VARIATION IN METHYLOMES DUE TO PHASE VARIATION IN GENES ENCODING METHYLTRANSFERASES. CONCLUSIONS: WE ANALYZED ADAPTATION OF A FULLY VIRULENT STRAIN OF H PYLORI TO 12 DIFFERENT VOLUNTEERS TO OBTAIN A ROBUST ESTIMATE OF THE FREQUENCY OF GENETIC AND EPIGENETIC CHANGES IN THE ABSENCE OF INTERSTRAIN RECOMBINATION. OUR FINDINGS INDICATE THAT THE LARGE AMOUNT OF GENETIC VARIATION IN H PYLORI POSES A CHALLENGE TO VACCINE DEVELOPMENT. CLINICALTRIALS.GOV NO: NCT00736476. 2018 17 4744 22 NOVEL INSIGHTS INTO THE GENETICS OF SMOKING BEHAVIOUR, LUNG FUNCTION, AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE (UK BILEVE): A GENETIC ASSOCIATION STUDY IN UK BIOBANK. BACKGROUND: UNDERSTANDING THE GENETIC BASIS OF AIRFLOW OBSTRUCTION AND SMOKING BEHAVIOUR IS KEY TO DETERMINING THE PATHOPHYSIOLOGY OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD). WE USED UK BIOBANK DATA TO STUDY THE GENETIC CAUSES OF SMOKING BEHAVIOUR AND LUNG HEALTH. METHODS: WE SAMPLED INDIVIDUALS OF EUROPEAN ANCESTRY FROM UK BIOBANK, FROM THE MIDDLE AND EXTREMES OF THE FORCED EXPIRATORY VOLUME IN 1 S (FEV1) DISTRIBUTION AMONG HEAVY SMOKERS (MEAN 35 PACK-YEARS) AND NEVER SMOKERS. WE DEVELOPED A CUSTOM ARRAY FOR UK BIOBANK TO PROVIDE OPTIMUM GENOME-WIDE COVERAGE OF COMMON AND LOW-FREQUENCY VARIANTS, DENSE COVERAGE OF GENOMIC REGIONS ALREADY IMPLICATED IN LUNG HEALTH AND DISEASE, AND TO ASSAY RARE CODING VARIANTS RELEVANT TO THE UK POPULATION. WE INVESTIGATED WHETHER THERE WERE SHARED GENETIC CAUSES BETWEEN DIFFERENT PHENOTYPES DEFINED BY EXTREMES OF FEV1. WE ALSO LOOKED FOR NOVEL VARIANTS ASSOCIATED WITH EXTREMES OF FEV1 AND SMOKING BEHAVIOUR AND ASSESSED REGIONS OF THE GENOME THAT HAD ALREADY SHOWN EVIDENCE FOR A ROLE IN LUNG HEALTH AND DISEASE. WE SET GENOME-WIDE SIGNIFICANCE AT P<5 X 10(-8). FINDINGS: UK BIOBANK PARTICIPANTS WERE RECRUITED FROM MARCH 15, 2006, TO JULY 7, 2010. SAMPLE SELECTION FOR THE UK BILEVE STUDY STARTED ON NOV 22, 2012, AND WAS COMPLETED ON DEC 20, 2012. WE SELECTED 50,008 UNIQUE SAMPLES: 10,002 INDIVIDUALS WITH LOW FEV1, 10,000 WITH AVERAGE FEV1, AND 5002 WITH HIGH FEV1 FROM EACH OF THE HEAVY SMOKER AND NEVER SMOKER GROUPS. WE NOTED A SUBSTANTIAL SHARING OF GENETIC CAUSES OF LOW FEV1 BETWEEN HEAVY SMOKERS AND NEVER SMOKERS (P=2.29 X 10(-16)) AND BETWEEN INDIVIDUALS WITH AND WITHOUT DOCTOR-DIAGNOSED ASTHMA (P=6.06 X 10(-11)). WE DISCOVERED SIX NOVEL GENOME-WIDE SIGNIFICANT SIGNALS OF ASSOCIATION WITH EXTREMES OF FEV1, INCLUDING SIGNALS AT FOUR NOVEL LOCI (KANSL1, TSEN54, TET2, AND RBM19/TBX5) AND INDEPENDENT SIGNALS AT TWO PREVIOUSLY REPORTED LOCI (NPNT AND HLA-DQB1/HLA-DQA2). THESE VARIANTS ALSO SHOWED ASSOCIATION WITH COPD, INCLUDING IN INDIVIDUALS WITH NO HISTORY OF SMOKING. THE NUMBER OF COPIES OF A 150 KB REGION CONTAINING THE 5' END OF KANSL1, A GENE THAT IS IMPORTANT FOR EPIGENETIC GENE REGULATION, WAS ASSOCIATED WITH EXTREMES OF FEV1. WE ALSO DISCOVERED FIVE NEW GENOME-WIDE SIGNIFICANT SIGNALS FOR SMOKING BEHAVIOUR, INCLUDING A VARIANT IN NCAM1 (CHROMOSOME 11) AND A VARIANT ON CHROMOSOME 2 (BETWEEN TEX41 AND PABPC1P2) THAT HAS A TRANS EFFECT ON EXPRESSION OF NCAM1 IN BRAIN TISSUE. INTERPRETATION: BY SAMPLING FROM THE EXTREMES OF THE LUNG FUNCTION DISTRIBUTION IN UK BIOBANK, WE IDENTIFIED NOVEL GENETIC CAUSES OF LUNG FUNCTION AND SMOKING BEHAVIOUR. THESE RESULTS PROVIDE NEW INSIGHT INTO THE SPECIFIC MECHANISMS UNDERLYING AIRFLOW OBSTRUCTION, COPD, AND TOBACCO ADDICTION, AND SHOW SUBSTANTIAL SHARED GENETIC ARCHITECTURE UNDERLYING AIRFLOW OBSTRUCTION ACROSS INDIVIDUALS, IRRESPECTIVE OF SMOKING BEHAVIOUR AND OTHER AIRWAY DISEASE. FUNDING: MEDICAL RESEARCH COUNCIL. 2015 18 5746 11 SMOKING-RELATED DNA METHYLATION IS ASSOCIATED WITH DNA METHYLATION PHENOTYPIC AGE ACCELERATION: THE VETERANS AFFAIRS NORMATIVE AGING STUDY. DNA METHYLATION MAY PLAY A CRITICAL ROLE IN AGING AND AGE-RELATED DISEASES. DNA METHYLATION PHENOTYPIC AGE (DNAMPHENOAGE) IS A NEW AGING BIOMARKER AND PREDICTOR OF CHRONIC DISEASE RISK. WHILE SMOKING IS A STRONG RISK FACTOR FOR CHRONIC DISEASES AND INFLUENCES METHYLATION, ITS INFLUENCE ON DNAMPHENOAGE IS UNKNOWN. WE INVESTIGATED ASSOCIATIONS OF SELF-REPORTED AND EPIGENETIC SMOKING INDICATORS WITH DNAMPHENOAGE ACCELERATION IN A LONGITUDINAL AGING STUDY IN EASTERN MASSACHUSETTS. DNA METHYLATION WAS MEASURED IN WHOLE BLOOD SAMPLES FROM MULTIPLE VISITS FOR 692 MALE PARTICIPANTS IN THE VETERANS AFFAIRS NORMATIVE AGING STUDY DURING 1999-2013. ACCELERATION WAS DEFINED USING RESIDUALS FROM LINEAR REGRESSION OF THE DNAMPHENOAGE ON THE CHRONOLOGICAL AGE. CUMULATIVE SMOKING (PACK-YEARS) WAS SIGNIFICANTLY ASSOCIATED WITH DNAMPHENOAGE ACCELERATION, WHEREAS SELF-REPORTED SMOKING STATUS WAS NOT. WE OBSERVED SIGNIFICANT VALIDATED ASSOCIATIONS BETWEEN SMOKING-RELATED LOCI AND DNAMPHENOAGE ACCELERATION FOR 52 CPG SITES, WHERE 18 WERE HYPOMETHYLATED AND 34 WERE HYPERMETHYLATED, MAPPED TO 16 GENES. THE AHRR GENE HAD THE MOST LOCI (N = 8) AMONG THE 16 GENES. WE GENERATED A SMOKING AGING INDEX BASED ON THESE 52 LOCI, WHICH SHOWED POSITIVE SIGNIFICANT ASSOCIATIONS WITH DNAMPHENOAGE ACCELERATION. THESE EPIGENETIC BIOMARKERS MAY HELP TO PREDICT AGE-RELATED RISKS DRIVEN BY SMOKING. 2019 19 2628 14 EPIGENOME-WIDE ASSOCIATION STUDY OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE AND LUNG FUNCTION IN KOREANS. AIM: TO IDENTIFY DIFFERENTIALLY METHYLATED PROBES (DMPS) AND REGIONS (DMRS) IN RELATION TO CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) AND LUNG FUNCTION TRAITS. METHODS: WE PERFORMED AN EPIGENOME-WIDE ASSOCIATION STUDY OF COPD AND SPIROMETRIC PARAMETERS, INCLUDING FORCED EXPIRATORY VOLUME IN 1 S (FEV1), FORCED VITAL CAPACITY (FVC) AND FEV1/FVC, IN BLOOD DNA USING THE INFINIUM HUMANMETHYLATION450 (N = 100, A KOREAN COPD COHORT). RESULTS: WE FOUND ONE SIGNIFICANT DMP (CG03559389, DIP2C) AND 104 SIGNIFICANT DMRS AFTER MULTIPLE-TESTING CORRECTION. OF THESE, 34 DMRS MAPPED TO GENES DIFFERENTIAL EXPRESSED WITH RESPECT TO THE SAME TRAIT. FIVE OF THE GENES WERE ASSOCIATED WITH MORE THAN TWO TRAITS: CTU2, USP36, ZNF516, KLK10 AND CPT1B. CONCLUSION: WE IDENTIFIED NOVEL DIFFERENTIAL METHYLATION LOCI RELATED TO COPD AND LUNG FUNCTION IN BLOOD DNA IN KOREANS AND CONFIRMED PREVIOUS FINDINGS IN NON-ASIANS. EPIGENETIC MODIFICATION COULD CONTRIBUTE TO THE ETIOLOGY OF THESE PHENOTYPES. 2017 20 1408 17 DIETARY INTAKE IS ASSOCIATED WITH RESPIRATORY HEALTH OUTCOMES AND DNA METHYLATION IN CHILDREN WITH ASTHMA. BACKGROUND: ASTHMA IS AN INCREASINGLY COMMON CHRONIC DISEASE AMONG CHILDREN, AND DATA POINT TOWARD A COMPLEX MECHANISM INVOLVING GENETIC, ENVIRONMENTAL AND EPIGENETIC FACTORS. EPIGENETIC MODIFICATIONS SUCH AS DNA HYPO- OR HYPER-METHYLATION HAVE BEEN SHOWN TO OCCUR IN RESPONSE TO ENVIRONMENTAL EXPOSURES INCLUDING DIETARY NUTRIENTS. METHODS: WITHIN THE CONTEXT OF THE ASTHMA RANDOMIZED TRIAL OF INDOOR WOOD SMOKE (ARTIS) STUDY, WE INVESTIGATED RELATIONSHIPS BETWEEN DIET, ASTHMA HEALTH MEASURES, AND DNA METHYLATION. ASTHMA HEALTH MEASURES INCLUDED A QUALITY OF LIFE INSTRUMENT, DIURNAL PEAK FLOW VARIABILITY (DPFV) AND FORCED EXPIRATORY VOLUME IN THE FIRST SECOND (FEV(1)). DIETARY INTAKE WAS ASSESSED WITH A FOOD FREQUENCY QUESTIONNAIRE. METHYLATION LEVELS OF LINE-1 REPETITIVE ELEMENT AND TWO PROMOTER CPG SITES FOR INTERFERON GAMMA (IFNGAMMA, -186 AND -54) FROM BUCCAL CELL DNA WERE MEASURED USING PYROSEQUENCING ASSAYS. RESULTS: DATA WERE COLLECTED ON 32 CHILDREN WITH ASTHMA LIVING IN WESTERN MONTANA WHO WERE RECRUITED TO THE ARTIS STUDY. SELENIUM AND SEVERAL METHYL DONOR DIETARY NUTRIENTS WERE POSITIVELY ASSOCIATED WITH THE ASTHMA QUALITY OF LIFE MEASURE. INTAKE OF METHYL DONATING NUTRIENTS INCLUDING FOLATE WAS POSITIVELY ASSOCIATED LINE-1 METHYLATION AND NEGATIVELY ASSOCIATED WITH IFNGAMMA CPG-186. HIGHER LEVELS OF LINE-1 METHYLATION WERE ASSOCIATED WITH GREATER DPFV. CONCLUSION: WE IDENTIFIED SEVERAL NUTRIENTS THAT WERE ASSOCIATED WITH IMPROVED QUALITY OF LIFE MEASURES AMONG CHILDREN WITH ASTHMA. THE IFNGAMMA PROMOTER CPG SITE -186 BUT NOT -54 WAS ASSOCIATED WITH THE INTAKE OF SELECTED DIETARY NUTRIENTS. HOWEVER, IN THIS SMALL POPULATION OF CHILDREN WITH ASTHMA, THE IFNGAMMA PROMOTER CPG SITES WERE NOT ASSOCIATED WITH RESPIRATORY HEALTH MEASURES SO IT REMAINS UNCLEAR THROUGH WHICH EPIGENETIC MECHANISM THESE NUTRIENTS ARE IMPACTING THE QUALITY OF LIFE MEASURE. THESE FINDINGS ADD TO THE EVIDENCE THAT DIETARY NUTRIENTS, PARTICULARLY FOODS CONTAINING METHYL DONORS, MAY BE IMPORTANT FOR EPIGENETIC REGULATION AS IT PERTAINS TO THE CONTROL OF ASTHMA. TRIAL REGISTRATION CLINCIALTRIALS.GOV NCT00807183. REGISTERED 10 DECEMBER 2008. 2017