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 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
4 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
5 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
6 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
7 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
8 3050 15 GENOME-WIDE ASSOCIATION ANALYSES FOR LUNG FUNCTION AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE IDENTIFY NEW LOCI AND POTENTIAL DRUGGABLE TARGETS. CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS CHARACTERIZED BY REDUCED LUNG FUNCTION AND IS THE THIRD LEADING CAUSE OF DEATH GLOBALLY. THROUGH GENOME-WIDE ASSOCIATION DISCOVERY IN 48,943 INDIVIDUALS, SELECTED FROM EXTREMES OF THE LUNG FUNCTION DISTRIBUTION IN UK BIOBANK, AND FOLLOW-UP IN 95,375 INDIVIDUALS, WE INCREASED THE YIELD OF INDEPENDENT SIGNALS FOR LUNG FUNCTION FROM 54 TO 97. A GENETIC RISK SCORE WAS ASSOCIATED WITH COPD SUSCEPTIBILITY (ODDS RATIO PER 1 S.D. OF THE RISK SCORE ( APPROXIMATELY 6 ALLELES) (95% CONFIDENCE INTERVAL) = 1.24 (1.20-1.27), P = 5.05 X 10(-49)), AND WE OBSERVED A 3.7-FOLD DIFFERENCE IN COPD RISK BETWEEN INDIVIDUALS IN THE HIGHEST AND LOWEST GENETIC RISK SCORE DECILES IN UK BIOBANK. THE 97 SIGNALS SHOW ENRICHMENT IN GENES FOR DEVELOPMENT, ELASTIC FIBERS AND EPIGENETIC REGULATION PATHWAYS. WE HIGHLIGHT TARGETS FOR DRUGS AND COMPOUNDS IN DEVELOPMENT FOR COPD AND ASTHMA (GENES IN THE INOSITOL PHOSPHATE METABOLISM PATHWAY AND CHRM3) AND DESCRIBE TARGETS FOR POTENTIAL DRUG REPOSITIONING FROM OTHER CLINICAL INDICATIONS.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
9 3764 16 INTEGRATIVE ANALYSIS OF DNA METHYLATION AND GENE EXPRESSION DATA IDENTIFIES EPAS1 AS A KEY REGULATOR OF COPD. CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS A COMPLEX DISEASE. GENETIC, EPIGENETIC, AND ENVIRONMENTAL FACTORS ARE KNOWN TO CONTRIBUTE TO COPD RISK AND DISEASE PROGRESSION. THEREFORE WE DEVELOPED A SYSTEMATIC APPROACH TO IDENTIFY KEY REGULATORS OF COPD THAT INTEGRATES GENOME-WIDE DNA METHYLATION, GENE EXPRESSION, AND PHENOTYPE DATA IN LUNG TISSUE FROM COPD AND CONTROL SAMPLES. OUR INTEGRATIVE ANALYSIS IDENTIFIED 126 KEY REGULATORS OF COPD. WE IDENTIFIED EPAS1 AS THE ONLY KEY REGULATOR WHOSE DOWNSTREAM GENES SIGNIFICANTLY OVERLAPPED WITH MULTIPLE GENES SETS ASSOCIATED WITH COPD DISEASE SEVERITY. EPAS1 IS DISTINCT IN COMPARISON WITH OTHER KEY REGULATORS IN TERMS OF METHYLATION PROFILE AND DOWNSTREAM TARGET GENES. GENES PREDICTED TO BE REGULATED BY EPAS1 WERE ENRICHED FOR BIOLOGICAL PROCESSES INCLUDING SIGNALING, CELL COMMUNICATIONS, AND SYSTEM DEVELOPMENT. WE CONFIRMED THAT EPAS1 PROTEIN LEVELS ARE LOWER IN HUMAN COPD LUNG TISSUE COMPARED TO NON-DISEASE CONTROLS AND THAT EPAS1 GENE EXPRESSION IS REDUCED IN MICE CHRONICALLY EXPOSED TO CIGARETTE SMOKE. AS EPAS1 DOWNSTREAM GENES WERE SIGNIFICANTLY ENRICHED FOR HYPOXIA RESPONSIVE GENES IN ENDOTHELIAL CELLS, WE TESTED EPAS1 FUNCTION IN HUMAN ENDOTHELIAL CELLS. EPAS1 KNOCKDOWN BY SIRNA IN ENDOTHELIAL CELLS IMPACTED GENES THAT SIGNIFICANTLY OVERLAPPED WITH EPAS1 DOWNSTREAM GENES IN LUNG TISSUE INCLUDING HYPOXIA RESPONSIVE GENES, AND GENES ASSOCIATED WITH EMPHYSEMA SEVERITY. OUR FIRST INTEGRATIVE ANALYSIS OF GENOME-WIDE DNA METHYLATION AND GENE EXPRESSION PROFILES ILLUSTRATES THAT NOT ONLY DOES DNA METHYLATION PLAY A 'CAUSAL' ROLE IN THE MOLECULAR PATHOPHYSIOLOGY OF COPD, BUT IT CAN BE LEVERAGED TO DIRECTLY IDENTIFY NOVEL KEY MEDIATORS OF THIS PATHOPHYSIOLOGY.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
10 3638 18 INCREASED EXPRESSION OF BETA-DEFENSIN 1 (DEFB1) IN CHRONIC OBSTRUCTIVE PULMONARY DISEASE. ON-GOING AIRWAY INFLAMMATION IS CHARACTERISTIC FOR THE PATHOPHYSIOLOGY OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD). HOWEVER, THE KEY FACTORS DETERMINING THE DECREASE IN LUNG FUNCTION, AN IMPORTANT CLINICAL PARAMETER OF COPD, ARE NOT CLEAR. GENOME-WIDE LINKAGE ANALYSES PROVIDE EVIDENCE FOR SIGNIFICANT LINKAGE TO AIRWAY OBSTRUCTION SUSCEPTIBILITY LOCI ON CHROMOSOME 8P23, THE LOCATION OF THE HUMAN DEFENSIN GENE CLUSTER. MOREOVER, A GENETIC VARIATION IN THE DEFENSIN BETA 1 (DEFB1) GENE WAS FOUND TO BE ASSOCIATED WITH COPD. THEREFORE, WE HYPOTHESIZED THAT DEFB1 IS DIFFERENTLY REGULATED AND EXPRESSED IN HUMAN LUNGS DURING COPD PROGRESSION. GENE EXPRESSION OF DEFB1 WAS ASSESSED IN BRONCHIAL EPITHELIUM AND BAL FLUID CELLS OF HEALTHY CONTROLS AND PATIENTS WITH COPD AND USING BISULFITE SEQUENCING AND CHIP ANALYSIS, THE EPIGENETIC CONTROL OF DEFB1 MRNA EXPRESSION WAS INVESTIGATED. WE CAN DEMONSTRATE THAT DEFB1 MRNA EXPRESSION WAS SIGNIFICANTLY INCREASED IN BRONCHOPULMONARY SPECIMEN OF PATIENTS WITH COPD (N = 34) VS. HEALTHY CONTROLS (N = 10) (P<0.0001). FURTHERMORE, A SIGNIFICANT CORRELATION COULD BE DETECTED BETWEEN DEFB1 AND FUNCTIONAL PARAMETERS SUCH AS FEV(1) (P = 0.0024) AND THE FEV(1)/VC RATIO (P = 0.0005). UPREGULATION OF DEFB1 MRNA WAS PARALLELED BY CHANGES IN HDAC1-3, HDAC5 AND HDAC8 MRNA EXPRESSION. WHEREAS BISULFITE SEQUENCING REVEALED NO DIFFERENCES IN THE METHYLATION STATE OF DEFB1 PROMOTER BETWEEN PATIENTS WITH COPD AND CONTROLS, CHIP ANALYSIS SHOWED THAT ENHANCED DEFB1 MRNA EXPRESSION WAS ASSOCIATED WITH THE ESTABLISHMENT OF AN ACTIVE HISTONE CODE. THUS, EXPRESSION OF HUMAN DEFB1 IS UPREGULATED AND RELATED TO THE DECREASE IN PULMONARY FUNCTION IN PATIENTS WITH COPD.	2011	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
11 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
12 1590 14 DNA METHYLATION PROFILING IN HUMAN LUNG TISSUE IDENTIFIES GENES ASSOCIATED WITH COPD. CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS A SMOKING-RELATED DISEASE CHARACTERIZED BY GENETIC AND PHENOTYPIC HETEROGENEITY. ALTHOUGH ASSOCIATION STUDIES HAVE IDENTIFIED MULTIPLE GENOMIC REGIONS WITH REPLICATED ASSOCIATIONS TO COPD, GENETIC VARIATION ONLY PARTIALLY EXPLAINS THE SUSCEPTIBILITY TO LUNG DISEASE, AND SUGGESTS THE RELEVANCE OF EPIGENETIC INVESTIGATIONS. WE PERFORMED GENOME-WIDE DNA METHYLATION PROFILING IN HOMOGENIZED LUNG TISSUE SAMPLES FROM 46 CONTROL SUBJECTS WITH NORMAL LUNG FUNCTION AND 114 SUBJECTS WITH COPD, ALL FORMER SMOKERS. THE DIFFERENTIALLY METHYLATED LOCI WERE INTEGRATED WITH PREVIOUS GENOME-WIDE ASSOCIATION STUDY RESULTS. THE TOP 535 DIFFERENTIALLY METHYLATED SITES, FILTERED FOR A MINIMUM MEAN METHYLATION DIFFERENCE OF 5% BETWEEN CASES AND CONTROLS, WERE ENRICHED FOR CPG SHELVES AND SHORES. PATHWAY ANALYSIS REVEALED ENRICHMENT FOR TRANSCRIPTION FACTORS. THE TOP DIFFERENTIALLY METHYLATED SITES FROM THE INTERSECTION WITH PREVIOUS GWAS WERE IN CHRM1, GLT1D1, AND C10ORF11; SORTED BY GWAS P-VALUE, THE TOP SITES INCLUDED FRMD4A, THSD4, AND C10ORF11. EPIGENETIC ASSOCIATION STUDIES COMPLEMENT GENETIC ASSOCIATION STUDIES TO IDENTIFY GENES POTENTIALLY INVOLVED IN COPD PATHOGENESIS. ENRICHMENT FOR GENES IMPLICATED IN ASTHMA AND LUNG FUNCTION AND FOR TRANSCRIPTION FACTORS SUGGESTS THE POTENTIAL PATHOGENIC RELEVANCE OF GENES IDENTIFIED THROUGH DIFFERENTIAL METHYLATION AND THE INTERSECTION WITH A BROADER RANGE OF GWAS ASSOCIATIONS.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
13 1619 25 DNA METHYLTRANSFERASE REGULATES NITRIC OXIDE HOMEOSTASIS AND VIRULENCE IN A CHRONICALLY ADAPTED PSEUDOMONAS AERUGINOSA STRAIN. OPPORTUNISTIC PATHOGENS SUCH AS PSEUDOMONAS AERUGINOSA ADAPT THEIR GENOMES RAPIDLY DURING CHRONIC INFECTIONS. UNDERSTANDING THEIR EPIGENETIC REGULATION MAY PROVIDE BIOMARKERS FOR DIAGNOSIS AND REVEAL NOVEL REGULATORY MECHANISMS. WE PERFORMED SINGLE-MOLECULE REAL-TIME SEQUENCING (SMRT-SEQ) TO CHARACTERIZE THE METHYLOME OF A CHRONICALLY ADAPTED P. AERUGINOSA CLINICAL STRAIN, TBCF10839. TWO N(6)-METHYLADENINE (6MA) METHYLATION RECOGNITION MOTIFS (RCCANNNNNNNTGAR AND TRGANNNNNNTGC [MODIFICATION SITES ARE IN BOLD]) WERE IDENTIFIED AND PREDICTED AS NEW TYPE I METHYLATION SITES USING REBASE ANALYSIS. WE CONFIRMED THAT THE MOTIF TRGANNNNNNTGC WAS METHYLATED BY THE METHYLTRANSFERASE (MTASE) M.PAETBCFII, ACCORDING TO METHYLATION SENSITIVITY ASSAYS IN VIVO AND VITRO. TRANSCRIPTOMIC ANALYSIS SHOWED THAT A DELTAPAETBCFIIM KNOCKOUT MUTANT SIGNIFICANTLY DOWNREGULATED NITRIC OXIDE REDUCTASE (NOR) REGULATION AND EXPRESSION OF CODING GENES SUCH AS NOSR AND NORB, WHICH CONTAIN METHYLATED MOTIFS IN THEIR PROMOTERS OR CODING REGIONS. THE DELTAPAETBCFIIM STRAIN EXHIBITED REDUCED INTERCELLULAR SURVIVAL CAPACITY IN NO-PRODUCING RAW264.7 MACROPHAGES AND ATTENUATED VIRULENCE IN A GALLERIA MELLONELLA INFECTION MODEL; THE COMPLEMENTED STRAIN RECOVERED THESE DEFECTIVE PHENOTYPES. FURTHER PHYLOGENETIC ANALYSIS DEMONSTRATED THAT HOMOLOGS OF M.PAETBCFII OCCUR FREQUENTLY IN P. AERUGINOSA AS WELL AS OTHER BACTERIAL SPECIES. OUR WORK THEREFORE PROVIDED NEW INSIGHTS INTO THE RELATIONSHIP BETWEEN DNA METHYLATION, NO DETOXIFICATION, AND BACTERIAL VIRULENCE, LAYING A FOUNDATION FOR FURTHER EXPLORING THE MOLECULAR MECHANISM OF DNA METHYLTRANSFERASE IN REGULATING THE PATHOGENICITY OF P. AERUGINOSA. IMPORTANCE PSEUDOMONAS AERUGINOSA IS AN OPPORTUNISTIC PATHOGEN WHICH CAUSES ACUTE AND CHRONIC INFECTIONS THAT ARE DIFFICULT TO TREAT. COMPARATIVE GENOMIC ANALYSIS HAS SHOWED BROAD GENOME DIVERSITY AMONG P. AERUGINOSA CLINICAL STRAINS AND REVEALED THEIR DIFFERENT REGULATORY TRAITS COMPARED TO THE LABORATORY STRAINS. WHILE CURRENT INVESTIGATION OF THE EPIGENETICS OF P. AERUGINOSA IS STILL LACKING, UNDERSTANDING EPIGENETIC REGULATION MAY PROVIDE BIOMARKERS FOR DIAGNOSIS AND FACILITATE DEVELOPMENT OF NOVEL THERAPIES. DENITRIFICATION CAPABILITY IS CRITICAL FOR MICROBIAL VERSATILITY IN RESPONSE TO DIFFERENT ENVIRONMENTAL STRESS CONDITIONS, INCLUDING THE BACTERIAL INFECTION PROCESS, WHERE NITRIC OXIDE (NO) CAN BE GENERATED BY PHAGOCYTIC CELLS. THE DENITRIFICATION REGULATION MECHANISMS HAVE BEEN STUDIED INTENSIVELY AT GENETIC AND BIOCHEMICAL LEVELS. HOWEVER, THERE IS VERY LITTLE EVIDENCE ABOUT THE EPIGENETIC REGULATION OF BACTERIAL DENITRIFICATION MECHANISM. P. AERUGINOSA TBCF10839 IS A CHRONICALLY HOST-ADAPTED STRAIN ISOLATED FROM A CYSTIC FIBROSIS (CF) PATIENT WITH SPECIAL ANTIPHAGOCYTOSIS CHARACTERISTICS. HERE, WE INVESTIGATED THE REGULATORY EFFECT OF AN ORPHAN DNA MTASE, M.PAETBCFII, IN P. AERUGINOSA TBCF10839. WE DEMONSTRATED THAT THE DNA MTASE REGULATES THE TRANSCRIPTION OF DENITRIFICATION GENES REPRESENTED BY NOR AND AFFECTS ANTIPHAGOCYTIC ABILITY IN BACTERIA. IN SILICO ANALYSIS SUGGESTED THAT DNA METHYLATION MODIFICATION MAY ENHANCE GENE EXPRESSION BY AFFECTING THE BINDING OF TRANSACTING FACTORS SUCH AS DNR AND RPON. OUR FINDINGS NOT ONLY DEEPEN THE UNDERSTANDING OF THE ROLE OF DNA MTASE IN TRANSCRIPTIONAL REGULATION IN P. AERUGINOSA BUT ALSO PROVIDE A THEORETICAL FOUNDATION FOR THE IN-DEPTH STUDY OF THE MOLECULAR MECHANISM OF THE EPIGENETIC REGULATION ON DENITRIFICATION, VIRULENCE, AND HOST-PATHOGEN INTERACTION.	2022	

14 5883 15 SYSTEMIC AND AIRWAY EPIGENETIC DISRUPTIONS ARE ASSOCIATED WITH HEALTH STATUS IN COPD. EPIGENETIC MODIFICATIONS ARE COMMON IN CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD); HOWEVER, THEIR CLINICAL RELEVANCE IS LARGELY UNKNOWN. WE HYPOTHESIZED THAT EPIGENETIC DISRUPTIONS ARE ASSOCIATED WITH SYMPTOMS AND HEALTH STATUS IN COPD. WE PROFILED THE BLOOD (N = 57) AND AIRWAYS (N = 62) OF COPD PATIENTS FOR DNA METHYLATION (N = 55 PAIRED). THE PATIENTS' HEALTH STATUS WAS ASSESSED USING THE ST. GEORGE'S RESPIRATORY QUESTIONNAIRE (SGRQ). WE CONDUCTED DIFFERENTIAL METHYLATION ANALYSES AND IDENTIFIED PATHWAYS CHARACTERIZED BY EPIGENETIC DISRUPTIONS ASSOCIATED WITH SGRQ SCORES AND ITS INDIVIDUAL DOMAINS. 29,211 AND 5044 DIFFERENTIALLY METHYLATED POSITIONS (DMPS) WERE ASSOCIATED WITH TOTAL SGRQ SCORES IN BLOOD AND AIRWAY SAMPLES, RESPECTIVELY. THE ACTIVITY, IMPACT, AND SYMPTOM DOMAINS WERE ASSOCIATED WITH 9161, 25,689 AND 17,293 DMPS IN BLOOD, RESPECTIVELY; AND 4674, 3730 AND 5063 DMPS IN AIRWAYS, RESPECTIVELY. THERE WAS A SUBSTANTIAL OVERLAP OF DMPS BETWEEN AIRWAY AND BLOOD. DMPS WERE ENRICHED FOR PATHWAYS RELATED TO COMMON CO-MORBIDITIES OF COPD (E.G., AGEING, CANCER AND NEUROLOGICAL) IN BOTH TISSUES. HEALTH STATUS IN COPD IS ASSOCIATED WITH AIRWAY AND SYSTEMIC EPIGENETIC CHANGES ESPECIALLY IN PATHWAYS RELATED TO CO-MORBIDITIES OF COPD. THERE ARE MORE BLOOD DMPS THAN IN THE AIRWAYS SUGGESTING THAT BLOOD EPIGENOME IS A PROMISING SOURCE TO DISCOVER BIOMARKERS FOR CLINICAL OUTCOMES IN COPD.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
15 3482 13 IDENTIFICATION OF CDC5L AS BRIDGE GENE BETWEEN CHRONIC OBSTRUCTIVE PULMONARY DISEASE AND LUNG ADENOCARCINOMA. AIM: THIS STUDY AIMED TO EXPLORE THE GENETIC AND EPIGENETIC SIMILARITIES BETWEEN CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) AND LUNG ADENOCARCINOMA (LUAD). MATERIALS & METHODS: WE MAINLY USED WEIGHTED CORRELATION NETWORK ANALYSIS, PROTEIN-PROTEIN INTERACTION NETWORK AND PIVOT ANALYSIS TO IDENTIFY HUB MODULES, BRIDGE REGULATORS, BRIDGE GENES AND HUB-DRIVING GENES IN BOTH DISEASES AND CARRIED OUT VERIFYING USING EXTERNAL DATASETS. RESULTS: WE IDENTIFIED EIGHT BRIDGE REGULATORS, 19 KEY MOLECULES IN THE COPD MODEL AND TEN KEY MOLECULES IN THE LUAD MODEL. MOREOVER, WE VALIDATED THAT CDC5L COULD BE A RELIABLE BIOMARKER IN COPD AND MAY REGULATE CELL PROLIFERATION AND METASTASIS IN LUAD VIA PROMOTER METHYLATION. CONCLUSION: OUR RESULTS MIGHT FORM A THEORETICAL FOUNDATION FOR FUTURE STUDY AT AN EPIGENETIC LEVEL.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
16 1591 17 DNA METHYLATION PROFILING IN PERIPHERAL LUNG TISSUES OF SMOKERS AND PATIENTS WITH COPD. BACKGROUND: EPIGENETICS CHANGES HAVE BEEN SHOWN TO BE AFFECTED BY CIGARETTE SMOKING. CIGARETTE SMOKE (CS)-MEDIATED DNA METHYLATION CAN POTENTIALLY AFFECT SEVERAL CELLULAR AND PATHOPHYSIOLOGICAL PROCESSES, ACUTE EXACERBATIONS, AND COMORBIDITY IN THE LUNGS OF PATIENTS WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD). WE SOUGHT TO DETERMINE WHETHER GENOME-WIDE LUNG DNA METHYLATION PROFILES OF SMOKERS AND PATIENTS WITH COPD WERE SIGNIFICANTLY DIFFERENT FROM NON-SMOKERS. WE ISOLATED DNA FROM PARENCHYMAL LUNG TISSUES OF PATIENTS INCLUDING EIGHT LIFELONG NON-SMOKERS, EIGHT CURRENT SMOKERS, AND EIGHT PATIENTS WITH COPD AND ANALYZED THE SAMPLES USING ILLUMINA'S INFINIUM HUMANMETHYLATION450 BEADCHIP. RESULTS: OUR DATA REVEALED THAT THE DIFFERENTIALLY METHYLATED GENES WERE RELATED TO TOP CANONICAL PATHWAYS (E.G., G BETA GAMMA SIGNALING, MECHANISMS OF CANCER, AND NNOS SIGNALING IN NEURONS), DISEASE AND DISORDERS (ORGANISMAL INJURY AND ABNORMALITIES, CANCER, AND RESPIRATORY DISEASE), AND MOLECULAR AND CELLULAR FUNCTIONS (CELL DEATH AND SURVIVAL, CELLULAR ASSEMBLY AND ORGANIZATION, CELLULAR FUNCTION AND MAINTENANCE) IN PATIENTS WITH COPD. THE GENOME-WIDE DNA METHYLATION ANALYSIS IDENTIFIED SUGGESTIVE GENES, SUCH AS NOS1AP, TNFAIP2, BID, GABRB1, ATXN7, AND THOC7 WITH DNA METHYLATION CHANGES IN COPD LUNG TISSUES THAT WERE FURTHER VALIDATED BY PYROSEQUENCING. PYROSEQUENCING VALIDATION CONFIRMED HYPER-METHYLATION IN SMOKERS AND PATIENTS WITH COPD AS COMPARED TO NON-SMOKERS. HOWEVER, WE DID NOT DETECT SIGNIFICANT DIFFERENCES IN DNA METHYLATION FOR TNFAIP2, ATXN7, AND THOC7 GENES IN SMOKERS AND COPD GROUPS DESPITE THE CHANGES OBSERVED IN THE GENOME-WIDE ANALYSIS. CONCLUSIONS: OUR STUDY SUGGESTS THAT DNA METHYLATION IN SUGGESTIVE GENES, SUCH AS NOS1AP, BID, AND GABRB1 MAY BE USED AS EPIGENETIC SIGNATURES IN SMOKERS AND PATIENTS WITH COPD IF THE SAME IS VALIDATED IN A LARGER COHORT. FUTURE STUDIES ARE REQUIRED TO CORRELATE DNA METHYLATION STATUS WITH TRANSCRIPTOMICS OF SELECTIVE GENES IDENTIFIED IN THIS STUDY AND ELUCIDATE THEIR ROLE AND INVOLVEMENT IN THE PROGRESSION OF COPD AND ITS EXACERBATIONS.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
17  546 15 ATTENUATED EXPRESSION OF SLCO2A1 CAUSED BY DNA METHYLATION IN PEDIATRIC INFLAMMATORY BOWEL DISEASE. BACKGROUND: SLCO2A1 ENCODES A PROSTAGLANDIN (PG) TRANSPORTER, AND AUTOSOMAL RECESSIVE PATHOGENIC VARIANTS OF THIS GENE CAUSE CHRONIC ENTEROPATHY ASSOCIATED WITH SLCO2A1. IT IS UNCLEAR WHETHER A HETEROZYGOUS PATHOGENIC VARIANT OF SLCO2A1 HAS A ROLE IN THE PATHOGENESIS OF OTHER TYPES OF INFLAMMATORY BOWEL DISEASE (IBD). IN THIS STUDY, WE INVESTIGATED THE POSSIBLE INVOLVEMENT OF A LOCAL EPIGENETIC ALTERATION IN SLCO2A1 IN PATIENTS WITH A HETEROZYGOUS PATHOGENIC VARIANT. METHODS: WE CONDUCTED WHOLE-EXOME SEQUENCING OF SAMPLES FROM 2 SISTERS WITH SUSPECTED MONOGENIC IBD. IN ADDITION, WE PERFORMED BISULFITE SEQUENCING USING DNA EXTRACTED FROM THEIR SMALL AND LARGE INTESTINE SAMPLES TO EXPLORE EPIGENETIC ALTERATIONS. RESULTS: A HETEROZYGOUS SPLICING SITE VARIANT, SLCO2A1:C.940 + 1G > A, WAS DETECTED IN BOTH PATIENTS. TO EXPLORE THE POSSIBLE INVOLVEMENT OF EPIGENETIC ALTERATIONS, WE ANALYZED PROTEIN AND MESSENGER RNA EXPRESSION OF SLCO2A1, AND OBSERVED ATTENUATED SLCO2A1 EXPRESSION IN THE INFLAMED LESIONS OF THESE PATIENTS COMPARED WITH THAT IN THE CONTROL INDIVIDUALS. FURTHERMORE, BISULFITE SEQUENCING INDICATED DENSE METHYLATION IN THE PROMOTER REGION OF SLCO2A1 ONLY IN THE INFLAMED LESIONS OF BOTH PATIENTS. THE URINARY PG METABOLITE LEVELS IN THESE PATIENTS WERE COMPARABLE TO THOSE IN PATIENTS WITH CHRONIC ENTEROPATHY ASSOCIATED WITH SLCO2A1 AND HIGHER THAN THOSE IN THE CONTROL INDIVIDUALS. WE FOUND CONSIDERABLY HIGHER LEVELS OF THE METABOLITES IN PATIENT 1, WHO SHOWED MORE SEVERE SYMPTOMS THAN PATIENT 2. CONCLUSIONS: LOCAL DNA METHYLATION ATTENUATED SLCO2A1 EXPRESSION, WHICH MAY EVOKE LOCAL INFLAMMATION OF THE MUCOSA BY THE UNINCORPORATED PG. THESE FINDINGS MAY IMPROVE OUR UNDERSTANDING OF THE EPIGENETIC MECHANISMS UNDERLYING IBD DEVELOPMENT.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
18 6642 20 UNRAVELING THE PATHOGENESIS OF ASTHMA AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE OVERLAP: FOCUSING ON EPIGENETIC MECHANISMS. ASTHMA AND COPD OVERLAP (ACO) IS CHARACTERIZED BY PATIENTS PRESENTING WITH PERSISTENT AIRFLOW LIMITATION AND FEATURES OF BOTH ASTHMA AND COPD. IT IS ASSOCIATED WITH A HIGHER FREQUENCY AND SEVERITY OF EXACERBATIONS, A FASTER LUNG FUNCTION DECLINE, AND A HIGHER HEALTHCARE COST. SYSTEMIC INFLAMMATION IN COPD AND ASTHMA IS DRIVEN BY TYPE 1 T HELPER (TH1) AND TH2 IMMUNE RESPONSES, RESPECTIVELY, BOTH OF WHICH MAY CONTRIBUTE TO AIRWAY REMODELING IN ACO. ACO-RELATED BIOMARKERS CAN BE CLASSIFIED INTO FOUR CATEGORIES: NEUTROPHIL-MEDIATED INFLAMMATION, TH2 CELL RESPONSES, ARACHIDONIC ACID-EICOSANOIDS PATHWAY, AND METABOLITES. GENE-ENVIRONMENT INTERACTIONS ARE KEY CONTRIBUTORS TO THE COMPLEXITY OF ACO AND ARE REGULATED BY EPIGENETIC MECHANISMS, INCLUDING DNA METHYLATION, HISTONE MODIFICATIONS, AND NON-CODING RNAS. THUS, THIS REVIEW FOCUSES ON THE LINK BETWEEN EPIGENETICS AND ACO, AND OUTLINES THE FOLLOWING: (I) INHERITING EPIGENOTYPES WITHOUT CHANGE WITH ENVIRONMENTAL STIMULI, OR EPIGENETIC CHANGES IN RESPONSE TO LONG-TERM EXPOSURE TO INHALED PARTICLES PLUS INTERMITTENT EXPOSURE TO SPECIFIC ALLERGENS; (II) EPIGENETIC MARKERS DISTINGUISHING ACO FROM COPD AND ASTHMA; (III) POTENTIAL EPIGENETIC DRUGS THAT CAN REVERSE OXIDATIVE STRESS, GLUCOCORTICOID INSENSITIVITY, AND CELL INJURY. IMPROVED UNDERSTANDING OF THE EPIGENETIC REGULATIONS HOLDS GREAT VALUE TO GIVE DEEPER INSIGHT INTO THE MECHANISMS, AND CLARIFY THEIR IMPLICATIONS FOR BIOMEDICAL RESEARCH IN ACO.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
19 6052 16 THE CROHN'S DISEASE ASSOCIATED SNP RS6651252 IMPACTS MYC GENE EXPRESSION IN HUMAN COLONIC EPITHELIAL CELLS. CROHN'S DISEASE (CD) IS A DEBILITATING INFLAMMATORY BOWEL DISEASE (IBD) THAT ARISES FROM CHRONIC INFLAMMATION IN THE GASTROINTESTINAL TRACT. GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE IDENTIFIED OVER 200 SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) THAT ARE ASSOCIATED WITH A PREDISPOSITION FOR DEVELOPING IBD. FOR THE MAJORITY, THE CAUSAL VARIANT AND TARGET GENES AFFECTED ARE UNKNOWN. HERE, WE INVESTIGATED THE CD-ASSOCIATED SNP RS6651252 THAT MAPS TO A GENE DESERT REGION ON CHROMOSOME 8. WE DEMONSTRATE THAT RS6651252 RESIDES WITHIN A WNT RESPONSIVE DNA ENHANCER ELEMENT (WRE) AND THAT THE DISEASE ASSOCIATED ALLELE AUGMENTS BINDING OF THE TCF7L2 TRANSCRIPTION FACTOR TO THIS REGION. USING CRISPR/CAS9 DIRECTED GENE EDITING AND EPIGENETIC MODULATION, WE FIND THAT THE RS6651252 ENHANCER REGULATES EXPRESSION OF THE C-MYC PROTO-ONCOGENE (MYC). FURTHERMORE, WE FOUND MYC TRANSCRIPT LEVELS ARE ELEVATED IN PATIENT-DERIVED COLONIC SEGMENTS HARBORING THE DISEASE-ASSOCIATED ALLELE IN COMPARISON TO THOSE CONTAINING THE ANCESTRAL ALLELE. THESE RESULTS SUGGEST THAT WNT/MYC SIGNALING CONTRIBUTES TO CD PATHOGENESIS AND THAT PATIENTS HARBORING THE DISEASE-ASSOCIATED ALLELE MAY BENEFIT FROM THERAPIES THAT TARGET MYC OR MYC-REGULATED GENES.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
20   11 14 15Q12 VARIANTS, SPUTUM GENE PROMOTER HYPERMETHYLATION, AND LUNG CANCER RISK: A GWAS IN SMOKERS. BACKGROUND: LUNG CANCER IS THE LEADING CAUSE OF CANCER-RELATED MORTALITY WORLDWIDE. DETECTION OF PROMOTER HYPERMETHYLATION OF TUMOR SUPPRESSOR GENES IN EXFOLIATED CELLS FROM THE LUNG PROVIDES AN ASSESSMENT OF FIELD CANCERIZATION THAT IN TURN PREDICTS LUNG CANCER. THE IDENTIFICATION OF GENETIC DETERMINANTS FOR THIS VALIDATED CANCER BIOMARKER SHOULD PROVIDE NOVEL INSIGHTS INTO MECHANISMS UNDERLYING EPIGENETIC REPROGRAMMING DURING LUNG CARCINOGENESIS. METHODS: A GENOME-WIDE ASSOCIATION STUDY USING GENERALIZED ESTIMATING EQUATIONS AND LOGISTIC REGRESSION MODELS WAS CONDUCTED IN TWO GEOGRAPHICALLY INDEPENDENT SMOKER COHORTS TO IDENTIFY LOCI AFFECTING THE PROPENSITY FOR CANCER-RELATED GENE METHYLATION THAT WAS ASSESSED BY A 12-GENE PANEL INTERROGATED IN SPUTUM. ALL STATISTICAL TESTS WERE TWO-SIDED. RESULTS: TWO SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) AT 15Q12 (RS73371737 AND RS7179575) THAT DROVE GENE METHYLATION WERE DISCOVERED AND REPLICATED WITH RS73371737 REACHING GENOME-WIDE SIGNIFICANCE (P = 3.3X10(-8)). A HAPLOTYPE CARRYING RISK ALLELES FROM THE TWO 15Q12 SNPS CONFERRED 57% INCREASED RISK FOR GENE METHYLATION (P = 2.5X10(-9)). RS73371737 REDUCED GABRB3 EXPRESSION IN LUNG CELLS AND INCREASED RISK FOR SMOKING-INDUCED CHRONIC MUCOUS HYPERSECRETION. FURTHERMORE, SUBJECTS WITH VARIANT HOMOZYGOTE OF RS73371737 HAD A TWO-FOLD INCREASE IN RISK FOR LUNG CANCER (P = .0043). PATHWAY ANALYSIS IDENTIFIED DNA DOUBLE-STRAND BREAK REPAIR BY HOMOLOGOUS RECOMBINATION (DSBR-HR) AS A MAJOR PATHWAY AFFECTING SUSCEPTIBILITY FOR GENE METHYLATION THAT WAS VALIDATED BY MEASURING CHROMATID BREAKS IN LYMPHOCYTES CHALLENGED BY BLEOMYCIN. CONCLUSIONS: A FUNCTIONAL 15Q12 VARIANT WAS IDENTIFIED AS A RISK FACTOR FOR GENE METHYLATION AND LUNG CANCER. THE ASSOCIATIONS COULD BE MEDIATED BY GABAERGIC SIGNALING THAT DRIVES THE SMOKING-INDUCED MUCOUS CELL METAPLASIA. OUR FINDINGS ALSO SUBSTANTIATE DSBR-HR AS A CRITICAL PATHWAY DRIVING EPIGENETIC GENE SILENCING.	2015