1 1118 155 COMPARATIVE GENOTYPING AND PHENOTYPING OF ASPERGILLUS FUMIGATUS ISOLATES FROM HUMANS, DOGS AND THE ENVIRONMENT. BACKGROUND: ASPERGILLUS FUMIGATUS IS A UBIQUITOUS SAPROTROPHIC FUNGUS AND AN OPPORTUNISTIC PATHOGEN OF HUMANS AND ANIMALS. HUMANS AND ANIMALS CAN INHALE HUNDREDS OF A. FUMIGATUS SPORES DAILY. NORMALLY THIS IS HARMLESS FOR HUMANS, BUT IN CASE OF IMMUNODEFICIENCY, INVASIVE PULMONARY ASPERGILLOSIS (IPA) CAN DEVELOP WITH A HIGH MORTALITY RATE. A. FUMIGATUS ALSO CAUSES NON-INVASIVE MYCOSES LIKE SINO-NASAL ASPERGILLOSIS (SNA) IN DOGS. RESULTS: IN THIS STUDY WE COMPARED A. FUMIGATUS ISOLATES FROM HUMANS WITH SUSPECTED IPA, DOGS WITH SNA, AND A SET OF ENVIRONMENTAL ISOLATES. PHYLOGENETIC INFERENCE BASED ON CALMODULIN (CAM) AND BETA-TUBULIN (BENA) SEQUENCES DID NOT REVEAL A. FUMIGATUS SUB-GROUPS LINKED TO THE ORIGIN OF THE ISOLATES. GENOTYPING AND MICROSATELLITE ANALYSIS SHOWED THAT EACH DOG WAS INFECTED BY ONE A. FUMIGATUS GENOTYPE, WHEREAS HUMAN PATIENTS HAD MIXED INFECTIONS. AZOLE RESISTANCE WAS DETERMINED BY ANTIFUNGAL SUSCEPTIBILITY TESTING AND SEQUENCING OF THE CYP51A GENE. A TOTAL OF 12 OUT OF 29 HUMAN ISOLATES AND 1 OUT OF 27 ENVIRONMENTAL ISOLATES WERE AZOLE RESISTANT. OF THE AZOLE RESISTANT STRAINS, 11 HUMAN ISOLATES SHOWED TR(34)/L98H (N = 6) OR TR46/Y121F/T289A (N = 5). PHENOTYPICALLY, ISOLATES FROM DOGS WERE MORE VARIABLE IN GROWTH SPEED AND MORPHOLOGY WHEN COMPARED TO THOSE ISOLATED FROM HUMAN AND THE ENVIRONMENT. CONCLUSIONS: 1. A. FUMIGATUS FROM DOGS WITH SNA ARE PHENOTYPICALLY VERY DIVERSE IN CONTRAST TO THEIR ENVIRONMENTAL AND HUMAN COUNTERPARTS. 2. PHENOTYPIC VARIABILITY CAN BE INDUCED DURING THE CHRONIC INFECTION PROCESS IN THE SINUS OF THE DOGS. THE BASIS OF THIS HETEROGENEITY MIGHT BE DUE TO GENOMIC DIFFERENCES AND/OR EPIGENETIC VARIATIONS. 3. DIFFERENCES IN DOGS IS A COULD BE A RESULT OF WITHIN-HOST ADAPTION AND MIGHT BE TRIGGERED BY ENVIRONMENTAL FACTORS IN THE SINUS, HOWEVER THIS HYPOTHESIS STILL NEEDS TO BE TESTED. 2018 2 1519 27 DNA METHYLATION AT ATP11A CG11702988 IS A BIOMARKER OF LUNG DISEASE SEVERITY IN CYSTIC FIBROSIS: A LONGITUDINAL STUDY. CYSTIC FIBROSIS (CF) IS A CHRONIC GENETIC DISEASE THAT MAINLY AFFECTS THE RESPIRATORY AND GASTROINTESTINAL SYSTEMS. NO CURATIVE TREATMENTS ARE AVAILABLE, BUT THE FOLLOW-UP IN SPECIALIZED CENTERS HAS GREATLY IMPROVED THE PATIENT LIFE EXPECTANCY. ROBUST BIOMARKERS ARE REQUIRED TO MONITOR THE DISEASE, GUIDE TREATMENTS, STRATIFY PATIENTS, AND PROVIDE OUTCOME MEASURES IN CLINICAL TRIALS. IN THE PRESENT STUDY, WE OUTLINE A STRATEGY TO SELECT PUTATIVE DNA METHYLATION BIOMARKERS OF LUNG DISEASE SEVERITY IN CYSTIC FIBROSIS PATIENTS. IN THE DISCOVERY STEP, WE SELECTED SEVEN POTENTIAL BIOMARKERS USING A GENOME-WIDE DNA METHYLATION DATASET THAT WE GENERATED IN NASAL EPITHELIAL SAMPLES FROM THE METHYLCF COHORT. IN THE REPLICATION STEP, WE ASSESSED THE SAME BIOMARKERS USING SPUTUM CELL SAMPLES FROM THE METHYLBIOMARK COHORT. OF INTEREST, DNA METHYLATION AT THE CG11702988 SITE (ATP11A GENE) POSITIVELY CORRELATED WITH LUNG FUNCTION AND BMI, AND NEGATIVELY CORRELATED WITH LUNG DISEASE SEVERITY, P. AERUGINOSA CHRONIC INFECTION, AND THE NUMBER OF EXACERBATIONS. THESE RESULTS WERE REPLICATED IN PROSPECTIVE SPUTUM SAMPLES COLLECTED AT FOUR TIME POINTS WITHIN AN 18-MONTH PERIOD AND LONGITUDINALLY. TO CONCLUDE, (I) WE IDENTIFIED A DNA METHYLATION BIOMARKER THAT CORRELATES WITH CF SEVERITY, (II) WE PROVIDED A METHOD TO EASILY ASSESS THIS BIOMARKER, AND (III) WE CARRIED OUT THE FIRST LONGITUDINAL ANALYSIS OF DNA METHYLATION IN CF PATIENTS. THIS NEW EPIGENETIC BIOMARKER COULD BE USED TO STRATIFY CF PATIENTS IN CLINICAL TRIALS. 2021 3 6817 38 [FACIOSCAPULOHUMERAL MUSCULAR DYSTROPHY: REPORT OF SEVEN PATIENTS]. BACKGROUND: FACIOSCAPULOHUMERAL MUSCULAR DYSTROPHY IS THE THIRD MOST COMMON MUSCULAR DYSTROPHY WITH AN ESTIMATED PREVALENCE OF 1 PER 20.000 AND A NORMAL LIFE EXPECTANCY IN THE MAJORITY OF PATIENTS. HOWEVER, APPROXIMATELY 15% OF PATIENTS BECOME WHEELCHAIR BOUND IN THE COURSE OF THEIR LIFE. IT IS A HEREDITARY AUTOSOMAL DOMINANT DISEASE WITH HIGH (95%) PENETRANCE BY THE AGE OF 20, BUT WITH VARIABLE DEGREE OF PHENOTYPIC EXPRESSION EVEN IN THE SAME FAMILY GROUP. SYMPTOMS FREQUENTLY START IN THE SECOND DECADE OF LIFE, WITH FACIAL AND SCAPULAR WEAKNESS. AIM: TO REPORT THE CLINICAL FEATURES OF SEVEN PATIENTS WITH THE DISEASE, SEEN AT A PUBLIC HOSPITAL. MATERIAL AND METHODS: ANALYSIS OF SEVEN PATIENTS WITH GENETIC STUDY SEEN IN A PUBLIC HOSPITAL IN SANTIAGO. RESULTS: THE AGE OF PATIENTS FLUCTUATED FROM 18 TO 61 YEARS AND FOUR WERE FEMALES. THE MEAN AGE AT ONSET OF SYMPTOMS WAS 29 YEARS AND FOUR HAD A FAMILY HISTORY OF THE DISEASE. THE USUAL PRESENTING COMPLAINT WAS ARM OR SHOULDER ASYMMETRIC WEAKNESS. FOUR PATIENTS HAD BONE PAIN. FACIAL INVOLVEMENT WAS PRESENT IN FOUR. A GENETIC STUDY WAS DONE IN FIVE PATIENTS, THE OTHER TWO PATIENTS WERE RELATIVES, CONFIRMING THE CONTRACTION OR LOWER NUMBER OF REPETITIONS IN D4Z4 REGION. AFTER 12 YEARS OF FOLLOW UP ONLY 2 PATIENTS OLDER THAN 60 YEARS CANNOT WORK AND ONE FEMALE PATIENTS IS IN A SEMI DEPENDENT STATE AT THE AGE OF 30. CONCLUSIONS: THE CLINICAL WORKUP IN THE DIAGNOSIS AND THE TIMELY INDICATION OF GENETIC STUDIES ARE HIGHLIGHTED, TO AVOID UNNECESSARY AND INVASIVE PROCEDURES. THE VARIABILITY IN THE PHENOTYPIC EXPRESSION IN A SIMILAR GENETIC DEFECT IS DISCUSSED AND THE GENETIC OR EPIGENETIC MECHANISMS OF THIS MUSCULAR DYSTROPHY ARE DESCRIBED. 2015 4 2820 25 FINE-MAPPING INFLAMMATORY BOWEL DISEASE LOCI TO SINGLE-VARIANT RESOLUTION. INFLAMMATORY BOWEL DISEASES ARE CHRONIC GASTROINTESTINAL INFLAMMATORY DISORDERS THAT AFFECT MILLIONS OF PEOPLE WORLDWIDE. GENOME-WIDE ASSOCIATION STUDIES HAVE IDENTIFIED 200 INFLAMMATORY BOWEL DISEASE-ASSOCIATED LOCI, BUT FEW HAVE BEEN CONCLUSIVELY RESOLVED TO SPECIFIC FUNCTIONAL VARIANTS. HERE WE REPORT FINE-MAPPING OF 94 INFLAMMATORY BOWEL DISEASE LOCI USING HIGH-DENSITY GENOTYPING IN 67,852 INDIVIDUALS. WE PINPOINT 18 ASSOCIATIONS TO A SINGLE CAUSAL VARIANT WITH GREATER THAN 95% CERTAINTY, AND AN ADDITIONAL 27 ASSOCIATIONS TO A SINGLE VARIANT WITH GREATER THAN 50% CERTAINTY. THESE 45 VARIANTS ARE SIGNIFICANTLY ENRICHED FOR PROTEIN-CODING CHANGES (N = 13), DIRECT DISRUPTION OF TRANSCRIPTION-FACTOR BINDING SITES (N = 3), AND TISSUE-SPECIFIC EPIGENETIC MARKS (N = 10), WITH THE LAST CATEGORY SHOWING ENRICHMENT IN SPECIFIC IMMUNE CELLS AMONG ASSOCIATIONS STRONGER IN CROHN'S DISEASE AND IN GUT MUCOSA AMONG ASSOCIATIONS STRONGER IN ULCERATIVE COLITIS. THE RESULTS OF THIS STUDY SUGGEST THAT HIGH-RESOLUTION FINE-MAPPING IN LARGE SAMPLES CAN CONVERT MANY DISCOVERIES FROM GENOME-WIDE ASSOCIATION STUDIES INTO STATISTICALLY CONVINCING CAUSAL VARIANTS, PROVIDING A POWERFUL SUBSTRATE FOR EXPERIMENTAL ELUCIDATION OF DISEASE MECHANISMS. 2017 5 4227 33 METHYLATION OF FREE-FLOATING DEOXYRIBONUCLEIC ACID FRAGMENTS IN THE BRONCHOALVEOLAR LAVAGE FLUID OF DOGS WITH CHRONIC BRONCHITIS EXPOSED TO ENVIRONMENTAL TOBACCO SMOKE. BACKGROUND: THE ETIOLOGY OF CANINE CHRONIC BRONCHITIS (CB) IS NOT COMPLETELY UNDERSTOOD, ALTHOUGH EXPOSURE TO ENVIRONMENTAL TOBACCO SMOKE (ETS) AFFECTS THE AIRWAY INFLAMMATORY RESPONSES IN SOME DOGS WITH CB. THE MECHANISM BY WHICH THIS OCCURS IS UNKNOWN. FINDINGS: WE INVESTIGATED THE CONCENTRATIONS AND METHYLATION RATES OF FREE-FLOATING DNA FRAGMENTS IN BRONCHOALVEOLAR LAVAGE FLUID (BALF) FROM DOGS WITH CHRONIC BRONCHITIS. BASED ON SERUM COTININE LEVELS, DOGS WITH CB WERE DIVIDED INTO 2 GROUPS: DOGS THAT EITHER HAD OR HAD NOT BEEN EXPOSED TO ETS. OUR RESULTS DEMONSTRATED THAT THE TOTAL NUCLEATED CELL AND MACROPHAGE NUMBERS INCREASED IN BALF OF ETS-EXPOSED DOGS WITH CB. THERE WERE NO SIGNIFICANT DIFFERENCES IN DNA CONCENTRATIONS AND METHYLATION RATES IN BALF BETWEEN THE 2 GROUPS. HOWEVER, 3 OUT OF 8 DOGS EXPOSED TO ETS HAD HIGH DNA METHYLATION RATES IN THEIR BALF SAMPLES. CONCLUSION: OUR RESULTS SUGGEST THAT ETS EXPOSURE LEADS TO EPIGENETIC MODIFICATIONS OF CELLULAR COMPONENTS IN BALF IN DOGS DIAGNOSED WITH CB. 2015 6 1345 31 DETECTION OF DIFFERENTIALLY METHYLATED REGIONS USING BAYES FACTOR FOR ORDINAL GROUP RESPONSES. RESEARCHERS IN GENOMICS ARE INCREASINGLY INTERESTED IN EPIGENETIC FACTORS SUCH AS DNA METHYLATION, BECAUSE THEY PLAY AN IMPORTANT ROLE IN REGULATING GENE EXPRESSION WITHOUT CHANGES IN THE DNA SEQUENCE. THERE HAVE BEEN SIGNIFICANT ADVANCES IN DEVELOPING STATISTICAL METHODS TO DETECT DIFFERENTIALLY METHYLATED REGIONS (DMRS) ASSOCIATED WITH BINARY DISEASE STATUS. MOST OF THESE METHODS ARE BEING DEVELOPED FOR DETECTING DIFFERENTIAL METHYLATION RATES BETWEEN CASES AND CONTROLS. WE CONSIDER MULTIPLE SEVERITY LEVELS OF DISEASE, AND DEVELOP A BAYESIAN STATISTICAL METHOD TO DETECT THE REGION WITH INCREASING (OR DECREASING) METHYLATION RATES AS THE DISEASE SEVERITY INCREASES. PATIENTS ARE CLASSIFIED INTO MORE THAN TWO GROUPS, BASED ON THE DISEASE SEVERITY (E.G., STAGES OF CANCER), AND DMRS ARE DETECTED BY USING MOVING WINDOWS ALONG THE GENOME. WITHIN EACH WINDOW, THE BAYES FACTOR IS CALCULATED TO TEST THE HYPOTHESIS OF MONOTONIC INCREASE IN METHYLATION RATES CORRESPONDING TO SEVERITY OF THE DISEASE VERSUS NO DIFFERENCE. A MIXED-EFFECT MODEL IS USED TO INCORPORATE THE CORRELATION OF METHYLATION RATES OF NEARBY CPG SITES IN THE REGION. RESULTS FROM EXTENSIVE SIMULATION INDICATE THAT OUR PROPOSED METHOD IS STATISTICALLY VALID AND REASONABLY POWERFUL. WE DEMONSTRATE OUR APPROACH ON A BISULFITE SEQUENCING DATASET FROM A CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) STUDY. 2019 7 3652 33 INDIVIDUAL DNA METHYLATION PATTERN SHIFTS IN NANOPARTICLES-EXPOSED WORKERS ANALYZED IN FOUR CONSECUTIVE YEARS. A DNA METHYLATION PATTERN REPRESENTS AN ORIGINAL PLAN OF THE FUNCTION SETTINGS OF INDIVIDUAL CELLS AND TISSUES. THE BASIC STRATEGIES OF ITS DEVELOPMENT AND CHANGES DURING THE HUMAN LIFETIME ARE KNOWN, BUT THE DETAILS RELATED TO ITS MODIFICATION OVER THE YEARS ON AN INDIVIDUAL BASIS HAVE NOT YET BEEN STUDIED. MOREOVER, CURRENT EVIDENCE SHOWS THAT ENVIRONMENTAL EXPOSURE COULD GENERATE CHANGES IN DNA METHYLATION SETTINGS AND, SUBSEQUENTLY, THE FUNCTION OF GENES. IN THIS STUDY, WE ANALYZED THE EFFECT OF CHRONIC EXPOSURE TO NANOPARTICLES (NP) IN OCCUPATIONALLY EXPOSED WORKERS REPEATEDLY SAMPLED IN FOUR CONSECUTIVE YEARS (2016-2019). A DETAILED METHYLATION PATTERN ANALYSIS OF 14 PERSONS (10 EXPOSED AND 4 CONTROLS) WAS PERFORMED ON AN INDIVIDUAL BASIS. A MICROARRAY-BASED APPROACH USING CHIPS, ALLOWING THE ASSESSMENT OF MORE THAN 850 K CPG LOCI, WAS USED. INDIVIDUAL DNA METHYLATION PATTERNS WERE COMPARED BY PRINCIPAL COMPONENT ANALYSIS (PCA). THE RESULTS SHOW THE SHIFT IN DNA METHYLATION PATTERNS IN INDIVIDUAL YEARS IN ALL THE EXPOSED AND CONTROL SUBJECTS. THE OVERALL RANGE OF DIFFERENCES VARIED BETWEEN THE YEARS IN INDIVIDUAL PERSONS. THE DIFFERENCES BETWEEN THE FIRST AND LAST YEAR OF EXAMINATION (A THREE-YEAR TIME PERIOD) SEEM TO BE CONSISTENTLY GREATER IN THE NP-EXPOSED SUBJECTS IN COMPARISON WITH THE CONTROLS. THE SELECTED 14 MOST DIFFERENTLY METHYLATED CG LOCI WERE RELATIVELY STABLE IN THE CHRONICALLY EXPOSED SUBJECTS. IN SUMMARY, THE SPECIFIC TYPE OF LONG-TERM EXPOSURE CAN CONTRIBUTE TO THE FIXING OF RELEVANT EPIGENETIC CHANGES RELATED TO A SPECIFIC ENVIRONMENT AS, E.G., NP INHALATION. 2021 8 6547 32 TRANSCRIPTOMICS OF LONG-TERM MEDITATION PRACTICE: EVIDENCE FOR PREVENTION OR REVERSAL OF STRESS EFFECTS HARMFUL TO HEALTH. BACKGROUND AND OBJECTIVES: STRESS CAN OVERLOAD ADAPTIVE MECHANISMS, LEADING TO EPIGENETIC EFFECTS HARMFUL TO HEALTH. RESEARCH ON THE REVERSAL OF THESE EFFECTS IS IN ITS INFANCY. EARLY RESULTS SUGGEST SOME MEDITATION TECHNIQUES HAVE HEALTH BENEFITS THAT GROW WITH REPEATED PRACTICE. THIS STUDY FOCUSED ON POSSIBLE TRANSCRIPTOMIC EFFECTS OF 38 YEARS OF TWICE-DAILY TRANSCENDENTAL MEDITATION((R)) (TM((R))) PRACTICE. MATERIALS AND METHODS: FIRST, USING ILLUMINA((R)) BEADCHIP MICROARRAY TECHNOLOGY, DIFFERENCES IN GLOBAL GENE EXPRESSION IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) WERE SOUGHT BETWEEN HEALTHY PRACTITIONERS AND TIGHTLY MATCHED CONTROLS (N = 12, AGE 65). SECOND, THESE MICROARRAY RESULTS WERE VERIFIED ON A SUBSET OF GENES USING QUANTITATIVE POLYMERASE CHAIN REACTION (QPCR) AND WERE VALIDATED USING QPCR IN LARGER TM AND CONTROL GROUPS (N = 45, AGE 63). BIOINFORMATICS INVESTIGATION EMPLOYED INGENUITY((R)) PATHWAY ANALYSIS (IPA((R))), DAVID, GENOMATIX, AND R PACKAGES. RESULTS: THE 200 GENES AND LOCI FOUND TO MEET STRICT CRITERIA FOR DIFFERENTIAL EXPRESSION IN THE MICROARRAY EXPERIMENT SHOWED CONTRASTING PATTERNS OF EXPRESSION THAT DISTINGUISHED THE TWO GROUPS. DIFFERENTIAL EXPRESSION RELATING TO IMMUNE FUNCTION AND ENERGY EFFICIENCY WERE MOST APPARENT. IN THE TM GROUP, RELATIVE TO THE CONTROL, ALL 49 GENES ASSOCIATED WITH INFLAMMATION WERE DOWNREGULATED, WHILE GENES ASSOCIATED WITH ANTIVIRAL AND ANTIBODY COMPONENTS OF THE DEFENSE RESPONSE WERE UPREGULATED. THE LARGEST EXPRESSION DIFFERENCES WERE SHOWN BY SIX GENES RELATED TO ERYTHROCYTE FUNCTION THAT APPEARED TO REFLECT A CONDITION OF LOWER ENERGY EFFICIENCY IN THE CONTROL GROUP. RESULTS SUPPORTING THESE GENE EXPRESSION DIFFERENCES WERE OBTAINED WITH QPCR-MEASURED EXPRESSION BOTH IN THE WELL-MATCHED MICROARRAY GROUPS AND IN THE LARGER, LESS WELL-MATCHED GROUPS. CONCLUSIONS: THESE FINDINGS ARE CONSISTENT WITH PREDICTIONS BASED ON RESULTS FROM EARLIER RANDOMIZED TRIALS OF MEDITATION AND MAY PROVIDE EVIDENCE FOR STRESS-RELATED MOLECULAR MECHANISMS UNDERLYING REDUCTIONS IN ANXIETY, POST-TRAUMATIC STRESS DISORDER (PTSD), CARDIOVASCULAR DISEASE (CVD), AND OTHER CHRONIC DISORDERS AND DISEASES. 2021 9 1537 33 DNA METHYLATION IN ADOLESCENTS WITH ANXIETY DISORDER: A LONGITUDINAL STUDY. ANXIETY DISORDERS (AD) TYPICALLY MANIFEST IN CHILDREN AND ADOLESCENTS AND MIGHT PERSIST INTO ADULTHOOD. HOWEVER, THERE ARE STILL FEW DATA CONCERNING EPIGENETIC MECHANISMS ASSOCIATED WITH ONSET, PERSISTENCE OR REMISSION OF AD OVER TIME. WE INVESTIGATED A COHORT OF ADOLESCENTS AND YOUNG ADULTS AT BASELINE (AGE; 13.19 +/- 2.38) AND AFTER 5 YEARS AND CLASSIFIED THEM ACCORDING TO THE AD DIAGNOSIS AND THEIR LONGITUDINAL TRAJECTORIES INTO 4 GROUPS: (1) TYPICALLY DEVELOPING COMPARISONS (TDC; CONTROL GROUP, N = 14); (2) INCIDENT (AD IN THE SECOND EVALUATION ONLY, N = 11); (3) PERSISTENT (AD IN BOTH EVALUATIONS, N = 14) AND (4) REMITTENT (AD IN THE FIRST EVALUATION ONLY, N = 8). DNA METHYLATION WAS EVALUATED WITH THE INFINIUM HUMANMETHYLATION450 BEADCHIP FROM SALIVA SAMPLES COLLECTED AT BOTH EVALUATIONS. GENE SET ENRICHMENT ANALYSIS WAS APPLIED TO CONSIDER BIOLOGICAL PATHWAYS. WE FOUND DECREASED DNA METHYLATION IN TDC GROUP WHILE THE CHRONIC CASES OF AD PRESENTED HYPERMETHYLATION IN CENTRAL NERVOUS SYSTEM DEVELOPMENT PATHWAYS. MOREOVER, WE SHOWED THAT THIS PERSISTENT GROUP ALSO PRESENTED HYPERMETHYLATION WHILE THE OTHER THREE GROUPS WERE ASSOCIATED WITH HYPOMETHYLATION IN NERVOUS SYSTEM DEVELOPMENT PATHWAY. INCIDENCE AND REMISSION GROUPS WERE ASSOCIATED WITH INCREASED AND DECREASED METHYLATION IN NEURON DEVELOPMENT PATHWAYS, RESPECTIVELY. LARGER STUDIES ARE LIKELY TO DETECT SPECIFIC GENES RELEVANT TO AD. 2018 10 5638 33 SERUM METABOLOMICS REVEALS PATHWAYS AND BIOMARKERS ASSOCIATED WITH ASTHMA PATHOGENESIS. BACKGROUND: ASTHMA IS A CHRONIC INFLAMMATORY DISEASE CAUSED BY COMPLEX INTERACTIONS OF GENETIC, EPIGENETIC, AND ENVIRONMENTAL FACTORS. FOR THIS REASON, NEW APPROACHES ARE REQUIRED TO CLARIFY THE PATHOGENESIS OF ASTHMA BY SYSTEMIC REVIEW. OBJECTIVE: WE APPLIED A (1)H-NMR METABOLOMICS APPROACH TO INVESTIGATE THE ALTERED METABOLIC PATTERN IN SERA FROM PATIENTS WITH ASTHMA AND SOUGHT TO IDENTIFY THE MECHANISM UNDERLYING ASTHMA AND POTENTIAL BIOMARKERS. METHOD: A GLOBAL PROFILE OF SERA FROM PATIENTS WITH ASTHMA (N = 39) AND CONTROLS (N = 26) WAS GENERATED USING (1)H-NMR SPECTROSCOPY COUPLED WITH MULTIVARIATE STATISTICAL ANALYSIS. ENDOGENOUS METABOLITES IN SERUM WERE RAPIDLY MEASURED USING THE TARGET-PROFILING PROCEDURE. RESULTS: MULTIVARIATE STATISTICAL ANALYSIS SHOWED A CLEAR DISTINCTION BETWEEN PATIENTS WITH ASTHMA AND HEALTHY SUBJECTS. SERA OF ASTHMA PATIENTS WERE CHARACTERIZED BY INCREASED LEVELS OF METHIONINE, GLUTAMINE, AND HISTIDINE AND BY DECREASED LEVELS OF FORMATE, METHANOL, ACETATE, CHOLINE, O-PHOSPHOCHOLINE, ARGININE, AND GLUCOSE. THE METABOLITES DETECTED IN THE SERA OF PATIENTS WITH ASTHMA ARE INVOLVED IN HYPERMETHYLATION, RESPONSE TO HYPOXIA, AND IMMUNE REACTION. FURTHERMORE, THE LEVELS OF SERUM METABOLITES FROM PATIENTS WITH ASTHMA CORRELATED WITH ASTHMA SEVERITY; IN PARTICULAR, LIPID METABOLISM WAS ALTERED IN PATIENTS WITH LOWER FORCED EXPIRATORY VOLUME IN 1 S PERCENTAGE (FEV(1)%) PREDICTED VALUES. IN ADDITION, POTENTIAL BIOMARKERS SHOWED STRONG PREDICTIVE POWER IN ROC ANALYSIS, AND THE PRESENCE OF ASTHMA IN EXTERNAL VALIDATION MODELS WAS PREDICTED WITH HIGH ACCURACY (90.9% FOR ASTHMA AND 100% FOR CONTROL SUBJECTS). CONCLUSION & CLINICAL RELEVANCE: THESE DATA SHOWED THAT (1)H-NMR-BASED METABOLITE PROFILING OF SERUM MAY BE USEFUL FOR THE EFFECTIVE DIAGNOSIS OF ASTHMA AND A FURTHER UNDERSTANDING OF ITS PATHOGENESIS. 2013 11 2908 28 GENE EXPRESSION PROFILE OF NORMAL BREAST TISSUE AND BODY MASS INDEX. BACKGROUND: IN HUMAN BREAST, ADIPOSE TISSUE REPRESENTS UP TO 80% OF THE TOTAL VOLUME AND PLAYS A CRITICAL ROLE IN MAMMARY GLAND REMODELING. GIVEN THE EMERGING ROLE OF OBESITY IN BREAST CANCER GROWTH AND DEVELOPMENT, WE EXPLORED THE RELATIONSHIP BETWEEN BODY MASS INDEX (BMI), AS A PROXY OF WOMAN'S OBESITY STATUS, AND THE EXPRESSION IN NORMAL BREAST TISSUE FROM HEALTHY WOMEN OF A SELECTED PANEL OF GENES, KNOWN TO BE INVOLVED IN MAMMARY GLAND HOMEOSTASIS. METHODS: TWO INDEPENDENT PUBLICLY AVAILABLE DATASETS, COMPOSED OF 180 SPECIMENS OF NORMAL BREAST TISSUE FROM REDUCTION MAMMOPLASTY WERE INTERROGATED. DIFFERENTIAL GENE EXPRESSION AMONG BMI CLASSES WAS EVALUATED BY ANOVA, AND PARTIAL CORRELATION COEFFICIENT WAS USED TO ASSAY THE CORRELATION BETWEEN GENES CONTROLLING FOR BMI. RESULTS: DESPITE THE DIFFERENCES IN MICROARRAY PLATFORMS AND ANALYTICAL PROCEDURES, THE TWO DATASETS SHARED A CORE OF 9 GENES DIFFERENTIALLY EXPRESSED IN BMI CLASSES AND SIGNIFICANTLY CORRELATED WITH BMI. FOUR (44%) OF THESE GENES BELONG TO THE FUNCTIONAL CLASS OF CYTOKINES AND CYTOKINE RECEPTORS (IL1R1, IL2RA, IL12A, AND IL12RB2). THE OTHERS BELONG TO THE FUNCTIONAL CLASS OF THE EPIGENETIC REGULATION (MEDAG AND SETD7), SIGNAL TRANSDUCTION (STAT1), CELL ADHESION (ITGAV), AND ENZYMATIC ACTIVITY (STS). CONCLUSIONS: ALTHOUGH EXPLORATORY, PRESENT FINDINGS ARE IN AGREEMENT WITH THE ROLE OF INFLAMMATION MODULATORS IN THE HOMEOSTASIS OF NORMAL BREAST TISSUE AND THE BELIEVE THAT AN INCREASE IN BODY ADIPOSE TISSUE MAY HAVE A POTENTIALLY DANGEROUS LOCAL EFFECT, THROUGH THE INCREASED EXPRESSION OF INFLAMMATION-RELATED GENES AND THE ESTABLISHMENT OF A LOW-GRADE CHRONIC INFLAMMATION. 2021 12 1948 46 EPIGENETIC ACQUISITION OF INDUCIBILITY OF TYPE III CYTOTOXICITY IN P. AERUGINOSA. BACKGROUND: PSEUDOMONAS AERUGINOSA, AN OPPORTUNISTIC PATHOGEN, IS OFTEN ENCOUNTERED IN CHRONIC LUNG DISEASES SUCH AS CYSTIC FIBROSIS OR CHRONIC OBSTRUCTIVE PNEUMONIA, AS WELL AS ACUTE SETTINGS LIKE MECHANICAL VENTILATION ACQUIRED PNEUMONIA OR NEUTROPENIC PATIENTS. IT IS A MAJOR CAUSE OF MORTALITY AND MORBIDITY IN THESE DISEASES. IN LUNGS, P. AERUGINOSA SETTLES IN A BIOFILM MODE OF GROWTH WITH THE SECRETION OF EXOPOLYSACCHARIDES IN WHICH IT IS ENCAPSULATED, ENHANCING ITS ANTIBIOTIC RESISTANCE AND CONTRIBUTING TO THE RESPIRATORY DEFICIENCY OF PATIENTS. HOWEVER, BACTERIA MUST FIRST MULTIPLY TO A HIGH DENSITY AND DISPLAY A CYTOTOXIC PHENOTYPE TO AVOID THE HOST'S DEFENCES. A VIRULENCE DETERMINANT IMPLICATED IN THIS STEP OF INFECTION IS THE TYPE III SECRETION SYSTEM (TTSS), ALLOWING TOXIN INJECTION DIRECTLY INTO HOST CELLS. AT THE BEGINNING OF THE INFECTION, MOST STRAINS ISOLATED FROM PATIENTS' LUNGS POSSESS AN INDUCIBLE TTSS ALLOWING TOXINS INJECTION OR SECRETION UPON IN VIVO OR IN VITRO ACTIVATION SIGNALS. AS THE INFECTION PERSISTS MOST OF THE BACTERIA PERMANENTLY LOOSE THIS CAPACITY, ALTHOUGH NO MUTATIONS HAVE BEEN EVIDENCED. WE NAME "NON INDUCIBLE" THIS PHENOTYPE. AS SUGGESTED BY THE PRESENCE OF A POSITIVE FEEDBACK CIRCUIT IN THE REGULATORY NETWORK CONTROLLING TTSS EXPRESSION, IT MAY BE DUE TO AN EPIGENETIC SWITCH ALLOWING HERITABLE PHENOTYPIC MODIFICATIONS WITHOUT GENOTYPE'S MUTATIONS. RESULTS: USING THE GENERALISED LOGICAL METHOD, WE DESIGNED A MINIMAL MODEL OF THE TTSS REGULATORY NETWORK THAT COULD SUPPORT THE EPIGENETIC HYPOTHESIS, AND STUDIED ITS DYNAMICS WHICH HELPED TO DEFINE A DISCRIMINATING EXPERIMENTAL SCENARIO SUFFICIENT TO VALIDATE THE EPIGENETIC HYPOTHESIS. A MATHEMATICAL FRAMEWORK BASED ON FORMAL METHODS FROM COMPUTER SCIENCE ALLOWED A RIGOROUS VALIDATION AND CERTIFICATION OF PARAMETERS OF THIS MODEL LEADING TO EPIGENETIC BEHAVIOUR. THEN, WE DEMONSTRATED THAT A NON INDUCIBLE STRAIN OF P. AERUGINOSA CAN STABLY ACQUIRE THE CAPACITY TO BE INDUCED BY CALCIUM DEPLETION FOR THE TTSS AFTER A SHORT PULSE OF A REGULATORY PROTEIN. FINALLY, THE INCREASED CYTOTOXICITY OF A STRAIN AFTER THIS EPIGENETIC SWITCH WAS DEMONSTRATED IN VIVO IN AN ACUTE PULMONARY INFECTION MODEL. CONCLUSION: THESE RESULTS MAY OFFER NEW PERSPECTIVES FOR THERAPEUTIC STRATEGIES TO PREVENT LETHAL INFECTIONS BY P. AERUGINOSA BY REVERTING THE EPIGENETIC INDUCIBILITY OF TYPE III CYTOTOXICITY. 2006 13 1607 24 DNA METHYLATION, COLON CANCER AND MEDITERRANEAN DIET: RESULTS FROM THE EPIC-ITALY COHORT. THE BIOLOGICAL MECHANISMS THROUGH WHICH ADHERENCE TO MEDITERRANEAN DIET (MD) PROTECTS AGAINST COLON CANCER (CC) ARE POORLY UNDERSTOOD. EVIDENCE SUGGESTS THAT CHRONIC INFLAMMATION MAY BE IMPLICATED IN THE PATHWAY. BOTH DIET AND CC ARE RELATED TO EPIGENETIC REGULATION. WE PERFORMED A NESTED CASE-CONTROL STUDY ON 161 PAIRS FROM THE ITALIAN COMPONENT OF THE EUROPEAN PROSPECTIVE INVESTIGATION INTO CANCER AND NUTRITION (EPIC) COHORT, IN WHICH WE LOOKED FOR THE METHYLATION SIGNALS IN DNA EXTRACTED FROM LEUCOCYTES ASSOCIATED WITH BOTH CC AND MD IN 995 CPGS LOCATED IN 48 INFLAMMATION GENES. THE DNA METHYLATION SIGNALS DETECTED IN THIS ANALYSIS WERE VALIDATED IN A SUBGROUP OF 47 CASE-CONTROL PAIRS AND FURTHER REPLICATED (WHERE VALIDATED) IN 95 NEW PAIRS BY MEANS OF PYROSEQUENCING. AMONG THE CPG SITES SELECTED A-PRIORI IN INFLAMMATION-RELATED GENES, SEVEN CPG SITES WERE FOUND TO BE ASSOCIATED WITH CC STATUS AND WITH MD, IN LINE WITH ITS PROTECTIVE EFFECT. ONLY TWO CPG SITES (CG17968347-SERPINE1 AND CG20674490-RUNX3) WERE VALIDATED USING BISULPHITE PYROSEQUENCING AND, AFTER REPLICATION, WE FOUND THAT DNA METHYLATION OF CG20674490-RUNX3 MAY BE A POTENTIAL MOLECULAR MEDIATOR EXPLAINING THE PROTECTIVE EFFECT OF MD ON CC ONSET. THE USE OF A 'MEET-IN-THE-MIDDLE' APPROACH TO IDENTIFY THE OVERLAP BETWEEN EXPOSURE AND PREDICTIVE MARKERS OF DISEASE IS INNOVATIVE IN STUDIES ON THE RELATIONSHIP BETWEEN DIET AND CANCER, IN WHICH EXPOSURE ASSESSMENT IS DIFFICULT AND THE MECHANISMS THROUGH WHICH THE NUTRIENTS EXERT THEIR PROTECTIVE EFFECT IS LARGELY UNKNOWN. 2019 14 344 37 ALTERED BDNF METHYLATION IN PATIENTS WITH CHRONIC MUSCULOSKELETAL PAIN AND HIGH BIOPSYCHOSOCIAL COMPLEXITY. PURPOSE: THE INTERMED INSTRUMENT, WHICH WAS DEVELOPED TO MEASURE PATIENT'S BIOPSYCHOSOCIAL (BPS) COMPLEXITY, REPRESENTS A POWERFUL DIAGNOSTIC AND THERAPEUTIC TOOL. EPIGENETIC CHANGES ARE THE INTERFACE BETWEEN SIGNALS FROM THE ENVIRONMENT AND GENETIC MODIFICATIONS, AFFECTING GENE EXPRESSION, IN PARTICULAR, BY DNA METHYLATION OF CPG DINUCLEOTIDES IN PROMOTOR REGIONS OF THE CORRESPONDING GENES. THE BRAIN-DERIVED NEUROTROPHIC FACTOR (BDNF) GENE PLAYS A CRUCIAL ROLE IN THE CENTRAL SENSITIZATION (CS) OF PAIN. IN THIS STUDY, WE HYPOTHESIZED THAT CHRONIC PAIN MODIFIES THE METHYLATION LEVELS OF THE BDNF GENE IN A MANNER THAT IS INTERCONNECTED WITH THE BPS STATUS. PATIENTS AND METHODS: FIFTY-EIGHT CHRONIC MUSCULOSKELETAL PAIN PATIENTS (CMSP) WERE ENROLLED IN THE STUDY. DNA WAS EXTRACTED FROM BLOOD SAMPLES, THE METHYLATION LEVELS OF 13 CPG SITES IN THE BDNF PROMOTER WERE MEASURED BY PYROSEQUENCING, AND ASSOCIATION STUDIES WITH VARIOUS PATIENT PARAMETERS AND THE INTERMED SCORES WERE PERFORMED. RESULTS: INTERESTINGLY, A NEGATIVE CORRELATION (-0.40) WAS FOUND BETWEEN THE TOTAL INTERMED SCORES AND THE AVERAGE CPG METHYLATION VALUES OF THE BDNF GENE, BUT NO CORRELATION WAS OBSERVED WITH THE SEVERITY OF PAIN, DEGREE OF ANXIETY, DEPRESSION, OR KINESIOPHOBIA AND CATASTROPHISM. MOREOVER, THE ASSOCIATION WAS INDEPENDENT OF AGE, SEX AND LEVEL OF COMORBIDITIES. CONCLUSION: THIS RESULT SHOWS THAT CMSP, IN ASSOCIATION WITH ITS BIOPSYCHOSOCIAL CONTEXT, EPIGENETICALLY DECREASES THE DEGREE OF METHYLATION OF THE BDNF PROMOTER AND SHOULD THEREFORE INCREASE THE LEVEL OF BDNF TRANSCRIPTION. IT ALSO SUGGESTS A ROLE OF THE INTERMED TOOL TO DETECT A RELATIONSHIP BETWEEN THE BPS COMPLEXITY AND THE EPIGENETIC CONTROL OF A TARGET GENE. THE POSSIBLE UPREGULATION OF BDNF EXPRESSION MIGHT BE, AT LEAST IN PART, THE SIGNAL FOR CHRONIC PAIN-INDUCED CENTRAL SENSITIZATION (CS). THIS COULD PARTLY EXPLAIN WHY PATIENTS WITH A HIGHER LEVEL OF COMPLEXITY FEEL MORE PAIN THAN THOSE WITH LOWER COMPLEXITY. 2020 15 2653 33 EPIGENOTYPING IN PERIPHERAL BLOOD CELL DNA AND BREAST CANCER RISK: A PROOF OF PRINCIPLE STUDY. BACKGROUND: EPIGENETIC CHANGES ARE EMERGING AS ONE OF THE MOST IMPORTANT EVENTS IN CARCINOGENESIS. TWO ALTERATIONS IN THE PATTERN OF DNA METHYLATION IN BREAST CANCER (BC) HAVE BEEN PREVIOUSLY REPORTED; ACTIVE ESTROGEN RECEPTOR-ALPHA (ER-ALPHA) IS ASSOCIATED WITH DECREASED METHYLATION OF ER-ALPHA TARGET (ERT) GENES, AND POLYCOMB GROUP TARGET (PCGT) GENES ARE MORE LIKELY THAN OTHER GENES TO HAVE PROMOTER DNA HYPERMETHYLATION IN CANCER. HOWEVER, WHETHER DNA METHYLATION IN NORMAL UNRELATED CELLS IS ASSOCIATED WITH BC RISK AND WHETHER THESE IMPRINTS CAN BE RELATED TO FACTORS WHICH CAN BE MODIFIED BY THE ENVIRONMENT, IS UNCLEAR. METHODOLOGY/PRINCIPAL FINDINGS: USING QUANTITATIVE METHYLATION ANALYSIS IN A CASE-CONTROL STUDY (N = 1,083) WE FOUND THAT DNA METHYLATION OF PERIPHERAL BLOOD CELL DNA PROVIDES GOOD PREDICTION OF BC RISK. WE ALSO REPORT THAT INVASIVE DUCTAL AND INVASIVE LOBULAR BC IS CHARACTERIZED BY TWO DIFFERENT SETS OF GENES, THE LATTER PARTICULAR BY GENES INVOLVED IN THE DIFFERENTIATION OF THE MESENCHYME (PITX2, TITF1, GDNF AND MYOD1). FINALLY WE DEMONSTRATE THAT ONLY ERT GENES PREDICT ER POSITIVE BC; LACK OF PERIPHERAL BLOOD CELL DNA METHYLATION OF ZNF217 PREDICTED BC INDEPENDENT OF AGE AND FAMILY HISTORY (ODDS RATIO 1.49; 95% CONFIDENCE INTERVAL 1.12-1.97; P = 0.006) AND WAS ASSOCIATED WITH ER-ALPHA BIOACTIVITY IN THE CORRESPONDING SERUM. CONCLUSION/SIGNIFICANCE: THIS FIRST LARGE-SCALE EPIGENOTYPING STUDY DEMONSTRATES THAT DNA METHYLATION MAY SERVE AS A LINK BETWEEN THE ENVIRONMENT AND THE GENOME. FACTORS THAT CAN BE MODULATED BY THE ENVIRONMENT (LIKE ESTROGENS) LEAVE AN IMPRINT IN THE DNA OF CELLS THAT ARE UNRELATED TO THE TARGET ORGAN AND INDICATE THE PREDISPOSITION TO DEVELOP A CANCER. FURTHER RESEARCH WILL NEED TO DEMONSTRATE WHETHER DNA METHYLATION PROFILES WILL BE ABLE TO SERVE AS A NEW TOOL TO PREDICT THE RISK OF DEVELOPING CHRONIC DISEASES WITH SUFFICIENT ACCURACY TO GUIDE PREVENTIVE MEASURES. 2008 16 2024 35 EPIGENETIC CHANGES CAUSED BY DIABETES AND THEIR POTENTIAL ROLE IN THE DEVELOPMENT OF PERIODONTITIS. AIMS/INTRODUCTION: PERIODONTAL DISEASE, A CHRONIC INFLAMMATION INDUCED BY BACTERIA, IS CLOSELY LINKED WITH DIABETES MELLITUS. MANY COMPLICATIONS ASSOCIATED WITH DIABETES ARE RELATED TO EPIGENETIC CHANGES. HOWEVER, THE EXACT EPIGENETIC CHANGES WHEREBY DIABETES AFFECTS PERIODONTAL DISEASE REMAIN LARGELY UNKNOWN. THUS, WE SOUGHT TO INVESTIGATE THE ROLE OF DIABETES-DEPENDENT EPIGENETIC CHANGES OF GINGIVAL TISSUE IN THE SUSCEPTIBILITY TO PERIODONTAL DISEASE. MATERIALS AND METHODS: WE STUDIED THE EFFECT OF STREPTOZOTOCIN-INDUCED DIABETES IN MINIPIGS ON GINGIVAL MORPHOLOGICAL AND EPIGENETIC TISSUE CHANGES. ACCORDINGLY, WE RANDOMLY DIVIDED SIX MINIPIGS INTO TWO GROUPS: STREPTOZOTOCIN-INDUCED DIABETES GROUP, N = 3; AND NON-DIABETES HEALTHY CONTROL GROUP, N = 3. AFTER 85 DAYS, ALL ANIMALS WERE KILLED, AND GINGIVAL TISSUE WAS COLLECTED FOR HISTOLOGY, DEOXYRIBONUCLEIC ACID METHYLATION ANALYSIS AND IMMUNOHISTOCHEMISTRY. RESULTS: A DIABETES MELLITUS MODEL WAS SUCCESSFULLY CREATED, AS EVIDENCED BY SIGNIFICANTLY INCREASED BLOOD GLUCOSE LEVELS, REDUCTION OF PANCREATIC INSULIN-PRODUCING BETA-CELLS AND HISTOPATHOLOGICAL CHANGES IN THE KIDNEYS. THE GINGIVAL TISSUES IN THE DIABETES GROUP PRESENTED ACANTHOSIS OF BOTH GINGIVAL SQUAMOUS EPITHELIUM AND SULCULAR/JUNCTIONAL EPITHELIUM, AND A SIGNIFICANT REDUCTION IN THE NUMBER AND LENGTH OF RETE PEGS. DEOXYRIBONUCLEIC ACID METHYLATION ANALYSIS SHOWED A TOTAL OF 1,163 AFFECTED GENES, OF WHICH 599 AND 564 WERE SIGNIFICANTLY HYPERMETHYLATED AND HYPOMETHYLATED, RESPECTIVELY. IMMUNOHISTOCHEMISTRY STAINING SHOWED THAT THE HYPOMETHYLATED GENES - TUMOR NECROSIS FACTOR-ALPHA AND INTERLEUKIN-6 - WERE POSITIVELY EXPRESSED UNDER THE JUNCTIONAL EPITHELIUM AREA IN THE DIABETES GROUP. CONCLUSIONS: DIABETES MELLITUS INDUCES MORPHOLOGICAL AND EPIGENETIC CHANGES IN PERIODONTAL TISSUE, WHICH MIGHT CONTRIBUTE TO THE INCREASED SUSCEPTIBILITY OF PERIODONTAL DISEASES IN PATIENTS WITH DIABETES. 2021 17 2142 45 EPIGENETIC INVESTIGATION OF VARIABLY X CHROMOSOME INACTIVATED GENES IN MONOZYGOTIC FEMALE TWINS DISCORDANT FOR PRIMARY BILIARY CIRRHOSIS. PRIMARY BILIARY CIRRHOSIS (PBC) IS AN AUTOIMMUNE CHRONIC CHOLESTATIC LIVER DISEASE WITH A STRONG GENETIC SUSCEPTIBILITY DUE TO THE HIGH CONCORDANCE IN MONOZYGOTIC (MZ) TWINS AND A STRIKING FEMALE PREDOMINANCE. WOMEN WITH PBC MANIFEST AN ENHANCED X MONOSOMY RATE IN PERIPHERAL LYMPHOCYTES AND WE THUS HYPOTHESIZED AN X CHROMOSOME EPIGENETIC COMPONENT TO EXPLAIN PBC FEMALE PREVALENCE. WHILE MOST GENES ON THE FEMALE INACTIVE X CHROMOSOME ARE SILENCED BY PROMOTER METHYLATION FOLLOWING X CHROMOSOME INACTIVATION (XCI), APPROXIMATELY 10% OF X- LINKED GENES EXHIBIT VARIABLE ESCAPE FROM XCI IN HEALTHY FEMALES. THIS STUDY WAS DESIGNED TO TEST THE HYPOTHESIS THAT SUSCEPTIBILITY TO PBC IS MODIFIED BY ONE OR MORE X-LINKED GENE WITH VARIABLE XCI STATUS. PERIPHERAL BLOOD MRNA AND DNA SAMPLES WERE OBTAINED FROM A UNIQUE COHORT OF MZ TWIN SETS DISCORDANT AND CONCORDANT FOR PBC. TRANSCRIPT LEVELS OF THE 125 VARIABLE XCI STATUS GENES WAS DETERMINED BY QUANTITATIVE RT-PCR ANALYSIS AND TWO GENES (CLIC2 AND PIN4) WERE IDENTIFIED AS CONSISTENTLY DOWNREGULATED IN THE AFFECTED TWIN OF DISCORDANT PAIRS. BOTH CLIC2 AND PIN4 DEMONSTRATED PARTIAL AND VARIABLE METHYLATION OF CPG SITES WITHIN 300 BP OF THE TRANSCRIPTION START SITE THAT DID NOT PREDICT THE XCI STATUS. PROMOTER METHYLATION OF CLIC2 MANIFESTED NO SIGNIFICANT DIFFERENCE BETWEEN SAMPLES AND NO SIGNIFICANT CORRELATION WITH TRANSCRIPT LEVELS. PIN4 METHYLATION SHOWED A POSITIVE TREND WITH TRANSCRIPTION IN ALL SAMPLES BUT NO DIFFERENTIAL METHYLATION WAS OBSERVED BETWEEN DISCORDANT TWINS. A GENETIC POLYMORPHISM AFFECTING THE NUMBER OF CPG SITES IN THE PIN4 PROMOTER DID NOT IMPACT METHYLATION OR TRANSCRIPT LEVELS IN A HETEROZYGOUS TWIN PAIR AND SHOWED A SIMILAR FREQUENCY IN INDEPENDENT SERIES OF UNRELATED PBC CASES AND CONTROLS. OUR RESULTS SUGGEST THAT EPIGENETIC FACTORS INFLUENCING PBC ONSET ARE MORE COMPLEX THAN METHYLATION DIFFERENCES AT X-LINKED PROMOTERS AND VARIABLY 3 INACTIVATED X-LINKED GENES MAY BE CHARACTERIZED BY PARTIAL PROMOTER METHYLATION AND BIALLELIC TRANSCRIPTION. 2011 18 3248 36 HEPATITIS B VIRUS GENOME ASYMMETRY IN HEPATOCELLULAR CARCINOMA. BACKGROUND: THE ASSOCIATION BETWEEN HEPATITIS B VIRUS (HBV) MUTATIONS AND HEPATOCARCINOGENESIS WERE REPORTED IN THE LITERATURE. PREFERENCE FOR G OVER C IN THE LEADING DNA STRAND HAS BEEN REPORTED TO ACCOUNT FOR THE ASYMMETRY IN NUCLEOTIDE (NT) COMPOSITION. THE AIM OF THIS STUDY WAS TO ANALYZE THE COMPLETE GENOME SEQUENCE AND COMPOSITIONAL ASYMMETRY OF HBV IN DIFFERENT STAGES OF HEPATITIS B. METHODS: FULL GENOME SEQUENCING OF 24 PATIENTS WITH CHRONIC HEPATITIS B, SOME OF WHOM ALSO HAD CIRRHOSIS AND HEPATOCELLULAR CARCINOMA (HCC) WAS PERFORMED. MUTATIONS ANALYSIS WAS IMPLEMENTED IN A COMPARISON WITH A HBV GENOTYPE D REFERENCE FROM AN INTERNATIONAL DNA DATABASE. CPGPROD, A WEB-BASED APPLICATION, WAS USED TO EVALUATE CG CONTENT AND PREDICT CPG ISLANDS. RESULTS: ALL STRAINS WERE 3182 BASE PAIRS (BP) IN LENGTH, EXCEPT FOR TWO CASES OF HCC IN WHICH 9 AND 21 NT, RESPECTIVELY, WERE DELETED IN PRES2. THE GENETIC RELATEDNESS OF THESE ISOLATES WAS 97%-100%. THERE WERE COMMON CPG-RICH REGIONS IN ALL 24 ISOLATED FULL GENOME SEQUENCES, HOWEVER A STRONG NEGATIVE GC SKEW FOR FORMING A CPG ISLAND IN THE MINUS STRAND WERE EXHIBITED IN OVERLAP WITH ENHANCER I IN THREE HCC PATIENTS, A CIRRHOTIC PATIENT AND THREE WITH CHRONIC HEPATITIS. CONCLUSION: THE HIGH PERCENTAGE OF SEQUENCE IDENTITY BETWEEN HBV ISOLATES IN OUR PATIENTS DEMONSTRATES THAT GENOMIC FACTORS, EXCEPT FOR GENOTYPE, ARE INVOLVED IN HEPATOCARCINOGENESIS. VARIATIONS IN GC CONTENT WHICH WERE CAUSED BY A DIFFERENT SPECTRUM OF MUTATIONS MAY AFFECT DNA COMPOSITIONAL ASYMMETRY AND EPIGENETIC MODIFICATION OF HBV DNA IN HCC. 2012 19 3936 36 LIVING IN ENDEMIC AREA FOR INFECTIOUS DISEASES ACCELERATES EPIGENETIC AGE. INFLAMMAGING IS A LOW-GRADE INFLAMMATORY STATE GENERATED BY THE AGING PROCESS THAT CAN CONTRIBUTE TO FRAILTY AND AGE-RELATED DISEASES IN THE ELDERLY. HOWEVER, IT CAN HAVE DISTINCT EFFECTS IN THE ELDERLY LIVING IN ENDEMIC AREAS FOR INFECTIOUS DISEASES. AN INCREASED INFLAMMATORY RESPONSE MAY CONFER PROTECTION AGAINST INFECTIOUS AGENTS IN THESE AREAS, ALTHOUGH THIS ADVANTAGE CAN CAUSE ACCELERATING EPIGENETIC AGING. IN THIS STUDY, WE EVALUATED THE INFLAMMATORY PROFILE AND THE EPIGENETIC AGE OF INFECTED AND NONINFECTED INDIVIDUALS FROM AN ENDEMIC AREA IN BRAZIL. THE PROFILE OF CYTOKINES, CHEMOKINES AND GROWTH FACTORS ANALYZED IN THE SERA OF THE TWO GROUPS OF INDIVIDUALS SHOWED SIMILARITIES, ALTHOUGH INFECTED INDIVIDUALS HAD A HIGHER CONCENTRATION OF THESE MEDIATORS. A SIGNIFICANT INCREASE IN IL-1RA, CXCL8, CCL2, CCL3 AND CCL4 PRODUCTION WAS ASSOCIATED WITH LEPROSY INFECTION. NOTABLY, ELDERLY INDIVIDUALS DISPLAYED DISTINCT IMMUNE RESPONSES ASSOCIATED WITH THEIR INFECTION STATUS WHEN COMPARED TO ADULTS SUGGESTING AN ADAPTIVE REMODELLING OF THEIR IMMUNE RESPONSES. EPIGENETIC ANALYSIS ALSO SHOWED THAT THERE WAS NO DIFFERENCE IN EPIGENETIC AGE BETWEEN THE TWO GROUPS OF INDIVIDUALS. HOWEVER, INDIVIDUALS FROM THE ENDEMIC AREA HAD A SIGNIFICANT ACCELERATED AGING WHEN COMPARED TO INDIVIDUALS FROM SAO PAULO, A NON-ENDEMIC AREA IN BRAZIL. MOREOVER, THE LATTER COHORT WAS ALSO EPIGENETICALLY AGED IN RELATION TO AN ITALIAN COHORT. OUR DATA SHOWS THAT LIVING IN ENDEMIC AREAS FOR CHRONIC INFECTIOUS DISEASES RESULTS IN REMODELLING OF INFLAMMAGING AND ACCELERATION OF EPIGENETIC AGING IN INDIVIDUALS REGARDLESS OF THEIR INFECTIOUS STATUS. IT ALSO HIGHLIGHTS THAT GEOGRAPHICAL, GENETIC AND ENVIRONMENTAL FACTORS INFLUENCE AGING AND IMMUNOSENESCENCE IN THEIR PACE AND PROFILE. 2022 20 519 26 ASSOCIATIONS BETWEEN GENETIC AND EPIGENETIC VARIATIONS IN CYTOKINE GENES AND MILD PERSISTENT BREAST PAIN IN WOMEN FOLLOWING BREAST CANCER SURGERY. PERSISTENT PAIN FOLLOWING BREAST CANCER SURGERY IS A SIGNIFICANT PROBLEM. BOTH INHERITED AND ACQUIRED MECHANISMS OF INFLAMMATION APPEAR TO PLAY A ROLE IN THE DEVELOPMENT AND MAINTENANCE OF PERSISTENT PAIN. IN THIS LONGITUDINAL STUDY, GROWTH MIXTURE MODELING WAS USED TO IDENTIFY PERSISTENT BREAST PAIN PHENOTYPES BASED ON PAIN ASSESSMENTS OBTAINED PRIOR TO AND MONTHLY FOR 6MONTHS FOLLOWING BREAST CANCER SURGERY. ASSOCIATIONS BETWEEN THE "NO PAIN" AND "MILD PAIN" PHENOTYPES AND SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) SPANNING 15 CYTOKINE GENES WERE EVALUATED. THE METHYLATION STATUS OF THE CPG SITES FOUND IN THE PROMOTERS OF GENES ASSOCIATED WITH PAIN GROUP MEMBERSHIP WAS DETERMINED USING BISULFITE SEQUENCING. IN THE MULTIVARIATE ANALYSIS, THREE SNPS (I.E., INTERLEUKIN 6 (IL6) RS2069840, C-X-C MOTIF CHEMOKINE LIGAND 8 (CXCL8) RS4073, TUMOR NECROSIS FACTOR (TNF) RS1800610) AND TWO TNF CPG SITES (I.E., C.-350C, C.-344C) WERE ASSOCIATED WITH PAIN GROUP MEMBERSHIP. THESE FINDINGS SUGGEST THAT VARIATIONS IN IL6, CXCL8, AND TNF ARE ASSOCIATED WITH THE DEVELOPMENT AND MAINTENANCE OF MILD PERSISTENT BREAST PAIN. CPG METHYLATION WITHIN THE TNF PROMOTER MAY PROVIDE AN ADDITIONAL MECHANISM THROUGH WHICH TNF ALTERS THE RISK FOR MILD PERSISTENT BREAST PAIN AFTER BREAST CANCER SURGERY. THESE GENETIC AND EPIGENETIC VARIATIONS MAY HELP TO IDENTIFY INDIVIDUALS WHO ARE PREDISPOSED TO THE DEVELOPMENT OF MILD LEVELS OF PERSISTENT BREAST PAIN FOLLOWING BREAST CANCER SURGERY. 2017