1 161 140 ABHD4-REGULATING RNA PANEL: NOVEL BIOMARKERS IN ACUTE CORONARY SYNDROME DIAGNOSIS. BACKGROUND: ACUTE CORONARY SYNDROME (ACS) IS A MAJOR CAUSE OF DEATH ALL OVER THE WORLD. STEMI REPRESENTS A TYPE OF MYOCARDIAL INFARCTION WITH ACUTE ST ELEVATION. WE AIMED TO ASSESS THE PREDICTIVE POWER OF POTENTIAL RNA PANEL EXPRESSION IN ACUTE CORONARY SYNDROME. METHOD: WE USED IN SILICO DATA ANALYSIS TO RETRIEVE RNAS RELATED TO GLYCEROPHOSPHOLIPID METABOLISM DYSREGULATION AND SPECIFIC TO ACS THAT RESULTS IN THE SELECTION OF ALPHA/BETA HYDROLASE FOLD DOMAIN4 (ABHD4) MRNA AND ITS EPIGENETIC REGULATORS (FOXF1 ADJACENT NONCODING DEVELOPMENTAL REGULATORY RNA (FENDRR) LNCRNA, MIRNA-221, AND MIRNA-197). WE ASSESSED THE EXPRESSION OF THE SERUM RNA PANEL IN 68 PATIENTS WITH ACS, 21 PATIENTS WITH CHEST PAIN DUE TO NON-CARDIAC CAUSES, AND 21 HEALTHY VOLUNTEERS BY QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION. RESULTS: THE STUDY DATA SHOWED SIGNIFICANT DOWN REGULATION IN THE EXPRESSION OF THE SERUM LEVELS OF FENDRR LNCRNA AND MIRNA-221-3P BY 120-FOLD AND 22-FOLD IN UNSTABLE ANGINA (UA) IN COMPARISON WITH HEALTHY VOLUNTEERS, AND BY 8.6-FOLD AND 2-FOLD IN ST SEGMENT ELEVATION MYOCARDIAL INFARCTION (STEMI) PATIENTS VERSUS UA; CONCOMITANT UPREGULATION IN THE EXPRESSION OF ABHD4 MRNA AND MIRNA-197-5P BY 444-FOLD AND 10-FOLD IN UA COMPARED WITH HEALTHY VOLUNTEERS, AND BY 1.54-FOLD AND 4.5-FOLD IN STEMI VERSUS UNSTABLE ANGINA. PERFORMANCE CHARACTERISTICS ANALYSIS SHOWED THAT THE ABHD4-REGULATING RNA PANEL WERE POTENTIAL BIOMARKERS FOR PREDICTION OF ACS. MOREOVER, THERE WAS A SIGNIFICANT ASSOCIATION BETWEEN THE 2 MIRNAS AND ABHD4 MRNA AND THE REGULATING FENDRR LNCRNA. CONCLUSION: COLLECTIVELY, ABHD4 MRNA REGULATING RNA PANEL BASED ON PUTATIVE INTERACTIONS SEEMS TO BE NOVEL NON-INVASIVE BIOMARKERS THAT COULD DETECT ACS EARLY AND STRATIFY SEVERITY OF THE CONDITION THAT COULD IMPROVE HEALTH OUTCOME. 2021 2 782 40 CELL-FREE MICRORNA-148A IS ASSOCIATED WITH RENAL ALLOGRAFT DYSFUNCTION: IMPLICATION FOR BIOMARKER DISCOVERY. BACKGROUND: CHRONIC ALLOGRAFT DYSFUNCTION (CAD), THE FOREMOST CAUSE OF RENAL GRAFT LOSS WORLDWIDE, IS A SERIOUS CHALLENGE FOR MOST OF THE RECIPIENTS. AS THE EPIGENETIC ERA IS EMERGING, EPIGENETIC BIOMARKERS ESPECIALLY MICRORNAS (MIRNAS) MAY REFLECT THE CURRENT STAGE OF THE DISEASE AND PATIENT'S THERAPY RESPONSE. THE CURRENT STUDY INVESTIGATED THE POTENTIAL SIGNIFICANCE OF CIRCULATING MIRNA-148A IN PREDICTING THE RENAL GRAFT FUNCTION. DESIGN AND METHODS: CIRCULATING MIRNAS WERE ISOLATED FROM 53 PLASMA SAMPLES OF RECIPIENTS WITH HISTOLOGICALLY VALIDATED INTERSTITIAL FIBROSIS AND TUBULAR ATROPHY (IFTA, N = 26), AND RECIPIENTS WITH STABLE GRAFT FUNCTION (SGF, N = 27), AND ALSO HEALTHY INDIVIDUALS ( N = 15). THE LEVEL OF MIRNA-148A WAS EVALUATED BY THE QUANTITATIVE POLYMERASE CHAIN REACTION (QPCR) AND CORRELATED WITH CLINICAL AND HISTOLOGICAL PARAMETERS. RESULTS: SIGNIFICANTLY, MIRNA-148A DECREASED IN IFTA COMPARED WITH SGF SUBJECTS (P < 0.001). MIRNA-148A LEVELS INDICATED A SIGNIFICANT ASSOCIATION WITH SERUM CREATININE LEVELS ( R = 0.451, P = 0.021) AND GLOMERULAR FILTRATION RATE ( R = -0.520, P = 0.006). MIRNA-148A EXPRESSION LEVELS COULD DISCRIMINATE IFTA CASES FROM SGF INDIVIDUALS WITH AN AREA UNDER THE CURVE OF 0.89 ( P < 0.001), 97% SENSITIVITY, AND 72% SPECIFICITY. A NUMBER OF PREDICTED TARGETS THAT MIGHT BE INVOLVED IN CAD BY MIRNA-148A WERE PREDICTED. CONCLUSION: PLASMA CELL-FREE MIRNA-148A CORRELATED WITH RENAL FUNCTION AND HISTOLOGICAL GRADES; THEREFORE, IT MAY BE FURTHER INVESTIGATED AS A NOVEL NONINVASIVE MOLECULAR MARKER OF THE PROGRESSION TO IFTA IN RENAL TRANSPLANT RECIPIENTS; MOREOVER, THE EMERGING BIOMARKER MAY BECOME A THERAPEUTIC TARGET IN THE FUTURE CLINIC. 2019 3 2331 32 EPIGENETIC REGULATION OF INFLAMMATION BY MICRORNAS IN POST-INFECTIOUS BRONCHIOLITIS OBLITERANS. OBJECTIVES: POST-INFECTIOUS BRONCHIOLITIS OBLITERANS (PIBO) IS A RARE, CHRONIC DISEASE INITIATED BY SEVERE INFECTION AND FOLLOWED BY PERPETUATING INFLAMMATION AND OBLITERATION OF THE SMALL AIRWAYS. MICRORNAS (MIRNAS) HAVE BEEN PROPOSED TO PLAY A CENTRAL ROLE AS EPIGENETIC REGULATORS, WHICH CONTROL RESOLUTION AND PREVENT THE UNCONTROLLED PROGRESS OF INFLAMMATION. THE AIM OF THIS STUDY WAS TO DEFINE BIOMARKERS ON THE LEVEL OF POST-TRANSCRIPTIONAL GENE REGULATION IN ORDER TO CHARACTERISE PIBO. METHODS: A TOTAL OF 39 PATIENTS WITH WELL-DEFINED PIBO AND 31 CONTROLS FROM TWO CENTRES, BARCELONA, SPAIN, AND FRANKFURT, GERMANY, WERE ANALYSED BY NEXT-GENERATION SEQUENCING (NGS). THE EVALUATION OF THE BIOLOGICAL TARGETS OF THE MIRNAS WAS PERFORMED BY PATHWAY ENRICHMENT ANALYSIS AND PROTEIN-PROTEIN INTERACTION NETWORK ANALYSIS RESPECTIVELY. RESULTS: PATIENTS WITH PIBO HAD SIGNIFICANTLY LOWER LUNG FUNCTION VALUES AND INCREASED AIRWAY INFLAMMATION IN INDUCED SPUTUM AS INDICATED BY TOTAL CELL COUNTS, NEUTROPHILS, IL-1BETA, IL-6, IL-8 AND TGF-BETA COMPARED TO CONTROLS.NEXT-GENERATION SEQUENCING ANALYSIS REVEALED A TOTAL OF 22 DYSREGULATED MIRNAS, WHICH PASSED SIGNIFICANCE THRESHOLD FOR PADJ 2]. DAVID BIOINFORMATICS PROGRAM WAS USED FOR GENE ONTOLOGY (GO) ANNOTATION AND ENRICHMENT ANALYSES OF STATISTICALLY SIGNIFICANT GENES BETWEEN CAP AND IMA TISSUE. RESULTS AND CONCLUSIONS: IN OUR STUDY, 345 DEGS WERE FOUND TO BE STATISTICALLY SIGNIFICANT (P < 0.05; FC > 2) BETWEEN CAP AND IMA. OF THESE, 65 WERE LNCRNA AND 280 WERE MRNA. THIRTY-THREE LNCRNAS WERE UPREGULATED, WHILE 32 LNCRNAS WERE DOWNREGULATED. SOME OF THE IMPORTANT MRNAS ARE SPP1, CYP4B1, CHRDL1, MYOC, AND ALKAL2, WHILE SOME OF THE LNCRNAS ARE LOC105377123, LINC01857, DIO3OS, LOC101928134, AND KCNA3 BETWEEN CAP AND IMA TISSUE. WE ALSO IDENTIFIED GENES THAT CORRELATED WITH STATISTICALLY SIGNIFICANT LNCRNAS. THE RESULTS OF THIS STUDY ARE EXPECTED TO BE AN IMPORTANT SOURCE OF DATA IN THE DEVELOPMENT OF NEW GENETICALLY BASED DRUGS TO PREVENT ATHEROSCLEROTIC PLAQUE. IN ADDITION, THE DATA OBTAINED MAY CONTRIBUTE TO THE EXPLANATION OF THE EPIGENETIC MECHANISMS THAT PLAY A ROLE IN THE PATHOLOGICAL BASIS OF THE PROCESS THAT PROTECTS THE IMA FROM ATHEROSCLEROSIS. 2023 5 487 33 ASPIRIN PROTECTS HUMAN CORONARY ARTERY ENDOTHELIAL CELLS AGAINST ATHEROGENIC ELECTRONEGATIVE LDL VIA AN EPIGENETIC MECHANISM: A NOVEL CYTOPROTECTIVE ROLE OF ASPIRIN IN ACUTE MYOCARDIAL INFARCTION. AIMS: L5 IS THE MOST NEGATIVELY CHARGED SUBFRACTION OF HUMAN LOW-DENSITY LIPOPROTEIN (LDL) AND IS THE ONLY SUBFRACTION OF LDL CAPABLE OF INDUCING APOPTOSIS IN CULTURED VASCULAR ENDOTHELIAL CELLS (ECS) BY INHIBITING FIBROBLAST GROWTH FACTOR-2 (FGF2) TRANSCRIPTION. WE EXAMINED WHETHER PLASMA L5 LEVELS ARE ELEVATED IN PATIENTS WITH ST-SEGMENT ELEVATION MYOCARDIAL INFARCTION (STEMI) AND WHETHER ASPIRIN PROVIDES EPIGENETIC PROTECTION OF HUMAN CORONARY ARTERY ECS (HCAECS) EXPOSED TO L5. METHODS AND RESULTS: PLASMA L5 LEVELS WERE COMPARED BETWEEN PATIENTS WITH STEMI (N = 10) AND CONTROL SUBJECTS WITH CHEST PAIN SYNDROME BUT A NORMAL CORONARY ARTERIOGRAM (N = 5). L5 WAS ISOLATED FROM THE PLASMA OF STEMI PATIENTS AND CONTROL SUBJECTS, AND APOPTOSIS, FGF2 EXPRESSION, AND FGF2 PROMOTER METHYLATION WERE EXAMINED IN HCAECS TREATED WITH L5 AND ASPIRIN. PLASMA L5 LEVELS WERE SIGNIFICANTLY HIGHER IN STEMI PATIENTS THAN IN CONTROL SUBJECTS (P < 0.001). TREATMENT OF HCAECS WITH L5 RESULTED IN REDUCED SURVIVAL AND FGF2 EXPRESSION AND INCREASED CPG METHYLATION OF THE FGF2 PROMOTER. CO-TREATMENT OF HCAECS WITH L5 AND A PHYSIOLOGICALLY RELEVANT, LOW CONCENTRATION OF ASPIRIN (0.2 MM) ATTENUATED THE ADVERSE EFFECTS OF L5 ON HCAEC SURVIVAL, FGF2 EXPRESSION, AND FGF2 PROMOTER METHYLATION. IN CONTRAST, HIGH CONCENTRATIONS OF ASPIRIN (>/=1.0 MM) ACCENTUATED THE EFFECTS OF L5. CONCLUSIONS: OUR RESULTS SHOW THAT L5 LEVELS ARE SIGNIFICANTLY INCREASED IN STEMI PATIENTS. FURTHERMORE, L5 IMPAIRS HCAEC FUNCTION THROUGH CPG METHYLATION OF THE FGF2 PROMOTER, WHICH IS SUPPRESSED IN THE PRESENCE OF LOW-CONCENTRATION ASPIRIN. OUR RESULTS PROVIDE EVIDENCE OF A NOVEL MECHANISM OF ASPIRIN IN THE PREVENTION OF MI. 2013 6 3125 20 GHSR DNA HYPERMETHYLATION IS A COMMON EPIGENETIC ALTERATION OF HIGH DIAGNOSTIC VALUE IN A BROAD SPECTRUM OF CANCERS. IDENTIFICATION OF A SINGLE MOLECULAR TRAIT THAT IS DETERMINANT OF COMMON MALIGNANCIES MAY SERVE AS A POWERFUL DIAGNOSTIC SUPPLEMENT TO CANCER TYPE-SPECIFIC MARKERS. HERE, WE REPORT A DNA METHYLATION MARK THAT IS CHARACTERISTIC OF SEVEN STUDIED MALIGNANCIES, NAMELY CANCERS OF LUNG, BREAST, PROSTATE, PANCREAS, COLORECTUM, GLIOBLASTOMA AND B CELL CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) (N = 137). THIS MARK WAS DEFINED BY SUBSTANTIAL HYPERMETHYLATION AT THE PROMOTER AND FIRST EXON OF GROWTH HORMONE SECRETAGOUGE RECEPTOR (GHSR) THROUGH BISULFITE PYROSEQUENCING. THE DEGREE OF ABERRANT METHYLATION WAS CAPABLE OF ACCURATE DISCRIMINATION BETWEEN CANCER AND CONTROL SAMPLES. THE HIGHEST SENSITIVITY AND SPECIFICITY OF CANCER DETECTION WAS ACHIEVED FOR CANCERS OF PANCREAS, LUNG, BREAST AND CLL YIELDING THE AREA UNDER THE CURVE (AUC) VALUES OF 1.0000, 0.9952, 0.9800 AND 0.9400, RESPECTIVELY. NARROWING TO A SINGLE CPG SITE WITHIN THE GENE'S PROMOTER OR FOUR CONSECUTIVE CPG UNITS OF THE HIGHEST METHYLATION LEVELS WITHIN THE FIRST EXON IMPROVED THE DETECTION POWER. GHSR HYPERMETHYLATION WAS DETECTED ALREADY AT THE EARLY STAGE TUMORS. THE ACCURATE PERFORMANCE OF THIS MARKER WAS FURTHER REPLICATED IN AN INDEPENDENT SET OF PANCREATIC CANCER AND CONTROL SAMPLES (N = 78). THESE FINDINGS SUPPORT THE CANDIDATURE OF GHSR METHYLATION AS A HIGHLY ACCURATE PAN-CANCER MARKER. 2015 7 1729 27 DYSREGULATION OF MIR-155 EXPRESSION IN PROFESSIONAL MIXED MARTIAL ARTS (MMA) FIGHTERS. PSYCHOLOGICAL AND PHYSICAL STRESS CAN INDUCE DYSREGULATION OF GENE EXPRESSION VIA CHANGES IN DNA METHYLATION AND MICRORNA (MIRNA) EXPRESSION. SUCH EPIGENETIC MODIFICATIONS ARE YET TO BE INVESTIGATED IN PROFESSIONAL MIXED MARTIAL ARTS (MMA) FIGHTERS SUBJECT TO HIGHLY STRESSFUL TRAINING INVOLVING REPETITIVE HEAD IMPACTS. THIS STUDY EXAMINED DIFFERENCES IN DNA METHYLATION AND MIRNA EXPRESSION IN ELITE MMA FIGHTERS COMPARED TO ACTIVE CONTROLS. GLOBAL METHYLATION DIFFERENCES BETWEEN GROUPS WERE ASSESSED VIA A LINE-1 ASSAY. AT THE SAME TIME, PCR ARRAYS WERE USED TO ESTIMATE DIFFERENTIAL EXPRESSION IN SAMPLES OF 21 FIGHTERS AND 15 CONTROLS FOR 192 DIFFERENT MIRNAS ASSOCIATED WITH INFLAMMATORY DISEASES. AN INDEPENDENT-SAMPLES T-TEST FOUND NO SIGNIFICANT DIFFERENCE IN LINE-1 METHYLATION BETWEEN GROUPS. HOWEVER, AN INDEPENDENT-SAMPLES MANN-WHITNEY U TEST REVEALED A SIGNIFICANT UPREGULATION IN THE EXPRESSION OF MIR-155 IN MMA FIGHTER PLASMA. SINCE MIR-155 HAS BEEN RECOGNIZED AS AN IMPORTANT REGULATOR OF NEUROINFLAMMATION, THIS DYSREGULATION SUGGESTS A POSSIBLE EPIGENETIC MECHANISM RESPONSIBLE FOR CHRONIC INFLAMMATION ASSOCIATED WITH PROFESSIONAL-LEVEL MMA TRAINING. CONSISTENT WITH OTHER PUBLISHED WORKS, THIS STUDY HIGHLIGHTS THE POTENTIAL OF MIR-155 NOT ONLY AS A BIOMARKER FOR MONITORING LONG-TERM HEALTH RISKS LINKED TO HEAD TRAUMA BUT ALSO AS A TARGET TO REMEDIATE THE IMPACT OF CHRONIC NEUROINFLAMMATION. 2023 8 5273 33 PROMOTER METHYLATION AND BDNF AND DAT1 GENE EXPRESSION PROFILES IN PATIENTS WITH DRUG ADDICTION. BACKGROUND: DRUG ADDICTION IS A BRAIN DISORDER THAT HAS NEGATIVE CONSEQUENCES FOR INDIVIDUALS AND SOCIETY. ADDICTIONS ARE CHRONIC RELAPSING DISEASES OF THE BRAIN THAT ARE CAUSED BY DIRECT DRUG-INDUCED EFFECTS AND PERSEVERING NEUROADAPTATIONS AT THE EPIGENETIC, NEUROPEPTIDE AND NEUROTRANSMITTER LEVELS. BECAUSE THE DOPAMINERGIC SYSTEM HAS A SIGNIFICANT ROLE IN DRUG ABUSE, THE PURPOSE OF THIS STUDY WAS TO ANALYZE THE METHYLATION AND EXPRESSION PROFILE OF BRAIN-DERIVED NEUROTROPHIC FACTOR (BDNF) AND DOPAMINE TRANSPORTER (DAT1) GENES IN INDIVIDUALS WITH DRUG ADDICTION. MATERIALS AND METHODS: BDNF AND DAT1 PROMOTER METHYLATION WERE INVESTIGATED WITH A METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (PCR) TECHNIQUE IN BLOOD SAMPLES FROM 75 INDIVIDUALS WITH DRUG ADDICTION AND 65 HEALTHY CONTROLS. THE EXPRESSION LEVELS OF BDNF AND DAT1 WERE ASSESSED IN 12 MRNA SAMPLES FROM THE BLOOD OF PATIENTS AND COMPARED TO THE SAMPLES OF HEALTHY CONTROLS (N = 12) WITH REAL-TIME QUANTITATIVE REVERSE TRANSCRIPTION PCR. RESULTS: NO SIGNIFICANT DIFFERENCES WERE FOUND IN THE METHYLATION OF BDNF AND DAT1 BETWEEN PATIENTS AND CONTROLS, BUT THE RELATIVE LEVELS OF EXPRESSION OF BDNF AND DAT1 MRNA DIFFERED SIGNIFICANTLY IN THE PATIENTS COMPARED TO CONTROLS (P < 0.0001). CONCLUSION: THESE RESULTS SHOWED THAT THE METHYLATION STATUS OF THE BDNF AND DAT1 GENES HAD NO SIGNIFICANT FUNCTION IN THE PROCESSES OF DRUG ADDICTION. 2015 9 2679 39 EVALUATION OF CIRCULATORY RNA-BASED BIOMARKER PANEL IN HEPATOCELLULAR CARCINOMA. BACKGROUND: THE CIRCULATING TRANSCRIPTOME (CODING AND NON-CODING) PLAYS A CRITICAL ROLE IN CANCER. NOVEL ACCURATE STRATEGIES FOR EARLY DETECTION OF HEPATOCELLULAR CARCINOMA (HCC) ARE STRONGLY NEEDED. PATIENTS AND METHODS: WE CHOSE AN HCC-SPECIFIC RNA-BASED BIOMARKER PANEL BASED ON THE INTEGRATION OF DIFFERENTIAL LYSOSOMAL-ASSOCIATED MEMBRANE PROTEIN 2 (LAMP2) GENE EXPRESSION WITH ITS SELECTED EPIGENETIC REGULATORS USING BIOINFORMATIC METHODS. THIS WAS FOLLOWED BY RT-QPCR VALIDATION IN SERUM OF 78 PATIENTS WITH HCC, 36 PATIENTS WITH CHRONIC HEPATITIS C (CHC) INFECTION AND 44 HEALTHY VOLUNTEERS. WE USED RISK-SCORE ANALYSIS TO EVALUATE THE DIAGNOSTIC EFFICACY OF THE SERUM PROFILING SYSTEM. MOREOVER, IN TWENTY OF THE 78 HCC CASES INVOLVED IN THE STUDY WE EXAMINED THE EXPRESSION OF RNA-BASED BIOMARKER PANEL IN BOTH HCC AND ADJACENT NON-TUMOR TISSUES AND ASSESSED THEIR CORRELATION WITH THE SERUM LEVEL OF THIS PANEL. RESULTS: THE FOUR RIBONUCLEIC ACID (RNA)-BASED BIOMARKER PANEL [LONG NON-CODING RNA-C TERMINAL BINDING PROTEIN, ANDROGEN RESPONSIVE (LNCRNA-CTBP), MICRORNA-16-2 (MIR-16-2), MICRORNA-21-5-P (MIR-21-5P) AND LAMP2], HAD HIGH SENSITIVITY AND SPECIFICITY FOR DISCRIMINATING HCC FROM HEALTHY CONTROLS AND ALSO FROM CHC PATIENTS. AMONG THESE FOUR RNAS, SERUM MIR-16-2 AND MIR-21-5P WERE INDEPENDENT PROGNOSTIC FACTORS. CONCLUSION: THE CIRCULATORY RNA-BASED BIOMARKER PANEL CAN SERVE AS A POTENTIAL BIOMARKER FOR HCC DIAGNOSIS AND PROGNOSIS. 2016 10 3638 32 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 5845 34 STUDY PROTOCOL FOR THE EPIGENETIC CHARACTERIZATION OF ANGOR PECTORIS ACCORDING TO THE AFFECTED CORONARY COMPARTMENT: GLOBAL AND COMPREHENSIVE ASSESSMENT OF THE RELATIONSHIP BETWEEN INVASIVE CORONARY PHYSIOLOGY AND MICRORNAS. BACKGROUND: MICRORNAS (MIRNAS) ARE NONCODING RNAS INVOLVED IN POST-TRANSCRIPTIONAL GENETIC REGULATION WITH A PROPOSED ROLE IN INTERCELLULAR COMMUNICATION. MIRNAS ARE CONSIDERED PROMISING BIOMARKERS IN ISCHEMIC HEART DISEASE. INVASIVE PHYSIOLOGICAL EVALUATION ALLOWS A PRECISE ASSESSMENT OF EACH AFFECTED CORONARY COMPARTMENT. ALTHOUGH SOME STUDIES HAVE ASSOCIATED THE EXPRESSION OF CIRCULATING MIRNAS WITH INVASIVE PHYSIOLOGICAL INDEXES, THEIR GLOBAL RELATIONSHIP WITH CORONARY COMPARTMENTS HAS NOT BEEN ASSESSED. HERE, WE WILL EVALUATE CIRCULATING MIRNAS PROFILES ACCORDING TO THE CORONARY PATTERN OF THE VASCULAR COMPARTMENT AFFECTATION. STUDY AND DESIGN: THIS IS AN INVESTIGATOR-INITIATED, MULTICENTRE, DESCRIPTIVE STUDY TO BE CONDUCTED AT THREE CENTRES IN SPAIN (NCT05374694). THE STUDY WILL INCLUDE ONE HUNDRED CONSECUTIVE PATIENTS OLDER THAN 18 YEARS WITH CHEST PAIN OF PRESUMED CORONARY CAUSE UNDERGOING INVASIVE PHYSIOLOGICAL EVALUATION, INCLUDING FRACTIONAL FLOW RESERVE (FFR) AND INDEX OF MICROVASCULAR RESISTANCE (IMR). PATIENTS WILL BE INITIALLY CLASSIFIED INTO FOUR GROUPS, ACCORDING TO FFR AND IMR: MACROVASCULAR AND MICROVASCULAR AFFECTATION (FFR/=25), ISOLATED MACROVASCULAR AFFECTATION (FFR0.80 / IMR >/=25) AND NORMAL CORONARY INDEXES (FFR>0.80 / IMR<25). PATIENTS WITH ISOLATED MICROVASCULAR AFFECTATION OR NORMAL INDEXES WILL ALSO UNDERGO THE ACETYLCHOLINE TEST AND MAY BE RECLASSIFIED AS A FIFTH GROUP IN THE PRESENCE OF SPASM. A PANEL OF MIRNAS PREVIOUSLY ASSOCIATED WITH MOLECULAR MECHANISMS LINKED TO CHRONIC CORONARY SYNDROME WILL BE ANALYSED USING RT-QPCR. CONCLUSIONS: THE RESULTS OF THIS STUDY WILL IDENTIFY MIRNA PROFILES ASSOCIATED WITH PATTERNS OF CORONARY AFFECTATION AND WILL CONTRIBUTE TO A BETTER UNDERSTANDING OF THE MECHANISTIC PATHWAYS OF CORONARY PATHOLOGY. 2023 12 3764 28 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 13 3468 33 HYPOXIA-INDUCED DNA HYPERMETHYLATION IN HUMAN PULMONARY FIBROBLASTS IS ASSOCIATED WITH THY-1 PROMOTER METHYLATION AND THE DEVELOPMENT OF A PRO-FIBROTIC PHENOTYPE. BACKGROUND: PULMONARY FIBROSIS IS A DEBILITATING AND LETHAL DISEASE WITH NO EFFECTIVE TREATMENT OPTIONS. UNDERSTANDING THE PATHOLOGICAL PROCESSES AT PLAY WILL DIRECT THE APPLICATION OF NOVEL THERAPEUTIC AVENUES. HYPOXIA HAS BEEN IMPLICATED IN THE PATHOGENESIS OF PULMONARY FIBROSIS YET THE PRECISE MECHANISM BY WHICH IT CONTRIBUTES TO DISEASE PROGRESSION REMAINS TO BE FULLY ELUCIDATED. IT HAS BEEN SHOWN THAT CHRONIC HYPOXIA CAN ALTER DNA METHYLATION PATTERNS IN TUMOUR-DERIVED CELL LINES. THIS EPIGENETIC ALTERATION CAN INDUCE CHANGES IN CELLULAR PHENOTYPE WITH PROMOTER METHYLATION BEING ASSOCIATED WITH GENE SILENCING. OF PARTICULAR RELEVANCE TO IDIOPATHIC PULMONARY FIBROSIS (IPF) IS THE OBSERVATION THAT THY-1 PROMOTER METHYLATION IS ASSOCIATED WITH A MYOFIBROBLAST PHENOTYPE WHERE LOSS OF THY-1 OCCURS ALONGSIDE INCREASED ALPHA SMOOTH MUSCLE ACTIN (ALPHA-SMA) EXPRESSION. THE INITIAL AIM OF THIS STUDY WAS TO DETERMINE WHETHER HYPOXIA REGULATES DNA METHYLATION IN NORMAL HUMAN LUNG FIBROBLASTS (CCD19LU). AS IT HAS BEEN REPORTED THAT HYPOXIA SUPPRESSES THY-1 EXPRESSION DURING LUNG DEVELOPMENT WE ALSO STUDIED THE EFFECT OF HYPOXIA ON THY-1 PROMOTER METHYLATION AND GENE EXPRESSION. METHODS: CCD19LU WERE GROWN FOR UP TO 8 DAYS IN HYPOXIA AND ASSESSED FOR GLOBAL CHANGES IN DNA METHYLATION USING FLOW CYTOMETRY. REAL-TIME PCR WAS USED TO QUANTIFY EXPRESSION OF THY-1, ALPHA-SMA, COLLAGEN I AND III. GENOMIC DNA WAS BISULPHITE TREATED AND METHYLATION SPECIFIC PCR (MSPCR) WAS USED TO EXAMINE THE METHYLATION STATUS OF THE THY-1 PROMOTER. RESULTS: SIGNIFICANT GLOBAL HYPERMETHYLATION WAS DETECTED IN HYPOXIC FIBROBLASTS RELATIVE TO NORMOXIC CONTROLS AND WAS ACCOMPANIED BY INCREASED EXPRESSION OF MYOFIBROBLAST MARKERS. THY-1 MRNA EXPRESSION WAS SUPPRESSED IN HYPOXIC CELLS, WHICH WAS RESTORED WITH THE DEMETHYLATING AGENT 5-AZA-2'-DEOXYCYTIDINE. MSPCR REVEALED THAT THY-1 BECAME METHYLATED FOLLOWING FIBROBLAST EXPOSURE TO 1% O2. CONCLUSION: THESE DATA SUGGEST THAT GLOBAL AND GENE-SPECIFIC CHANGES IN DNA METHYLATION MAY PLAY AN IMPORTANT ROLE IN FIBROBLAST FUNCTION IN HYPOXIA. 2012 14 5673 32 SHARED EPIGENETIC ALTERATIONS BETWEEN ORAL CANCER AND PERIODONTITIS: A PRELIMINARY STUDY. INTRODUCTION: WE RECENTLY DEVELOPED A NON-INVASIVE SAMPLING PROCEDURE FOR ORAL SQUAMOUS CELL CARCINOMA (OSCC) DETECTION BASED ON DNA METHYLATION ANALYSIS OF A PANEL OF 13 GENES. ORAL CANCER, AS WELL AS ACUTE AND CHRONIC INFLAMMATORY DISEASES, MAY INFLUENCE THE METHYLATION LEVEL OF SEVERAL GENES IN THE ORAL CAVITY. IN THE PRESENT STUDY, WE EVALUATED THE PRESENCE OF PERIODONTAL DISEASE (PD) AND THE METHYLATION STATUS USING OUR 13-GENE PANEL. METHODS: ORAL BRUSHING SPECIMENS WERE COLLECTED FROM THREE DIFFERENT PATIENT GROUPS: 23 GINGIVAL OSCC PATIENTS, 15 PATIENTS AFFECTED BY PD, AND 15 HEALTHY VOLUNTEERS LACKING EVIDENCE OF PD. DNA METHYLATION ANALYSIS WAS PERFORMED AND EACH SAMPLE WAS DETERMINED TO BE POSITIVE OR NEGATIVE BASED ON A PREDEFINED CUT-OFF VALUE. RESULTS: POSITIVE RESULTS WERE FOUND FOR 23/23 OSCC PATIENTS, 3/15 PD PATIENTS, AND 0/15 SAMPLES FROM HEALTHY VOLUNTEERS. THE GP1BB AND MIR193 GENES IN THE PD GROUP EXHIBITED MEAN METHYLATION LEVELS SIMILAR TO OSCC PATIENTS. ZAP70 SHOWED DIFFERENT METHYLATION LEVELS AMONG THREE GROUPS. CONCLUSION: PRELIMINARY DATA IDENTIFIED SHARED EPIGENETIC ALTERATIONS BETWEEN PD AND OSCC PATIENTS IN TWO INFLAMMATORY GENES (GP1BB AND MIR193). THIS STUDY MAY HELP TO IDENTIFY POTENTIAL LINKS BETWEEN THE TWO DISEASES AND SERVE AS A STARTING POINT FOR THE FUTURE RESEARCH FOCUSED ON PATHOGENESIS. 2023 15 2753 30 EXPRESSION OF BCL2L12 IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS: ASSOCIATION WITH CLINICAL AND MOLECULAR PROGNOSTIC MARKERS. DYSREGULATION OF APOPTOSIS IS A DISTINCTIVE FEATURE OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), ALTHOUGH A UNIQUE MECHANISM UNDERLYING APOPTOSIS RESISTANCE OF CLL B LYMPHOCYTES HAS NOT BEEN IDENTIFIED YET. ABERRANT EXPRESSION AS WELL AS GENETIC AND EPIGENETIC ALTERATIONS OF NUMEROUS GENES INVOLVED IN DIFFERENT PATHWAYS OF APOPTOSIS REGULATION HAS BEEN DESCRIBED IN CLL. HERE, WE REPORT THE EXPRESSION ANALYSIS OF BCL2L12 (BCL2-LIKE 12), A NOVEL APOPTOTIC GENE BELONGING TO BCL2 FAMILY, IN 58 SERBIAN CLL PATIENTS. QUANTITATIVE REVERSE-TRANSCRIPTASE POLYMERASE CHAIN REACTION (QRT-PCR) ANALYSIS REVEALED A SIGNIFICANT OVEREXPRESSION OF BCL2L12 MRNA IN CLL SAMPLES COMPARED TO NON-LEUKEMIC SAMPLES, IMPLYING ITS ROLE IN THE PATHOGENESIS OF THE DISEASE. RECEIVER OPERATING CHARACTERISTIC (ROC) ANALYSIS SHOWED THAT BCL2L12 EXPRESSION EFFICIENTLY DISCRIMINATES CLL CASES FROM HEALTHY CONTROLS. HOWEVER, RELATIVELY HOMOGENOUS BCL2L12 MRNA EXPRESSION AMONG PATIENTS DID NOT REFLECT THEIR CLINICAL CHARACTERISTICS (WITH THE EXCEPTION OF LACTATE DEHYDROGENASE STATUS AND TIME FROM DIAGNOSIS TO TREATMENT) AND FAILED TO SHOW ASSOCIATION WITH THE MOST INFORMATIVE PROGNOSTIC MARKERS, NAMELY THE MUTATIONAL STATUS OF REARRANGED IMMUNOGLOBULIN HEAVY CHAIN VARIABLE REGION GENES, CD38 AND LIPOPROTEIN LIPASE GENE (LPL) EXPRESSION. 2013 16 1023 36 CIRCULATING MICRORNA PROFILES FOR PREMATURE CARDIOVASCULAR DEATH IN PATIENTS WITH KIDNEY FAILURE WITH REPLACEMENT THERAPY. INTRODUCTION: PATIENTS WITH KIDNEY FAILURE WITH REPLACEMENT THERAPY (KFRT) SUFFER FROM A DISPROPORTIONATELY HIGH CARDIOVASCULAR DISEASE BURDEN. CIRCULATING SMALL NON-CODING RNAS (C-SNCRNAS) HAVE EMERGED AS NOVEL EPIGENETIC REGULATORS AND ARE SUGGESTED AS NOVEL BIOMARKERS AND THERAPEUTIC TARGETS FOR CARDIOVASCULAR DISEASE; HOWEVER, LITTLE IS KNOWN ABOUT THE ASSOCIATIONS OF C-SNCRNAS WITH PREMATURE CARDIOVASCULAR DEATH IN KFRT. METHODS: IN A PILOT CASE-CONTROL STUDY OF 50 HEMODIALYSIS PATIENTS WHO DIED OF CARDIOVASCULAR EVENTS AS CASES, AND 50 MATCHED HEMODIALYSIS CONTROLS WHO REMAINED ALIVE DURING A MEDIAN FOLLOW-UP OF 2.0 YEARS, WE PERFORMED C-SNCRNAS PROFILES USING NEXT-GENERATION SEQUENCING TO IDENTIFY DIFFERENTIALLY EXPRESSED CIRCULATING MICRORNAS (C-MIRNAS) BETWEEN THE PLASMA OF CASES AND THAT OF CONTROLS. MRNA TARGET PREDICTION AND PATHWAY ENRICHMENT ANALYSIS WERE PERFORMED TO EXAMINE THE FUNCTIONAL RELEVANCE OF DIFFERENTIALLY EXPRESSED C-MIRNAS TO CARDIOVASCULAR PATHOPHYSIOLOGY. THE ASSOCIATION OF DIFFERENTIALLY EXPRESSED C-MIRNAS WITH CARDIOVASCULAR MORTALITY WAS EXAMINED USING MULTIVARIABLE CONDITIONAL LOGISTIC REGRESSION. RESULTS: THE PATIENT CHARACTERISTICS WERE SIMILAR BETWEEN CASES AND CONTROLS, WITH A MEAN AGE OF 63 YEARS, 48% MALE, AND 54% AFRICAN AMERICAN IN BOTH GROUPS. WE DETECTED A TOTAL OF 613 MIRNAS IN THE PLASMA, AMONG WHICH FIVE MIRNAS (I.E., MIR-129-1-5P, MIR-500B-3P, MIR-125B-1-3P, MIR-3648-2-5P, AND MIR-3150B-3P) WERE IDENTIFIED TO BE DIFFERENTIALLY EXPRESSED BETWEEN CASES AND CONTROLS WITH CUT-OFFS OF P < 0.05 AND LOG2 FOLD-CHANGE (LOG2FC) > 1. WHEN USING MORE STRINGENT CUT-OFFS OF P-ADJUSTED < 0.05 AND LOG2FC > 1, ONLY MIR-129-1-5P REMAINED SIGNIFICANTLY DIFFERENTIALLY EXPRESSED, WITH HIGHER LEVELS OF MIR-129-1-5P IN THE CASES THAN IN THE CONTROLS. THE PATHWAY ENRICHMENT ANALYSIS USING PREDICTED MIR-129-1-5P MRNA TARGETS DEMONSTRATED ENRICHMENT IN ADRENERGIC SIGNALING IN CARDIOMYOCYTES, ARRHYTHMOGENIC RIGHT VENTRICULAR CARDIOMYOPATHY, AND OXYTOCIN SIGNALING PATHWAYS. IN PARALLEL, THE CIRCULATING MIR-129-1-5P LEVELS WERE SIGNIFICANTLY ASSOCIATED WITH THE RISK OF CARDIOVASCULAR DEATH (ADJUSTED OR [95% CI], 1.68 [1.01-2.81] FOR ONE INCREASE IN LOG-TRANSFORMED MIR-129-1-5P COUNTS), INDEPENDENT OF POTENTIAL CONFOUNDERS. CONCLUSIONS: CIRCULATING MIR-129-1-5P MAY SERVE AS A NOVEL BIOMARKER FOR PREMATURE CARDIOVASCULAR DEATH IN KFRT. 2023 17 3504 41 IDENTIFICATION OF POTENTIALLY FUNCTIONAL CIRCRNAS AND PREDICTION OF CIRCRNA-MIRNA-MRNA REGULATORY NETWORK IN PERIODONTITIS: BRIDGING THE GAP BETWEEN BIOINFORMATICS AND CLINICAL NEEDS. BACKGROUND AND OBJECTIVE: PERIODONTITIS IS A MULTIFACTORIAL CHRONIC INFLAMMATORY DISEASE THAT CAN LEAD TO THE IRREVERSIBLE DESTRUCTION OF DENTAL SUPPORT TISSUES. AS AN EPIGENETIC FACTOR, THE EXPRESSION OF CIRCRNA IS TISSUE-DEPENDENT AND DISEASE-DEPENDENT. THIS STUDY AIMED TO IDENTIFY NOVEL PERIODONTITIS-ASSOCIATED CIRCRNAS AND PREDICT RELEVANT CIRCRNA-PERIODONTITIS REGULATORY NETWORK BY USING RECENTLY DEVELOPED BIOINFORMATIC TOOLS AND INTEGRATING SEQUENCING PROFILING WITH CLINICAL INFORMATION FOR GETTING A BETTER AND MORE THOROUGH IMAGE OF PERIODONTITIS PATHOGENESIS, FROM GENE TO CLINIC. MATERIAL AND METHODS: HIGH-THROUGHPUT SEQUENCING AND RT-QPCR WERE CONDUCTED TO IDENTIFY DIFFERENTIALLY EXPRESSED CIRCRNAS IN GINGIVAL TISSUES FROM PERIODONTITIS PATIENTS. THE RELATIONSHIP BETWEEN UPREGULATED CIRCRNAS EXPRESSION AND PROBING DEPTH (PD) WAS PERFORMED USING SPEARMAN'S CORRELATION ANALYSIS. BIOINFORMATIC ANALYSES INCLUDING GO ANALYSIS, CIRCRNA-DISEASE ASSOCIATION PREDICTION, AND CIRCRNA-MIRNA-MRNA NETWORK PREDICTION WERE PERFORMED TO CLARIFY POTENTIAL REGULATORY FUNCTIONS OF IDENTIFIED CIRCRNAS IN PERIODONTITIS. A RECEIVER-OPERATING CHARACTERISTIC (ROC) CURVE WAS ESTABLISHED TO ASSESS THE DIAGNOSTIC SIGNIFICANCE OF IDENTIFIED CIRCRNAS. RESULTS: HIGH-THROUGHPUT SEQUENCING IDENTIFIED 70 DIFFERENTIALLY EXPRESSED CIRCRNAS (68 UPREGULATED AND 2 DOWNREGULATED CIRCRNAS) IN HUMAN PERIODONTITIS (FOLD CHANGE >2.0 AND P < .05). THE TOP FIVE UPREGULATED CIRCRNAS WERE VALIDATED BY RT-QPCR THAT HAD STRONG ASSOCIATIONS WITH MULTIPLE HUMAN DISEASES, INCLUDING PERIODONTITIS. THE UPREGULATION OF CIRCRNAS WERE POSITIVELY CORRELATED WITH PD (R = .40-.69, P < .05, MODERATE). A CIRCRNA-MIRNA-MRNA NETWORK WITH THE TOP FIVE UPREGULATED CIRCRNAS, DIFFERENTIALLY EXPRESSED MRNAS, AND OVERLAPPED PREDICTED MIRNAS INDICATED POTENTIAL ROLES OF CIRCRNAS IN IMMUNE RESPONSE, CELL APOPTOSIS, MIGRATION, ADHESION, AND REACTION TO OXIDATIVE STRESS. THE ROC CURVE SHOWED THAT CIRCRNAS HAD POTENTIAL VALUE IN PERIODONTITIS DIAGNOSIS (AUC = 0.7321-0.8667, P < .05). CONCLUSION: CIRCRNA-DISEASE ASSOCIATIONS WERE PREDICTED BY ONLINE BIOINFORMATIC TOOLS. POSITIVE CORRELATION BETWEEN UPREGULATED CIRCRNAS, CIRCPTP4A2, CHR22:23101560-23135351+, CIRCARHGEF28, CIRCBARD1 AND CIRCRASA2, AND PD SUGGESTED FUNCTION OF CIRCRNAS IN PERIODONTITIS. NETWORK PREDICTION FURTHER FOCUSED ON DOWNSTREAM TARGETS REGULATED BY CIRCRNAS DURING PERIODONTITIS PATHOGENESIS. 2022 18 1144 32 CONCOMITANT HETEROCHROMATINISATION AND DOWN-REGULATION OF GENE EXPRESSION UNVEILS EPIGENETIC SILENCING OF RELB IN AN AGGRESSIVE SUBSET OF CHRONIC LYMPHOCYTIC LEUKEMIA IN MALES. BACKGROUND: THE SENSITIVITY OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) CELLS TO CURRENT TREATMENTS, BOTH IN VITRO AND IN VIVO, RELIES ON THEIR ABILITY TO ACTIVATE APOPTOTIC DEATH. CLL CELLS RESISTANT TO DNA DAMAGE-INDUCED APOPTOSIS DISPLAY DEREGULATION OF A SPECIFIC SET OF GENES. METHODS: MICROARRAY HYBRIDIZATION (HUMAN GENECHIP, AFFYMETRIX), IMMUNOFLUORESCENT IN SITU LABELING COUPLED WITH VIDEO-MICROSCOPY RECORDING/ANALYSES, CHROMATIN-IMMUNOPRECIPITATION (CHIP), POLYMERASE CHAIN REACTIONS (PCR), REAL-TIME QUANTITATIVE PCR (RT-QPCR) AND BISULFITE GENOME SEQUENCING WERE THE MAIN METHODS APPLIED. STATISTICAL ANALYSES WERE PERFORMED BY APPLYING GCRMA AND SAM ANALYSIS (MICROARRAY DATA) AND STUDENT'S T-TEST OR MANN & WHITNEY'S U-TEST. RESULTS: HEREIN WE SHOW THAT, REMARKABLY, IN A RESISTANT MALE CLL CELLS THE VAST MAJORITY OF GENES WERE DOWN-REGULATED COMPARED WITH SENSITIVE CELLS, WHEREAS THIS WAS NOT THE CASE IN CELLS DERIVED FROM FEMALES. THIS GENE DOWN-REGULATION WAS FOUND TO BE ASSOCIATED WITH AN OVERALL GAIN OF HETEROCHROMATIN AS EVIDENCED BY IMMUNOFLUORESCENT LABELING OF HETEROCHROMATIN PROTEIN 1ALPHA (HP-1), TRIMETHYLATED HISTONE 3 LYSINE 9 (3METH3K9), AND 5-METHYLCYTIDINE (5METC). NOTABLY, 17 GENES WERE FOUND TO BE COMMONLY DEREGULATED IN RESISTANT MALE AND FEMALE CELL SAMPLES. AMONG THESE, RELB WAS IDENTIFIED AS A DISCRIMINATORY CANDIDATE GENE REPRESSED IN THE MALE AND UPREGULATED IN THE FEMALE RESISTANT CELLS. CONCLUSION: THE MOLECULAR DEFECTS IN THE SILENCING OF RELB INVOLVE AN INCREASE IN H3K9- BUT NOT CPG-ISLAND METHYLATION IN THE PROMOTER REGIONS. INCREASE IN ACETYL-H3 IN RESISTANT FEMALE BUT NOT MALE CLL SAMPLES AS WELL AS A DECREASE OF TOTAL CELLULAR LEVEL OF RELB AFTER AN INHIBITION OF HISTONE DEACETYLASE (HDAC) BY TRICHOSTATIN A (TSA), FURTHER EMPHASIZE THE ROLE OF EPIGENETIC MODIFICATIONS WHICH COULD DISCRIMINATE TWO CLL SUBSETS. TOGETHER, THESE RESULTS HIGHLIGHTED THE EPIGENETIC RELB SILENCING AS A NEW MARKER OF THE PROGRESSIVE DISEASE IN MALES. 2010 19 5841 22 STRUCTURAL CHROMATIN ALTERATIONS IN PERIPHERAL BLOOD LEUKOCYTES OF ALCOHOL-DEPENDENT INDIVIDUALS DURING DETOXIFICATION THERAPY. BACKGROUND/AIM: THE AIM OF THIS STUDY WAS TO INVESTIGATE THE STATE OF CHROMATIN CONDENSATION IN PERIPHERAL BLOOD LEUKOCYTES OF ALCOHOLICS, DURING THE EARLY DETOXIFICATION PERIOD, IN ORDER TO HIGHLIGHT STRUCTURAL MODIFICATIONS, INDICATING EPIGENETIC MECHANISMS REGULATED BY ALCOHOL. MATERIALS AND METHODS: BLOOD SAMPLES WERE OBTAINED FROM ALCOHOLIC PATIENTS, WHO WERE ADMITTED FOR DETOXIFICATION ON AN INPATIENT BASIS, AND FROM HEALTHY CONTROLS. THE LEVEL OF CONDENSED HETEROCHROMATIN AND DE-CONDENSED EUCHROMATIN WERE DETECTED THROUGH THE RATIO OF LYSINE TO ARGININE RESIDUES, BY THE APPLICATION OF THE AMMONIACAL SILVER REACTION (ASR) STAINING ON LEUKOCYTE PELLETS, AND THROUGH IMMUNOHISTOCHEMICAL LOCALIZATION OF HISTONE H1 ON PERIPHERAL BLOOD SMEARS. RESULTS: LYMPHOCYTES AND NEUTROPHILS WITH RELAXED DE-CONDENSED CHROMATIN WERE FOUND, INDICATING A MORE REACTIVE GENOME IN ALCOHOLICS, EVEN AT THE STAGE OF DETOXIFICATION. CONCLUSION: THE RESULTS UNDERLINE THE IMPORTANCE OF CHROMATIN STRUCTURE OF LEUKOCYTES AS A SENSITIVE, PERIPHERAL, BIOLOGICAL MARKER FOR EPIGENETIC STUDIES IN LIVING CHRONIC ALCOHOLICS. 2014 20 1607 26 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