1 3904 165 LEPROSY PIRNOME: EXPLORING NEW POSSIBILITIES FOR AN OLD DISEASE. LEPROSY, WHICH IS CAUSED BY THE HUMAN PATHOGEN MYCOBACTERIUM LEPRAE, CAUSES NERVE DAMAGE, DEFORMITY AND DISABILITY IN OVER 200,000 PEOPLE EVERY YEAR. BECAUSE OF THE LONG DOUBLING TIME OF M. LEPRAE (13 DAYS) AND THE DELAYED ONSET OF DETECTABLE SYMPTOMS, WHICH IS ESTIMATED TO BE APPROXIMATELY 3-7 YEARS AFTER INFECTION, THERE IS ALWAYS A LARGE PERCENTAGE OF SUBCLINICALLY INFECTED INDIVIDUALS IN THE POPULATION WHO WILL EVENTUALLY DEVELOP THE DISEASE, MAINLY IN ENDEMIC COUNTRIES. PIRNAS COMPRISE THE LARGEST GROUP OF SMALL NONCODING RNAS FOUND IN HUMANS, AND THEY ARE DISTINCT FROM MICRORNAS (MIRNAS) AND SMALL INTERFERING RNAS (SIRNAS). PIRNAS FUNCTION IN TRANSPOSON SILENCING, EPIGENETIC REGULATION, AND GERMLINE DEVELOPMENT. THE FUNCTIONAL ROLE OF PIRNAS AND THEIR ASSOCIATED PIWI PROTEINS HAVE STARTED TO EMERGE IN THE DEVELOPMENT OF HUMAN CANCERS AND VIRAL INFECTIONS, BUT THEIR RELEVANCE TO BACTERIAL DISEASES HAS NOT BEEN INVESTIGATED. THE PRESENT STUDY REPORTS THE PIRNOME OF HUMAN SKIN, REVEALING THAT ALL BUT ONE OF THE PIRNAS EXAMINED ARE DOWNREGULATED IN LEPROSY SKIN LESIONS. CONSIDERING THAT ONE OF THE BEST CHARACTERIZED FUNCTIONS OF PIRNAS IN HUMANS IS POSTTRANSCRIPTIONAL MRNA SILENCING, THEIR FUNCTIONS ARE SIMILAR TO WHAT WE HAVE DESCRIBED FOR MIRNAS, INCLUDING ACTING ON APOPTOSIS, M. LEPRAE RECOGNITION AND ENGULFMENT, SCHWANN CELL (SC) DEMYELINATION, EPITHELIAL-MESENCHYMAL TRANSITION (EMT), LOSS OF SENSATION AND NEUROPATHIC PAIN. IN ADDITION TO NEW FINDINGS ON LEPROSY PHYSIOPATHOLOGY, THE DISCOVERY OF RELEVANT PIRNAS INVOLVED IN DISEASE PROCESSES IN HUMAN SKIN MAY PROVIDE NEW CLUES FOR THERAPEUTIC TARGETS, SPECIFICALLY TO CONTROL NERVE DAMAGE, A PROMINENT FEATURE OF LEPROSY THAT HAS NO CURRENTLY AVAILABLE PHARMACEUTICAL TREATMENT. 2020 2 3501 35 IDENTIFICATION OF POTENTIAL BIOMARKERS FOR SYSTEMIC LUPUS ERYTHEMATOSUS BY INTEGRATED ANALYSIS OF GENE EXPRESSION AND METHYLATION DATA. INTRODUCTION: SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A HETEROGENEOUS AND CHRONIC AUTOIMMUNE DISEASE. ABERRANT DNA METHYLATION OCCURS DURING VARIOUS PROCESSES OF SLE DEVELOPMENT REGULATING THE MRNA EXPRESSION OF INTERRELATED GENES. THIS STUDY AIMS TO SCREEN POTENTIAL DNA METHYLATION MARKERS FOR SLE. METHODS: GENE EXPRESSION AND METHYLATION DATASETS WERE DOWNLOADED FROM THE GENE EXPRESSION OMNIBUS (GEO) DATABASE. DIFFERENTIALLY EXPRESSED GENES (DEGS) BETWEEN SLE PATIENTS AND HEALTHY CONTROLS WERE SCREENED USING THE LIMMA R PACKAGE, AND DIFFERENTIALLY METHYLATED POSITIONS (DMPS) AND REGIONS (DMRS) WERE IDENTIFIED USING DMPFINDER AND BUMPHUNTER (MINFI). ADDITIONALLY, THE DNA METHYLATION MARKERS TO DISTINGUISH SLE PATIENTS FROM HEALTHY CONTROLS WERE EXPLORED THROUGH RECEIVER OPERATING CHARACTERISTIC (ROC) CURVES AND LOGISTIC REGRESSION ANALYSES. FINALLY, WE VALIDATED THE RESULTS OF THE BIOINFORMATIC ANALYSIS BY PYROSEQUENCING. RESULTS: IN TOTAL, 91 DEGS, 90,092 DMPS, 15 DMRS, AND 13 DMR-ASSOCIATED GENES WERE IDENTIFIED. THROUGH THE INTEGRATIVE ANALYSIS OF DEG- AND DMR-ASSOCIATED GENES, WE IDENTIFIED FIVE TYPE I INTERFERON (IFN)-RELATED GENES AS KEY EPIGENETIC-DRIVEN GENES IN SLE. GO ENRICHMENT ANALYSIS SHOWED THAT THE FIVE SLE-ASSOCIATED EPIGENETIC-DRIVEN GENES WERE MAINLY ENRICHED IN THE TYPE I IFN SIGNALING PATHWAY INVOLVED IN IMMUNE RESPONSE AND DEFENSE RESPONSE TO VIRUS. MOREOVER, WE IDENTIFIED TWO SLE-SPECIFIC DNA METHYLATION MARKERS, THREE SLE WITHOUT LUPUS NEPHRITIS (SLE-LN(-))-SPECIFIC DNA METHYLATION MARKERS, AND TWO SLE WITH LUPUS NEPHRITIS (SLE-LN(+))-SPECIFIC DNA METHYLATION MARKERS BY STEPWISE LOGISTIC REGRESSION. CONCLUSIONS: OVERALL, OUR STUDY DEMONSTRATES POTENTIAL DNA METHYLATION MARKERS OF SLE, SLE-LN(-), AND SLE-LN(+), WHICH MAY HELP THE DIAGNOSIS, BOOST THE DEVELOPMENT OF NEW EPIGENETIC THERAPY, AND CONTRIBUTE TO INDIVIDUALIZED TREATMENT. KEY POINTS * THIS STUDY IDENTIFIED FIVE TYPE I IFN-RELATED GENES AS KEY EPIGENETIC-DRIVEN GENES IN SLE, WHICH SUPPORT THE IMPORTANCE OF THE TYPE I IFN PATHWAY IN THE PATHOGENESIS OF SLE * WE IDENTIFIED NOVEL DNA METHYLATION BIOMARKERS IN SLE, SLE-LN-, AND SLE-LN+ BY A COMPREHENSIVE ANALYSIS OF BIOINFORMATICS METHODS AND EXECUTED EXPERIMENTAL VALIDATION, AND BINARY LOGISTIC REGRESSION ANALYSIS SHOWED THAT THEY HAVE EXCELLENT POTENTIAL * THESE RESULTS MAY PROVIDE NEW INSIGHTS INTO THE BIOLOGICAL MECHANISMS OF SLE, AND IDENTIFY RELIABLE BIOMARKERS FOR SLE, SLE-LN-, AND SLE-LN+, WHICH MAY CONTRIBUTE TO DIAGNOSIS AND INDIVIDUALIZED TREATMENT. 2023 3 1294 45 DECREASED EXPRESSION OF MIR-20A AND MIR-92A IN THE SERUM FROM SULFUR MUSTARD-EXPOSED PATIENTS DURING THE CHRONIC PHASE OF RESULTING ILLNESS. CONTEXT: SULFUR MUSTARD (SM), WITH EXTENSIVE NUCLEOPHILIC AND ALKYLATING PROPERTIES, WAS EMPLOYED DURING THE IRAN-IRAQ WAR BY IRAQI FORCES. THE MOST CRITICAL COMPLICATIONS ATTRIBUTED TO SM ARE RELATED TO DANGEROUS PULMONARY DISORDERS COLLECTIVELY KNOWN AS "MUSTARD LUNG". THE SYMPTOMS GRADUALLY EMERGE OVER A LONG PERIOD, BECOMING CHRONIC, AND ARE DEPENDENT ON TIME AND THE AMOUNT OF EXPOSED SM. BECAUSE OF THE UNKNOWN AND COMPLEX NATURE OF THE DISEASE, NO DIFFERENTIAL DIAGNOSTIC METHOD OR ABSOLUTE TREATMENT STRATEGY HAS BEEN FORMALLY DEVELOPED. OBJECTIVE: THE AIM OF OUR STUDY WAS TO DETERMINE THE EXPRESSION PATTERN OF THE MICRORNAS (MIRNAS) MIR-92A AND MIR-20A IN THE SERUM OF PATIENTS WITH MUSTARD LUNG ALONG WITH THAT OF NORMAL INDIVIDUALS. MIRNAS HAVE BEEN SHOWN TO POSSESS STABLE PERSISTENCE IN BIOFLUIDS LIKE PLASMA AND SERUM AND ARE CONSIDERED NON-AGGRESSIVE BIOMARKERS HELPFUL FOR DIAGNOSIS AND TREATMENT OF MANY DISEASES. MATERIALS AND METHODS: A HIGHLY SENSITIVE APPROACH CALLED STEM-LOOP REAL-TIME QUANTITATIVE POLYMERASE CHAIN REACTION WAS EMPLOYED TO STUDY THE EXPRESSION OF MIRNAS. RESULTS: THE EXPRESSION OF MIR-92A AND MIR-20A WAS SIGNIFICANTLY DOWN-REGULATED IN THE SERUM OF PATIENTS WITH MUSTARD LUNG COMPARED TO THE CONTROL GROUP. DISCUSSION: DOWN-REGULATION OF MIR-92A AND MIR-20A MAY BE DUE TO CHRONIC EPIGENETIC ALTERATIONS AFTER SM EXPOSURE, WHICH FINALLY LEADS TO CHANGES IN VITAL CELLULAR PROCESSES SUCH AS DIFFERENTIATION, PROLIFERATION AND SO FORTH. CONCLUSION: OUR FINDINGS MAY PROVIDE A DIFFERENTIAL DIAGNOSTIC METHOD THAT IS EFFECTIVE FOR DIAGNOSING LUNG DISEASES CAUSED BY SM EXPOSURE. ADDITIONALLY, THESE MIRNAS MAY BE REGARDED AS PROBABLE TARGETS FOR TREATMENT OF LUNG INJURIES. 2015 4 4373 42 MIRNAS: IMPORTANT TARGETS FOR ORAL CANCER PAIN RESEARCH. PAIN IS A SYMPTOM SHARED BY AN INCREDIBLE NUMBER OF DISEASES. IT IS ALSO ONE OF THE PRIMARY CONDITIONS THAT PROMPT INDIVIDUALS TO SEEK MEDICAL TREATMENT. HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) CORRESPONDS TO A HETEROGENEOUS DISEASE THAT MAY ARISE FROM MANY DISTINCT STRUCTURES OF A LARGE, HIGHLY COMPLEX, AND INTRICATE REGION. HNSCC AFFECTS A GREAT NUMBER OF PATIENTS WORLDWIDE AND IS DIRECTLY ASSOCIATED WITH CHRONIC PAIN, WHICH IS ESPECIALLY PROMINENT DURING THE ADVANCED STAGES OF ORAL SQUAMOUS CELL CARCINOMA (OSCC), AN ANATOMICAL AND CLINICAL SUBTYPE THAT CORRESPONDS TO THE GREAT MAJORITY ORAL CANCERS. ALTHOUGH THE CELLULAR AND MOLECULAR BASES OF ORAL CANCER PAIN HAVE NOT BEEN FULLY ESTABLISHED YET, THE RESULTS OF RECENT STUDIES SUGGEST THAT DIFFERENT EPIGENETIC MECHANISMS MAY CONTRIBUTE TO THIS PROCESS. FOR INSTANCE, THERE IS STRONG SCIENTIFIC EVIDENCE THAT MICRORNAS (MIRNAS), SMALL RNA MOLECULES THAT DO NOT ENCODE PROTEINS, MIGHT ACT BY REGULATING THE MECHANISMS UNDERLYING CANCER-RELATED PAIN. AMONG THE MIRNAS THAT COULD POSSIBLY INTERFERE IN PAIN-SIGNALING PATHWAYS, MIR-125B, MIR-181, AND MIR-339 EMERGE AS SOME OF THE MOST PROMISING CANDIDATES. IN FACT, SUCH MOLECULES APPARENTLY CONTRIBUTE TO INFLAMMATORY PAIN. MOREOVER, THESE MOLECULES POSSIBLY INFLUENCE THE ACTIVITY OF ENDOGENOUS PAIN CONTROL SYSTEMS (E.G., OPIOIDERGIC AND SEROTONERGIC SYSTEMS), WHICH COULD ULTIMATELY RESULT IN PERIPHERAL AND CENTRAL SENSITIZATION, CENTRAL NERVOUS SYSTEM (CNS) PHENOMENA INNATELY ASSOCIATED WITH CHRONIC PAIN. THIS REVIEW PAPER FOCUSES ON THE CURRENT SCIENTIFIC KNOWLEDGE REGARDING THE INVOLVEMENT OF MIRNAS IN CANCER PAIN, WITH SPECIAL ATTENTION DEDICATED TO OSCC-RELATED PAIN. 2017 5 4050 27 MALADAPTIVE TRAINED IMMUNITY AND CLONAL HEMATOPOIESIS AS POTENTIAL MECHANISTIC LINKS BETWEEN PERIODONTITIS AND INFLAMMATORY COMORBIDITIES. PERIODONTITIS IS BIDIRECTIONALLY ASSOCIATED WITH SYSTEMIC INFLAMMATORY DISORDERS. THE PREVALENCE AND SEVERITY OF THIS ORAL DISEASE AND LINKED COMORBIDITIES INCREASES WITH AGING. HERE, WE REVIEW TWO NEWLY EMERGED CONCEPTS, TRAINED INNATE IMMUNITY (TII) AND CLONAL HEMATOPOIESIS OF INDETERMINATE POTENTIAL (CHIP), WHICH TOGETHER SUPPORT A POTENTIAL HYPOTHESIS ON HOW PERIODONTITIS AFFECTS AND IS AFFECTED BY COMORBIDITIES AND WHY THE SUSCEPTIBILITY TO PERIODONTITIS AND COMORBIDITIES INCREASES WITH AGING. GIVEN THAT CHRONIC DISEASES ARE LARGELY TRIGGERED BY THE ACTION OF INFLAMMATORY IMMUNE CELLS, MODULATION OF THEIR BONE MARROW PRECURSORS, THE HEMATOPOIETIC STEM AND PROGENITOR CELLS (HSPCS), MAY AFFECT MULTIPLE DISORDERS THAT EMERGE AS COMORBIDITIES. SUCH ALTERATIONS IN HSPCS CAN BE MEDIATED BY TII AND/OR CHIP, TWO NON-MUTUALLY EXCLUSIVE PROCESSES SHARING A BIAS FOR ENHANCED MYELOPOIESIS AND PRODUCTION OF INNATE IMMUNE CELLS WITH HEIGHTENED PROINFLAMMATORY POTENTIAL. TII IS A STATE OF ELEVATED IMMUNE RESPONSIVENESS BASED ON INNATE IMMUNE (EPIGENETIC) MEMORY. SYSTEMIC INFLAMMATION CAN INITIATE TII IN THE BONE MARROW VIA SUSTAINED REWIRING OF HSPCS, WHICH THEREBY DISPLAY A SKEWING TOWARD THE MYELOID LINEAGE, RESULTING IN GENERATION OF HYPER-REACTIVE OR "TRAINED" MYELOID CELLS. CHIP ARISES FROM AGING-RELATED SOMATIC MUTATIONS IN HSPCS, WHICH CONFER A SURVIVAL AND PROLIFERATION ADVANTAGE TO THE MUTANT HSPCS AND GIVE RISE TO AN OUTSIZED FRACTION OF HYPER-INFLAMMATORY MUTANT MYELOID CELLS IN THE CIRCULATION AND TISSUES. THIS REVIEW DISCUSSES EMERGING EVIDENCE THAT SUPPORTS THE NOTION THAT TII AND CHIP MAY UNDERLIE A CAUSAL AND AGE-RELATED ASSOCIATION BETWEEN PERIODONTITIS AND COMORBIDITIES. A HOLISTIC MECHANISTIC UNDERSTANDING OF THE PERIODONTITIS-SYSTEMIC DISEASE CONNECTION MAY OFFER NOVEL DIAGNOSTIC AND THERAPEUTIC TARGETS FOR TREATING INFLAMMATORY COMORBIDITIES. 2022 6 3056 31 GENOME-WIDE DNA METHYLATION ANALYSIS IMPLICATES ENRICHMENT OF INTERFERON PATHWAY IN AFRICAN AMERICAN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS AND EUROPEAN AMERICANS WITH LUPUS NEPHRITIS. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC, MULTISYSTEM, INFLAMMATORY AUTOIMMUNE DISEASE THAT DISPROPORTIONATELY AFFECTS WOMEN. TRENDS IN SLE PREVALENCE AND CLINICAL COURSE DIFFER BY ANCESTRY, WITH THOSE OF AFRICAN AMERICAN ANCESTRY PRESENTING WITH MORE ACTIVE, SEVERE AND RAPIDLY PROGRESSIVE DISEASE THAN EUROPEAN AMERICANS. PREVIOUS RESEARCH ESTABLISHED ALTERED EPIGENETIC SIGNATURES IN SLE PATIENTS COMPARED TO CONTROLS. HOWEVER, THE CONTRIBUTION OF ABERRANT DNA METHYLATION (DNAM) TO THE RISK OF SLE BY ANCESTRY AND DIFFERENCES AMONG PATIENTS WITH SLE-ASSOCIATED LUPUS NEPHRITIS (LN) HAS NOT BEEN WELL DESCRIBED. WE EVALUATED THE DNA METHYLOMES OF 87 INDIVIDUALS INCLUDING 41 SLE PATIENTS, WITH AND WITHOUT LN, AND 46 CONTROLS ENROLLED IN AN ANCESTRY DIVERSE, WELL-CHARACTERIZED COHORT STUDY OF ESTABLISHED SLE (41 SLE PATIENTS [20 SLE-LN+, 21 SLE-LN-] AND 46 SEX-, RACE- AND AGE-MATCHED CONTROLS; 55% AFRICAN AMERICAN, 45% EUROPEAN AMERICAN). PARTICIPANTS WERE GENOTYPED USING THE INFINIUM GLOBAL DIVERSITY ARRAY (GDA), AND GENETIC ANCESTRY WAS ESTIMATED USING PRINCIPAL COMPONENTS. GENOME-WIDE DNA METHYLATION WAS INITIALLY MEASURED USING THE ILLUMINA METHYLATIONEPIC 850K BEADCHIP ARRAY FOLLOWED BY METHYLATION-SPECIFIC QPCR TO VALIDATE THE METHYLATION STATUS AT PUTATIVE LOCI. DIFFERENTIALLY METHYLATED POSITIONS (DMP) WERE IDENTIFIED USING A CASE-CONTROL APPROACH ADJUSTED FOR ANCESTRY. WE IDENTIFIED A TOTAL OF 51 DMPS IN CPGS AMONG SLE PATIENTS COMPARED TO CONTROLS. GENES PROXIMAL TO THESE CPGS WERE HIGHLY ENRICHED FOR INVOLVEMENT IN TYPE I INTERFERON SIGNALING. DMPS AMONG EUROPEAN AMERICAN SLE PATIENTS WITH LN WERE SIMILAR TO AFRICAN AMERICAN SLE PATIENTS WITH AND WITHOUT LN. OUR FINDINGS WERE VALIDATED USING AN ORTHOGONAL, METHYL-SPECIFIC PCR FOR THREE SLE-ASSOCIATED DMPS NEAR OR PROXIMAL TO MX1, USP18, AND IFITM1. OUR STUDY CONFIRMS PREVIOUS REPORTS THAT DMPS IN CPGS ASSOCIATED WITH SLE ARE ENRICHED IN TYPE I INTERFERON GENES. HOWEVER, WE SHOW THAT EUROPEAN AMERICAN SLE PATIENTS WITH LN HAVE SIMILAR DNAM PATTERNS TO AFRICAN AMERICAN SLE PATIENTS IRRESPECTIVE OF LN, SUGGESTING THAT ABERRANT DNAM ALTERS ACTIVITY OF TYPE I INTERFERON PATHWAY LEADING TO MORE SEVERE DISEASE INDEPENDENT OF ANCESTRY. 2023 7 3575 33 IMPACT OF MOLECULAR PROFILING ON THE MANAGEMENT OF PATIENTS WITH MYELOFIBROSIS. MYELOFIBROSIS (MF) IS A CHRONIC MYELOPROLIFERATIVE NEOPLASM (MPN) CHARACTERIZED BY A HIGHLY HETEROGENEOUS CLINICAL COURSE, WHICH CAN BE COMPLICATED BY SEVERE CONSTITUTIONAL SYMPTOMS, MASSIVE SPLENOMEGALY, PROGRESSIVE BONE MARROW FAILURE, CARDIOVASCULAR EVENTS, AND DEVELOPMENT OF ACUTE LEUKEMIA. CONSTITUTIVE SIGNALING THROUGH THE JAK-STAT PATHWAY PLAYS A FUNDAMENTAL ROLE IN ITS PATHOGENESIS, GENERALLY DUE TO ACTIVATING MUTATIONS OF JAK2, CALR AND MPL GENES (I.E., THE MPN DRIVER MUTATIONS), PRESENT IN MOST MF PATIENTS. NEXT GENERATION SEQUENCING (NGS) PANEL TESTING HAS SHOWN THAT ADDITIONAL SOMATIC MUTATIONS CAN ALREADY BE DETECTED AT THE TIME OF DIAGNOSIS IN MORE THAN HALF OF PATIENTS, AND THAT THEY ACCUMULATE ALONG THE DISEASE COURSE. THESE MUTATIONS, MOSTLY AFFECTING EPIGENETIC MODIFIERS OR SPLICEOSOME COMPONENTS, MAY COOPERATE WITH MPN DRIVERS TO FAVOR CLONAL DOMINANCE OR INFLUENCE THE CLINICAL PHENOTYPE, AND SOME, SUCH AS HIGH MOLECULAR RISK MUTATIONS, CORRELATE WITH A MORE AGGRESSIVE CLINICAL COURSE WITH POOR TREATMENT RESPONSE. THE CURRENT MAIN ROLE OF MOLECULAR PROFILING IN CLINICAL PRACTICE IS PROGNOSTICATION, PRINCIPALLY FOR SELECTING HIGH-RISK PATIENTS WHO MAY BE CANDIDATES FOR TRANSPLANTATION, THE ONLY CURATIVE TREATMENT FOR MF TO DATE. TO THIS END, CONTEMPORARY PROGNOSTIC MODELS INCORPORATING MOLECULAR DATA ARE USEFUL TOOLS TO DISCRIMINATE DIFFERENT RISK CATEGORIES. ASIDE FROM CERTAIN CLINICAL SITUATIONS, DECISIONS REGARDING MEDICAL TREATMENT ARE NOT BASED ON PATIENT MOLECULAR PROFILING, YET THIS APPROACH MAY BECOME MORE RELEVANT IN NOVEL TREATMENT STRATEGIES, SUCH AS THE USE OF VACCINES AGAINST THE MUTANT FORMS OF JAK2 OR CALR, OR DRUGS DIRECTED AGAINST ACTIONABLE MOLECULAR TARGETS. 2022 8 2895 26 GASTRIC CANCER DEVELOPMENT AFTER THE SUCCESSFUL ERADICATION OF HELICOBACTER PYLORI. GASTRIC CANCER (GC) DEVELOPS AS A RESULT OF INFLAMMATION-ASSOCIATED CARCINOGENESIS DUE TO HELICOBACTER PYLORI (H. PYLORI) INFECTION AND SUBSEQUENT DEFECTS IN GENETIC/EPIGENETIC EVENTS. ALTHOUGH THE INDICATION FOR ERADICATION THERAPY HAS BECOME WIDESPREAD, CLINICAL STUDIES HAVE REVEALED ITS LIMITED EFFECTS IN DECREASING THE INCIDENCE OF GC. MOREOVER, RESEARCH ON BIOPSY SPECIMENS OBTAINED BY CONVENTIONAL ENDOSCOPY HAS DEMONSTRATED THE FEASIBILITY OF THE RESTORATION OF SOME GENETIC/EPIGENETIC ALTERATIONS IN THE GASTRIC MUCOSA. PRACTICALLY, THE NUMBER OF SPORADIC CASES OF PRIMARY/METACHRONOUS GC THAT EMERGE AFTER SUCCESSFUL ERADICATION HAS INCREASED, WHILE ON-GOING GUIDELINES RECOMMEND ERADICATION THERAPY FOR PATIENTS WITH CHRONIC GASTRITIS AND THOSE WITH BACKGROUND MUCOSA AFTER ENDOSCOPIC RESECTION FOR GC. ACCORDINGLY, REGULAR SURVEILLANCE OF NUMEROUS INDIVIDUALS WHO HAVE RECEIVED ERADICATION THERAPY IS RECOMMENDED DESPITE THE LACK OF BIOMARKERS. RECENTLY, THE FOCUS HAS BEEN ON FUNCTIONAL REVERSIBILITY AFTER SUCCESSFUL ERADICATION AS ANOTHER CUE TO ELUCIDATE THE MECHANISMS OF RESTORATION AS WELL AS THOSE OF CARCINOGENESIS IN THE GASTRIC MUCOSA AFTER H. PYLORI ERADICATION. WE DEMONSTRATED THAT CONGO-RED CHROMOENDOSCOPY ENABLED THE IDENTIFICATION OF THE MULTI-FOCAL DISTRIBUTION OF FUNCTIONALLY IRREVERSIBLE MUCOSA COMPARED WITH THAT OF RESTORED MUCOSA AFTER SUCCESSFUL ERADICATION IN INDIVIDUALS AT EXTREMELY HIGH RISK FOR GC. FURTHER RESEARCH THAT USES FUNCTIONAL IMAGING MAY PROVIDE NEW INSIGHTS INTO THE MECHANISMS OF REGENERATION AND CARCINOGENESIS IN THE GASTRIC MUCOSA POST-ERADICATION AND MAY ALLOW FOR THE DEVELOPMENT OF USEFUL BIOMARKERS. 2016 9 2530 35 EPIGENETICS IN ALLERGIC DISEASES. PURPOSE OF REVIEW: ALLERGIC DISEASES ARE AMONG THE MOST PREVALENT CHRONIC DISEASES OF CHILDHOOD, AFFECTING MORE THAN 7 MILLION CHILDREN IN THE UNITED STATES. EPIDEMIOLOGICAL EVIDENCE SUPPORTS THE IDEA THAT THE INCEPTION OF ALLERGIC DISEASES IS TYPICALLY BEFORE THE PRESCHOOL YEARS, EVEN WHEN CHRONIC SYMPTOMS DO NOT EMERGE UNTIL ADULTHOOD. THE ROLE OF EPIGENETIC MECHANISMS (PARTICULARLY DNA METHYLATION) IN ALLERGIC DISEASE IS UNDER ACTIVE INVESTIGATION BECAUSE THESE MECHANISMS ARE KNOWN TO BE AT THE INTERFACE OF GENE REGULATION, ENVIRONMENTAL STIMULI, AND DEVELOPMENTAL PROCESSES, ALL OF WHICH ARE ESSENTIAL FOR THE PATHOGENESIS FOR ASTHMA AND ALLERGY. THIS ARTICLE SPECIFICALLY REVIEWS GENOME-WIDE DNA METHYLATION STUDIES IN ALLERGIC DISEASE. RECENT FINDINGS: DIFFERENTIAL DNA METHYLATION AT SPECIFIC REGIONS APPEARS TO BE ASSOCIATED WITH CONCURRENT ALLERGIC DISEASE. A FEW STUDIES HAVE IDENTIFIED METHYLATION SIGNATURES PREDICTIVE OF DISEASE. SUMMARY: DNA METHYLATION SIGNATURES HAVE BEEN SHOWN TO BE ASSOCIATED WITH SEVERAL ALLERGIC DISEASE PHENOTYPES, TYPICALLY CONCURRENTLY WITH DISEASE. THE FEW THAT HAVE BEEN FOUND TO PRECEDE DIAGNOSIS ARE ESPECIALLY INTERESTING BECAUSE THEY HIGHLIGHT AN EARLY TRAJECTORY TO DISEASE. 2015 10 2662 42 EPSTEIN-BARR VIRUS AND MULTIPLE SCLEROSIS: A CONVOLUTED INTERACTION AND THE OPPORTUNITY TO UNRAVEL PREDICTIVE BIOMARKERS. SINCE THE EARLY 1980S, EPSTEIN-BARR VIRUS (EBV) INFECTION HAS BEEN DESCRIBED AS ONE OF THE MAIN RISK FACTORS FOR DEVELOPING MULTIPLE SCLEROSIS (MS), AND RECENTLY, NEW EPIDEMIOLOGICAL EVIDENCE HAS REINFORCED THIS PREMISE. EBV SEROCONVERSION PRECEDES ALMOST 99% OF THE NEW CASES OF MS AND LIKELY PREDATES THE FIRST CLINICAL SYMPTOMS. THE MOLECULAR MECHANISMS OF THIS ASSOCIATION ARE COMPLEX AND MAY INVOLVE DIFFERENT IMMUNOLOGICAL ROUTES, PERHAPS ALL RUNNING IN PARALLEL (I.E., MOLECULAR MIMICRY, THE BYSTANDER DAMAGE THEORY, ABNORMAL CYTOKINE NETWORKS, AND COINFECTION OF EBV WITH RETROVIRUSES, AMONG OTHERS). HOWEVER, DESPITE THE LARGE AMOUNT OF EVIDENCE AVAILABLE ON THESE TOPICS, THE ULTIMATE ROLE OF EBV IN THE PATHOGENESIS OF MS IS NOT FULLY UNDERSTOOD. FOR INSTANCE, IT IS UNCLEAR WHY AFTER EBV INFECTION SOME INDIVIDUALS DEVELOP MS WHILE OTHERS EVOLVE TO LYMPHOPROLIFERATIVE DISORDERS OR SYSTEMIC AUTOIMMUNE DISEASES. IN THIS REGARD, RECENT STUDIES SUGGEST THAT THE VIRUS MAY EXERT EPIGENETIC CONTROL OVER MS SUSCEPTIBILITY GENES BY MEANS OF SPECIFIC VIRULENCE FACTORS. SUCH GENETIC MANIPULATION HAS BEEN DESCRIBED IN VIRALLY-INFECTED MEMORY B CELLS FROM PATIENTS WITH MS AND ARE THOUGHT TO BE THE MAIN SOURCE OF AUTOREACTIVE IMMUNE RESPONSES. YET, THE ROLE OF EBV INFECTION IN THE NATURAL HISTORY OF MS AND IN THE INITIATION OF NEURODEGENERATION IS EVEN LESS CLEAR. IN THIS NARRATIVE REVIEW, WE WILL DISCUSS THE AVAILABLE EVIDENCE ON THESE TOPICS AND THE POSSIBILITY OF HARNESSING SUCH IMMUNOLOGICAL ALTERATIONS TO UNCOVER PREDICTIVE BIOMARKERS FOR THE ONSET OF MS AND PERHAPS FACILITATE PROGNOSTICATION OF THE CLINICAL COURSE. 2023 11 5770 32 SPECIFIC MOLECULAR SIGNATURES OF NON-TUMOR LIVER TISSUE MAY PREDICT A RISK OF HEPATOCARCINOGENESIS. HEPATOCELLULAR CARCINOMA (HCC) IS ONE OF THE MOST COMMON HUMAN CANCERS AND A MAJOR CAUSE OF CANCER-RELATED DEATH WORLDWIDE. THE BLEAK OUTCOMES OF HCC PATIENTS EVEN AFTER CURATIVE TREATMENT HAVE BEEN, AT LEAST PARTIALLY, ATTRIBUTED TO ITS MULTICENTRIC ORIGIN. THEREFORE, IT IS NECESSARY TO EXAMINE NOT ONLY TUMOR TISSUE BUT ALSO NON-TUMOR LIVER TISSUE TO INVESTIGATE THE MOLECULAR MECHANISMS OPERATING DURING HEPATOCARCINOGENESIS BASED ON THE CONCEPT OF "FIELD CANCERIZATION". SEVERAL STUDIES PREVIOUSLY INVESTIGATED THE ASSOCIATION OF MOLECULAR ALTERATIONS IN NON-TUMOR LIVER TISSUE WITH CLINICAL FEATURES AND PROGNOSIS IN HCC PATIENTS ON A GENOME-WIDE SCALE. IN PARTICULAR, SPECIFIC ALTERATIONS OF DNA METHYLATION PROFILES HAVE BEEN CONFIRMED IN NON-TUMOR LIVER TISSUE. THIS REVIEW FOCUSES ON THE POSSIBLE CLINICAL VALUE OF ARRAY-BASED COMPREHENSIVE ANALYSES OF MOLECULAR ALTERATIONS, ESPECIALLY ABERRANT DNA METHYLATION, IN NON-TUMOR LIVER TISSUE TO CLARIFY THE RISK OF HEPATOCARCINOGENESIS. CARCINOGENETIC RISK ESTIMATION BASED ON SPECIFIC METHYLATION SIGNATURES MAY BE ADVANTAGEOUS FOR CLOSE FOLLOW-UP OF PATIENTS WHO ARE AT HIGH RISK OF HCC DEVELOPMENT. FURTHERMORE, EPIGENETIC THERAPIES FOR PATIENTS WITH CHRONIC LIVER DISEASES MAY BE HELPFUL TO REDUCE THE RISK OF HCC DEVELOPMENT BECAUSE EPIGENETIC ALTERATIONS ARE POTENTIALLY REVERSIBLE, AND THUS PROVIDE PROMISING MOLECULAR TARGETS FOR THERAPEUTIC INTERVENTION. 2014 12 1028 40 CIRCULATING MIRNAS RELATED TO EPITHELIAL-MESENCHYMAL TRANSITIONS (EMT) AS THE NEW MOLECULAR MARKERS IN ENDOMETRIOSIS. ENDOMETRIOSIS IS A CHRONIC GYNECOLOGICAL DISEASE DEFINED BY THE PRESENCE OF ENDOMETRIAL-LIKE TISSUE FOUND OUTSIDE THE UTERUS, MOST COMMONLY IN THE PERITONEAL CAVITY. ENDOMETRIOSIS LESIONS ARE HETEROGENOUS BUT USUALLY CONTAIN ENDOMETRIAL STROMAL CELLS AND EPITHELIAL GLANDS, IMMUNE CELL INFILTRATES AND ARE VASCULARIZED AND INNERVATED BY NERVES. THE COMPLEX ETIOPATHOGENESIS AND HETEROGENITY OF THE CLINICAL SYMPTOMS, AS WELL AS THE LACK OF A SPECIFIC NON-INVASIVE DIAGNOSTIC BIOMARKERS, UNDERLINE THE NEED FOR MORE ADVANCED DIAGNOSTIC TOOLS. UNFORTUNATELY, THE CONTRIBUTION OF ENVIRONMENTAL, HORMONAL AND IMMUNOLOGICAL FACTORS IN THE DISEASE ETIOLOGY IS INSUFFICIENT, AND THE CONTRIBUTION OF GENETIC/EPIGENETIC FACTORS IS STILL FRAGMENTARY. THEREFORE, THERE IS A NEED FOR MORE FOCUSED STUDY ON THE MOLECULAR MECHANISMS OF ENDOMETRIOSIS AND NON-INVASIVE DIAGNOSTIC MONITORING SYSTEMS. MICRORNAS (MIRNAS) DEMONSTRATE HIGH STABILITY AND TISSUE SPECIFICITY AND PLAY A SIGNIFICANT ROLE IN MODULATING A RANGE OF MOLECULAR PATHWAYS, AND HENCE MAY BE SUITABLE DIAGNOSTIC BIOMARKERS FOR THE ORIGIN AND DEVELOPMENT OF ENDOMETRIOSIS. OF THESE, THE MOST FREQUENTLY STUDIED ARE THOSE RELATED TO ENDOMETRIOSIS, INCLUDING THOSE INVOLVED IN EPITHELIAL-MESENCHYMAL TRANSITION (EMT), WHOSE EXPRESSION IS ALTERED IN PLASMA OR ENDOMETRIOTIC LESION BIOPSIES; HOWEVER, THE RESULTS ARE AMBIGUOUS. SPECIFIC MIRNAS EXPRESSED IN ENDOMETRIOSIS MAY SERVE AS DIAGNOSTICS MARKERS WITH PROGNOSTIC VALUE, AND THEY HAVE BEEN PROPOSED AS MOLECULAR TARGETS FOR TREATMENT. THE AIM OF THIS REVIEW IS TO PRESENT SELECTED MIRNAS ASSOCIATED WITH EMT KNOWN TO HAVE EXPERIMENTALLY CONFIRMED SIGNIFICANCE, AND DISCUSS THEIR UTILITY AS BIOMARKERS IN ENDOMETRIOSIS. 2021 13 4316 26 MICRORNAS AS NON-INVASIVE DIAGNOSTIC BIOMARKERS FOR GASTRIC CANCER: CURRENT INSIGHTS AND FUTURE PERSPECTIVES. NON-INVASIVE DIAGNOSTIC BIOMARKERS MAY CONTRIBUTE TO AN EARLY IDENTIFICATION OF GASTRIC CANCER (GC) AND IMPROVE THE CLINICAL MANAGEMENT. UNFORTUNATELY, NO SENSITIVE AND SPECIFIC SCREENING BIOMARKERS ARE AVAILABLE YET AND THE CURRENTLY AVAILABLE APPROACHES ARE LIMITED BY THE NATURE OF THE DISEASE. GC IS A HETEROGENIC DISEASE WITH VARIOUS DISTINCT GENETIC AND EPIGENETIC EVENTS THAT OCCUR DURING THE MULTIFACTORIAL CASCADE OF CARCINOGENESIS. MICRORNAS (MIRNAS) ARE COMMONLY DEREGULATED IN GASTRIC MUCOSA DURING THE HELICOBACTER PYLORI INFECTION AND IN STEPWISE MANNER FROM CHRONIC GASTRITIS, THROUGH PRENEOPLASTIC CONDITIONS SUCH AS ATROPHIC GASTRITIS AND INTESTINAL METAPLASIA, TO EARLY DYSPLASIA AND INVASIVE CANCER. IDENTIFICATION OF MIRNAS IN BLOOD IN 2008 LED TO A GREAT INTEREST ON MIRNA-BASED DIAGNOSTIC, PROGNOSTIC BIOMARKERS IN GC. IN THIS REVIEW, WE PROVIDE THE MOST RECENT SYSTEMATIC REVIEW ON THE EXISTING STUDIES RELATED TO MIRNAS AS DIAGNOSTIC BIOMARKERS FOR GC. HERE, WE SYSTEMATICALLY EVALUATE 75 STUDIES RELATED TO DIFFERENTIAL EXPRESSION OF CIRCULATING MIRNAS IN GC PATIENTS AND PROVIDE NOVEL VIEW ON VARIOUS HETEROGENIC ASPECTS OF THE EXISTING DATA AND SUMMARIZE THE METHODOLOGICAL DIFFERENCES. FINALLY, WE HIGHLIGHT SEVERAL IMPORTANT ASPECTS CRUCIAL TO IMPROVE THE FUTURE TRANSLATIONAL AND CLINICAL RESEARCH IN THE FIELD. 2018 14 5685 30 SHOULD WE INVEST IN BIOLOGICAL AGE PREDICTORS TO TREAT COLORECTAL CANCER IN OLDER ADULTS? COLORECTAL CANCER (CRC) IS A CHRONIC DISEASE OF THE OLD POPULATION WITH SLOW DEVELOPMENT PROGRESSING INTO CLINICAL SIGNS AND SYMPTOMS. BIOLOGICAL AGING IS CHARACTERIZED BY E.G. MITOCHONDRIAL DYSFUNCTION AND EPIGENETIC ALTERATIONS (E.G. METHYLATION) - MECHANISMS THAT ARE ALSO IMPORTANT IN CANCER DEVELOPMENT. FOR CRC, SPECIFIC TYPES OF TUMORS ARE DISTINGUISHABLE BY THEIR METHYLATION PATTERNS AND SEVERAL DETECTION METHODS USING DIFFERENT EPIGENETIC MARKS HAVE BEEN DEVELOPED AS SIGNATURES FOR THE DISEASE. BIOLOGICAL AGE ASSESSED BY DNA METHYLATION PATTERNS FROM BLOOD, I.E. THE EPIGENETIC CLOCK, IS HIGHER IN CRC PATIENTS COMPARED TO CONTROLS, AND MAY BE A TOOL FOR IDENTIFYING INDIVIDUALS AT INCREASED RISK FOR CRC. OTHER TYPES OF BIOMARKERS OF AGING ARE USEFUL TO CALCULATE BIOLOGICAL AGE, SUCH AS METABOLITES, PROTEIN LEVELS, INFLAMMATORY MARKERS AND CLINICAL BIOMARKERS, WHERE COMPOSITE SCORES OF BIOMARKERS HAVE BEEN USED TO ASSESS THE RISK OF CRC AND COLORECTAL ADENOMAS. CLINICAL ASSESSMENTS OF BIOLOGICAL AGING INCLUDES FRAILTY, WHICH IS A GERIATRIC SYNDROME CHARACTERIZED BY INCREASED VULNERABILITY TO ADVERSE OUTCOMES. MORE THAN HALF OF THE CRC PATIENTS ARE ESTIMATED TO BE FRAIL OR PRE-FRAIL, AND THESE INDIVIDUALS ARE AT INCREASED RISK OF POSTOPERATIVE COMPLICATIONS, POORER PROGNOSIS, TREATMENT INTOLERANCE AND DEATH. HENCE, CONSIDERING FRAILTY AS PART OF BIOLOGICAL AGE IN CRC PATIENTS MAY HELP IDENTIFYING THOSE AT NEED OF CLOSE MONITORING. IN SUMMARY, FUTURE SCREENING PROGRAMS FOR CRC MAY MAKE USE OF BIOLOGICAL AGE ASSESSMENTS, E.G. BY EPIGENETIC CLOCK OR COMPOSITE SCORES. MONITORING DISEASE RELAPSE AND TREATMENT RESPONSE SHOULD BE ENHANCED IN FRAIL INDIVIDUALS FOR BETTER PROGNOSIS. 2020 15 1888 30 ENDOMETRIOSIS AND IN VITRO FERTILISATION. THE AIM OF THE PRESENT REVIEW WAS TO DISCUSS A MATTER OF CONCERN IN THE CLINICAL FIELD OF OBSTETRICS/GYNECOLOGY, NAMELY THE POTENCY OF IN VITRO FERTILIZATION (IVF) IN THE MANAGEMENT OF ENDOMETRIOSIS-ASSOCIATED INFERTILITY. ENDOMETRIOSIS IS A MEDICAL CONDITION AFFECTING ONE TENTH OF WOMEN IN THEIR FERTILE YEARS, AND ACCOUNTS FOR UP TO 50% OF INFERTILE WOMEN. THUS, SUCH HIGH PREVALENCE HAS ESTABLISHED THE NECESSITY FOR INVESTIGATING THE EFFECTIVENESS OF AVAILABLE TECHNIQUES IN ERADICATING THE DISEASE AND CONSTRAINING INFERTILITY AS WELL AS THE ACCOMPANYING PAIN SYMPTOMS OF ENDOMETRIOSIS. THE UNDERLYING MECHANISMS CONNECTING ENDOMETRIOSIS WITH LOW FECUNDITY HAVE BEEN EXTENSIVELY STUDIED, BOTH IN TERMS OF GENETIC ALTERATIONS AND EPIGENETIC EVENTS THAT CONTRIBUTE TO THE MANIFESTATION OF AN INFERTILITY PHENOTYPE IN WOMEN WITH THE DISEASE. SEVERAL STUDIES HAVE DEALT WITH THE IMPACT OF IVF IN PREGNANCY RATES (PRS) ON PATIENTS WITH ENDOMETRIOSIS, PARTICULARLY REGARDING WOMEN WHO WISH TO CONCEIVE. RESULTS RETRIEVED FROM STUDIES AND META-ANALYSES DEPICT A DIVERSE PATTERN OF IVF SUCCESS, UNDERLINING THE INVOLVEMENT OF INDIVIDUAL PARAMETERS IN THE CONFIGURATION OF THE FINAL OUTCOME. THE ULTIMATE DECISION ON UNDERGOING IVF TREATMENT SHOULD BE BASED ON OBJECTIVE CRITERIA AND CLINICIANS' EXPERIENCE, CUSTOMIZED ACCORDING TO PATIENTS' INDIVIDUAL NEEDS. 2018 16 777 25 CELL-FREE CIRCULATING EPIGENOMIC SIGNATURES: NON-INVASIVE BIOMARKER FOR CARDIOVASCULAR AND OTHER AGE-RELATED CHRONIC DISEASES. THE BURDEN OF CARDIO-VASCULAR AND OTHER AGE-RELATED NON-COMMUNICABLE DISEASES ARE RAPIDLY INCREASING WORLDWIDE. MAJORITY OF THESE CHRONIC AILMENTS ARE CURABLE, IF DIAGNOSED AT EARLY STAGES. CANDIDATE BIOMARKERS OF EARLY DETECTION ARE THEREFORE ESSENTIAL FOR IDENTIFICATION OF HIGH-RISK INDIVIDUALS, PROMPT AND ACCURATE DISEASE DIAGNOSIS, AND TO MONITOR THERAPEUTIC RESPONSE. THE FUNCTIONAL SIGNIFICANCE OF CIRCULATING NUCLEIC ACIDS THAT RECAPITULATE SPECIFIC DISEASE PROFILES IS NOW WELL ESTABLISHED. BUT SUBTLE CHANGES IN DNA SEQUENCE MAY NOT SOLELY REFLECT THE DIFFERENTIATION OF GENE EXPRESSION PATTERNS OBSERVED IN DIVERSE SET OF DISEASES AS EPIGENETIC PHENOMENA PLAY A LARGER ROLE IN AETIOLOGY AND PATHO-PHYSIOLOGY. UNLIKE GENETIC MARKERS, KNOWLEDGE ABOUT THE DIAGNOSTIC UTILITY OF CIRCULATING EPIGENETIC SIGNATURES: METHYLATED DNA; MICRO RNA AND MODIFIED HISTONES ARE DEFICIENT. CHARACTERIZATION OF THESE NOVEL ENTITIES THROUGH OMICS-BASED MOLECULAR TECHNOLOGIES MIGHT PROMPT DEVELOPMENT OF A RANGE OF LABORATORY-BASED STRATEGIES, THEREBY ACCELERATING THEIR BROADER TRANSLATIONAL PURPOSE FOR EARLY DISEASE DIAGNOSIS, MONITORING THERAPEUTIC RESPONSE AND DRUG RESISTANCE. HOWEVER, LARGEST OPPORTUNITY FOR INNOVATION LIES IN DEVELOPING POINT-OF-CARE TESTS WITH ACCURATE DIAGNOSTIC AND HIGHER PROGNOSTIC SCORE THAT IS APPLICABLE FOR SCREENING OF HIGH-RISK POPULATIONS. 2017 17 2256 28 EPIGENETIC PATHWAYS IN MACROPHAGES EMERGE AS NOVEL TARGETS IN ATHEROSCLEROSIS. ATHEROSCLEROSIS IS A LIPID-DRIVEN CHRONIC INFLAMMATORY DISORDER. MONOCYTES AND MACROPHAGES ARE KEY IMMUNE CELLS IN THE DEVELOPMENT OF DISEASE AND CLINICAL OUTCOME. IT IS BECOMING INCREASINGLY CLEAR THAT EPIGENETIC PATHWAYS GOVERN MANY ASPECTS OF MONOCYTE AND MACROPHAGE DIFFERENTIATION AND ACTIVATION. THE DYNAMIC REGULATION OF EPIGENETIC PATTERNS PROVIDES OPPORTUNITIES TO ALTER DISEASE-ASSOCIATED EPIGENETIC STATES. THEREFORE, PHARMACEUTICAL COMPANIES HAVE EMBRACED THE TARGETING OF EPIGENETIC PROCESSES AS NEW APPROACHES FOR INTERVENTIONS. PARTICULARLY HISTONE DEACETYLASE (HDAC) INHIBITORS AND DNA-METHYLTRANSFERASE INHIBITORS HAVE LONG RECEIVED ATTENTION AND SEVERAL OF THEM HAVE BEEN APPROVED FOR CLINICAL USE IN RELATION TO HEMATOLOGICAL MALIGNANCIES. THE KEY FOCUS IS STILL ON ONCOLOGY, BUT ALZHEIMER'S DISEASE, HUNTINGTON'S DISEASE AND INFLAMMATORY DISORDERS ARE COMING IN FOCUS AS WELL. THESE DEVELOPMENTS RAISE OPPORTUNITIES FOR THE EPIGENETIC TARGETING IN CARDIOVASCULAR DISEASE (CVD). IN THIS REVIEW WE DISCUSS THE EPIGENETIC REGULATION OF THE INFLAMMATORY PATHWAYS IN RELATION TO ATHEROSCLEROSIS WITH A SPECIFIC ATTENTION TO MONOCYTE- AND MACROPHAGE-RELATED PROCESSES. WHAT ARE THE OPPORTUNITIES FOR FUTURE THERAPY OF ATHEROSCLEROSIS BY EPIGENETIC INTERVENTIONS? 2015 18 5702 21 SINGLE-CELL GENOMICS FOR INVESTIGATING PATHOGENESIS OF INFLAMMATORY DISEASES. RECENT TECHNICAL ADVANCES HAVE ENABLED UNBIASED TRANSCRIPTOMIC AND EPIGENETIC ANALYSIS OF EACH CELL, KNOWN AS "SINGLE-CELL ANALYSIS". SINGLE-CELL ANALYSIS HAS A VARIETY OF TECHNICAL APPROACHES TO INVESTIGATE THE STATE OF EACH CELL, INCLUDING MRNA LEVELS (TRANSCRIPTOME), THE IMMUNE REPERTOIRE (IMMUNE REPERTOIRE ANALYSIS), CELL SURFACE PROTEINS (SURFACE PROTEOME ANALYSIS), CHROMATIN ACCESSIBILITY (EPIGENOME), AND ACCORDANCE WITH GENOME VARIANTS (EQTLS; EXPRESSION QUANTITATIVE TRAIT LOCI). AS AN EFFECTIVE TOOL FOR INVESTIGATING ROBUST IMMUNE RESPONSES IN CORONAVIRUS DISEASE 2019 (COVID-19), MANY RESEARCHERS PERFORMED SINGLE-CELL ANALYSIS TO CAPTURE THE DIVERSE, UNBIASED IMMUNE CELL ACTIVATION AND DIFFERENTIATION. DESPITE CHALLENGES ELUCIDATING THE COMPLICATED IMMUNE MICROENVIRONMENTS OF CHRONIC INFLAMMATORY DISEASES USING EXISTING EXPERIMENTAL METHODS, IT IS NOW POSSIBLE TO CAPTURE THE SIMULTANEOUS IMMUNE FEATURES OF DIFFERENT CELL TYPES ACROSS INFLAMED TISSUES USING VARIOUS SINGLE-CELL TOOLS. IN THIS REVIEW, WE INTRODUCE PATIENT-BASED AND EXPERIMENTAL MOUSE MODEL RESEARCH UTILIZING SINGLE-CELL ANALYSES IN THE FIELD OF CHRONIC INFLAMMATORY DISEASES, AS WELL AS MULTI-ORGAN ATLAS TARGETING IMMUNE CELLS. 2023 19 311 29 ALCOHOL AND THE METHYLOME: DESIGN AND ANALYSIS CONSIDERATIONS FOR RESEARCH USING HUMAN SAMPLES. BACKGROUND: A GROWING NUMBER OF STUDIES IN HUMAN SAMPLES HAVE SOUGHT TO DETERMINE WHETHER CHRONIC ALCOHOL USE AND ALCOHOL USE DISORDERS (AUDS) MAY BE ASSOCIATED WITH EPIGENETIC FACTORS, SUCH AS DNA METHYLATION. WE REVIEW THE EXTANT LITERATURE IN LIGHT OF SOME OF THE CHALLENGES THAT CURRENTLY AFFECT THE DESIGN AND INTERPRETATION OF EPIGENETIC RESEARCH IN HUMAN SAMPLES. METHOD: A LITERATURE SEARCH WAS USED TO IDENTIFY STUDIES THAT HAVE EXAMINED DNA METHYLATION IN RELATION TO ALCOHOL USE OR AUDS IN HUMAN SAMPLES (THROUGH JULY 2013). A TOTAL OF 22 STUDIES WERE IDENTIFIED. RESULTS: ASSOCIATIONS WITH QUANTITATIVE OR DIAGNOSTIC PHENOTYPES OF ALCOHOL USE OR AUDS HAVE BEEN REPORTED FOR SEVERAL GENES. HOWEVER, ALL STUDIES TO DATE HAVE RELIED ON RELATIVELY SMALL SAMPLES AND CROSS-SECTIONAL STUDY DESIGNS. ADDITIONALLY, ATTEMPTS TO REPLICATE RESULTS HAVE BEEN RARE. MORE GENERALLY, RESEARCH PROGRESS IS HAMPERED BY SEVERAL ISSUES, INCLUDING LIMITATIONS OF THE TECHNOLOGIES USED TO ASSESS DNA METHYLATION, TISSUE- AND CELL-SPECIFICITY OF METHYLATION PATTERNS, THE DIFFICULTIES OF RELATING OBSERVED METHYLATION DIFFERENCES AT A GIVEN LOCUS TO A FUNCTIONAL EFFECT, AND LIMITED KNOWLEDGE ABOUT THE MOLECULAR MECHANISMS UNDERLYING THE EFFECTS OF ALCOHOL ON DNA METHYLATION. CONCLUSIONS: ALTHOUGH WE SHARE THE OPTIMISM THAT EPIGENETICS MAY LEAD TO NEW INSIGHTS INTO THE ETIOLOGY AND PATHOPHYSIOLOGY OF AUDS, THE METHODOLOGICAL AND SCIENTIFIC CHALLENGES ASSOCIATED WITH CONDUCTING METHYLOMIC RESEARCH IN HUMAN SAMPLES NEED TO BE CAREFULLY CONSIDERED WHEN DESIGNING AND EVALUATING SUCH STUDIES. 2013 20 835 30 CHEMICAL CARCINOGEN MECHANISMS OF ACTION AND IMPLICATIONS FOR TESTING METHODOLOGY. CHEMICAL CARCINOGENS ARE OF TWO DISTINCT TYPES, DNA-REACTIVE AND EPIGENETIC. TESTING METHODOLOGY CAN BE DIRECTED TOWARD DETECTING EFFECTS OF BOTH TYPES OF CARCINOGEN. CARCINOGENS OF THE DNA-REACTIVE TYPE ARE DEFINED BY THE FORMATION OF COVALENTLY BOUND DNA ADDUCTS. THESE CHEMICALS HAVE STRUCTURES THAT YIELD ELECTROPHILIC REACTANTS EITHER DIRECTLY OR AFTER BIOACTIVATION. THESE AGENTS CAUSE GENOMIC ALTERATION IN THE STRUCTURE OR FUNCTION OF DNA IN THE TARGET CELL. IN ADDITION, THESE COMPOUNDS CAN EXERT OTHER CELLULAR AND TISSUE EPIGENETIC EFFECTS, SUCH AS CELL PROLIFERATION AND GROWTH PROMOTION. CARCINOGENS OF THE EPIGENETIC (PARAGENETIC) TYPE, IN CONTRAST, DO NOT REACT WITH DNA, BUT RATHER DISPLAY CELLULAR EFFECTS SUCH AS NEOPLASM GROWTH PROMOTION, CYTOTOXICITY, INHIBITION OF TISSUE GROWTH REGULATION, PEROXISOME PROLIFERATION, ENDOCRINE MODIFICATION, IMMUNOSUPPRESSION AND/OR SUSTAINED TISSUE ISCHEMIA THAT CAN BE THE BASIS FOR INCREASES IN NEOPLASIA. THEIR CHEMICAL STRUCTURE IS SUCH THAT THEY DO NOT GIVE RISE TO A REACTIVE ELECTROPHILE. THE TESTING METHODOLOGIES TO IDENTIFY EITHER TYPE FOLLOW A DECISION POINT APPROACH DESIGNED TO IDENTIFY POTENTIAL CARCINOGENICITY AND YIELD MECHANISTIC INFORMATION ON THE PRODUCTION OF EFFECTS THAT UNDERLIE CARCINOGENICITY. IT HAS 5 STAGES FOCUSING ON THE CHEMICAL STRUCTURE, DNA-REACTIVITY, EPIGENETIC EFFECTS, LIMITED BIOASSAYS AND FINALLY THE APPLICATION OF THE ACCELERATED BIOASSAY (ABA). ABA REQUIRES 40 WEEKS AND APPLIES THE USE OF SENSITIVE MARKERS FOR INDUCTION OF NEOPLASIA IN COMPARISON TO POSITIVE CONTROL COMPOUNDS FOR IMPORTANT ORGANS IN HUMAN CARCINOGENESIS. IT ENABLES DATA ACQUISITION OF THE ENTIRE CARCINOGENIC PROCESS DIRECTED TOWARD DEVELOPING MECHANISTIC INFORMATION. THE ABA HAS THE POTENTIAL TO REPLACE THE CHRONIC BIOASSAY IN RODENTS IN SOME CIRCUMSTANCES AND CAN SERVE AS AN ALTERNATIVE TO A CHRONIC BIOASSAY IN A SECOND SPECIES. 1996