1 4594 169 NATURAL HISTORY AND LONG-TERM CLINICAL COURSE OF CROHN'S DISEASE. CROHN'S DISEASE IS A CHRONIC INFLAMMATORY DISEASE PROCESS INVOLVING DIFFERENT SITES IN THE GASTROINTESTINAL TRACT. OCCASIONALLY, SO-CALLED METASTATIC DISEASE OCCURS IN EXTRA-INTESTINAL SITES. GRANULOMATOUS INFLAMMATION MAY BE DETECTED IN ENDOSCOPIC BIOPSIES OR RESECTED TISSUES. GENETIC, EPIGENETIC AND ENVIRONMENTAL FACTORS APPEAR TO PLAY A ROLE. MULTIPLE SUSCEPTIBILITY GENES HAVE BEEN DESCRIBED IN BOTH FAMILIAL AND NON-FAMILIAL FORMS WHILE THE DISEASE IS PHENOTYPICALLY HETEROGENEOUS WITH A FEMALE PREDOMINANCE. THE DISORDER OCCURS OVER A BROAD AGE SPECTRUM, FROM EARLY CHILDHOOD TO LATE ADULTHOOD. MORE THAN 80% ARE DIAGNOSED BEFORE AGE 40 YEARS USUALLY WITH TERMINAL ILEAL AND COLONIC INVOLVEMENT. PEDIATRIC-ONSET DISEASE IS MORE SEVERE AND MORE EXTENSIVE, USUALLY WITH A HIGHER CHANCE OF UPPER GASTROINTESTINAL TRACT DISEASE, COMPARED TO ADULT-ONSET DISEASE. LONG-TERM STUDIES HAVE SHOWN THAT THE DISORDER MAY EVOLVE WITH TIME INTO MORE COMPLEX DISEASE WITH STRICTURE FORMATION AND PENETRATING DISEASE COMPLICATIONS (I.E., FISTULA, ABSCESS). ALTHOUGH PROLONGED REMISSION MAY OCCUR, DISCRETE PERIODS OF SYMPTOMATIC DISEASE MAY RE-APPEAR OVER MANY DECADES SUGGESTING RECURRENCE OR RE-ACTIVATION OF THIS INFLAMMATORY PROCESS. EVENTUAL DEVELOPMENT OF A CURE WILL LIKELY DEPEND ON IDENTIFICATION OF AN ETIOLOGIC CAUSE AND A FUNDAMENTAL UNDERSTANDING OF ITS PATHOGENESIS. UNTIL NOW, TREATMENT HAS FOCUSED ON REMOVING RISK FACTORS, PARTICULARLY CIGARETTE SMOKING, AND IMPROVING SYMPTOMS. IN CLINICAL TRIALS, CLINICAL REMISSION IS LARGELY DEFINED AS IMPROVED NUMERICAL AND ENDOSCOPIC INDICES FOR "MUCOSAL HEALING". "DEEP REMISSION" IS A CONCEPTUAL, MORE "EXTENDED" GOAL THAT MAY OR MAY NOT ALTER THE LONG-TERM NATURAL HISTORY OF THE DISEASE IN SELECTED PATIENTS, ALBEIT AT A SIGNIFICANT RISK FOR TREATMENT COMPLICATIONS, INCLUDING SERIOUS AND UNUSUAL OPPORTUNISTIC INFECTIONS. 2014 2 5643 37 SEX AND AUTOIMMUNITY: PROPOSED MECHANISMS OF DISEASE ONSET AND SEVERITY. CHRONIC AUTOIMMUNE DISEASES AFFECT 5-10% OF THE POPULATION WORLDWIDE AND ARE LARGELY PREDOMINANT IN WOMEN. SEX HORMONE CHANGES HAVE BEEN WIDELY INVESTIGATED BASED ON CHANGES IN THE CLINICAL PHENOTYPES OBSERVED DURING PREGNANCY AND MENOPAUSE. IT IS KNOWN THAT FEMALES WITH AUTOIMMUNE DISEASES MANIFEST A HIGHER RATE OF CIRCULATING LEUKOCYTES WITH A SINGLE X CHROMOSOME, AND THERE HAVE BEEN SEVERAL REPORTS ON THE ROLE OF X CHROMOSOME GENE DOSAGE THROUGH INACTIVATION OR DUPLICATION IN AUTOIMMUNITY. HOWEVER, IT IS ALSO IMPORTANT NOT TO OVERLOOK MEN WITH AUTOIMMUNE DISEASES, WHO MIGHT MANIFEST A MORE FREQUENT LOSS OF THE Y CHROMOSOME IN CIRCULATING LEUKOCYTES. AREAS COVERED: IN THE PRESENT REVIEW, WE WILL DISCUSS THE CURRENT EVIDENCE SUPPORTING THE MECHANISMS OF FEMALE PREDOMINANCE IN RHEUMATIC DISEASES, BY DISCUSSING THE ROLE OF REPRODUCTIVE HISTORY, SEX HORMONES AND ABNORMALITIES RELATED TO THEM, CLINICAL DIFFERENCES BETWEEN MALE AND FEMALE PATIENTS, AND EPIGENETIC CHANGES THAT HAVE BEEN EVALUATED THROUGH TWIN STUDIES ON GENETIC AND ENVIRONMENTAL CHANGES IN RHEUMATIC PATIENTS. EXPERT OPINION: THE INFLUENCE OF SEX HORMONES AND CHROMOSOMES ON THE FUNCTION OF THE INNATE AND ADAPTIVE IMMUNE SYSTEMS NEEDS TO BE CLARIFIED, TO BETTER UNDERSTAND THE RISK OF AUTOIMMUNE DISEASES, EARLY DIAGNOSTIC TOOLS, AND THERAPEUTIC RESPONSE. 2019 3 938 32 CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) RISK IS MEDIATED BY MULTIPLE ENHANCER VARIANTS WITHIN CLL RISK LOCI. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS THE MOST COMMON ADULT LEUKEMIA IN WESTERN COUNTRIES. IT HAS A STRONG GENETIC BASIS, SHOWING A ~ 8-FOLD INCREASED RISK OF CLL IN FIRST-DEGREE RELATIVES. GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE IDENTIFIED 41 RISK VARIANTS ACROSS 41 LOCI. HOWEVER, FOR A MAJORITY OF THE LOCI, THE FUNCTIONAL VARIANTS AND THE MECHANISMS UNDERLYING THEIR CAUSAL ROLES REMAIN UNDEFINED. HERE, WE EXAMINED THE GENETIC AND EPIGENETIC FEATURES ASSOCIATED WITH 12 INDEX VARIANTS, ALONG WITH ANY CORRELATED (R2 >/= 0.5) VARIANTS, AT THE CLL RISK LOCI LOCATED OUTSIDE OF GENE PROMOTERS. BASED ON PUBLICLY AVAILABLE CHIP-SEQ AND CHROMATIN ACCESSIBILITY DATA AS WELL AS OUR OWN CHIP-SEQ DATA FROM CLL PATIENTS, WE IDENTIFIED SIX CANDIDATE FUNCTIONAL VARIANTS AT SIX LOCI AND AT LEAST TWO CANDIDATE FUNCTIONAL VARIANTS AT EACH OF THE REMAINING SIX LOCI. THE FUNCTIONAL VARIANTS ARE PREDOMINANTLY LOCATED WITHIN ENHANCERS OR SUPER-ENHANCERS, INCLUDING BI-DIRECTIONALLY TRANSCRIBED ENHANCERS, WHICH ARE OFTEN RESTRICTED TO IMMUNE CELL TYPES. FURTHERMORE, WE FOUND THAT, AT 78% OF THE FUNCTIONAL VARIANTS, THE ALTERNATIVE ALLELES ALTERED THE TRANSCRIPTION FACTOR BINDING MOTIFS OR HISTONE MODIFICATIONS, INDICATING THE INVOLVEMENT OF THESE VARIANTS IN THE CHANGE OF LOCAL CHROMATIN STATE. FINALLY, THE ENHANCERS CARRYING FUNCTIONAL VARIANTS PHYSICALLY INTERACTED WITH GENES ENRICHED IN THE TYPE I INTERFERON SIGNALING PATHWAY, APOPTOSIS, OR TP53 NETWORK THAT ARE KNOWN TO PLAY KEY ROLES IN CLL. THESE RESULTS SUPPORT THE REGULATORY ROLES FOR INHERITED NONCODING VARIANTS IN THE PATHOGENESIS OF CLL. 2020 4 2512 41 EPIGENETICS AND PRIMARY BILIARY CIRRHOSIS: A COMPREHENSIVE REVIEW AND IMPLICATIONS FOR AUTOIMMUNITY. PRIMARY BILIARY CIRRHOSIS (PBC) IS A CHRONIC INFLAMMATORY AUTOIMMUNE DISEASE THAT DEVELOPS BASED UPON THE INTERACTION OF GENETIC AND ENVIRONMENTAL FACTORS. RECENT GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE IDENTIFIED DOZENS OF PREDISPOSING VARIANTS INCLUDING HLA, IL12A, AND CTLA4 BUT HAVE BEEN DISAPPOINTED IN IDENTIFYING A "SMOKING GUN." THESE DISCOVERIES HIGHLIGHT THE IMPORTANCE OF THE GENETIC BACKGROUND INVOLVED IN IMMUNOLOGICAL DYSREGULATION. ALTHOUGH CONCORDANCE RATE OF PBC IN MONOZYGOTIC (MZ) TWINS IS AMONG THE HIGHEST REPORTED IN AUTOIMMUNE DISORDERS, INCOMPLETE DISEASE CONCORDANCE IN TWINS ASSOCIATED WITH DIFFERENTIALLY EXPRESSED GENES HAS BEEN DEMONSTRATED. HOWEVER, LITTLE IS UNDERSTOOD ABOUT HOW ENVIRONMENTAL ASPECTS CONTRIBUTE TO THE DISEASE AND WHY MIDDLE-AGED WOMEN ARE MORE SUSCEPTIBLE. AS A RESULT, EPIGENETIC FACTORS, WHICH CONVERT SIGNALS INDICATING ENVIRONMENTAL CHANGES INTO DYNAMIC AND HERITABLE ALTERATIONS OF TRANSCRIPTIONAL POTENTIAL, ARE GETTING INCREASED ATTENTION BY RESEARCHERS IN BOTH BASIC AND CLINICAL STUDIES. AMONG EPIGENETIC MECHANISMS, THE INSTABILITY AND SKEWED GENE EXPRESSION IN THE X CHROMOSOME MAY ACCOUNT FOR THE FEMALE PREPONDERANCE IN PBC. IN ADDITION, TRANSCRIPTIONAL REGULATION OF HISTONE MODIFICATION AND DNA METHYLATION UNDERSCORES POTENTIAL INVOLVEMENT IN DISEASE PATHOGENESIS. HIGH-THROUGHPUT TECHNIQUES ARE BEING USED TO IDENTIFY EPIGENETIC REGULATORS. IN THIS REVIEW, WE ATTEMPT TO OUTLINE RECENT PROGRESS REGARDING EPIGENETICS IN PBC AND OTHER AUTOIMMUNE DISEASES. 2016 5 6631 40 UNDERSTANDING THE MANIFESTATION OF DIABETES IN SUB SAHARAN AFRICA TO INFORM THERAPEUTIC APPROACHES AND PREVENTIVE STRATEGIES: A NARRATIVE REVIEW. BACKGROUND: GLOBALLY, THE BURDEN OF DIABETES MELLITUS HAS INCREASED TO EPIDEMIC PROPORTIONS. ESTIMATES FROM THE INTERNATIONAL DIABETES FEDERATION PREDICT THAT THE GREATEST FUTURE INCREASE IN THE PREVALENCE OF DIABETES MELLITUS WILL OCCUR IN AFRICA. METHODS: THIS ARTICLE REVIEWS LITERATURE ON THE MANIFESTATION OF DIABETES IN ADULT PATIENTS IN SUB-SAHARAN AFRICA HIGHLIGHTING THE DISTINCT PHENOTYPES, PLAUSIBLE EXPLANATIONS FOR THIS UNIQUE MANIFESTATION AND THE CLINICAL SIGNIFICANCE OF COMPREHENSIVELY DEFINING AND UNDERSTANDING THE AFRICAN DIABETES PHENOTYPE. RESULTS: THERE ARE FEW STUDIES ON THE MANIFESTATION OR PHENOTYPE OF DIABETES IN AFRICA. THE LIMITED DATA AVAILABLE SUGGESTS THAT, COMPARED TO THE WESTERN WORLD, THE MAJORITY OF PATIENTS WITH DIABETES IN AFRICA ARE YOUNG AND RELATIVELY LEAN IN BODY SIZE. IN ADDITION, HYPERGLYCAEMIA IN MOST CASES IS CHARACTERISED BY A SIGNIFICANTLY BLUNTED ACUTE FIRST PHASE OF INSULIN SECRETION IN RESPONSE TO AN ORAL OR INTRAVENOUS GLUCOSE LOAD AND PANCREATIC BETA CELL SECRETORY DYSFUNCTION, RATHER THAN PERIPHERAL INSULIN RESISTANCE PREDOMINATES. GENETIC AND ENVIRONMENTAL FACTORS LIKE CHRONIC INFECTIONS/INFLAMMATION, EARLY LIFE MALNUTRITION AND EPIGENETIC MODIFICATIONS ARE THOUGHT TO CONTRIBUTE TO THESE DISTINCT DIFFERENCES IN MANIFESTATION. CONCLUSIONS: WHILE PUBLISHED DATA IS LIMITED, THERE APPEARS TO BE DISTINCT PHENOTYPES OF DIABETES IN SUB-SAHARAN AFRICA. LARGE AND MORE DETAILED STUDIES ARE NEEDED ESPECIALLY AMONG NEWLY DIAGNOSED PATIENTS TO FULLY CHARACTERIZE DIABETES IN THIS REGION. THIS WILL FURTHER IMPROVE THE UNDERSTANDING OF MANIFESTATION OF DIABETES AND GUIDE THE FORMULATION OF OPTIMAL THERAPEUTIC APPROACHES AND PREVENTIVE STRATEGIES OF THE CONDITION ON THE CONTINENT. 2019 6 3021 37 GENETICS AND EPIGENETICS OF PRIMARY SJOGREN SYNDROME: IMPLICATIONS FOR FUTURE THERAPIES. IN PRIMARY SJOGREN SYNDROME (PSS), CHRONIC INFLAMMATION OF EXOCRINE GLANDS RESULTS IN TISSUE DESTRUCTION AND SICCA SYMPTOMS, PRIMARILY OF THE MOUTH AND EYES. FATIGUE, ARTHRALGIA AND MYALGIA ARE ALSO COMMON SYMPTOMS, WHEREAS EXTRAGLANDULAR MANIFESTATIONS THAT INVOLVE THE RESPIRATORY, NERVOUS AND VASCULAR SYSTEMS OCCUR IN A SUBSET OF PATIENTS. THE DISEASE PREDOMINANTLY AFFECTS WOMEN, WITH AN ESTIMATED FEMALE TO MALE RATIO OF 14 TO 1. THE AETIOLOGY OF PSS, HOWEVER, REMAINS INCOMPLETELY UNDERSTOOD, AND EFFECTIVE TREATMENT IS LACKING. LARGE-SCALE GENETIC AND EPIGENETIC INVESTIGATIONS HAVE REVEALED ASSOCIATIONS BETWEEN PSS AND GENES IN BOTH INNATE AND ADAPTIVE IMMUNE PATHWAYS. THE GENETIC VARIANTS MEDIATE CONTEXT-DEPENDENT EFFECTS, AND BOTH SEX AND ENVIRONMENTAL FACTORS CAN INFLUENCE THE OUTCOME. AS SUCH, GENETIC AND EPIGENETIC STUDIES CAN PROVIDE INSIGHT INTO THE DYSREGULATED MOLECULAR MECHANISMS, WHICH IN TURN MIGHT REVEAL NEW THERAPEUTIC POSSIBILITIES. THIS REVIEW DISCUSSES THE GENETIC AND EPIGENETIC FEATURES THAT HAVE BEEN ROBUSTLY CONNECTED WITH PSS, PUTTING THEM INTO THE CONTEXT OF CELLULAR FUNCTION, CARRIER SEX AND ENVIRONMENTAL CHALLENGES. IN ALL, THE OBSERVATIONS POINT TO SEVERAL NOVEL OPPORTUNITIES FOR EARLY DETECTION, TREATMENT DEVELOPMENT AND THE PATHWAY TOWARDS PERSONALIZED MEDICINE. 2023 7 406 31 ANALYSIS OF FIVE CHRONIC INFLAMMATORY DISEASES IDENTIFIES 27 NEW ASSOCIATIONS AND HIGHLIGHTS DISEASE-SPECIFIC PATTERNS AT SHARED LOCI. WE SIMULTANEOUSLY INVESTIGATED THE GENETIC LANDSCAPE OF ANKYLOSING SPONDYLITIS, CROHN'S DISEASE, PSORIASIS, PRIMARY SCLEROSING CHOLANGITIS AND ULCERATIVE COLITIS TO INVESTIGATE PLEIOTROPY AND THE RELATIONSHIP BETWEEN THESE CLINICALLY RELATED DISEASES. USING HIGH-DENSITY GENOTYPE DATA FROM MORE THAN 86,000 INDIVIDUALS OF EUROPEAN ANCESTRY, WE IDENTIFIED 244 INDEPENDENT MULTIDISEASE SIGNALS, INCLUDING 27 NEW GENOME-WIDE SIGNIFICANT SUSCEPTIBILITY LOCI AND 3 UNREPORTED SHARED RISK LOCI. COMPLEX PLEIOTROPY WAS SUPPORTED WHEN CONTRASTING MULTIDISEASE SIGNALS WITH EXPRESSION DATA SETS FROM HUMAN, RAT AND MOUSE TOGETHER WITH EPIGENETIC AND EXPRESSED ENHANCER PROFILES. THE COMORBIDITIES AMONG THE FIVE IMMUNE DISEASES WERE BEST EXPLAINED BY BIOLOGICAL PLEIOTROPY RATHER THAN HETEROGENEITY (A SUBGROUP OF CASES GENETICALLY IDENTICAL TO THOSE WITH ANOTHER DISEASE, POSSIBLY OWING TO DIAGNOSTIC MISCLASSIFICATION, MOLECULAR SUBTYPES OR EXCESSIVE COMORBIDITY). IN PARTICULAR, THE STRONG COMORBIDITY BETWEEN PRIMARY SCLEROSING CHOLANGITIS AND INFLAMMATORY BOWEL DISEASE IS LIKELY THE RESULT OF A UNIQUE DISEASE, WHICH IS GENETICALLY DISTINCT FROM CLASSICAL INFLAMMATORY BOWEL DISEASE PHENOTYPES. 2016 8 5912 28 TARGETED THERAPIES IN SYSTEMIC LUPUS ERYTHEMATOSUS. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC, MULTISYSTEM DISORDER CHARACTERISED BY LOSS OF TOLERANCE TO ENDOGENOUS NUCLEAR ANTIGENS AND AUTOANTIBODY FORMATION. RECENT INSIGHT INTO THE IMMUNOPATHOGENESIS OF LUPUS HAS PROVIDED THE FOUNDATION FOR A NOVEL CLASS OF AGENTS WHICH TARGET SPECIFIC, DYSREGULATED COMPONENTS OF THE IMMUNE SYSTEM. EFFORTS HAVE FOCUSED PREDOMINANTLY ON B-CELL DEPLETING THERAPIES, OF WHICH BELIMUMAB WAS THE FIRST TO DEMONSTRATE SUCCESS IN PHASE III STUDIES AND THUS RECEIVE MARKETING AUTHORISATION. OFF-LABEL PRESCRIBING OF RITUXIMAB IN REFRACTORY CASES IS COMMON AND SUPPORTED BY UNCONTROLLED STUDIES, WHICH SUGGEST A FAVOURABLE RISK:BENEFIT PROFILE. HOWEVER, TWO PLACEBO-CONTROLLED TRIALS FAILED TO SHOW BENEFIT, POSSIBLY BECAUSE OF INAPPROPRIATE PATIENT SELECTION AND OTHER ASPECTS OF TRIAL METHODOLOGY. INHIBITION OF DYSREGULATED CO-STIMULATORY SIGNALS AND CYTOKINES ARE OTHER THERAPEUTIC STRATEGIES CURRENTLY UNDER INVESTIGATION. SOME CANDIDATE DRUGS FAILED TO MEET PRIMARY ENDPOINTS IN EARLY-PHASE CLINICAL TRIALS, YET DEMONSTRATED CLINICAL BENEFIT WHEN ALTERNATIVE ASSESSMENT CRITERIA WERE APPLIED OR SPECIFIC PATIENT SUB-GROUPS ANALYSED. WELL-DESIGNED STUDIES OF GREATER SIZE AND DURATION ARE NEEDED TO CLARIFY THE THERAPEUTIC UTILITY OF THESE AGENTS. FUTURE IMMUNOMODULATORY STRATEGIES TARGETING INTERFERON-ALPHA, T CELLS, OXIDATIVE STRESS AND EPIGENETIC ABNORMALITIES MAY REDUCE MULTISYSTEM DISEASE ACTIVITY AND PROLONG SURVIVAL IN THIS COMPLEX AND HETEROGENEIC DISEASE. 2013 9 6142 35 THE EVALUATION OF CYTOKINES TO HELP ESTABLISH DIAGNOSIS AND GUIDE TREATMENT OF AUTOINFLAMMATORY AND AUTOIMMUNE DISEASES. OUR KNOWLEDGE OF THE ROLE OF CYTOKINES IN PATHOLOGIC CONDITIONS HAS INCREASED CONSIDERABLY WITH THE EMERGENCE OF MOLECULAR AND GENETIC STUDIES, PARTICULARLY IN THE CASE OF AUTOINFLAMMATORY MONOGENIC DISEASES. MANY RARE DISORDERS, CONSIDERED ORPHAN UNTIL RECENTLY, ARE DIRECTLY RELATED TO ABNORMAL GENE REGULATION, AND THE TREATMENT WITH BIOLOGIC AGENTS (BIOLOGICS) TARGETING CYTOKINE RECEPTORS, INTRACELLULAR SIGNALING OR SPECIFIC CYTOKINES IMPROVE THE SYMPTOMS OF AN INCREASING NUMBER OF CHRONIC INFLAMMATORY DISEASES. AS IT IS CURRENTLY IMPOSSIBLE TO SYSTEMATICALLY CONDUCT GENETIC STUDIES FOR ALL PATIENTS WITH AUTOINFLAMMATORY AND AUTOIMMUNE DISEASES, THE EVALUATION OF CYTOKINES CAN BE SEEN AS A SIMPLE, LESS TIME CONSUMING, AND LESS EXPENSIVE ALTERNATIVE. THIS APPROACH COULD BE ESPECIALLY USEFUL WHEN THE DIAGNOSIS OF SYNDROMES OF DISEASES OF UNKNOWN ETIOLOGY REMAINS PROBLEMATIC. THE EVALUATION OF CYTOKINES COULD ALSO HELP AVOID THE CURRENT TRIAL-AND-ERROR APPROACH, WHICH HAS THE DISADVANTAGES OF EXPOSING PATIENTS TO INEFFECTIVE DRUGS WITH POSSIBLE UNNECESSARY SIDE EFFECTS AND PERMANENT ORGAN DAMAGES. IN THIS REVIEW, WE DISCUSS THE VARIOUS POSSIBILITIES, AS WELL AS THE LIMITATIONS OF EVALUATING THE CYTOKINE PROFILES OF PATIENTS SUFFERING FROM AUTOINFLAMMATORY AND AUTOIMMUNE DISEASES, WITH METHODS SUCH AS DIRECT DETECTION OF CYTOKINES IN THE PLASMA/SERUM OR FOLLOWING EX VIVO STIMULATION OF PBMCS LEADING TO THE PRODUCTION OF THEIR CYTOKINE SECRETOME. THE PATIENTS' SECRETOME, COMBINED WITH BIOMARKERS RANGING FROM GENETIC AND EPIGENETIC ANALYSES TO IMMUNOLOGIC BIOMARKERS, MAY HELP NOT ONLY THE DIAGNOSIS BUT ALSO GUIDE THE CHOICE OF BIOLOGICS FOR MORE EFFICIENT AND RAPID TREATMENTS. 2020 10 605 40 BEYOND ENDOMETRIOSIS GENOME-WIDE ASSOCIATION STUDY: FROM GENOMICS TO PHENOMICS TO THE PATIENT. ENDOMETRIOSIS IS A HERITABLE, COMPLEX CHRONIC INFLAMMATORY DISEASE, FOR WHICH MUCH OF THE CAUSAL PATHOGENIC MECHANISM REMAINS UNKNOWN. GENOME-WIDE ASSOCIATION STUDIES (GWAS) TO DATE HAVE IDENTIFIED 12 SINGLE NUCLEOTIDE POLYMORPHISMS AT 10 INDEPENDENT GENETIC LOCI ASSOCIATED WITH ENDOMETRIOSIS. MOST OF THESE WERE MORE STRONGLY ASSOCIATED WITH REVISED AMERICAN FERTILITY SOCIETY STAGE III/IV, RATHER THAN STAGE I/II. THE LOCI ARE ALMOST ALL LOCATED IN INTERGENIC REGIONS THAT ARE KNOWN TO PLAY A ROLE IN THE REGULATION OF EXPRESSION OF TARGET GENES YET TO BE IDENTIFIED. TO IDENTIFY THE TARGET GENES AND PATHWAYS PERTURBED BY THE IMPLICATED VARIANTS, STUDIES ARE REQUIRED INVOLVING FUNCTIONAL GENOMIC ANNOTATION OF THE SURROUNDING CHROMOSOMAL REGIONS, IN TERMS OF TRANSCRIPTION FACTOR BINDING, EPIGENETIC MODIFICATION (E.G., DNA METHYLATION AND HISTONE MODIFICATION) SITES, AS WELL AS THEIR CORRELATION WITH RNA TRANSCRIPTION. THESE STUDIES NEED TO BE CONDUCTED IN TISSUE TYPES RELEVANT TO ENDOMETRIOSIS-IN PARTICULAR, ENDOMETRIUM. IN ADDITION, TO ALLOW BIOLOGICALLY AND CLINICALLY RELEVANT INTERPRETATION OF MOLECULAR PROFILING DATA, THEY NEED TO BE COMBINED AND CORRELATED WITH DETAILED, SYSTEMATICALLY COLLECTED PHENOTYPIC INFORMATION (SURGICAL AND CLINICAL). THE WERF ENDOMETRIOSIS PHENOME AND BIOBANKING HARMONISATION PROJECT IS A GLOBAL STANDARDIZATION INITIATIVE THAT HAS PRODUCED CONSENSUS DATA AND SAMPLE COLLECTION PROTOCOLS FOR ENDOMETRIOSIS RESEARCH. THESE NOW PAVE THE WAY FOR COLLABORATIVE STUDIES INTEGRATING PHENOMIC WITH GENOMIC DATA, TO IDENTIFY INFORMATIVE SUBTYPES OF ENDOMETRIOSIS THAT WILL ENHANCE UNDERSTANDING OF THE PATHOGENIC MECHANISMS OF THE DISEASE AND DISCOVERY OF NOVEL, TARGETED TREATMENTS. 2016 11 2552 35 EPIGENETICS IN PRIMARY SJOGREN'S SYNDROME. PRIMARY SJOGREN'S SYNDROME (SJS) IS A CHRONIC AND SYSTEMIC AUTOIMMUNE EPITHELITIS WITH PREDOMINANT FEMALE INCIDENCE, WHICH IS CHARACTERIZED BY EXOCRINE GLAND DYSFUNCTION. INCOMPLETELY UNDERSTOOD, THE ETIOLOGY OF SJS IS MULTI-FACTORIAL AND EVIDENCE IS GROWING TO CONSIDER THAT EPIGENETIC FACTORS ARE PLAYING A CRUCIAL ROLE IN ITS DEVELOPMENT. INDEPENDENT FROM DNA SEQUENCE MUTATIONS, EPIGENETICS IS DESCRIBED AS INHERITABLE AND REVERSIBLE PROCESSES THAT MODIFY GENE EXPRESSION. EPIGENETIC MODIFICATIONS REPORTED IN MINOR SALIVARY GLAND AND LYMPHOCYTES FROM SJS PATIENTS ARE RELATED TO (I) AN ABNORMAL DNA METHYLATION PROCESS INDUCING IN TURN DEFECTIVE CONTROL OF NORMALLY REPRESSED GENES INVOLVING SUCH MATTERS AS AUTOANTIGENS, RETROTRANSPOSONS, AND THE X CHROMOSOME IN WOMEN; (II) ALTERED NUCLEOSOME POSITIONING ASSOCIATED WITH AUTOANTIBODY PRODUCTION; AND (III) ALTERED CONTROL OF MICRORNA. RESULTS FROM EPIGENOME-WIDE ASSOCIATION STUDIES HAVE FURTHER REVEALED THE IMPORTANCE OF THE INTERFERON PATHWAY IN DISEASE PROGRESSION, THE CALCIUM SIGNALING PATHWAY FOR CONTROLLING FLUID SECRETIONS, AND A CELL-SPECIFIC CROSS TALK WITH RISK FACTORS ASSOCIATED WITH SJS. IMPORTANTLY, EPIGENETIC MODIFICATIONS ARE REVERSIBLE THUS OPENING OPPORTUNITIES FOR THERAPEUTIC PROCEDURES IN THIS CURRENTLY INCURABLE DISEASE. 2020 12 3027 37 GENETICS OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE. CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS A COMPLEX DISEASE WITH MULTIFACTORIAL BACKGROUND, BASED ON THE INTERACTION OF ENVIRONMENTAL AND GENETIC FACTORS. ENVIRONMENTAL FACTORS ARE CLEARLY RELATED TO THE DEVELOPMENT OF THE DISEASE. HOWEVER, FAMILY AND TWIN STUDIES SUGGESTED GENETICS FACTORS TO BE ONE OF THE IMPORTANT DETERMINANTS FOR THE DEVELOPMENT OF COPD. DIFFERENT APPROACHES HAVE BEEN USED TO IDENTIFY GENES OF INTEREST. GENOMEWIDE LINKAGE ANALYSIS FOUND AREAS OF INTEREST ON DIFFERENT CHROMOSOMES, WITH SOME GENES LOCATED IN THIS REGIONS BEING IDENTIFIED AND REPLICATED AS SUSCEPTIBILITY GENES. NUMEROUS OF CANDIDATE GENES THAT COULD BE LINKED TO DISEASE PATHOGENESIS HAVE BEEN IMPLICATED IN COPD GENETICS. HOWEVER, THE CANDIDATE GENE APPROACH IS OFTEN LIMITED BY INCONSISTENT RESULTS IN OTHER STUDY POPULATIONS. RECENTLY, A COMBINATION OF DIFFERENT METHODS IS USED GIVING MORE EVIDENCE FOR SOME CANDIDATE GENES, INCLUDING TGFBETA-1, SURFACTANT, SERPINE2 AND MICROSOMAL EPOXIDE HYDROLASE. IN THE FUTURE ONGOING EXACT PHENOTYPE DEFINITION, COMBINATION OF SEVERAL APPROACHES, GENOME-WIDE ASSOCIATION STUDIES AND ANIMAL MODEL GENETICS WILL LEAD TO NEW INSIGHTS INTO THE GENETICS OF COPD, WITH EPIGENETIC FACTORS NEEDS TO BE FURTHER INVESTIGATED AND CONSIDERED IN CONCERT WITH GENETIC FINDINGS. 2007 13 3934 50 LIVER TUMOR INDUCTION. THE SIGNIFICANCE OF THE DEVELOPMENT OF NODULAR LIVER LESIONS IN RODENTS FOLLOWING THE ADMINISTRATION OF TEST AGENTS RAISES SEVERAL QUESTIONS WHICH COULD BE PLACED IN ONE OF TWO GENERAL CATEGORIES: DIAGNOSTIC AND INTERPRETATIONAL. FROM A DIAGNOSTIC POINT OF VIEW, THE PROPER CLASSIFICATION OF LIVER TUMORS INTO A BENIGN AND MALIGNANT CATEGORY HAS TO BE BASED ON THE DIRECT CORRELATION BETWEEN THE MORPHOLOGY AND THE BIOLOGIC BEHAVIOR OF THE LESIONS. THEREFORE, EXTREME CARE SHOULD BE TAKEN TO SEPARATE THE MALIGNANT TUMORS FROM THE BENIGN AND THE BENIGN NEOPLASIA FROM THE HYPERPLASIA. THE SUBSTITUTION OF THE TERM "NEOPLASTIC NODULE" FOR HYPERPLASTIC NODULE IN RATS IS MISLEADING. MOST OF THESE NODULES, WHEN INDUCED UNDER SPECIAL EXPERIMENTAL CONDITIONS, MAY REGRESS OR REMODEL AND THUS THEY ARE NOT NEOPLASTIC IN NATURE. CHRONIC CARCINOGENICITY BIOASSAYS SHOULD INCLUDE "STOP" TYPE OF TREATMENT LEAVING ENOUGH OF THE OBSERVATIONAL TIME TO ESTABLISH THE FATE OF INDUCED NODULAR LESIONS. THE INDUCTION OF HISTOCHEMICALLY CHANGED FOCI CAN SERVE ONLY AS AN INDICATION OF POTENTIAL HEPATOCARCINOGENICITY AND SHOULD NOT BE EQUATED WITH THE INDUCTION OF BONA FIDE CANCER. THE BIOLOGIC INTERPRETATION OF NODULAR LIVER LESIONS, ESPECIALLY IN MICE, NEEDS FURTHER SCRUTINY BECAUSE THESE LESIONS HAVE A TENDENCY TO DEVELOP SPONTANEOUSLY WITH HIGH INCIDENCE IN SOME STRAINS. THIS CHARACTERISTIC THEN RAISES THE QUESTION AS TO THE MECHANISM BY WHICH VARIOUS AGENTS AUGMENT AND/OR ACCELERATE THE DEVELOPMENT OF SUCH TUMORS. IS THIS ACTION PRIMARILY PROMOTING OR INITIATING IN NATURE OR DOES IT REPRESENT THE INDUCTION OF TUMORS DE NOVO? THE ANSWER TO THIS DILEMMA MAY HAVE A DECISIVE BEARING ON CARCINOGENIC RISK ASSESSMENT AND THE TYPE OF REGULATORY ACTION, SINCE THE PROMOTING AGENTS POSSESS A THRESHOLD EFFECT AND THE PROMOTED CHANGES MAY REGRESS FOLLOWING WITHDRAWAL OF TREATMENT. THE INTERPRETATION OF HEPATOCARCINOGENESIS IS FURTHER COMPLICATED BY THE FACT THAT SEVERAL FACTORS, SUCH AS SEX HORMONAL ENVIRONMENT, INCREASED MITOTIC ACTIVITY FOLLOWING AN EXCESSIVE LOSS OF PARENCHYMAL CELLS, DEGREE OF CALORIC INTAKE, ENZYMATIC COMPLEMENT, AND ANIMALS' AGE AT THE TIME OF THE EXPOSURE TO A TEST AGENT, MAY INFLUENCE THE OUTCOME OF LIVER TUMOR DEVELOPMENT BY MODULATING "INITIATION" AND/OR "PROMOTION" OF CARCINOGENESIS. BROAD FLUCTUATION IN THE HISTORIC INCIDENCE OF LIVER TUMORS FURTHER COMPOUNDS THE COMPLEXITY OF THE PROPER BIOASSAY INTERPRETATION. THE SPECIFICALLY DESIGNED EXPERIMENTS MAY HAVE THE OBJECTIVE TO EXPLORE PREDOMINANTLY THE INITIATING OR PROMOTING EFFECTS OF THE AGENT. SUCH PROTOCOLS SHOULD BE USED WHENEVER NECESSARY TO DIFFERENTIATE BETWEEN THESE TWO MECHANISMS OF ACTION. IN THE CAUCASIANS, THE "SPONTANEOUS" DEVELOPMENT OF THE PRIMARY HEPATOCELLULAR TUMORS IS RARE. THE MAJORITY OF THESE TUMORS ARE MALIGNANT AND RAPIDLY FATAL. ACCORDING TO SOME HUMAN PATHOLOGISTS, THE BENIGN VARIETY OF LIVER TUMORS IS RARE AND IT DOES NOT REPRESENT NECESSARILY A PREMALIGNANT STAGE IN TUMOR DEVELOPMENT. CARCINOMA OF THE LIVER MAY OCCUR IN INFANCY, ESPECIALLY IN MALES BEFORE THE AGE OF 2 YEARS. THIS SUGGESTS A GENETIC CAUSATION OR CARCINOGENIC EXPOSURE IN UTERO. ONE OF THE GEOGRAPHIC FACTORS WHICH SIGNIFICANTLY ENHANCES THE INCIDENCE OF HEPATOCELLULAR CARCINOMA IN HUMANS IS EXPOSURE TO AFLATOXIN B(1) WHICH IS APPARENTLY POTENTIATED BY CONCURRENT LIVER CIRRHOSIS. BECAUSE MANY MORE AGENTS HAVE BEEN FOUND TO BE HEPATOCARCINOGENIC IN MICE AND RATS THAN IN MEN, A QUESTION ARISES AS TO THE DIRECT RELEVANCE OF RODENT STUDIES TO HUMANS. A BALANCED ASSESSMENT OF THE CARCINOGENICITY OF THE AGENT COULD ONLY BE REACHED IN CONSIDERING BOTH THE PHARMACOKINETICS AND THE DEVELOPMENT OF MALIGNANT NEOPLASIA IN OTHER ORGANS. IN THE CASE OF POSITIVE CARCINOGENICITY ASSESSMENT, THE OUTCOME OF THE MUTAGENICITY BIOASSAYS CAN SUGGEST GENIC (GENOTOXIC) OR PARAGENIC (EPIGENETIC) MODE OF ACTION IN MAMMALIAN SYSTEMS. 1982 14 6050 30 THE CONTRIBUTION OF EPIGENETICS IN SJOGREN'S SYNDROME. SJOGREN'S SYNDROME (SS) IS A CHRONIC AUTOIMMUNE EPITHELITIS THAT COMBINES EXOCRINE GLAND DYSFUNCTIONS AND LYMPHOCYTIC INFILTRATIONS. WHILE THE PATHOGENESIS OF SS REMAINS UNCLEAR, ITS ETIOLOGY IS MULTIFUNCTIONAL AND INCLUDES A COMBINATION OF GENETIC PREDISPOSITIONS, ENVIRONMENTAL FACTORS, AND EPIGENETIC FACTORS. RECENTLY, INTEREST HAS GROWN IN THE INVOLVEMENT OF EPIGENETICS IN AUTOIMMUNE DISEASES. EPIGENETICS IS DEFINED AS CHANGES IN GENE EXPRESSION, THAT ARE INHERITABLE AND THAT DO NOT ENTAIL CHANGES IN THE DNA SEQUENCE. IN SS, SEVERAL EPIGENETIC MECHANISMS ARE DEFECTIVE INCLUDING DNA DEMETHYLATION THAT PREDOMINATES IN EPITHELIAL CELLS, AN ABNORMAL EXPRESSION OF MICRORNAS, AND ABNORMAL CHROMATIN POSITIONING-ASSOCIATED WITH AUTOANTIBODY PRODUCTION. LAST BUT NOT LEAST, EPIGENETIC MODIFICATIONS ARE REVERSIBLE AS OBSERVED IN MINOR SALIVARY GLANDS FROM SS PATIENTS AFTER B CELL DEPLETION USING RITUXIMAB. THUS EPIGENETIC FINDINGS IN SS OPEN NEW PERSPECTIVES FOR THERAPEUTIC APPROACHES AS WELL AS THE POSSIBLE IDENTIFICATION OF NEW BIOMARKERS. 2014 15 1481 31 DIVERSITY OF GENOME PROFILES IN MALIGNANT LYMPHOMA. CHARACTERISTIC CHROMOSOME TRANSLOCATIONS ARE ASSOCIATED WITH SPECIFIC DISEASE ENTITIES, AND ARE KNOWN TO PLAY A PIVOTAL ROLE IN LYMPHOMA DEVELOPMENT. CHROMOSOME TRANSLOCATION ALONE, HOWEVER, IS NOT SUFFICIENT TO PRODUCE TUMORS. FACTORS INCLUDING THE MICROENVIRONMENT AND EPIGENETIC AND GENETIC ALTERATIONS OTHER THAN CHROMOSOME TRANSLOCATIONS HAVE BEEN SHOWN TO PLAY A ROLE IN LYMPHOMA DEVELOPMENT. FOLLICULAR LYMPHOMA CELLS PROLIFERATE IN CLOSE CONTACT WITH FOLLICULAR DENDRITIC CELLS. MUCOSA-ASSOCIATED LYMPHOID TISSUE (MALT) LYMPHOMA CELLS PROLIFERATE AT THE MARGINAL ZONE AREA OF REACTIVE FOLLICLES WHICH ARE FORMED BY PRECEDING CHRONIC INFLAMMATION. THE IMPORTANCE OF GENETIC ALTERATIONS OTHER THAN CHROMOSOME TRANSLOCATION HAS BEEN RECOGNIZED SINCE THE INTRODUCTION OF ARRAY COMPARATIVE GENOMIC HYBRIDIZATION (ARRAY CGH). VARIATIONS IN THE GENOMIC PROFILE AMONG PATIENTS WITH THE SAME DISEASE ENTITY HAVE BEEN FOUND BY ARRAY CGH ANALYSES. THESE VARIATIONS INDICATE THAT MULTIPLE GENETIC PATHWAYS LEADING TO THE DEVELOPMENT OF LYMPHOMAS MAY EXIST AND HENCE RESULT IN THE VARIABLE CLINICOPATHOLOGICAL FEATURES OBSERVED. 2010 16 3026 38 GENETICS OF BEHCET'S DISEASE: FUNCTIONAL GENETIC ANALYSIS AND ESTIMATING DISEASE HERITABILITY. BEHCET'S DISEASE IS A CHRONIC MULTISYSTEMIC INFLAMMATORY DISORDER CHARACTERIZED BY RECURRENT ORAL AND GENITAL ULCERS. ALTHOUGH ITS ETIOLOGY REMAINS UNCLEAR, IT IS THOUGHT THAT BOTH GENETIC AND ENVIRONMENTAL FACTORS CONTRIBUTE TO THE ONSET AND PROGRESSION OF BEHCET'S DISEASE. HERE, WE PROVIDE AN UPDATED VIEW OF THE GENETIC LANDSCAPE AND ARCHITECTURE OF BEHCET'S DISEASE. LARGE-SCALE GENETIC STUDIES PERFORMED TO DATE REVEALED 21 GENETIC SUSCEPTIBILITY LOCI ASSOCIATED WITH THE DISEASE AT A GWAS LEVEL OF SIGNIFICANCE (P-VALUE = 5 X 10(-8)). WE PERFORMED EPIGENETIC PATTERN ENRICHMENT ANALYSIS IN BEHCET'S DISEASE ASSOCIATED LOCI, PROVIDING NEW INSIGHTS INTO THE MOLECULAR MECHANISMS UNDERLYING ITS PATHOPHYSIOLOGY. OUR DATA SUGGEST THE CRUCIAL INVOLVEMENT OF SEVERAL IMMUNE CELL TYPES, INCLUDING NATURAL KILLER CELLS, MONOCYTES, AND B CELLS IN THE PATHOGENESIS OF THE DISEASE. PATHWAY ENRICHMENT ANALYSIS IDENTIFIED IMPORTANT BIOLOGICAL PROCESSES INVOLVED. USING LARGE-SCALE GENETIC DATA AVAILABLE FROM ~200 IMMUNE-RELATED LOCI (IMMUNOCHIP), WE ESTIMATE BEHCET'S DISEASE HERITABILITY TO BE AT LEAST 16%. WE FURTHER USED THE SAME APPROACH TO ESTIMATE THE HERITABILITY EXPLAINED BY THE KNOWN BEHCET'S DISEASE-ASSOCIATED LOCI, SUGGESTING THAT THEY EXPLAIN ~ 60% OF THE GENETIC COMPONENT UNDERLYING BEHCET'S DISEASE. THESE RESULTS INDICATE A SIGNIFICANT ROLE OF NON-GENETIC FACTORS IN CAUSING BEHCET'S DISEASE AND THAT ADDITIONAL GENETIC VARIATION INFLUENCING THE RISK OF BEHCET'S DISEASE REMAINS TO BE IDENTIFIED. FINALLY, WE CALCULATED A CUMULATIVE GENETIC RISK SCORE ACROSS POPULATIONS REINFORCING THE LINK BETWEEN GEOGRAPHIC VARIATIONS IN DISEASE PREVALENCE WITH ITS GENETIC COMPONENT. 2021 17 3743 53 INSIGHTS FROM GENOMIC STUDIES ON THE ROLE OF SEX STEROIDS IN THE AETIOLOGY OF ENDOMETRIOSIS. ENDOMETRIOSIS IS A CHRONIC NEURO-INFLAMMATORY DISORDER THE DEFINING FEATURE OF WHICH IS THE GROWTH OF TISSUE (LESIONS) THAT RESEMBLES THE ENDOMETRIUM OUTSIDE THE UTERUS. ESTIMATES OF PREVALENCE QUOTE RATES OF ~10% OF WOMEN OF REPRODUCTIVE AGE, EQUATING TO AT LEAST 190 MILLION WOMEN WORLD-WIDE. GENETIC, HORMONAL AND IMMUNOLOGICAL FACTORS HAVE ALL BEEN PROPOSED AS CONTRIBUTING TO RISK FACTORS ASSOCIATED WITH THE DEVELOPMENT OF LESIONS. TWIN STUDIES REPORT THE HERITABLE COMPONENT OF ENDOMETRIOSIS AS ~50%. GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE IDENTIFIED SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) THAT APPEAR OVER-REPRESENTED IN PATIENTS WITH ENDOMETRIOSIS, PARTICULARLY THOSE WITH MORE EXTENSIVE DISEASE (STAGE III/IV). IN DIFFERENT SAMPLE POPULATIONS, THERE HAS BEEN REPLICATION OF SNPS NEAR GENES INVOLVED IN OESTROGEN AND OTHER STEROID REGULATED PATHWAYS INCLUDING ESR1 (OESTROGEN RECEPTOR ALPHA), GREB1, HOXA10, WNT4 AND MAPK KINASE SIGNALLING. COMPARISONS WITH GWAS CONDUCTED ON OTHER PATIENT COHORTS HAVE FOUND LINKS WITH REPRODUCTIVE TRAITS (AGE AT MENARCHE) AND DISORDERS (FIBROIDS, ENDOMETRIAL AND OVARIAN CANCER) AND COMMON CO-MORBIDITIES (MIGRAINE, DEPRESSION, ASTHMA). IN SUMMARY, GENETIC ANALYSES HAVE PROVIDED NEW INSIGHTS INTO THE HORMONE-REGULATED PATHWAYS THAT MAY CONTRIBUTE TO INCREASED RISK OF DEVELOPING ENDOMETRIOSIS SOME OF WHICH MAY ACT IN EARLY LIFE. NEW STUDIES ARE NEEDED TO CLARIFY THE RELATIONSHIP BETWEEN THE MANY SNPS IDENTIFIED, THE GENES THAT THEY REGULATE AND THEIR CONTRIBUTION(S) TO DEVELOPMENT OF DIFFERENT FORMS OF ENDOMETRIOSIS. WE HOPE THAT MORE ADVANCED METHODS ALLOWING INTEGRATION BETWEEN GWAS, EPIGENETIC AND TISSUE EXPRESSION DATA WILL IMPROVE RISK ANALYSIS AND REDUCE DIAGNOSITIC DELAY. LAY SUMMARY: ENDOMETRIOSIS IS A DEBILITATING REPRODUCTIVE DISORDER AFFECTING ~10% OF REPRODUCTIVE-AGE WOMEN, AND THOSE ASSIGNED FEMALE AT BIRTH, WHICH CAUSES A RANGE OF SYMPTOMS INCLUDING CHRONIC PAIN AND INFERTILITY. THE REASON WHY SOME, BUT NOT ALL THESE INDIVIDUALS, DEVELOP THE LESIONS THAT CHARACTERISE THE DISEASE ARE POORLY UNDERSTOOD, BUT RECENTLY ATTENTION HAS FOCUSED ON GENETIC RISK FACTORS TO EXPLAIN WHY THE INCIDENCE IS HIGHER IN SOME FAMILIES. STUDIES ON LARGE COHORTS OF PATIENTS WITH COMPARISON OF THEIR DNA TO WOMEN WITHOUT ENDOMETRIOSIS OR WITH OTHER DISORDERS HAVE DOCUMENTED CHANGES IN GENES ASSOCIATED WITH STEROID HORMONE PRODUCTION OR ACTION. THE RESULTS PROVIDE FURTHER EVIDENCE THAT ENDOMETRIOSIS SHARES GENETIC RISK FACTORS WITH OTHER DISORDERS OF THE REPRODUCTIVE SYSTEM AND A PLATFORM FOR NEW IDEAS RELATED TO RISK, BIOMARKERS AND THERAPIES. 2022 18 3012 35 GENETICS AND EPIGENETICS IN THE PATHOGENESIS OF PRIMARY BILIARY CHOLANGITIS. PRIMARY BILIARY CHOLANGITIS (PBC) IS A CHRONIC, SLOWLY PROGRESSIVE CHOLESTATIC AUTOIMMUNE LIVER DISEASE PREDOMINANTLY AFFLICTING WOMEN. PBC IS CHARACTERIZED BY THE PRESENCE OF DISEASE-SPECIFIC ANTIMITOCHONDRIAL ANTIBODIES AND THE HISTOLOGICAL DESTRUCTION OF INTRAHEPATIC BILE DUCTS, WHICH EVENTUALLY LEAD TO CIRRHOSIS AND HEPATIC FAILURE. FORTUNATELY, URSODEOXYCHOLIC ACID THERAPY HAS IMPROVED THE OUTCOME OF THE VAST MAJORITY OF PBC CASES. ALTHOUGH THE ETIOLOGY OF PBC HAS NOT YET BEEN ELUCIDATED, HUMAN LEUKOCYTE ANTIGEN (HLA) CLASS II ALLELES HAVE BEEN CONSISTENTLY ASSOCIATED WITH DISEASE ONSET FOR DECADES. PBC PATIENTS MAY ALSO HAVE GENETICALLY DETERMINED RISK FACTORS IN NON-HLA REGIONS. MEANWHILE, EXPOSURE TO ENVIRONMENTAL FACTORS, SUCH AS INFECTIOUS DISEASES AND HARMFUL CHEMICALS, CAN PRODUCE EPIGENETIC ALTERATIONS IN SOME INDIVIDUALS AND SUBSEQUENT PBC ONSET. IN THIS REVIEW, WE DESCRIBE THE INFLUENCE OF HLA ALLELES AND OTHER GENE POLYMORPHISMS ON PBC ALONG WITH THE RESULTS OF GENOME-WIDE ASSOCIATION STUDIES ON THIS DISEASE AND ITS FUTURE PROSPECTS IN TERMS OF EPIGENETICS. 2018 19 1599 39 DNA METHYLATION SIGNATURE OF CHILDHOOD CHRONIC PHYSICAL AGGRESSION IN T CELLS OF BOTH MEN AND WOMEN. BACKGROUND: HIGH FREQUENCY OF PHYSICAL AGGRESSION IS THE CENTRAL FEATURE OF SEVERE CONDUCT DISORDER AND IS ASSOCIATED WITH A WIDE RANGE OF SOCIAL, MENTAL AND PHYSICAL HEALTH PROBLEMS. WE HAVE PREVIOUSLY TESTED THE HYPOTHESIS THAT DIFFERENTIAL DNA METHYLATION SIGNATURES IN PERIPHERAL T CELLS ARE ASSOCIATED WITH A CHRONIC AGGRESSION TRAJECTORY IN MALES. DESPITE THE FACT THAT SEX DIFFERENCES APPEAR TO PLAY A PIVOTAL ROLE IN DETERMINING THE DEVELOPMENT, MAGNITUDE AND FREQUENCY OF AGGRESSION, MOST OF PREVIOUS STUDIES FOCUSED ON MALES, SO LITTLE IS KNOWN ABOUT FEMALE CHRONIC PHYSICAL AGGRESSION. WE THEREFORE TESTED HERE WHETHER OR NOT THERE IS A SIGNATURE OF PHYSICAL AGGRESSION IN FEMALE DNA METHYLATION AND, IF THERE IS, HOW IT RELATES TO THE SIGNATURE OBSERVED IN MALES. METHODOLOGY/PRINCIPAL FINDINGS: METHYLATION PROFILES WERE CREATED USING THE METHOD OF METHYLATED DNA IMMUNOPRECIPITATION (MEDIP) FOLLOWED BY MICROARRAY HYBRIDIZATION AND STATISTICAL AND BIOINFORMATIC ANALYSES ON T CELL DNA OBTAINED FROM ADULT WOMEN WHO WERE FOUND TO BE ON A CHRONIC PHYSICAL AGGRESSION TRAJECTORY (CPA) BETWEEN 6 AND 12 YEARS OF AGE COMPARED TO WOMEN WHO FOLLOWED A NORMAL PHYSICAL AGGRESSION TRAJECTORY. WE CONFIRMED THE EXISTENCE OF A WELL-DEFINED, GENOME-WIDE SIGNATURE OF DNA METHYLATION ASSOCIATED WITH CHRONIC PHYSICAL AGGRESSION IN THE PERIPHERAL T CELLS OF ADULT FEMALES THAT INCLUDES MANY OF THE GENES SIMILARLY ASSOCIATED WITH PHYSICAL AGGRESSION IN THE SAME CELL TYPES OF ADULT MALES. CONCLUSIONS: THIS STUDY IN A SMALL NUMBER OF WOMEN PRESENTS PRELIMINARY EVIDENCE FOR A GENOME-WIDE VARIATION IN PROMOTER DNA METHYLATION THAT ASSOCIATES WITH CPA IN WOMEN THAT WARRANT LARGER STUDIES FOR FURTHER VERIFICATION. A SIGNIFICANT PROPORTION OF THESE ASSOCIATIONS WERE PREVIOUSLY OBSERVED IN MEN WITH CPA SUPPORTING THE HYPOTHESIS THAT THE EPIGENETIC SIGNATURE OF EARLY LIFE AGGRESSION IN FEMALES IS COMPOSED OF A COMPONENT SPECIFIC TO FEMALES AND ANOTHER COMMON TO BOTH MALES AND FEMALES. 2014 20 492 33 ASSESSMENT OF HIV-1 INTEGRATION IN TISSUES AND SUBSETS ACROSS INFECTION STAGES. THE INTEGRATION OF HIV DNA INTO THE HOST GENOME CONTRIBUTES TO LIFELONG INFECTION IN MOST INDIVIDUALS. FEW STUDIES HAVE EXAMINED INTEGRATION IN LYMPHOID TISSUE, WHERE HIV PREDOMINANTLY PERSISTS BEFORE AND AFTER ANTIRETROVIRAL TREATMENT (ART). OF PARTICULAR INTEREST IS WHETHER INTEGRATION SITE DISTRIBUTIONS DIFFER BETWEEN INFECTION STAGES WITH PAIRED BLOOD AND TISSUE COMPARISONS. HERE, WE PROFILED HIV INTEGRATION SITE DISTRIBUTIONS IN SORTED MEMORY, TISSUE-RESIDENT, AND/OR FOLLICULAR HELPER CD4+ T CELL SUBSETS FROM PAIRED BLOOD AND LYMPHOID TISSUE SAMPLES FROM ACUTE, CHRONIC, AND ART-TREATED INDIVIDUALS. WE OBSERVED MINOR DIFFERENCES IN THE FREQUENCY OF NONINTRONIC AND NONDISTAL INTERGENIC SITES, VARYING WITH TISSUE AND RESIDENCY PHENOTYPES DURING ART. GENOMIC AND EPIGENETIC ANNOTATIONS WERE GENERALLY SIMILAR. CLONAL EXPANSION OF CELLS MARKED BY IDENTICAL INTEGRATION SITES WAS DETECTED, WITH INCREASED DETECTION IN CHRONIC AND ART-TREATED INDIVIDUALS. HOWEVER, OVERLAP BETWEEN OR WITHIN CD4+ T CELL SUBSETS OR TISSUE COMPARTMENTS WAS ONLY OBSERVED IN 8 UNIQUE SITES OF THE 3540 SITES STUDIED. TOGETHER, THESE FINDINGS SUGGEST THAT SHARED INTEGRATION SITES BETWEEN BLOOD AND TISSUE MAY, DEPENDING ON THE TISSUE SITE, BE THE EXCEPTION RATHER THAN THE RULE AND INDICATE THAT ADDITIONAL STUDIES ARE NECESSARY TO FULLY UNDERSTAND THE HETEROGENEITY OF TISSUE-SEQUESTERED HIV RESERVOIRS. 2020