1 4816 129 OCCULT HEPATITIS B VIRUS INFECTION: A COMPLEX ENTITY WITH RELEVANT CLINICAL IMPLICATIONS. OCCULT HEPATITIS B VIRUS (HBV) INFECTION IS A WORLD-WIDE ENTITY, FOLLOWING THE GEOGRAPHICAL DISTRIBUTION OF DETECTABLE HEPATITIS B. THIS ENTITY IS DEFINED AS THE PERSISTENCE OF VIRAL GENOMES IN THE LIVER TISSUE AND IN SOME INSTANCES ALSO IN THE SERUM, ASSOCIATED TO NEGATIVE HBV SURFACE ANTIGEN SEROLOGY. THE MOLECULAR BASIS OF THE OCCULT INFECTION IS RELATED TO THE LIFE CYCLE OF HBV, WHICH PRODUCES A COVALENTLY CLOSED CIRCULAR DNA THAT PERSISTS IN THE CELL NUCLEI AS AN EPISOME, AND SERVES AS A TEMPLATE FOR GENE TRANSCRIPTION. THE MECHANISM RESPONSIBLE FOR THE HBSAG NEGATIVE STATUS IN OCCULT HBV CARRIERS IS A STRONG SUPPRESSION OF VIRAL REPLICATION, PROBABLY DUE TO THE HOST'S IMMUNE RESPONSE, CO-INFECTION WITH OTHER INFECTIOUS AGENTS AND EPIGENETIC FACTORS. THERE IS EMERGING EVIDENCE OF THE POTENTIAL CLINICAL RELEVANCE OF OCCULT HBV INFECTION, SINCE THIS COULD BE INVOLVED IN OCCULT HBV TRANSMISSION THROUGH ORTHOTOPIC LIVER TRANSPLANT AND BLOOD TRANSFUSION, REACTIVATION OF HBV INFECTION DURING IMMUNOSUPPRESSION, IMPAIRING CHRONIC LIVER DISEASE OUTCOME AND ACTING AS A RISK FACTOR FOR HEPATOCELLULAR CARCINOMA. THEREFORE IT IS IMPORTANT TO BEAR IN MIND THIS ENTITY IN CRYPTOGENETIC LIVER DISEASES, HEPATITIS C VIRUS/HIV INFECTED PATIENTS AND IMMUNOSUPRESSED INDIVIDUALS. IT IS ALSO NECESSARY TO INCREASE OUR KNOWLEDGE IN THIS FASCINATING FIELD TO DEFINE BETTER STRATEGIES TO DIAGNOSE AND TREAT THIS INFECTION. 2011 2 2516 33 EPIGENETICS AND SYSTEMIC LUPUS ERYTHEMATOSUS: UNMET NEEDS. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC RELAPSING-REMITTING AUTOIMMUNE DISEASE AFFECTING SEVERAL ORGANS. ALTHOUGH THE MANAGEMENT OF LUPUS PATIENTS HAS IMPROVED IN THE LAST YEARS, SEVERAL ASPECTS STILL REMAIN CHALLENGING. MORE SENSITIVE AND SPECIFIC BIOMARKERS FOR AN EARLY DIAGNOSIS AS WELL AS FOR MONITORING DISEASE ACTIVITY AND TISSUE DAMAGE ARE NEEDED. GENOME-WIDE ASSOCIATION AND GENE MAPPING STUDIES HAVE SUPPORTED THE GENETIC BACKGROUND FOR SLE SUSCEPTIBILITY. HOWEVER, THE RELATIVELY MODEST RISK ASSOCIATION AND THE STUDIES IN TWINS HAVE SUGGESTED A ROLE FOR ENVIRONMENTAL AND EPIGENETIC FACTORS, AS WELL AS GENETIC-EPIGENETIC INTERACTION. ACCORDINGLY, THERE IS EVIDENCE THAT DIFFERENCES IN DNA METHYLATION, HISTONE MODIFICATIONS, AND MIRNA PROFILING CAN BE FOUND IN LUPUS PATIENTS VERSUS NORMAL SUBJECTS. MOREOVER, IMPAIRED DNA METHYLATION ON THE INACTIVE X-CHROMOSOME WAS SUGGESTED TO EXPLAIN, AT LEAST IN PART, THE FEMALE PREVALENCE OF THE DISEASE. EPIGENETIC MARKERS MAY BE HELP IN FULFILLING THE UNMET NEEDS FOR SLE BY OFFERING NEW DIAGNOSTIC TOOLS, NEW BIOMARKERS FOR MONITORING DISEASE ACTIVITY, OR TO BETTER CHARACTERIZE PATIENTS WITH A SILENT CLINICAL DISEASE BUT WITH AN ACTIVE SEROLOGY. ANTI-DNA, ANTI-PHOSPHOLIPID, AND ANTI-RO/SSA AUTOANTIBODIES ARE THOUGHT TO BE PATHOGENIC FOR GLOMERULONEPHRITIS, RECURRENT THROMBOSIS AND MISCARRIAGES, AND NEONATAL LUPUS, RESPECTIVELY. HOWEVER, TISSUE DAMAGE OCCURS OCCASIONALLY OR, IN SOME PATIENTS, ONLY IN SPITE OF THE PERSISTENT PRESENCE OF THE ANTIBODIES. PRELIMINARY STUDIES SUGGEST THAT EPIGENETIC MECHANISMS MAY EXPLAIN WHY THE DAMAGE TAKES PLACE IN SOME PATIENTS ONLY OR AT A GIVEN TIME. 2016 3 6862 68 [OCCULT HEPATITIS B VIRUS INFECTION]. OCCULT HEPATITIS B VIRUS (HBV) INFECTION IS A PECULIAR FORM OF CHRONIC VIRAL INFECTION IDENTIFIED SINCE THE EARLY 80'S AND CAN BE DEFINED AS THE PRESENCE OF HBV DNA IN THE SERUM AND/OR IN THE LIVER TISSUE OF PATIENTS NEGATIVE FOR THE HBV SURFACE ANTIGEN (HBSAG) USING USUAL SEROLOGICAL TESTS. THE DATA ABOUT THE PREVALENCE OF OCCULT HBV INFECTION ARE CONTRASTING AND THE REPORTED PREVALENCES IN VARIOUS CATEGORIES OF INDIVIDUALS ARE HIGHLY DIVERSE. THE MOLECULAR BASIS OF THE OCCULT HBV INFECTION IS THE COVALENTLY CLOSED-CIRCULAR DNA (CCCDNA) THAT PERSISTS IN THE CELL NUCLEI AND THAT SERVES AS A TEMPLATE FOR GENE TRANSCRIPTION. THE PHYSIOPATHOLOGY OF OCCULT HBV INFECTION IS STILL UNCLEAR. HOWEVER, THE AVAILABLE DATA SUGGEST THAT THE HOST'S IMMUNE RESPONSE, THE CO-INFECTIONS WITH OTHER INFECTIOUS AGENTS AND EPIGENETIC FACTORS MAY PLAY IMPORTANT ROLES IN INDICING THE OCCULT STATUS. THE CLINICAL RELEVANCE OF OCCULTHBVINFECTION REMAINS DEBATED BUT IT MAY IMPACT IN FOUR CLINICAL CONTEXTS: 1) THE TRANSMISSION OF THE INFECTION BY BLOOD TRANSFUSION OR ORGAN TRANSPLANTATION; 2) THE ACUTE REACTIVATION WHEN AN IMMUNOSUPPRESSIVE STATUS OCCURS MAINLY IN PATIENTS WITH ISOLATED ANTI-HBC (CHEMOTHERAPY, TRANSPLANTATIONS, IMMUNODEPRESSION, NEW IMMUNOSUPPRESSIVE THERAPY AS ANTI-CD20 OR ANTI TNF); 3) THE POTENT BUT NON PROVED PROGRESSION OF LIVER FIBROSIS IN HCV INFECTED PATIENTS OR IN PATIENTS WITH CRYPTOGENETIC LIVER DISEASE; AND, 4. THE RISK FACTOR FOR HEPATOCELLULAR CARCINOMA DEVELOPMENT. 2008 4 4815 54 OCCULT HEPATITIS B INFECTION AND HEPATOCELLULAR CARCINOMA: EPIDEMIOLOGY, VIROLOGY, HEPATOCARCINOGENESIS AND CLINICAL SIGNIFICANCE. OCCULT HEPATITIS B INFECTION (OBI) REFERS TO A CONDITION WHERE REPLICATION-COMPETENT HBV DNA IS PRESENT IN THE LIVER, WITH OR WITHOUT HBV DNA IN THE BLOOD, IN INDIVIDUALS WITH SERUM HBSAG NEGATIVITY ASSESSED BY CURRENTLY AVAILABLE ASSAYS. THE EPISOMAL COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) IN OBI IS IN A LOW REPLICATIVE STATE. VIRAL GENE EXPRESSION IS MEDIATED BY EPIGENETIC CONTROL OF HBV TRANSCRIPTION, INCLUDING THE HBV CPG ISLAND METHYLATION PATHWAY AND POST-TRANSLATIONAL MODIFICATION OF CCCDNA-BOUND HISTONE, WITH A DIFFERENT PATTERN FROM PATIENTS WITH CHRONIC HBV INFECTION. THE PREVALENCE OF OBI VARIES TREMENDOUSLY ACROSS PATIENT POPULATIONS OWING TO NUMEROUS FACTORS, SUCH AS GEOGRAPHIC LOCATION, ASSAY CHARACTERISTICS, HOST IMMUNE RESPONSE, COINFECTION WITH OTHER VIRUSES, AND VACCINATION STATUS. APART FROM THE RISK OF VIRAL REACTIVATION UPON IMMUNOSUPPRESSION AND THE RISK OF TRANSMISSION OF HBV, OBI HAS BEEN IMPLICATED IN HEPATOCELLULAR CARCINOMA (HCC) DEVELOPMENT IN PATIENTS WITH CHRONIC HCV INFECTION, THOSE WITH CRYPTOGENIC OR KNOWN LIVER DISEASE, AND IN PATIENTS WITH HBSAG SEROCLEARANCE AFTER CHRONIC HBV INFECTION. AN INCREASING NUMBER OF PROSPECTIVE STUDIES AND META-ANALYSES HAVE REPORTED A HIGHER INCIDENCE OF HCC IN PATIENTS WITH HCV AND OBI, AS WELL AS MORE ADVANCED TUMOUR HISTOLOGICAL GRADES AND EARLIER AGE OF HCC DIAGNOSIS, COMPARED WITH PATIENTS WITHOUT OBI. THE PROPOSED PATHOGENETIC MECHANISMS OF OBI-RELATED HCC INCLUDE THE INFLUENCE OF HBV DNA INTEGRATION ON THE HEPATOCYTE CELL CYCLE, THE PRODUCTION OF PRO-ONCOGENIC PROTEINS (HBX PROTEIN AND MUTATED SURFACE PROTEINS), AND PERSISTENT LOW-GRADE NECROINFLAMMATION (CONTRIBUTING TO THE DEVELOPMENT OF FIBROSIS AND CIRRHOSIS). THERE REMAIN UNCERTAINTIES ABOUT EXACTLY HOW, AND IN WHAT ORDER, THESE MECHANISMS DRIVE THE DEVELOPMENT OF TUMOURS IN PATIENTS WITH OBI. 2020 5 4817 58 OCCULT HEPATITIS B VIRUS INFECTION: AN UPDATE. OCCULT HEPATITIS B VIRUS (HBV) INFECTION (OBI) REFERS TO A CONDITION IN WHICH REPLICATION-COMPETENT VIRAL DNA IS PRESENT IN THE LIVER (WITH DETECTABLE OR UNDETECTABLE HBV DNA IN THE SERUM) OF INDIVIDUALS TESTING NEGATIVE FOR THE HBV SURFACE ANTIGEN (HBSAG). IN THIS PECULIAR PHASE OF HBV INFECTION, THE COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) IS IN A LOW STATE OF REPLICATION. MANY ADVANCES HAVE BEEN MADE IN CLARIFYING THE MECHANISMS INVOLVED IN SUCH A SUPPRESSION OF VIRAL ACTIVITY, WHICH SEEMS TO BE MAINLY RELATED TO THE HOST'S IMMUNE CONTROL AND EPIGENETIC FACTORS. OBI IS DIFFUSED WORLDWIDE, BUT ITS PREVALENCE IS HIGHLY VARIABLE AMONG PATIENT POPULATIONS. THIS DEPENDS ON DIFFERENT GEOGRAPHIC AREAS, RISK FACTORS FOR PARENTERAL INFECTIONS, AND ASSAYS USED FOR HBSAG AND HBV DNA DETECTION. OBI HAS AN IMPACT IN SEVERAL CLINICAL CONTEXTS: (A) IT CAN BE TRANSMITTED, CAUSING A CLASSIC FORM OF HEPATITIS B, THROUGH BLOOD TRANSFUSION OR LIVER TRANSPLANTATION; (B) IT MAY REACTIVATE IN THE CASE OF IMMUNOSUPPRESSION, LEADING TO THE POSSIBLE DEVELOPMENT OF EVEN FULMINANT HEPATITIS; (C) IT MAY ACCELERATE THE PROGRESSION OF CHRONIC LIVER DISEASE DUE TO DIFFERENT CAUSES TOWARD CIRRHOSIS; (D) IT MAINTAINS THE PRO-ONCOGENIC PROPERTIES OF THE "OVERT" INFECTION, FAVORING THE DEVELOPMENT OF HEPATOCELLULAR CARCINOMA. 2022 6 1134 36 COMPREHENSIVE GENETIC AND EPIGENETIC ANALYSIS OF OCCULT HEPATITIS B FROM LIVER TISSUE SAMPLES. BACKGROUND: OCCULT INFECTION WITH HEPATITIS B VIRUS (HBV) IS A TYPE OF CHRONIC HBV INFECTION THAT IS CHARACTERIZED BY THE ABSENCE OF A DETECTABLE HEPATITIS B SURFACE ANTIGEN IN THE BLOOD AND BY VERY LOW LEVELS OF HBV DNA IN THE BLOOD AND LIVER. THE MECHANISMS LEADING TO OCCULT HBV INFECTION REMAIN POORLY UNDERSTOOD BUT INCLUDE POSSIBLE GENETIC MUTATIONS AND DELETIONS. RECENTLY, IT HAS BEEN SHOWN THAT HBV HAS CPG ISLANDS THAT ARE METHYLATED, RAISING THE POSSIBILITY THAT EPIGENETIC CHANGES MAY ALSO BE IMPORTANT. METHODS: THE FULL-LENGTH GENOMES OF ISOLATES FROM 5 CASES OF OCCULT HBV INFECTION WERE CLONED AND ANALYZED FOR MUTATIONS AND DELETIONS. ADDITIONAL STUDIES WERE PERFORMED TO EXAMINE FOR APOBEC3G (1 MEMBER OF A FAMILY OF DEAMINATING PROTEINS THAT ARE PART OF THE INNATE IMMUNE SYSTEM'S DEFENSE AGAINST VIRAL INFECTION) HYPEREDITING AND METHYLATION OF VIRAL DNA. RESULTS: NUMEROUS MUTATIONS AND DELETIONS WERE FOUND IN THE GENOMES OF OCCULT HBV. HOWEVER, SIMILAR TYPES AND LOCATIONS OF POLYMORPHISMS WERE ALSO NOTED IN THE GENOME SEQUENCES OF HBV ISOLATED FROM CONTROL LIVER TISSUE SAMPLES OBTAINED FROM INDIVIDUALS WITH NONOCCULT HBV INFECTION. EVIDENCE OF APOBEC3G HYPEREDITING WAS FOUND IN 1 CASE OF OCCULT HBV INFECTION, BUT HYPEREDITED SEQUENCES MADE UP ONLY A SMALL PROPORTION OF THE VIRAL SEQUENCES. METHYLATION OF HBV CPG ISLANDS 1 AND 2 WAS EVIDENT IN BOTH OCCULT AND NONOCCULT HBV SEQUENCES, WITH ISLAND 2 MORE DENSELY METHYLATED IN OCCULT HBV SEQUENCES AND ISLAND 1 MORE DENSELY METHYLATED IN NONOCCULT HBV SEQUENCES. CONCLUSION: DELETIONS AND MUTATIONS ARE COMMON IN OCCULT HBV BUT ARE ALSO FOUND IN CONTROL NONOCCULT HBV, AND NO UNIQUE GENETIC SIGNATURE FOR OCCULT HBV WAS FOUND. METHYLATION PATTERNS DIFFER BETWEEN CASES OF OCCULT AND NONOCCULT HBV INFECTION, SUGGESTING THAT EPIGENETIC CHANGES MAY BE RELEVANT TO OCCULT HBV. TOGETHER, THESE FINDINGS SUGGEST THAT MULTIPLE MECHANISMS CAN CONTRIBUTE TO OCCULT HBV INFECTION. 2008 7 5689 41 SILENCING HEPATITIS B VIRUS COVALENTLY CLOSED CIRCULAR DNA: THE POTENTIAL OF AN EPIGENETIC THERAPY APPROACH. GLOBAL PROPHYLACTIC VACCINATION PROGRAMMES HAVE HELPED TO CURB NEW HEPATITIS B VIRUS (HBV) INFECTIONS. HOWEVER, IT IS ESTIMATED THAT NEARLY 300 MILLION PEOPLE ARE CHRONICALLY INFECTED AND HAVE A HIGH RISK OF DEVELOPING HEPATOCELLULAR CARCINOMA. AS SUCH, HBV REMAINS A SERIOUS HEALTH PRIORITY AND THE DEVELOPMENT OF NOVEL CURATIVE THERAPEUTICS IS URGENTLY NEEDED. CHRONIC HBV INFECTION HAS BEEN ATTRIBUTED TO THE PERSISTENCE OF THE COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) WHICH ESTABLISHES ITSELF AS A MINICHROMOSOME IN THE NUCLEUS OF HEPATOCYTES. AS THE VIRAL TRANSCRIPTION INTERMEDIATE, THE CCCDNA IS RESPONSIBLE FOR PRODUCING NEW VIRIONS AND PERPETUATING INFECTION. HBV IS DEPENDENT ON VARIOUS HOST FACTORS FOR CCCDNA FORMATION AND THE MINICHROMOSOME IS AMENABLE TO EPIGENETIC MODIFICATIONS. TWO HBV PROTEINS, X (HBX) AND CORE (HBC) PROMOTE VIRAL REPLICATION BY MODULATING THE CCCDNA EPIGENOME AND REGULATING HOST CELL RESPONSES. THIS INCLUDES VIRAL AND HOST GENE EXPRESSION, CHROMATIN REMODELING, DNA METHYLATION, THE ANTIVIRAL IMMUNE RESPONSE, APOPTOSIS, AND UBIQUITINATION. ELIMINATION OF THE CCCDNA MINICHROMOSOME WOULD RESULT IN A STERILIZING CURE; HOWEVER, THIS MAY BE DIFFICULT TO ACHIEVE. EPIGENETIC THERAPIES COULD PERMANENTLY SILENCE THE CCCDNA MINICHROMOSOME AND PROMOTE A FUNCTIONAL CURE. THIS REVIEW EXPLORES THE CCCDNA EPIGENOME, HOW HOST AND VIRAL FACTORS INFLUENCE TRANSCRIPTION, AND THE RECENT EPIGENETIC THERAPIES AND EPIGENOME ENGINEERING APPROACHES THAT HAVE BEEN DESCRIBED. 2021 8 3209 22 HEALTH DISPARITIES IN SYSTEMIC LUPUS ERYTHEMATOSUS. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC MULTISYSTEM AUTOIMMUNE DISEASE CHARACTERIZED BY AUTOANTIBODY PRODUCTION AND DIVERSE CLINICAL MANIFESTATIONS. THE MANY COMPLEX, OVERLAPPING, AND CLOSELY ASSOCIATED FACTORS THAT INFLUENCE SLE SUSCEPTIBILITY AND OUTCOMES INCLUDE ETHNIC DISPARITIES, LOW ADHERENCE TO MEDICATIONS, AND POVERTY, AND GEOGRAPHY. EPIGENETIC MECHANISMS MAY PROVIDE THE LINK BETWEEN THESE ENVIRONMENTAL EXPOSURES AND BEHAVIORS AND THE DISPROPORTIONATE BURDEN OF SLE SEEN IN ETHNIC MINORITIES. ATTENTION TO THESE MODIFIABLE SOCIAL DETERMINANTS OF HEALTH WOULD NOT ONLY IMPROVE OUTCOMES FOR VULNERABLE PATIENTS WITH SLE BUT LIKELY REDUCE SUSCEPTIBILITY TO SLE AS WELL THROUGH EPIGENETIC CHANGES. 2020 9 5368 29 RECENT ADVANCES IN THE STUDY OF HEPATITIS B VIRUS COVALENTLY CLOSED CIRCULAR DNA. CHRONIC HEPATITIS B INFECTION IS CAUSED BY HEPATITIS B VIRUS (HBV) AND A TOTAL CURE IS YET TO BE ACHIEVED. THE VIRAL COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) IS THE KEY TO ESTABLISH A PERSISTENT INFECTION WITHIN HEPATOCYTES. CURRENT ANTIVIRAL STRATEGIES HAVE NO EFFECT ON THE PRE-EXISTING CCCDNA RESERVOIR. THEREFORE, THE STUDY OF THE MOLECULAR MECHANISM OF CCCDNA FORMATION IS BECOMING A MAJOR FOCUS OF HBV RESEARCH. THIS REVIEW SUMMARIZES THE CURRENT ADVANCES IN CCCDNA MOLECULAR BIOLOGY AND THE LATEST STUDIES ON THE ELIMINATION OR INACTIVATION OF CCCDNA, INCLUDING THREE MAJOR AREAS: (1) EPIGENETIC REGULATION OF CCCDNA BY HBV X PROTEIN, (2) IMMUNE-MEDIATED DEGRADATION, AND (3) GENOME-EDITING NUCLEASES. ALL THESE ASPECTS PROVIDE CLUES ON HOW TO FINALLY ATTAIN A CURE FOR CHRONIC HEPATITIS B INFECTION. 2017 10 5936 30 TARGETING HEPATITIS B VIRUS COVALENTLY CLOSED CIRCULAR DNA AND HEPATITIS B VIRUS X PROTEIN: RECENT ADVANCES AND NEW APPROACHES. CHRONIC HEPATITIS B VIRUS (HBV) INFECTION REMAINS A WORLDWIDE CONCERN AND PUBLIC HEALTH PROBLEM. TWO KEY ASPECTS OF THE HBV LIFE CYCLE ARE ESSENTIAL FOR VIRAL REPLICATION AND THUS THE DEVELOPMENT OF CHRONIC INFECTIONS: THE ESTABLISHMENT OF THE VIRAL MINICHROMOSOME, COVALENTLY CLOSED CIRCULAR (CCC) DNA, WITHIN THE NUCLEUS OF INFECTED HEPATOCYTES AND THE EXPRESSION OF THE REGULATORY HEPATITIS B VIRUS X PROTEIN (HBX). INTERESTINGLY, NUCLEAR HBX REDIRECTS HOST EPIGENETIC MACHINERY TO ACTIVATE CCCDNA TRANSCRIPTION. IN THIS PERSPECTIVE, WE PROVIDE AN OVERVIEW OF RECENT ADVANCES IN UNDERSTANDING THE REGULATION OF CCCDNA AND THE MECHANISTIC AND FUNCTIONAL ROLES OF HBX. WE ALSO DESCRIBE THE PROGRESS TOWARD TARGETING BOTH CCCDNA AND HBX FOR THERAPEUTIC PURPOSES. FINALLY, WE OUTLINE STANDING QUESTIONS IN THE FIELD AND PROPOSE COMPLEMENTARY CHEMICAL BIOLOGY APPROACHES TO ADDRESS THEM. 2019 11 2731 22 EXPLORING THE COMPLEX RELATIONSHIP BETWEEN MICROBIOTA AND SYSTEMIC LUPUS ERYTHEMATOSUS. PURPOSE OF REVIEW: SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC AUTOIMMUNE DISEASE CHARACTERIZED BY VARIOUS AUTOANTIBODIES AND MULTI-ORGAN. MICROBIOTA DYSBIOSIS IN THE GUT, SKIN, ORAL, AND OTHER SURFACES HAS A SIGNIFICANT IMPACT ON SLE DEVELOPMENT. THIS ARTICLE SUMMARIZES RELEVANT RESEARCH AND PROVIDES NEW MICROBIOME-RELATED STRATEGIES FOR EXPLORING THE MECHANISMS AND TREATING PATIENTS WITH SLE. RECENT FINDINGS: SLE PATIENTS HAVE DISRUPTIONS IN MULTIPLE MICROBIOMES, WITH THE GUT MICROBIOTA (BACTERIA, VIRUSES, AND FUNGI) AND THEIR METABOLITES BEING THE MOST THOROUGHLY RESEARCHED. THIS DYSBIOSIS CAN PROMOTE SLE PROGRESSION THROUGH MECHANISMS SUCH AS THE LEAKY GUT, MOLECULAR MIMICRY, AND EPIGENETIC REGULATION. NOTWITHSTANDING STUDY CONSTRAINTS ON THE RELATIONSHIP BETWEEN MICROBIOTA AND SLE, SPECIFIC INTERVENTIONS TARGETING THE GUT MICROBIOTA, SUCH AS PROBIOTICS, DIETARY MANAGEMENT, AND FECAL MICROBIOTA TRANSPLANTATION, HAVE EMERGED AS PROMISING SLE THERAPEUTICS. 2023 12 1052 36 CLINICAL IMPLICATIONS OF HEPATITIS B VIRUS RNA AND COVALENTLY CLOSED CIRCULAR DNA IN MONITORING PATIENTS WITH CHRONIC HEPATITIS B TODAY WITH A GAZE INTO THE FUTURE: THE FIELD IS UNPREPARED FOR A STERILIZING CURE. . CHRONIC HEPATITIS B VIRUS (HBV) INFECTION HAS LONG REMAINED A CRITICAL GLOBAL HEALTH ISSUE. COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) IS A PERSISTENT FORM OF THE HBV GENOME THAT MAINTAINS HBV CHRONICITY. DECADES OF EXTENSIVE RESEARCH RESULTED IN THE TWO THERAPEUTIC OPTIONS CURRENTLY AVAILABLE: NUCLEOT(S)IDE ANALOGS AND INTERFERON (IFN) THERAPY. A PLETHORA OF RELIABLE MARKERS TO MONITOR HBV PATIENTS HAS BEEN ESTABLISHED, INCLUDING THE RECENTLY DISCOVERED ENCAPSIDATED PREGENOMIC RNA IN SERUM, WHICH CAN BE USED TO DETERMINE TREATMENT END-POINTS AND TO PREDICT THE SUSCEPTIBILITY OF PATIENTS TO IFN. ADDITIONALLY, HBV RNA SPLICE VARIANTS AND CCCDNA AND ITS EPIGENETIC MODIFICATIONS ARE ASSOCIATED WITH THE CLINICAL COURSE AND RISKS OF HEPATOCELLULAR CARCINOMA (HCC) AND LIVER FIBROSIS. HOWEVER, NEW ANTIVIRALS, INCLUDING CRISPR/CAS9, APOBEC-MEDIATED DEGRADATION OF CCCDNA, AND T-CELL THERAPIES AIM AT COMPLETELY ELIMINATING HBV, AND IT IS CLEAR THAT THE DIAGNOSTIC ARSENAL FOR DEFINING THE LONG-AWAITED STERILIZING CURE IS MISSING. IN THIS REVIEW, WE DISCUSS THE CURRENTLY AVAILABLE TOOLS FOR DETECTING AND MEASURING HBV RNAS AND CCCDNA, AS WELL AS THE STATE-OF-THE-ART IN CLINICAL IMPLICATIONS OF THESE MARKERS, AND DEBATE NEEDS AND GOALS WITHIN THE CONTEXT OF THE STERILIZING CURE THAT IS SOON TO COME. 2018 13 2324 34 EPIGENETIC REGULATION OF HEPATITIS B VIRUS COVALENTLY CLOSED CIRCULAR DNA: IMPLICATIONS FOR EPIGENETIC THERAPY AGAINST CHRONIC HEPATITIS B. HEPATITIS B VIRUS (HBV) INFECTION REPRESENTS A SIGNIFICANT PUBLIC HEALTH BURDEN WORLDWIDE. ALTHOUGH CURRENT THERAPEUTICS MANAGE TO CONTROL THE DISEASE PROGRESSION, LIFELONG TREATMENT AND SURVEILLANCE ARE REQUIRED BECAUSE DRUG RESISTANCE DEVELOPS DURING TREATMENT AND REACTIVATIONS FREQUENTLY OCCUR FOLLOWING MEDICATION CESSATION. THUS, THE OCCURRENCE OF HEPATOCELLULAR CARCINOMA IS DECREASED, BUT NOT ELIMINATED. ONE MAJOR REASON FOR FAILURE OF HBV TREATMENT IS THE INABILITY TO ERADICATE OR INACTIVATE THE VIRAL COVALENTLY CLOSED CIRCULAR DNA (CCCDNA), WHICH IS A STABLE EPISOMAL FORM OF THE VIRAL GENOME DECORATED WITH HOST HISTONES AND NONHISTONE PROTEINS. ACCUMULATING EVIDENCE SUGGESTS THAT EPIGENETIC MODIFICATIONS OF CCCDNA CONTRIBUTE TO VIRAL REPLICATION AND THE OUTCOME OF CHRONIC HBV INFECTION. HERE, WE SUMMARIZE CURRENT PROGRESS ON HBV EPIGENETICS RESEARCH AND THE THERAPEUTIC IMPLICATIONS FOR CHRONIC HBV INFECTION BY LEARNING FROM THE EPIGENETIC THERAPIES FOR CANCER AND OTHER VIRAL DISEASES, WHICH MAY OPEN A NEW VENUE TO CURE CHRONIC HEPATITIS B. (HEPATOLOGY 2017;66:2066-2077). 2017 14 2257 20 EPIGENETIC PERSPECTIVES IN SYSTEMIC LUPUS ERYTHEMATOSUS: PATHOGENESIS, BIOMARKERS, AND THERAPEUTIC POTENTIALS. SYSTEM LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC AUTOIMMUNE DISEASE CHARACTERIZED BY THE PRODUCTION OF AUTOANTIBODIES THAT CAUSE WIDESPREAD TISSUE DAMAGE. THE UNDERLYING ETIOLOGY REMAINS LARGELY UNKNOWN. ABERRANT EPIGENETICS PLAYS ESSENTIAL ROLES IN THE PATHOGENESIS OF SLE. THIS REVIEW EXPLORES THE LINKS BETWEEN DNA METHYLATION, HISTONE MODIFICATIONS, AND MIRNAS IN SLE AND HIGHLIGHTS HOW THESE FACTORS MAY INTERACT IN SLE PATHOGENESIS. WE ALSO DISCUSS HOW FURTHERING OUR KNOWLEDGE OF EPIGENETICS IN LUPUS PROVIDES HOPE FOR FINDING NEW DIAGNOSTIC AND PROGNOSTIC BIOMARKERS AND NOVEL THERAPEUTIC TARGETS AND STRATEGIES. 2010 15 2915 35 GENE THERAPY FOR CHRONIC HBV-CAN WE ELIMINATE CCCDNA? CHRONIC INFECTION WITH THE HEPATITIS B VIRUS (HBV) IS A GLOBAL HEALTH CONCERN AND ACCOUNTS FOR APPROXIMATELY 1 MILLION DEATHS ANNUALLY. AMONGST OTHER LIMITATIONS OF CURRENT ANTI-HBV TREATMENT, FAILURE TO ELIMINATE THE VIRAL COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) AND EMERGENCE OF RESISTANCE REMAIN THE MOST WORRISOME. VIRAL REBOUND FROM LATENT EPISOMAL CCCDNA RESERVOIRS OCCURS FOLLOWING CESSATION OF THERAPY, PATIENT NON-COMPLIANCE, OR THE DEVELOPMENT OF ESCAPE MUTANTS. SIMULTANEOUS VIRAL CO-INFECTIONS, SUCH AS BY HIV-1, FURTHER COMPLICATE THERAPEUTIC INTERVENTIONS. THESE CHALLENGES HAVE PROMPTED DEVELOPMENT OF NOVEL TARGETED HEPATITIS B THERAPIES. GIVEN THE EASE WITH WHICH HIGHLY SPECIFIC AND POTENT NUCLEIC ACID THERAPEUTICS CAN BE RATIONALLY DESIGNED, GENE THERAPY HAS GENERATED INTEREST FOR ANTIVIRAL APPLICATION. GENE THERAPY STRATEGIES DEVELOPED FOR HBV INCLUDE GENE SILENCING BY HARNESSING RNA INTERFERENCE, TRANSCRIPTIONAL INHIBITION THROUGH EPIGENETIC MODIFICATION OF TARGET DNA, GENOME EDITING BY DESIGNER NUCLEASES, AND IMMUNE MODULATION WITH CYTOKINES. DNA-BINDING DOMAINS AND EFFECTORS BASED ON THE ZINC FINGER (ZF), TRANSCRIPTION ACTIVATOR-LIKE EFFECTOR (TALE), AND CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT (CRISPR) SYSTEMS ARE REMARKABLY WELL SUITED TO TARGETING EPISOMAL CCCDNA. THIS REVIEW DISCUSSES RECENT DEVELOPMENTS AND CHALLENGES FACING THE FIELD OF ANTI-HBV GENE THERAPY, ITS POTENTIAL CURATIVE SIGNIFICANCE AND THE PROGRESS TOWARDS CLINICAL APPLICATION. 2018 16 3782 36 INTERFERON THERAPY OF CHRONIC HEPATITIS B. CHRONIC HEPATITIS B (CHB) RESULTS FROM THE INABILITY OF THE HOST'S IMMUNE SYSTEM TO CONTROL VIRAL REPLICATION. INTERFERON-ALPHA (IFN-ALPHA) THERAPY CAN CONVERT CHB INTO INACTIVE HEPATITIS B VIRUS (HBV) INFECTION IN 20-30% OF THE TREATED PATIENTS. IN SPITE OF THE LOW RESPONSE RATE, IFN-ALPHA THERAPY HAS THE ADVANTAGE OF HAVING A LIMITED DURATION AND BEING EFFECTIVE EVEN AFTER THERAPY, AS DEMONSTRATED BY A MUCH HIGHER INCIDENCE OF HBSAG CLEARANCE IN RESPONDERS TO IFN-ALPHA THAN IN NATURALLY OCCURRING INACTIVE HBSAG CARRIERS. IFN-ALPHA HAS MULTIPLE ANTIVIRAL, ANTIPROLIFERATIVE, AND IMMUNOMODULATORY ACTIVITIES AND TARGETS: CELLULAR GENES (IFN-STIMULATED GENES) ACTIVATING DIFFERENT PATHWAYS OF ANTIVIRAL DEFENSE IN INFECTED AND NONINFECTED CELLS, HBV REPLICATION BLOCKING THE RNA-CONTAINING CORE PARTICLE FORMATION AND ACCELERATING THEIR DECAY, DEGRADING PREGENOMIC RNA, AND MODULATING THE NUCLEAR VIRAL MINICHROMOSOME (COVALENTLY CLOSED CIRCULAR DNA) ACTIVITY BY TARGETING ITS EPIGENETIC REGULATION AND BOTH INNATE AND ADAPTIVE IMMUNE RESPONSE. THE INTERFERENCE OF VIRAL HETEROGENEITY AND GENETIC POLYMORPHISMS OF THE HOST ON IFN-ALPHA SUSCEPTIBILITY IS UNDER INVESTIGATION. ONLY A BETTER UNDERSTANDING OF THE COMPLEX INTERPLAY BETWEEN THE DIFFERENT ACTIVITIES OF IFN-ALPHA WOULD WARRANT THE AMELIORATION OF CURRENT THERAPEUTIC STRATEGIES AND THE DESIGN OF NEW THERAPEUTIC APPROACHES. THE STUDY OF ON-TREATMENT DYNAMICS OF HBV INFECTION BY MEANS OF COMBINED QUANTITATIVE MONITORING OF SERUM HBV DNA AND HBSAG WARRANT TAILORING TREATMENT AT THE SINGLE-PATIENT LEVEL AND CAN HELP TO MAKE TREATMENT MORE COST-EFFECTIVE BY USING THE DIFFERENT COMBINATIONS OF CURRENTLY AVAILABLE ANTIVIRALS, INCLUDING IFN, MORE APPROPRIATELY. INTEGRATED MOLECULAR AND CLINICAL KNOWLEDGE IN A SYSTEMS MEDICINE FASHION IS MANDATORY TO FURTHER IMPROVE ANTIVIRAL THERAPY IN CHB. 2014 17 5952 37 TARGETING VIRAL CCCDNA FOR CURE OF CHRONIC HEPATITIS B. PURPOSE OF REVIEW: CHRONIC HEPATITIS B (CHB), CAUSED BY HEPATITIS B VIRUS (HBV), IS A MAJOR CAUSE OF ADVANCED LIVER DISEASE AND HEPATOCELLULAR CARCINOMA (HCC) WORLDWIDE. HBV REPLICATION IS CHARACTERIZED BY THE SYNTHESIS OF COVALENTLY CLOSED CIRCULAR (CCC) DNA WHICH IS NOT TARGETED BY ANTIVIRAL NUCLEOS(T)IDE ANALOGUES (NUCS) THE KEY MODALITY OF STANDARD OF CARE. WHILE HBV REPLICATION IS SUCCESSFULLY SUPPRESSED IN TREATED PATIENTS, THEY REMAIN AT RISK FOR DEVELOPING HCC. WHILE FUNCTIONAL CURE, CHARACTERIZED BY LOSS OF HBSAG, IS THE FIRST GOAL OF NOVEL ANTIVIRAL THERAPIES, CURATIVE TREATMENTS ELIMINATING CCCDNA REMAIN THE ULTIMATE GOAL. THIS REVIEW SUMMARIZES RECENT ADVANCES IN THE DISCOVERY AND DEVELOPMENT OF NOVEL THERAPEUTIC STRATEGIES AND THEIR IMPACT ON CCCDNA BIOLOGY. RECENT FINDINGS: WITHIN THE LAST DECADE, SUBSTANTIAL PROGRESS HAS BEEN MADE IN THE UNDERSTANDING OF CCCDNA BIOLOGY INCLUDING THE DISCOVERY OF HOST DEPENDENCY FACTORS, EPIGENETIC REGULATION OF CCCDNA TRANSCRIPTION AND IMMUNE-MEDIATED DEGRADATION. SEVERAL APPROACHES TARGETING CCCDNA EITHER IN A DIRECT OR INDIRECT MANNER ARE CURRENTLY AT THE STAGE OF DISCOVERY, PRECLINICAL OR EARLY CLINICAL DEVELOPMENT. EXAMPLES INCLUDE GENOME-EDITING APPROACHES, STRATEGIES TARGETING HOST DEPENDENCY FACTORS OR EPIGENETIC GENE REGULATION, NUCLEOCAPSID MODULATORS AND IMMUNE-MEDIATED DEGRADATION. SUMMARY: WHILE DIRECT-TARGETING CCCDNA STRATEGIES ARE STILL LARGELY AT THE PRECLINICAL STAGE OF DEVELOPMENT, CAPSID ASSEMBLY MODULATORS AND IMMUNE-BASED APPROACHES HAVE REACHED THE CLINICAL PHASE. CLINICAL TRIALS ARE ONGOING TO ASSESS THEIR EFFICACY AND SAFETY IN PATIENTS INCLUDING THEIR IMPACT ON VIRAL CCCDNA. COMBINATION THERAPIES PROVIDE ADDITIONAL OPPORTUNITIES TO OVERCOME CURRENT LIMITATIONS OF INDIVIDUAL APPROACHES. 2020 18 6754 40 WILL WE NEED NOVEL COMBINATIONS TO CURE HBV INFECTION? CHRONIC HEPATITIS B IS A NUMERICALLY IMPORTANT CAUSE OF CIRRHOSIS AND HEPATOCELLULAR CARCINOMA. NUCLEOSIDE ANALOGUE THERAPY MAY MODIFY THE RISK. HOWEVER, MAINTENANCE SUPPRESSIVE THERAPY IS REQUIRED, AS A FUNCTIONAL CURE (GENERALLY DEFINED AS LOSS OF HBSAG OFF TREATMENT) IS AN UNCOMMON OUTCOME OF ANTIVIRAL TREATMENT. CHRONIC HEPATITIS B IS A NUMERICALLY IMPORTANT CAUSE OF CIRRHOSIS AND HEPATOCELLULAR CARCINOMA. NUCLEOSIDE ANALOGUE THERAPY MAY MODIFY THE RISK. HOWEVER, MAINTENANCE SUPPRESSIVE THERAPY IS REQUIRED, AS A FUNCTIONAL CURE (GENERALLY DEFINED AS LOSS OF HBSAG OFF TREATMENT) IS AN UNCOMMON OUTCOME OF ANTIVIRAL TREATMENT. CURRENTLY NUMEROUS INVESTIGATIONAL AGENTS BEING DEVELOPED TO EITHER INTERFERE WITH SPECIFIC STEPS IN HBV REPLICATION OR AS HOST CELLULAR TARGETING AGENTS, THAT INHIBIT VIRAL REPLICATION, AND DEPLETE OR INACTIVATE CCCDNA, OR AS IMMUNE MODULATORS. SYNERGISTIC MECHANISMS WILL BE NEEDED TO INCORPORATE A DECREASE IN HBV TRANSCRIPTION, IMPAIRMENT OF TRANSCRIPTION FROM HBV GENOMES, LOSS OF CCCDNA OR ALTERED EPIGENETIC REGULATION OF CCCDNA TRANSCRIPTION, AND IMMUNE MODULATION OR IMMUNOLOGICALLY STIMULATED HEPATOCYTE CELL TURNOVER. NUCLEOSIDE ANALOGUE SUPPRESSED PATIENTS ARE BEING INCLUDED IN MANY CURRENT TRIALS. TRIALS ARE PROGRESSING TO COMBINATION THERAPY AS ADDITIVE OR SYNERGISTIC EFFECTS ARE SOUGHT. THESE TRIALS WILL PROVIDE IMPORTANT INSIGHTS INTO THE BIOLOGY OF HBV AND PERTURBATIONS OF THE IMMUNE RESPONSE, REQUIRED TO EFFECT HBSAG LOSS AT DIFFERENT STAGES OF THE DISEASE. THE PROSPECT OF CURES OF HEPATITIS B WOULD ENSURE THAT A WIDE RANGE OF PATIENTS COULD BE DEEMED CANDIDATES FOR TREATMENT WITH NEW COMPOUNDS IF THESE WERE HIGHLY EFFECTIVE, FINITE AND SAFE. WITHDRAWAL OF THERAPY IN SHORT-TERM TRIALS IS CHALLENGING BECAUSE SHORT-TERM THERAPIES MAY RISK SEVERE HEPATITIS FLARES, AND HEPATIC DECOMPENSATION. THE LIMITED CLINICAL TRIAL DATA TO DATE SUGGEST THAT COMBINATION THERAPY IS INEVITABLE. 2020 19 4055 43 MAPPING OF HISTONE MODIFICATIONS IN EPISOMAL HBV CCCDNA UNCOVERS AN UNUSUAL CHROMATIN ORGANIZATION AMENABLE TO EPIGENETIC MANIPULATION. CHRONIC HEPATITIS B VIRUS (HBV) INFECTION AFFECTS 240 MILLION PEOPLE WORLDWIDE AND IS A MAJOR RISK FACTOR FOR LIVER FAILURE AND HEPATOCELLULAR CARCINOMA. CURRENT ANTIVIRAL THERAPY INHIBITS CYTOPLASMIC HBV GENOMIC REPLICATION, BUT IS NOT CURATIVE BECAUSE IT DOES NOT DIRECTLY AFFECT NUCLEAR HBV CLOSED CIRCULAR DNA (CCCDNA), THE GENOMIC FORM THAT TEMPLATES VIRAL TRANSCRIPTION AND SUSTAINS VIRAL PERSISTENCE. NOVEL APPROACHES THAT DIRECTLY TARGET CCCDNA REGULATION WOULD THEREFORE BE HIGHLY DESIRABLE. CCCDNA IS ASSEMBLED WITH CELLULAR HISTONE PROTEINS INTO CHROMATIN, BUT LITTLE IS KNOWN ABOUT THE REGULATION OF HBV CHROMATIN BY HISTONE POSTTRANSLATIONAL MODIFICATIONS (PTMS). HERE, USING A NEW CCCDNA CHIP-SEQ APPROACH, WE REPORT, TO OUR KNOWLEDGE, THE FIRST GENOME-WIDE MAPS OF PTMS IN CCCDNA-CONTAINING CHROMATIN FROM DE NOVO INFECTED HEPG2 CELLS, PRIMARY HUMAN HEPATOCYTES, AND FROM HBV-INFECTED LIVER TISSUE. WE FIND HIGH LEVELS OF PTMS ASSOCIATED WITH ACTIVE TRANSCRIPTION ENRICHED AT SPECIFIC SITES WITHIN THE HBV GENOME AND, SURPRISINGLY, VERY LOW LEVELS OF PTMS LINKED TO TRANSCRIPTIONAL REPRESSION EVEN AT SILENT HBV PROMOTERS. WE SHOW THAT TRANSCRIPTION AND ACTIVE PTMS IN HBV CHROMATIN ARE REDUCED BY THE ACTIVATION OF AN INNATE IMMUNITY PATHWAY, AND THAT THIS EFFECT CAN BE RECAPITULATED WITH A SMALL MOLECULE EPIGENETIC MODIFYING AGENT, OPENING THE POSSIBILITY THAT CHROMATIN-BASED REGULATION OF CCCDNA TRANSCRIPTION COULD BE A NEW THERAPEUTIC APPROACH TO CHRONIC HBV INFECTION. 2015 20 1478 26 DIVERSE ROLES OF HEPATITIS B VIRUS IN LIVER CANCER. HEPATITIS B VIRUS (HBV) IS A WIDESPREAD HUMAN PATHOGEN RESPONSIBLE FOR ACUTE AND CHRONIC LIVER DISEASES. THE HEPATITIS B BURDEN IS PARTICULARLY HEAVY IN ENDEMIC COUNTRIES, WHERE LIVER CIRRHOSIS AND HEPATOCELLULAR CARCINOMA ARE LEADING CAUSES OF DEATH. HOWEVER, THE ONCOGENIC ROLE OF HBV REMAINS ENIGMATIC. AS THE VIRUS HAS NO CYTOPATHIC EFFECT, LIVER DAMAGE IS ATTRIBUTED TO IMMUNE RESPONSES THAT INDUCE INFLAMMATION, APOPTOSIS AND REGENERATION, FOSTERING THE ACCUMULATION OF GENETIC AND EPIGENETIC ALTERATIONS. IN A MORE DIRECT ACTION, FREQUENT INTEGRATION OF HBV DNA INTO HOST CHROMOSOMES MAY LEAD TO INSERTIONAL MUTAGENESIS OF CANCER-RELATED GENES AND CHROMOSOMAL INSTABILITY. HBV PROTEINS, NOTABLY THE HBX TRANSACTIVATOR, PARTICIPATE AS CO-FACTORS IN ONCOGENESIS. BETTER UNDERSTANDING OF HEPATITIS B PATHOGENESIS IS MANDATORY FOR IMPROVING DISEASE MANAGEMENT. 2012