1 1239 120 CURE AND LONG-TERM REMISSION STRATEGIES. THE MAJORITY OF VIRALLY SUPPRESSED INDIVIDUALS WILL EXPERIENCE RAPID VIRAL REBOUND UPON ANTIRETROVIRAL THERAPY (ART) INTERRUPTION, PROVIDING A STRONG RATIONALE FOR THE DEVELOPMENT OF CURE STRATEGIES. MOREOVER, DESPITE ART VIROLOGICAL CONTROL, HIV INFECTION IS STILL ASSOCIATED WITH CHRONIC IMMUNE ACTIVATION, INFLAMMATION, COMORBIDITIES, AND ACCELERATED AGING. THESE EFFECTS ARE BELIEVED TO BE DUE, IN PART, TO LOW-GRADE PERSISTENT TRANSCRIPTION AND TRICKLING PRODUCTION OF VIRAL PROTEINS FROM THE POOL OF LATENT PROVIRUSES CONSTITUTING THE VIRAL RESERVOIR. IN RECENT YEARS THERE HAS BEEN AN INCREASING INTEREST IN DEVELOPING WHAT HAS BEEN TERMED A FUNCTIONAL CURE FOR HIV. THIS APPROACH ENTAILS THE LONG-TERM, DURABLE CONTROL OF VIRAL EXPRESSION IN THE ABSENCE OF THERAPY, PREVENTING DISEASE PROGRESSION AND TRANSMISSION, DESPITE THE PRESENCE OF DETECTABLE INTEGRATED PROVIRUSES. ONE SUCH STRATEGY, THE BLOCK-AND-LOCK APPROACH FOR A FUNCTIONAL CURE, PROPOSES THE EPIGENETIC SILENCING OF PROVIRAL EXPRESSION, LOCKING THE VIRUS IN A PROFOUND LATENT STATE, FROM WHICH REACTIVATION IS VERY UNLIKELY. THE PROOF-OF-CONCEPT FOR THIS APPROACH WAS DEMONSTRATED WITH THE USE OF A SPECIFIC SMALL MOLECULE TARGETING HIV TRANSCRIPTION. HERE WE REVIEW THE PRINCIPLES BEHIND THE BLOCK-AND-LOCK APPROACH AND SOME OF THE ADDITIONAL STRATEGIES PROPOSED TO SILENCE HIV EXPRESSION. 2022 2 2073 29 EPIGENETIC CROSSTALK IN CHRONIC INFECTION WITH HIV-1. HUMAN IMMUNODEFICIENCY VIRUS 1 (HIV-1) REPLICATES THROUGH THE INTEGRATION OF ITS VIRAL DNA INTO THE GENOME OF HUMAN IMMUNE TARGET CELLS. CHRONICALLY INFECTED INDIVIDUALS THUS CARRY A GENOMIC BURDEN OF VIRUS-DERIVED SEQUENCES THAT PERSISTS THROUGH ANTIRETROVIRAL THERAPY. THIS BURDEN CONSISTS OF A SMALL FRACTION OF INTACT, BUT TRANSCRIPTIONALLY SILENCED, I.E. LATENT, VIRAL GENOMES AND A DOMINANT FRACTION OF DEFECTIVE SEQUENCES. REMARKABLY, ALL VIRAL-DERIVED SEQUENCES ARE SUBJECT TO INTERACTION WITH HOST CELLULAR PHYSIOLOGY AT VARIOUS LEVELS. IN THIS REVIEW, WE FOCUS ON EPIGENETIC ASPECTS OF THIS INTERACTION. WE PROVIDE A COMPREHENSIVE OVERVIEW OF HOW EPIGENETIC MECHANISMS CONTRIBUTE TO ESTABLISHMENT AND MAINTENANCE OF HIV-1 GENE REPRESSION DURING LATENCY. WE FURTHERMORE SUMMARIZE FINDINGS INDICATING THAT HIV-1 INFECTION LEADS TO CHANGES IN THE EPIGENOME OF TARGET AND BYSTANDER IMMUNE CELLS. FINALLY, WE DISCUSS HOW AN IMPROVED UNDERSTANDING OF EPIGENETIC FEATURES AND MECHANISMS INVOLVED IN HIV-1 INFECTION COULD BE EXPLOITED FOR CLINICAL USE. 2020 3 3938 36 LNC(ING)RNAS TO THE "SHOCK AND KILL" STRATEGY FOR HIV-1 CURE. THE ADVENT OF ANTIRETROVIRAL THERAPY ALMOST 25 YEARS AGO HAS TRANSFORMED HIV-1 INFECTION INTO A MANAGEABLE CHRONIC CONDITION, ALBEIT STILL INCURABLE. THE INABILITY OF THE TREATMENT REGIMEN TO ELIMINATE LATENTLY INFECTED CELLS THAT HARBOR THE VIRUS IN AN EPIGENETICALLY SILENT STATE POSES A MAJOR HURDLE. CURRENT CURE APPROACHES ARE FOCUSED ON A "SHOCK AND KILL" STRATEGY THAT USES LATENCY-REVERSING AGENTS TO CHEMICALLY REVERSE THE PROVIRAL QUIESCENCE IN LATENTLY INFECTED CELLS, FOLLOWED BY IMMUNE-MEDIATED CLEARANCE OF REACTIVATED CELLS. TO DATE, HUNDREDS OF COMPOUNDS HAVE BEEN INVESTIGATED FOR VIRAL REACTIVATION, YET NONE HAS RESULTED IN A FUNCTIONAL CURE. THE INSUFFICIENCY OF THESE LATENCY-REVERSING AGENTS (LRAS) ALONE INDICATES A CRITICAL NEED FOR ADDITIONAL, ALTERNATE APPROACHES SUCH AS GENETIC MANIPULATION. LONG NON-CODING RNAS (LNCRNAS) ARE AN EMERGING CLASS OF REGULATORY RNAS WITH FUNCTIONAL ROLES IN MANY CELLULAR PROCESSES, INCLUDING EPIGENETIC MODULATION. A NUMBER OF LNCRNAS HAVE ALREADY BEEN IMPLICATED TO PLAY IMPORTANT ROLES IN HIV-1 LATENCY AND, AS SUCH, PHARMACOLOGICAL MODULATION OF LNCRNAS CONSTITUTES A RATIONAL ALTERNATIVE APPROACH IN HIV-1 CURE RESEARCH. IN THIS REVIEW, WE DISCUSS THE CURRENT STATE OF KNOWLEDGE OF THE ROLE OF LNCRNAS IN HIV-1 INFECTION AND EXPLORE THE SCOPE FOR A LNCRNA-MEDIATED GENETIC APPROACH WITHIN THE SHOCK AND KILL STRATEGY OF HIV-1 CURE. 2021 4 4849 36 OPIOID-MEDIATED HIV-1 IMMUNOPATHOGENESIS. DESPITE THE ABILITY OF COMBINATION ANTIRETROVIRAL THERAPY TO DRAMATICALLY SUPPRESS VIREMIA, THE BRAIN CONTINUES TO BE A RESERVOIR OF HIV-1 LOW-LEVEL REPLICATION. ADDING FURTHER COMPLEXITY TO THIS IS THE COMORBIDITY OF DRUG ABUSE WITH HIV-1 ASSOCIATED NEUROCOGNITIVE DISORDERS AND NEUROHIV. AMONG SEVERAL ABUSED DRUGS, THE USE OF OPIATES IS HIGHLY PREVALENT IN HIV-1 INFECTED INDIVIDUALS, BOTH AS AN ABUSED DRUG AS WELL AS FOR PAIN MANAGEMENT. OPIOIDS AND THEIR RECEPTORS HAVE ATTAINED NOTABLE ATTENTION OWING TO THEIR ABILITY TO MODULATE IMMUNE FUNCTIONS, IN TURN, IMPACTING DISEASE PROGRESSION. VARIOUS CELL CULTURE, ANIMAL AND HUMAN STUDIES HAVE IMPLICATED THE ROLE OF OPIOIDS AND THEIR RECEPTORS IN MODULATING VIRAL REPLICATION AND VIRUS-MEDIATED PATHOLOGY BOTH POSITIVELY AND NEGATIVELY. FURTHER, THE COMBINATORIAL EFFECTS OF HIV-1/HIV-1 PROTEINS AND MORPHINE HAVE DEMONSTRATED ACTIVATION OF INFLAMMATORY SIGNALING IN THE HOST SYSTEM. HEREIN, WE SUMMARIZED THE CURRENT KNOWLEDGE ON THE ROLE OF OPIOIDS ON PERIPHERAL IMMUNOPATHOGENESIS, VIRAL IMMUNOPATHOGENESIS, EPIGENETIC PROFILES OF THE HOST AND VIRAL GENOME, NEUROPATHOGENESIS OF SIV/SHIV-INFECTED NON-HUMAN PRIMATES, BLOOD-BRAIN-BARRIER, HIV-1 VIRAL LATENCY, AND VIRAL REBOUND. OVERALL, THIS REVIEW PROVIDES RECENT INSIGHTS INTO THE ROLE OF OPIOIDS IN HIV-1 IMMUNOPATHOGENESIS. GRAPHICAL ABSTRACT. 2020 5 6706 29 VIRAL GENE PRODUCTS ACTIVELY PROMOTE LATENT INFECTION BY EPIGENETIC SILENCING MECHANISMS. MANY VIRUSES UNDERGO AN ACUTE INFECTION IN THE HOST ORGANISM AND THEN ARE CLEARED BY THE ENSUING HOST IMMUNE RESPONSE, BUT OTHER VIRUSES ESTABLISH A PERSISTENT INFECTION INVOLVING A LATENT INFECTION OR A CHRONIC INFECTION. LATENT INFECTION BY THE HERPESVIRUSES OR HUMAN IMMUNODEFICIENCY VIRUS INVOLVES EPIGENETIC SILENCING OF THE DNA GENOME OR PROVIRAL GENOME, RESPECTIVELY. LATENT INFECTION WAS PREVIOUSLY THOUGHT TO BE A DEFAULT PATHWAY RESULTING FROM INFECTION OF A NONPERMISSIVE CELL, BUT RECENT STUDIES HAVE SHOWN THAT VIRAL GENE PRODUCTS CAN PROMOTE EPIGENETIC SILENCING AND LATENT INFECTION. THIS REVIEW WILL SUMMARIZE THE VIRAL GENE PRODUCTS THAT HAVE BEEN SHOWN TO PROMOTE EPIGENETIC SILENCING OF THE GENOMES AND THEIR POTENTIAL FOR THERAPEUTICS TO TARGET THESE VIRAL GENE PRODUCTS AND DISRUPT OR LOCK IN LATENT INFECTION. 2017 6 2115 31 EPIGENETIC HETEROGENEITY IN HIV-1 LATENCY ESTABLISHMENT. DESPITE PROLONGED ANTIRETROVIRAL THERAPY, HIV-1 PERSISTS AS TRANSCRIPTIONALLY INACTIVE PROVIRUSES. THE HIV-1 LATENCY REMAINS A PRINCIPAL OBSTACLE IN CURING AIDS. IT IS IMPORTANT TO UNDERSTAND MECHANISMS BY WHICH HIV-1 LATENCY IS ESTABLISHED TO MAKE THE LATENT RESERVOIR SMALLER. WE PRESENT A MOLECULAR CHARACTERIZATION OF DISTINCT POPULATIONS AT AN EARLY PHASE OF INFECTION. WE DEVELOPED AN ORIGINAL DUAL-COLOR REPORTER VIRUS TO MONITOR LTR KINETICS FROM ESTABLISHMENT TO MAINTENANCE STAGE. WE FOUND THAT THERE ARE TWO WAYS OF LATENCY ESTABLISHMENT I.E., BY IMMEDIATE SILENCING AND SLOW INACTIVATION FROM ACTIVE INFECTION. HISTONE COVALENT MODIFICATIONS, PARTICULARLY POLYCOMB REPRESSIVE COMPLEX 2 (PRC2)-MEDIATED H3K27 TRIMETHYLATION, APPEARED TO DOMINATE VIRAL TRANSCRIPTION AT THE EARLY PHASE. PRC2 ALSO CONTRIBUTES TO TIME-DEPENDENT LTR DORMANCY IN THE CHRONIC PHASE OF THE INFECTION. SIGNIFICANT DIFFERENCES IN SENSITIVITY AGAINST SEVERAL STIMULI WERE OBSERVED BETWEEN THESE TWO DISTINCT POPULATIONS. THESE RESULTS WILL EXPAND OUR UNDERSTANDING OF HETEROGENEOUS ESTABLISHMENT OF HIV-1 LATENCY POPULATIONS. 2015 7 3379 27 HIV LATENCY AND THE NONCODING RNA THERAPEUTIC LANDSCAPE. THE HUMAN IMMUNODEFICIENCY VIRUS (HIV) BELONGS TO THE SUBFAMILY OF LENTIVIRUSES THAT ARE CHARACTERIZED BY LONG INCUBATION PERIODS AND CHRONIC, PERSISTENT INFECTION. THE VIRUS INTEGRATES INTO THE GENOME OF INFECTED CD4+ CELLS AND, IN A SUBPOPULATION OF CELLS, ADOPTS A TRANSCRIPTIONALLY SILENT STATE, A PROCESS REFERRED TO A VIRAL LATENCY. THIS PROPERTY MAKES IT EXCEEDINGLY DIFFICULT TO THERAPEUTICALLY TARGET THE VIRUS AND ERADICATE INFECTION. IF LEFT UNTREATED, THE INEXORABLE DEMISE OF THE INFECTED INDIVIDUAL'S IMMUNE SYSTEM ENSUES, A CAUSAL RESULT OF ACQUIRED IMMUNODEFICIENCY SYNDROME (AIDS). LATENTLY INFECTED CELLS PROVIDE A RESERVOIR THAT MAINTAINS VIRAL INFECTION INDEFINITELY. IN THIS CHAPTER WE EXPLORE THE ROLE OF NONCODING RNAS IN HIV INFECTION AND IN THE ESTABLISHMENT AND MAINTENANCE OF VIRAL LATENCY. BOTH SHORT AND LONG NONCODING RNAS ARE ENDOGENOUS MODULATORS OF EPIGENETIC REGULATION IN HUMAN CELLS AND PLAY AN ACTIVE ROLE IN GENE EXPRESSION. LASTLY, WE EXPLORE THERAPEUTIC MODALITIES BASED ON EXPRESSED RNAS THAT ARE CAPABLE OF COUNTERING INFECTION, TRANSCRIPTIONALLY REGULATING THE VIRUS, AND SUPPRESSING OR ACTIVATING THE LATENT STATE. 2015 8 6044 34 THE COMPLEX BIOLOGY OF HUMAN CYTOMEGALOVIRUS LATENCY. WHILE MANY VIRAL INFECTIONS ARE LIMITED AND EVENTUALLY RESOLVED BY THE HOST IMMUNE RESPONSE OR BY DEATH OF THE HOST, OTHER VIRUSES ESTABLISH LONG-TERM RELATIONSHIPS WITH THE HOST BY WAY OF A PERSISTENT INFECTION, THAT RANGE FROM CHRONIC VIRUSES THAT MAY BE EVENTUALLY CLEARED TO THOSE THAT ESTABLISH LIFE-LONG PERSISTENT OR LATENT INFECTION. VIRUSES INFECTING HOSTS FROM BACTERIA TO HUMANS ESTABLISH QUIESCENT INFECTIONS THAT MUST BE REACTIVATED TO PRODUCE PROGENY. FOR MAMMALIAN VIRUSES, MOST NOTABLY HERPESVIRUSES, THIS QUIESCENT MAINTENANCE OF VIRAL GENOMES IN THE ABSENCE OF VIRUS REPLICATION IS REFERRED TO AS LATENCY. THE LATENT STRATEGY ALLOWS THE VIRUS TO PERSIST QUIESCENTLY WITHIN A SINGLE HOST UNTIL CONDITIONS INDICATE A NEED TO REACTIVATE TO REACH A NEW HOST OR, TO RE-SEED A RESERVOIR WITHIN THE HOST. HERE, I REVIEW COMMON THEMES IN VIRAL STRATEGIES TO REGULATE THE LATENT CYCLE AND REACTIVATE FROM IT RANGING FROM BACTERIOPHAGE TO HERPESVIRUSES WITH A FOCUS ON HUMAN CYTOMEGALOVIRUS (HCMV). THEMES CENTRAL TO HERPESVIRUS LATENCY INCLUDE, EPIGENETIC REPRESSION OF VIRAL GENE EXPRESSION AND MECHANISMS TO REGULATE HOST SIGNALING AND SURVIVAL. CRITICAL TO THE SUCCESS OF A LATENT PROGRAM ARE MECHANISMS BY WHICH THE VIRUS CAN "SENSE" FLUCTUATIONS IN HOST BIOLOGY (WITHIN THE HOST) OR ENVIRONMENT (OUTSIDE THE HOST) AND MAKE APPROPRIATE "DECISIONS" TO MAINTAIN LATENCY OR RE-INITIATE THE REPLICATIVE PROGRAM. THE SIGNALS OR ENVIRONMENTS THAT INDICATE THE ESTABLISHMENT OF A LATENT STATE, THE VERY NATURE OF THE LATENT STATE, AS WELL AS THE SIGNALS DRIVING REACTIVATION HAVE BEEN TOPICS OF INTENSE STUDY FROM BACTERIOPHAGE TO HUMAN VIRUSES, AS THESE QUESTIONS ENCOMPASS THE HEIGHT OF COMPLEXITY IN VIRUS-HOST INTERACTIONS-WHERE THE HOST AND THE VIRUS COEXIST. 2022 9 6712 32 VIRUS-HOST INTERPLAY IN HEPATITIS B VIRUS INFECTION AND EPIGENETIC TREATMENT STRATEGIES. WORLDWIDE, CHRONIC HEPATITIS B VIRUS (HBV) INFECTION IS A MAJOR HEALTH PROBLEM AND NO CURE EXISTS. IMPORTANTLY, HEPATOCYTE INTRUSION BY HBV PARTICLES RESULTS IN A COMPLEX DEREGULATION OF BOTH VIRAL AND HOST CELLULAR GENETIC AND EPIGENETIC PROCESSES. AMONG THE ATTEMPTS TO DEVELOP NOVEL THERAPEUTIC APPROACHES AGAINST HBV INFECTION, SEVERAL OPTIONS TARGETING THE EPIGENOMIC REGULATION OF HBV REPLICATION ARE GAINING ATTENTION. THESE INCLUDE THE EXPERIMENTAL TREATMENT WITH 'EPIDRUGS'. MOREOVER, AS A TARGETED APPROACH, THE PRINCIPLE OF 'EPIGENETIC EDITING' RECENTLY IS BEING EXPLOITED TO CONTROL VIRAL REPLICATION. SILENCING OF HBV BY SPECIFIC REWRITING OF EPIGENETIC MARKS MIGHT DIMINISH VIRAL REPLICATION, VIREMIA, AND INFECTIVITY, EVENTUALLY CONTROLLING THE DISEASE AND ITS COMPLICATIONS. ADDITIONALLY, EPIGENETIC EDITING CAN BE USED AS AN EXPERIMENTAL TOOL TO INCREASE OUR LIMITED UNDERSTANDING REGARDING THE ROLE OF EPIGENETIC MODIFICATIONS IN VIRAL INFECTIONS. AIMING FOR PERMANENT EPIGENETIC REPROGRAMMING OF THE VIRAL GENOME WITHOUT UNSPECIFIC SIDE EFFECTS, THIS BREAKTHROUGH MAY PAVE THE ROADS FOR AN AMBITIOUS TECHNOLOGICAL PURSUIT: TO START DESIGNING A CURATIVE APPROACH UTILIZING MANIPULATIVE MOLECULAR THERAPIES FOR VIRAL INFECTIONS IN VIVO. 2017 10 6641 30 UNRAVELING THE MULTIFACETED NATURE OF CD8 T CELL EXHAUSTION PROVIDES THE MOLECULAR BASIS FOR THERAPEUTIC T CELL RECONSTITUTION IN CHRONIC HEPATITIS B AND C. IN CHRONIC HEPATITIS B AND C VIRUS INFECTIONS PERSISTENTLY ELEVATED ANTIGEN LEVELS DRIVE CD8+ T CELLS TOWARD A PECULIAR DIFFERENTIATION STATE KNOWN AS T CELL EXHAUSTION, WHICH POSES CRUCIAL CONSTRAINTS TO ANTIVIRAL IMMUNITY. AVAILABLE EVIDENCE INDICATES THAT T CELL EXHAUSTION IS ASSOCIATED WITH A SERIES OF METABOLIC AND SIGNALING DEREGULATIONS AND WITH A VERY PECULIAR EPIGENETIC STATUS WHICH ALL TOGETHER LEAD TO REDUCED EFFECTOR FUNCTIONS. A CLEAR MECHANISTIC NETWORK EXPLAINING HOW INTRACELLULAR METABOLIC DERANGEMENTS, TRANSCRIPTIONAL AND SIGNALING ALTERATIONS SO FAR DESCRIBED ARE INTERCONNECTED IN A COMPREHENSIVE AND UNIFIED VIEW OF THE T CELL EXHAUSTION DIFFERENTIATION PROFILE IS STILL LACKING. ADDRESSING THIS ISSUE IS OF KEY IMPORTANCE FOR THE DEVELOPMENT OF INNOVATIVE STRATEGIES TO BOOST HOST IMMUNITY IN ORDER TO ACHIEVE VIRAL CLEARANCE. THIS REVIEW WILL DISCUSS THE CURRENT KNOWLEDGE IN HBV AND HCV INFECTIONS, ADDRESSING HOW INNATE IMMUNITY, METABOLIC DERANGEMENTS, EXTENSIVE STRESS RESPONSES AND ALTERED EPIGENETIC PROGRAMS MAY BE TARGETED TO RESTORE FUNCTIONALITY AND RESPONSIVENESS OF VIRUS-SPECIFIC CD8 T CELLS IN THE CONTEXT OF CHRONIC VIRUS INFECTIONS. 2021 11 1057 27 CLINICAL MANIFESTATIONS AND EPIGENETIC REGULATION OF ORAL HERPESVIRUS INFECTIONS. THE ORAL CAVITY IS OFTEN THE FIRST SITE WHERE VIRUSES INTERACT WITH THE HUMAN BODY. THE ORAL EPITHELIUM IS A MAJOR SITE OF VIRAL ENTRY, REPLICATION AND SPREAD TO OTHER CELL TYPES, WHERE CHRONIC INFECTION CAN BE ESTABLISHED. IN ADDITION, SALIVA HAS BEEN SHOWN AS A PRIMARY ROUTE OF PERSON-TO-PERSON TRANSMISSION FOR MANY VIRUSES. FROM A CLINICAL PERSPECTIVE, VIRAL INFECTION CAN LEAD TO SEVERAL ORAL MANIFESTATIONS, RANGING FROM COMMON INTRAORAL LESIONS TO TUMORS. DESPITE THE CLINICAL AND BIOLOGICAL RELEVANCE OF INITIAL ORAL INFECTION, LITTLE IS KNOWN ABOUT THE MECHANISM OF REGULATION OF THE VIRAL LIFE CYCLE IN THE ORAL CAVITY. SEVERAL VIRUSES UTILIZE HOST EPIGENETIC MACHINERY TO PROMOTE THEIR OWN LIFE CYCLE. IMPORTANTLY, VIRAL HIJACKING OF HOST CHROMATIN-MODIFYING ENZYMES CAN ALSO LEAD TO THE DYSREGULATION OF HOST FACTORS AND IN THE CASE OF ONCOGENIC VIRUSES MAY ULTIMATELY PLAY A ROLE IN PROMOTING TUMORIGENESIS. GIVEN THE KNOWN ROLES OF EPIGENETIC REGULATION OF VIRAL INFECTION, EPIGENETIC-TARGETED ANTIVIRAL THERAPY HAS BEEN RECENTLY EXPLORED AS A THERAPEUTIC OPTION FOR CHRONIC VIRAL INFECTION. IN THIS REVIEW, WE HIGHLIGHT THREE HERPESVIRUSES WITH KNOWN ROLES IN ORAL INFECTION, INCLUDING HERPES SIMPLEX VIRUS TYPE 1, EPSTEIN-BARR VIRUS AND KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS. WE FOCUS ON THE RESPECTIVE ORAL CLINICAL MANIFESTATIONS OF THESE VIRUSES AND THEIR EPIGENETIC REGULATION, WITH A SPECIFIC EMPHASIS ON THE VIRAL LIFE CYCLE IN THE ORAL EPITHELIUM. 2021 12 2600 23 EPIGENETICS REGULATION DURING VIRUS-HOST INTERACTION AND THEIR EFFECTS ON THE VIRUS AND HOST CELL. EPIGENETICS, A FIELD OF STUDY FOCUSED ON CELLULAR GENE REGULATION INDEPENDENT OF DNA SEQUENCE ALTERATIONS, ENCOMPASSES DNA METHYLATION, HISTONE MODIFICATION AND MICRORNA MODIFICATION. EPIGENETICS PROCESSES PLAY A PIVOTAL ROLE IN GOVERNING THE LIFE CYCLES OF VIRUSES, ENABLING THEIR TRANSMISSION, PERSISTENCE, AND MAINTENANCE WITH IN HOST ORGANISMS. THIS REVIEW EXAMINES THE EPIGENETICS REGULATION OF DIVERSE VIRUS INCLUDING ORTHOMOXYVIRUSES, CORONAVIRUS, RETROVIRIDAE, MONONEGAVIRALES, AND POXVIRUSES AMONG OTHERS. THE INVESTIGATION ENCOMPASSES TEN REPRESENTATIVE VIRUSES FROM THESE FAMILIES. DETAILED EXPLORATION OF THE EPIGENETIC MECHANISMS UNDERLYING EACH VIRUS TYPE, INVOLVING MIRNA MODIFICATION, HISTONE MODIFICATION AND DNA METHYLATION, SHEDS LIGHT ON THE INTRICATE AND MULTIFACETED EPIGENETIC INTERPLAY BETWEEN VIRUSES AND THEIR HOSTS. FURTHERMORE, THIS REVIEW INVESTIGATES THE INFLUENCE OF THESE EPIGENETIC PROCESSES ON INFECTION CYCLES, EMPHASIZING THE UTILIZATION OF EPIGENETICS BY VIRUSES SUCH AS EPSTEIN-BARR VIRUS AND HUMAN IMMUNODEFICIENCY VIRUS (HIV) TO REGULATE GENE EXPRESSION DURING CHRONIC OR LATENT INFECTIONS, CONTROL LATENCY, AND TRANSITION TO LYTIC INFECTION. FINALLY, THE PAPER EXPLORES THE NOVEL TREATMENTS POSSIBILITIES STEMMING FROM THIS EPIGENETIC UNDERSTANDING. 2023 13 5901 26 T-CELL HETEROGENEITY, PROGENITOR-PROGENY RELATIONSHIPS, AND FUNCTION DURING LATENT AND CHRONIC VIRAL INFECTIONS. UPON RESOLUTION OF AN ACUTE VIRAL INFECTION, DURING LATENT-REACTIVATING INFECTION AND DURING CHRONIC ACTIVE INFECTIONS VIRUS-SPECIFIC T-CELLS DIFFERENTIATE INTO DISTINCT SUBSETS THAT DIFFER IN PHENOTYPE, LONGEVITY, TRANSCRIPTIONAL, METABOLIC, AND EPIGENETIC PROFILES, AND EFFECTOR FUNCTIONS. WITH RECENT ADVANCES IN SINGLE-CELL PROFILING, THIS SUBSTANTIAL HETEROGENEITY HAS BECOME APPARENT AND NEW SUBSETS OF VIRUS-SPECIFIC T CELLS, EITHER OF STABLE OR TRANSITORY NATURE, ARE BEING IDENTIFIED. A UNIFYING PRINCIPLE OF T CELLS EMERGING IN THESE DIFFERENT CONDITIONS IS THEIR PRECURSOR-PROGENY RELATIONSHIP. FOR ACUTE AND RESOLVED VIRAL INFECTIONS, THIS RELATIONSHIP BECOMES APPARENT DURING RE-CHALLENGE, WHEREAS A CONSTANT DIFFERENTIATION OF PROGENITOR T CELLS INTO MORE DIFFERENTIATED CELLS OCCURS DURING LATENT-REACTIVATING AND ACTIVE CHRONIC VIRAL INFECTIONS. IN THIS REVIEW, WE SUMMARIZE AND DISCUSS CURRENT KNOWLEDGE ABOUT T-CELL HETEROGENEITY AND PROGENITOR-PROGENY RELATIONSHIPS IN THE SETTING OF PERSISTENT VIRAL INFECTIONS. 2023 14 6754 32 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 15 4434 23 MOLECULAR DISSECTION OF CD8(+) T-CELL DYSFUNCTION. CHRONIC VIRAL INFECTIONS AND CANCER OFTEN LEAD TO THE EMERGENCE OF DYSFUNCTIONAL OR 'EXHAUSTED' CD8(+) T CELLS, AND THE RESTORATION OF THEIR FUNCTIONS IS CURRENTLY THE FOCUS OF THERAPEUTIC INTERVENTIONS. IN THIS REVIEW, WE DETAIL RECENT ADVANCES IN THE ANNOTATION OF THE GENE MODULES AND THE EPIGENETIC LANDSCAPE ASSOCIATED WITH T-CELL DYSFUNCTION. TOGETHER WITH ANALYSIS OF SINGLE-CELL TRANSCRIPTOMES, THESE FINDINGS HAVE ENABLED A DEEPER AND MORE PRECISE UNDERSTANDING OF THE TRANSCRIPTIONAL MECHANISMS THAT INDUCE AND MAINTAIN THE DYSFUNCTIONAL STATE AND HIGHLIGHT THE HETEROGENEITY OF CD8(+) T-CELL PHENOTYPES PRESENT IN CHRONICALLY INFLAMED TISSUE. WE DISCUSS THE RELEVANCE OF THESE FINDINGS FOR UNDERSTANDING THE TRANSCRIPTIONAL AND SPATIAL REGULATION OF DYSFUNCTIONAL T CELLS AND FOR THE DESIGN OF THERAPEUTICS. 2017 16 451 37 APPLICATION OF ATAC-SEQ IN TUMOR-SPECIFIC T CELL EXHAUSTION. RESEARCHES SHOW THAT CHRONIC VIRAL INFECTION AND PERSISTENT ANTIGEN AND/OR INFLAMMATORY SIGNAL EXPOSURE IN CANCER CAUSES THE FUNCTIONAL STATUS OF T CELLS TO BE ALTERED, MAINLY BY MAJOR CHANGES IN THE EPIGENETIC AND METABOLIC ENVIRONMENT, WHICH THEN LEADS TO T CELL EXHAUSTION. THE DISCOVERY OF THE IMMUNE CHECKPOINT PATHWAY IS AN IMPORTANT MILESTONE IN UNDERSTANDING AND REVERSING T CELL EXHAUSTION. ANTIBODIES TARGETING THESE PATHWAYS HAVE SHOWN SUPERIOR ABILITY TO REVERSE T CELL EXHAUSTION. HOWEVER, THERE ARE STILL SOME LIMITATIONS IN IMMUNE CHECKPOINT BLOCKING THERAPY, SUCH AS THE SHORT-TERM NATURE OF THERAPEUTIC EFFECTS AND HIGH INDIVIDUAL HETEROGENEITY. ASSAY FOR TRANSPOSASE-ACCESSIBLE CHROMATIN WITH SEQUENCING(ATAC-SEQ) IS A METHOD USED TO ANALYZE THE ACCESSIBILITY OF WHOLE-GENOME CHROMATIN. IT USES HYPERACTIVE TN5 TRANSPOSASE TO ASSESS CHROMATIN ACCESSIBILITY. RECENTLY, A GROWING NUMBER OF STUDIES HAVE REPORTED THAT ATAC-SEQ CAN BE USED TO CHARACTERIZE THE DYNAMIC CHANGES OF EPIGENETICS IN THE PROCESS OF T CELL EXHAUSTION. IT HAS BEEN DETERMINED THAT IMMUNE CHECKPOINT BLOCKING CAN ONLY TEMPORARILY RESTORE THE FUNCTION OF EXHAUSTED T CELLS BECAUSE OF AN IRREVERSIBLE CHANGE IN THE EPIGENETICS OF EXHAUSTED T CELLS. IN THIS STUDY, WE REVIEW THE LATEST DEVELOPMENTS, WHICH PROVIDE A CLEARER MOLECULAR UNDERSTANDING OF T CELL EXHAUSTION, REVEAL POTENTIAL NEW THERAPEUTIC TARGETS FOR PERSISTENT VIRAL INFECTION AND CANCER, AND PROVIDE NEW INSIGHTS FOR DESIGNING EFFECTIVE IMMUNOTHERAPY FOR TREATING CANCER AND CHRONIC INFECTION. 2023 17 6449 41 THERAPEUTIC TARGETING OF TELOMERASE. TELOMERE LENGTH AND CELL FUNCTION CAN BE PRESERVED BY THE HUMAN REVERSE TRANSCRIPTASE TELOMERASE (HTERT), WHICH SYNTHESIZES THE NEW TELOMERIC DNA FROM A RNA TEMPLATE, BUT IS NORMALLY RESTRICTED TO CELLS NEEDING A HIGH PROLIFERATIVE CAPACITY, SUCH AS STEM CELLS. CONSEQUENTLY, TELOMERASE-BASED THERAPIES TO ELONGATE SHORT TELOMERES ARE DEVELOPED, SOME OF WHICH HAVE SUCCESSFULLY REACHED THE STAGE I IN CLINICAL TRIALS. TELOMERASE IS ALSO PERMISSIVE FOR TUMORIGENESIS AND 90% OF ALL MALIGNANT TUMORS USE TELOMERASE TO OBTAIN IMMORTALITY. THUS, REVERSAL OF TELOMERASE UPREGULATION IN TUMOR CELLS IS A POTENTIAL STRATEGY TO TREAT CANCER. NATURAL AND SMALL-MOLECULE TELOMERASE INHIBITORS, IMMUNOTHERAPEUTIC APPROACHES, OLIGONUCLEOTIDE INHIBITORS, AND TELOMERASE-DIRECTED GENE THERAPY ARE USEFUL TREATMENT STRATEGIES. TELOMERASE IS MORE WIDELY EXPRESSED THAN ANY OTHER TUMOR MARKER. THE LOW EXPRESSION IN NORMAL TISSUES, TOGETHER WITH THE LONGER TELOMERES IN NORMAL STEM CELLS VERSUS CANCER CELLS, PROVIDES SOME DEGREE OF SPECIFICITY WITH LOW RISK OF TOXICITY. HOWEVER, LONG TERM TELOMERASE INHIBITION MAY ELICIT NEGATIVE EFFECTS IN HIGHLY-PROLIFERATIVE CELLS WHICH NEED TELOMERASE FOR SURVIVAL, AND IT MAY INTERFERE WITH TELOMERE-INDEPENDENT PHYSIOLOGICAL FUNCTIONS. MOREOVER, ONLY A FEW HTERT MOLECULES ARE REQUIRED TO OVERCOME SENESCENCE IN CANCER CELLS, AND TELOMERASE INHIBITION REQUIRES PROLIFERATING CELLS OVER A SUFFICIENT NUMBER OF POPULATION DOUBLINGS TO INDUCE TUMOR SUPPRESSIVE SENESCENCE. THESE LIMITATIONS MAY EXPLAIN THE MODERATE SUCCESS RATES IN MANY CLINICAL STUDIES. DESPITE EXTENSIVE STUDIES, ONLY ONE VACCINE AND ONE TELOMERASE ANTAGONIST ARE ROUTINELY USED IN CLINICAL WORK. FOR COMPLETE ERADICATION OF ALL SUBPOPULATIONS OF CANCER CELLS A SIMULTANEOUS TARGETING OF SEVERAL MECHANISMS WILL LIKELY BE NEEDED. POSSIBLE TECHNICAL IMPROVEMENTS HAVE BEEN PROPOSED INCLUDING THE DEVELOPMENT OF MORE SPECIFIC INHIBITORS, METHODS TO INCREASE THE EFFICACY OF VACCINATION METHODS, AND PERSONALIZED APPROACHES. TELOMERASE ACTIVATION AND CELL REJUVENATION IS SUCCESSFULLY USED IN REGENERATIVE MEDICINE FOR TISSUE ENGINEERING AND RECONSTRUCTIVE SURGERY. HOWEVER, THERE ARE ALSO A NUMBER OF PITFALLS IN THE TREATMENT WITH TELOMERASE ACTIVATING PROCEDURES FOR THE WHOLE ORGANISM AND FOR LONGER PERIODS OF TIME. EXTENDED CELL LIFESPAN MAY ACCUMULATE RARE GENETIC AND EPIGENETIC ABERRATIONS THAT CAN CONTRIBUTE TO MALIGNANT TRANSFORMATION. THEREFORE, NOVEL VECTOR SYSTEMS HAVE BEEN DEVELOPED FOR A 'MILD' INTEGRATION OF TELOMERASE INTO THE HOST GENOME AND LOSS OF THE VECTOR IN RAPIDLY-PROLIFERATING CELLS. IT IS CURRENTLY UNCLEAR IF THIS TECHNIQUE CAN ALSO BE USED IN HUMAN BEINGS TO TREAT CHRONIC DISEASES, SUCH AS ATHEROSCLEROSIS. 2016 18 4340 27 MIGRATION OF STEM-LIKE CD8 T CELLS BETWEEN TISSUE MICROENVIRONMENTS UNDERPINS SUCCESSFUL ANTI-TUMOUR IMMUNE RESPONSES. THE CLINICAL SUCCESS OF IMMUNE CHECKPOINT BLOCKADE IN SOME PATIENTS HAS TRANSFORMED TREATMENT APPROACHES IN CANCER AND OFFERS THE HOPE OF DURABLE CURATIVE RESPONSES. BUILDING FROM STUDIES OF CHRONIC INFECTION, THE COMPOSITION OF TUMOUR INFILTRATING LYMPHOCYTES AND IN PARTICULAR, THE SPECTRUM OF EXHAUSTED CD8 T CELLS HAS NOW BEEN CHARACTERIZED IN DETAIL, PROFILING THE PHENOTYPE, FUNCTION, TRANSCRIPTIONAL REGULATION AND EVEN THE EPIGENETIC CHANGES. HOWEVER, WHAT REMAINS LESS CLEAR IS HOW INTRATUMOURAL IMMUNE CELLS INTERFACE WITH POPULATIONS IN THE PERIPHERY, BOTH IN TERMS OF SUSTAINING THE RESPONSE IN CANCER, BUT ALSO IN ESTABLISHING SYSTEMIC MEMORY RESPONSES THAT CAN PROVIDE LONG-TERM PROTECTION. HERE WE WILL SUCCINCTLY REVIEW THE CURRENT UNDERSTANDING OF THE ANTI-TUMOUR RESPONSE, CONSIDER THE TISSUE MICROENVIRONMENTS THAT SUPPORT KEY CELLULAR SUBSETS AND THE EXTENT TO WHICH CELLULAR MIGRATION BETWEEN THESE SITES IMPACTS THE RESPONSE. 2023 19 6479 39 TOWARD A NEW ERA OF HEPATITIS B VIRUS THERAPEUTICS: THE PURSUIT OF A FUNCTIONAL CURE. HEPATITIS B VIRUS (HBV) INFECTION, ALTHOUGH PREVENTABLE BY VACCINATION, REMAINS A GLOBAL HEALTH PROBLEM AND A MAJOR CAUSE OF CHRONIC LIVER DISEASE. ALTHOUGH CURRENT TREATMENT STRATEGIES SUPPRESS VIRAL REPLICATION VERY EFFICIENTLY, THE OPTIMAL ENDPOINT OF HEPATITIS B SURFACE ANTIGEN (HBSAG) CLEARANCE IS RARELY ACHIEVED. MOREOVER, THE THORNY PROBLEMS OF PERSISTENT CHROMATIN-LIKE COVALENTLY CLOSED CIRCULAR DNA AND THE PRESENCE OF INTEGRATED HBV DNA IN THE HOST GENOME ARE IGNORED. THEREFORE, THE SCIENTIFIC COMMUNITY HAS FOCUSED ON DEVELOPING INNOVATIVE THERAPEUTIC APPROACHES TO ACHIEVE A FUNCTIONAL CURE OF HBV, DEFINED AS UNDETECTABLE HBV DNA AND HBSAG LOSS OVER A LIMITED TREATMENT PERIOD. A DEEPER UNDERSTANDING OF THE HBV LIFE CYCLE HAS LED TO THE INTRODUCTION OF NOVEL DIRECT-ACTING ANTIVIRALS THAT EXERT THEIR FUNCTION THROUGH MULTIPLE MECHANISMS, INCLUDING INHIBITION OF VIRAL ENTRY, TRANSCRIPTIONAL SILENCING, EPIGENETIC MANIPULATION, INTERFERENCE WITH CAPSID ASSEMBLY, AND DISRUPTION OF HBSAG RELEASE. IN PARALLEL, ANOTHER CATEGORY OF NEW DRUGS AIMS TO RESTORE DYSREGULATED IMMUNE FUNCTION IN CHRONIC HEPATITIS B ACCOMPANIED BY LETHARGIC CELLULAR AND HUMORAL RESPONSES. STIMULATION OF INNATE IMMUNITY BY PATTERN-RECOGNITION RECEPTOR AGONISTS LEADS TO UPREGULATION OF ANTIVIRAL CYTOKINE EXPRESSION AND APPEARS TO CONTRIBUTE TO HBV CONTAINMENT. IMMUNE CHECKPOINT INHIBITORS AND ADOPTIVE TRANSFER OF GENETICALLY ENGINEERED T CELLS ARE BREAKTHROUGH TECHNOLOGIES CURRENTLY BEING EXPLORED THAT MAY ELICIT POTENT HBV-SPECIFIC T-CELL RESPONSES. IN ADDITION, SEVERAL CLINICAL TRIALS ARE ATTEMPTING TO CLARIFY THE ROLE OF THERAPEUTIC VACCINATION IN THIS SETTING. ULTIMATELY, IT IS INCREASINGLY RECOGNIZED THAT ELIMINATION OF HBV REQUIRES A TREATMENT REGIMEN BASED ON A COMBINATION OF MULTIPLE DRUGS. THIS REVIEW DESCRIBES THE RATIONALE FOR PROGRESSIVE THERAPEUTIC INTERVENTIONS AND DISCUSSES THE LATEST FINDINGS IN THE FIELD OF HBV THERAPEUTICS. 2021 20 3731 22 INNATE AND ADAPTIVE IMMUNE REGULATION DURING CHRONIC VIRAL INFECTIONS. CHRONIC VIRAL INFECTIONS REPRESENT A UNIQUE CHALLENGE TO THE INFECTED HOST. PERSISTENTLY REPLICATING VIRUSES OUTCOMPETE OR SUBVERT THE INITIAL ANTIVIRAL RESPONSE, ALLOWING THE ESTABLISHMENT OF CHRONIC INFECTIONS THAT RESULT IN CONTINUOUS STIMULATION OF BOTH THE INNATE AND ADAPTIVE IMMUNE COMPARTMENTS. THIS CAUSES A PROFOUND REPROGRAMMING OF THE HOST IMMUNE SYSTEM, INCLUDING ATTENUATION AND PERSISTENT LOW LEVELS OF TYPE I INTERFERONS, PROGRESSIVE LOSS (OR EXHAUSTION) OF CD8(+) T CELL FUNCTIONS, AND SPECIALIZATION OF CD4(+) T CELLS TO PRODUCE INTERLEUKIN-21 AND PROMOTE ANTIBODY-MEDIATED IMMUNITY AND IMMUNE REGULATION. EPIGENETIC, TRANSCRIPTIONAL, POSTTRANSCRIPTIONAL, AND METABOLIC CHANGES UNDERLIE THIS ADAPTATION OR RECALIBRATION OF IMMUNE CELLS TO THE EMERGING NEW ENVIRONMENT IN ORDER TO STRIKE AN OFTEN IMPERFECT BALANCE BETWEEN THE HOST AND THE INFECTIOUS PATHOGEN. IN THIS REVIEW WE DISCUSS THE COMMON IMMUNOLOGICAL HALLMARKS OBSERVED ACROSS A RANGE OF DIFFERENT PERSISTENTLY REPLICATING VIRUSES AND HOST SPECIES, THE UNDERLYING MOLECULAR MECHANISMS, AND THE BIOLOGICAL AND CLINICAL IMPLICATIONS. 2015