1 6802 49 [EPIGENETIC MECHANISMS IN MODELS OF CHRONIC PAIN - A TARGET FOR NOVEL THERAPY?]. EVIDENCE OF EPIGENETICS' ROLE IN PAIN RESPONSE IS ACCUMULATING IN RECENT YEARS. TIGHTLY REGULATED EPIGENETIC ALTERATIONS ON DNA AND HISTONES IN THE SENSORY CIRCUIT SHAPE THE PHYSIOLOGICAL RESPONSE TO INJURY. ALTERING THOSE EPIGENETIC PROCESSES HINDERS THERAPEUTIC POTENTIAL IN PAIN. THIS REVIEW PROVIDES AN OVERVIEW OF EPIGENOMIC MODIFICATION IN THE DEVELOPMENT OF CHRONIC PAIN, AND SUMMARIZES THE THERAPEUTIC POTENTIAL TO ALTER EPIGENETIC PROCESSES. 2018 2 2315 25 EPIGENETIC REGULATION OF FERROPTOSIS-ASSOCIATED GENES AND ITS IMPLICATION IN CANCER THERAPY. FERROPTOSIS IS AN EVOLUTIONARILY CONSERVED FORM OF REGULATED CELL DEATH TRIGGERED BY IRON-DEPENDENT PHOSPHOLIPID PEROXIDATION. FERROPTOSIS CONTRIBUTES TO THE MAINTENANCE OF TISSUE HOMEOSTASIS UNDER PHYSIOLOGICAL CONDITIONS WHILE ITS ABERRATION IS TIGHTLY CONNECTED WITH LOTS OF PATHOPHYSIOLOGICAL PROCESSES SUCH AS ACUTE TISSUE INJURY, CHRONIC DEGENERATIVE DISEASE, AND TUMORIGENESIS. EPIGENETIC REGULATION CONTROLS CHROMATIN STRUCTURE AND GENE EXPRESSION BY WRITING/READING/ERASING THE COVALENT MODIFICATIONS ON DNA, HISTONE, AND RNA, WITHOUT ALTERING THE DNA SEQUENCE. ACCUMULATING EVIDENCES SUGGEST THAT EPIGENETIC REGULATION IS INVOLVED IN THE DETERMINATION OF CELLULAR VULNERABILITY TO FERROPTOSIS. HERE, WE SUMMARIZE THE RECENT ADVANCES ON THE EPIGENETIC MECHANISMS THAT CONTROL THE EXPRESSION OF FERROPTOSIS-ASSOCIATED GENES AND THEREBY THE FERROPTOSIS PROCESS. MOREOVER, THE POTENTIAL VALUE OF EPIGENETIC DRUGS IN TARGETING OR SYNERGIZING FERROPTOSIS DURING CANCER THERAPY IS ALSO DISCUSSED. 2022 3 2344 18 EPIGENETIC REGULATION OF MACROPHAGES: FROM HOMEOSTASIS MAINTENANCE TO HOST DEFENSE. MACROPHAGES ARE CRUCIAL MEMBERS OF THE INNATE IMMUNE RESPONSE AND IMPORTANT REGULATORS. THE DIFFERENTIATION AND ACTIVATION OF MACROPHAGES REQUIRE THE TIMELY REGULATION OF GENE EXPRESSION, WHICH DEPENDS ON THE INTERACTION OF A VARIETY OF FACTORS, INCLUDING TRANSCRIPTION FACTORS AND EPIGENETIC MODIFICATIONS. EPIGENETIC CHANGES ALSO GIVE MACROPHAGES THE ABILITY TO SWITCH RAPIDLY BETWEEN CELLULAR PROGRAMS, INDICATING THE ABILITY OF EPIGENETIC MECHANISMS TO AFFECT PHENOTYPE PLASTICITY. IN THIS REVIEW, WE FOCUS ON KEY EPIGENETIC EVENTS ASSOCIATED WITH MACROPHAGE FATE, HIGHLIGHTING EVENTS RELATED TO THE MAINTENANCE OF TISSUE HOMEOSTASIS, RESPONSES TO DIFFERENT STIMULI AND THE FORMATION OF INNATE IMMUNE MEMORY. FURTHER UNDERSTANDING OF THE EPIGENETIC REGULATION OF MACROPHAGES WILL BE HELPFUL FOR MAINTAINING TISSUE INTEGRITY, PREVENTING CHRONIC INFLAMMATORY DISEASES AND DEVELOPING THERAPIES TO ENHANCE HOST DEFENSE. 2020 4 6322 32 THE ROLE FOR EPIGENETIC MODIFICATIONS IN PAIN AND ANALGESIA RESPONSE. PAIN REMAINS A POORLY UNDERSTOOD AND MANAGED SYMPTOM. A LIMITED MECHANISTIC UNDERSTANDING OF INTERINDIVIDUAL DIFFERENCES IN PAIN AND ANALGESIA RESPONSE SHAPES CURRENT APPROACHES TO ASSESSMENT AND TREATMENT. OPPORTUNITIES EXIST TO IMPROVE PAIN CARE THROUGH INCREASED UNDERSTANDING OF HOW DYNAMIC EPIGENOMIC REMODELING SHAPES INJURY, ILLNESS, PAIN, AND TREATMENT RESPONSE. TIGHTLY REGULATED ALTERATIONS OF THE DNA-HISTONE CHROMATIN COMPLEX ENABLE CELLS TO CONTROL TRANSCRIPTION, REPLICATION, GENE EXPRESSION, AND PROTEIN PRODUCTION. PATHOLOGICAL ALTERATIONS TO CHROMATIN SHAPE THE ABILITY OF THE CELL TO RESPOND TO PHYSIOLOGIC AND ENVIRONMENTAL CUES LEADING TO DISEASE AND REDUCED TREATMENT EFFECTIVENESS. THIS REVIEW PROVIDES AN OVERVIEW OF CRITICAL EPIGENETIC PROCESSES SHAPING PATHOLOGY AND PAIN, HIGHLIGHTS CURRENT RESEARCH SUPPORT FOR THE ROLE OF EPIGENOMIC MODIFICATION IN THE DEVELOPMENT OF CHRONIC PAIN, AND SUMMARIZES THE THERAPEUTIC POTENTIAL TO ALTER EPIGENETIC PROCESSES TO IMPROVE HEALTH OUTCOMES. 2013 5 700 23 BROMODOMAIN-CONTAINING PROTEIN 4 (BRD4): A KEY PLAYER IN INFLAMMATORY BOWEL DISEASE AND POTENTIAL TO INSPIRE EPIGENETIC THERAPEUTICS. INTRODUCTION: INFLAMMATORY BOWEL DISEASES (IBDS) ARE DEBILITATING CHRONIC INFLAMMATORY DISORDERS WITH INCREASING PREVALENCE WORLDWIDE. EPIGENETIC REGULATOR BROMODOMAIN-CONTAINING PROTEIN 4 (BRD4) IS CRITICAL IN CONTROLLING GENE EXPRESSION OF IBD-ASSOCIATED INFLAMMATORY CYTOKINE NETWORKS. BRD4 AS A PROMISING THERAPEUTIC TARGET IS ALSO TIGHTLY ASSOCIATED WITH MANY OTHER DISEASES, SUCH AS AIRWAY INFLAMMATION AND FIBROSIS, CANCERS, INFECTIOUS DISEASES AND CENTRAL NERVOUS SYSTEM DISORDERS. AREAS COVERED: THIS REVIEW BRIEFLY SUMMARIZED THE CRITICAL ROLE OF BRD4 IN THE PATHOGENESIS OF IBDS AND THE CURRENT CLINICAL LANDSCAPE OF DEVELOPING BROMODOMAIN AND EXTRA TERMINAL DOMAIN (BET) INHIBITORS. THE CHALLENGES AND OPPORTUNITIES AS WELL AS FUTURE DIRECTIONS OF TARGETING BRD4 INHIBITION FOR POTENTIAL IBD MEDICATIONS WERE ALSO DISCUSSED. EXPERT OPINION: TARGETING BRD4 WITH POTENT AND SPECIFIC INHIBITORS MAY OFFER NOVEL EFFECTIVE THERAPEUTICS FOR IBD PATIENTS, PARTICULARLY THOSE WHO ARE REFRACTORY TO ANTI-TNFALPHA THERAPY AND IBD-RELATED PROFIBROTIC. DEVELOPING HIGHLY SPECIFIC BRD4 INHIBITORS FOR IBD MEDICATIONS MAY HELP ERASE THE DRAWBACKS OF MOST CURRENT PAN-BET/BRD4 INHIBITORS, SUCH AS OFF-TARGET EFFECTS, POOR ORAL BIOAVAILABILITY, AND LOW GUT MUCOSAL ABSORBANCE. NOVEL STRATEGIES SUCH AS COMBINATORIAL THERAPY, BRD4-BASED DUAL INHIBITORS AND PROTEOLYSIS TARGETING CHIMERAS (PROTACS) MAY ALSO HAVE GREAT POTENTIAL TO MITIGATE SIDE EFFECTS AND OVERCOME DRUG RESISTANCE DURING IBD TREATMENT. 2023 6 4773 19 NUCLEAR TRAFFICKING OF BACTERIAL EFFECTOR PROTEINS. BACTERIAL PATHOGENS CAN SUBVERT HOST RESPONSES BY PRODUCING EFFECTOR PROTEINS THAT DIRECTLY TARGET THE NUCLEUS OF EUKARYOTIC CELLS IN ANIMALS AND PLANTS. NUCLEAR-TARGETING PROTEINS ARE CATEGORISED AS EITHER: "NUCLEOMODULINS," WHICH HAVE EPIGENETIC-MODULATING ACTIVITIES; OR "CYCLOMODULINS," WHICH SPECIFICALLY INTERFERE WITH THE HOST CELL CYCLE. BACTERIA CAN DELIVER THESE EFFECTOR PROTEINS TO EUKARYOTIC CELLS VIA A RANGE OF STRATEGIES. DESPITE AN INCREASING NUMBER OF REPORTS DESCRIBING THE EFFECTS OF BACTERIAL EFFECTOR PROTEINS ON NUCLEAR PROCESSES IN HOST CELLS, THE INTRACELLULAR PATHWAYS USED BY THESE PROTEINS TO TRAFFIC TO THE NUCLEUS HAVE YET TO BE FULLY ELUCIDATED. THIS REVIEW WILL DESCRIBE CURRENT KNOWLEDGE ABOUT HOW NUCLEOMODULINS AND CYCLOMODULINS ENTER EUKARYOTIC CELLS, EXPLOIT ENDOCYTIC PATHWAYS AND TRANSLOCATE TO THE NUCLEUS. WE WILL ALSO DISCUSS THE SECRETION OF NUCLEAR-TARGETING PROTEINS OR THEIR RELEASE IN BACTERIAL MEMBRANE VESICLES AND THE TRAFFICKING PATHWAYS EMPLOYED BY EACH OF THESE FORMS. BESIDES THEIR IMPORTANCE FOR BACTERIAL PATHOGENESIS, SOME NUCLEAR-TARGETING PROTEINS HAVE BEEN IMPLICATED IN THE DEVELOPMENT OF CHRONIC DISEASES AND EVEN CANCER. A GREATER UNDERSTANDING OF NUCLEAR-TARGETING PROTEINS AND THEIR ACTIONS WILL PROVIDE NEW INSIGHTS INTO THE PATHOGENESIS OF INFECTIOUS DISEASES, AS WELL AS CONTRIBUTE TO ADVANCES IN THE DEVELOPMENT OF NOVEL THERAPIES AGAINST BACTERIAL INFECTIONS AND POSSIBLY CANCER. 2021 7 6532 15 TRANSCRIPTIONAL REGULATION OF INFLAMMASOMES. INFLAMMASOMES ARE MULTIMOLECULAR COMPLEXES WITH POTENT INFLAMMATORY ACTIVITY. AS SUCH, THEIR ACTIVITY IS TIGHTLY REGULATED AT THE TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL LEVELS. IN THIS REVIEW, WE PRESENT THE TRANSCRIPTIONAL REGULATION OF INFLAMMASOME GENES FROM SENSORS (E.G., NLRP3) TO SUBSTRATES (E.G., IL-1BETA). LINEAGE-DETERMINING TRANSCRIPTION FACTORS SHAPE INFLAMMASOME RESPONSES IN DIFFERENT CELL TYPES WITH PROFOUND CONSEQUENCES ON THE RESPONSIVENESS TO INFLAMMASOME-ACTIVATING STIMULI. PRO-INFLAMMATORY SIGNALS (STERILE OR MICROBIAL) HAVE A KEY TRANSCRIPTIONAL IMPACT ON INFLAMMASOME GENES, WHICH IS LARGELY MEDIATED BY NF-KAPPAB AND THAT TRANSLATES INTO HIGHER ANTIMICROBIAL IMMUNE RESPONSES. FURTHERMORE, DIVERSE INTRINSIC (E.G., CIRCADIAN CLOCK, METABOLITES) OR EXTRINSIC (E.G., XENOBIOTICS) SIGNALS ARE INTEGRATED BY SIGNAL-DEPENDENT TRANSCRIPTION FACTORS AND CHROMATIN STRUCTURE CHANGES TO MODULATE TRANSCRIPTIONALLY INFLAMMASOME RESPONSES. FINALLY, ANTI-INFLAMMATORY SIGNALS (E.G., IL-10) COUNTERBALANCE INFLAMMASOME GENES INDUCTION TO LIMIT DELETERIOUS INFLAMMATION. TRANSCRIPTIONAL REGULATIONS THUS APPEAR AS THE FIRST LINE OF INFLAMMASOME REGULATION TO RAISE THE DEFENSE LEVEL IN FRONT OF STRESS AND INFECTIONS BUT ALSO TO LIMIT EXCESSIVE OR CHRONIC INFLAMMATION. 2020 8 2367 17 EPIGENETIC REGULATION OF T CELL EXHAUSTION. CHRONIC ANTIGEN STIMULATION DURING VIRAL INFECTIONS AND CANCER CAN LEAD TO T CELL EXHAUSTION, WHICH IS CHARACTERIZED BY REDUCED EFFECTOR FUNCTION AND PROLIFERATION, AND THE EXPRESSION OF INHIBITORY IMMUNE CHECKPOINT RECEPTORS. RECENT STUDIES HAVE DEMONSTRATED THAT T CELL EXHAUSTION RESULTS IN WHOLESCALE EPIGENETIC REMODELING THAT CONFERS PHENOTYPIC STABILITY TO THESE CELLS AND PREVENTS T CELL REINVIGORATION BY CHECKPOINT BLOCKADE. HERE, WE REVIEW FOUNDATIONAL TECHNOLOGIES TO PROFILE THE EPIGENOME AT MULTIPLE SCALES, INCLUDING MAPPING THE LOCATIONS OF TRANSCRIPTION FACTORS AND HISTONE MODIFICATIONS, DNA METHYLATION AND THREE-DIMENSIONAL GENOME CONFORMATION. WE DISCUSS HOW THESE TECHNOLOGIES HAVE ELUCIDATED THE DEVELOPMENT AND EPIGENETIC REGULATION OF EXHAUSTED T CELLS AND FUNCTIONAL IMPLICATIONS ACROSS VIRAL INFECTION, CANCER, AUTOIMMUNITY AND ENGINEERED T CELL THERAPIES. FINALLY, WE COVER EMERGING MULTI-OMIC AND GENOME ENGINEERING TECHNOLOGIES, CURRENT AND UPCOMING OPPORTUNITIES TO APPLY THESE TO T CELL EXHAUSTION, AND THERAPEUTIC OPPORTUNITIES FOR T CELL ENGINEERING IN THE CLINIC. 2022 9 790 13 CELLULAR AND MOLECULAR MECHANISMS OF CD8(+) T CELL DIFFERENTIATION, DYSFUNCTION AND EXHAUSTION. T CELLS FOLLOW A TRIPHASIC DISTINCT PATHWAY OF ACTIVATION, PROLIFERATION AND DIFFERENTIATION BEFORE BECOMING FUNCTIONALLY AND PHENOTYPICALLY "EXHAUSTED" IN SETTINGS OF CHRONIC INFECTION, AUTOIMMUNITY AND IN CANCER. EXHAUSTED T CELLS PROGRESSIVELY LOSE CANONICAL EFFECTOR FUNCTIONS, EXHIBIT ALTERED TRANSCRIPTIONAL NETWORKS AND EPIGENETIC SIGNATURES AND GAIN CONSTITUTIVE EXPRESSION OF A BROAD COINHIBITORY RECEPTOR SUITE. THIS REVIEW OUTLINES RECENT ADVANCES IN OUR UNDERSTANDING OF EXHAUSTED T CELL BIOLOGY AND EXAMINES CELLULAR AND MOLECULAR MECHANISMS BY WHICH A STATE OF DYSFUNCTION OR EXHAUSTION IS ESTABLISHED, AND MECHANISMS BY WHICH EXHAUSTED T CELLS MAY STILL CONTRIBUTE TO PATHOGEN OR TUMOUR CONTROL. FURTHER, THIS REVIEW DESCRIBES OUR UNDERSTANDING OF EXHAUSTED T CELL HETEROGENEITY AND OUTLINES THE MECHANISMS BY WHICH CHECKPOINT BLOCKADE DIFFERENTIALLY ENGAGES EXHAUSTED T CELL SUBSETS TO OVERCOME EXHAUSTION AND RECOVER T CELL FUNCTION. 2020 10 1876 18 EMERGING ROLES FOR EPIGENETIC PROGRAMMING IN THE CONTROL OF INFLAMMATORY SIGNALING INTEGRATION IN HEATH AND DISEASE. MACROPHAGES AND DENDRITIC CELLS INITIATE THE INNATE IMMUNE RESPONSE TO INFECTION AND INJURY AND CONTRIBUTE TO INFLAMMATORY SIGNALING TO MAINTAIN THE HOMEOSTASIS OF VARIOUS TISSUES, WHICH INCLUDES RESIDENT MACROPHAGES FOR THE ELIMINATION OF INVADING MICROORGANISMS AND TISSUE DAMAGE. INAPPROPRIATE INFLAMMATORY SIGNALING CAN LEAD TO PERSISTENT INFLAMMATION AND FURTHER DEVELOP INTO AUTOIMMUNE AND INFLAMMATION-ASSOCIATED DISEASES. INFLAMMATORY SIGNALING PATHWAYS HAVE BEEN WELL CHARACTERIZED, BUT HOW THESE SIGNALING PATHWAYS ARE CONVERTED INTO SUSTAINED AND DIVERSE PATTERNS OF EXPRESSION OF CYTOKINES, CHEMOKINES, AND OTHER GENES IN RESPONSE TO ENVIRONMENTAL CHALLENGES IS UNCLEAR. EMERGING EVIDENCE SUGGESTS THE IMPORTANT ROLE OF EPIGENETIC MECHANISMS IN FINELY TUNING THE OUTCOME OF THE HOST INNATE IMMUNE RESPONSE. AN UNDERSTANDING OF EPIGENETIC REGULATION OF INNATE IMMUNE CELL IDENTITY AND FUNCTION WILL ENABLE THE IDENTIFICATION OF THE MECHANISM BETWEEN GENE-SPECIFIC HOST DEFENSES AND INFLAMMATORY DISEASE AND WILL ALSO ALLOW FOR EXPLORATION OF THE PROGRAM OF INNATE IMMUNE MEMORY IN HEALTH AND DISEASE. THIS INFORMATION COULD BE USED TO DEVELOP THERAPEUTIC AGENTS TO ENHANCE THE HOST RESPONSE, PREVENTING CHRONIC INFLAMMATION THROUGH PRESERVING TISSUES AND SIGNALING INTEGRITY. 2017 11 4749 18 NOVEL PROSPECTS FOR SCARLESS WOUND HEALING: THE ROLES OF MYOFIBROBLASTS AND ADIPOCYTES. DISTURBANCES OR DEFECTS IN THE PROCESS OF WOUND REPAIR CAN DISRUPT THE DELICATE BALANCE OF CELLS AND MOLECULES NECESSARY FOR COMPLETE WOUND HEALING, THUS LEADING TO CHRONIC WOUNDS OR FIBROTIC SCARS. MYOFIBROBLASTS ARE ONE OF THE MOST IMPORTANT CELLS INVOLVED IN FIBROTIC SCARS, AND REPROGRAMMING PROVIDES A POTENTIAL AVENUE TO INCREASE MYOFIBROBLAST CLEARANCE. ALTHOUGH MYOFIBROBLASTS HAVE LONG BEEN RECOGNIZED AS TERMINALLY DIFFERENTIATED CELLS, RECENT STUDIES HAVE SHOWN THAT MYOFIBROBLASTS HAVE THE CAPACITY TO BE REPROGRAMMED INTO ADIPOCYTES. THIS REVIEW INTENDS TO SUMMARIZE THE POTENTIAL OF REPROGRAMMING MYOFIBROBLASTS INTO ADIPOCYTES. WE WILL DISCUSS MYOFIBROBLAST LINEAGE TRACING, AS WELL AS THE KNOWN MECHANISMS UNDERLYING ADIPOCYTE REGENERATION FROM MYOFIBROBLASTS. IN ADDITION, WE INVESTIGATED DIFFERENT CHANGES IN MYOFIBROBLAST GENE EXPRESSION, TRANSCRIPTIONAL REGULATORS, SIGNALLING PATHWAYS AND EPIGENETIC REGULATORS DURING SKIN WOUND HEALING. IN THE FUTURE, MYOFIBROBLAST REPROGRAMMING IN WOUND HEALING WILL BE BETTER UNDERSTOOD AND APPRECIATED, WHICH MAY PROVIDE NEW IDEAS FOR THE TREATMENT OF SCARLESS WOUND HEALING. 2022 12 769 17 CD8 T CELL EXHAUSTION DURING CHRONIC VIRAL INFECTION AND CANCER. EXHAUSTED CD8 T (TEX) CELLS ARE A DISTINCT CELL LINEAGE THAT ARISE DURING CHRONIC INFECTIONS AND CANCERS IN ANIMAL MODELS AND HUMANS. TEX CELLS ARE CHARACTERIZED BY PROGRESSIVE LOSS OF EFFECTOR FUNCTIONS, HIGH AND SUSTAINED INHIBITORY RECEPTOR EXPRESSION, METABOLIC DYSREGULATION, POOR MEMORY RECALL AND HOMEOSTATIC SELF-RENEWAL, AND DISTINCT TRANSCRIPTIONAL AND EPIGENETIC PROGRAMS. THE ABILITY TO REINVIGORATE TEX CELLS THROUGH INHIBITORY RECEPTOR BLOCKADE, SUCH AS ALPHAPD-1, HIGHLIGHTS THE THERAPEUTIC POTENTIAL OF TARGETING THIS POPULATION. EMERGING INSIGHTS INTO THE MECHANISMS OF EXHAUSTION ARE INFORMING IMMUNOTHERAPIES FOR CANCER AND CHRONIC INFECTIONS. HOWEVER, LIKE OTHER IMMUNE CELLS, TEX CELLS ARE HETEROGENEOUS AND INCLUDE PROGENITOR AND TERMINAL SUBSETS WITH UNIQUE CHARACTERISTICS AND RESPONSES TO CHECKPOINT BLOCKADE. HERE, WE REVIEW OUR CURRENT UNDERSTANDING OF TEX CELL BIOLOGY, INCLUDING THE DEVELOPMENTAL PATHS, TRANSCRIPTIONAL AND EPIGENETIC FEATURES, AND CELL INTRINSIC AND EXTRINSIC FACTORS CONTRIBUTING TO EXHAUSTION AND HOW THIS KNOWLEDGE MAY INFORM THERAPEUTIC TARGETING OF TEX CELLS IN CHRONIC INFECTIONS, AUTOIMMUNITY, AND CANCER. 2019 13 3920 17 LINKING IMMUNITY, EPIGENETICS, AND CANCER IN INFLAMMATORY BOWEL DISEASE. MOST OF WHAT IS KNOWN ABOUT THE PATHOGENESIS OF INFLAMMATORY BOWEL DISEASE (IBD) PERTAINS TO COMPLEX INTERPLAY BETWEEN HOST GENETICS, IMMUNITY, AND ENVIRONMENTAL FACTORS. EPIGENETIC MODIFICATIONS PLAY PIVOTAL ROLES IN INTESTINAL IMMUNITY AND MUCOSAL HOMEOSTASIS AS WELL AS MEDIATING GENE-ENVIRONMENT INTERACTIONS. IN THIS ARTICLE, WE PROVIDE A HISTORICAL ACCOUNT OF EPIGENETIC RESEARCH EITHER DIRECTLY RELATED OR PERTINENT TO THE PATHOGENESIS AND MANAGEMENT OF IBD. WE FURTHER COLLATE EMERGING EVIDENCE SUPPORTING ROLES FOR EPIGENETIC MECHANISMS IN RELEVANT ASPECTS OF IBD BIOLOGY, INCLUDING DEREGULATED IMMUNITY, HOST-PATHOGEN RECOGNITION AND MUCOSAL INTEGRITY. FINALLY, WE HIGHLIGHT KEY EPIGENETIC MECHANISMS THAT LINK CHRONIC INFLAMMATION TO SPECIFIC IBD COMORBIDITIES, INCLUDING COLITIS-ASSOCIATED CANCER AND DISCUSS THEIR POTENTIAL UTILITY AS NOVEL BIOMARKERS OR PHARMACOLOGIC TARGETS IN IBD THERAPY. 2014 14 127 13 A TRANSCRIPTIONAL PERSPECTIVE ON HUMAN MACROPHAGE BIOLOGY. MACROPHAGES ARE A MAJOR CELL TYPE IN TISSUE HOMEOSTASIS AND CONTRIBUTE TO BOTH PATHOLOGY AND RESOLUTION IN ALL ACUTE AND CHRONIC INFLAMMATORY DISEASES RANGING FROM INFECTIONS, CANCER, OBESITY, ATHEROSCLEROSIS, AUTOIMMUNE DISORDERS TO NEURODEGENERATIVE DISEASES SUCH AS ALZHEIMER'S DISEASE. THE CELLULAR AND FUNCTIONAL DIVERSITY OF MACROPHAGES DEPENDS UPON TIGHTLY REGULATED TRANSCRIPTION. THE INNATE IMMUNE SYSTEM IS UNDER PROFOUND EVOLUTIONARY SELECTION. THERE IS INCREASING RECOGNITION THAT HUMAN MACROPHAGE BIOLOGY DIFFERS VERY SIGNIFICANTLY FROM THAT OF COMMONLY STUDIED ANIMAL MODELS, WHICH THEREFORE CAN HAVE A LIMITED PREDICTIVE VALUE. HERE WE REPORT ON THE NEWEST FINDINGS ON TRANSCRIPTIONAL CONTROL OF MACROPHAGE ACTIVATION, AND HOW WE ENVISION INTEGRATING STUDIES ON TRANSCRIPTIONAL AND EPIGENETIC REGULATION, AND MORE CLASSICAL APPROACHES IN MURINE MODELS. MOREOVER, WE PROVIDE NEW INSIGHTS INTO HOW WE CAN LEARN ABOUT TRANSCRIPTIONAL REGULATION IN THE HUMAN SYSTEM FROM LARGER EFFORTS SUCH AS THE FANTOM (FUNCTIONAL ANNOTATION OF THE MAMMALIAN GENOME) CONSORTIUM. 2015 15 2342 18 EPIGENETIC REGULATION OF MACROPHAGE POLARIZATION AND FUNCTION. MACROPHAGE POLARIZATION REFERS TO DEVELOPMENT OF A SPECIFIC PHENOTYPE IMPORTANT FOR TISSUE HOMEOSTASIS OR HOST DEFENSE IN RESPONSE TO ENVIRONMENTAL CUES. ENVIRONMENTAL FACTORS THAT INDUCE MACROPHAGE POLARIZATION INCLUDE CYTOKINES AND MICROBIAL FACTORS PRODUCED BY PATHOGENS OR COMMENSAL MICROBIOTA. SIGNALING PATHWAYS UTILIZED BY THESE POLARIZING FACTORS HAVE BEEN WELL CHARACTERIZED, BUT IT IS LESS CLEAR HOW SIGNALS ARE CONVERTED INTO COMPLEX AND SUSTAINED PATTERNS OF GENE EXPRESSION, AND HOW MACROPHAGES ARE REPROGRAMMED DURING POLARIZATION TO ALTER THEIR RESPONSES TO SUBSEQUENT ENVIRONMENTAL CHALLENGES. EMERGING EVIDENCE, REVIEWED HERE, SUGGESTS AN IMPORTANT ROLE FOR EPIGENETIC MECHANISMS IN MODULATING AND TRANSMITTING SIGNALS DURING MACROPHAGE POLARIZATION AND REPROGRAMMING. DEEPER UNDERSTANDING OF EPIGENETIC REGULATION OF MACROPHAGE PHENOTYPE WILL ENABLE DEVELOPMENT OF GENE-SPECIFIC THERAPEUTIC APPROACHES TO ENHANCE HOST DEFENSE WHILE PRESERVING TISSUE INTEGRITY AND PREVENTING CHRONIC INFLAMMATORY DISEASES. 2013 16 6255 21 THE MICROBIOTA AND EPIGENETIC REGULATION OF T HELPER 17/REGULATORY T CELLS: IN SEARCH OF A BALANCED IMMUNE SYSTEM. IMMUNE CELLS NOT ONLY AFFECT TISSUE HOMEOSTASIS AT THE SITE OF INFLAMMATION BUT ALSO EXERT SYSTEMIC EFFECTS CONTRIBUTING TO MULTIPLE CHRONIC CONDITIONS. RECENT EVIDENCE CLEARLY SUPPORTS AN ALTERED T HELPER 17/REGULATORY T CELL (TH17/TREG) BALANCE LEADING TO THE DEVELOPMENT AND PROGRESSION OF INFLAMMATORY DISEASES THAT NOT ONLY AFFECT THE GASTROINTESTINAL TRACT BUT ALSO HAVE WHOLE-BODY MANIFESTATIONS, INCLUDING INSULIN RESISTANCE. EPIGENETIC MECHANISMS ARE AMENABLE TO BOTH ENVIRONMENTAL AND CIRCULATING FACTORS AND CONTRIBUTE TO DETERMINING THE T CELL LANDSCAPE. THE RECENTLY IDENTIFIED PARTICIPATION OF THE GUT MICROBIOTA IN THE REMODELING OF THE EPIGENOME OF IMMUNE CELLS HAS TRIGGERED A PARADIGM SHIFT IN OUR UNDERSTANDING OF THE ETIOLOGY OF VARIOUS INFLAMMATORY DISEASES AND OPENED NEW PATHS TOWARD THERAPEUTIC STRATEGIES. IN THIS REVIEW, WE PROVIDE AN OVERVIEW OF THE CONTRIBUTION OF THE TH17/TREG BALANCE IN THE DEVELOPMENT AND PROGRESSION OF INFLAMMATORY BOWEL DISEASES AND METABOLIC DISEASES. WE DISCUSS THE INVOLVEMENT OF EPIGENETIC MECHANISMS IN THE REGULATION OF T CELL FUNCTION IN THE PARTICULAR CONTEXT OF DYSBIOSIS. FINALLY, WE EXAMINE THE POTENTIAL FOR NUTRITIONAL INTERVENTIONS AFFECTING THE GUT MICROBIOTA TO RESHAPE THE T CELL EPIGENOME AND ADDRESS THE INFLAMMATORY COMPONENT OF VARIOUS DISEASES. 2017 17 5620 16 SCHRODINGER'S T CELLS: MOLECULAR INSIGHTS INTO STEMNESS AND EXHAUSTION. T CELL STEMNESS AND EXHAUSTION COEXIST AS TWO KEY CONTRASTING PHENOMENA DURING CHRONIC ANTIGEN STIMULATION, SUCH AS INFECTION, TRANSPLANT, CANCER, AND AUTOIMMUNITY. T CELL EXHAUSTION REFERS TO THE PROGRESSIVE LOSS OF EFFECTOR FUNCTION CAUSED BY CHRONIC ANTIGEN EXPOSURE. EXHAUSTED T (T(EX)) CELLS HIGHLY EXPRESS MULTIPLE INHIBITORY RECEPTORS AND EXHIBIT SEVERE DEFECTS IN CELL PROLIFERATION AND CYTOKINE PRODUCTION. THE TERM T CELL STEMNESS DESCRIBES THE STEM CELL-LIKE BEHAVIORS OF T CELLS, INCLUDING SELF-RENEWAL, MULTIPOTENCY, AND FUNCTIONAL PERSISTENCE. IT IS WELL ACCEPTED THAT NAIVE AND SOME MEMORY T CELL SUBSETS HAVE STEM CELL-LIKE PROPERTIES. WHEN INVESTIGATING THE EXHAUSTIVE DIFFERENTIATION OF T CELLS IN CHRONIC INFECTION AND CANCER, RECENT STUDIES HIGHLIGHTED THE STEMNESS OF "PRECURSORS OF EXHAUSTED" T (T(PEX)) CELLS PRIOR TO THEIR TERMINAL DIFFERENTIATION TO T(EX) CELLS. CLINICALLY SUCCESSFUL CHECKPOINT BLOCKADES FOR CANCER TREATMENT APPEAR TO INVIGORATE ANTITUMOR T(PEX) CELLS BUT NOT T(EX) CELLS. HERE WE DISCUSS THE TRANSCRIPTIONAL AND EPIGENETIC REGULATIONS OF T CELL STEMNESS AND EXHAUSTION, WITH A FOCUS ON HOW SYSTEMS IMMUNOLOGY WAS AND WILL BE UTILIZED TO DEFINE THE MOLECULAR BASIS UNDERLYING THE TRANSITION OF T(PEX) TO T(EX) CELLS. WE SUGGEST A "STEPWISE MODEL" OF T CELL STEMNESS AND EXHAUSTION, IN WHICH LOSS OF STEMNESS AND EXHAUSTION PROGRESSION ARE GRADUAL MULTI-STEP PROCESSES. WE PROVIDE PERSPECTIVES ON THE RESEARCH NEEDED TO DEFINE T CELL STEMNESS AND EXHAUSTION IN THE TRANSPLANTATION SETTING, IN WHICH ALLOGENIC T CELLS ARE ALSO CHRONICALLY EXPOSED TO ALLOANTIGENS. A BETTER UNDERSTANDING OF T CELL STEMNESS AND EXHAUSTION WILL SHED LIGHT ON DEVELOPING NOVEL STRATEGIES FOR IMMUNOTHERAPIES. 2021 18 2821 15 FINE-TUNING AUTOPHAGY: FROM TRANSCRIPTIONAL TO POSTTRANSLATIONAL REGULATION. MACROAUTOPHAGY (HEREAFTER CALLED AUTOPHAGY) IS A VACUOLAR LYSOSOMAL PATHWAY FOR DEGRADATION OF INTRACELLULAR MATERIAL IN EUKARYOTIC CELLS. AUTOPHAGY PLAYS CRUCIAL ROLES IN TISSUE HOMEOSTASIS, IN ADAPTATION TO STRESS SITUATIONS, AND IN IMMUNE AND INFLAMMATORY RESPONSES. ALTERATION OF AUTOPHAGY IS ASSOCIATED WITH CANCER, DIABETES AND OBESITY, CARDIOVASCULAR DISEASE, NEURODEGENERATIVE DISEASE, AUTOIMMUNE DISEASE, INFECTION, AND CHRONIC INFLAMMATORY DISEASE. AUTOPHAGY IS CONTROLLED BY AUTOPHAGY-RELATED (ATG) PROTEINS THAT ACT IN A COORDINATED MANNER TO BUILD UP THE INITIAL AUTOPHAGIC VACUOLE NAMED THE AUTOPHAGOSOME. IT IS NOW KNOWN THAT THE ACTIVITIES OF ATG PROTEINS ARE MODULATED BY POSTTRANSLATIONAL MODIFICATIONS SUCH AS PHOSPHORYLATION, UBIQUITINATION, AND ACETYLATION. MOREOVER, TRANSCRIPTIONAL AND EPIGENETIC CONTROLS ARE INVOLVED IN THE REGULATION OF AUTOPHAGY IN STRESS SITUATIONS. HERE WE SUMMARIZE AND DISCUSS HOW POSTTRANSLATIONAL MODIFICATIONS AND TRANSCRIPTIONAL AND EPIGENETIC CONTROLS REGULATE THE INVOLVEMENT OF AUTOPHAGY IN THE PROTEOSTASIS NETWORK. 2016 19 4196 13 METABOLIC PLASTICITY AND REGULATION OF T CELL EXHAUSTION. THE METABOLIC REPROGRAMMING DURING T CELL ACTIVATION AND DIFFERENTIATION AFFECTS T CELL FATE AND IMMUNE RESPONSES. CELL METABOLISM MAY SERVE AS THE DRIVING FORCE THAT INDUCES EPIGENETIC MODIFICATIONS, CONTRIBUTING TO REGULATING T CELL DIFFERENTIATION. PERSISTENT PATHOGEN INFECTION LEADS TO T CELL EXHAUSTION, WHICH IS COMPOSED OF TWO MAIN SUBSETS AND WITH DISTINCT METABOLIC CHARACTERISTICS. THE PROGENITOR EXHAUSTED T CELLS UTILIZE MITOCHONDRIAL FATTY ACID OXIDATION (FAO) AND OXIDATIVE PHOSPHORYLATION (OXPHOS) FOR ENERGY, WHILE TERMINALLY EXHAUSTED T CELLS MAINLY RELY ON GLYCOLYTIC METABOLISM WITH IMPAIRED GLYCOLYSIS AND OXPHOS. HERE, WE COMPILED THE LATEST RESEARCH ON HOW T CELL METABOLISM DEFINES DIFFERENTIATION, FOCUSING ON T CELL EXHAUSTION DURING CHRONIC INFECTIONS. IN ADDITION, METABOLIC-RELATED FACTORS INCLUDING ANTIGEN STIMULATION SIGNALS STRENGTH, CYTOKINES AND EPIGENETICS AFFECTING T CELL EXHAUSTION WERE ALSO REVIEWED. FURTHERMORE, THE INTERVENTION STRATEGIES ON METABOLISM AND EPIGENETICS TO REVERSE T CELL EXHAUSTION WERE DISCUSSED IN DETAIL, WHICH MAY CONTRIBUTE TO ACHIEVING THE GOAL OF PREVENTION AND TREATMENT OF T CELL EXHAUSTION. 2022 20 5432 17 REJUVENATION OF MESENCHYMAL STEM CELLS TO AMELIORATE SKELETAL AGING. ADVANCED AGE IS A SHARED RISK FACTOR FOR MANY CHRONIC AND DEBILITATING SKELETAL DISEASES INCLUDING OSTEOPOROSIS AND PERIODONTITIS. MESENCHYMAL STEM CELLS DEVELOP VARIOUS AGING PHENOTYPES INCLUDING THE ONSET OF SENESCENCE, INTRINSIC LOSS OF REGENERATIVE POTENTIAL AND EXACERBATION OF INFLAMMATORY MICROENVIRONMENT VIA SECRETORY FACTORS. THIS REVIEW ELABORATES ON THE EMERGING CONCEPTS ON THE MOLECULAR AND EPIGENETIC MECHANISMS OF MSC SENESCENCE, SUCH AS THE ACCUMULATION OF OXIDATIVE STRESS, DNA DAMAGE AND MITOCHONDRIAL DYSFUNCTION. SENESCENT MSCS AGGRAVATE LOCAL INFLAMMATION, DISRUPT BONE REMODELING AND BONE-FAT BALANCE, THEREBY CONTRIBUTING TO THE PROGRESSION OF AGE-RELATED BONE DISEASES. VARIOUS REJUVENATION STRATEGIES TO TARGET SENESCENT MSCS COULD PRESENT A PROMISING PARADIGM TO RESTORE SKELETAL AGING. 2023