1 6571 113 TRANSPOSABLE ELEMENTS CROSS KINGDOM BOUNDARIES AND CONTRIBUTE TO INFLAMMATION AND AGEING: SOMATIC ACQUISITION OF FOREIGN TRANSPOSABLE ELEMENTS AS A CATALYST OF GENOME INSTABILITY, EPIGENETIC DYSREGULATION, INFLAMMATION, SENESCENCE, AND AGEING. THE DE-REPRESSION OF TRANSPOSABLE ELEMENTS (TES) IN MAMMALIAN GENOMES IS THOUGHT TO CONTRIBUTE TO GENOME INSTABILITY, INFLAMMATION, AND AGEING, YET IS VIEWED AS A CELL-AUTONOMOUS EVENT. IN CONTRAST TO MAMMALIAN CELLS, PROKARYOTES CONSTANTLY EXCHANGE GENETIC MATERIAL THROUGH TES, CROSSING BOTH CELL AND SPECIES BARRIERS, CONTRIBUTING TO RAPID MICROBIAL EVOLUTION AND DIVERSITY IN COMPLEX COMMUNITIES SUCH AS THE MAMMALIAN GUT. HERE, IT IS PROPOSED THAT TES RELEASED FROM PROKARYOTES IN THE MICROBIOME OR FROM PATHOGENIC INFECTIONS REGULARLY CROSS THE KINGDOM BARRIER TO THE SOMATIC CELLS OF THEIR EUKARYOTIC HOSTS. IT IS PROPOSED THIS HORIZONTAL TRANSFER OF TES FROM MICROBE TO HOST IS A STOCHASTIC, ONGOING CATALYST OF GENOME DESTABILIZATION, RESULTING IN STRUCTURAL AND EPIGENETIC VARIATIONS, AND ACTIVATION OF WELL-EVOLVED HOST DEFENSE MECHANISMS CONTRIBUTING TO INFLAMMATION, SENESCENCE, AND BIOLOGICAL AGEING. IT IS PROPOSED THAT INNATE IMMUNITY PATHWAYS DEFEND AGAINST THE HORIZONTAL ACQUISITION OF MICROBIAL TES, AND THAT ACTIVATION OF THIS PATHWAY DURING HORIZONTAL TRANSPOSON TRANSFER PROMOTES CHRONIC INFLAMMATION DURING AGEING. FINALLY, IT IS SUGGESTED THAT HORIZONTAL ACQUISITION OF PROKARYOTIC TES INTO MAMMALIAN GENOMES HAS BEEN MASKED AND SUBSEQUENTLY UNDER-REPORTED DUE TO FLAWS IN CURRENT SEQUENCING PIPELINES, AND NEW STRATEGIES TO UNCOVER THESE EVENTS ARE PROPOSED. 2020 2 6397 24 THE ROLE OF TRANSPOSABLE ELEMENTS IN AGING AND CANCER. TRANSPOSABLE ELEMENTS (TES) CONSTITUTE A LARGE PORTION OF THE HUMAN GENOME. VARIOUS MECHANISMS AT THE TRANSCRIPTION AND POST-TRANSCRIPTION LEVELS DEVELOPED TO SUPPRESS TE ACTIVITY IN HEALTHY CONDITIONS. HOWEVER, A GROWING BODY OF EVIDENCE SUGGESTS THAT TE DYSREGULATION IS INVOLVED IN VARIOUS HUMAN DISEASES, INCLUDING AGE-RELATED DISEASES AND CANCER. IN THIS REVIEW, WE EXPLAINED HOW SENSING TES BY THE IMMUNE SYSTEM COULD INDUCE INNATE IMMUNE RESPONSES, CHRONIC INFLAMMATION, AND FOLLOWING AGE-RELATED DISEASES. WE ALSO NOTED THAT INFLAMMAGEING AND EXOGENOUS CARCINOGENS COULD TRIGGER THE UPREGULATION OF TES IN PRECANCEROUS CELLS. INCREASED INFLAMMATION COULD ENHANCE EPIGENETIC PLASTICITY AND UPREGULATION OF EARLY DEVELOPMENTAL TES, WHICH REWIRES THE TRANSCRIPTIONAL NETWORKS AND GIFT THE SURVIVAL ADVANTAGE TO THE PRECANCEROUS CELLS. IN ADDITION, UPREGULATED TES COULD INDUCE GENOME INSTABILITY, ACTIVATION OF ONCOGENES, OR INHIBITION OF TUMOR SUPPRESSORS AND CONSEQUENT CANCER INITIATION AND PROGRESSION. SO, WE SUGGEST THAT TES COULD BE CONSIDERED THERAPEUTIC TARGETS IN AGING AND CANCER. 2023 3 4273 26 MICROBIOTA AND EPIGENETICS: HEALTH IMPACT. EPIGENETIC CHANGES ASSOCIATED WITH DISEASE DEVELOPMENT AND PROGRESSIONS ARE OF INCREASING IMPORTANCE BECAUSE OF THEIR POTENTIAL DIAGNOSTIC AND THERAPEUTIC APPLICATIONS. SEVERAL EPIGENETIC CHANGES ASSOCIATED WITH CHRONIC METABOLIC DISORDERS HAVE BEEN STUDIED IN VARIOUS DISEASES. EPIGENETIC CHANGES ARE MOSTLY MODULATED BY ENVIRONMENTAL FACTORS, INCLUDING THE HUMAN MICROBIOTA LIVING IN DIFFERENT PARTS OF OUR BODIES. THE MICROBIAL STRUCTURAL COMPONENTS AND THE MICROBIALLY DERIVED METABOLITES DIRECTLY INTERACT WITH HOST CELLS, THEREBY MAINTAINING HOMEOSTASIS. MICROBIOME DYSBIOSIS, ON THE OTHER HAND, IS KNOWN TO PRODUCE ELEVATED LEVELS OF DISEASE-LINKED METABOLITES, WHICH MAY DIRECTLY AFFECT A HOST METABOLIC PATHWAY OR INDUCE EPIGENETIC CHANGES THAT CAN LEAD TO DISEASE DEVELOPMENT. DESPITE THEIR IMPORTANT ROLE IN HOST PHYSIOLOGY AND SIGNAL TRANSDUCTION, THERE HAS BEEN LITTLE RESEARCH INTO THE MECHANICS AND PATHWAYS ASSOCIATED WITH EPIGENETIC MODIFICATIONS. THIS CHAPTER FOCUSES ON THE RELATIONSHIP BETWEEN MICROBES AND THEIR EPIGENETIC EFFECTS IN DISEASED PATHOLOGY, AS WELL AS ON THE REGULATION AND METABOLISM OF THE DIETARY OPTIONS AVAILABLE TO THE MICROBES. FURTHERMORE, THIS CHAPTER ALSO PROVIDES A PROSPECTIVE LINK BETWEEN THESE TWO IMPORTANT PHENOMENA, TERMED "MICROBIOME AND EPIGENETICS." 2023 4 6135 32 THE EPIGENETICS OF INFLAMMAGING: THE CONTRIBUTION OF AGE-RELATED HETEROCHROMATIN LOSS AND LOCUS-SPECIFIC REMODELLING AND THE MODULATION BY ENVIRONMENTAL STIMULI. A GROWING AMOUNT OF EVIDENCES INDICATES THAT INFLAMMAGING - THE CHRONIC, LOW GRADE INFLAMMATION STATE CHARACTERISTIC OF THE ELDERLY - IS THE RESULT OF GENETIC AS WELL AS ENVIRONMENTAL OR STOCHASTIC FACTORS. SOME OF THESE, SUCH AS THE ACCUMULATION OF SENESCENT CELLS THAT ARE PERSISTENT DURING AGING OR ACCOMPANY ITS PROGRESSION, SEEM TO BE SUFFICIENT TO INITIATE THE AGING PROCESS AND TO FUEL IT. OTHERS, LIKE EXPOSURE TO ENVIRONMENTAL COMPOUNDS OR INFECTIONS, ARE TEMPORARY AND RESOLVE WITHIN A (RELATIVELY) SHORT TIME. IN BOTH CASES, HOWEVER, A CELLULAR MEMORY OF THE EVENT CAN BE ESTABLISHED BY MEANS OF EPIGENETIC MODULATION OF THE GENOME. IN THIS REVIEW WE WILL SPECIFICALLY DISCUSS THE RELATIONSHIP BETWEEN EPIGENETICS AND INFLAMMAGING. IN PARTICULAR, WE WILL SHOW HOW AGE-ASSOCIATED EPIGENETIC MODIFICATIONS CONCERNED WITH HETEROCHROMATIN LOSS AND GENE-SPECIFIC REMODELLING, CAN PROMOTE INFLAMMAGING. FURTHERMORE, WE WILL RECALL HOW THE EXPOSURE TO SPECIFIC NUTRITIONAL, ENVIRONMENTAL AND MICROBIAL STIMULI CAN AFFECT THE RATE OF INFLAMMAGING THROUGH EPIGENETIC MECHANISMS, TOUCHING ALSO ON THE RECENT INSIGHT GIVEN BY THE CONCEPT OF TRAINED IMMUNITY. 2018 5 4200 34 METABOLIC REQUIREMENTS OF TH17 CELLS AND OF B CELLS: REGULATION AND DEFECTS IN HEALTH AND IN INFLAMMATORY DISEASES. THE IMMUNE SYSTEM PROTECTS FROM INFECTIONS AND CANCER THROUGH COMPLEX CELLULAR NETWORKS. FOR THIS PURPOSE, IMMUNE CELLS REQUIRE WELL-DEVELOPED MECHANISMS OF ENERGY GENERATION. HOWEVER, THE IMMUNE SYSTEM ITSELF CAN ALSO CAUSE DISEASES WHEN DEFECTIVE REGULATION RESULTS IN THE EMERGENCE OF AUTOREACTIVE LYMPHOCYTES. RECENT STUDIES PROVIDE INSIGHTS INTO HOW DIFFERENTIAL PATTERNS OF IMMUNE CELL RESPONSES ARE ASSOCIATED WITH SELECTIVE METABOLIC PATHWAYS. THIS REVIEW WILL EXAMINE THE CHANGING METABOLIC REQUIREMENTS OF TH17 CELLS AND OF B CELLS AT DIFFERENT STAGES OF THEIR DEVELOPMENT AND ACTIVATION. BOTH CELLS PROVIDE PROTECTION BUT CAN ALSO MEDIATE DISEASES THROUGH THE PRODUCTION OF AUTOANTIBODIES AND THE PRODUCTION OF PROINFLAMMATORY MEDIATORS. IN HEALTH, B CELLS PRODUCE ANTIBODIES AND CYTOKINES AND PRESENT ANTIGENS TO T CELLS TO MOUNT SPECIFIC IMMUNITY. TH17 CELLS, ON THE OTHER HAND, PROVIDE PROTECTION AGAINST EXTRA CELLULAR PATHOGENS AT MUCOSAL SURFACES BUT CAN ALSO DRIVE CHRONIC INFLAMMATION. THE LATTER CELLS CAN ALSO PROMOTE THE DIFFERENTIATION OF B CELLS TO PLASMA CELLS TO PRODUCE MORE AUTOANTIBODIES. METABOLISM-REGULATED CHECKPOINTS AT DIFFERENT STAGES OF THEIR DEVELOPMENT ENSURE THE THAT SELF-REACTIVE B CELLS CLONES AND NEEDLESS PRODUCTION OF INTERLEUKIN (IL-)17 ARE LIMITED. THE METABOLIC REGULATION OF THE TWO CELL TYPES HAS SOME SIMILARITIES, E.G. THE UTILITY OF HYPOXIA INDUCED FACTOR (HIF)1ALPHA DURING LOW OXYGEN TENSION, TO PREVENT AUTOIMMUNITY AND REGULATE INFLAMMATION. THERE ARE ALSO CLEAR DIFFERENCES, AS TH17 CELLS ONLY ARE VULNERABLE TO THE LACK OF CERTAIN AMINO ACIDS. B CELLS, UNLIKE TH17 CELLS, ARE ALSO DEPENDENT OF MECHANISTIC TARGET OF RAPAMYCIN 2 (MTORC2) TO FUNCTION. SIGNIFICANT KNOWLEDGE HAS RECENTLY BEEN GAINED, PARTICULARLY ON TH17 CELLS, ON HOW METABOLISM REGULATES THESE CELLS THROUGH INFLUENCING THEIR EPIGENOME. METABOLIC DYSREGULATION OF TH17 CELLS AND B CELLS CAN LEAD TO CHRONIC INFLAMMATION. DISEASE ASSOCIATED ALTERATIONS IN THE GENOME CAN, IN ADDITION, CAUSE DYSREGULATION TO METABOLISM AND, THEREBY, RESULT IN EPIGENETIC ALTERATIONS IN THESE CELLS. RECENT STUDIES HIGHLIGHT HOW PATHOLOGY CAN RESULT FROM THE COOPERATION BETWEEN THE TWO CELL TYPES BUT ONLY FEW HAVE SO FAR ADDRESSED THE KEY METABOLIC ALTERATIONS IN SUCH SETTINGS. KNOWLEDGE OF THE IMPACT OF METABOLIC DYSFUNCTION ON CHRONIC INFLAMMATION AND PATHOLOGY CAN REVEAL NOVEL THERAPEUTIC TARGETS TO TREAT SUCH DISEASES. 2022 6 5581 29 ROLE OF NF-KAPPAB IN AGEING AND AGE-RELATED DISEASES: LESSONS FROM GENETICALLY MODIFIED MOUSE MODELS. AGEING IS A COMPLEX PROCESS, INDUCED BY MULTIFACETED INTERACTION OF GENETIC, EPIGENETIC, AND ENVIRONMENTAL FACTORS. IT IS MANIFESTED BY A DECLINE IN THE PHYSIOLOGICAL FUNCTIONS OF ORGANISMS AND ASSOCIATED TO THE DEVELOPMENT OF AGE-RELATED CHRONIC DISEASES AND CANCER DEVELOPMENT. IT IS CONSIDERED THAT AGEING FOLLOWS A STRICTLY-REGULATED PROGRAM, IN WHICH SOME SIGNALING PATHWAYS CRITICALLY CONTRIBUTE TO THE ESTABLISHMENT AND MAINTENANCE OF THE AGED STATE. CHRONIC INFLAMMATION IS A MAJOR MECHANISM THAT PROMOTES THE BIOLOGICAL AGEING PROCESS AND COMORBIDITY, WITH THE TRANSCRIPTION FACTOR NF-KAPPAB (NUCLEAR FACTOR KAPPA-LIGHT-CHAIN-ENHANCER OF ACTIVATED B CELLS) AS A CRUCIAL MEDIATOR OF INFLAMMATORY RESPONSES. THIS, TOGETHER WITH THE FINDING THAT THE ACTIVATION OR INHIBITION OF NF-KAPPAB CAN INDUCE OR REVERSE RESPECTIVELY THE MAIN FEATURES OF AGED ORGANISMS, HAS BROUGHT IT UNDER CONSIDERATION AS A KEY TRANSCRIPTION FACTOR THAT ACTS AS A DRIVER OF AGEING. IN THIS REVIEW, WE FOCUSED ON THE DATA OBTAINED ENTIRELY THROUGH THE GENERATION OF KNOCKOUT AND TRANSGENIC MOUSE MODELS OF EITHER PROTEIN INVOLVED IN THE NF-KAPPAB SIGNALING PATHWAY THAT HAVE PROVIDED RELEVANT INFORMATION ABOUT THE INTRICATE PROCESSES OR MOLECULAR MECHANISMS THAT CONTROL AGEING. WE HAVE REVIEWED THE RELATIONSHIP OF NF-KAPPAB AND PREMATURE AGEING; THE DEVELOPMENT OF CANCER ASSOCIATED WITH AGEING AND THE IMPLICATION OF NF-KAPPAB ACTIVATION IN THE DEVELOPMENT OF AGE-RELATED DISEASES, SOME OF WHICH GREATLY INCREASE THE RISK OF DEVELOPING CANCER. 2021 7 2601 29 EPIGENETICS, DNA ORGANIZATION, AND INFLAMMATORY BOWEL DISEASE. INFLAMMATORY BOWEL DISEASES (IBDS) ARE CHRONIC INFLAMMATORY DISORDERS AFFECTING THE GASTROINTESTINAL TRACT. THE INCIDENCE OF IBD IS INCREASING, WITH MORE CASES OCCURRING IN DEVELOPED COUNTRIES. MULTIPLE FACTORS SUCH AS GENETICS, ENVIRONMENTAL CHANGES, GUT MICROBIOTA, AND IMMUNE ABNORMALITIES HAVE BEEN ASSOCIATED WITH DEVELOPMENT OF IBD. IN RECENT YEARS, IT HAS BECOME INCREASINGLY APPARENT THAT EPIGENETIC MODIFICATIONS OF CHROMATIN AND THE MANNER IN WHICH CHROMATIN IS ORGANIZED IN THE NUCLEUS ARE ADDITIONALLY IMPORTANT ELEMENTS THAT CAN INFLUENCE RESPONSES INDUCED BY THE FACTORS DESCRIBED ABOVE, AND MAY THEREFORE CONTRIBUTE TO THE ONSET AND PATHOGENESIS OF IBD. EPIGENETICS AND CHROMATIN ORGANIZATION REGULATE DIVERSE FUNCTIONS THAT INCLUDE MAINTENANCE OF HOMEOSTASIS IN THE INTESTINAL EPITHELIUM, THE DEVELOPMENT AND DIFFERENTIATION OF IMMUNE CELLS, AND MODULATION OF RESPONSES GENERATED BY THE IMMUNE SYSTEM TO DEFEND AGAINST POTENTIAL PATHOGENS. FURTHERMORE, CHANGES IN EPIGENETIC CHROMATIN MARKS AND IN CHROMATIN ORGANIZATION HAVE NOW BEEN LINKED TO DIFFERENTIAL GENE EXPRESSION IN IBD PATIENT CELLS. ALTHOUGH DIRECT EVIDENCE FOR A ROLE OF HISTONE MODIFICATIONS IN IBD IS CURRENTLY VERY LIMITED, IN THIS REVIEW, WE SUMMARIZE THE LINKS BETWEEN VARIOUS EPIGENETIC MODIFICATIONS, THE PROTEINS THAT CATALYZE OR RECOGNIZE THESE MODIFICATIONS, AND THE DEVELOPMENT OR PROGRESSION OF IBD IN HUMAN AND EXPERIMENTAL IBD. WE ALSO DISCUSS HOW EPIGENETICS INFLUENCE THE ORGANIZATION OF DNA CONTACTS TO REGULATE GENE EXPRESSION AND THE IMPLICATIONS THIS MAY HAVE FOR DIAGNOSING AND TREATING IBD. 2019 8 2177 21 EPIGENETIC MECHANISMS OF HYPERGLYCEMIC MEMORY. RECENTLY THE CONCEPT EMERGED THAT PROLONGED EXPOSURE TO ALTERED METABOLIC CONDITIONS, INCLUDING HYPERGLYCEMIA, MAY EPIGENETICALLY IMPRINT HUMAN CELLS PERMITTING VERTICAL OR HORIZONTAL TRANSFER TO "DESCENDANTS". ALTHOUGH MECHANISTICALLY ILL UNDERSTOOD, THE HYPERGLYCEMIC/EPIGENETIC MEMORY MAY REPRESENT ONE OF THE MAJOR LIMITATIONS FOR THE APPLICATION OF CELL THERAPY TO TREATMENT OF CHRONIC HEART DISEASE WHERE A RELATIVELY PROLONGED PERIOD OF EX VIVO CELLULAR EXPANSION IS REQUIRED. HYPERGLYCEMIC MEMORY, IN FACT, SEEMS TO CONTRIBUTE TO THE ESTABLISHMENT OF AN EPIGENETIC "REMINISCENCE" OF THE ALTERED METABOLIC STATE, TO WHICH, CELLS FROM DISEASED BODIES HAVE BEEN EXPOSED. THIS REVIEW SUMMARIZES THE MOST RELEVANT CONCEPTS AND OBSERVATIONS ABOUT THE MECHANISMS UNDERLYING THE ONSET OF STABLE INFORMATION INSIDE THE EPIGENOME LEADING TO THE DEVELOPMENT OF A DISEASED PHENOTYPE. SPECIAL ATTENTION IS GIVEN TO EPIGENETIC DRUGS AND HOW THEY HAVE BEEN USED IN EXPERIMENTAL, PRECLINICAL AND CLINICAL SETTINGS TO TREAT DYSMETABOLISM, DIABETES AND THEIR COMPLICATIONS. 2014 9 2812 24 FIBROBLAST MEMORY IN DEVELOPMENT, HOMEOSTASIS AND DISEASE. FIBROBLASTS ARE THE MAJOR CELL POPULATION IN THE CONNECTIVE TISSUE OF MOST ORGANS, WHERE THEY ARE ESSENTIAL FOR THEIR STRUCTURAL INTEGRITY. THEY ARE BEST KNOWN FOR THEIR ROLE IN REMODELLING THE EXTRACELLULAR MATRIX, HOWEVER MORE RECENTLY THEY HAVE BEEN RECOGNISED AS A FUNCTIONALLY HIGHLY DIVERSE CELL POPULATION THAT CONSTANTLY RESPONDS AND ADAPTS TO THEIR ENVIRONMENT. BIOLOGICAL MEMORY IS THE PROCESS OF A SUSTAINED ALTERED CELLULAR STATE AND FUNCTIONS IN RESPONSE TO A TRANSIENT OR PERSISTENT ENVIRONMENTAL STIMULUS. WHILE IT IS WELL ESTABLISHED THAT FIBROBLASTS RETAIN A MEMORY OF THEIR ANATOMICAL LOCATION, HOW OTHER ENVIRONMENTAL STIMULI INFLUENCE FIBROBLAST BEHAVIOUR AND FUNCTION IS LESS CLEAR. THE ABILITY OF FIBROBLASTS TO RESPOND AND MEMORISE DIFFERENT ENVIRONMENTAL STIMULI IS ESSENTIAL FOR TISSUE DEVELOPMENT AND HOMEOSTASIS AND MAY BECOME DYSREGULATED IN CHRONIC DISEASE CONDITIONS SUCH AS FIBROSIS AND CANCER. HERE WE SUMMARISE THE FOUR EMERGING KEY AREAS OF FIBROBLAST ADAPTATION: POSITIONAL, MECHANICAL, INFLAMMATORY, AND METABOLIC MEMORY AND HIGHLIGHT THE UNDERLYING MECHANISMS AND THEIR IMPLICATIONS IN TISSUE HOMEOSTASIS AND DISEASE. 2021 10 733 31 CANCER EPIGENETICS: LINKING BASIC BIOLOGY TO CLINICAL MEDICINE. CANCER EVOLUTION AT ALL STAGES IS DRIVEN BY BOTH EPIGENETIC ABNORMALITIES AS WELL AS GENETIC ALTERATIONS. DYSREGULATION OF EPIGENETIC CONTROL EVENTS MAY LEAD TO ABNORMAL PATTERNS OF DNA METHYLATION AND CHROMATIN CONFIGURATIONS, BOTH OF WHICH ARE CRITICAL CONTRIBUTORS TO THE PATHOGENESIS OF CANCER. THESE EPIGENETIC ABNORMALITIES ARE SET AND MAINTAINED BY MULTIPLE PROTEIN COMPLEXES AND THE INTERPLAY BETWEEN THEIR INDIVIDUAL COMPONENTS INCLUDING DNA METHYLATION MACHINERY, HISTONE MODIFIERS, PARTICULARLY, POLYCOMB (PCG) PROTEINS, AND CHROMATIN REMODELING PROTEINS. RECENT ADVANCES IN GENOME-WIDE TECHNOLOGY HAVE REVEALED THAT THE INVOLVEMENT OF THESE DYSREGULATED EPIGENETIC COMPONENTS APPEARS TO BE EXTENSIVE. MOREOVER, THERE IS A GROWING CONNECTION BETWEEN EPIGENETIC ABNORMALITIES IN CANCER AND CONCEPTS CONCERNING STEM-LIKE CELL SUBPOPULATIONS AS A DRIVING FORCE FOR CANCER. EMERGING DATA SUGGEST THAT ASPECTS OF THE EPIGENETIC LANDSCAPE INHERENT TO NORMAL EMBRYONIC AND ADULT STEM/PROGENITOR CELLS MAY HELP FOSTER, UNDER THE STRESS OF CHRONIC INFLAMMATION OR ACCUMULATING REACTIVE OXYGEN SPECIES, EVOLUTION OF MALIGNANT SUBPOPULATIONS. FINALLY, UNDERSTANDING MOLECULAR MECHANISMS INVOLVED IN INITIATION AND MAINTENANCE OF EPIGENETIC ABNORMALITIES IN ALL TYPES OF CANCER HAS GREAT POTENTIAL FOR TRANSLATIONAL PURPOSES. THIS IS ALREADY EVIDENT FOR EPIGENETIC BIOMARKER DEVELOPMENT, AND FOR PHARMACOLOGICAL TARGETING AIMED AT REVERSING CANCER-SPECIFIC EPIGENETIC ALTERATIONS. 2011 11 5816 22 STRESS AND STEM CELLS. THE UNIQUE PROPERTIES AND FUNCTIONS OF STEM CELLS MAKE THEM PARTICULARLY SUSCEPTIBLE TO STRESSES AND ALSO LEAD TO THEIR REGULATION BY STRESS. STEM CELL DIVISION MUST RESPOND TO THE DEMAND TO REPLENISH CELLS DURING NORMAL TISSUE TURNOVER AS WELL AS IN RESPONSE TO DAMAGE. OXIDATIVE STRESS, MECHANICAL STRESS, GROWTH FACTORS, AND CYTOKINES SIGNAL STEM CELL DIVISION AND DIFFERENTIATION. MANY OF THE CONSERVED PATHWAYS REGULATING STEM CELL SELF-RENEWAL AND DIFFERENTIATION ARE ALSO STRESS-RESPONSE PATHWAYS. THE LONG LIFE SPAN AND DIVISION POTENTIAL OF STEM CELLS CREATE A PROPENSITY FOR TRANSFORMATION (CANCER) AND SPECIFIC STRESS RESPONSES SUCH AS APOPTOSIS AND SENESCENCE ACT AS ANTITUMOR MECHANISMS. QUIESCENCE REGULATED BY CDK INHIBITORS AND A HYPOXIC NICHE REGULATED BY FOXO TRANSCRIPTION FACTOR FUNCTION TO REDUCE STRESS FOR SEVERAL TYPES OF STEM CELLS TO FACILITATE LONG-TERM MAINTENANCE. AGING IS A PARTICULARLY RELEVANT STRESS FOR STEM CELLS, BECAUSE REPEATED DEMANDS ON STEM CELL FUNCTION OVER THE LIFE SPAN CAN HAVE CUMULATIVE CELL-AUTONOMOUS EFFECTS INCLUDING EPIGENETIC DYSREGULATION, MUTATIONS, AND TELOMERE EROSION. IN ADDITION, AGING OF THE ORGANISM IMPAIRS FUNCTION OF THE STEM CELL NICHE AND SYSTEMIC SIGNALS, INCLUDING CHRONIC INFLAMMATION AND OXIDATIVE STRESS. 2012 12 4738 27 NOVEL FIBROBLAST PHENOTYPES IN HOMEOSTASIS AND CHRONIC INFLAMMATION: FROM FUNCTIONS TO POTENTIAL REGULATORS. FIBROBLASTS ARE ESSENTIAL COMPONENTS OF THE STROMA, SUSTAINING A VARIETY OF TISSUES AND BEING KEY TO THE PROCESS OF TISSUE REPAIR AFTER INJURY. THEIR ROLE IN TISSUE REPAIR HAS BEEN ATTRIBUTED TO THEIR ABILITY TO ACQUIRE A CONTRACTILE, EXTRACELLULAR MATRIX-PRODUCING PHENOTYPE KNOWN AS MYOFIBROBLASTS. THIS PROPERTY IS PRIMARILY DEPENDENT ON THEIR RESPONSE TO THE PLEIOTROPIC CYTOKINE TRANSFORMING GROWTH FACTOR-BETA1. UNTIL RECENTLY, THE POTENTIAL ROLE OF FIBROBLASTS IN OTHER HOMEOSTATIC AND DISEASE-RELATED PROCESSES WAS LESS WELL UNDERSTOOD. ALTHOUGH IN VITRO STUDIES INDICATED THAT FIBROBLASTS ARE ABLE TO RESPOND TO AND SECRETE INFLAMMATORY MEDIATORS, DEFINITIVE EVIDENCE OF THEIR CONTRIBUTION TO CHRONIC INFLAMMATION WAS LIMITED. HOWEVER, THE EMERGENCE OF TECHNIQUES THAT ALLOW EXPLORATION OF TISSUES AT THE SINGLE CELL LEVEL HAS CHALLENGED THE PREVIOUS PARADIGMS ON FIBROBLAST IDENTITY AND FUNCTIONS, AND HAS LED TO THE DISCOVERY OF SIGNIFICANT DIVERSITY, SHOWING THE PRESENCE OF FIBROBLASTS WITH ALTERNATE TRANSCRIPTIONAL PROFILES IN A VARIETY OF TISSUES. THESE STUDIES HAVE ALSO SUGGESTED POTENTIAL ROLES OF NOVEL FIBROBLAST SUBTYPES AS REGULATORS OF EPITHELIAL HOMEOSTASIS AND RENEWAL, INFLAMMATORY CELL INFILTRATION AND ACTIVATION, AND ANTIGEN PRESENTATION. HERE, WE PROVIDE A COMPREHENSIVE REVIEW OF THE RECENT LITERATURE ON FIBROBLAST DIVERSITY IN THE DIGESTIVE TRACT, SKIN, LUNGS AND JOINTS. WE ALSO REVIEW EVIDENCE OF THEIR CONTRIBUTION TO THE REGULATION OF HOMEOSTASIS AND CHRONIC INFLAMMATION, AS WELL AS THEIR INTERACTIONS WITH OTHER CELLS IN VARIOUS TISSUE COMPARTMENTS. WE DISCUSS EVIDENCE OF DIFFERENT FACTORS INVOLVED IN THE CONTROL OF FIBROBLAST FUNCTION, ADDRESSING THE ROLE OF VARIOUS CYTOKINES, TRANSCRIPTION FACTORS AND EPIGENETIC CHANGES, AS WELL AS MICROENVIRONMENTAL FACTORS, INCLUDING EXTRACELLULAR MATRIX STIFFNESS, HYPOXIA, AND METABOLIC SHIFTS. 2023 13 6213 22 THE INTESTINAL EPITHELIAL CELL CYCLE: UNCOVERING ITS 'CRYPTIC' NATURE. PURPOSE OF REVIEW: TO DISCUSS THE RECENT LANDMARK FINDINGS THAT HAVE INCREASED OUR UNDERSTANDING NOT ONLY OF THE ROLE OF THE EPITHELIAL CELL CYCLE IN THE HOMEOSTASIS OF THE SMALL INTESTINE, BUT ALSO ITS RELEVANCE TO INFLAMMATION AND CANCER. RECENT FINDINGS: RECENT DATA HAVE UNVEILED NOVEL INFORMATION ON PROTEIN INTERACTIONS DIRECTLY INVOLVED IN THE CELL CYCLE AS WELL AS IN THE PATHWAYS THAT TRANSDUCE EXTERNAL ENVIRONMENTAL SIGNALS TO THE CELL CYCLE. A GROWING BODY OF THE RECENT EVIDENCE CONFIRMS THE IMPORTANCE OF FOOD AS WELL AS HORMONAL REGULATION IN THE GUT ON CELL CYCLE. INFORMATION ON THE CONTRIBUTION OF THE EPITHELIAL MICROENVIRONMENT, INCLUDING THE MICROBIOTA, HAS GROWN SUBSTANTIALLY IN THE RECENT YEARS AS WELL AS ON THE GENE-ENVIRONMENT INTERACTIONS AND THE MULTIPLE EPIGENETIC MECHANISMS INVOLVED IN REGULATING CELL-CYCLE PROTEINS AND SIGNALLING. FINALLY, FURTHER STUDIES INVESTIGATING THE DYSREGULATION OF THE CELL CYCLE DURING INFLAMMATION AND PROLIFERATION HAVE INCREASED OUR UNDERSTANDING OF THE PATHOPHYSIOLOGY OF CHRONIC INFLAMMATORY DISEASES AND CANCER. SUMMARY: THIS REVIEW HIGHLIGHTS SOME OF THE MOST RECENT ADVANCES THAT FURTHER EMPHASIZE THE IMPORTANCE OF THE CELL CYCLE IN THE SMALL INTESTINE DURING HOMEOSTASIS AS WELL AS IN INFLAMMATION AND CANCER. 2015 14 2644 31 EPIGENOMIC DRIVERS OF IMMUNE DYSFUNCTION IN AGING. AGING INEVITABLY LEADS TO REDUCED IMMUNE FUNCTION, LEAVING THE ELDERLY MORE SUSCEPTIBLE TO INFECTIONS, LESS ABLE TO RESPOND TO PATHOGEN CHALLENGES, AND LESS RESPONSIVE TO PREVENTATIVE VACCINATIONS. NO CELL TYPE IS EXEMPT FROM THE RAVAGES OF AGE, AND EXTENSIVE STUDIES HAVE FOUND AGE-RELATED ALTERATIONS IN THE FREQUENCIES AND FUNCTIONS OF BOTH STEM AND PROGENITOR CELLS, AS WELL AS EFFECTOR CELLS OF BOTH THE INNATE AND ADAPTIVE IMMUNE SYSTEMS. THE INTRINSIC FUNCTIONAL REDUCTION IN IMMUNE COMPETENCE IS ALSO ASSOCIATED WITH LOW-GRADE CHRONIC INFLAMMATION, TERMED "INFLAMM-AGING," WHICH FURTHER PERPETUATES IMMUNE DYSFUNCTION. WHILE MANY OF THESE AGE-RELATED CELLULAR CHANGES ARE WELL CHARACTERIZED, UNDERSTANDING THE MOLECULAR CHANGES THAT UNDERPIN THE FUNCTIONAL DECLINE HAS PROVEN MORE DIFFICULT. CHANGES IN CHROMATIN ARE INCREASINGLY APPRECIATED AS A CAUSATIVE MECHANISM OF CELLULAR AND ORGANISMAL AGING ACROSS SPECIES. THESE CHANGES INCLUDE INCREASED GENOMIC INSTABILITY THROUGH LOSS OF HETEROCHROMATIN AND INCREASED DNA DAMAGE, TELOMERE ATTRITION, AND EPIGENETIC ALTERATIONS. IN THIS REVIEW, WE DISCUSS THE CONNECTIONS BETWEEN CHROMATIN, IMMUNOCOMPETENCE, AND THE LOSS OF FUNCTION ASSOCIATED WITH MAMMALIAN IMMUNE AGING. THROUGH UNDERSTANDING THE MOLECULAR EVENTS WHICH UNDERPIN THE PHENOTYPIC CHANGES OBSERVED IN THE AGED IMMUNE SYSTEM, IT IS HOPED THAT THE AGED IMMUNE SYSTEM CAN BE RESTORED TO PROVIDE YOUTHFUL IMMUNITY ONCE MORE. 2019 15 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 16 6101 20 THE EMERGING ROLE OF EPIGENETICS IN THE IMMUNE RESPONSE TO VACCINATION AND INFECTION: A SYSTEMATIC REVIEW. EXTENSIVE RESEARCH HAS HIGHLIGHTED THE ROLE OF INFECTION-INDUCED EPIGENETIC EVENTS IN THE DEVELOPMENT OF CANCER. MORE RECENTLY, ATTENTION HAS FOCUSED ON THE ABILITY OF NON-CARCINOGENIC INFECTIONS, AS WELL AS VACCINES, TO MODIFY THE HUMAN EPIGENOME AND MODULATE THE IMMUNE RESPONSE. THIS REVIEW EXPLORES THIS RAPIDLY EVOLVING AREA OF INVESTIGATION AND OUTLINES THE MANY AND VARIED WAYS IN WHICH VACCINATION AND NATURAL INFECTION CAN INFLUENCE THE HUMAN EPIGENOME FROM MODULATION OF THE INNATE AND ADAPTIVE IMMUNE RESPONSE, TO BIOLOGICAL AGEING AND MODIFICATION OF DISEASE RISK. THE IMPLICATIONS OF THESE EPIGENETIC CHANGES ON IMMUNE REGULATION AND THEIR POTENTIAL APPLICATION TO THE DIAGNOSIS AND TREATMENT OF CHRONIC INFECTION AND VACCINE DEVELOPMENT ARE ALSO DISCUSSED. 2020 17 6715 20 VITAMIN A AND THE EPIGENOME. THE EPIGENETIC PHENOMENA REFER TO HERITABLE CHANGES IN GENE EXPRESSION OTHER THAN THOSE IN THE DNA SEQUENCE, SUCH AS DNA METHYLATION AND HISTONE MODIFICATIONS. MAJOR RESEARCH PROGRESS IN THE LAST FEW YEARS HAS PROVIDED FURTHER PROOF THAT ENVIRONMENTAL FACTORS, INCLUDING DIET AND NUTRITION, CAN INFLUENCE PHYSIOLOGIC AND PATHOLOGIC PROCESSES THROUGH EPIGENETIC ALTERATIONS, WHICH IN TURN INFLUENCE GENE EXPRESSION. THIS INFLUENCE IS TERMED NUTRITIONAL EPIGENETICS, AND ONE PROMINENT EXAMPLE IS THE REGULATION OF GENE TRANSCRIPTION BY VITAMIN A THROUGH INTERACTION TO ITS NUCLEAR RECEPTOR. VITAMIN A IS CRITICAL THROUGHOUT LIFE. TOGETHER WITH ITS DERIVATIVES, IT REGULATES DIVERSE PROCESSES INCLUDING REPRODUCTION, EMBRYOGENESIS, VISION, GROWTH, CELLULAR DIFFERENTIATION AND PROLIFERATION, MAINTENANCE OF EPITHELIAL CELLULAR INTEGRITY AND IMMUNE FUNCTION. HERE WE REVIEW THE EPIGENETIC ROLE OF VITAMIN A IN CANCER, STEM CELLS DIFFERENTIATION, PROLIFERATION, AND IMMUNITY. THE DATA PRESENTED HERE SHOW THAT RETINOIC ACID IS A POTENT AGENT CAPABLE OF INDUCING ALTERATIONS IN EPIGENETIC MODIFICATIONS THAT PRODUCE VARIOUS EFFECTS ON THE PHENOTYPE. MEDICAL BENEFITS OF VITAMIN A AS AN EPIGENETIC MODULATOR, ESPECIALLY WITH RESPECT TO ITS CHRONIC USE AS NUTRITIONAL SUPPLEMENT, SHOULD RELY ON OUR FURTHER UNDERSTANDING OF ITS EPIGENETIC EFFECTS DURING HEALTH AND DISEASE, AS WELL AS THROUGH DIFFERENT GENERATIONS. 2017 18 5632 28 SENESCENT CELLS: SASPECTED DRIVERS OF AGE-RELATED PATHOLOGIES. THE PROGRESSION OF PHYSIOLOGICAL AGEING IS DRIVEN BY INTRACELLULAR ABERRATIONS INCLUDING TELOMERE ATTRITION, GENOMIC INSTABILITY, EPIGENETIC ALTERATIONS AND LOSS OF PROTEOSTASIS. THESE IN TURN DAMAGE CELLS AND COMPROMISE THEIR FUNCTIONALITY. CELLULAR SENESCENCE, A STABLE IRREVERSIBLE CELL-CYCLE ARREST, IS ELICITED IN DAMAGED CELLS AND PREVENTS THEIR PROPAGATION IN THE ORGANISM. UNDER NORMAL CONDITIONS, SENESCENT CELLS RECRUIT THE IMMUNE SYSTEM WHICH FACILITATES THEIR REMOVAL FROM TISSUES. NEVERTHELESS, DURING AGEING, TISSUE-RESIDING SENESCENT CELLS TEND TO ACCUMULATE, AND MIGHT NEGATIVELY IMPACT THEIR MICROENVIRONMENT VIA PROFOUND SECRETORY PHENOTYPE WITH PRO-INFLAMMATORY CHARACTERISTICS, TERMED SENESCENCE-ASSOCIATED SECRETORY PHENOTYPE (SASP). INDEED, SENESCENT CELLS ARE MOSTLY ABUNDANT AT SITES OF AGE-RELATED PATHOLOGIES, INCLUDING DEGENERATIVE DISORDERS AND MALIGNANCIES. INTERESTINGLY, STUDIES ON PROGEROID MICE INDICATE THAT SELECTIVE ELIMINATION OF SENESCENT CELLS CAN DELAY AGE-RELATED DETERIORATION. THIS SUGGESTS THAT CHRONIC INFLAMMATION INDUCED BY SENESCENT CELLS MIGHT BE A MAIN DRIVER OF THESE PATHOLOGIES. IMPORTANTLY, SENESCENT CELLS ACCUMULATE AS A RESULT OF DEFICIENT IMMUNE SURVEILLANCE, AND THEIR REMOVAL IS INCREASED UPON THE USE OF IMMUNE STIMULATORY AGENTS. INSIGHTS INTO MECHANISMS OF SENESCENCE SURVEILLANCE COULD BE COMBINED WITH CURRENT APPROACHES FOR CANCER IMMUNOTHERAPY TO PROPOSE NEW PREVENTIVE AND THERAPEUTIC STRATEGIES FOR AGE-RELATED DISEASES. 2014 19 5633 21 SENESCENT REMODELING OF THE INNATE AND ADAPTIVE IMMUNE SYSTEM IN THE ELDERLY MEN WITH PROSTATE CANCER. DESPITE YEARS OF INTENSIVE INVESTIGATION THAT HAS BEEN MADE IN UNDERSTANDING PROSTATE CANCER, IT REMAINS A MAJOR CAUSE OF DEATH IN MEN WORLDWIDE. PROSTATE CANCER EMERGES FROM MULTIPLE ALTERATIONS THAT INDUCE CHANGES IN EXPRESSION PATTERNS OF GENES AND PROTEINS THAT FUNCTION IN NETWORKS CONTROLLING CRITICAL CELLULAR EVENTS. BASED ON THE EXPONENTIAL AGING OF THE POPULATION AND THE INCREASING LIFE EXPECTANCY IN INDUSTRIALIZED WESTERN COUNTRIES, PROSTATE CANCER IN THE ELDERLY MEN IS BECOMING A DISEASE OF INCREASING SIGNIFICANCE. AGING IS A PROGRESSIVE DEGENERATIVE PROCESS STRICTLY INTEGRATED WITH INFLAMMATION. SEVERAL THEORIES HAVE BEEN PROPOSED THAT ATTEMPT TO DEFINE THE ROLE OF CHRONIC INFLAMMATION IN AGING INCLUDING REDOX STRESS, MITOCHONDRIAL DAMAGE, IMMUNOSENESCENCE, AND EPIGENETIC MODIFICATIONS. HERE, WE REVIEW THE INNATE AND ADAPTIVE IMMUNE SYSTEMS AND THEIR SENESCENT REMODELING IN ELDERLY MEN WITH PROSTATE CANCER. 2014 20 1876 24 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