1 6054 162 THE CURRENT STATE AND FUTURE OF T-CELL EXHAUSTION RESEARCH. 'EXHAUSTION' IS A TERM USED TO DESCRIBE A STATE OF NATIVE AND REDIRECTED T-CELL HYPO-RESPONSIVENESS RESULTING FROM PERSISTENT ANTIGEN EXPOSURE DURING CHRONIC VIRAL INFECTIONS OR CANCER. ALTHOUGH A WELL-ESTABLISHED PHENOTYPE ACROSS MICE AND HUMANS, EXHAUSTION AT THE MOLECULAR LEVEL REMAINS POORLY DEFINED AND INCONSISTENT ACROSS THE LITERATURE. THIS IS, IN PART, DUE TO AN OVERRELIANCE ON SURFACE RECEPTORS TO DEFINE THESE CELLS AND EXPLAIN EXHAUSTIVE BEHAVIOURS, AN INCOMPLETE UNDERSTANDING OF HOW EXHAUSTION ARISES, AND A LACK OF CLARITY OVER WHETHER EXHAUSTION IS THE SAME ACROSS CONTEXTS, E.G. CHRONIC VIRAL INFECTIONS VERSUS CANCER. WITH THE DEVELOPMENT OF SYSTEMS-BASED GENETIC APPROACHES SUCH AS SINGLE-CELL RNA-SEQ AND CRISPR SCREENS APPLIED TO IN VIVO DATA, WE ARE MOVING CLOSER TO A CONSENSUS VIEW OF EXHAUSTION, ALTHOUGH UNDERSTANDING HOW IT ARISES REMAINS CHALLENGING GIVEN THE DIFFICULTY IN MANIPULATING THE IN VIVO SETTING. ACCORDINGLY, PRODUCING AND STUDYING EXHAUSTED T-CELLS EX VIVO ARE BURGEONING, ALLOWING EXPERIMENTS TO BE CONDUCTED AT SCALE UP AND WITH HIGH THROUGHPUT. HERE, WE FIRST REVIEW WHAT IS CURRENTLY KNOWN ABOUT T-CELL EXHAUSTION AND HOW IT'S BEING STUDIED. WE THEN DISCUSS HOW IMPROVEMENTS IN THEIR METHOD OF ISOLATION/PRODUCTION AND EXAMINING THE IMPACT OF DIFFERENT MICROENVIRONMENTAL SIGNALS AND CELL INTERACTIONS HAVE NOW BECOME AN ACTIVE AREA OF RESEARCH. FINALLY, WE DISCUSS WHAT THE FUTURE HOLDS FOR THE ANALYSIS OF THIS PHYSIOLOGICAL CONDITION AND, GIVEN THE DIVERSITY OF WAYS IN WHICH EXHAUSTED CELLS ARE NOW BEING GENERATED, PROPOSE THE ADOPTION OF A UNIFIED APPROACH TO CLEARLY DEFINING EXHAUSTION USING A SET OF METABOLIC-, EPIGENETIC-, TRANSCRIPTIONAL-, AND ACTIVATION-BASED PHENOTYPIC MARKERS, THAT WE CALL 'M.E.T.A'. 2023 2 2812 31 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 3 5631 36 SENESCENCE-INFLAMMATORY REGULATION OF REPARATIVE CELLULAR REPROGRAMMING IN AGING AND CANCER. THE INABILITY OF ADULT TISSUES TO TRANSITORILY GENERATE CELLS WITH FUNCTIONAL STEM CELL-LIKE PROPERTIES IS A MAJOR OBSTACLE TO TISSUE SELF-REPAIR. NUCLEAR REPROGRAMMING-LIKE PHENOMENA THAT INDUCE A TRANSIENT ACQUISITION OF EPIGENETIC PLASTICITY AND PHENOTYPE MALLEABILITY MAY CONSTITUTE A REPARATIVE ROUTE THROUGH WHICH HUMAN TISSUES RESPOND TO INJURY, STRESS, AND DISEASE. HOWEVER, TISSUE REJUVENATION SHOULD INVOLVE NOT ONLY THE TRANSIENT EPIGENETIC REPROGRAMMING OF DIFFERENTIATED CELLS, BUT ALSO THE COMMITTED RE-ACQUISITION OF THE ORIGINAL OR ALTERNATIVE COMMITTED CELL FATE. CHRONIC OR UNRESTRAINED EPIGENETIC PLASTICITY WOULD DRIVE AGING PHENOTYPES BY IMPAIRING THE REPAIR OR THE REPLACEMENT OF DAMAGED CELLS; SUCH UNCONTROLLED PHENOMENA OF IN VIVO REPROGRAMMING MIGHT ALSO GENERATE CANCER-LIKE CELLULAR STATES. WE HEREIN PROPOSE THAT THE ABILITY OF SENESCENCE-ASSOCIATED INFLAMMATORY SIGNALING TO REGULATE IN VIVO REPROGRAMMING CYCLES OF TISSUE REPAIR OUTLINES A THRESHOLD MODEL OF AGING AND CANCER. THE DEGREE OF SENESCENCE/INFLAMMATION-ASSOCIATED DEVIATION FROM THE HOMEOSTATIC STATE MAY DELINEATE A TYPE OF THRESHOLDING ALGORITHM DISTINGUISHING BENEFICIAL FROM DELETERIOUS EFFECTS OF IN VIVO REPROGRAMMING. FIRST, TRANSIENT ACTIVATION OF NF-KAPPAB-RELATED INNATE IMMUNITY AND SENESCENCE-ASSOCIATED INFLAMMATORY COMPONENTS (E.G., IL-6) MIGHT FACILITATE REPARATIVE CELLULAR REPROGRAMMING IN RESPONSE TO ACUTE INFLAMMATORY EVENTS. SECOND, PARA-INFLAMMATION SWITCHES MIGHT PROMOTE LONG-LASTING BUT REVERSIBLE REFRACTORINESS TO REPARATIVE CELLULAR REPROGRAMMING. THIRD, CHRONIC SENESCENCE-ASSOCIATED INFLAMMATORY SIGNALING MIGHT LOCK CELLS IN HIGHLY PLASTIC EPIGENETIC STATES DISABLED FOR REPARATIVE DIFFERENTIATION. THE CONSIDERATION OF A CELLULAR REPROGRAMMING-CENTERED VIEW OF EPIGENETIC PLASTICITY AS A FUNDAMENTAL ELEMENT OF A TISSUE'S CAPACITY TO UNDERGO SUCCESSFUL REPAIR, AGING DEGENERATION OR MALIGNANT TRANSFORMATION SHOULD PROVIDE CHALLENGING STOCHASTIC INSIGHTS INTO THE CURRENT DETERMINISTIC GENETIC PARADIGM FOR MOST CHRONIC DISEASES, THEREBY INCREASING THE SPECTRUM OF THERAPEUTIC APPROACHES FOR PHYSIOLOGICAL AGING AND CANCER. 2017 4 5315 40 PSYCHOLOGICAL STRESS IN CHILDHOOD AND SUSCEPTIBILITY TO THE CHRONIC DISEASES OF AGING: MOVING TOWARD A MODEL OF BEHAVIORAL AND BIOLOGICAL MECHANISMS. AMONG PEOPLE EXPOSED TO MAJOR PSYCHOLOGICAL STRESSORS IN EARLY LIFE, THERE ARE ELEVATED RATES OF MORBIDITY AND MORTALITY FROM CHRONIC DISEASES OF AGING. THE MOST COMPELLING DATA COME FROM STUDIES OF CHILDREN RAISED IN POVERTY OR MALTREATED BY THEIR PARENTS, WHO SHOW HEIGHTENED VULNERABILITY TO VASCULAR DISEASE, AUTOIMMUNE DISORDERS, AND PREMATURE MORTALITY. THESE FINDINGS RAISE CHALLENGING THEORETICAL QUESTIONS. HOW DOES CHILDHOOD STRESS GET UNDER THE SKIN, AT THE MOLECULAR LEVEL, TO AFFECT RISK FOR LATER DISEASES? AND HOW DOES IT INCUBATE THERE, GIVING RISE TO DISEASES SEVERAL DECADES LATER? HERE WE PRESENT A BIOLOGICAL EMBEDDING MODEL, WHICH ATTEMPTS TO ADDRESS THESE QUESTIONS BY SYNTHESIZING KNOWLEDGE ACROSS SEVERAL BEHAVIORAL AND BIOMEDICAL LITERATURES. THIS MODEL MAINTAINS THAT CHILDHOOD STRESS GETS "PROGRAMMED" INTO MACROPHAGES THROUGH EPIGENETIC MARKINGS, POSTTRANSLATIONAL MODIFICATIONS, AND TISSUE REMODELING. AS A CONSEQUENCE THESE CELLS ARE ENDOWED WITH PROINFLAMMATORY TENDENCIES, MANIFEST IN EXAGGERATED CYTOKINE RESPONSES TO CHALLENGE AND DECREASED SENSITIVITY TO INHIBITORY HORMONAL SIGNALS. THE MODEL GOES ON TO PROPOSE THAT OVER THE LIFE COURSE, THESE PROINFLAMMATORY TENDENCIES ARE EXACERBATED BY BEHAVIORAL PROCLIVITIES AND HORMONAL DYSREGULATION, THEMSELVES THE PRODUCTS OF EXPOSURE TO EARLY STRESS. BEHAVIORALLY, THE MODEL POSITS THAT CHILDHOOD STRESS GIVES RISE TO EXCESSIVE THREAT VIGILANCE, MISTRUST OF OTHERS, POOR SOCIAL RELATIONSHIPS, IMPAIRED SELF-REGULATION, AND UNHEALTHY LIFESTYLE CHOICES. HORMONALLY, EARLY STRESS CONFERS ALTERED PATTERNS OF ENDOCRINE AND AUTONOMIC DISCHARGE. THIS MILIEU AMPLIFIES THE PROINFLAMMATORY ENVIRONMENT ALREADY INSTANTIATED BY MACROPHAGES. ACTING IN CONCERT WITH OTHER EXPOSURES AND GENETIC LIABILITIES, THE RESULTING INFLAMMATION DRIVES FORWARD PATHOGENIC MECHANISMS THAT ULTIMATELY FOSTER CHRONIC DISEASE. 2011 5 5817 22 STRESS AND THE EPIGENETIC LANDSCAPE: A LINK TO THE PATHOBIOLOGY OF HUMAN DISEASES? ACCUMULATING EVIDENCE POINTS TO A MAJOR ROLE FOR CHRONIC STRESS OF CELL RENEWAL SYSTEMS IN THE PATHOGENESIS OF IMPORTANT HUMAN DISEASES, INCLUDING CANCER, ATHEROSCLEROSIS AND DIABETES. HERE WE DISCUSS EMERGING EVIDENCE THAT EPIGENETIC ABNORMALITIES MAY MAKE SUBSTANTIAL CONTRIBUTIONS TO THESE STRESS-INDUCED PATHOLOGIES. ALTHOUGH THE MECHANISMS REMAIN TO BE FULLY ELUCIDATED, WE SUGGEST THAT CHRONIC STRESS CAN ELICIT HERITABLE CHANGES IN THE CHROMATIN LANDSCAPE THAT 'LOCK' CELLS IN ABNORMAL STATES, WHICH THEN LEAD TO DISEASE. WE EMPHASIZE THE NEED TO INVESTIGATE EPIGENETIC STATES IN DISEASE AND LINKS TO STRESS AND TO CONSIDER HOW THE KNOWLEDGE GAINED THROUGH THESE STUDIES MAY FOSTER NEW MEANS OF DISEASE PREVENTION AND MANAGEMENT. 2010 6 1748 32 EARLY LIFE EVENTS AND THEIR CONSEQUENCES FOR LATER DISEASE: A LIFE HISTORY AND EVOLUTIONARY PERSPECTIVE. BIOMEDICAL SCIENCE HAS LITTLE CONSIDERED THE RELEVANCE OF LIFE HISTORY THEORY AND EVOLUTIONARY AND ECOLOGICAL DEVELOPMENTAL BIOLOGY TO CLINICAL MEDICINE. HOWEVER, THE OBSERVATIONS THAT EARLY LIFE INFLUENCES CAN ALTER LATER DISEASE RISK--THE "DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE" (DOHAD) PARADIGM--HAVE LED TO A RECOGNITION THAT THESE PERSPECTIVES CAN INFORM OUR UNDERSTANDING OF HUMAN BIOLOGY. WE PROPOSE THAT THE DOHAD PHENOMENON CAN BE CONSIDERED AS A SUBSET OF THE BROADER PROCESSES OF DEVELOPMENTAL PLASTICITY BY WHICH ORGANISMS ADAPT TO THEIR ENVIRONMENT DURING THEIR LIFE COURSE. SUCH ADAPTIVE PROCESSES ALLOW GENOTYPIC VARIATION TO BE PRESERVED THROUGH TRANSIENT ENVIRONMENTAL CHANGES. CUES FOR PLASTICITY OPERATE PARTICULARLY DURING EARLY DEVELOPMENT; THEY MAY AFFECT A SINGLE ORGAN OR SYSTEM, BUT GENERALLY THEY INDUCE INTEGRATED ADJUSTMENTS IN THE MATURE PHENOTYPE, A PROCESS UNDERPINNED BY EPIGENETIC MECHANISMS AND INFLUENCED BY PREDICTION OF THE MATURE ENVIRONMENT. IN MAMMALS, AN ADVERSE INTRAUTERINE ENVIRONMENT RESULTS IN AN INTEGRATED SUITE OF RESPONSES, SUGGESTING THE INVOLVEMENT OF A FEW KEY REGULATORY GENES, THAT RESETS THE DEVELOPMENTAL TRAJECTORY IN EXPECTATION OF POOR POSTNATAL CONDITIONS. MISMATCH BETWEEN THE ANTICIPATED AND THE ACTUAL MATURE ENVIRONMENT EXPOSES THE ORGANISM TO RISK OF ADVERSE CONSEQUENCES-THE GREATER THE MISMATCH, THE GREATER THE RISK. FOR HUMANS, PREDICTION IS INACCURATE FOR MANY INDIVIDUALS BECAUSE OF CHANGES IN THE POSTNATAL ENVIRONMENT TOWARD ENERGY-DENSE NUTRITION AND LOW ENERGY EXPENDITURE, CONTRIBUTING TO THE EPIDEMIC OF CHRONIC NONCOMMUNICABLE DISEASE. THIS VIEW OF HUMAN DISEASE FROM THE PERSPECTIVES OF LIFE HISTORY BIOLOGY AND EVOLUTIONARY THEORY OFFERS NEW APPROACHES TO PREVENTION, DIAGNOSIS AND INTERVENTION. 2007 7 1310 21 DEFINING TRAINED IMMUNITY AND ITS ROLE IN HEALTH AND DISEASE. IMMUNE MEMORY IS A DEFINING FEATURE OF THE ACQUIRED IMMUNE SYSTEM, BUT ACTIVATION OF THE INNATE IMMUNE SYSTEM CAN ALSO RESULT IN ENHANCED RESPONSIVENESS TO SUBSEQUENT TRIGGERS. THIS PROCESS HAS BEEN TERMED 'TRAINED IMMUNITY', A DE FACTO INNATE IMMUNE MEMORY. RESEARCH IN THE PAST DECADE HAS POINTED TO THE BROAD BENEFITS OF TRAINED IMMUNITY FOR HOST DEFENCE BUT HAS ALSO SUGGESTED POTENTIALLY DETRIMENTAL OUTCOMES IN IMMUNE-MEDIATED AND CHRONIC INFLAMMATORY DISEASES. HERE WE DEFINE 'TRAINED IMMUNITY' AS A BIOLOGICAL PROCESS AND DISCUSS THE INNATE STIMULI AND THE EPIGENETIC AND METABOLIC REPROGRAMMING EVENTS THAT SHAPE THE INDUCTION OF TRAINED IMMUNITY. 2020 8 4717 25 NON-GENOMIC TRANSGENERATIONAL INHERITANCE OF DISEASE RISK. THAT THERE IS A HERITABLE OR FAMILIAL COMPONENT OF SUSCEPTIBILITY TO CHRONIC NON-COMMUNICABLE DISEASES SUCH AS TYPE 2 DIABETES, OBESITY AND CARDIOVASCULAR DISEASE IS WELL ESTABLISHED, BUT THERE IS INCREASING EVIDENCE THAT SOME ELEMENTS OF SUCH HERITABILITY ARE TRANSMITTED NON-GENOMICALLY AND THAT THE PROCESSES WHEREBY ENVIRONMENTAL INFLUENCES ACT DURING EARLY DEVELOPMENT TO SHAPE DISEASE RISK IN LATER LIFE CAN HAVE EFFECTS BEYOND A SINGLE GENERATION. SUCH HERITABILITY MAY OPERATE THROUGH EPIGENETIC MECHANISMS INVOLVING REGULATION OF EITHER IMPRINTED OR NON-IMPRINTED GENES BUT ALSO THROUGH BROADER MECHANISMS RELATED TO PARENTAL PHYSIOLOGY OR BEHAVIOUR. WE REVIEW EVIDENCE AND POTENTIAL MECHANISMS FOR NON-GENOMIC TRANSGENERATIONAL INHERITANCE OF 'LIFESTYLE' DISEASE AND PROPOSE THAT THE 'DEVELOPMENTAL ORIGINS OF DISEASE' PHENOMENON IS A MALADAPTIVE CONSEQUENCE OF AN ANCESTRAL MECHANISM OF DEVELOPMENTAL PLASTICITY THAT MAY HAVE HAD ADAPTIVE VALUE IN THE EVOLUTION OF GENERALIST SPECIES SUCH AS HOMO SAPIENS. 2007 9 3700 32 INFLAMMATORY MEMORY AND TISSUE ADAPTATION IN SICKNESS AND IN HEALTH. OUR BODY HAS A REMARKABLE ABILITY TO REMEMBER ITS PAST ENCOUNTERS WITH ALLERGENS, PATHOGENS, WOUNDS AND IRRITANTS, AND TO REACT MORE QUICKLY TO THE NEXT EXPERIENCE. THIS ACCENTUATED SENSITIVITY ALSO HELPS US TO COPE WITH NEW THREATS. DESPITE MAINTAINING A STATE OF READINESS AND BROADENED RESISTANCE TO SUBSEQUENT PATHOGENS, MEMORIES CAN ALSO BE MALADAPTIVE, LEADING TO CHRONIC INFLAMMATORY DISORDERS AND CANCERS. WITH THE EVER-INCREASING EMERGENCE OF NEW PATHOGENS, ALLERGENS AND POLLUTANTS IN OUR WORLD, THE URGENCY TO UNRAVEL THE MOLECULAR UNDERPINNINGS OF THESE PHENOMENA HAS RISEN TO NEW HEIGHTS. HERE WE REFLECT ON HOW THE FIELD OF INFLAMMATORY MEMORY HAS EVOLVED, SINCE 2007, WHEN RESEARCHERS REALIZED THAT NON-SPECIFIC MEMORY IS CONTAINED IN THE NUCLEUS AND PROPAGATED AT THE EPIGENETIC LEVEL. WE REVIEW THE FLURRY OF RECENT DISCOVERIES REVEALING THAT MEMORY IS NOT JUST A PRIVILEGE OF THE IMMUNE SYSTEM BUT ALSO EXTENDS TO EPITHELIA OF THE SKIN, LUNG, INTESTINE AND PANCREAS, AND TO NEURONS. ALTHOUGH STILL UNFOLDING, EPIGENETIC MEMORIES OF INFLAMMATION HAVE NOW BEEN LINKED TO POSSIBLE BRAIN DISORDERS SUCH AS ALZHEIMER DISEASE, AND TO AN ELEVATED RISK OF CANCER. IN THIS REVIEW, WE CONSIDER THE CONSEQUENCES-GOOD AND BAD-OF THESE EPIGENETIC MEMORIES AND THEIR IMPLICATIONS FOR HUMAN HEALTH AND DISEASE. 2022 10 2103 29 EPIGENETIC EPIDEMIOLOGY OF THE DEVELOPMENTAL ORIGINS HYPOTHESIS. EXTENSIVE HUMAN EPIDEMIOLOGIC AND ANIMAL MODEL DATA INDICATE THAT DURING CRITICAL PERIODS OF PRENATAL AND POSTNATAL MAMMALIAN DEVELOPMENT, NUTRITION AND OTHER ENVIRONMENTAL STIMULI INFLUENCE DEVELOPMENTAL PATHWAYS AND THEREBY INDUCE PERMANENT CHANGES IN METABOLISM AND CHRONIC DISEASE SUSCEPTIBILITY. THE BIOLOGIC MECHANISMS UNDERLYING THIS "DEVELOPMENTAL ORIGINS HYPOTHESIS" ARE POORLY UNDERSTOOD. THIS REVIEW FOCUSES ON THE LIKELY INVOLVEMENT OF EPIGENETIC MECHANISMS IN THE DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE (DOHAD). WE DESCRIBE PERMANENT EFFECTS OF TRANSIENT ENVIRONMENTAL INFLUENCES ON THE DEVELOPMENTAL ESTABLISHMENT OF EPIGENETIC GENE REGULATION AND EVIDENCE LINKING EPIGENETIC DYSREGULATION WITH HUMAN DISEASE. WE PROPOSE A DEFINITION OF "EPIGENETIC EPIDEMIOLOGY" AND DELINEATE HOW THIS EMERGING FIELD PROVIDES A BASIS FROM WHICH TO EXPLORE THE ROLE OF EPIGENETIC MECHANISMS IN DOHAD. WE SUGGEST STRATEGIES FOR FUTURE HUMAN EPIDEMIOLOGIC STUDIES TO IDENTIFY CAUSAL ASSOCIATIONS BETWEEN EARLY EXPOSURES, LONG-TERM CHANGES IN EPIGENETIC REGULATION, AND DISEASE, WHICH MAY ULTIMATELY ENABLE SPECIFIC EARLY-LIFE INTERVENTIONS TO IMPROVE HUMAN HEALTH. 2007 11 5829 25 STRESS, PSYCHIATRIC DISORDERS, MOLECULAR TARGETS, AND MORE. MENTAL HEALTH IS CENTRAL TO NORMAL HEALTH OUTCOMES. A WIDELY ACCEPTED THEORY IS THAT CHRONIC PERSISTENT STRESS DURING ADULTHOOD AS WELL AS DURING EARLY LIFE TRIGGERS ONSET OF NEUROPSYCHIATRIC AILMENTS. HOWEVER, QUESTIONS RELATED TO HOW THAT OCCURS, AND WHY ARE SOME INDIVIDUALS RESISTANT TO STRESS WHILE OTHERS ARE NOT, REMAIN UNANSWERED. AN INTEGRATED, MULTISYSTEMIC STRESS RESPONSE INVOLVING NEUROINFLAMMATORY, NEUROENDOCRINE, EPIGENETIC AND METABOLIC CASCADES HAVE BEEN SUGGESTED TO HAVE CAUSATIVE LINKS. SEVERAL THEORIES HAVE BEEN PROPOSED OVER THE YEARS TO CONCEPTUALIZE THIS LINK INCLUDING THE CYTOKINE HYPOTHESIS, THE ENDOCRINE HYPOTHESIS, THE OXIDATIVE STRESS HYPOTHESIS AND THE OXIDO-NEUROINFLAMMATION HYPOTHESIS. THE DATA DISCUSSED IN THIS REVIEW DESCRIBES POTENTIAL BIOCHEMICAL BASIS OF THE LINK BETWEEN STRESS, AND STRESS-INDUCED NEURONAL, BEHAVIORAL AND EMOTIONAL DEFICITS, PROVIDING INSIGHTS INTO POTENTIALLY NOVEL DRUG TARGETS. 2019 12 2264 40 EPIGENETIC PROGRAMMING BY STRESS AND GLUCOCORTICOIDS ALONG THE HUMAN LIFESPAN. PSYCHOSOCIAL STRESS TRIGGERS A SET OF BEHAVIORAL, NEURAL, HORMONAL, AND MOLECULAR RESPONSES THAT CAN BE A DRIVING FORCE FOR SURVIVAL WHEN ADAPTIVE AND TIME-LIMITED, BUT MAY ALSO CONTRIBUTE TO A HOST OF DISEASE STATES IF DYSREGULATED OR CHRONIC. THE BENEFICIAL OR DETRIMENTAL EFFECTS OF STRESS ARE LARGELY MEDIATED BY THE HYPOTHALAMIC-PITUITARY AXIS, A HIGHLY CONSERVED NEUROHORMONAL CASCADE THAT CULMINATES IN SYSTEMIC SECRETION OF GLUCOCORTICOIDS. GLUCOCORTICOIDS ACTIVATE THE GLUCOCORTICOID RECEPTOR, A UBIQUITOUS NUCLEAR RECEPTOR THAT NOT ONLY CAUSES WIDESPREAD CHANGES IN TRANSCRIPTIONAL PROGRAMS, BUT ALSO INDUCES LASTING EPIGENETIC MODIFICATIONS IN MANY TARGET TISSUES. WHILE THE EPIGENOME REMAINS SENSITIVE TO STRESSORS THROUGHOUT LIFE, WE PROPOSE TWO KEY PRINCIPLES THAT MAY GOVERN THE EPIGENETICS OF STRESS AND GLUCOCORTICOIDS ALONG THE LIFESPAN: FIRST, THE PRESENCE OF DISTINCT LIFE PERIODS, DURING WHICH THE EPIGENOME SHOWS HEIGHTENED PLASTICITY TO STRESS EXPOSURE, SUCH AS IN EARLY DEVELOPMENT AND AT ADVANCED AGE; AND, SECOND, THE POTENTIAL OF STRESS-INDUCED EPIGENETIC CHANGES TO ACCUMULATE THROUGHOUT LIFE BOTH IN SELECT CHROMATIN REGIONS AND AT THE GENOME-WIDE LEVEL. THESE PRINCIPLES HAVE IMPORTANT CLINICAL AND TRANSLATIONAL IMPLICATIONS, AND THEY SHOW STRIKING PARALLELS WITH THE EXISTENCE OF SENSITIVE DEVELOPMENTAL PERIODS AND THE CUMULATIVE IMPACT OF STRESSFUL EXPERIENCES ON THE DEVELOPMENT OF STRESS-RELATED PHENOTYPES. WE HOPE THAT THIS CONCEPTUAL MECHANISTIC FRAMEWORK WILL STIMULATE FRUITFUL RESEARCH THAT AIMS AT UNRAVELING THE MOLECULAR PATHWAYS THROUGH WHICH OUR LIFE STORIES SCULPT GENOMIC FUNCTION TO CONTRIBUTE TO COMPLEX BEHAVIORAL AND SOMATIC PHENOTYPES. 2017 13 2525 32 EPIGENETICS AND TRAINED IMMUNITY. SIGNIFICANCE: A GROWING BODY OF CLINICAL AND EXPERIMENTAL EVIDENCE HAS CHALLENGED THE TRADITIONAL UNDERSTANDING THAT ONLY THE ADAPTIVE IMMUNE SYSTEM CAN MOUNT IMMUNOLOGICAL MEMORY. RECENT FINDINGS DESCRIBE THE ADAPTIVE CHARACTERISTICS OF THE INNATE IMMUNE SYSTEM, UNDERSCORED BY ITS ABILITY TO REMEMBER ANTECEDENT FOREIGN ENCOUNTERS AND RESPOND IN A NONSPECIFIC SENSITIZED MANNER TO REINFECTION. THIS HAS BEEN TERMED TRAINED INNATE IMMUNITY. ALTHOUGH BENEFICIAL IN THE CONTEXT OF RECURRENT INFECTIONS, THIS MIGHT ACTUALLY CONTRIBUTE TO CHRONIC IMMUNE-MEDIATED DISEASES, SUCH AS ATHEROSCLEROSIS. RECENT ADVANCES: IN LINE WITH ITS PROPOSED ROLE IN SUSTAINING CELLULAR MEMORIES, EPIGENETIC REPROGRAMMING HAS EMERGED AS A CRITICAL DETERMINANT OF TRAINED IMMUNITY. RECENT TECHNOLOGICAL AND COMPUTATIONAL ADVANCES THAT IMPROVE UNBIASED ACQUISITION OF EPIGENOMIC PROFILES HAVE SIGNIFICANTLY ENHANCED OUR APPRECIATION FOR THE COMPLEXITIES OF CHROMATIN ARCHITECTURE IN THE CONTEXTS OF DIVERSE IMMUNOLOGICAL CHALLENGES. CRITICAL ISSUES: KEY TO RESOLVING THE DISTINCT CHROMATIN SIGNATURES OF INNATE IMMUNE MEMORY IS A COMPREHENSIVE UNDERSTANDING OF THE PRECISE PHYSIOLOGICAL TARGETS OF REGULATORY PROTEINS THAT RECOGNIZE, DEPOSIT, AND REMOVE CHEMICAL MODIFICATIONS FROM CHROMATIN AS WELL AS OTHER GENE-REGULATING FACTORS. DRAWING FROM A RAPIDLY EXPANDING COMPENDIUM OF EXPERIMENTAL AND CLINICAL STUDIES, THIS REVIEW DETAILS A CURRENT PERSPECTIVE OF THE EPIGENETIC PATHWAYS THAT SUPPORT THE ADAPTED PHENOTYPES OF MONOCYTES AND MACROPHAGES. FUTURE DIRECTIONS: WE EXPLORE FUTURE STRATEGIES THAT ARE AIMED AT EXPLOITING THE MECHANISM OF TRAINED IMMUNITY TO IMPROVE THE PREVENTION AND TREATMENT OF INFECTIONS AND IMMUNE-MEDIATED CHRONIC DISORDERS. 2018 14 6513 26 TRANSCRIPTION-ASSOCIATED EVENTS AFFECTING GENOMIC INTEGRITY. ACCURATE MAINTENANCE OF GENOMIC AS WELL AS EPIGENOMIC INTEGRITY IS CRITICAL FOR PROPER CELL AND ORGAN FUNCTION. CONTINUOUS EXPOSURE TO DNA DAMAGE IS, THUS, OFTEN ASSOCIATED WITH MALIGNANT TRANSFORMATION AND DEGENERATIVE DISEASES. A SIGNIFICANT, CHRONIC THREAT TO GENOME INTEGRITY LIES IN THE PROCESS OF TRANSCRIPTION, WHICH CAN RESULT IN THE FORMATION OF POTENTIALLY HARMFUL RNA : DNA HYBRID STRUCTURES (R-LOOPS) AND HAS BEEN LINKED TO DNA DAMAGE ACCUMULATION AS WELL AS DYNAMIC CHROMATIN REORGANIZATION. IN SHARP CONTRAST, RECENT EVIDENCE SUGGESTS THAT ACTIVE TRANSCRIPTION, THE RESULTING TRANSCRIPTS AS WELL AS R-LOOP FORMATION CAN PLAY MULTI-FACETED ROLES IN MAINTAINING AND RESTORING GENOME INTEGRITY. HERE, WE WILL DISCUSS THE EMERGING CONTRIBUTIONS OF TRANSCRIPTION AS BOTH A SOURCE OF DNA DAMAGE AND A MEDIATOR OF DNA REPAIR. WE PROPOSE THAT BOTH ASPECTS HAVE SIGNIFICANT IMPLICATIONS FOR GENOME MAINTENANCE, AND WILL SPECULATE ON POSSIBLE LONG-TERM CONSEQUENCES FOR THE EPIGENETIC INTEGRITY OF TRANSCRIBING CELLS.THIS ARTICLE IS PART OF THE THEMED ISSUE 'CHROMATIN MODIFIERS AND REMODELLERS IN DNA REPAIR AND SIGNALLING'. 2017 15 357 33 ALTERNATIVE MODELS FOR TRANSGENERATIONAL EPIGENETIC INHERITANCE: MOLECULAR PSYCHIATRY BEYOND MICE AND MAN. MENTAL ILLNESS REMAINS THE GREATEST CHRONIC HEALTH BURDEN GLOBALLY WITH FEW IN-ROADS HAVING BEEN MADE DESPITE SIGNIFICANT ADVANCES IN GENOMIC KNOWLEDGE IN RECENT DECADES. THE FIELD OF PSYCHIATRY IS CONSTANTLY CHALLENGED TO BRING NEW APPROACHES AND TOOLS TO ADDRESS AND TREAT THE NEEDS OF VULNERABLE INDIVIDUALS AND SUBPOPULATIONS, AND THAT HAS TO BE SUPPORTED BY A CONTINUOUS GROWTH IN KNOWLEDGE. THE MAJORITY OF NEUROPSYCHIATRIC SYMPTOMS REFLECT COMPLEX GENE-ENVIRONMENT INTERACTIONS, WITH EPIGENETICS BRIDGING THE GAP BETWEEN GENETIC SUSCEPTIBILITY AND ENVIRONMENTAL STRESSORS THAT TRIGGER DISEASE ONSET AND DRIVE THE ADVANCEMENT OF SYMPTOMS. IT HAS MORE RECENTLY BEEN DEMONSTRATED IN PRECLINICAL MODELS THAT EPIGENETICS UNDERPINS THE TRANSGENERATIONAL INHERITANCE OF STRESS-RELATED BEHAVIOURAL PHENOTYPES IN BOTH PATERNAL AND MATERNAL LINEAGES, PROVIDING FURTHER SUPPORTING EVIDENCE FOR HERITABILITY IN HUMANS. HOWEVER, UNBIASED PROSPECTIVE STUDIES OF THIS NATURE ARE PRACTICALLY IMPOSSIBLE TO CONDUCT IN HUMANS SO PRECLINICAL MODELS REMAIN OUR BEST OPTION FOR RESEARCHING THE MOLECULAR PATHOPHYSIOLOGIES UNDERLYING MANY NEUROPSYCHIATRIC CONDITIONS. WHILE RODENTS WILL REMAIN THE DOMINANT MODEL SYSTEM FOR PRECLINICAL STUDIES (ESPECIALLY FOR ADDRESSING COMPLEX BEHAVIOURAL PHENOTYPES), THERE IS SCOPE TO EXPAND CURRENT RESEARCH OF THE MOLECULAR AND EPIGENETIC PATHOLOGIES BY USING INVERTEBRATE MODELS. HERE, WE WILL DISCUSS THE UTILITY AND ADVANTAGES OF TWO ALTERNATIVE MODEL ORGANISMS-CAENORHABDITIS ELEGANS AND DROSOPHILA MELANOGASTER-AND SUMMARISE THE COMPELLING INSIGHTS OF THE EPIGENETIC REGULATION OF TRANSGENERATIONAL INHERITANCE THAT ARE POTENTIALLY RELEVANT TO HUMAN PSYCHIATRY. 2021 16 6501 29 TRAINED IMMUNITY: LINKING OBESITY AND CARDIOVASCULAR DISEASE ACROSS THE LIFE-COURSE? OBESITY, A CHRONIC INFLAMMATORY DISEASE, IS THE MOST PREVALENT MODIFIABLE RISK FACTOR FOR CARDIOVASCULAR DISEASE. THE MECHANISMS UNDERLYING INFLAMMATION IN OBESITY ARE INCOMPLETELY UNDERSTOOD. RECENT DEVELOPMENTS HAVE CHALLENGED THE DOGMA OF IMMUNOLOGICAL MEMORY OCCURRING EXCLUSIVELY IN THE ADAPTIVE IMMUNE SYSTEM AND SHOW THAT THE INNATE IMMUNE SYSTEM HAS POTENTIAL TO BE REPROGRAMMED. THIS INNATE IMMUNE MEMORY (TRAINED IMMUNITY) IS CHARACTERIZED BY EPIGENETIC AND METABOLIC REPROGRAMMING OF MYELOID CELLS FOLLOWING ENDOGENOUS OR EXOGENOUS STIMULATION, RESULTING IN ENHANCED INFLAMMATION TO SUBSEQUENT STIMULI. TRAINED IMMUNITY PHENOTYPES HAVE NOW BEEN REPORTED FOR OTHER IMMUNE AND NON-IMMUNE CELLS. HERE, WE PROVIDE A NOVEL PERSPECTIVE ON THE PUTATIVE ROLE OF TRAINED IMMUNITY IN MEDIATING THE ADVERSE CARDIOVASCULAR EFFECTS OF OBESITY AND HIGHLIGHT POTENTIAL TRANSLATIONAL PATHWAYS. 2020 17 2069 37 EPIGENETIC CONTROL OF SKELETAL MUSCLE REGENERATION: INTEGRATING GENETIC DETERMINANTS AND ENVIRONMENTAL CHANGES. DURING EMBRYONIC DEVELOPMENT, PLURIPOTENT CELLS ARE GENETICALLY COMMITTED TO SPECIFIC LINEAGES BY THE EXPRESSION OF CELL-TYPE-SPECIFIC TRANSCRIPTIONAL ACTIVATORS THAT DIRECT THE FORMATION OF SPECIALIZED TISSUES AND ORGANS IN RESPONSE TO DEVELOPMENTAL CUES. CHROMATIN-MODIFYING PROTEINS ARE EMERGING AS ESSENTIAL COMPONENTS OF THE EPIGENETIC MACHINERY, WHICH ESTABLISHES THE NUCLEAR LANDSCAPE THAT ULTIMATELY DETERMINES THE FINAL IDENTITY AND FUNCTIONAL SPECIALIZATION OF ADULT CELLS. RECENT EVIDENCE HAS REVEALED THAT DISCRETE POPULATIONS OF ADULT CELLS CAN RETAIN THE ABILITY TO ADOPT ALTERNATIVE CELL FATES IN RESPONSE TO ENVIRONMENTAL CUES. THESE CELLS INCLUDE CONVENTIONAL ADULT STEM CELLS AND A STILL POORLY DEFINED COLLECTION OF CELL TYPES ENDOWED WITH FACULTATIVE PHENOTYPE AND FUNCTIONAL PLASTICITY. UNDER PHYSIOLOGICAL CONDITIONS OR ADAPTIVE STATES, THESE CELLS COOPERATE TO SUPPORT TISSUE AND ORGAN HOMEOSTASIS, AND TO PROMOTE GROWTH OR COMPENSATORY REGENERATION. HOWEVER, DURING CHRONIC DISEASES AND AGING THESE CELLS CAN ADOPT A PATHOLOGICAL PHENOTYPE AND MEDIATE MALADAPTIVE RESPONSES, SUCH AS THE FORMATION OF FIBROTIC SCARS AND FAT DEPOSITION THAT PROGRESSIVELY REPLACES STRUCTURAL AND FUNCTIONAL UNITS OF TISSUES AND ORGANS. THE MOLECULAR DETERMINANTS OF THESE PHENOTYPIC TRANSITIONS ARE ONLY EMERGING FROM RECENT STUDIES THAT REVEAL HOW DYNAMIC CHROMATIN STATES CAN GENERATE FLEXIBLE EPIGENETIC LANDSCAPES, WHICH CONFER ON CELLS THE ABILITY TO RETAIN PARTIAL PLURIPOTENCY AND ADAPT TO ENVIRONMENTAL CHANGES. THIS REVIEW SUMMARIZES OUR CURRENT KNOWLEDGE ON THE ROLE OF THE EPIGENETIC MACHINERY AS A 'FILTER' BETWEEN GENETIC COMMITMENT AND ENVIRONMENTAL SIGNALS IN CELL TYPES THAT CAN ALTERNATIVELY PROMOTE SKELETAL MUSCLE REGENERATION OR FIBRO-ADIPOGENIC DEGENERATION. 2013 18 2177 36 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 19 6656 31 UPDATED UNDERSTANDING OF CANCER AS A METABOLIC AND TELOMERE-DRIVEN DISEASE, AND PROPOSAL FOR COMPLEX PERSONALIZED TREATMENT, A HYPOTHESIS. IN THIS REVIEW, WE PROPOSE A HOLISTIC APPROACH TO UNDERSTANDING CANCER AS A METABOLIC DISEASE. OUR SEARCH FOR RELEVANT STUDIES IN MEDICAL DATABASES CONCLUDES THAT CANCER CELLS DO NOT EVOLVE DIRECTLY FROM NORMAL HEALTHY CELLS. WE HYPOTHESIZE THAT ABERRANT DNA DAMAGE ACCUMULATES OVER TIME-AVOIDING THE NATURAL DNA CONTROLS THAT OTHERWISE REPAIR OR REPLACE THE RAPIDLY REPLICATING CELLS. DNA DAMAGE STARTS TO ACCUMULATE IN NON-REPLICATING CELLS, LEADING TO SENESCENCE AND AGING. DNA DAMAGE IS LINKED WITH GENETIC AND EPIGENETIC FACTORS, BUT THE DEVELOPMENT OF CANCER IS FAVORED BY TELOMERASE ACTIVITY. EVIDENCE INDICATES THAT TELOMERE LENGTH IS AFFECTED BY CHRONIC INFLAMMATIONS, ALTERATIONS OF MITOCHONDRIAL DNA, AND VARIOUS ENVIRONMENTAL FACTORS. EMOTIONAL STRESS ALSO INFLUENCES TELOMERE LENGTH. CHRONIC INFLAMMATION CAN CAUSE OXIDATIVE DNA DAMAGE. OXIDATIVE STRESS, IN TURN, CAN TRIGGER MITOCHONDRIAL CHANGES, WHICH ULTIMATELY ALTER NUCLEAR GENE EXPRESSION. THIS VICIOUS CYCLE HAS LED SEVERAL SCIENTISTS TO VIEW CANCER AS A METABOLIC DISEASE. WE HAVE PROPOSED COMPLEX PERSONALIZED TREATMENTS THAT SEEK TO CORRECT MULTIPLE CHANGES SIMULTANEOUSLY USING A PSYCHOLOGICAL APPROACH TO REDUCE CHRONIC STRESS, IMMUNE CHECKPOINT THERAPY WITH REDUCED DOSES OF CHEMO AND RADIOTHERAPY, MINIMAL SURGICAL INTERVENTION, IF ANY, AND MITOCHONDRIAL METABOLIC REPROGRAMMING PROTOCOLS SUPPLEMENTED BY INTERMITTENT FASTING AND PERSONALIZED DIETARY PLANS WITHOUT INTERFERING WITH THE OTHER THERAPIES. 2020 20 6189 31 THE IMPACT OF LIFE STRESS ON HALLMARKS OF AGING AND ACCELERATED SENESCENCE: CONNECTIONS IN SICKNESS AND IN HEALTH. CHRONIC STRESS IS A RISK FACTOR FOR NUMEROUS AGING-RELATED DISEASES AND HAS BEEN SHOWN TO SHORTEN LIFESPAN IN HUMANS AND OTHER SOCIAL MAMMALS. YET HOW LIFE STRESS CAUSES SUCH A VAST RANGE OF DISEASES IS STILL LARGELY UNCLEAR. IN RECENT YEARS, THE IMPACT OF STRESS ON HEALTH AND AGING HAS BEEN INCREASINGLY ASSOCIATED WITH THE DYSREGULATION OF THE SO-CALLED HALLMARKS OF AGING. THESE ARE BASIC BIOLOGICAL MECHANISMS THAT INFLUENCE INTRINSIC CELLULAR FUNCTIONS AND WHOSE ALTERATION CAN LEAD TO ACCELERATED AGING. HERE, WE REVIEW CORRELATIONAL AND EXPERIMENTAL LITERATURE (PRIMARILY FOCUSING ON EVIDENCE FROM HUMANS AND MURINE MODELS) ON THE CONTRIBUTION OF LIFE STRESS - PARTICULARLY STRESS DERIVED FROM ADVERSE SOCIAL ENVIRONMENTS - TO TRIGGER HALLMARKS OF AGING, INCLUDING CELLULAR SENESCENCE, STERILE INFLAMMATION, TELOMERE SHORTENING, PRODUCTION OF REACTIVE OXYGEN SPECIES, DNA DAMAGE, AND EPIGENETIC CHANGES. WE ALSO EVALUATE THE VALIDITY OF STRESS-INDUCED SENESCENCE AND ACCELERATED AGING AS AN ETIOPATHOLOGICAL PROPOSITION. FINALLY, WE HIGHLIGHT CURRENT GAPS OF KNOWLEDGE AND FUTURE DIRECTIONS FOR THE FIELD, AND DISCUSS PERSPECTIVES FOR TRANSLATIONAL GEROSCIENCE. 2023