1 2307 102 EPIGENETIC REGULATION OF CELLULAR FUNCTIONS IN WOUND HEALING. STRINGENT SPATIOTEMPORAL REGULATION OF THE WOUND HEALING PROCESS INVOLVING MULTIPLE CELL TYPES IS ASSOCIATED WITH EPIGENETIC MECHANISMS OF GENE REGULATION, SUCH AS DNA METHYLATION, HISTONE MODIFICATION AND CHROMATIN REMODELLING, AS WELL AS NON-CODING RNAS. HERE, WE DISCUSS THE EPIGENETIC CHANGES THAT OCCUR DURING WOUND HEALING AND THE RAPIDLY EXPANDING UNDERSTANDING OF HOW THESE MECHANISMS AFFECT HEALING RESOLUTION IN BOTH ACUTE AND CHRONIC WOUND MILIEU. WE PROVIDE A FOCUSSED OVERVIEW OF CURRENT RESEARCH INTO EPIGENETIC REGULATORS THAT CONTRIBUTE TO WOUND HEALING BY SPECIFIC CELL TYPE. WE HIGHLIGHT THE ROLE OF EPIGENETIC REGULATORS IN THE MOLECULAR PATHOPHYSIOLOGY OF CHRONIC WOUND CONDITIONS. THE UNDERSTANDING OF HOW EPIGENETIC REGULATORS CAN AFFECT CELLULAR FUNCTIONS DURING NORMAL AND IMPAIRED WOUND HEALING COULD LEAD TO NOVEL THERAPEUTIC APPROACHES, AND WE OUTLINE QUESTIONS THAT CAN PROVIDE GUIDANCE FOR FUTURE RESEARCH ON EPIGENETIC-BASED INTERVENTIONS TO PROMOTE HEALING. DISSECTING THE DYNAMIC INTERPLAY BETWEEN CELLULAR SUBTYPES INVOLVED IN WOUND HEALING AND EPIGENETIC PARAMETERS DURING BARRIER REPAIR WILL DEEPEN OUR UNDERSTANDING OF HOW TO IMPROVE HEALING OUTCOMES IN PATIENTS AFFECTED BY CHRONIC NON-HEALING WOUNDS. 2021 2 6322 27 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 3 2642 28 EPIGENOMIC AND TRANSCRIPTOMIC ANALYSIS OF CHRONIC INFLAMMATORY DISEASES. CHRONIC INFLAMMATORY DISEASES (CIDS) HAVE COMPLEX PATHOLOGIES THAT RESULT FROM ABERRANT AND PERSISTENT IMMUNE RESPONSES. HOWEVER, THE PRECISE TRIGGERS AND MECHANISMS REMAIN ELUSIVE. AN IMPORTANT ASPECT OF CID RESEARCH FOCUSES ON EPIGENETICS MODIFICATIONS, WHICH REGULATE GENE EXPRESSION AND PROVIDE A DYNAMIC TRANSCRIPTIONAL RESPONSE TO INFLAMMATION. IN RECENT YEARS, MOUNTING EVIDENCE HAS DEMONSTRATED AN ASSOCIATION BETWEEN EPIGENOMIC AND TRANSCRIPTOMIC DYSREGULATION AND THE PHENOTYPES OF CIDS. IN PARTICULAR, EPIGENETIC CHANGES AT CIS-REGULATORY ELEMENTS HAVE PROVIDED NEW INSIGHTS FOR IMMUNE CELL-SPECIFIC ALTERATIONS THAT CONTRIBUTE TO DISEASE ETIOLOGY. FURTHERMORE, THE ADVANCEMENTS IN SINGLE-CELL GENOMICS PROVIDE NOVEL SOLUTIONS TO CELL TYPE HETEROGENEITY, WHICH HAS LONG POSED CHALLENGES FOR CID DIAGNOSIS AND TREATMENT. IN THIS REVIEW, WE DISCUSS THE CURRENT STATE OF EPIGENOMICS RESEARCH OF CID AND THE INSIGHTS DERIVED FROM SINGLE-CELL TRANSCRIPTOMIC AND EPIGENOMIC STUDIES. 2021 4 5929 33 TARGETING EPIGENETIC MECHANISMS IN PERIODONTAL DISEASES. EPIGENETIC FACTORS ARE HERITABLE GENOME MODIFICATIONS THAT POTENTIALLY IMPACT GENE TRANSCRIPTION, CONTRIBUTING TO DISEASE STATES. EPIGENETIC MARKS PLAY AN IMPORTANT ROLE IN CHRONIC INFLAMMATORY CONDITIONS, AS OBSERVED IN PERIODONTAL DISEASES, BY ALLOWING MICROBIAL PERSISTENCE OR BY PERMITTING MICROBIAL INSULT TO PLAY A ROLE IN THE SO-CALLED 'HIT-AND-RUN' INFECTIOUS MECHANISM, LEADING TO LASTING PATHOGEN INTERFERENCE WITH THE HOST GENOME. EPIGENETICS ALSO AFFECTS THE HEALTH SCIENCES BY PROVIDING A DYNAMIC MECHANISTIC FRAMEWORK TO EXPLAIN THE WAY IN WHICH ENVIRONMENTAL AND BEHAVIORAL FACTORS INTERACT WITH THE GENOME TO ALTER DISEASE RISK. IN THIS ARTICLE WE REVIEW CURRENT KNOWLEDGE OF EPIGENOME REGULATION IN LIGHT OF THE MULTIFACTORIAL NATURE OF PERIODONTAL DISEASES. WE DISCUSS EPIGENETIC TAGGING IN IDENTIFIED GENES, AND CONSIDER THE POTENTIAL IMPLICATIONS OF EPIGENETIC CHANGES ON HOST-MICROBIOME DYNAMICS IN CHRONIC INFLAMMATORY STATES AND IN RESPONSE TO ENVIRONMENTAL STRESSORS. THE MOST RECENT ADVANCES IN GENOMIC TECHNOLOGIES HAVE PLACED US IN A POSITION TO ANALYZE INTERACTION EFFECTS (EG, BETWEEN PERIODONTAL DISEASE AND TYPE 2 DIABETES MELLITUS), WHICH CAN BE INVESTIGATED THROUGH EPIGENOME-WIDE ASSOCIATION ANALYSIS. FINALLY, BECAUSE OF THE INDIVIDUALIZED TRAITS OF EPIGENETIC BIOMARKERS, PHARMACOEPIGENOMIC PERSPECTIVES ARE ALSO CONSIDERED AS POTENTIALLY NOVEL THERAPEUTIC APPROACHES FOR IMPROVING PERIODONTAL DISEASE STATUS. 2018 5 2069 32 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 6 4342 24 MINIREVIEW: EPIGENETICS OF OBESITY AND DIABETES IN HUMANS. UNDERSTANDING THE DETERMINANTS OF HUMAN HEALTH AND DISEASE IS OVERWHELMINGLY COMPLEX, PARTICULARLY FOR COMMON, LATE-ONSET, CHRONIC DISORDERS, SUCH AS OBESITY AND DIABETES. ELUCIDATING THE GENETIC AND ENVIRONMENTAL FACTORS THAT INFLUENCE SUSCEPTIBILITY TO DISRUPTIONS IN ENERGY HOMEOSTASIS AND METABOLIC REGULATION REMAIN A CHALLENGE, AND PROGRESS WILL ENTAIL THE INTEGRATION OF MULTIPLE ASSESSMENTS OF TEMPORALLY DYNAMIC ENVIRONMENTAL EXPOSURES IN THE CONTEXT OF EACH INDIVIDUAL'S GENOTYPE. TO MEET THIS CHALLENGE, RESEARCHERS ARE INCREASINGLY EXPLORING THE EPIGENOME, WHICH IS THE MALLEABLE INTERFACE OF GENE-ENVIRONMENT INTERACTIONS. EPIGENETIC VARIATION, WHETHER INNATE OR INDUCED, CONTRIBUTES TO VARIATION IN GENE EXPRESSION, THE RANGE OF POTENTIAL INDIVIDUAL RESPONSES TO INTERNAL AND EXTERNAL CUES, AND RISK FOR METABOLIC DISEASE. ULTIMATELY, ADVANCEMENT IN OUR UNDERSTANDING OF CHRONIC DISEASE SUSCEPTIBILITY IN HUMANS WILL DEPEND ON REFINEMENT OF EXPOSURE ASSESSMENT TOOLS AND SYSTEMS BIOLOGY APPROACHES TO INTERPRETATION. IN THIS REVIEW, WE PRESENT RECENT PROGRESS IN EPIGENETICS OF HUMAN OBESITY AND DIABETES, EXISTING CHALLENGES, AND THE POTENTIAL FOR NEW APPROACHES TO UNRAVEL THE COMPLEX BIOLOGY OF METABOLIC DYSREGULATION. 2012 7 2174 31 EPIGENETIC MECHANISMS INVOLVED IN MODULATION OF INFLAMMATORY DISEASES. PURPOSE OF REVIEW: THE ACTIVATION OF INFLAMMATORY RESPONSE IS DEPENDENT UPON GENETIC FACTORS AND EPIGENETIC CONTROL MECHANISMS. THIS OVERVIEW WILL HIGHLIGHT RECENT ADVANCES IN THE UNDERSTANDING OF EPIGENETIC DYNAMICS DURING CELLULAR INFLAMMATION. RECENT FINDINGS: THERE IS A GROWING BODY OF EVIDENCE INDICATING THAT ALTERATIONS OF THE CHROMATIN STATE ASSOCIATE WITH AN INCREASED RISK OF CHRONIC DISEASE DEVELOPMENT AND INFLAMMATION. EPIGENETIC ALTERATIONS RESPOND RAPIDLY TO ENVIRONMENTAL CHANGES AND HAVE A PROFOUND EFFECT ON GENE REGULATORY CROSS-WIRINGS AND TRANSCRIPTIONAL REGULATION. SUMMARY: SYSTEMATIC DISSECTION OF THE MECHANISMS UNDERLYING EPIGENETIC EFFECTS DURING INFLAMMATORY RESPONSE IS A CRITICAL STEP TOWARD ELUCIDATION OF THE CELL'S MOLECULAR PROCESSES AND HOLDS POTENTIAL FOR THE DEVELOPMENT OF NOVEL THERAPIES FOR THE TREATMENT OF CHRONIC DISEASES. 2016 8 2543 34 EPIGENETICS IN LIVER DISEASE. EPIGENETICS IS A TERM THAT ENCOMPASSES A VARIETY OF REGULATORY PROCESSES THAT ARE ABLE TO CROSSTALK IN ORDER TO INFLUENCE GENE EXPRESSION AND CELL PHENOTYPE IN RESPONSE TO ENVIRONMENTAL CUES. A DEEP UNDERSTANDING OF EPIGENETICS OFFERS THE POTENTIAL FOR FRESH INSIGHTS INTO THE BASIS FOR COMPLEX CHRONIC DISEASES AND IMPROVED DIAGNOSTIC AND PROGNOSTIC TOOLS. MOREOVER, AS EPIGENETIC MODIFICATIONS ARE HIGHLY PLASTIC AND RESPONSIVE TO THE ENVIRONMENT, THERE IS MUCH EXCITEMENT AROUND THE THEME OF EPIGENETIC THERAPEUTICS, INCLUDING NOT ONLY NEW DRUGS BUT ALSO MORE INFORMED PATIENT ADVICE ON LIFESTYLE CHOICES AND THEIR IMPACT ON PATHOLOGY. THIS REVIEW BRIEFLY EXPLAINS THE MOLECULAR NATURE OF THE INDIVIDUAL REGULATORY PROCESS THAT CONSTITUTE EPIGENETICS, INCLUDING DNA METHYLATION, HISTONE MODIFICATIONS, CHROMATIN REMODELING, TRANSCRIPTIONAL CONTROL, AND NONCODING RNAS. THE WAYS IN WHICH THESE EPIGENETIC MECHANISMS INFLUENCE LIVER PHYSIOLOGY AND DISEASE WILL BE CONSIDERED IN DETAIL, PARTICULARLY IN THE CONTEXT OF CANCER, FIBROSIS, AND NONALCOHOLIC STEATOHEPATITIS. THE CURRENT LIMITATIONS ASSOCIATED WITH EPIGENETIC PROFILING AND THERAPEUTICS IN LIVER DISEASE ARE DISCUSSED, AS IS THE INTRIGUING POSSIBILITY THAT ENVIRONMENTAL-INDUCED EPIGENETIC CHANGES MAY BECOME STABLE AND HERITABLE. CONCLUSION: THE AIM OF THE REVIEW IS TO INFORM HEPATOLOGISTS OF THE EMERGING KEY EPIGENETIC IDEAS OF RELEVANCE TO LIVER DISEASES THAT ARE HIGHLY LIKELY TO FORM A COMPONENT OF PATIENT MANAGEMENT AND CARE IN THE NEXT DECADE. 2014 9 2291 31 EPIGENETIC REGULATION IN PATHOLOGY OF ATHEROSCLEROSIS: A NOVEL PERSPECTIVE. ATHEROSCLEROSIS, CHARACTERIZED BY ATHEROSCLEROTIC PLAQUES, IS A COMPLEX PATHOLOGICAL PROCESS THAT INVOLVES DIFFERENT CELL TYPES AND CAN BE SEEN AS A CHRONIC INFLAMMATORY DISEASE. IN THE ADVANCED STAGE, THE RUPTURED ATHEROSCLEROTIC PLAQUE CAN INDUCE DEADLY ACCIDENTS INCLUDING ISCHEMIC STROKE AND MYOCARDIAL INFARCTION. EPIGENETICS REGULATION, INCLUDING DNA METHYLATION, HISTONE MODIFICATION, AND NON-CODING RNA MODIFICATION. MAINTAINS CELLULAR IDENTITY VIA AFFECTING THE CELLULAR TRANSCRIPTOME. THE EPIGENETIC MODIFICATION PROCESS, MEDIATING BY EPIGENETIC ENZYMES, IS DYNAMIC UNDER VARIOUS STIMULI, WHICH CAN BE REVERSELY ALTERED. RECENTLY, NUMEROUS STUDIES HAVE EVIDENCED THE CLOSE RELATIONSHIP BETWEEN ATHEROSCLEROSIS AND EPIGENETIC REGULATIONS IN ATHEROSCLEROSIS, PROVIDING US WITH A NOVEL PERSPECTIVE IN RESEARCHING MECHANISMS AND FINDING NOVEL THERAPEUTIC TARGETS OF THIS SERIOUS DISEASE. HERE, WE CRITICALLY REVIEW THE RECENT DISCOVERIES BETWEEN EPIGENETIC REGULATION MECHANISMS IN ATHEROSCLEROSIS. 2021 10 4422 35 MOLECULAR AND GENETIC INFLAMMATION NETWORKS IN MAJOR HUMAN DISEASES. IT HAS BEEN WELL-RECOGNIZED THAT INFLAMMATION ALONGSIDE TISSUE REPAIR AND DAMAGE MAINTAINING TISSUE HOMEOSTASIS DETERMINES THE INITIATION AND PROGRESSION OF COMPLEX DISEASES. ALBEIT WITH THE ACCOMPLISHMENT OF HAVING CAPTURED THE MOST CRITICAL INFLAMMATION-INVOLVED MOLECULES, GENETIC SUSCEPTIBILITIES, EPIGENETIC FACTORS, AND ENVIRONMENTAL FACTORS, OUR SCHEMATA ON THE ROLE OF INFLAMMATION IN COMPLEX DISEASES REMAIN LARGELY PATCHY, IN PART DUE TO THE SUCCESS OF REDUCTIONISM IN TERMS OF RESEARCH METHODOLOGY PER SE. OMICS DATA ALONGSIDE THE ADVANCES IN DATA INTEGRATION TECHNOLOGIES HAVE ENABLED RECONSTRUCTION OF MOLECULAR AND GENETIC INFLAMMATION NETWORKS WHICH SHED LIGHT ON THE UNDERLYING PATHOPHYSIOLOGY OF COMPLEX DISEASES OR CLINICAL CONDITIONS. GIVEN THE PROVEN BENEFICIAL ROLE OF ANTI-INFLAMMATION IN CORONARY HEART DISEASE AS WELL AS OTHER COMPLEX DISEASES AND IMMUNOTHERAPY AS A REVOLUTIONARY TRANSITION IN ONCOLOGY, IT BECOMES TIMELY TO REVIEW OUR CURRENT UNDERSTANDING OF THE MOLECULAR AND GENETIC INFLAMMATION NETWORKS UNDERLYING MAJOR HUMAN DISEASES. IN THIS REVIEW, WE FIRST BRIEFLY DISCUSS THE COMPLEXITY OF INFECTIOUS DISEASES AND THEN HIGHLIGHT RECENTLY UNCOVERED MOLECULAR AND GENETIC INFLAMMATION NETWORKS IN OTHER MAJOR HUMAN DISEASES INCLUDING OBESITY, TYPE II DIABETES, CORONARY HEART DISEASE, LATE ONSET ALZHEIMER'S DISEASE, PARKINSON'S DISEASE, AND SPORADIC CANCER. THE COMMONALITY AND SPECIFICITY OF THESE MOLECULAR NETWORKS ARE ADDRESSED IN THE CONTEXT OF GENETICS BASED ON GENOME-WIDE ASSOCIATION STUDY (GWAS). THE DOUBLE-SWORD ROLE OF INFLAMMATION, SUCH AS HOW THE ABERRANT TYPE 1 AND/OR TYPE 2 IMMUNITY LEADS TO CHRONIC AND SEVERE CLINICAL CONDITIONS, REMAINS OPEN IN TERMS OF THE INFLAMMASOME AND THE CORE INFLAMMATOME NETWORK FEATURES. INCREASINGLY AVAILABLE LARGE OMICS AND CLINICAL DATA IN TANDEM WITH SYSTEMS BIOLOGY APPROACHES HAVE OFFERED AN EXCITING YET CHALLENGING OPPORTUNITY TOWARD RECONSTRUCTION OF MORE COMPREHENSIVE AND DYNAMIC MOLECULAR AND GENETIC INFLAMMATION NETWORKS, WHICH HOLD GREAT PROMISE IN TRANSITING NETWORK SNAPSHOTS TO VIDEO-STYLE MULTI-SCALE INTERPLAYS OF DISEASE MECHANISMS, IN TURN LEADING TO EFFECTIVE CLINICAL INTERVENTION. 2016 11 6513 32 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 12 6630 29 UNDERSTANDING THE INTERPLAY BETWEEN HEALTH DISPARITIES AND EPIGENOMICS. SOCIAL EPIGENOMICS HAS EMERGED AS AN INTEGRATIVE FIELD OF RESEARCH FOCUSED ON IDENTIFICATION OF SOCIO-ENVIRONMENTAL FACTORS, THEIR INFLUENCE ON HUMAN BIOLOGY THROUGH EPIGENOMIC MODIFICATIONS, AND HOW THEY CONTRIBUTE TO CURRENT HEALTH DISPARITIES. SEVERAL HEALTH DISPARITIES STUDIES HAVE BEEN PUBLISHED USING GENETIC-BASED APPROACHES; HOWEVER, INCREASING ACCESSIBILITY AND AFFORDABILITY OF MOLECULAR TECHNOLOGIES HAVE ALLOWED FOR AN IN-DEPTH INVESTIGATION OF THE INFLUENCE OF EXTERNAL FACTORS ON EPIGENETIC MODIFICATIONS (E.G., DNA METHYLATION, MICRO-RNA EXPRESSION). CURRENTLY, RESEARCH IS FOCUSED ON EPIGENETIC CHANGES IN RESPONSE TO ENVIRONMENT, AS WELL AS TARGETED EPIGENETIC THERAPIES AND ENVIRONMENTAL/SOCIAL STRATEGIES FOR POTENTIALLY MINIMIZING CERTAIN HEALTH DISPARITIES. HERE, WE WILL REVIEW RECENT FINDINGS IN THIS FIELD PERTAINING TO CONDITIONS AND DISEASES OVER LIFE SPAN ENCOMPASSING PRENATAL TO ADULT STAGES. 2020 13 4460 35 MOLECULAR MECHANISMS OF ENVIRONMENTAL EXPOSURES AND HUMAN DISEASE. A SUBSTANTIAL PROPORTION OF DISEASE RISK FOR COMMON COMPLEX DISORDERS IS ATTRIBUTABLE TO ENVIRONMENTAL EXPOSURES AND POLLUTANTS. AN APPRECIATION OF HOW ENVIRONMENTAL POLLUTANTS ACT ON OUR CELLS TO PRODUCE DELETERIOUS HEALTH EFFECTS HAS LED TO ADVANCES IN OUR UNDERSTANDING OF THE MOLECULAR MECHANISMS UNDERLYING THE PATHOGENESIS OF CHRONIC DISEASES, INCLUDING CANCER AND CARDIOVASCULAR, NEURODEGENERATIVE AND RESPIRATORY DISEASES. HERE, WE DISCUSS EMERGING RESEARCH ON THE INTERPLAY OF ENVIRONMENTAL POLLUTANTS WITH THE HUMAN GENOME AND EPIGENOME. WE REVIEW EVIDENCE SHOWING THE ENVIRONMENTAL IMPACT ON GENE EXPRESSION THROUGH EPIGENETIC MODIFICATIONS, INCLUDING DNA METHYLATION, HISTONE MODIFICATION AND NON-CODING RNAS. WE ALSO HIGHLIGHT RECENT STUDIES THAT EVALUATE RECENTLY DISCOVERED MOLECULAR PROCESSES THROUGH WHICH THE ENVIRONMENT CAN EXERT ITS EFFECTS, INCLUDING EXTRACELLULAR VESICLES, THE EPITRANSCRIPTOME AND THE MITOCHONDRIAL GENOME. FINALLY, WE DISCUSS CURRENT CHALLENGES WHEN STUDYING THE EXPOSOME - THE CUMULATIVE MEASURE OF ENVIRONMENTAL INFLUENCES OVER THE LIFESPAN - AND ITS INTEGRATION INTO FUTURE ENVIRONMENTAL HEALTH RESEARCH. 2023 14 2503 20 EPIGENETICS AND METABOLISM AT THE CROSSROADS OF STRESS-INDUCED PLASTICITY, STEMNESS AND THERAPEUTIC RESISTANCE IN CANCER. DESPITE THE RECENT ADVANCES IN THE TREATMENT OF CANCERS, ACQUIRED DRUG RESISTANCE REMAINS A MAJOR CHALLENGE IN CANCER MANAGEMENT. WHILE EARLIER STUDIES SUGGEST DARWINIAN FACTORS DRIVING ACQUIRED DRUG RESISTANCE, RECENT STUDIES POINT TO A MORE DYNAMIC PROCESS INVOLVING PHENOTYPIC PLASTICITY AND TUMOR HETEROGENEITY IN THE EVOLUTION OF ACQUIRED DRUG RESISTANCE. CHRONIC STRESS AFTER DRUG TREATMENT INDUCES INTRINSIC CELLULAR REPROGRAMMING AND CANCER STEMNESS THROUGH A SLOW-CYCLING PERSISTER STATE, WHICH SUBSEQUENTLY DRIVES CANCER PROGRESSION. BOTH EPIGENETIC AND METABOLIC MECHANISMS PLAY AN IMPORTANT ROLE IN THIS DYNAMIC PROCESS. IN THIS REVIEW, WE DISCUSS HOW EPIGENETIC AND METABOLIC REPROGRAMMING LEADS TO STRESS-INDUCED PHENOTYPIC PLASTICITY AND ACQUIRED DRUG RESISTANCE, AND HOW THE TWO REPROGRAMMING MECHANISMS CROSSTALK WITH EACH OTHER. 2020 15 2812 25 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 16 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 17 6268 32 THE NEUROEPIGENOME: IMPLICATIONS OF CHEMICAL AND PHYSICAL MODIFICATIONS OF GENOMIC DNA IN SCHIZOPHRENIA. SCHIZOPHRENIA IS A CHRONIC MENTAL ILLNESS WITH A SUBSTANTIAL GENETIC COMPONENT. TO UNFOLD THE COMPLEX ETIOLOGY OF SCHIZOPHRENIA, IT IS IMPORTANT TO UNDERSTAND THE INTERPLAY BETWEEN GENETIC AND NONGENETIC FACTORS. GENETIC FACTORS INVOLVE VARIATION IN THE DNA SEQUENCES OF PROTEIN-CODING GENES, WHICH DIRECTLY CONTRIBUTE TO PHENOTYPIC TRAITS, AND VARIATION IN NONCODING SEQUENCES, WHICH COMPRISE 98% OF THE GENOME AND CONTAIN DNA ELEMENTS KNOWN TO PLAY A ROLE IN REGULATING GENE EXPRESSION. THE EPIGENOME REFERS TO THE CHEMICAL MODIFICATIONS ON BOTH DNA AND THE STRUCTURAL PROTEINS THAT PACKAGE DNA INTO THE NUCLEUS, WHICH TOGETHER REGULATE GENE EXPRESSION IN SPECIFIC CELL TYPES, CONDITIONS, AND DEVELOPMENTAL STAGES. THE DYNAMIC NATURE OF THE EPIGENOME MAKES IT AN IDEAL TOOL TO INVESTIGATE THE RELATIONSHIP BETWEEN INHERITED GENETIC MUTATIONS ASSOCIATED WITH SCHIZOPHRENIA AND ALTERED GENE REGULATION THROUGHOUT THE COURSE OF BRAIN DEVELOPMENT. IN THIS REVIEW, WE FOCUS ON THE CURRENT UNDERSTANDING OF THE ROLE OF EPIGENETIC MARKS AND THEIR THREE-DIMENSIONAL NUCLEAR ORGANIZATION IN THE DEVELOPMENTAL TRAJECTORY OF DISTINCT BRAIN CELL TYPES TO DECIPHER THE COMPLEX GENE REGULATORY MECHANISMS THAT ARE DISRUPTED IN SCHIZOPHRENIA. 2022 18 2168 26 EPIGENETIC MECHANISMS IN MONOCYTES/MACROPHAGES REGULATE INFLAMMATION IN CARDIOMETABOLIC AND VASCULAR DISEASE. CARDIOMETABOLIC AND VASCULAR DISEASE, WITH THEIR ASSOCIATED SECONDARY COMPLICATIONS, ARE THE LEADING CAUSE OF MORBIDITY AND MORTALITY IN WESTERN SOCIETY. CHRONIC INFLAMMATION IS A COMMON THEME THAT UNDERLIES INITIATION AND PROGRESSION OF CARDIOVASCULAR DISEASE. IN THIS REGARD, MONOCYTES/MACROPHAGES ARE KEY PLAYERS IN THE DEVELOPMENT OF A CHRONIC INFLAMMATORY STATE. OVER THE PAST DECADE, EPIGENETIC MODIFICATIONS, SUCH AS DNA METHYLATION AND POSTTRANSLATIONAL HISTONE PROCESSING, HAVE EMERGED AS IMPORTANT REGULATORS OF IMMUNE CELL PHENOTYPES. ACCUMULATING STUDIES REVEAL THE IMPORTANCE OF EPIGENETIC ENZYMES IN THE DYNAMIC REGULATION OF KEY SIGNALING PATHWAYS THAT ALTER MONOCYTE/MACROPHAGE PHENOTYPES IN RESPONSE TO ENVIRONMENTAL STIMULI. IN THIS REVIEW, WE HIGHLIGHT THE CURRENT PARADIGMS OF MONOCYTE/MACROPHAGE POLARIZATION AND THE EMERGING ROLE OF EPIGENETIC MODIFICATION IN THE REGULATION OF MONOCYTE/MACROPHAGE PHENOTYPE IN OBESITY, DIABETES MELLITUS, ATHEROSCLEROSIS, AND ABDOMINAL AORTIC ANEURYSMS. 2019 19 838 35 CHEMISTRY MEETS BIOLOGY IN COLITIS-ASSOCIATED CARCINOGENESIS. THE INTESTINE COMPRISES AN EXCEPTIONAL VENUE FOR A DYNAMIC AND COMPLEX INTERPLAY OF NUMEROUS CHEMICAL AND BIOLOGICAL PROCESSES. HERE, MULTIPLE CHEMICAL AND BIOLOGICAL SYSTEMS, INCLUDING THE INTESTINAL TISSUE ITSELF, ITS ASSOCIATED IMMUNE SYSTEM, THE GUT MICROBIOTA, XENOBIOTICS, AND METABOLITES MEET AND INTERACT TO FORM A SOPHISTICATED AND TIGHTLY REGULATED STATE OF TISSUE HOMOEOSTASIS. DISTURBANCE OF THIS HOMEOSTASIS CAN CAUSE INFLAMMATORY BOWEL DISEASE (IBD)-A CHRONIC DISEASE OF MULTIFACTORIAL ETIOLOGY THAT IS STRONGLY ASSOCIATED WITH INCREASED RISK FOR CANCER DEVELOPMENT. THIS REVIEW ADDRESSES RECENT DEVELOPMENTS IN RESEARCH INTO CHEMICAL AND BIOLOGICAL MECHANISMS UNDERLYING THE ETIOLOGY OF INFLAMMATION-INDUCED COLON CANCER. BEGINNING WITH A GENERAL OVERVIEW OF REACTIVE CHEMICAL SPECIES GENERATED DURING COLONIC INFLAMMATION, THE MECHANISTIC INTERPLAY BETWEEN CHEMICAL AND BIOLOGICAL MEDIATORS OF INFLAMMATION, THE ROLE OF GENETIC TOXICOLOGY, AND MICROBIAL PATHOGENESIS IN DISEASE DEVELOPMENT ARE DISCUSSED. WHEN POSSIBLE, WE SYSTEMATICALLY COMPARE EVIDENCE FROM STUDIES UTILIZING HUMAN IBD PATIENTS WITH EXPERIMENTAL INVESTIGATIONS IN MICE. THE COMPARISON REVEALS THAT MANY STRONG PATHOLOGICAL AND MECHANISTIC CORRELATES EXIST BETWEEN MOUSE MODELS OF COLITIS-ASSOCIATED CANCER, AND THE CLINICALLY RELEVANT SITUATION IN HUMANS. WE ALSO SUMMARIZE SEVERAL EMERGING ISSUES IN THE FIELD, SUCH AS THE CARCINOGENIC POTENTIAL OF NOVEL INFLAMMATION-RELATED DNA ADDUCTS AND GENOTOXIC MICROBIAL FACTORS, THE SYSTEMIC DIMENSION OF INFLAMMATION-INDUCED GENOTOXICITY, AND THE COMPLEX ROLE OF GENOME MAINTENANCE MECHANISMS DURING THESE PROCESSES. TAKEN TOGETHER, CURRENT EVIDENCE POINTS TO THE INDUCTION OF GENETIC AND EPIGENETIC ALTERATIONS BY CHEMICAL AND BIOLOGICAL INFLAMMATORY STIMULI ULTIMATELY LEADING TO CANCER FORMATION. 2013 20 5376 39 RECENT DEVELOPMENTS IN EPIGENETICS OF ACUTE AND CHRONIC KIDNEY DISEASES. THE GROWING EPIDEMIC OF OBESITY AND DIABETES, THE AGING POPULATION AS WELL AS PREVALENCE OF DRUG ABUSE HAS LED TO SIGNIFICANT INCREASES IN THE RATES OF THE CLOSELY ASSOCIATED ACUTE AND CHRONIC KIDNEY DISEASES, INCLUDING DIABETIC NEPHROPATHY. FURTHERMORE, EVIDENCE SHOWS THAT PARENTAL BEHAVIOR AND DIET CAN AFFECT THE PHENOTYPE OF SUBSEQUENT GENERATIONS VIA EPIGENETIC TRANSMISSION MECHANISMS. THESE DATA SUGGEST A STRONG INFLUENCE OF THE ENVIRONMENT ON DISEASE SUSCEPTIBILITY AND THAT, APART FROM GENETIC SUSCEPTIBILITY, EPIGENETIC MECHANISMS NEED TO BE EVALUATED TO GAIN CRITICAL NEW INFORMATION ABOUT KIDNEY DISEASES. EPIGENETICS IS THE STUDY OF PROCESSES THAT CONTROL GENE EXPRESSION AND PHENOTYPE WITHOUT ALTERATIONS IN THE UNDERLYING DNA SEQUENCE. EPIGENETIC MODIFICATIONS, INCLUDING CYTOSINE DNA METHYLATION AND COVALENT POST-TRANSLATIONAL MODIFICATIONS OF HISTONES IN CHROMATIN, ARE PART OF THE EPIGENOME, THE INTERFACE BETWEEN THE STABLE GENOME AND THE VARIABLE ENVIRONMENT. THIS DYNAMIC EPIGENETIC LAYER RESPONDS TO EXTERNAL ENVIRONMENTAL CUES TO INFLUENCE THE EXPRESSION OF GENES ASSOCIATED WITH DISEASE STATES. THE FIELD OF EPIGENETICS HAS SEEN REMARKABLE GROWTH IN THE PAST FEW YEARS WITH SIGNIFICANT ADVANCES IN BASIC BIOLOGY, CONTRIBUTIONS TO HUMAN DISEASE, AS WELL AS EPIGENOMICS TECHNOLOGIES. FURTHER UNDERSTANDING OF HOW THE RENAL CELL EPIGENOME IS ALTERED BY METABOLIC AND OTHER STIMULI CAN YIELD NOVEL NEW INSIGHTS INTO THE PATHOGENESIS OF KIDNEY DISEASES. IN THIS REVIEW, WE HAVE DISCUSSED THE CURRENT KNOWLEDGE ON THE ROLE OF EPIGENETIC MECHANISMS (PRIMARILY DNAME AND HISTONE MODIFICATIONS) IN ACUTE AND CHRONIC KIDNEY DISEASES, AND THEIR TRANSLATIONAL POTENTIAL TO IDENTIFY MUCH NEEDED NEW THERAPIES. 2015