1 4376 111 MITOCHONDRIAL (DYS) FUNCTION IN INFLAMMAGING: DO MITOMIRS INFLUENCE THE ENERGETIC, OXIDATIVE, AND INFLAMMATORY STATUS OF SENESCENT CELLS? A RELEVANT FEATURE OF AGING IS CHRONIC LOW-GRADE INFLAMMATION, TERMED INFLAMMAGING, A KEY PROCESS PROMOTING THE DEVELOPMENT OF ALL MAJOR AGE-RELATED DISEASES. SENESCENT CELLS CAN ACQUIRE THE SENESCENCE-ASSOCIATED (SA) SECRETORY PHENOTYPE (SASP), CHARACTERIZED BY THE SECRETION OF PROINFLAMMATORY FACTORS FUELLING INFLAMMAGING. CELLULAR SENESCENCE IS ALSO ACCOMPANIED BY A DEEP RESHAPING OF MICRORNA EXPRESSION AND BY THE MODULATION OF MITOCHONDRIA ACTIVITY, BOTH MASTER REGULATORS OF THE SASP. HERE, WE SYNTHESIZE NOVEL FINDINGS REGARDING THE ROLE OF MITOCHONDRIA IN THE SASP AND IN THE INFLAMMAGING PROCESS AND PROPOSE A NETWORK LINKING NUCLEAR-ENCODED SA-MIRNAS TO MITOCHONDRIAL GENE REGULATION AND FUNCTION IN AGING CELLS. IN THIS CONCEPTUAL STRUCTURE, SA-MIRNAS CAN TRANSLOCATE TO MITOCHONDRIA (SA-MITOMIRS) AND MAY AFFECT THE ENERGETIC, OXIDATIVE, AND INFLAMMATORY STATUS OF SENESCENT CELLS. WE DISCUSS THE POTENTIAL ROLE OF SEVERAL OF SA-MITOMIRS (I.E., LET-7B, MIR-1, MIR-130A-3P, MIR-133A, MIR-146A-5P, MIR-181C-5P, AND MIR-378-5P), USING MIR-146A AS A PROOF-OF-PRINCIPLE MODEL. FINALLY, WE PROPOSE A COMPREHENSIVE, METABOLIC, AND EPIGENETIC VIEW OF THE SENESCENCE PROCESS, IN ORDER TO AMPLIFY THE RANGE OF POSSIBLE APPROACHES TO TARGET INFLAMMAGING, WITH THE ULTIMATE GOAL OF DECELERATING THE AGING RATE, POSTPONING OR BLUNTING THE DEVELOPMENT OF AGE-RELATED DISEASES. 2017 2 5671 28 SHARED AND DISTINCT BIOLOGICAL CIRCUITS IN EFFECTOR, MEMORY AND EXHAUSTED CD8(+) T CELLS REVEALED BY TEMPORAL SINGLE-CELL TRANSCRIPTOMICS AND EPIGENETICS. NAIVE CD8(+) T CELLS CAN DIFFERENTIATE INTO EFFECTOR (T(EFF)), MEMORY (T(MEM)) OR EXHAUSTED (T(EX)) T CELLS. THESE DEVELOPMENTAL PATHWAYS ARE ASSOCIATED WITH DISTINCT TRANSCRIPTIONAL AND EPIGENETIC CHANGES THAT ENDOW CELLS WITH DIFFERENT FUNCTIONAL CAPACITIES AND THEREFORE THERAPEUTIC POTENTIAL. THE MOLECULAR CIRCUITRY UNDERLYING THESE DEVELOPMENTAL TRAJECTORIES AND THE EXTENT OF HETEROGENEITY WITHIN T(EFF), T(MEM) AND T(EX) POPULATIONS REMAIN POORLY UNDERSTOOD. HERE, WE USED THE LYMPHOCYTIC CHORIOMENINGITIS VIRUS MODEL OF ACUTE-RESOLVING AND CHRONIC INFECTION TO ADDRESS THESE GAPS BY APPLYING LONGITUDINAL SINGLE-CELL RNA-SEQUENCING (SCRNA-SEQ) AND SINGLE-CELL ASSAY FOR TRANSPOSASE-ACCESSIBLE CHROMATIN SEQUENCING (SCATAC-SEQ) ANALYSES. THESE ANALYSES UNCOVERED NEW SUBSETS, INCLUDING A SUBPOPULATION OF T(EX) CELLS EXPRESSING NATURAL KILLER CELL-ASSOCIATED GENES THAT IS DEPENDENT ON THE TRANSCRIPTION FACTOR ZEB2, AS WELL AS MULTIPLE DISTINCT TCF-1(+) STEM/PROGENITOR-LIKE SUBSETS IN ACUTE AND CHRONIC INFECTION. THESE DATA ALSO REVEALED INSIGHTS INTO THE RESHAPING OF T(EX) SUBSETS FOLLOWING PROGRAMMED DEATH 1 (PD-1) PATHWAY BLOCKADE AND IDENTIFIED A KEY ROLE FOR THE CELL STRESS REGULATOR, BTG1, IN ESTABLISHING THE T(EX) POPULATION. FINALLY, THESE RESULTS HIGHLIGHTED HOW THE SAME BIOLOGICAL CIRCUITS SUCH AS CYTOTOXICITY OR STEM/PROGENITOR PATHWAYS CAN BE USED BY CD8(+) T CELL SUBSETS WITH HIGHLY DIVERGENT UNDERLYING CHROMATIN LANDSCAPES GENERATED DURING DIFFERENT INFECTIONS. 2022 3 862 22 CHROMATIN REMODELING IN MONOCYTE AND MACROPHAGE ACTIVATION. INCREASING EVIDENCE COLLECTED DURING THE LAST YEARS SUPPORTS THE IDEA THAT MONOCYTE AND MACROPHAGE ACTIVATION IS NOT ONLY ASSOCIATED WITH TRANSCRIPTIONAL CHANGES BUT ALSO CHANGES IN THE CHROMATIN LANDSCAPE. MOREOVER, THE INTRODUCTION OF A MULTIDIMENSIONAL MODEL OF MACROPHAGE ACTIVATION ALLOWS A MORE PRECISE DESCRIPTION OF MONOCYTES AND MACROPHAGES UNDER HOMEOSTATIC AND PATHOPHYSIOLOGICAL CONDITIONS. MONOCYTES AND MACROPHAGES ARE MASTERS OF INTEGRATING MICROENVIRONMENTAL SIGNALS, THEREBY RESHAPING THEIR CHROMATIN LANDSCAPE AND AS A CONSEQUENCE THEIR TRANSCRIPTIONAL AND FUNCTIONAL PROGRAMS. ALBEIT THESE CELLS SHARE A LARGE NUMBER OF EPIGENETIC LANDMARKS, THEIR CHROMATIN IS SIGNIFICANTLY SHAPED BY ENVIRONMENTAL SIGNALS. THE CHROMATIN LANDSCAPE OF ANY GIVEN TISSUE MACROPHAGE IS A RATHER SPECIFIC FINGERPRINT OF THESE CELLS, WHICH IS DIRECTLY LINKED TO TISSUE-SPECIFIC FUNCTIONS OF THESE CELLS. MOREOVER, CHROMATIN REMODELING IN RESPONSE TO STRESS SIGNALS ALSO SEEMS TO BE AN IMPORTANT MECHANISM OF THESE CELLS TO INCREASE THEIR READINESS FOR FUTURE STRESSORS. UNDERSTANDING THIS SOPHISTICATED EPIGENETIC REGULATORY NETWORK IN MONOCYTES AND MACROPHAGES WILL OPEN UP NEW AVENUES TOWARD TISSUE- AND DISEASE-SPECIFIC THERAPEUTIC STRATEGIES IN MANY OF THE CHRONIC INFLAMMATORY DISEASES OUR SOCIETIES ARE CURRENTLY FACING. 2017 4 2663 25 EPSTEIN-BARR VIRUS PROMOTES B CELL LYMPHOMAS BY MANIPULATING THE HOST EPIGENETIC MACHINERY. DURING THE PAST DECADE, THE RAPID DEVELOPMENT OF HIGH-THROUGHPUT NEXT-GENERATION SEQUENCING TECHNOLOGIES HAS SIGNIFICANTLY REINFORCED OUR UNDERSTANDING OF THE ROLE OF EPIGENETICS IN HEALTH AND DISEASE. ALTERED FUNCTIONS OF EPIGENETIC MODIFIERS LEAD TO THE DISRUPTION OF THE HOST EPIGENOME, ULTIMATELY INDUCING CARCINOGENESIS AND DISEASE PROGRESSION. EPSTEIN-BARR VIRUS (EBV) IS AN ENDEMIC HERPESVIRUS THAT IS ASSOCIATED WITH SEVERAL MALIGNANT TUMOURS, INCLUDING B-CELL RELATED LYMPHOMAS. IN EBV-INFECTED CELLS, THE EPIGENOMIC LANDSCAPE IS EXTENSIVELY RESHAPED BY VIRAL ONCOPROTEINS, WHICH DIRECTLY INTERACT WITH EPIGENETIC MODIFIERS AND MODULATE THEIR FUNCTION. THIS PROCESS IS FUNDAMENTAL FOR THE EBV LIFE CYCLE, PARTICULARLY FOR THE ESTABLISHMENT AND MAINTENANCE OF LATENCY IN B CELLS; HOWEVER, THE ALTERATION OF THE HOST EPIGENETIC MACHINERY ALSO CONTRIBUTES TO THE DYSREGULATED EXPRESSION OF SEVERAL CELLULAR GENES, INCLUDING TUMOUR SUPPRESSOR GENES, WHICH CAN DRIVE LYMPHOMA DEVELOPMENT. THIS REVIEW OUTLINES THE MOLECULAR MECHANISMS UNDERLYING THE EPIGENETIC MANIPULATION INDUCED BY EBV THAT LEAD TO TRANSFORMED B CELLS, AS WELL AS NOVEL THERAPEUTIC INTERVENTIONS TO TARGET EBV-ASSOCIATED B-CELL LYMPHOMAS. 2020 5 1468 24 DISTINCT EPIGENETIC PROGRAMS REGULATE CARDIAC MYOCYTE DEVELOPMENT AND DISEASE IN THE HUMAN HEART IN VIVO. EPIGENETIC MECHANISMS AND TRANSCRIPTION FACTOR NETWORKS ESSENTIAL FOR DIFFERENTIATION OF CARDIAC MYOCYTES HAVE BEEN UNCOVERED. HOWEVER, RESHAPING OF THE EPIGENOME OF THESE TERMINALLY DIFFERENTIATED CELLS DURING FETAL DEVELOPMENT, POSTNATAL MATURATION, AND IN DISEASE REMAINS UNKNOWN. HERE, WE INVESTIGATE THE DYNAMICS OF THE CARDIAC MYOCYTE EPIGENOME DURING DEVELOPMENT AND IN CHRONIC HEART FAILURE. WE FIND THAT PRENATAL DEVELOPMENT AND POSTNATAL MATURATION ARE CHARACTERIZED BY A COOPERATION OF ACTIVE CPG METHYLATION AND HISTONE MARKS AT CIS-REGULATORY AND GENIC REGIONS TO SHAPE THE CARDIAC MYOCYTE TRANSCRIPTOME. IN CONTRAST, PATHOLOGICAL GENE EXPRESSION IN TERMINAL HEART FAILURE IS ACCOMPANIED BY CHANGES IN ACTIVE HISTONE MARKS WITHOUT MAJOR ALTERATIONS IN CPG METHYLATION AND REPRESSIVE CHROMATIN MARKS. NOTABLY, CIS-REGULATORY REGIONS IN CARDIAC MYOCYTES ARE SIGNIFICANTLY ENRICHED FOR CARDIOVASCULAR DISEASE-ASSOCIATED VARIANTS. THIS STUDY UNCOVERS DISTINCT LAYERS OF EPIGENETIC REGULATION NOT ONLY DURING PRENATAL DEVELOPMENT AND POSTNATAL MATURATION BUT ALSO IN DISEASED HUMAN CARDIAC MYOCYTES. 2018 6 2944 18 GENETIC AND EPIGENETIC BASIS OF CHRONIC LYMPHOCYTIC LEUKEMIA. PURPOSE OF REVIEW: NEXT-GENERATION SEQUENCING OF WHOLE GENOMES, EXOMES AND DNA METHYLOMES IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) HAS PROVIDED THE FIRST COMPREHENSIVE VIEW OF SOMATIC MUTATIONS AND METHYLATION CHANGES IN THIS DISEASE. THIS REVIEW SUMMARIZES THE RECENT FINDINGS IN THIS FIELD AND THEIR IMPACT ON OUR CURRENT UNDERSTANDING OF THIS NEOPLASM. RECENT FINDINGS: GENOMIC STUDIES HAVE REVEALED A REMARKABLE MOLECULAR HETEROGENEITY OF THE DISEASE, WITH ONLY FEW GENES MUTATED IN UP TO 10-15% OF THE PATIENTS AND A RELATIVELY LARGE NUMBER OF GENES RECURRENTLY MUTATED AT LOW FREQUENCY. THE MUTATED GENES TEND TO CLUSTER IN DIFFERENT PATHWAYS THAT INCLUDE NOTCH1 SIGNALING, RNA SPLICING, PROCESSING AND TRANSPORT MACHINERY, INNATE INFLAMMATORY RESPONSE, AND DNA DAMAGE AND CELL CYCLE CONTROL, AMONG OTHERS. NOTCH1 AND SF3B1 MUTATIONS ARE EMERGING AS NEW DRIVERS OF AGGRESSIVE FORMS OF THE DISEASE. GENOME-WIDE METHYLATION STUDIES HAVE SHOWN THAT CLL TRANSFORMATION IS ASSOCIATED WITH A MASSIVE HYPOMETHYLATION PHENOMENON FREQUENTLY AFFECTING THE ENHANCER REGIONS. THIS EPIGENETIC REPROGRAMMING MAINTAINS AN IMPRINT OF THE PUTATIVE CELL OF ORIGIN FROM NAIVE AND MEMORY B-CELLS. SUMMARY: GENOMIC AND EPIGENOMIC STUDIES OF CLL ARE RESHAPING OUR UNDERSTANDING OF THE DISEASE AND PROVIDE NEW PERSPECTIVE FOR A MORE INDIVIDUALIZED DIAGNOSIS AND NEW POTENTIAL THERAPEUTIC TARGETS. 2013 7 4291 31 MICRORNA PROFILES IN INTESTINAL EPITHELIAL CELLS IN A MOUSE MODEL OF SEPSIS. SEPSIS IS A SYSTEMIC INFLAMMATORY DISORDER THAT LEADS TO THE DYSFUNCTION OF MULTIPLE ORGANS. IN THE INTESTINE, THE DEREGULATION OF THE EPITHELIAL BARRIER CONTRIBUTES TO THE DEVELOPMENT OF SEPSIS BY TRIGGERING CONTINUOUS EXPOSURE TO HARMFUL FACTORS. HOWEVER, SEPSIS-INDUCED EPIGENETIC CHANGES IN GENE-REGULATION NETWORKS WITHIN INTESTINAL EPITHELIAL CELLS (IECS) REMAIN UNEXPLORED. IN THIS STUDY, WE ANALYZED THE EXPRESSION PROFILE OF MICRORNAS (MIRNAS) IN IECS ISOLATED FROM A MOUSE MODEL OF SEPSIS GENERATED VIA CECAL SLURRY INJECTION. AMONG 239 MIRNAS, 14 MIRNAS WERE UPREGULATED, AND 9 MIRNAS WERE DOWNREGULATED IN THE IECS BY SEPSIS. UPREGULATED MIRNAS IN IECS FROM SEPTIC MICE, PARTICULARLY MIR-149-5P, MIR-466Q, MIR-495, AND MIR-511-3P, WERE SEEN TO EXHIBIT COMPLEX AND GLOBAL EFFECTS ON GENE REGULATION NETWORKS. INTERESTINGLY, MIR-511-3P HAS EMERGED AS A DIAGNOSTIC MARKER IN THIS SEPSIS MODEL DUE TO ITS INCREASE IN BLOOD IN ADDITION TO IECS. AS EXPECTED, MRNAS IN THE IECS WERE REMARKABLY ALTERED BY SEPSIS; SPECIFICALLY, 2248 MRNAS WERE DECREASED, WHILE 612 MRNAS WERE INCREASED. THIS QUANTITATIVE BIAS MAY BE POSSIBLY DERIVED, AT LEAST PARTLY, FROM THE DIRECT EFFECTS OF THE SEPSIS-INCREASED MIRNAS ON THE COMPREHENSIVE EXPRESSION OF MRNAS. THUS, CURRENT IN SILICO DATA INDICATE THAT THERE ARE DYNAMIC REGULATORY RESPONSES OF MIRNAS TO SEPSIS IN IECS. IN ADDITION, THE MIRNAS THAT WERE INCREASED WITH SEPSIS HAD ENRICHED DOWNSTREAM PATHWAYS INCLUDING WNT SIGNALING, WHICH IS ASSOCIATED WITH WOUND HEALING, AND FGF/FGFR SIGNALING, WHICH HAS BEEN LINKED TO CHRONIC INFLAMMATION AND FIBROSIS. THESE MODIFICATIONS IN MIRNA NETWORKS IN IECS MAY LEAD TO BOTH PRO- AND ANTI-INFLAMMATORY EFFECTS IN SEPSIS. THE FOUR MIRNAS DISCOVERED ABOVE WERE SHOWN TO PUTATIVELY TARGET LOX, PTCH1, COL22A1, FOXO1, OR HMGA2, VIA IN SILICO ANALYSIS, WHICH WERE ASSOCIATED WITH WNT OR INFLAMMATORY PATHWAYS AND SELECTED FOR FURTHER STUDY. THE EXPRESSIONS OF THESE TARGET GENES WERE DOWNREGULATED IN SEPSIS IECS, POSSIBLY THROUGH POSTTRANSCRIPTIONAL MODIFICATIONS OF THESE MIRNAS. TAKEN TOGETHER, OUR STUDY SUGGESTS THAT IECS DISPLAY A DISTINCTIVE MIRNA PROFILE WHICH IS CAPABLE OF COMPREHENSIVELY AND FUNCTIONALLY RESHAPING THE IEC-SPECIFIC MRNA LANDSCAPE IN A SEPSIS MODEL. 2023 8 4178 18 MEMORY T-CELL HETEROGENEITY AND TERMINOLOGY. IMMUNOLOGICAL MEMORY AND EXHAUSTION ARE FUNDAMENTAL FEATURES OF ADAPTIVE IMMUNITY. RECENT ADVANCES REVEAL INCREASING HETEROGENEITY AND DIVERSITY AMONG CD8 T-CELL SUBSETS, RESULTING IN NEW SUBSETS TO ANNOTATE AND UNDERSTAND. HERE, WE REVIEW OUR CURRENT KNOWLEDGE OF DIFFERENTIATION AND MAINTENANCE OF MEMORY AND EXHAUSTED CD8 T CELLS, INCLUDING PHENOTYPIC CLASSIFICATION, DEVELOPMENTAL PATHS, TRANSCRIPTIONAL AND EPIGENETIC FEATURES, AND CELL INTRINSIC AND EXTRINSIC FACTORS. ADDITIONALLY, WE USE THIS OUTLINE TO DISCUSS THE NOMENCLATURE OF EFFECTOR, MEMORY, AND EXHAUSTED CD8 T CELLS. FINALLY, WE DISCUSS HOW NEW FINDINGS ABOUT THESE CELL TYPES MAY IMPACT THE THERAPEUTIC EFFICACY AND DEVELOPMENT OF IMMUNOTHERAPIES TARGETING EFFECTOR, MEMORY, AND/OR EXHAUSTED CD8 T CELLS IN CHRONIC INFECTIONS AND CANCER. 2021 9 6307 17 THE REFERENCE EPIGENOME AND REGULATORY CHROMATIN LANDSCAPE OF CHRONIC LYMPHOCYTIC LEUKEMIA. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS A FREQUENT HEMATOLOGICAL NEOPLASM IN WHICH UNDERLYING EPIGENETIC ALTERATIONS ARE ONLY PARTIALLY UNDERSTOOD. HERE, WE ANALYZE THE REFERENCE EPIGENOME OF SEVEN PRIMARY CLLS AND THE REGULATORY CHROMATIN LANDSCAPE OF 107 PRIMARY CASES IN THE CONTEXT OF NORMAL B CELL DIFFERENTIATION. WE IDENTIFY THAT THE CLL CHROMATIN LANDSCAPE IS LARGELY INFLUENCED BY DISTINCT DYNAMICS DURING NORMAL B CELL MATURATION. BEYOND THIS, WE DEFINE EXTENSIVE CATALOGUES OF REGULATORY ELEMENTS DE NOVO REPROGRAMMED IN CLL AS A WHOLE AND IN ITS MAJOR CLINICO-BIOLOGICAL SUBTYPES CLASSIFIED BY IGHV SOMATIC HYPERMUTATION LEVELS. WE UNCOVER THAT IGHV-UNMUTATED CLLS HARBOR MORE ACTIVE AND OPEN CHROMATIN THAN IGHV-MUTATED CASES. FURTHERMORE, WE SHOW THAT DE NOVO ACTIVE REGIONS IN CLL ARE ENRICHED FOR NFAT, FOX AND TCF/LEF TRANSCRIPTION FACTOR FAMILY BINDING SITES. ALTHOUGH MOST GENETIC ALTERATIONS ARE NOT ASSOCIATED WITH CONSISTENT EPIGENETIC PROFILES, CLLS WITH MYD88 MUTATIONS AND TRISOMY 12 SHOW DISTINCT CHROMATIN CONFIGURATIONS. FURTHERMORE, WE OBSERVE THAT NON-CODING MUTATIONS IN IGHV-MUTATED CLLS ARE ENRICHED IN H3K27AC-ASSOCIATED REGULATORY ELEMENTS OUTSIDE ACCESSIBLE CHROMATIN. OVERALL, THIS STUDY PROVIDES AN INTEGRATIVE PORTRAIT OF THE CLL EPIGENOME, IDENTIFIES EXTENSIVE NETWORKS OF ALTERED REGULATORY ELEMENTS AND SHEDS LIGHT ON THE RELATIONSHIP BETWEEN THE GENETIC AND EPIGENETIC ARCHITECTURE OF THE DISEASE. 2018 10 4434 21 MOLECULAR DISSECTION OF CD8(+) T-CELL DYSFUNCTION. CHRONIC VIRAL INFECTIONS AND CANCER OFTEN LEAD TO THE EMERGENCE OF DYSFUNCTIONAL OR 'EXHAUSTED' CD8(+) T CELLS, AND THE RESTORATION OF THEIR FUNCTIONS IS CURRENTLY THE FOCUS OF THERAPEUTIC INTERVENTIONS. IN THIS REVIEW, WE DETAIL RECENT ADVANCES IN THE ANNOTATION OF THE GENE MODULES AND THE EPIGENETIC LANDSCAPE ASSOCIATED WITH T-CELL DYSFUNCTION. TOGETHER WITH ANALYSIS OF SINGLE-CELL TRANSCRIPTOMES, THESE FINDINGS HAVE ENABLED A DEEPER AND MORE PRECISE UNDERSTANDING OF THE TRANSCRIPTIONAL MECHANISMS THAT INDUCE AND MAINTAIN THE DYSFUNCTIONAL STATE AND HIGHLIGHT THE HETEROGENEITY OF CD8(+) T-CELL PHENOTYPES PRESENT IN CHRONICALLY INFLAMED TISSUE. WE DISCUSS THE RELEVANCE OF THESE FINDINGS FOR UNDERSTANDING THE TRANSCRIPTIONAL AND SPATIAL REGULATION OF DYSFUNCTIONAL T CELLS AND FOR THE DESIGN OF THERAPEUTICS. 2017 11 4185 23 METABOLIC ADAPTIONS/REPROGRAMMING IN ISLET BETA-CELLS IN RESPONSE TO PHYSIOLOGICAL STIMULATORS-WHAT ARE THE CONSEQUENCES. IRREVERSIBLE PANCREATIC BETA-CELL DAMAGE MAY BE A RESULT OF CHRONIC EXPOSURE TO SUPRAPHYSIOLOGICAL GLUCOSE OR LIPID CONCENTRATIONS OR CHRONIC EXPOSURE TO THERAPEUTIC ANTI-DIABETIC DRUGS. THE BETA-CELLS ARE ABLE TO RESPOND TO BLOOD GLUCOSE IN A NARROW CONCENTRATION RANGE AND RELEASE INSULIN IN RESPONSE, FOLLOWING ACTIVATION OF METABOLIC PATHWAYS SUCH AS GLYCOLYSIS AND THE TCA CYCLE. THE BETA-CELL CANNOT PROTECT ITSELF FROM GLUCOSE TOXICITY BY BLOCKING GLUCOSE UPTAKE, BUT INDEED RELIES ON ALTERNATIVE METABOLIC PROTECTION MECHANISMS TO AVOID DYSFUNCTION AND DEATH. ALTERATION OF NORMAL METABOLIC PATHWAY FUNCTION OCCURS AS A COUNTER REGULATORY RESPONSE TO HIGH NUTRIENT, INFLAMMATORY FACTOR, HORMONE OR THERAPEUTIC DRUG CONCENTRATIONS. METABOLIC REPROGRAMMING IS A TERM WIDELY USED TO DESCRIBE A CHANGE IN REGULATION OF VARIOUS METABOLIC ENZYMES AND TRANSPORTERS, USUALLY ASSOCIATED WITH CELL GROWTH AND PROLIFERATION AND MAY INVOLVE RESHAPING EPIGENETIC RESPONSES, IN PARTICULAR THE ACETYLATION AND METHYLATION OF HISTONE PROTEINS AND DNA. OTHER METABOLIC MODIFICATIONS SUCH AS MALONYLATION, SUCCINYLATION, HYDROXYBUTYRYLATION, ADP-RIBOSYLATION, AND LACTYLATION, MAY IMPACT REGULATORY PROCESSES, MANY OF WHICH NEED TO BE INVESTIGATED IN DETAIL TO CONTRIBUTE TO CURRENT ADVANCES IN METABOLISM. BY DESCRIBING MULTIPLE MECHANISMS OF METABOLIC ADAPTION THAT ARE AVAILABLE TO THE BETA-CELL ACROSS ITS LIFESPAN, WE HOPE TO IDENTIFY SITES FOR METABOLIC REPROGRAMMING MECHANISMS, MOST OF WHICH ARE INCOMPLETELY DESCRIBED OR UNDERSTOOD. MANY OF THESE MECHANISMS ARE RELATED TO PROMINENT ANTIOXIDANT RESPONSES. HERE, WE HAVE ATTEMPTED TO DESCRIBE THE KEY BETA-CELL METABOLIC ADAPTIONS AND CHANGES WHICH ARE REQUIRED FOR SURVIVAL AND FUNCTION IN VARIOUS PHYSIOLOGICAL, PATHOLOGICAL AND PHARMACOLOGICAL CONDITIONS. 2022 12 2409 19 EPIGENETIC SCARRING OF EXHAUSTED T CELLS HINDERS MEMORY DIFFERENTIATION UPON ELIMINATING CHRONIC ANTIGENIC STIMULATION. EXHAUSTED CD8 T CELLS (T(EX)) ARE A DISTINCT STATE OF T CELL DIFFERENTIATION ASSOCIATED WITH FAILURE TO CLEAR CHRONIC VIRUSES AND CANCER. IMMUNOTHERAPIES SUCH AS PD-1 BLOCKADE CAN REINVIGORATE T(EX) CELLS, BUT REINVIGORATION IS NOT DURABLE. A MAJOR UNANSWERED QUESTION IS WHETHER T(EX) CELLS DIFFERENTIATE INTO FUNCTIONAL DURABLE MEMORY T CELLS (T(MEM)) UPON ANTIGEN CLEARANCE. HERE, USING A MOUSE MODEL, WE FOUND THAT UPON ELIMINATING CHRONIC ANTIGENIC STIMULATION, T(EX) CELLS PARTIALLY (RE)ACQUIRE PHENOTYPIC AND TRANSCRIPTIONAL FEATURES OF T(MEM) CELLS. THESE 'RECOVERING' T(EX) CELLS ORIGINATED FROM THE T CELL FACTOR (TCF-1(+)) T(EX) PROGENITOR SUBSET. NEVERTHELESS, THE RECALL CAPACITY OF THESE RECOVERING T(EX) CELLS REMAINED COMPROMISED AS COMPARED TO T(MEM) CELLS. CHROMATIN-ACCESSIBILITY PROFILING REVEALED A FAILURE TO RECOVER CORE MEMORY EPIGENETIC CIRCUITS AND MAINTENANCE OF A LARGELY EXHAUSTED OPEN CHROMATIN LANDSCAPE. THUS, DESPITE SOME PHENOTYPIC AND TRANSCRIPTIONAL RECOVERY UPON ANTIGEN CLEARANCE, EXHAUSTION LEAVES DURABLE EPIGENETIC SCARS CONSTRAINING FUTURE IMMUNE RESPONSES. THESE RESULTS SUPPORT EPIGENETIC REMODELING INTERVENTIONS FOR T(EX) CELL-TARGETED IMMUNOTHERAPIES. 2021 13 1476 26 DIVERSE EPIGENETIC REGULATIONS OF MACROPHAGES IN ATHEROSCLEROSIS. EMERGING RESEARCH ON EPIGENETICS HAS RESULTED IN MANY NOVEL DISCOVERIES IN ATHEROSCLEROSIS (AS), AN INFLAMMAGING-ASSOCIATED DISEASE CHARACTERIZED BY CHRONIC INFLAMMATION PRIMARILY DRIVEN BY MACROPHAGES. THE BULK OF EVIDENCE HAS DEMONSTRATED THE CENTRAL ROLE OF EPIGENETIC MACHINERY IN MACROPHAGE POLARIZATION TO PRO- (M1-LIKE) OR ANTI-INFLAMMATORY (M2-LIKE) PHENOTYPE. AN INCREASING NUMBER OF EPIGENETIC ALTERATIONS AND THEIR MODIFIERS INVOLVED IN REPROGRAMMING MACROPHAGES BY REGULATING DNA METHYLATION OR HISTONE MODIFICATIONS (E.G., METHYLATION, ACETYLATION, AND RECENTLY LACTYLATION) HAVE BEEN IDENTIFIED. THEY MAY ACT TO DETERMINE OR SKEW THE DIRECTION OF MACROPHAGE POLARIZATION IN AS LESIONS, THEREBY REPRESENTING A PROMISING TARGET. HERE WE DESCRIBE THE CURRENT UNDERSTANDING OF THE EPIGENETIC MACHINERY INVOLVING MACROPHAGE POLARIZATION, TO SHED LIGHT ON CHRONIC INFLAMMATION-DRIVING ONSET AND PROGRESSION OF INFLAMMAGING-ASSOCIATED DISEASES, USING AS AS A PROTOTYPIC EXAMPLE, AND DISCUSS THE CHALLENGE FOR DEVELOPING EFFECTIVE THERAPIES TARGETING THE EPIGENETIC MODIFIERS AGAINST THESE DISEASES, PARTICULARLY HIGHLIGHTING A POTENTIAL STRATEGY BASED ON EPIGENETICALLY-GOVERNED REPOLARIZATION FROM M1-LIKE TO M2-LIKE PHENOTYPE. 2022 14 4049 24 MAKING MEMORIES THAT LAST A LIFETIME: HERITABLE FUNCTIONS OF SELF-RENEWING MEMORY CD8 T CELLS. CLONAL EXPANSION OF VIRUS-SPECIFIC NAIVE T CELLS DURING AN ACUTE VIRAL INFECTION RESULTS IN THE FORMATION OF MEMORY CD8 T CELLS THAT PROVIDE THE HOST WITH LONG-TERM PROTECTIVE IMMUNITY AGAINST THE PATHOGEN. MEMORY CD8 T CELLS DISPLAY ENHANCED EFFECTOR FUNCTIONS COMPARED WITH THEIR NAIVE PRECURSORS, ALLOWING THEM TO RESPOND MORE RAPIDLY AND EFFECTIVELY TO ANTIGEN RE-ENCOUNTER. THE ENHANCED FUNCTIONS OF MEMORY CD8 T CELLS ARE MEDIATED BY HERITABLE CHANGES IN GENE REGULATION. EXPRESSION OF SELECT TRANSCRIPTION FACTORS ALONG WITH LOCUS-SPECIFIC EPIGENETIC MODIFICATIONS ARE COUPLED TO AND ARE ESSENTIAL IN THE FORMATION OF MEMORY-SPECIFIC GENE EXPRESSION PATTERNS. HERE, WE WILL REVIEW THE CHANGES IN GENE EXPRESSION THAT ACCOMPANY DEVELOPMENT OF MEMORY CD8 T CELLS AND DISCUSS CHROMATIN MODIFICATIONS AS A POTENTIAL MEANS FOR HERITABLE PROPAGATION OF THESE CHANGES DURING HOMEOSTATIC CELL DIVISION OF SELF-RENEWING MEMORY CD8 T CELLS. ALSO, WE WILL DISCUSS THERAPIES THAT MANIPULATE HERITABLE GENE REGULATION AS A POTENTIAL MECHANISM TO RESTORE FUNCTION TO NON-FUNCTIONAL MEMORY CD8 T CELLS TO COMBAT CHRONIC VIRAL INFECTION. 2010 15 3768 24 INTEGRATIVE EPIGENOMICS IN CHRONIC LYMPHOCYTIC LEUKAEMIA: BIOLOGICAL INSIGHTS AND CLINICAL APPLICATIONS. CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) IS NOT ONLY CHARACTERISED BY DRIVER GENETIC ALTERATIONS BUT BY EXTENSIVE EPIGENETIC CHANGES. OVER THE LAST DECADE, EPIGENOMIC STUDIES HAVE DESCRIBED THE DNA METHYLOME, CHROMATIN ACCESSIBILITY, HISTONE MODIFICATIONS AND THE THREE-DIMENSIONAL (3D) GENOME ARCHITECTURE OF CLL. BEYOND ITS REGULATORY ROLE, THE DNA METHYLOME CONTAINS IMPRINTS OF THE CELLULAR ORIGIN AND PROLIFERATIVE HISTORY OF CLL CELLS. THESE TWO ASPECTS ARE STRONG INDEPENDENT PROGNOSTIC FACTORS. INTEGRATIVE ANALYSES OF CHROMATIN MARKS HAVE UNCOVERED NOVEL REGULATORY ELEMENTS AND ALTERED TRANSCRIPTION FACTOR NETWORKS AS NON-GENETIC MEANS MEDIATING GENE DEREGULATION IN CLL. ADDITIONALLY, CLL CELLS DISPLAY A DISEASE-SPECIFIC PATTERN OF 3D GENOME INTERACTIONS. FROM THE TECHNOLOGICAL PERSPECTIVE, WE ARE CURRENTLY WITNESSING A TRANSITION FROM BULK OMICS TO SINGLE-CELL ANALYSES. THIS REVIEW AIMS AT SUMMARISING THE MAJOR FINDINGS FROM THE EPIGENOMICS FIELD AS WELL AS PROVIDING A PROSPECT OF THE PRESENT AND FUTURE OF SINGLE-CELL ANALYSES IN CLL. 2023 16 771 22 CD8(+) T CELL EXHAUSTION. CD8(+) T CELLS ARE IMPORTANT FOR THE PROTECTIVE IMMUNITY AGAINST INTRACELLULAR PATHOGENS AND TUMOR. IN THE CASE OF CHRONIC INFECTION OR CANCER, CD8(+) T CELLS ARE EXPOSED TO PERSISTENT ANTIGEN AND/OR INFLAMMATORY SIGNALS. THIS EXCESSIVE AMOUNT OF SIGNALS OFTEN LEADS CD8(+) T CELLS TO GRADUAL DETERIORATION OF T CELL FUNCTION, A STATE CALLED "EXHAUSTION." EXHAUSTED T CELLS ARE CHARACTERIZED BY PROGRESSIVE LOSS OF EFFECTOR FUNCTIONS (CYTOKINE PRODUCTION AND KILLING FUNCTION), EXPRESSION OF MULTIPLE INHIBITORY RECEPTORS (SUCH AS PD-1 AND LAG3), DYSREGULATED METABOLISM, POOR MEMORY RECALL RESPONSE, AND HOMEOSTATIC PROLIFERATION. THESE ALTERED FUNCTIONS ARE CLOSELY RELATED WITH ALTERED TRANSCRIPTIONAL PROGRAM AND EPIGENETIC LANDSCAPE THAT CLEARLY DISTINGUISH EXHAUSTED T CELLS FROM NORMAL EFFECTOR AND MEMORY T CELLS. T CELL EXHAUSTION IS OFTEN ASSOCIATED WITH INEFFICIENT CONTROL OF PERSISTING INFECTIONS AND CANCERS, BUT RE-INVIGORATION OF EXHAUSTED T CELLS WITH INHIBITORY RECEPTOR BLOCKADE CAN PROMOTE IMPROVED IMMUNITY AND DISEASE OUTCOME. ACCUMULATING EVIDENCES SUPPORT THE THERAPEUTIC POTENTIAL OF TARGETING EXHAUSTED T CELLS. HOWEVER, EXHAUSTED T CELLS COMPRISE HETEROGENOUS CELL POPULATION WITH DISTINCT RESPONSIVENESS TO INTERVENTION. UNDERSTANDING MOLECULAR MECHANISM OF T CELL EXHAUSTION IS ESSENTIAL TO ESTABLISH RATIONAL IMMUNOTHERAPEUTIC INTERVENTIONS. 2019 17 6121 19 THE EPIGENETIC LANDSCAPE OF T CELL EXHAUSTION. EXHAUSTED T CELLS IN CANCER AND CHRONIC VIRAL INFECTION EXPRESS DISTINCTIVE PATTERNS OF GENES, INCLUDING SUSTAINED EXPRESSION OF PROGRAMMED CELL DEATH PROTEIN 1 (PD-1). HOWEVER, THE REGULATION OF GENE EXPRESSION IN EXHAUSTED T CELLS IS POORLY UNDERSTOOD. HERE, WE DEFINE THE ACCESSIBLE CHROMATIN LANDSCAPE IN EXHAUSTED CD8(+) T CELLS AND SHOW THAT IT IS DISTINCT FROM FUNCTIONAL MEMORY CD8(+) T CELLS. EXHAUSTED CD8(+) T CELLS IN HUMANS AND A MOUSE MODEL OF CHRONIC VIRAL INFECTION ACQUIRE A STATE-SPECIFIC EPIGENETIC LANDSCAPE ORGANIZED INTO FUNCTIONAL MODULES OF ENHANCERS. GENOME EDITING SHOWS THAT PD-1 EXPRESSION IS REGULATED IN PART BY AN EXHAUSTION-SPECIFIC ENHANCER THAT CONTAINS ESSENTIAL RAR, T-BET, AND SOX3 MOTIFS. FUNCTIONAL ENHANCER MAPS MAY OFFER TARGETS FOR GENOME EDITING THAT ALTER GENE EXPRESSION PREFERENTIALLY IN EXHAUSTED CD8(+) T CELLS. 2016 18 5896 27 T CELLS IN HEALTH AND DISEASE. T CELLS ARE CRUCIAL FOR IMMUNE FUNCTIONS TO MAINTAIN HEALTH AND PREVENT DISEASE. T CELL DEVELOPMENT OCCURS IN A STEPWISE PROCESS IN THE THYMUS AND MAINLY GENERATES CD4(+) AND CD8(+) T CELL SUBSETS. UPON ANTIGEN STIMULATION, NAIVE T CELLS DIFFERENTIATE INTO CD4(+) HELPER AND CD8(+) CYTOTOXIC EFFECTOR AND MEMORY CELLS, MEDIATING DIRECT KILLING, DIVERSE IMMUNE REGULATORY FUNCTION, AND LONG-TERM PROTECTION. IN RESPONSE TO ACUTE AND CHRONIC INFECTIONS AND TUMORS, T CELLS ADOPT DISTINCT DIFFERENTIATION TRAJECTORIES AND DEVELOP INTO A RANGE OF HETEROGENEOUS POPULATIONS WITH VARIOUS PHENOTYPE, DIFFERENTIATION POTENTIAL, AND FUNCTIONALITY UNDER PRECISE AND ELABORATE REGULATIONS OF TRANSCRIPTIONAL AND EPIGENETIC PROGRAMS. ABNORMAL T-CELL IMMUNITY CAN INITIATE AND PROMOTE THE PATHOGENESIS OF AUTOIMMUNE DISEASES. IN THIS REVIEW, WE SUMMARIZE THE CURRENT UNDERSTANDING OF T CELL DEVELOPMENT, CD4(+) AND CD8(+) T CELL CLASSIFICATION, AND DIFFERENTIATION IN PHYSIOLOGICAL SETTINGS. WE FURTHER ELABORATE THE HETEROGENEITY, DIFFERENTIATION, FUNCTIONALITY, AND REGULATION NETWORK OF CD4(+) AND CD8(+) T CELLS IN INFECTIOUS DISEASE, CHRONIC INFECTION AND TUMOR, AND AUTOIMMUNE DISEASE, HIGHLIGHTING THE EXHAUSTED CD8(+) T CELL DIFFERENTIATION TRAJECTORY, CD4(+) T CELL HELPER FUNCTION, T CELL CONTRIBUTIONS TO IMMUNOTHERAPY AND AUTOIMMUNE PATHOGENESIS. WE ALSO DISCUSS THE DEVELOPMENT AND FUNCTION OF GAMMADELTA T CELLS IN TISSUE SURVEILLANCE, INFECTION, AND TUMOR IMMUNITY. FINALLY, WE SUMMARIZED CURRENT T-CELL-BASED IMMUNOTHERAPIES IN BOTH CANCER AND AUTOIMMUNE DISEASES, WITH AN EMPHASIS ON THEIR CLINICAL APPLICATIONS. A BETTER UNDERSTANDING OF T CELL IMMUNITY PROVIDES INSIGHT INTO DEVELOPING NOVEL PROPHYLACTIC AND THERAPEUTIC STRATEGIES IN HUMAN DISEASES. 2023 19 2056 24 EPIGENETIC CONTROL OF CD8(+) T CELL DIFFERENTIATION. UPON STIMULATION, SMALL NUMBERS OF NAIVE CD8(+) T CELLS PROLIFERATE AND DIFFERENTIATE INTO A VARIETY OF MEMORY AND EFFECTOR CELL TYPES. CD8(+) T CELLS CAN PERSIST FOR YEARS AND KILL TUMOUR CELLS AND VIRALLY INFECTED CELLS. THE FUNCTIONAL AND PHENOTYPIC CHANGES THAT OCCUR DURING CD8(+) T CELL DIFFERENTIATION ARE WELL CHARACTERIZED, BUT THE EPIGENETIC STATES THAT UNDERLIE THESE CHANGES ARE INCOMPLETELY UNDERSTOOD. HERE, WE REVIEW THE EPIGENETIC PROCESSES THAT DIRECT CD8(+) T CELL DIFFERENTIATION AND FUNCTION. WE FOCUS ON EPIGENETIC MODIFICATION OF DNA AND ASSOCIATED HISTONES AT GENES AND THEIR REGULATORY ELEMENTS. WE ALSO DESCRIBE STRUCTURAL CHANGES IN CHROMATIN ORGANIZATION THAT AFFECT GENE EXPRESSION. FINALLY, WE EXAMINE THE TRANSLATIONAL POTENTIAL OF EPIGENETIC INTERVENTIONS TO IMPROVE CD8(+) T CELL FUNCTION IN INDIVIDUALS WITH CHRONIC INFECTIONS AND CANCER. 2018 20 2562 24 EPIGENETICS IN THE PRIMARY AND SECONDARY PREVENTION OF CARDIOVASCULAR DISEASE: INFLUENCE OF EXERCISE AND NUTRITION. INCREASING EVIDENCE LINKS CHANGES IN EPIGENETIC SYSTEMS, SUCH AS DNA METHYLATION, HISTONE MODIFICATION, AND NON-CODING RNA EXPRESSION, TO THE OCCURRENCE OF CARDIOVASCULAR DISEASE (CVD). THESE EPIGENETIC MODIFICATIONS CAN CHANGE GENETIC FUNCTION UNDER INFLUENCE OF EXOGENOUS STIMULI AND CAN BE TRANSFERRED TO NEXT GENERATIONS, PROVIDING A POTENTIAL MECHANISM FOR INHERITANCE OF BEHAVIOURAL INTERVENTION EFFECTS. THE BENEFITS OF EXERCISE AND NUTRITIONAL INTERVENTIONS IN THE PRIMARY AND SECONDARY PREVENTION OF CVD ARE WELL ESTABLISHED, BUT THE MECHANISMS ARE NOT COMPLETELY UNDERSTOOD. IN THIS REVIEW, WE DESCRIBE THE ACUTE AND CHRONIC EPIGENETIC EFFECTS OF PHYSICAL ACTIVITY AND DIETARY CHANGES. WE PROPOSE EXERCISE AND NUTRITION AS POTENTIAL TRIGGERS OF EPIGENETIC SIGNALS, PROMOTING THE RESHAPING OF TRANSCRIPTIONAL PROGRAMMES WITH EFFECTS ON CVD PHENOTYPES. FINALLY, WE HIGHLIGHT RECENT DEVELOPMENTS IN EPIGENETIC THERAPEUTICS WITH IMPLICATIONS FOR PRIMARY AND SECONDARY CVD PREVENTION. 2022