1 6121 73 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 2 5671 36 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 6482 32 TOX TRANSCRIPTIONALLY AND EPIGENETICALLY PROGRAMS CD8(+) T CELL EXHAUSTION. EXHAUSTED CD8(+) T (T(EX)) CELLS IN CHRONIC INFECTIONS AND CANCER HAVE LIMITED EFFECTOR FUNCTION, HIGH CO-EXPRESSION OF INHIBITORY RECEPTORS AND EXTENSIVE TRANSCRIPTIONAL CHANGES COMPARED WITH EFFECTOR (T(EFF)) OR MEMORY (T(MEM)) CD8(+) T CELLS. T(EX) CELLS ARE IMPORTANT CLINICAL TARGETS OF CHECKPOINT BLOCKADE AND OTHER IMMUNOTHERAPIES. EPIGENETICALLY, T(EX) CELLS ARE A DISTINCT IMMUNE SUBSET, WITH A UNIQUE CHROMATIN LANDSCAPE COMPARED WITH T(EFF) AND T(MEM) CELLS. HOWEVER, THE MECHANISMS THAT GOVERN THE TRANSCRIPTIONAL AND EPIGENETIC DEVELOPMENT OF T(EX) CELLS REMAIN UNKNOWN. HERE WE IDENTIFY THE HMG-BOX TRANSCRIPTION FACTOR TOX AS A CENTRAL REGULATOR OF T(EX) CELLS IN MICE. TOX IS LARGELY DISPENSABLE FOR THE FORMATION OF T(EFF) AND T(MEM) CELLS, BUT IT IS CRITICAL FOR EXHAUSTION: IN THE ABSENCE OF TOX, T(EX) CELLS DO NOT FORM. TOX IS INDUCED BY CALCINEURIN AND NFAT2, AND OPERATES IN A FEED-FORWARD LOOP IN WHICH IT BECOMES CALCINEURIN-INDEPENDENT AND SUSTAINED IN T(EX) CELLS. ROBUST EXPRESSION OF TOX THEREFORE RESULTS IN COMMITMENT TO T(EX) CELLS BY TRANSLATING PERSISTENT STIMULATION INTO A DISTINCT T(EX) CELL TRANSCRIPTIONAL AND EPIGENETIC DEVELOPMENTAL PROGRAM. 2019 4 6481 31 TOX IS EXPRESSED BY EXHAUSTED AND POLYFUNCTIONAL HUMAN EFFECTOR MEMORY CD8(+) T CELLS. CD8(+) T CELL EXHAUSTION IS A HALLMARK OF MANY CANCERS AND CHRONIC INFECTIONS. IN MICE, T CELL FACTOR 1 (TCF-1) MAINTAINS EXHAUSTED CD8(+) T CELL RESPONSES, WHEREAS THYMOCYTE SELECTION-ASSOCIATED HMG BOX (TOX) IS REQUIRED FOR THE EPIGENETIC REMODELING AND SURVIVAL OF EXHAUSTED CD8(+) T CELLS. HOWEVER, IT HAS REMAINED UNCLEAR TO WHAT EXTENT THESE TRANSCRIPTION FACTORS PLAY ANALOGOUS ROLES IN HUMANS. IN THIS STUDY, WE MAPPED THE EXPRESSION OF TOX AND TCF-1 AS A FUNCTION OF DIFFERENTIATION AND SPECIFICITY IN THE HUMAN CD8(+) T CELL LANDSCAPE. HERE, WE DEMONSTRATE THAT CIRCULATING TOX(+) CD8(+) T CELLS EXIST IN MOST HUMANS, BUT THAT TOX IS NOT EXCLUSIVELY ASSOCIATED WITH EXHAUSTION. EFFECTOR MEMORY CD8(+) T CELLS GENERALLY EXPRESSED TOX, WHEREAS NAIVE AND EARLY-DIFFERENTIATED MEMORY CD8(+) T CELLS GENERALLY EXPRESSED TCF-1. CYTOLYTIC GENE AND PROTEIN EXPRESSION SIGNATURES WERE ALSO DEFINED BY THE EXPRESSION OF TOX. IN THE CONTEXT OF A RELENTLESS IMMUNE CHALLENGE, EXHAUSTED HIV-SPECIFIC CD8(+) T CELLS COMMONLY EXPRESSED TOX, OFTEN IN CLUSTERS WITH VARIOUS ACTIVATION MARKERS AND INHIBITORY RECEPTORS, AND EXPRESSED LESS TCF-1. HOWEVER, POLYFUNCTIONAL MEMORY CD8(+) T CELLS SPECIFIC FOR CYTOMEGALOVIRUS (CMV) OR EPSTEIN-BARR VIRUS (EBV) ALSO EXPRESSED TOX, EITHER WITH OR WITHOUT TCF-1. A SIMILAR PHENOTYPE WAS OBSERVED AMONG HIV-SPECIFIC CD8(+) T CELLS FROM INDIVIDUALS WHO MAINTAINED EXCEPTIONAL IMMUNE CONTROL OF VIRAL REPLICATION. COLLECTIVELY, THESE DATA DEMONSTRATE THAT TOX IS EXPRESSED BY MOST CIRCULATING EFFECTOR MEMORY CD8(+) T CELL SUBSETS AND NOT EXCLUSIVELY LINKED TO EXHAUSTION. 2020 5 2410 30 EPIGENETIC SCARS OF CD8(+) T CELL EXHAUSTION PERSIST AFTER CURE OF CHRONIC INFECTION IN HUMANS. T CELL EXHAUSTION IS AN INDUCED STATE OF DYSFUNCTION THAT ARISES IN RESPONSE TO CHRONIC INFECTION AND CANCER. EXHAUSTED CD8(+) T CELLS ACQUIRE A DISTINCT EPIGENETIC STATE, BUT IT IS NOT KNOWN WHETHER THAT CHROMATIN LANDSCAPE IS FIXED OR PLASTIC FOLLOWING THE RESOLUTION OF A CHRONIC INFECTION. HERE WE SHOW THAT THE EPIGENETIC STATE OF EXHAUSTION IS LARGELY IRREVERSIBLE, EVEN AFTER CURATIVE THERAPY. ANALYSIS OF CHROMATIN ACCESSIBILITY IN HCV- AND HIV-SPECIFIC RESPONSES IDENTIFIES A CORE EPIGENETIC PROGRAM OF EXHAUSTION IN CD8(+) T CELLS, WHICH UNDERGOES ONLY LIMITED REMODELING BEFORE AND AFTER RESOLUTION OF INFECTION. MOREOVER, CANONICAL FEATURES OF EXHAUSTION, INCLUDING SUPER-ENHANCERS NEAR THE GENES TOX AND HIF1A, REMAIN 'EPIGENETICALLY SCARRED.' T CELL EXHAUSTION IS THEREFORE A CONSERVED EPIGENETIC STATE THAT BECOMES FIXED AND PERSISTS INDEPENDENT OF CHRONIC ANTIGEN STIMULATION AND INFLAMMATION. THERAPEUTIC EFFORTS TO REVERSE T CELL EXHAUSTION MAY REQUIRE NEW APPROACHES THAT INCREASE THE EPIGENETIC PLASTICITY OF EXHAUSTED T CELLS. 2021 6 5015 31 PERSISTENCE OF SELF-REACTIVE CD8+ T CELLS IN THE CNS REQUIRES TOX-DEPENDENT CHROMATIN REMODELING. SELF-REACTIVE CD8(+) T CELLS ARE IMPORTANT MEDIATORS OF PROGRESSIVE TISSUE DAMAGE IN AUTOIMMUNE DISEASES, BUT THE MOLECULAR PROGRAM UNDERLYING THESE CELLS' FUNCTIONAL ADAPTATION IS UNCLEAR. HERE WE CHARACTERIZE THE TRANSCRIPTIONAL AND EPIGENETIC LANDSCAPE OF SELF-REACTIVE CD8(+) T CELLS IN A MOUSE MODEL OF PROTRACTED CENTRAL NERVOUS SYSTEM (CNS) AUTOIMMUNITY AND COMPARE IT TO POPULATIONS OF CNS-RESIDENT MEMORY CD8(+) T CELLS EMERGING FROM ACUTE VIRAL INFECTION. WE FIND THAT AUTOIMMUNE CD8(+) T CELLS PERSISTING AT SITES OF SELF-ANTIGEN EXHIBIT CHARACTERISTIC TRANSCRIPTIONAL REGULATION TOGETHER WITH DISTINCT EPIGENETIC REMODELING. THIS SELF-REACTIVE CD8(+) T CELL FATE DEPENDS ON THE TRANSCRIPTIONAL REGULATION BY THE DNA-BINDING HMG-BOX PROTEIN TOX WHICH REMODELS MORE THAN 400 GENOMIC REGIONS INCLUDING LOCI SUCH AS TCF7, WHICH IS CENTRAL TO STEMNESS OF CD8(+) T CELLS. CONTINUOUS EXPOSURE TO CNS SELF-ANTIGEN SUSTAINS TOX LEVELS IN SELF-REACTIVE CD8(+) T CELLS, WHEREAS GENETIC ABLATION OF TOX IN CD8(+) T CELLS RESULTS IN SHORTENED PERSISTENCE OF SELF-REACTIVE CD8(+) T CELLS IN THE INFLAMED CNS. OUR STUDY ESTABLISHES AND CHARACTERIZES THE GENETIC DIFFERENTIATION PROGRAM ENABLING CHRONIC T CELL-DRIVEN IMMUNOPATHOLOGY IN CNS AUTOIMMUNITY. 2021 7 2409 27 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 8 1379 25 DEVELOPMENTAL RELATIONSHIPS OF FOUR EXHAUSTED CD8(+) T CELL SUBSETS REVEALS UNDERLYING TRANSCRIPTIONAL AND EPIGENETIC LANDSCAPE CONTROL MECHANISMS. CD8(+) T CELL EXHAUSTION IS A MAJOR BARRIER TO CURRENT ANTI-CANCER IMMUNOTHERAPIES. DESPITE THIS, THE DEVELOPMENTAL BIOLOGY OF EXHAUSTED CD8(+) T CELLS (TEX) REMAINS POORLY DEFINED, RESTRAINING IMPROVEMENT OF STRATEGIES AIMED AT "RE-INVIGORATING" TEX CELLS. HERE, WE DEFINED A FOUR-CELL-STAGE DEVELOPMENTAL FRAMEWORK FOR TEX CELLS. TWO TCF1(+) PROGENITOR SUBSETS WERE IDENTIFIED, ONE TISSUE RESTRICTED AND QUIESCENT AND ONE MORE BLOOD ACCESSIBLE, THAT GRADUALLY LOST TCF1 AS IT DIVIDED AND CONVERTED TO A THIRD INTERMEDIATE TEX SUBSET. THIS INTERMEDIATE SUBSET RE-ENGAGED SOME EFFECTOR BIOLOGY AND INCREASED UPON PD-L1 BLOCKADE BUT ULTIMATELY CONVERTED INTO A FOURTH, TERMINALLY EXHAUSTED SUBSET. BY USING TRANSCRIPTIONAL AND EPIGENETIC ANALYSES, WE IDENTIFIED THE CONTROL MECHANISMS UNDERLYING SUBSET TRANSITIONS AND DEFINED A KEY INTERPLAY BETWEEN TCF1, T-BET, AND TOX IN THE PROCESS. THESE DATA REVEAL A FOUR-STAGE DEVELOPMENTAL HIERARCHY FOR TEX CELLS AND DEFINE THE MOLECULAR, TRANSCRIPTIONAL, AND EPIGENETIC MECHANISMS THAT COULD PROVIDE OPPORTUNITIES TO IMPROVE CANCER IMMUNOTHERAPY. 2020 9 6307 23 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 3054 23 GENOME-WIDE CRISPR SCREENS OF T CELL EXHAUSTION IDENTIFY CHROMATIN REMODELING FACTORS THAT LIMIT T CELL PERSISTENCE. T CELL EXHAUSTION LIMITS ANTITUMOR IMMUNITY, BUT THE MOLECULAR DETERMINANTS OF THIS PROCESS REMAIN POORLY UNDERSTOOD. USING A CHRONIC STIMULATION ASSAY, WE PERFORMED GENOME-WIDE CRISPR-CAS9 SCREENS TO SYSTEMATICALLY DISCOVER REGULATORS OF T CELL EXHAUSTION, WHICH IDENTIFIED AN ENRICHMENT OF EPIGENETIC FACTORS. IN VIVO CRISPR SCREENS IN MURINE AND HUMAN TUMOR MODELS DEMONSTRATED THAT PERTURBATION OF THE INO80 AND BAF CHROMATIN REMODELING COMPLEXES IMPROVED T CELL PERSISTENCE IN TUMORS. IN VIVO PERTURB-SEQ REVEALED DISTINCT TRANSCRIPTIONAL ROLES OF EACH COMPLEX AND THAT DEPLETION OF CANONICAL BAF COMPLEX MEMBERS, INCLUDING ARID1A, RESULTED IN THE MAINTENANCE OF AN EFFECTOR PROGRAM AND DOWNREGULATION OF EXHAUSTION-RELATED GENES IN TUMOR-INFILTRATING T CELLS. FINALLY, ARID1A DEPLETION LIMITED THE ACQUISITION OF EXHAUSTION-ASSOCIATED CHROMATIN ACCESSIBILITY AND LED TO IMPROVED ANTITUMOR IMMUNITY. IN SUMMARY, WE PROVIDE AN ATLAS OF THE GENETIC REGULATORS OF T CELL EXHAUSTION AND DEMONSTRATE THAT MODULATION OF EPIGENETIC STATE CAN IMPROVE T CELL RESPONSES IN CANCER IMMUNOTHERAPY. 2022 11 5620 29 SCHRODINGER'S T CELLS: MOLECULAR INSIGHTS INTO STEMNESS AND EXHAUSTION. T CELL STEMNESS AND EXHAUSTION COEXIST AS TWO KEY CONTRASTING PHENOMENA DURING CHRONIC ANTIGEN STIMULATION, SUCH AS INFECTION, TRANSPLANT, CANCER, AND AUTOIMMUNITY. T CELL EXHAUSTION REFERS TO THE PROGRESSIVE LOSS OF EFFECTOR FUNCTION CAUSED BY CHRONIC ANTIGEN EXPOSURE. EXHAUSTED T (T(EX)) CELLS HIGHLY EXPRESS MULTIPLE INHIBITORY RECEPTORS AND EXHIBIT SEVERE DEFECTS IN CELL PROLIFERATION AND CYTOKINE PRODUCTION. THE TERM T CELL STEMNESS DESCRIBES THE STEM CELL-LIKE BEHAVIORS OF T CELLS, INCLUDING SELF-RENEWAL, MULTIPOTENCY, AND FUNCTIONAL PERSISTENCE. IT IS WELL ACCEPTED THAT NAIVE AND SOME MEMORY T CELL SUBSETS HAVE STEM CELL-LIKE PROPERTIES. WHEN INVESTIGATING THE EXHAUSTIVE DIFFERENTIATION OF T CELLS IN CHRONIC INFECTION AND CANCER, RECENT STUDIES HIGHLIGHTED THE STEMNESS OF "PRECURSORS OF EXHAUSTED" T (T(PEX)) CELLS PRIOR TO THEIR TERMINAL DIFFERENTIATION TO T(EX) CELLS. CLINICALLY SUCCESSFUL CHECKPOINT BLOCKADES FOR CANCER TREATMENT APPEAR TO INVIGORATE ANTITUMOR T(PEX) CELLS BUT NOT T(EX) CELLS. HERE WE DISCUSS THE TRANSCRIPTIONAL AND EPIGENETIC REGULATIONS OF T CELL STEMNESS AND EXHAUSTION, WITH A FOCUS ON HOW SYSTEMS IMMUNOLOGY WAS AND WILL BE UTILIZED TO DEFINE THE MOLECULAR BASIS UNDERLYING THE TRANSITION OF T(PEX) TO T(EX) CELLS. WE SUGGEST A "STEPWISE MODEL" OF T CELL STEMNESS AND EXHAUSTION, IN WHICH LOSS OF STEMNESS AND EXHAUSTION PROGRESSION ARE GRADUAL MULTI-STEP PROCESSES. WE PROVIDE PERSPECTIVES ON THE RESEARCH NEEDED TO DEFINE T CELL STEMNESS AND EXHAUSTION IN THE TRANSPLANTATION SETTING, IN WHICH ALLOGENIC T CELLS ARE ALSO CHRONICALLY EXPOSED TO ALLOANTIGENS. A BETTER UNDERSTANDING OF T CELL STEMNESS AND EXHAUSTION WILL SHED LIGHT ON DEVELOPING NOVEL STRATEGIES FOR IMMUNOTHERAPIES. 2021 12 771 28 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 13 2367 24 EPIGENETIC REGULATION OF T CELL EXHAUSTION. CHRONIC ANTIGEN STIMULATION DURING VIRAL INFECTIONS AND CANCER CAN LEAD TO T CELL EXHAUSTION, WHICH IS CHARACTERIZED BY REDUCED EFFECTOR FUNCTION AND PROLIFERATION, AND THE EXPRESSION OF INHIBITORY IMMUNE CHECKPOINT RECEPTORS. RECENT STUDIES HAVE DEMONSTRATED THAT T CELL EXHAUSTION RESULTS IN WHOLESCALE EPIGENETIC REMODELING THAT CONFERS PHENOTYPIC STABILITY TO THESE CELLS AND PREVENTS T CELL REINVIGORATION BY CHECKPOINT BLOCKADE. HERE, WE REVIEW FOUNDATIONAL TECHNOLOGIES TO PROFILE THE EPIGENOME AT MULTIPLE SCALES, INCLUDING MAPPING THE LOCATIONS OF TRANSCRIPTION FACTORS AND HISTONE MODIFICATIONS, DNA METHYLATION AND THREE-DIMENSIONAL GENOME CONFORMATION. WE DISCUSS HOW THESE TECHNOLOGIES HAVE ELUCIDATED THE DEVELOPMENT AND EPIGENETIC REGULATION OF EXHAUSTED T CELLS AND FUNCTIONAL IMPLICATIONS ACROSS VIRAL INFECTION, CANCER, AUTOIMMUNITY AND ENGINEERED T CELL THERAPIES. FINALLY, WE COVER EMERGING MULTI-OMIC AND GENOME ENGINEERING TECHNOLOGIES, CURRENT AND UPCOMING OPPORTUNITIES TO APPLY THESE TO T CELL EXHAUSTION, AND THERAPEUTIC OPPORTUNITIES FOR T CELL ENGINEERING IN THE CLINIC. 2022 14 769 31 CD8 T CELL EXHAUSTION DURING CHRONIC VIRAL INFECTION AND CANCER. EXHAUSTED CD8 T (TEX) CELLS ARE A DISTINCT CELL LINEAGE THAT ARISE DURING CHRONIC INFECTIONS AND CANCERS IN ANIMAL MODELS AND HUMANS. TEX CELLS ARE CHARACTERIZED BY PROGRESSIVE LOSS OF EFFECTOR FUNCTIONS, HIGH AND SUSTAINED INHIBITORY RECEPTOR EXPRESSION, METABOLIC DYSREGULATION, POOR MEMORY RECALL AND HOMEOSTATIC SELF-RENEWAL, AND DISTINCT TRANSCRIPTIONAL AND EPIGENETIC PROGRAMS. THE ABILITY TO REINVIGORATE TEX CELLS THROUGH INHIBITORY RECEPTOR BLOCKADE, SUCH AS ALPHAPD-1, HIGHLIGHTS THE THERAPEUTIC POTENTIAL OF TARGETING THIS POPULATION. EMERGING INSIGHTS INTO THE MECHANISMS OF EXHAUSTION ARE INFORMING IMMUNOTHERAPIES FOR CANCER AND CHRONIC INFECTIONS. HOWEVER, LIKE OTHER IMMUNE CELLS, TEX CELLS ARE HETEROGENEOUS AND INCLUDE PROGENITOR AND TERMINAL SUBSETS WITH UNIQUE CHARACTERISTICS AND RESPONSES TO CHECKPOINT BLOCKADE. HERE, WE REVIEW OUR CURRENT UNDERSTANDING OF TEX CELL BIOLOGY, INCLUDING THE DEVELOPMENTAL PATHS, TRANSCRIPTIONAL AND EPIGENETIC FEATURES, AND CELL INTRINSIC AND EXTRINSIC FACTORS CONTRIBUTING TO EXHAUSTION AND HOW THIS KNOWLEDGE MAY INFORM THERAPEUTIC TARGETING OF TEX CELLS IN CHRONIC INFECTIONS, AUTOIMMUNITY, AND CANCER. 2019 15 4178 19 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 16 790 21 CELLULAR AND MOLECULAR MECHANISMS OF CD8(+) T CELL DIFFERENTIATION, DYSFUNCTION AND EXHAUSTION. T CELLS FOLLOW A TRIPHASIC DISTINCT PATHWAY OF ACTIVATION, PROLIFERATION AND DIFFERENTIATION BEFORE BECOMING FUNCTIONALLY AND PHENOTYPICALLY "EXHAUSTED" IN SETTINGS OF CHRONIC INFECTION, AUTOIMMUNITY AND IN CANCER. EXHAUSTED T CELLS PROGRESSIVELY LOSE CANONICAL EFFECTOR FUNCTIONS, EXHIBIT ALTERED TRANSCRIPTIONAL NETWORKS AND EPIGENETIC SIGNATURES AND GAIN CONSTITUTIVE EXPRESSION OF A BROAD COINHIBITORY RECEPTOR SUITE. THIS REVIEW OUTLINES RECENT ADVANCES IN OUR UNDERSTANDING OF EXHAUSTED T CELL BIOLOGY AND EXAMINES CELLULAR AND MOLECULAR MECHANISMS BY WHICH A STATE OF DYSFUNCTION OR EXHAUSTION IS ESTABLISHED, AND MECHANISMS BY WHICH EXHAUSTED T CELLS MAY STILL CONTRIBUTE TO PATHOGEN OR TUMOUR CONTROL. FURTHER, THIS REVIEW DESCRIBES OUR UNDERSTANDING OF EXHAUSTED T CELL HETEROGENEITY AND OUTLINES THE MECHANISMS BY WHICH CHECKPOINT BLOCKADE DIFFERENTIALLY ENGAGES EXHAUSTED T CELL SUBSETS TO OVERCOME EXHAUSTION AND RECOVER T CELL FUNCTION. 2020 17 5407 26 REGULATION AND IMMUNOTHERAPEUTIC TARGETING OF THE EPIGENOME IN EXHAUSTED CD8 T CELL RESPONSES. EXHAUSTION IS A STATE OF CD8 T CELL DIFFERENTIATION THAT OCCURS IN SETTINGS OF CHRONIC AG SUCH AS TUMORS, CHRONIC VIRAL INFECTION, AND AUTOIMMUNITY. CELLULAR DIFFERENTIATION IS DRIVEN BY A SERIES OF ENVIRONMENTAL SIGNALS THAT PROMOTE EPIGENETIC LANDSCAPES THAT SET TRANSCRIPTOMES NEEDED FOR FUNCTION. FOR CD8 T CELLS, THE EPIGENOME THAT UNDERLIES EXHAUSTION IS DISTINCT FROM EFFECTOR AND MEMORY CELL DIFFERENTIATION, SUGGESTING THAT SIGNALS EARLY ON SET IN MOTION A PROCESS WHERE THE EPIGENOME IS MODIFIED TO PROMOTE A TRAJECTORY TOWARD A DYSFUNCTIONAL STATE. ALTHOUGH WE KNOW MANY SIGNALS THAT PROMOTE EXHAUSTION, PUTTING THIS IN THE CONTEXT OF THE EPIGENETIC CHANGES THAT OCCUR DURING DIFFERENTIATION HAS BEEN LESS CLEAR. IN THIS REVIEW, WE AIM TO SUMMARIZE THE EPIGENETIC CHANGES ASSOCIATED WITH EXHAUSTION IN THE CONTEXT OF SIGNALS THAT PROMOTE IT, HIGHLIGHTING IMMUNOTHERAPEUTIC STUDIES THAT SUPPORT THESE OBSERVATIONS OR AREAS FOR FUTURE THERAPEUTIC OPPORTUNITIES. 2023 18 2718 24 EXHAUSTED T CELLS AND EPIGENETIC STATUS. EXHAUSTED T CELLS ARE A GROUP OF DYSFUNCTIONAL T CELLS, WHICH ARE PRESENT IN CHRONIC INFECTIONS OR TUMORS. THE MOST SIGNIFICANT CHARACTERISTICS OF EXHAUSTED T CELLS ARE ATTENUATED EFFECTOR CYTOTOXICITY, REDUCED CYTOKINE PRODUCTION, AND UPREGULATION OF MULTIPLE INHIBITORY MOLECULAR RECEPTORS (E.G., PD-1, TIM-3, AND LAG-3). THE INTRACELLULAR METABOLIC CHANGES, ALTERED EXPRESSION OF TRANSCRIPTION FACTORS, AND A UNIQUE EPIGENETIC LANDSCAPE CONSTITUTE THE EXHAUSTION PROGRAM. RECENTLY, RESEARCHERS HAVE MADE PROGRESS IN UNDERSTANDING EXHAUSTED T CELLS, WITH THE DEFINITION AND IDENTIFICATION OF EXHAUSTED T CELLS CHANGING FROM PHENOTYPE-BASED TO BEING CLASSIFIED AT THE TRANSCRIPTIONAL AND EPIGENETIC LEVELS. RECENT STUDIES HAVE REVEALED THAT EXHAUSTED T CELLS CAN BE SEPARATED INTO TWO SUBGROUPS, NAMELY TCF1(+)PD-1(+) PROGENITOR-LIKE PRECURSOR EXHAUSTED CELLS AND TCF1(-)PD-1(+) TERMINALLY DIFFERENTIATED EXHAUSTED T CELLS. MOREOVER, THE PROGENITOR-LIKE PRECURSOR CELL POPULATION MAY BE A SUBSET OF T CELLS THAT CAN RESPOND TO IMMUNOTHERAPY. STUDIES HAVE ALSO FOUND THAT TOX INITIATES AND DOMINATES THE DEVELOPMENT OF EXHAUSTED T CELLS AT THE TRANSCRIPTIONAL AND EPIGENETIC LEVELS. TOX ALSO MAINTAINS T CELL SURVIVAL AND MAY AFFECT DECISIONS REGARDING TREATMENT STRATEGIES. IN THIS REVIEW, WE DISCUSS THE LATEST DEVELOPMENTS IN T CELL EXHAUSTION IN REGARDS TO DEFINITIONS, SUBPOPULATIONS, DEVELOPMENT MECHANISMS, DIFFERENCES IN DIVERSE DISEASES, AND TREATMENT PROSPECTS FOR EXHAUSTED T CELLS. FURTHERMORE, WE HYPOTHESIZE THAT THE EPIGENETIC STATE REGULATED BY TOX MIGHT BE THE KEY POINT, WHICH CAN DETERMINE THE REVERSIBILITY OF EXHAUSTION AND THE EFFICACY OF IMMUNOTHERAPY. 2020 19 4434 24 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 20 2056 27 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