1 2764 105 EXPRESSION PATTERN, REGULATION, AND CLINICAL SIGNIFICANCE OF TOX IN BREAST CANCER. THYMOCYTE SELECTION-ASSOCIATED HIGH MOBILITY GROUP BOX PROTEIN (TOX) IS A TRANSCRIPTION FACTOR IMPLICATED IN THE REGULATION OF T CELL EXHAUSTION DURING CHRONIC INFECTION AND CANCER. WHILE TOX IS BEING TARGETED FOR CANCER IMMUNOTHERAPY, LIMITED INFORMATION IS AVAILABLE ABOUT ITS SIGNIFICANCE IN BREAST CANCER AND OTHER SOLID TUMORS. WE PERFORMED A COMPREHENSIVE ANALYSIS OF TOX GENE EXPRESSION, ITS EPIGENETIC REGULATION, PROTEIN LOCALIZATION, RELATION TO TUMOR INFILTRATING IMMUNE CELL COMPOSITION, AND PROGNOSTIC SIGNIFICANCE IN BREAST CANCER USING PUBLICLY AVAILABLE DATASETS. OUR RESULTS SUGGEST AN INVERSE CORRELATION BETWEEN TOX EXPRESSION AND DNA METHYLATION IN TUMOR CELLS. HOWEVER, ITS EXPRESSION IS ELEVATED IN TUMOR INFILTRATING IMMUNE CELLS (TIICS), WHICH MAY COMPENSATES FOR THE TOTAL TOX LEVELS IN THE TUMOR AS A WHOLE. FURTHERMORE, HIGHER TOX LEVELS IN TUMORS ARE ASSOCIATED WITH T CELL EXHAUSTION SIGNATURES ALONG WITH PRESENCE OF ACTIVE INFLAMMATORY RESPONSE, INCLUDING ELEVATED LEVELS OF T CELL EFFECTOR CYTOKINES. SURVIVAL ANALYSIS ALSO CONFIRMED THAT HIGHER EXPRESSION OF TOX IS ASSOCIATED WITH BETTER PROGNOSIS IN BREAST CANCER. THEREFORE, EXPRESSION OF TOX MAY SERVE AS A NOVEL PROGNOSTIC MARKER FOR THIS MALIGNANCY. 2021 2 5593 39 ROLE, FUNCTION AND REGULATION OF THE THYMOCYTE SELECTION-ASSOCIATED HIGH MOBILITY GROUP BOX PROTEIN IN CD8(+) T CELL EXHAUSTION. THYMOCYTE SELECTION-ASSOCIATED HIGH MOBILITY GROUP BOX PROTEIN (TOX), A MEMBER OF THE HIGH-MOTILITY GROUP BOX (HMG) PROTEIN SUPERFAMILY, IS AN EVOLUTIONARILY CONSERVED DNA-BINDING PROTEIN. IT FUNCTIONS AS A TRANSCRIPTION FACTOR THAT MODULATES TRANSCRIPTIONAL PROGRAMS BY BINDING TO DNA IN A STRUCTURE-DEPENDENT MANNER. IT HAS BEEN WELL ESTABLISHED THAT TOX IS REQUIRED FOR THE DEVELOPMENT OF CD4(+) T CELLS, NATURAL KILLER (NK) CELLS AND INNATE LYMPHOID CELLS (ILCS), AS WELL AS THE AUTOIMMUNITY MEDIATED BY CD8(+) T CELLS. RECENTLY, EMERGING EVIDENCE SUPPORTS AN ESSENTIAL ROLE FOR TOX IN THE INDUCTION OF T CELL EXHAUSTION IN THE SETTING OF TUMOR OR CHRONIC VIRAL INFECTION BY MEDIATING TRANSCRIPTIONAL AND EPIGENETIC CHANGES, WHICH ARE CARDINAL HALLMARKS OF EXHAUSTED T CELLS. MOREOVER, TOX PLAYS A KEY ROLE IN THE PERSISTENCE OF ANTIGEN-SPECIFIC T CELLS AND IN THE MITIGATION OF TISSUE DAMAGE CAUSED BY IMMUNOPATHOLOGY OVER THE COURSE OF TUMORIGENESIS AND CHRONIC INFECTION. ADDITIONALLY, TOX CONTRIBUTES TO THE HIGH LEVEL OF PROGRAMMED CELL DEATH PROTEIN 1 (PD-1) ON THE CELL SURFACE BY PARTICIPATING IN THE PROCESS OF ENDOCYTIC RECYCLING OF PD-1. IN THIS REVIEW, WE SUMMARIZE THE MOST RECENT INFORMATION ABOUT THE ROLE OF TOX IN THE PROCESS OF T CELL EXHAUSTION, WHICH ENRICHES OUR UNDERSTANDING OF THE MOLECULAR MECHANISMS OF CD8(+) T CELL EXHAUSTION UPON CHRONIC ANTIGEN STIMULATION AND REVEALS PROMISING THERAPEUTIC TARGETS FOR PERSISTING INFECTION AND CANCER. 2021 3 2056 26 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 4 2718 36 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 5 5704 37 SINGLE-CELL RNA-SEQ REVEALS TOX AS A KEY REGULATOR OF CD8(+) T CELL PERSISTENCE IN CHRONIC INFECTION. PROGENITOR-LIKE CD8(+) T CELLS MEDIATE LONG-TERM IMMUNITY TO CHRONIC INFECTION AND CANCER AND RESPOND POTENTLY TO IMMUNE CHECKPOINT BLOCKADE. THESE CELLS SHARE TRANSCRIPTIONAL REGULATORS WITH MEMORY PRECURSOR CELLS, INCLUDING T CELL-SPECIFIC TRANSCRIPTION FACTOR 1 (TCF1), BUT IT IS UNCLEAR WHETHER THEY ADOPT DISTINCT PROGRAMS TO ADAPT TO THE IMMUNOSUPPRESSIVE ENVIRONMENT. BY COMPARING THE SINGLE-CELL TRANSCRIPTOMES AND EPIGENETIC PROFILES OF CD8(+) T CELLS RESPONDING TO ACUTE AND CHRONIC VIRAL INFECTIONS, WE FOUND THAT PROGENITOR-LIKE CD8(+) T CELLS BECAME DISTINCT FROM MEMORY PRECURSOR CELLS BEFORE THE PEAK OF THE T CELL RESPONSE. WE DISCOVERED A COEXPRESSION GENE MODULE CONTAINING TOX THAT EXHIBITED HIGHER TRANSCRIPTIONAL ACTIVITY ASSOCIATED WITH MORE ABUNDANT ACTIVE HISTONE MARKS IN PROGENITOR-LIKE CELLS THAN MEMORY PRECURSOR CELLS. MOREOVER, THYMOCYTE SELECTION-ASSOCIATED HIGH MOBILITY GROUP BOX PROTEIN TOX (TOX) PROMOTED THE PERSISTENCE OF ANTIVIRAL CD8(+) T CELLS AND WAS REQUIRED FOR THE PROGRAMMING OF PROGENITOR-LIKE CD8(+) T CELLS. THUS, LONG-TERM CD8(+) T CELL IMMUNITY TO CHRONIC VIRAL INFECTION REQUIRES UNIQUE TRANSCRIPTIONAL AND EPIGENETIC PROGRAMS ASSOCIATED WITH THE TRANSCRIPTION FACTOR TOX. 2019 6 6530 32 TRANSCRIPTIONAL REGULATION AND T CELL EXHAUSTION. PURPOSE OF REVIEW: THIS REVIEW HIGHLIGHTS THE CONTROL OF TRANSCRIPTIONAL NETWORKS, INCLUDING INDUCTION OF INHIBITORY RECEPTORS, BY T CELL-SPECIFIC TRANSCRIPTION FACTORS IN EXHAUSTED T CELLS THAT ACCUMULATE IN CHRONIC VIRAL INFECTIONS INCLUDING HIV. RECENT FINDINGS: TRANSCRIPTIONAL PROFILING HAS ESTABLISHED DISTINCT MOLECULAR PHENOTYPES FOR EXHAUSTED CD4 AND CD8 T CELLS IN CHRONIC VIRAL INFECTION MODELS. THERE EXISTS A SUBSET OF TRANSCRIPTION FACTORS ASSOCIATED WITH EXHAUSTION, NOTABLY BLIMP-1, BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR, ATF-LIKE AND HELIOS. EPIGENETIC PHENOMENA ARE LIKELY IMPORTANT IN REGULATING GENE EXPRESSION NETWORKS DURING EXHAUSTION AS ILLUSTRATED BY PROGRAMMED DEATH 1 PROMOTER METHYLATION PATTERNS. SUMMARY: FOLLOWING CHRONIC VIRAL INFECTIONS, CD4 AND CD8 T CELLS DEFINED FUNCTIONALLY AND PHENOTYPICALLY AS EXHAUSTED HAVE DISTINCT TRANSCRIPTIONAL PROFILES. THESE STUDIES HAVE IDENTIFIED A CORE SET OF TRANSCRIPTION FACTORS THAT HAVE BEEN IMPLICATED IN PROMOTING EXHAUSTION. HOWEVER, NO SINGLE FACTOR APPEARS TO BE AN EXHAUSTION DETERMINING FACTOR, SUGGESTING THAT T CELL EXHAUSTION REFLECTS A COMBINATORIAL MECHANISM WITH MULTIPLE TRANSCRIPTION FACTORS INTERACTING TO INFLUENCE THE DEVELOPMENT OF FUNCTIONALLY EXHAUSTED T CELLS AS WELL AS DIFFERENT T EFFECTOR POPULATIONS. 2014 7 451 29 APPLICATION OF ATAC-SEQ IN TUMOR-SPECIFIC T CELL EXHAUSTION. RESEARCHES SHOW THAT CHRONIC VIRAL INFECTION AND PERSISTENT ANTIGEN AND/OR INFLAMMATORY SIGNAL EXPOSURE IN CANCER CAUSES THE FUNCTIONAL STATUS OF T CELLS TO BE ALTERED, MAINLY BY MAJOR CHANGES IN THE EPIGENETIC AND METABOLIC ENVIRONMENT, WHICH THEN LEADS TO T CELL EXHAUSTION. THE DISCOVERY OF THE IMMUNE CHECKPOINT PATHWAY IS AN IMPORTANT MILESTONE IN UNDERSTANDING AND REVERSING T CELL EXHAUSTION. ANTIBODIES TARGETING THESE PATHWAYS HAVE SHOWN SUPERIOR ABILITY TO REVERSE T CELL EXHAUSTION. HOWEVER, THERE ARE STILL SOME LIMITATIONS IN IMMUNE CHECKPOINT BLOCKING THERAPY, SUCH AS THE SHORT-TERM NATURE OF THERAPEUTIC EFFECTS AND HIGH INDIVIDUAL HETEROGENEITY. ASSAY FOR TRANSPOSASE-ACCESSIBLE CHROMATIN WITH SEQUENCING(ATAC-SEQ) IS A METHOD USED TO ANALYZE THE ACCESSIBILITY OF WHOLE-GENOME CHROMATIN. IT USES HYPERACTIVE TN5 TRANSPOSASE TO ASSESS CHROMATIN ACCESSIBILITY. RECENTLY, A GROWING NUMBER OF STUDIES HAVE REPORTED THAT ATAC-SEQ CAN BE USED TO CHARACTERIZE THE DYNAMIC CHANGES OF EPIGENETICS IN THE PROCESS OF T CELL EXHAUSTION. IT HAS BEEN DETERMINED THAT IMMUNE CHECKPOINT BLOCKING CAN ONLY TEMPORARILY RESTORE THE FUNCTION OF EXHAUSTED T CELLS BECAUSE OF AN IRREVERSIBLE CHANGE IN THE EPIGENETICS OF EXHAUSTED T CELLS. IN THIS STUDY, WE REVIEW THE LATEST DEVELOPMENTS, WHICH PROVIDE A CLEARER MOLECULAR UNDERSTANDING OF T CELL EXHAUSTION, REVEAL POTENTIAL NEW THERAPEUTIC TARGETS FOR PERSISTENT VIRAL INFECTION AND CANCER, AND PROVIDE NEW INSIGHTS FOR DESIGNING EFFECTIVE IMMUNOTHERAPY FOR TREATING CANCER AND CHRONIC INFECTION. 2023 8 1464 30 DISSECTING THE HETEROGENEITY OF EXHAUSTED T CELLS AT THE MOLECULAR LEVEL. OUR UNDERSTANDING OF MECHANISMS UNDERLYING T-CELL EXHAUSTION HAS BEEN REFINED BY ANALYSIS OF EXHAUSTED T CELLS AT THE MOLECULAR LEVEL. THE DEVELOPMENT AND FUNCTIONS OF EXHAUSTED T CELLS ARE REGULATED BY A NUMBER OF TRANSCRIPTION FACTORS, EPIGENETIC FACTORS AND METABOLIC ENZYMES. IN ADDITION, RECENT WORK TO DISSECT EXHAUSTED T CELLS AT THE SINGLE-CELL LEVEL HAS ENABLED US TO DISCOVER A PRECURSOR EXHAUSTED T-CELL SUBSET EQUIPPED WITH LONG-TERM SURVIVAL CAPACITY. STARTING FROM THE ANALYSIS OF MOUSE MODELS, THE EXISTENCE OF PRECURSOR EXHAUSTED T CELLS HAS ALSO BEEN DOCUMENTED IN HUMAN T CELLS IN THE CONTEXT OF CHRONIC VIRUS INFECTIONS OR TUMORS. CLINICAL DATA SUGGEST THAT EVALUATING THE QUALITY OF EXHAUSTED T CELLS ON THE BASIS OF THEIR DIFFERENTIATION STATUS MAY BE HELPFUL TO PREDICT THE THERAPEUTIC RESPONSE TO INHIBITION OF PROGRAMMED DEATH 1 (PD1). MOREOVER, BEYOND IMMUNE-CHECKPOINT BLOCKADE, NOVEL THERAPEUTIC APPROACHES TO RE-INVIGORATE EXHAUSTED T CELLS HAVE BEEN EXPLORED BASED ON MOLECULAR INSIGHTS INTO T-CELL EXHAUSTION. HERE I WILL DISCUSS KEY MOLECULAR PROFILES ASSOCIATED WITH THE DEVELOPMENT, MAINTENANCE AND DIFFERENTIATION OF EXHAUSTED T CELLS AND HOW THESE FINDINGS CAN BE APPLICABLE IN THE FIELD OF CANCER IMMUNOTHERAPY. 2022 9 2033 32 EPIGENETIC CHANGES IN SOLID AND HEMATOPOIETIC TUMORS. THERE ARE THREE CONNECTED MOLECULAR MECHANISMS OF EPIGENETIC CELLULAR MEMORY IN MAMMALIAN CELLS: DNA METHYLATION, HISTONE MODIFICATIONS, AND RNA INTERFERENCE. THE FIRST TWO HAVE NOW BEEN FIRMLY LINKED TO NEOPLASTIC TRANSFORMATION. HYPERMETHYLATION OF CPG-RICH PROMOTERS TRIGGERS LOCAL HISTONE CODE MODIFICATIONS RESULTING IN A CELLULAR CAMOUFLAGE MECHANISM THAT SEQUESTERS GENE PROMOTERS AWAY FROM TRANSCRIPTION FACTORS AND RESULTS IN STABLE SILENCING. THIS NORMALLY RESTRICTED MECHANISM IS UBIQUITOUSLY USED IN CANCER TO SILENCE HUNDREDS OF GENES, AMONG WHICH SOME CRITICALLY CONTRIBUTE TO THE NEOPLASTIC PHENOTYPE. VIRTUALLY EVERY PATHWAY IMPORTANT TO CANCER FORMATION IS AFFECTED BY THIS PROCESS. METHYLATION PROFILING OF HUMAN CANCERS REVEALS TISSUE-SPECIFIC EPIGENETIC SIGNATURES, AS WELL AS TUMOR-SPECIFIC SIGNATURES, REFLECTING IN PARTICULAR THE PRESENCE OF EPIGENETIC INSTABILITY IN A SUBSET OF CANCERS AFFECTED BY THE CPG ISLAND METHYLATOR PHENOTYPE. GENERALLY, METHYLATION PATTERNS CAN BE TRACED TO A TISSUE-SPECIFIC, PROLIFERATION-DEPENDENT ACCUMULATION OF ABERRANT PROMOTER METHYLATION IN AGING TISSUES, A PROCESS THAT CAN BE ACCELERATED BY CHRONIC INFLAMMATION AND LESS WELL-DEFINED MECHANISMS INCLUDING, POSSIBLY, DIET AND GENETIC PREDISPOSITION. THE EPIGENETIC MACHINERY CAN ALSO BE ALTERED IN CANCER BY SPECIFIC LESIONS IN EPIGENETIC EFFECTOR GENES, OR BY ABERRANT RECRUITMENT OF THESE GENES BY MUTANT TRANSCRIPTION FACTORS AND COACTIVATORS. EPIGENETIC PATTERNS ARE PROVING CLINICALLY USEFUL IN HUMAN ONCOLOGY VIA RISK ASSESSMENT, EARLY DETECTION, AND PROGNOSTIC CLASSIFICATION. PHARMACOLOGIC MANIPULATION OF THESE PATTERNS-EPIGENETIC THERAPY-IS ALSO POISED TO CHANGE THE WAY WE TREAT CANCER IN THE CLINIC. 2005 10 2146 27 EPIGENETIC MANIPULATION RESTORES FUNCTIONS OF DEFECTIVE CD8(+) T CELLS FROM CHRONIC VIRAL INFECTION. FUNCTIONAL EXHAUSTION OF ANTIGEN-SPECIFIC T CELLS IS A DEFINING CHARACTERISTIC OF MANY CHRONIC INFECTIONS, BUT THE UNDERLYING MECHANISMS OF T CELL DYSFUNCTION ARE NOT WELL UNDERSTOOD. EPIGENETICS PLAYS AN IMPORTANT ROLE IN THE CONTROL OF T CELL DEVELOPMENT, DIFFERENTIATION, AND FUNCTION. TO EXAMINE IF EPIGENETICS ALSO PLAYS A ROLE IN T CELL EXHAUSTION, WE ANALYZED CHROMATIN REMODELING IN CD8(+) T CELLS FROM MICE WITH CHRONIC LYMPHOCYTIC CHORIOMENINGITIS VIRUS INFECTION. WE OBSERVED DOWNREGULATION OF DIACETYLATED HISTONE H3 IN BOTH VIRUS-SPECIFIC AND TOTAL CD8(+) T CELLS, AND FUNCTIONAL DEFECTS NOT ONLY IN VIRUS-SPECIFIC CD8(+) T CELLS BUT ALSO WITHIN THE TOTAL CD8(+) T CELL POPULATION. IN VITRO TREATMENT OF THESE EXHAUSTED CD8(+) T CELLS WITH HISTONE DEACETYLASE INHIBITORS RESTORED DIACETYLATED HISTONE H3 LEVELS, AND IMPROVED THEIR IMMUNE FUNCTIONS. UPON ADOPTIVE TRANSFER, THESE TREATED CD8(+) T CELLS DEVELOPED INTO FUNCTIONAL MEMORY T CELLS IN VIVO THAT ENHANCED PROTECTIVE IMMUNITY. THESE RESULTS DEFINE A ROLE OF EPIGENETICS IN T CELL EXHAUSTION AND SUGGEST EPIGENETIC MANIPULATION AS A NOVEL MOLECULAR THERAPY TO RESTORE IMMUNE FUNCTIONS. 2014 11 3895 34 LANDSCAPES AND MECHANISMS OF CD8(+) T CELL EXHAUSTION IN GASTROINTESTINAL CANCER. CD8(+) T CELLS, A CYTOTOXIC T LYMPHOCYTE, ARE A KEY COMPONENT OF THE TUMOR IMMUNE SYSTEM, BUT THEY ENTER A HYPOREACTIVE T CELL STATE IN LONG-TERM CHRONIC INFLAMMATION, AND HOW TO RESCUE THIS DEPLETED STATE IS A KEY DIRECTION OF RESEARCH. CURRENT STUDIES ON CD8(+) T CELL EXHAUSTION HAVE FOUND THAT THE MECHANISMS RESPONSIBLE FOR THEIR HETEROGENEITY AND DIFFERENTIAL KINETICS MAY BE CLOSELY RELATED TO TRANSCRIPTION FACTORS AND EPIGENETIC REGULATION, WHICH MAY SERVE AS BIOMARKERS AND POTENTIAL IMMUNOTHERAPEUTIC TARGETS TO GUIDE TREATMENT. ALTHOUGH THE IMPORTANCE OF T CELL EXHAUSTION IN TUMOR IMMUNOTHERAPY CANNOT BE OVERSTATED, STUDIES HAVE POINTED OUT THAT GASTRIC CANCER TISSUES HAVE A BETTER ANTI-TUMOR T CELL COMPOSITION COMPARED TO OTHER CANCER TISSUES, WHICH MAY INDICATE THAT GASTROINTESTINAL CANCERS HAVE MORE PROMISING PROSPECTS FOR THE DEVELOPMENT OF PRECISION-TARGETED IMMUNOTHERAPY. THEREFORE, THE PRESENT STUDY WILL FOCUS ON THE MECHANISMS INVOLVED IN THE DEVELOPMENT OF CD8(+) T CELL EXHAUSTION, AND THEN REVIEW THE LANDSCAPES AND MECHANISMS OF T CELL EXHAUSTION IN GASTROINTESTINAL CANCER AS WELL AS CLINICAL APPLICATIONS, WHICH WILL PROVIDE A CLEAR VISION FOR THE DEVELOPMENT OF FUTURE IMMUNOTHERAPIES. 2023 12 6060 30 THE DEVELOPMENT OF CD8 T-CELL EXHAUSTION HETEROGENEITY AND THE THERAPEUTIC POTENTIALS IN CANCER. CD8(+) T CELLS ARE ESSENTIAL LYMPHOCYTES WITH CYTOTOXIC PROPERTIES FOR ANTITUMOR IMMUNOTHERAPY. HOWEVER, DURING CHRONIC INFECTION OR TUMORIGENESIS, THESE CELLS OFTEN BECOME DYSFUNCTIONAL WITH A GRADUALLY DEPLETED ABILITY TO RELEASE CYTOKINES AND THE EXHIBITION OF REDUCED CYTOTOXICITY, THE STATE REFERRED TO AS "T-CELL EXHAUSTION" (TEX). THIS UNIQUE STATE WAS CHARACTERIZED BY THE INCREASING EXPRESSION OF INHIBITORY CHECKPOINT RECEPTORS, AND INTERVENTIONS TARGETING IMMUNE CHECKPOINT BLOCKADES (ICBS) HAVE BEEN CONSIDERED AS A PROMISING STRATEGY TO STIMULATE T-CELL KILLING. RECENT INVESTIGATIONS HAVE DEMONSTRATED THAT EXHAUSTED T CELLS NOT ONLY DISPLAY FUNCTIONAL, METABOLIC, TRANSCRIPTIONAL, AND EPIGENETIC DIFFERENCES BUT ALSO COMPRISE A HETEROGENEOUS GROUP OF CELLS. IN THIS REVIEW, WE SUMMARIZE THE CURRENT FINDINGS ON DYNAMIC DIFFERENTIATION PROCESS DURING TEX HETEROGENEITY DEVELOPMENT IN CANCER AND CHRONIC INFECTION. WE DISCUSS HOW THE RESPONSES TO IMMUNOTHERAPY ARE DETERMINED BY THESE DISTINCT SUBSETS AND HIGHLIGHT PROSPECTIVE APPROACHES FOR IMPROVING THE EFFICACY OF ICB THERAPY FOR CANCER BY LEVERAGING THE HETEROGENEITY OF T CELLS. 2023 13 2410 27 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 14 925 33 CHRONIC INFLAMMATION INDUCES A NOVEL EPIGENETIC PROGRAM THAT IS CONSERVED IN INTESTINAL ADENOMAS AND IN COLORECTAL CANCER. CHRONIC INFLAMMATION REPRESENTS A MAJOR RISK FACTOR FOR TUMOR FORMATION, BUT THE UNDERLYING MECHANISMS HAVE REMAINED LARGELY UNKNOWN. EPIGENETIC MECHANISMS CAN RECORD THE EFFECTS OF ENVIRONMENTAL CHALLENGES ON THE GENOME LEVEL AND COULD THEREFORE PLAY AN IMPORTANT ROLE IN THE PATHOGENESIS OF INFLAMMATION-ASSOCIATED TUMORS. USING SINGLE-BASE METHYLATION MAPS AND TRANSCRIPTOME ANALYSES OF A COLITIS-INDUCED MOUSE COLON CANCER MODEL, WE IDENTIFIED A NOVEL EPIGENETIC PROGRAM THAT IS CHARACTERIZED BY HYPERMETHYLATION OF DNA METHYLATION VALLEYS THAT ARE CHARACTERIZED BY LOW CPG DENSITY AND ACTIVE CHROMATIN MARKS. THIS PROGRAM IS CONSERVED AND FUNCTIONAL IN MOUSE INTESTINAL ADENOMAS AND RESULTS IN SILENCING OF ACTIVE INTESTINAL GENES THAT ARE INVOLVED IN GASTROINTESTINAL HOMEOSTASIS AND INJURY RESPONSE. FURTHER ANALYSES REVEAL THAT THE PROGRAM REPRESENTS A PROMINENT FEATURE OF HUMAN COLORECTAL CANCER AND CAN BE USED TO CORRECTLY CLASSIFY COLORECTAL CANCER SAMPLES WITH HIGH ACCURACY. TOGETHER, OUR RESULTS SHOW THAT INFLAMMATORY SIGNALS ESTABLISH A NOVEL EPIGENETIC PROGRAM THAT SILENCES A SPECIFIC SET OF GENES THAT CONTRIBUTE TO INFLAMMATION-INDUCED CELLULAR TRANSFORMATION. 2015 15 2650 31 EPIGENOMIC-GUIDED MASS CYTOMETRY PROFILING REVEALS DISEASE-SPECIFIC FEATURES OF EXHAUSTED CD8 T CELLS. EXHAUSTED CD8 T (TEX) CELLS ARE IMMUNOTHERAPY TARGETS IN CHRONIC INFECTION AND CANCER, BUT A COMPREHENSIVE ASSESSMENT OF TEX CELL DIVERSITY IN HUMAN DISEASE IS LACKING. HERE, WE DEVELOPED A TRANSCRIPTOMIC- AND EPIGENETIC-GUIDED MASS CYTOMETRY APPROACH TO DEFINE CORE EXHAUSTION-SPECIFIC GENES AND DISEASE-INDUCED CHANGES IN TEX CELLS IN HIV AND HUMAN CANCER. SINGLE-CELL PROTEOMIC PROFILING IDENTIFIED 9 DISTINCT TEX CELL CLUSTERS USING PHENOTYPIC, FUNCTIONAL, TRANSCRIPTION FACTOR, AND INHIBITORY RECEPTOR CO-EXPRESSION PATTERNS. AN EXHAUSTION SEVERITY METRIC WAS DEVELOPED AND INTEGRATED WITH HIGH-DIMENSIONAL PHENOTYPES TO DEFINE TEX CELL CLUSTERS THAT WERE PRESENT IN HEALTHY SUBJECTS, COMMON ACROSS CHRONIC INFECTION AND CANCER OR ENRICHED IN EITHER DISEASE, LINKED TO DISEASE SEVERITY, AND CHANGED WITH HIV THERAPY. COMBINATORIAL PATTERNS OF IMMUNOTHERAPY TARGETS ON DIFFERENT TEX CELL CLUSTERS WERE ALSO DEFINED. THIS APPROACH AND ASSOCIATED DATASETS PRESENT A RESOURCE FOR INVESTIGATING HUMAN TEX CELL BIOLOGY, WITH IMPLICATIONS FOR IMMUNE MONITORING AND IMMUNOMODULATION IN CHRONIC INFECTIONS, AUTOIMMUNITY, AND CANCER. 2018 16 1319 32 DEMETHYLATION OF THE PD-1 PROMOTER IS IMPRINTED DURING THE EFFECTOR PHASE OF CD8 T CELL EXHAUSTION. PD-1 IS AN INHIBITORY RECEPTOR THAT HAS A MAJOR ROLE IN T CELL DYSFUNCTION DURING CHRONIC INFECTIONS AND CANCER. WHILE DEMETHYLATION OF THE PD-1 PROMOTER DNA IS OBSERVED IN EXHAUSTED T CELLS ISOLATED FROM CHRONICALLY INFECTED INDIVIDUALS, LITTLE IS KNOWN ABOUT WHEN THIS STABLE DEMETHYLATION OF PD-1 PROMOTER DNA IS PROGRAMMED DURING THE COURSE OF A CHRONIC INFECTION. TO ASSESS IF PD-1 PROMOTER DNA DEMETHYLATION IS IMPACTED BY PROLONGED STIMULATION DURING EFFECTOR PHASE OF CHRONIC INFECTION, WE ADOPTIVELY TRANSFERRED VIRUS-SPECIFIC DAY 8 EFFECTOR CD8 T CELLS FROM MICE INFECTED WITH LYMPHOCYTIC CHORIOMENINGITIS VIRUS (LCMV) CLONE 13 INTO RECIPIENT MICE THAT HAD CLEARED AN ACUTE INFECTION. WE OBSERVED THAT LCMV-SPECIFIC CD8 T CELLS FROM CHRONICALLY INFECTED MICE MAINTAINED THEIR SURFACE EXPRESSION OF PD-1 EVEN AFTER TRANSFER INTO ACUTE IMMUNE MICE UNTIL DAY 45 POSTTRANSFER. INTERESTINGLY, THE PD-1 TRANSCRIPTIONAL REGULATORY REGION CONTINUED TO REMAIN UNMETHYLATED IN THESE DONOR CD8 T CELLS GENERATED FROM A CHRONIC INFECTION. THE OBSERVED MAINTENANCE OF PD-1 SURFACE EXPRESSION AND THE DEMETHYLATED PD-1 PROMOTER WERE NOT A RESULT OF RESIDUAL ANTIGEN IN THE RECIPIENT MICE, BECAUSE SIMILAR RESULTS WERE SEEN WHEN CHRONIC INFECTION-INDUCED EFFECTOR CELLS WERE TRANSFERRED INTO MICE INFECTED WITH A VARIANT STRAIN OF LCMV (LCMV V35A) BEARING A MUTATION IN THE COGNATE MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I (MHC-I) EPITOPE THAT IS RECOGNIZED BY THE DONOR CD8 T CELLS. IMPORTANTLY, THE MAINTENANCE OF PD-1 PROMOTER DEMETHYLATION IN MEMORY CD8 T CELLS WAS COUPLED WITH IMPAIRED CLONAL EXPANSION AND HIGHER PD-1 RE-EXPRESSION UPON SECONDARY CHALLENGE. THESE DATA SHOW THAT THE IMPRINTING OF THE EPIGENETIC PROGRAM OF THE INHIBITORY RECEPTOR PD-1 OCCURS DURING THE EFFECTOR PHASE OF CHRONIC VIRAL INFECTION. IMPORTANCE: SINCE PD-1 IS A MAJOR INHIBITORY RECEPTOR REGULATING T CELL DYSFUNCTION DURING CHRONIC VIRAL INFECTION AND CANCERS, A BETTER UNDERSTANDING OF THE MECHANISMS THAT REGULATE PD-1 EXPRESSION IS IMPORTANT. IN THIS WORK, WE DEMONSTRATE THAT THE PD-1 EPIGENETIC PROGRAM IN ANTIGEN-SPECIFIC CD8 T CELLS IS FIXED DURING THE PRIMING PHASE OF CHRONIC INFECTION. 2016 17 5900 37 T-CELL EXHAUSTION IN ORGAN TRANSPLANTATION. EXHAUSTION OF T CELLS OCCURS IN RESPONSE TO LONG-TERM EXPOSURE TO SELF AND FOREIGN ANTIGENS. IT LIMITS T CELL CAPACITY TO PROLIFERATE AND PRODUCE CYTOKINES, LEADING TO AN IMPAIRED ABILITY TO CLEAR CHRONIC INFECTIONS OR ERADICATE TUMORS. T-CELL EXHAUSTION IS ASSOCIATED WITH A SPECIFIC TRANSCRIPTIONAL, EPIGENETIC, AND METABOLIC PROGRAM AND CHARACTERISTIC CELL SURFACE MARKERS' EXPRESSION. RECENT STUDIES HAVE BEGUN TO ELUCIDATE THE ROLE OF T-CELL EXHAUSTION IN TRANSPLANT. HIGHER LEVELS OF EXHAUSTED T CELLS HAVE BEEN ASSOCIATED WITH BETTER GRAFT FUNCTION IN KIDNEY TRANSPLANT RECIPIENTS. IN CONTRAST, REINVIGORATING EXHAUSTED T CELLS BY IMMUNE CHECKPOINT BLOCKADE THERAPIES, WHILE PROMOTING TUMOR CLEARANCE, INCREASES THE RISK OF ACUTE REJECTION. LYMPHOCYTE DEPLETION AND HIGH ALLOANTIGEN LOAD HAVE BEEN IDENTIFIED AS MAJOR DRIVERS OF T-CELL EXHAUSTION. THIS COULD ACCOUNT, AT LEAST IN PART, FOR THE REDUCED RATES OF ACUTE REJECTION IN ORGAN TRANSPLANT RECIPIENTS INDUCED WITH THYMOGLOBULIN AND FOR THE PRO-TOLEROGENIC EFFECTS OF A LARGE ORGAN SUCH AS THE LIVER. AMONG THE DRUGS THAT ARE WIDELY USED FOR MAINTENANCE IMMUNOSUPPRESSION, CALCINEURIN INHIBITORS HAVE A CONTRASTING INHIBITORY EFFECT ON EXHAUSTION OF T CELLS, WHILE THE INFLUENCE OF MTOR INHIBITORS IS STILL UNCLEAR. HARNESSING OR ENCOURAGING THE NATURAL PROCESSES OF EXHAUSTION MAY PROVIDE A NOVEL STRATEGY TO PROMOTE GRAFT SURVIVAL AND TRANSPLANTATION TOLERANCE. 2022 18 6677 25 USING EPIGENETICS TO DEFINE VACCINE-INDUCED MEMORY T CELLS. MEMORY T CELLS GENERATED FROM ACUTE INFECTION OR VACCINATION HAVE THE POTENTIAL TO PROVIDE THE HOST WITH LIFE-LONG IMMUNITY AGAINST RE-INFECTION. PROTECTION BY MEMORY T CELLS IS ACHIEVED THROUGH THEIR ACQUIRED ABILITY TO PERSIST AT ANATOMICAL SITES OF THE PRIMARY INFECTION AS WELL AS MAINTAINING A HEIGHTENED ABILITY TO RECALL EFFECTOR FUNCTIONS. THE MAINTENANCE OF CD8 AND CD4 T CELL FUNCTION IN A STATE OF READINESS IS KEY TO LIFE-LONG IMMUNITY AND MANIFEST THROUGH CHANGES IN TRANSCRIPTIONAL REGULATION. YET, THE ABILITY TO IDENTIFY POISED TRANSCRIPTIONAL PROGRAMS AT THE MAINTENANCE STAGE OF THE RESPONSE IS LACKING FROM MOST TRANSCRIPTIONAL PROFILING STUDIES OF MEMORY T CELLS. EPIGENETIC PROFILING ALLOWS FOR THE ASSESSMENT OF TRANSCRIPTIONALLY POISED (PROMOTERS THAT ARE READILY ACCESSIBLE FOR TRANSCRIPTION) STATES OF ANTIGEN-SPECIFIC T CELLS WITHOUT MANIPULATION OF THE ACTIVATION STATE OF THE CELL. HERE WE REVIEW RECENT STUDIES THAT HAVE EXAMINED EPIGENETIC PROGRAMS OF EFFECTOR AND MEMORY T CELL SUBSETS. THESE REPORTS DEMONSTRATE THAT ACQUISITION OF EPIGENETIC PROGRAMS DURING MEMORY T CELL DIFFERENTIATION TO ACUTE AND CHRONIC INFECTIONS IS COUPLED TO, AND POTENTIALLY REGULATE, THE CELL'S RECALL RESPONSE. WE DISCUSS THE USEFULNESS OF EPIGENETIC PROFILING IN CHARACTERIZING T CELL DIFFERENTIATION STATE AND FUNCTION FOR PRECLINICAL EVALUATION OF VACCINES AND THE CURRENT METHODOLOGIES FOR SINGLE LOCUS VERSUS GENOME-WIDE EPIGENETIC PROFILING. 2013 19 3799 32 INTERPLAY BETWEEN INFLAMMATION AND EPIGENETIC CHANGES IN CANCER. IMMUNE RESPONSES CAN SUPPRESS TUMORIGENESIS, BUT ALSO CONTRIBUTE TO CANCER INITIATION AND PROGRESSION SUGGESTING A COMPLEX INTERACTION BETWEEN THE IMMUNE SYSTEM AND CANCER. EPIGENETIC ALTERATIONS, WHICH ARE HERITABLE CHANGES IN GENE EXPRESSION WITHOUT CHANGES TO THE DNA SEQUENCE, ALSO PLAY A ROLE IN CARCINOGENESIS THROUGH SILENCING EXPRESSION OF TUMOR SUPPRESSOR GENES AND ACTIVATING ONCOGENIC SIGNALING. INTERESTINGLY, EPITHELIAL CELLS AT SITES OF CHRONIC INFLAMMATION UNDERGO DNA METHYLATION ALTERATIONS THAT ARE SIMILAR TO THOSE PRESENT IN CANCER CELLS, SUGGESTING THAT INFLAMMATION MAY INITIATE CANCER-SPECIFIC EPIGENETIC CHANGES IN EPITHELIAL CELLS. FURTHERMORE, EPIGENETIC CHANGES OCCUR DURING IMMUNE CELL DIFFERENTIATION AND PARTICIPATE IN REGULATING THE IMMUNE RESPONSE, INCLUDING THE REGULATION OF INFLAMMATORY CYTOKINES. CANCER CELLS UTILIZE EPIGENETIC SILENCING OF IMMUNE-RELATED GENES TO EVADE THE IMMUNE RESPONSE. THIS CHAPTER WILL DETAIL THE INTERACTIONS BETWEEN INFLAMMATION AND EPIGENETICS IN TUMOR INITIATION, PROMOTION, AND IMMUNE EVASION AND HOW THESE CONNECTIONS ARE BEING LEVERAGED IN CANCER PREVENTION AND TREATMENT. 2016 20 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