1 2421 123 EPIGENETIC SIGNATURE OF PD-1+ TCF1+ CD8 T CELLS THAT ACT AS RESOURCE CELLS DURING CHRONIC VIRAL INFECTION AND RESPOND TO PD-1 BLOCKADE. WE HAVE RECENTLY DEFINED A NOVEL POPULATION OF PD-1 (PROGRAMMED CELL DEATH 1)+ TCF1 (T CELL FACTOR 1)+ VIRUS-SPECIFIC CD8 T CELLS THAT FUNCTION AS RESOURCE CELLS DURING CHRONIC LCMV INFECTION AND PROVIDE THE PROLIFERATIVE BURST SEEN AFTER PD-1 BLOCKADE. SUCH CD8 T CELLS HAVE BEEN FOUND IN OTHER CHRONIC INFECTIONS AND ALSO IN CANCER IN MICE AND HUMANS. THESE CD8 T CELLS EXHIBIT STEM-LIKE PROPERTIES UNDERGOING SELF-RENEWAL AND ALSO DIFFERENTIATING INTO THE TERMINALLY EXHAUSTED CD8 T CELLS. HERE WE COMPARED THE EPIGENETIC SIGNATURE OF STEM-LIKE CD8 T CELLS WITH EXHAUSTED CD8 T CELLS. ATAC-SEQ ANALYSIS SHOWED THAT STEM-LIKE CD8 T CELLS HAD A UNIQUE SIGNATURE IMPLICATING ACTIVITY OF HMG (TCF) AND RHD (NF-KAPPAB) TRANSCRIPTION FACTOR FAMILY MEMBERS IN CONTRAST TO HIGHER ACCESSIBILITY TO ETS AND RUNX MOTIFS IN EXHAUSTED CD8 T CELLS. IN ADDITION, REGULATORY REGIONS OF THE TRANSCRIPTION FACTORS TCF7 AND ID3 WERE MORE ACCESSIBLE IN STEM-LIKE CELLS WHEREAS PRDM1 AND ID2 WERE MORE ACCESSIBLE IN EXHAUSTED CD8 T CELLS. WE ALSO COMPARED THE EPIGENETIC SIGNATURES OF THE 2 CD8 T CELL SUBSETS FROM CHRONICALLY INFECTED MICE WITH EFFECTOR AND MEMORY CD8 T CELLS GENERATED AFTER AN ACUTE LCMV INFECTION. BOTH CD8 T CELL SUBSETS GENERATED DURING CHRONIC INFECTION WERE STRIKINGLY DIFFERENT FROM CD8 T CELL SUBSETS FROM ACUTE INFECTION. INTERESTINGLY, THE STEM-LIKE CD8 T CELL SUBSET FROM CHRONIC INFECTION, DESPITE SHARING KEY FUNCTIONAL PROPERTIES WITH MEMORY CD8 T CELLS, HAD A VERY DISTINCT EPIGENETIC PROGRAM. THESE RESULTS SHOW THAT THE CHRONIC STEM-LIKE CD8 T CELL PROGRAM REPRESENTS A SPECIFIC ADAPTATION OF THE T CELL RESPONSE TO PERSISTENT ANTIGENIC STIMULATION. 2019 2 771 33 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 3 6522 42 TRANSCRIPTIONAL AND EPIGENETIC REGULATION OF T CELL HYPORESPONSIVENESS. NAIVE CD8(+) T CELLS DIFFERENTIATE INTO EFFECTOR AND MEMORY CYTOLYTIC T CELLS (CTLS) DURING AN ACUTE INFECTION. IN CONTRAST, IN SCENARIOS OF PERSISTENT ANTIGEN STIMULATION, SUCH AS CHRONIC INFECTIONS AND CANCER, ANTIGEN-SPECIFIC CTLS SHOW A GRADUAL DECREASE IN EFFECTOR FUNCTION, A PHENOMENON THAT HAS BEEN TERMED CD8(+) T CELL "EXHAUSTION" OR "DYSFUNCTION." ANOTHER HYPORESPONSIVE STATE, TERMED "ANERGY", IS OBSERVED WHEN T CELLS ARE ACTIVATED IN THE ABSENCE OF POSITIVE COSTIMULATORY SIGNALS. AMONG THE MANY NEGATIVE REGULATORS INDUCED IN HYPORESPONSIVE T CELLS ARE INHIBITORY CELL-SURFACE RECEPTORS, SUCH AS PD-1, LAG-3, CTLA-4, AND TIM-3; "CHECKPOINT BLOCKADE" THERAPIES THAT INVOLVE TREATMENT OF PATIENTS WITH CANCER WITH BLOCKING ANTIBODIES TO THOSE RECEPTORS SHOW CONSIDERABLE PROMISE IN THE CLINIC BECAUSE THE BLOCKING ANTIBODIES CAN MITIGATE HYPORESPONSIVENESS AND PROMOTE TUMOR REJECTION. IN THIS REVIEW, WE DESCRIBE RECENT ADVANCES IN OUR MOLECULAR UNDERSTANDING OF THESE HYPORESPONSIVE STATES. WE REVIEW EVIDENCE FOR THE INVOLVEMENT OF DIVERSE TRANSCRIPTION FACTORS, METABOLIC PROGRAMS, AND CHROMATIN ACCESSIBILITY CHANGES IN HYPORESPONSIVE T CELLS, AND WE DISCUSS HOW CHECKPOINT BLOCKADE THERAPIES AFFECT THE MOLECULAR PROGRAM OF CD8(+) T CELL EXHAUSTION. 2017 4 559 36 BACH2 ENFORCES THE TRANSCRIPTIONAL AND EPIGENETIC PROGRAMS OF STEM-LIKE CD8(+) T CELLS. DURING CHRONIC INFECTION AND CANCER, A SELF-RENEWING CD8(+) T CELL SUBSET MAINTAINS LONG-TERM IMMUNITY AND IS CRITICAL TO THE EFFECTIVENESS OF IMMUNOTHERAPY. THESE STEM-LIKE CD8(+) T CELLS DIVERGE FROM OTHER CD8(+) SUBSETS EARLY AFTER CHRONIC VIRAL INFECTION. HOWEVER, PATHWAYS GUARDING STEM-LIKE CD8(+) T CELLS AGAINST TERMINAL EXHAUSTION REMAIN UNCLEAR. HERE, WE SHOW THAT THE GENE ENCODING TRANSCRIPTIONAL REPRESSOR BACH2 IS TRANSCRIPTIONALLY AND EPIGENETICALLY ACTIVE IN STEM-LIKE CD8(+) T CELLS BUT NOT TERMINALLY EXHAUSTED CELLS EARLY AFTER INFECTION. BACH2 OVEREXPRESSION ENFORCED STEM-LIKE CELL FATE, WHEREAS BACH2 DEFICIENCY IMPAIRED STEM-LIKE CD8(+) T CELL DIFFERENTIATION. SINGLE-CELL TRANSCRIPTOMIC AND EPIGENOMIC APPROACHES REVEALED THAT BACH2 ESTABLISHED THE TRANSCRIPTIONAL AND EPIGENETIC PROGRAMS OF STEM-LIKE CD8(+) T CELLS. IN ADDITION, BACH2 SUPPRESSED THE MOLECULAR PROGRAM DRIVING TERMINAL EXHAUSTION THROUGH TRANSCRIPTIONAL REPRESSION AND EPIGENETIC SILENCING. THUS, OUR STUDY REVEALS A NEW PATHWAY THAT ENFORCES COMMITMENT TO STEM-LIKE CD8(+) LINEAGE AND PREVENTS AN ALTERNATIVE TERMINALLY EXHAUSTED CELL FATE. 2021 5 6481 42 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 6 1007 35 CHRONIC VIRUS INFECTION ENFORCES DEMETHYLATION OF THE LOCUS THAT ENCODES PD-1 IN ANTIGEN-SPECIFIC CD8(+) T CELLS. FUNCTIONALLY EXHAUSTED T CELLS HAVE HIGH EXPRESSION OF THE PD-1 INHIBITORY RECEPTOR, AND THERAPIES THAT BLOCK PD-1 SIGNALING SHOW PROMISE FOR RESOLVING CHRONIC VIRAL INFECTIONS AND CANCER. BY USING HUMAN AND MURINE SYSTEMS OF ACUTE AND CHRONIC VIRAL INFECTIONS, WE ANALYZED EPIGENETIC REGULATION OF PD-1 EXPRESSION DURING CD8(+) T CELL DIFFERENTIATION. DURING ACUTE INFECTION, NAIVE TO EFFECTOR CD8(+) T CELL DIFFERENTIATION WAS ACCOMPANIED BY A TRANSIENT LOSS OF DNA METHYLATION OF THE PDCD1 LOCUS THAT WAS DIRECTLY COUPLED TO THE DURATION AND STRENGTH OF T CELL RECEPTOR SIGNALING. FURTHER DIFFERENTIATION INTO FUNCTIONAL MEMORY CELLS COINCIDED WITH PDCD1 REMETHYLATION, PROVIDING AN ADAPTED PROGRAM FOR REGULATION OF PD-1 EXPRESSION. IN CONTRAST, THE PDCD1 REGULATORY REGION WAS COMPLETELY DEMETHYLATED IN EXHAUSTED CD8(+) T CELLS AND REMAINED UNMETHYLATED EVEN WHEN VIRUS TITERS DECREASED. THIS LACK OF DNA REMETHYLATION LEAVES THE PDCD1 LOCUS POISED FOR RAPID EXPRESSION, POTENTIALLY PROVIDING A SIGNAL FOR PREMATURE TERMINATION OF ANTIVIRAL FUNCTIONS. 2011 7 1319 48 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 8 1759 33 EARLY PRECURSOR T CELLS ESTABLISH AND PROPAGATE T CELL EXHAUSTION IN CHRONIC INFECTION. CD8(+) T CELLS RESPONDING TO CHRONIC INFECTIONS OR TUMORS ACQUIRE AN 'EXHAUSTED' STATE ASSOCIATED WITH ELEVATED EXPRESSION OF INHIBITORY RECEPTORS, INCLUDING PD-1, AND IMPAIRED CYTOKINE PRODUCTION. EXHAUSTED T CELLS ARE CONTINUOUSLY REPLENISHED BY T CELLS WITH PRECURSOR CHARACTERISTICS THAT SELF-RENEW AND DEPEND ON THE TRANSCRIPTION FACTOR TCF1; HOWEVER, THEIR DEVELOPMENTAL REQUIREMENTS ARE POORLY UNDERSTOOD. IN THE PRESENT STUDY, WE DEMONSTRATE THAT HIGH ANTIGEN LOAD PROMOTED THE DIFFERENTIATION OF PRECURSOR T CELLS, WHICH ACQUIRED HALLMARKS OF EXHAUSTION WITHIN DAYS OF INFECTION, WHEREAS EARLY EFFECTOR CELLS RETAINED POLYFUNCTIONAL FEATURES. EARLY PRECURSOR T CELLS SHOWED EPIGENETIC IMPRINTING CHARACTERISTIC OF T CELL RECEPTOR-DEPENDENT TRANSCRIPTION FACTOR BINDING AND WERE RESTRICTED TO THE GENERATION OF CELLS DISPLAYING EXHAUSTION CHARACTERISTICS. TRANSCRIPTION FACTORS BACH2 AND BATF WERE KEY REGULATORS WITH OPPOSING FUNCTIONS IN THE GENERATION OF EARLY PRECURSOR T CELLS. OVERALL, WE DEMONSTRATE THAT EXHAUSTION MANIFESTS FIRST IN TCF1(+) PRECURSOR T CELLS AND IS PROPAGATED SUBSEQUENTLY TO THE POOL OF ANTIGEN-SPECIFIC T CELLS. 2020 9 5704 40 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 10 6851 36 [MOLECULAR PROFILES OF EXHAUSTED T CELLS AND THEIR IMPACT ON RESPONSE TO IMMUNE CHECKPOINT BLOCKADE]. T CELL EXHAUSTION IS INDUCED IN THE CONTEXT OF CHRONIC VIRUS INFECTION AND TUMOR MICROENVIRONMENT, IN WHICH CYTOTOXIC T CELLS ARE REPEATEDLY EXPOSED TO THE TARGET ANTIGEN AND DEPRIVED OF THEIR EFFECTOR FUNCTIONS. MULTIPLE STUDIES HAVE ALREADY SHOWN THE SIGNIFICANT IMPACT OF IMMUNE CHECKPOINT MOLECULES SUCH AS PD1 ON FUNCTIONAL PROPERTIES OF EXHAUSTED T CELLS. IN ADDITION TO THESE SIGNALS, EXHAUSTED T CELLS POSSESS DISTINCT TRANSCRIPTIONAL AND EPIGENETIC PROFILES COMPARED WITH CONVENTIONAL EFFECTOR AND MEMORY T CELLS. IMPORTANTLY, MOST OF THESE FEATURES ARE NOT AFFECTED BY IMMUNE CHECKPOINT BLOCKADE, SUGGESTING THAT GENETIC AND EPIGENETIC REMODELING OF T CELLS IS AN UNDERLYING MOLECULAR MECHANISM ESSENTIAL FOR T CELL EXHAUSTION. MOREOVER, IT HAS NOW BEEN EVIDENT THAT EXHAUSTED T CELLS ARE A HETEROGENEOUS CELL POPULATION COMPOSED OF DISTINCT T CELL SUBSETS, AND THESE FUNCTIONAL DIFFERENCES PROFOUNDLY AFFECT THERAPEUTIC EFFICACY OF CANCER IMMUNOTHERAPY. IN THIS REVIEW, I WILL DISCUSS RECENT STUDIES INVESTIGATING MOLECULAR MECHANISMS OF T CELL EXHAUSTION, INCLUDING NOVEL KEY MOLECULES ESSENTIALLY ASSOCIATED WITH T CELL EXHAUSTION. THESE FINDINGS ARE POTENTIALLY APPLICABLE TO REINVIGORATE EFFECTOR FUNCTIONS OF EXHAUSTED T CELLS. 2022 11 6521 27 TRANSCRIPTIONAL AND EPIGENETIC REGULATION OF PD-1 EXPRESSION. PROGRAMMED CELL DEATH-1 (PD-1) IS A CO-INHIBITORY RECEPTOR THAT PLAYS IMPORTANT ROLES IN REGULATING T CELL IMMUNITY AND PERIPHERAL TOLERANCE. PD-1 SIGNALING PREVENTS T CELLS FROM OVERACTIVATION DURING ACUTE INFECTIONS, BUT IT MAINTAINS T CELL EXHAUSTION DURING CHRONIC INFECTIONS. TUMOR CELLS CAN EXPLOIT THE PD-1 SIGNALING PATHWAY TO EVADE ANTITUMOR IMMUNE RESPONSES. THE PD-1 SIGNALING PATHWAY IS ALSO ESSENTIAL FOR MAINTAINING PERIPHERAL TOLERANCE AND PREVENTION OF AUTOIMMUNITY. PD-1 EXPRESSION IS STRICTLY AND DIFFERENTIALLY REGULATED BY DIVERSE MECHANISMS IN IMMUNE CELLS. IT IS ACTIVATED AND REPRESSED BY DISTINCT TRANSCRIPTION FACTORS IN DIFFERENT CIRCUMSTANCES. MOREOVER, EPIGENETIC MECHANISMS ARE ALSO INVOLVED IN REGULATING PD-1 EXPRESSION. IN THIS REVIEW, WE SUMMARIZE THE KNOWLEDGE OF THE TRANSCRIPTIONAL AND EPIGENETIC REGULATION OF PD-1 EXPRESSION DURING DIFFERENT IMMUNE RESPONSES. 2021 12 6121 33 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 13 2145 30 EPIGENETIC MAINTENANCE OF ACQUIRED GENE EXPRESSION PROGRAMS DURING MEMORY CD8 T CELL HOMEOSTASIS. MEMORY CD8 T CELLS HAVE A UNIQUE ABILITY TO PROVIDE LIFELONG IMMUNITY AGAINST PATHOGENS CONTAINING THEIR COGNATE EPITOPE. BECAUSE OF THEIR ABILITY TO PROVIDE LIFELONG PROTECTION, THE GENERATION OF MEMORY T CELLS IS NOW A MAJOR FOCUS FOR CURRENT VACCINATION OR ADOPTIVE CELL THERAPY APPROACHES TO TREAT CHRONIC VIRAL INFECTIONS AND CANCER. IT IS NOW CLEAR THAT MAINTENANCE OF MEMORY CD8 T CELLS OCCURS THROUGH A PROCESS OF ANTIGEN-INDEPENDENT HOMEOSTATIC PROLIFERATION, WHICH IS REGULATED IN PART BY THE GAMMA CHAIN CYTOKINES IL-7 AND IL-15. HERE, WE WILL DESCRIBE THE ROLE OF THESE CYTOKINES IN THE SURVIVAL AND SELF-RENEWAL OF MEMORY CD8 T CELLS. FURTHER, WE WILL DESCRIBE THE ROLE OF EPIGENETICS IN THE MAINTENANCE OF ACQUIRED FUNCTIONS AMONG MEMORY CD8 T CELLS DURING HOMEOSTATIC PROLIFERATION. 2018 14 4726 26 NOT-SO-OPPOSITE ENDS OF THE SPECTRUM: CD8(+) T CELL DYSFUNCTION ACROSS CHRONIC INFECTION, CANCER AND AUTOIMMUNITY. CD8(+) T CELLS ARE CRITICAL MEDIATORS OF CYTOTOXIC EFFECTOR FUNCTION IN INFECTION, CANCER AND AUTOIMMUNITY. IN CANCER AND CHRONIC VIRAL INFECTION, CD8(+) T CELLS UNDERGO A PROGRESSIVE LOSS OF CYTOKINE PRODUCTION AND CYTOTOXICITY, A STATE TERMED T CELL EXHAUSTION. IN AUTOIMMUNITY, AUTOREACTIVE CD8(+) T CELLS RETAIN THE CAPACITY TO EFFECTIVELY MEDIATE THE DESTRUCTION OF HOST TISSUES. ALTHOUGH THE CLINICAL OUTCOME DIFFERS IN EACH CONTEXT, CD8(+) T CELLS ARE CHRONICALLY EXPOSED TO ANTIGEN IN ALL THREE. THESE CHRONICALLY STIMULATED CD8(+) T CELLS SHARE SOME COMMON PHENOTYPIC FEATURES, AS WELL AS TRANSCRIPTIONAL AND EPIGENETIC PROGRAMMING, ACROSS DISEASE CONTEXTS. A BETTER UNDERSTANDING OF THESE CD8(+) T CELL STATES MAY REVEAL NOVEL STRATEGIES TO AUGMENT CLEARANCE OF CHRONIC VIRAL INFECTION AND CANCER AND TO MITIGATE SELF-REACTIVITY LEADING TO TISSUE DAMAGE IN AUTOIMMUNITY. 2021 15 3288 30 HIERARCHICAL TRANSCRIPTIONAL NETWORK GOVERNING HETEROGENEOUS T CELL EXHAUSTION AND ITS IMPLICATIONS FOR IMMUNE CHECKPOINT BLOCKADE. THE FUNDAMENTAL PRINCIPLE OF IMMUNE CHECKPOINT BLOCKADE (ICB) IS TO PROTECT TUMOR-INFILTRATING T CELLS FROM BEING EXHAUSTED. DESPITE THE REMARKABLE SUCCESS ACHIEVED BY ICB TREATMENT, ONLY A SMALL GROUP OF PATIENTS BENEFIT FROM IT. CHARACTERIZED BY A HYPOFUNCTIONAL STATE WITH THE EXPRESSION OF MULTIPLE INHIBITORY RECEPTORS, EXHAUSTED T (TEX) CELLS ARE A MAJOR OBSTACLE IN IMPROVING ICB. T CELL EXHAUSTION IS A PROGRESSIVE PROCESS WHICH ADAPTS TO PERSISTENT ANTIGEN STIMULATION IN CHRONIC INFECTIONS AND CANCERS. IN THIS REVIEW, WE ELUCIDATE THE HETEROGENEITY OF TEX CELLS AND OFFER NEW INSIGHTS INTO THE HIERARCHICAL TRANSCRIPTIONAL REGULATION OF T CELL EXHAUSTION. FACTORS AND SIGNALING PATHWAYS THAT INDUCE AND PROMOTE EXHAUSTION ARE ALSO SUMMARIZED. MOREOVER, WE REVIEW THE EPIGENETIC AND METABOLIC ALTERATIONS OF TEX CELLS AND DISCUSS HOW PD-1 SIGNALING AFFECTS THE BALANCE BETWEEN T CELL ACTIVATION AND EXHAUSTION, AIMING TO PROVIDE MORE THERAPEUTIC TARGETS FOR APPLICATIONS OF COMBINATIONAL IMMUNOTHERAPIES. 2023 16 2879 39 FUNDAMENTALS TO THERAPEUTICS: EPIGENETIC MODULATION OF CD8(+) T CELL EXHAUSTION IN THE TUMOR MICROENVIRONMENT. IN THE SETTING OF CHRONIC ANTIGEN EXPOSURE IN THE TUMOR MICROENVIRONMENT (TME), CYTOTOXIC CD8(+) T CELLS (CTLS) LOSE THEIR IMMUNE SURVEILLANCE CAPABILITIES AND ABILITY TO CLEAR TUMOR CELLS AS A RESULT OF THEIR DIFFERENTIATION INTO TERMINALLY EXHAUSTED CD8(+) T CELLS. IMMUNE CHECKPOINT BLOCKADE (ICB) THERAPIES REINVIGORATE EXHAUSTED CD8(+) T CELLS BY TARGETING SPECIFIC INHIBITORY RECEPTORS, THUS PROMOTING THEIR CYTOLYTIC ACTIVITY TOWARDS TUMOR CELLS. DESPITE EXCITING RESULTS WITH ICB THERAPIES, MANY PATIENTS WITH SOLID TUMORS STILL FAIL TO RESPOND TO SUCH THERAPIES AND PATIENTS WHO INITIALLY RESPOND CAN DEVELOP RESISTANCE. RECENTLY, THROUGH NEW SEQUENCING TECHNOLOGIES SUCH AS THE ASSAY FOR TRANSPOSASE-ACCESSIBLE CHROMATIN WITH SEQUENCING (ATAC-SEQ), EPIGENETICS HAS BEEN APPRECIATED AS A CONTRIBUTING FACTOR THAT ENFORCES T CELL DIFFERENTIATION TOWARD EXHAUSTION IN THE TME. IMPORTANTLY, SPECIFIC EPIGENETIC ALTERATIONS AND EPIGENETIC FACTORS HAVE BEEN FOUND TO CONTROL CD8(+) T CELL EXHAUSTION PHENOTYPES. IN THIS REVIEW, WE WILL EXPLAIN THE BACKGROUND OF T CELL DIFFERENTIATION AND VARIOUS EXHAUSTION STATES AND DISCUSS HOW EPIGENETICS PLAY AN IMPORTANT ROLE IN THESE PROCESSES. THEN WE WILL OUTLINE SPECIFIC EPIGENETIC CHANGES AND CERTAIN EPIGENETIC AND TRANSCRIPTION FACTORS THAT ARE KNOWN TO CONTRIBUTE TO CD8(+) T CELL EXHAUSTION. WE WILL ALSO DISCUSS THE MOST RECENT METHODOLOGIES THAT ARE USED TO STUDY AND DISCOVER SUCH EPIGENETIC MODULATIONS. FINALLY, WE WILL EXPLAIN HOW EPIGENETIC REPROGRAMMING IS A PROMISING APPROACH THAT MIGHT FACILITATE THE DEVELOPMENT OF NOVEL EXHAUSTED T CELL-TARGETING IMMUNOTHERAPIES. 2022 17 3188 26 HBV-SPECIFIC CD8+ T-CELL TOLERANCE IN THE LIVER. HEPATITIS B VIRUS (HBV) REMAINS A LEADING CAUSE OF LIVER-RELATED MORBIDITY AND MORTALITY THROUGH CHRONIC HEPATITIS THAT MAY PROGRESS TO LIVER CIRRHOSIS AND CANCER. THE CENTRAL ROLE PLAYED BY HBV-SPECIFIC CD8+ T CELLS IN THE CLEARANCE OF ACUTE HBV INFECTION, AND HBV-RELATED LIVER INJURY IS NOW WELL ESTABLISHED. VIGOROUS, MULTIFUNCTIONAL CD8+ T CELL RESPONSES ARE USUALLY INDUCED IN MOST ADULT-ONSET HBV INFECTIONS, WHILE CHRONIC HEPATITIS B (CHB) IS CHARACTERIZED BY QUANTITATIVELY AND QUALITATIVELY WEAK HBV-SPECIFIC CD8+ T CELL RESPONSES. THE MOLECULAR BASIS OF THIS DICHOTOMY IS POORLY UNDERSTOOD. GENOMIC ANALYSIS OF DYSFUNCTIONAL HBV-SPECIFIC CD8+ T CELLS IN CHB PATIENTS AND VARIOUS MOUSE MODELS SUGGEST THAT MULTIFACETED MECHANISMS INCLUDING NEGATIVE SIGNALING AND METABOLIC ABNORMALITIES COOPERATIVELY ESTABLISH CD8+ T CELL DYSFUNCTION. IMMUNOREGULATORY CELL POPULATIONS IN THE LIVER, INCLUDING LIVER RESIDENT DENDRITIC CELLS (DCS), HEPATIC STELLATE CELLS (HSCS), MYELOID-DERIVED SUPPRESSOR CELLS (MDSCS), MAY CONTRIBUTE TO INTRAHEPATIC CD8+ T CELL DYSFUNCTION THROUGH THE PRODUCTION OF SOLUBLE MEDIATORS, SUCH AS ARGINASE, INDOLEAMINE 2,3-DIOXYGENASE (IDO) AND SUPPRESSIVE CYTOKINES AND THE EXPRESSION OF CO-INHIBITORY MOLECULES. A SERIES OF RECENT STUDIES WITH MOUSE MODELS OF HBV INFECTION SUGGEST THAT GENETIC AND EPIGENETIC CHANGES IN DYSFUNCTIONAL CD8+ T CELLS ARE THE MANIFESTATION OF PROLONGED ANTIGENIC STIMULATION, AS WELL AS THE ABSENCE OF CO-STIMULATORY OR CYTOKINE SIGNALING. THESE NEW FINDINGS MAY PROVIDE POTENTIAL NEW TARGETS FOR IMMUNOTHERAPY AIMING AT INVIGORATING HBV-SPECIFIC CD8+ T CELLS, WHICH HOPEFULLY CURES CHB. 2021 18 991 35 CHRONIC STIMULATION DRIVES HUMAN NK CELL DYSFUNCTION AND EPIGENETIC REPROGRAMING. A POPULATION OF NATURAL KILLER (NK) CELLS EXPRESSING THE ACTIVATING RECEPTOR NKG2C AND THE MATURATION MARKER CD57 EXPANDS IN RESPONSE TO HUMAN CYTOMEGALOVIRUS (HCMV) INFECTION. CD3-CD56DIMCD57+NKG2C+ NK CELLS ARE SIMILAR TO CD8+ MEMORY T CELLS WITH RAPID AND ROBUST EFFECTOR FUNCTION UPON RE-STIMULATION, PERSISTENCE, AND EPIGENETIC REMODELING OF THE IFNG LOCUS. CHRONIC ANTIGEN STIMULATION DRIVES CD8+ MEMORY T CELL PROLIFERATION WHILE ALSO INDUCING GENOME-WIDE EPIGENETIC REPROGRAMING AND DYSFUNCTION. WE HYPOTHESIZED THAT CHRONIC STIMULATION COULD SIMILARLY INDUCE EPIGENETIC REPROGRAMING AND DYSFUNCTION IN NK CELLS. HERE WE SHOW THAT CHRONIC STIMULATION OF ADAPTIVE NK CELLS THROUGH NKG2C USING PLATE-BOUND AGONISTIC ANTIBODIES IN COMBINATION WITH IL-15 DROVE ROBUST PROLIFERATION AND ACTIVATION OF CD3-CD56DIMCD57+NKG2C+ NK CELLS WHILE SIMULTANEOUSLY INDUCING HIGH EXPRESSION OF THE CHECKPOINT INHIBITORY RECEPTORS LAG-3 AND PD-1. MARKED INDUCTION OF CHECKPOINT INHIBITORY RECEPTORS WAS ALSO OBSERVED ON THE SURFACE OF ADAPTIVE NK CELLS CO-CULTURED WITH HCMV-INFECTED ENDOTHELIAL CELLS. CHRONICALLY STIMULATED ADAPTIVE NK CELLS WERE DYSFUNCTIONAL WHEN CHALLENGED WITH TUMOR TARGETS. THESE CELLS EXHIBITED A PATTERN OF EPIGENETIC REPROGRAMING, WITH GENOME-WIDE ALTERATIONS IN DNA METHYLATION. OUR STUDY HAS IMPORTANT IMPLICATIONS FOR CANCER IMMUNOTHERAPY AND SUGGEST THAT EXHAUSTED NK CELLS COULD BE TARGETED WITH INHIBITORY CHECKPOINT RECEPTOR BLOCKADE. 2019 19 5896 35 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 20 233 17 ADAPTIVE T CELL TUNING IN IMMUNE REGULATION AND IMMUNOTHERAPY OF AUTOIMMUNE DISEASES(?). LYMPHOCYTE RECEPTORS CONFER ANTIGEN SPECIFICITY ON THE ADAPTIVE IMMUNE RESPONSE. INCREASING EVIDENCE POINTS TO THE ROLE OF ADAPTIVE TUNING PARTICULARLY AMONGST CD4(+) T CELL RESPONSES. THIS REVIEW SUMMARISES HOW T CELL TUNING IMPACTS ON CRITICALLY IMPORTANT ASPECTS OF IMMUNE REGULATION INCLUDING THYMIC SELECTION, THE IMMUNE RESPONSE TO CHRONIC ANTIGEN EXPOSURE AND ANTIGEN-SPECIFIC IMMUNOTHERAPY OF AUTOIMMUNE CONDITIONS. RECENT WORK HAS REVEALED A NOVEL MECHANISM FOR T CELL ANERGY AND REGULATORY TYPE 1 T CELL DIFFERENTIATION THROUGH A LIMITATION OF T CELL RECEPTOR MEDIATED SIGNALLING COMBINED WITH EPIGENETIC PRIMING OF TOLERANCE ASSOCIATED GENES. 2022