1 568 99 BATF REGULATES PROGENITOR TO CYTOLYTIC EFFECTOR CD8(+) T CELL TRANSITION DURING CHRONIC VIRAL INFECTION. DURING CHRONIC VIRAL INFECTION, CD8(+) T CELLS DEVELOP INTO THREE MAJOR PHENOTYPICALLY AND FUNCTIONALLY DISTINCT SUBSETS: LY108(+)TCF-1(+) PROGENITORS, LY108(-)CX(3)CR1(-) TERMINALLY EXHAUSTED CELLS AND THE RECENTLY IDENTIFIED CX(3)CR1(+) CYTOTOXIC EFFECTOR CELLS. NEVERTHELESS, HOW CX(3)CR1(+) EFFECTOR CELL DIFFERENTIATION IS TRANSCRIPTIONALLY AND EPIGENETICALLY REGULATED REMAINS ELUSIVE. HERE, WE IDENTIFY DISTINCT GENE REGULATORY NETWORKS AND EPIGENETIC LANDSCAPES UNDERPINNING THE FORMATION OF THESE SUBSETS. NOTABLY, OUR DATA DEMONSTRATE THAT CX(3)CR1(+) EFFECTOR CELLS BEAR A STRIKING SIMILARITY TO SHORT-LIVED EFFECTOR CELLS DURING ACUTE INFECTION. GENETIC DELETION OF TBX21 SIGNIFICANTLY DIMINISHED FORMATION OF THE CX(3)CR1(+) SUBSET. IMPORTANTLY, WE FURTHER IDENTIFY A PREVIOUSLY UNAPPRECIATED ROLE FOR THE TRANSCRIPTION FACTOR BATF IN MAINTAINING A PERMISSIVE CHROMATIN STRUCTURE THAT ALLOWS THE TRANSITION FROM TCF-1(+) PROGENITORS TO CX(3)CR1(+) EFFECTOR CELLS. BATF DIRECTLY BOUND TO REGULATORY REGIONS NEAR TBX21 AND KLF2, MODULATING THEIR ENHANCER ACCESSIBILITY TO FACILITATE THE TRANSITION. THESE MECHANISTIC INSIGHTS CAN POTENTIALLY BE HARNESSED TO OVERCOME T CELL EXHAUSTION DURING CHRONIC INFECTION AND CANCER. 2021 2 1763 32 EARLY TRANSCRIPTIONAL AND EPIGENETIC DIVERGENCE OF CD8+ T CELLS RESPONDING TO ACUTE VERSUS CHRONIC INFECTION. DURING A MICROBIAL INFECTION, RESPONDING CD8+ T CELLS GIVE RISE TO EFFECTOR CELLS THAT PROVIDE ACUTE HOST DEFENSE AND MEMORY CELLS THAT PROVIDE SUSTAINED PROTECTION. AN ALTERNATIVE OUTCOME IS EXHAUSTION, A STATE OF T CELL DYSFUNCTION THAT OCCURS IN THE CONTEXT OF CHRONIC INFECTIONS AND CANCER. ALTHOUGH IT IS EVIDENT THAT EXHAUSTED CD8+ T (TEX) CELLS ARE PHENOTYPICALLY AND MOLECULARLY DISTINCT FROM EFFECTOR AND MEMORY CD8+ T CELLS, THE FACTORS REGULATING THE EARLIEST EVENTS IN THE DIFFERENTIATION PROCESS OF TEX CELLS REMAIN INCOMPLETELY UNDERSTOOD. HERE, WE PERFORMED SINGLE-CELL RNA-SEQUENCING AND SINGLE-CELL ATAC-SEQUENCING OF CD8+ T CELLS RESPONDING TO LCMV-ARMSTRONG (LCMV-ARM) OR LCMV-CLONE 13 (LCMV-CL13), WHICH RESULT IN ACUTE OR CHRONIC INFECTIONS, RESPECTIVELY. COMPARED TO CD8+ T CELLS THAT HAD UNDERGONE THEIR FIRST DIVISION IN RESPONSE TO LCMV-ARM (DIV1ARM) CELLS, CD8+ T CELLS THAT HAD UNDERGONE THEIR FIRST DIVISION IN RESPONSE TO LCMV-CL13 (DIV1CL13) EXPRESSED HIGHER LEVELS OF GENES ENCODING TRANSCRIPTION FACTORS PREVIOUSLY ASSOCIATED WITH EXHAUSTION, ALONG WITH HIGHER LEVELS OF EZH2, THE CATALYTIC COMPONENT OF THE POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) COMPLEX, WHICH MEDIATES EPIGENETIC SILENCING. MODULATION OF EZH2 RESULTED IN ALTERED EXPRESSION OF EXHAUSTION-ASSOCIATED MOLECULES BY CD8+ T CELLS RESPONDING TO LCMV-CL13, THOUGH THE SPECIFIC CELLULAR AND INFECTIOUS CONTEXTS, RATHER THAN SIMPLY THE LEVEL OF EZH2 EXPRESSION, LIKELY DETERMINE THE EVENTUAL OUTCOME. TAKEN TOGETHER, THESE FINDINGS SUGGEST THAT THE DIFFERENTIATION PATHS OF CD8+ T CELLS RESPONDING TO ACUTE VERSUS CHRONIC INFECTIONS MAY DIVERGE EARLIER THAN PREVIOUSLY APPRECIATED. 2023 3 5853 30 SUBSETS OF EXHAUSTED CD8(+) T CELLS DIFFERENTIALLY MEDIATE TUMOR CONTROL AND RESPOND TO CHECKPOINT BLOCKADE. T CELL DYSFUNCTION IS A HALLMARK OF MANY CANCERS, BUT THE BASIS FOR T CELL DYSFUNCTION AND THE MECHANISMS BY WHICH ANTIBODY BLOCKADE OF THE INHIBITORY RECEPTOR PD-1 (ANTI-PD-1) REINVIGORATES T CELLS ARE NOT FULLY UNDERSTOOD. HERE WE SHOW THAT SUCH THERAPY ACTS ON A SPECIFIC SUBPOPULATION OF EXHAUSTED CD8(+) TUMOR-INFILTRATING LYMPHOCYTES (TILS). DYSFUNCTIONAL CD8(+) TILS POSSESS CANONICAL EPIGENETIC AND TRANSCRIPTIONAL FEATURES OF EXHAUSTION THAT MIRROR THOSE SEEN IN CHRONIC VIRAL INFECTION. EXHAUSTED CD8(+) TILS INCLUDE A SUBPOPULATION OF 'PROGENITOR EXHAUSTED' CELLS THAT RETAIN POLYFUNCTIONALITY, PERSIST LONG TERM AND DIFFERENTIATE INTO 'TERMINALLY EXHAUSTED' TILS. CONSEQUENTLY, PROGENITOR EXHAUSTED CD8(+) TILS ARE BETTER ABLE TO CONTROL TUMOR GROWTH THAN ARE TERMINALLY EXHAUSTED T CELLS. PROGENITOR EXHAUSTED TILS CAN RESPOND TO ANTI-PD-1 THERAPY, BUT TERMINALLY EXHAUSTED TILS CANNOT. PATIENTS WITH MELANOMA WHO HAVE A HIGHER PERCENTAGE OF PROGENITOR EXHAUSTED CELLS EXPERIENCE A LONGER DURATION OF RESPONSE TO CHECKPOINT-BLOCKADE THERAPY. THUS, APPROACHES TO EXPAND THE POPULATION OF PROGENITOR EXHAUSTED CD8(+) T CELLS MIGHT BE AN IMPORTANT COMPONENT OF IMPROVING THE RESPONSE TO CHECKPOINT BLOCKADE. 2019 4 4866 30 ORTHOGONAL CRISPR SCREENS TO IDENTIFY TRANSCRIPTIONAL AND EPIGENETIC REGULATORS OF HUMAN CD8 T CELL FUNCTION. THE CLINICAL RESPONSE TO ADOPTIVE T CELL THERAPIES IS STRONGLY ASSOCIATED WITH TRANSCRIPTIONAL AND EPIGENETIC STATE. THUS, TECHNOLOGIES TO DISCOVER REGULATORS OF T CELL GENE NETWORKS AND THEIR CORRESPONDING PHENOTYPES HAVE GREAT POTENTIAL TO IMPROVE THE EFFICACY OF T CELL THERAPIES. WE DEVELOPED POOLED CRISPR SCREENING APPROACHES WITH COMPACT EPIGENOME EDITORS TO SYSTEMATICALLY PROFILE THE EFFECTS OF ACTIVATION AND REPRESSION OF 120 TRANSCRIPTION FACTORS AND EPIGENETIC MODIFIERS ON HUMAN CD8+ T CELL STATE. THESE SCREENS NOMINATED KNOWN AND NOVEL REGULATORS OF T CELL PHENOTYPES WITH BATF3 EMERGING AS A HIGH CONFIDENCE GENE IN BOTH SCREENS. WE FOUND THAT BATF3 OVEREXPRESSION PROMOTED SPECIFIC FEATURES OF MEMORY T CELLS SUCH AS INCREASED IL7R EXPRESSION AND GLYCOLYTIC CAPACITY, WHILE ATTENUATING GENE PROGRAMS ASSOCIATED WITH CYTOTOXICITY, REGULATORY T CELL FUNCTION, AND T CELL EXHAUSTION. IN THE CONTEXT OF CHRONIC ANTIGEN STIMULATION, BATF3 OVEREXPRESSION COUNTERED PHENOTYPIC AND EPIGENETIC SIGNATURES OF T CELL EXHAUSTION. CAR T CELLS OVEREXPRESSING BATF3 SIGNIFICANTLY OUTPERFORMED CONTROL CAR T CELLS IN BOTH IN VITRO AND IN VIVO TUMOR MODELS. MOREOVER, WE FOUND THAT BATF3 PROGRAMMED A TRANSCRIPTIONAL PROFILE THAT CORRELATED WITH POSITIVE CLINICAL RESPONSE TO ADOPTIVE T CELL THERAPY. FINALLY, WE PERFORMED CRISPR KNOCKOUT SCREENS WITH AND WITHOUT BATF3 OVEREXPRESSION TO DEFINE CO-FACTORS AND DOWNSTREAM FACTORS OF BATF3, AS WELL AS OTHER THERAPEUTIC TARGETS. THESE SCREENS POINTED TO A MODEL WHERE BATF3 INTERACTS WITH JUNB AND IRF4 TO REGULATE GENE EXPRESSION AND ILLUMINATED SEVERAL OTHER NOVEL TARGETS FOR FURTHER INVESTIGATION. 2023 5 1278 27 DE NOVO EPIGENETIC PROGRAMS INHIBIT PD-1 BLOCKADE-MEDIATED T CELL REJUVENATION. IMMUNE-CHECKPOINT-BLOCKADE (ICB)-MEDIATED REJUVENATION OF EXHAUSTED T CELLS HAS EMERGED AS A PROMISING APPROACH FOR TREATING VARIOUS CANCERS AND CHRONIC INFECTIONS. HOWEVER, T CELLS THAT BECOME FULLY EXHAUSTED DURING PROLONGED ANTIGEN EXPOSURE REMAIN REFRACTORY TO ICB-MEDIATED REJUVENATION. WE REPORT THAT BLOCKING DE NOVO DNA METHYLATION IN ACTIVATED CD8 T CELLS ALLOWS THEM TO RETAIN THEIR EFFECTOR FUNCTIONS DESPITE CHRONIC STIMULATION DURING A PERSISTENT VIRAL INFECTION. WHOLE-GENOME BISULFITE SEQUENCING OF ANTIGEN-SPECIFIC MURINE CD8 T CELLS AT THE EFFECTOR AND EXHAUSTION STAGES OF AN IMMUNE RESPONSE IDENTIFIED PROGRESSIVELY ACQUIRED HERITABLE DE NOVO METHYLATION PROGRAMS THAT RESTRICT T CELL EXPANSION AND CLONAL DIVERSITY DURING PD-1 BLOCKADE TREATMENT. MOREOVER, THESE EXHAUSTION-ASSOCIATED DNA-METHYLATION PROGRAMS WERE ACQUIRED IN TUMOR-INFILTRATING PD-1HI CD8 T CELLS, AND APPROACHES TO REVERSE THESE PROGRAMS IMPROVED T CELL RESPONSES AND TUMOR CONTROL DURING ICB. THESE DATA ESTABLISH DE NOVO DNA-METHYLATION PROGRAMMING AS A REGULATOR OF T CELL EXHAUSTION AND BARRIER OF ICB-MEDIATED T CELL REJUVENATION. 2017 6 4990 35 PD-1-CIS IL-2R AGONISM YIELDS BETTER EFFECTORS FROM STEM-LIKE CD8(+) T CELLS. EXPANSION AND DIFFERENTIATION OF ANTIGEN-EXPERIENCED PD-1(+)TCF-1(+) STEM-LIKE CD8(+) T CELLS INTO EFFECTOR CELLS IS CRITICAL FOR THE SUCCESS OF IMMUNOTHERAPIES BASED ON PD-1 BLOCKADE(1-4). HASHIMOTO ET AL. HAVE SHOWN THAT, IN CHRONIC INFECTIONS, ADMINISTRATION OF THE CYTOKINE INTERLEUKIN (IL)-2 TRIGGERS AN ALTERNATIVE DIFFERENTIATION PATH OF STEM-LIKE T CELLS TOWARDS A DISTINCT POPULATION OF 'BETTER EFFECTOR' CD8(+) T CELLS SIMILAR TO THOSE GENERATED IN AN ACUTE INFECTION(5). IL-2 BINDING TO THE IL-2 RECEPTOR ALPHA-CHAIN (CD25) WAS ESSENTIAL IN TRIGGERING THIS ALTERNATIVE DIFFERENTIATION PATH AND EXPANDING BETTER EFFECTORS WITH DISTINCT TRANSCRIPTIONAL AND EPIGENETIC PROFILES. HOWEVER, CONSTITUTIVE EXPRESSION OF CD25 ON REGULATORY T CELLS AND SOME ENDOTHELIAL CELLS ALSO CONTRIBUTES TO UNWANTED SYSTEMIC EFFECTS FROM IL-2 THERAPY. THEREFORE, ENGINEERED IL-2 RECEPTOR BETA- AND GAMMA-CHAIN (IL-2RBETAGAMMA)-BIASED AGONISTS ARE CURRENTLY BEING DEVELOPED(6-10). HERE WE SHOW THAT IL-2RBETAGAMMA-BIASED AGONISTS ARE UNABLE TO PREFERENTIALLY EXPAND BETTER EFFECTOR T CELLS IN CANCER MODELS AND DESCRIBE PD1-IL2V, A NEW IMMUNOCYTOKINE THAT OVERCOMES THE NEED FOR CD25 BINDING BY DOCKING IN CIS TO PD-1. CIS BINDING OF PD1-IL2V TO PD-1 AND IL-2RBETAGAMMA ON THE SAME CELL RECOVERS THE ABILITY TO DIFFERENTIATE STEM-LIKE CD8(+) T CELLS INTO BETTER EFFECTORS IN THE ABSENCE OF CD25 BINDING IN BOTH CHRONIC INFECTION AND CANCER MODELS AND PROVIDES SUPERIOR EFFICACY. BY CONTRAST, PD-1- OR PD-L1-BLOCKING ANTIBODIES ALONE, OR THEIR COMBINATION WITH CLINICALLY RELEVANT DOSES OF NON-PD-1-TARGETED IL2V, CANNOT EXPAND THIS UNIQUE SUBSET OF BETTER EFFECTOR T CELLS AND INSTEAD LEAD TO THE ACCUMULATION OF TERMINALLY DIFFERENTIATED, EXHAUSTED T CELLS. THESE FINDINGS PROVIDE THE BASIS FOR THE DEVELOPMENT OF A NEW GENERATION OF PD-1 CIS-TARGETED IL-2R AGONISTS WITH ENHANCED THERAPEUTIC POTENTIAL FOR THE TREATMENT OF CANCER AND CHRONIC INFECTIONS. 2022 7 198 33 ACQUIRED TRANSCRIPTIONAL PROGRAMMING IN FUNCTIONAL AND EXHAUSTED VIRUS-SPECIFIC CD8 T CELLS. PURPOSE OF REVIEW: FAILURE TO CONTROL VIRAL INFECTIONS SUCH AS HIV RESULTS IN T-CELL RECEPTOR (TCR) AND INHIBITORY RECEPTOR DRIVEN EXHAUSTION OF ANTIGEN-SPECIFIC T CELLS. PERSISTENT SIGNALING BY THESE RECEPTORS DURING CHRONIC VIRAL INFECTION SCULPTS THE TRANSCRIPTIONAL REGULATORY PROGRAMS OF VIRUS-SPECIFIC T CELLS. THE RESULTING GENE EXPRESSION PROFILE IS TAILORED TO TEMPER THE POTENTIALLY DAMAGING EFFECTOR FUNCTIONS OF CYTOTOXIC T CELLS AND ADAPT THEM TO AN ANTIGEN-RICH AND INFLAMMATION-RICH ENVIRONMENT. HERE WE REVIEW RECENT STUDIES INVESTIGATING MECHANISMS OF TRANSCRIPTIONAL REGULATION OF EFFECTOR, FUNCTIONAL MEMORY, AND EXHAUSTED T-CELL FUNCTIONS DURING ACUTE VERSUS CHRONIC INFECTIONS. RECENT FINDINGS: PATTERNS OF GENE EXPRESSION IN VIRUS-SPECIFIC CD8 T CELLS ARE A RESULT OF A COMBINATION OF PRO AND INHIBITORY SIGNALS FROM ANTIGEN PRESENTATION (TCR-MEDIATED) AND CO-INHIBITORY RECEPTOR LIGATION (PD-1, 2B4). FURTHER, MEMORY-SPECIFIC TRANSCRIPTIONAL REGULATION OF 2B4 EXPRESSION AND SIGNALING IMPOSE A SELF-LIMITING SECONDARY EFFECTOR RESPONSE TO A PROLONGED VIRAL INFECTION. ADDITIONALLY, DIFFERENTIATION OF FUNCTIONAL MEMORY CD8 T CELLS IS COUPLED WITH ACQUISITION OF A REPRESSIVE EPIGENETIC PROGRAM FOR PD-1 EXPRESSION. HOWEVER, CHRONIC INFECTION PROVIDES A SIGNAL THAT BLOCKS THE ACQUISITION OF THESE EPIGENETIC MODIFICATIONS REINFORCING THE SUPPRESSION OF CYTOTOXIC LYMPHOCYTE (CTL) FUNCTIONS IN EXHAUSTED CELLS. SUMMARY: CURRENT FINDINGS SUGGEST THAT THE MECHANISM(S) THAT DELINEATE FUNCTIONAL MEMORY VERSUS EXHAUSTION ARE COUPLED WITH ACQUISITION OF TRANSCRIPTIONAL PROGRAMS AT THE EFFECTOR STAGE OF DIFFERENTIATION, REINFORCED BY CESSATION OR PERSISTENCE OF TCR SIGNALING. 2012 8 5358 25 REBALANCING TGFBETA1/BMP SIGNALS IN EXHAUSTED T CELLS UNLOCKS RESPONSIVENESS TO IMMUNE CHECKPOINT BLOCKADE THERAPY. T CELL DYSFUNCTIONALITY PREVENTS THE CLEARANCE OF CHRONIC INFECTIONS AND CANCER. FURTHERMORE, EPIGENETIC PROGRAMMING IN DYSFUNCTIONAL CD8(+) T CELLS LIMITS THEIR RESPONSE TO IMMUNOTHERAPIES, INCLUDING IMMUNE CHECKPOINT BLOCKADE (ICB). HOWEVER, IT IS UNCLEAR WHICH UPSTREAM SIGNALS DRIVE ACQUISITION OF DYSFUNCTIONAL EPIGENETIC PROGRAMS, AND WHETHER THERAPEUTICALLY TARGETING THESE SIGNALS CAN REMODEL TERMINALLY DYSFUNCTIONAL T CELLS TO AN ICB-RESPONSIVE STATE. HERE WE INNOVATE AN IN VITRO MODEL SYSTEM OF STABLE HUMAN T CELL DYSFUNCTION AND SHOW THAT CHRONIC TGFBETA1 SIGNALING IN POSTEFFECTOR CD8(+) T CELLS ACCELERATES THEIR TERMINAL DYSFUNCTION THROUGH STABLE EPIGENETIC CHANGES. CONVERSELY, BOOSTING BONE MORPHOGENETIC PROTEIN (BMP) SIGNALING WHILE BLOCKING TGFBETA1 PRESERVED EFFECTOR AND MEMORY PROGRAMS IN CHRONICALLY STIMULATED HUMAN CD8(+) T CELLS, INDUCING SUPERIOR RESPONSES TO TUMORS AND SYNERGIZING THE ICB RESPONSES DURING CHRONIC VIRAL INFECTION. THUS, REBALANCING TGFBETA1/BMP SIGNALS PROVIDES AN EXCITING NEW APPROACH TO UNLEASH DYSFUNCTIONAL CD8(+) T CELLS AND ENHANCE T CELL IMMUNOTHERAPIES. 2023 9 5081 29 PI3KDELTA COORDINATES TRANSCRIPTIONAL, CHROMATIN, AND METABOLIC CHANGES TO PROMOTE EFFECTOR CD8(+) T CELLS AT THE EXPENSE OF CENTRAL MEMORY. PATIENTS WITH ACTIVATED PHOSPHATIDYLINOSITOL 3-KINASE DELTA (PI3KDELTA) SYNDROME (APDS) PRESENT WITH SINOPULMONARY INFECTIONS, LYMPHADENOPATHY, AND CYTOMEGALVIRUS (CMV) AND/OR EPSTEIN-BARR VIRUS (EBV) VIREMIA, YET WHY PATIENTS FAIL TO CLEAR CERTAIN CHRONIC VIRAL INFECTIONS REMAINS INCOMPLETELY UNDERSTOOD. USING PATIENT SAMPLES AND A MOUSE MODEL (PIK3CD(E1020K/+) MICE), WE DEMONSTRATE THAT, UPON ACTIVATION, PIK3CD(E1020K/+) CD8(+) T CELLS EXHIBIT EXAGGERATED FEATURES OF EFFECTOR POPULATIONS BOTH IN VITRO AND AFTER VIRAL INFECTION THAT ARE ASSOCIATED WITH INCREASED FAS-MEDIATED APOPTOSIS DUE TO SUSTAINED FOXO1 PHOSPHORYLATION AND FASL DEREPRESSION, ENHANCED MTORC1 AND C-MYC SIGNATURES, METABOLIC PERTURBATIONS, AND AN ALTERED CHROMATIN LANDSCAPE. CONVERSELY, PIK3CD(E1020K/+) CD8(+) CELLS FAIL TO SUSTAIN EXPRESSION OF PROTEINS CRITICAL FOR CENTRAL MEMORY, INCLUDING TCF1. STRIKINGLY, ACTIVATED PIK3CD(E1020K/+) CD8(+) CELLS EXHIBIT ALTERED TRANSCRIPTIONAL AND EPIGENETIC CIRCUITS CHARACTERIZED BY PRONOUNCED INTERLEUKIN-2 (IL-2)/STAT5 SIGNATURES AND HEIGHTENED IL-2 RESPONSES THAT PREVENT DIFFERENTIATION TO MEMORY-LIKE CELLS IN IL-15. OUR DATA POSITION PI3KDELTA AS INTEGRATING MULTIPLE SIGNALING NODES THAT PROMOTE CD8(+) T CELL EFFECTOR DIFFERENTIATION, PROVIDING INSIGHT INTO PHENOTYPES OF PATIENTS WITH APDS. 2021 10 5895 22 T CELL EXHAUSTION: AN EPIGENETICALLY IMPRINTED PHENOTYPIC AND FUNCTIONAL MAKEOVER. A RECENT ARTICLE IN CELL DEMONSTRATES THAT THE ABSENCE OF A SINGLE DNA METHYLTRANSFERASE, DNMT3A, PREVENTS CYTOTOXIC T CELLS FROM ACQUIRING THE HYPOFUNCTIONAL OR EXHAUSTED PHENOTYPE TYPICALLY SEEN IN CHRONIC VIRAL INFECTIONS AND TUMORS. UPON ESTABLISHING A CAUSAL RELATIONSHIP BETWEEN EXHAUSTION-ASSOCIATED EPIGENETIC CHANGES AND REDUCED CD8(+) T CELL FUNCTION, THE AUTHORS PROVIDED MECHANISTIC EVIDENCE THAT EXHAUSTION CONSTITUTES A SPECIFIC DIFFERENTIATION PROGRAM. 2017 11 6055 23 THE CXXC1 SUBUNIT OF THE TRITHORAX COMPLEX DIRECTS EPIGENETIC LICENSING OF CD4+ T CELL DIFFERENTIATION. DIFFERENT DYNAMICS OF GENE EXPRESSION ARE OBSERVED DURING CELL DIFFERENTIATION. IN T CELLS, GENES THAT ARE TURNED ON EARLY OR TURNED OFF AND STAY OFF HAVE BEEN THOROUGHLY STUDIED. HOWEVER, GENES THAT ARE INITIALLY TURNED OFF BUT THEN TURNED ON AGAIN AFTER STIMULATION HAS CEASED HAVE NOT BEEN DEFINED; THEY ARE OBVIOUSLY IMPORTANT, ESPECIALLY IN THE CONTEXT OF ACUTE VERSUS CHRONIC INFLAMMATION. USING THE TH1/TH2 DIFFERENTIATION PARADIGM, WE FOUND THAT THE CXXC1 SUBUNIT OF THE TRITHORAX COMPLEX DIRECTS TRANSCRIPTION OF GENES INITIALLY DOWN-REGULATED BY TCR STIMULATION BUT UP-REGULATED AGAIN IN A LATER PHASE. THE LATE UP-REGULATION OF THESE GENES WAS IMPAIRED EITHER BY PROLONGED TCR STIMULATION OR CXXC1 DEFICIENCY, WHICH LED TO DECREASED EXPRESSION OF TRIB3 AND KLF2 IN TH1 AND TH2 CELLS, RESPECTIVELY. LOSS OF CXXC1 RESULTED IN ENHANCED PATHOGENICITY IN ALLERGIC AIRWAY INFLAMMATION IN VIVO. THUS, CXXC1 PLAYS ESSENTIAL ROLES IN THE ESTABLISHMENT OF A PROPER CD4+ T CELL IMMUNE SYSTEM VIA EPIGENETIC CONTROL OF A SPECIFIC SET OF GENES. 2021 12 1309 35 DEFINING AND TARGETING PATTERNS OF T CELL DYSFUNCTION IN INBORN ERRORS OF IMMUNITY. INBORN ERRORS OF IMMUNITY (IEIS) ARE A GROUP OF MORE THAN 450 MONOGENIC DISORDERS THAT IMPAIR IMMUNE DEVELOPMENT AND FUNCTION. A SUBSET OF IEIS BLEND INCREASED SUSCEPTIBILITY TO INFECTION, AUTOIMMUNITY, AND MALIGNANCY AND ARE KNOWN COLLECTIVELY AS PRIMARY IMMUNE REGULATORY DISORDERS (PIRDS). WHILE MANY ASPECTS OF IMMUNE FUNCTION ARE ALTERED IN PIRDS, ONE KEY IMPACT IS ON T-CELL FUNCTION. BY THEIR NATURE, PIRDS PROVIDE UNIQUE INSIGHTS INTO HUMAN T-CELL SIGNALING; ALTERATIONS IN INDIVIDUAL SIGNALING MOLECULES TUNE DOWNSTREAM SIGNALING PATHWAYS AND EFFECTOR FUNCTION. QUANTIFYING T-CELL DYSFUNCTION IN PIRDS AND THE UNDERLYING CAUSATIVE MECHANISMS IS CRITICAL TO IDENTIFYING EXISTING THERAPIES AND POTENTIAL NOVEL THERAPEUTIC TARGETS TO TREAT OUR RARE PATIENTS AND GAIN DEEPER INSIGHT INTO THE BASIC MECHANISMS OF T-CELL FUNCTION. THOUGH THERE ARE MANY TYPES OF T-CELL DYSFUNCTION, HERE WE WILL FOCUS ON T-CELL EXHAUSTION, A KEY PATHOPHYSIOLOGICAL STATE. EXHAUSTION HAS BEEN DESCRIBED IN BOTH HUMAN AND MOUSE MODELS OF DISEASE, WHERE THE CHRONIC PRESENCE OF ANTIGEN AND INFLAMMATION (E.G., CHRONIC INFECTION OR MALIGNANCY) INDUCES A STATE OF ALTERED IMMUNE PROFILE, TRANSCRIPTIONAL AND EPIGENETIC STATES, AS WELL AS IMPAIRED T-CELL FUNCTION. SINCE A SUBSET OF PIRDS AMPLIFY T-CELL RECEPTOR (TCR) SIGNALING AND/OR INFLAMMATORY CYTOKINE SIGNALING CASCADES, IT IS POSSIBLE THAT THEY COULD INDUCE T-CELL EXHAUSTION BY GENETICALLY MIMICKING CHRONIC INFECTION. HERE, WE REVIEW THE FUNDAMENTALS OF T-CELL EXHAUSTION AND ITS POSSIBLE ROLE IN IEIS IN WHICH GENETIC MUTATIONS MIMIC PROLONGED OR AMPLIFIED T-CELL RECEPTOR AND/OR CYTOKINE SIGNALING. GIVEN THE POTENTIAL INSIGHT FROM THE MANY FORMS OF PIRDS IN UNDERSTANDING T-CELL FUNCTION AND THE CHALLENGES IN OBTAINING PRIMARY CELLS FROM THESE RARE DISORDERS, WE ALSO DISCUSS ADVANCES IN CRISPR-CAS9 GENOME-EDITING TECHNOLOGIES AND POTENTIAL APPLICATIONS TO EDIT HEALTHY DONOR T CELLS THAT COULD FACILITATE FURTHER STUDY OF MECHANISMS OF IMMUNE DYSFUNCTIONS IN PIRDS. EDITING T CELLS TO MATCH PIRD PATIENT GENETIC VARIANTS WILL ALLOW INVESTIGATIONS INTO THE MECHANISMS UNDERPINNING STATES OF DYSREGULATED T-CELL FUNCTION, INCLUDING T-CELL EXHAUSTION. 2022 13 5806 28 STRATEGIES TO REINVIGORATE EXHAUSTED CD8(+) T CELLS IN TUMOR MICROENVIRONMENT. CD8(+) T CELL EXHAUSTION IS A STABLE DYSFUNCTIONAL STATE DRIVEN BY CHRONIC ANTIGEN STIMULATION IN THE TUMOR MICROENVIRONMENT (TME). DIFFERENTIATION OF EXHAUSTED CD8(+) T CELLS (CD8(+) TEXS) IS ACCOMPANIED BY EXTENSIVE TRANSCRIPTIONAL, EPIGENETIC AND METABOLIC REPROGRAMMING. CD8(+) TEXS ARE MAINLY CHARACTERIZED BY IMPAIRED PROLIFERATIVE AND CYTOTOXIC CAPACITY AS WELL AS THE INCREASED EXPRESSION OF MULTIPLE CO-INHIBITORY RECEPTORS. PRECLINICAL TUMOR STUDIES AND CLINICAL COHORTS HAVE DEMONSTRATED THAT T CELL EXHAUSTION IS FIRMLY ASSOCIATED WITH POOR CLINICAL OUTCOMES IN A VARIETY OF CANCERS. MORE IMPORTANTLY, CD8(+) TEXS ARE REGARDED AS THE MAIN RESPONDER TO IMMUNE CHECKPOINT BLOCKADE (ICB). HOWEVER, TO DATE, A LARGE NUMBER OF CANCER PATIENTS HAVE FAILED TO ACHIEVE DURABLE RESPONSES AFTER ICB. THEREFORE, IMPROVING CD8(+) TEXS MAY BE A BREAKTHROUGH POINT TO REVERSE THE CURRENT DILEMMA OF CANCER IMMUNOTHERAPY AND ELIMINATE CANCERS. STRATEGIES TO REINVIGORATE CD8(+) TEXS IN TME MAINLY INCLUDE ICB, TRANSCRIPTION FACTOR-BASED THERAPY, EPIGENETIC THERAPY, METABOLISM-BASED THERAPY AND CYTOKINE THERAPY, WHICH TARGET ON DIFFERENT ASPECTS OF EXHAUSTION PROGRESSION. EACH OF THEM HAS ITS ADVANTAGES AND APPLICATION SCOPE. IN THIS REVIEW, WE MAINLY FOCUS ON THE MAJOR ADVANCES OF CURRENT STRATEGIES TO REINVIGORATE CD8(+) TEXS IN TME. WE SUMMARIZE THEIR EFFICACY AND MECHANISMS, IDENTIFY THE PROMISING MONOTHERAPY AND COMBINED THERAPY AND PROPOSE SUGGESTIONS TO ENHANCE THE TREATMENT EFFICACY TO SIGNIFICANTLY BOOST ANTI-TUMOR IMMUNITY AND ACHIEVE BETTER CLINICAL OUTCOMES. 2023 14 5918 27 TARGETING BMI-1 IN B CELLS RESTORES EFFECTIVE HUMORAL IMMUNE RESPONSES AND CONTROLS CHRONIC VIRAL INFECTION. INEFFECTIVE ANTIBODY-MEDIATED RESPONSES ARE A KEY CHARACTERISTIC OF CHRONIC VIRAL INFECTION. HOWEVER, OUR UNDERSTANDING OF THE INTRINSIC MECHANISMS THAT DRIVE THIS DYSREGULATION ARE UNCLEAR. HERE, WE IDENTIFY THAT TARGETING THE EPIGENETIC MODIFIER BMI-1 IN MICE IMPROVES HUMORAL RESPONSES TO CHRONIC LYMPHOCYTIC CHORIOMENINGITIS VIRUS. BMI-1 WAS UPREGULATED BY GERMINAL CENTER B CELLS IN CHRONIC VIRAL INFECTION, CORRELATING WITH CHANGES TO THE ACCESSIBLE CHROMATIN LANDSCAPE, COMPARED TO ACUTE INFECTION. B CELL-INTRINSIC DELETION OF BMI1 ACCELERATED VIRAL CLEARANCE, REDUCED SPLENOMEGALY AND RESTORED SPLENIC ARCHITECTURE. DELETION OF BMI1 RESTORED C-MYC EXPRESSION IN B CELLS, CONCOMITANT WITH IMPROVED QUALITY OF ANTIBODY AND COUPLED WITH REDUCED ANTIBODY-SECRETING CELL NUMBERS. SPECIFICALLY, BMI-1-DEFICIENCY INDUCED ANTIBODY WITH INCREASED NEUTRALIZING CAPACITY AND ENHANCED ANTIBODY-DEPENDENT EFFECTOR FUNCTION. USING A SMALL MOLECULE INHIBITOR TO MURINE BMI-1, WE COULD DEPLETE ANTIBODY-SECRETING CELLS AND PROHIBIT DETRIMENTAL IMMUNE COMPLEX FORMATION IN VIVO. THIS STUDY DEFINES BMI-1 AS A CRUCIAL IMMUNE MODIFIER THAT CONTROLS ANTIBODY-MEDIATED RESPONSES IN CHRONIC INFECTION. 2022 15 5248 29 PROGRAMMED CELL DEATH 1-DIRECTED IMMUNOTHERAPY FOR ENHANCING T-CELL FUNCTION. T-CELL EXHAUSTION IS A UNIQUE STATE THAT APPEARS DURING MANY CHRONIC INFECTIONS AND CANCER AND IS CHARACTERIZED BY LOSS OF PROLIFERATIVE CAPACITY AND EFFECTOR FUNCTION. COMPLEX MECHANISMS ARE INVOLVED IN THIS T-CELL DYSFUNCTION BUT AN INHIBITORY RECEPTOR, PD-1, HAS BEEN IDENTIFIED AS A MAJOR REGULATOR OF T-CELL EXHAUSTION. BLOCKADE OF THE PD-1 PATHWAY CAN REINVIGORATE EXHAUSTED T CELLS, RESULTING IN BETTER CONTROL OF CHRONIC INFECTIONS AND CANCER. NOTABLY, RECENT CLINICAL STUDIES HAVE REVEALED THAT PD-1-DIRECTED IMMUNOTHERAPY IS HIGHLY EFFECTIVE IN CANCER PATIENTS, DEMONSTRATING THAT PD-1 IS A PROMISING THERAPEUTIC TARGET IN HUMANS. IN THIS REVIEW, WE SUMMARIZE OUR CURRENT UNDERSTANDING OF THE EPIGENETIC REGULATION OF PD-1 EXPRESSION IN T CELLS AND DISCUSS POTENTIAL COMBINATION THERAPY WITH PD-1 BLOCKADE TOWARD DEVELOPING MORE EFFECTIVE TREATMENT FOR CHRONIC INFECTIONS AND CANCER. 2013 16 5153 21 PPP2R2B HYPERMETHYLATION CAUSES ACQUIRED APOPTOSIS DEFICIENCY IN SYSTEMIC AUTOIMMUNE DISEASES. CHRONIC INFLAMMATION CAUSES TARGET ORGAN DAMAGE IN PATIENTS WITH SYSTEMIC AUTOIMMUNE DISEASES. THE FACTORS THAT ALLOW THIS PROTRACTED RESPONSE ARE POORLY UNDERSTOOD. WE ANALYZED THE TRANSCRIPTIONAL REGULATION OF PPP2R2B (B55SS), A MOLECULE NECESSARY FOR THE TERMINATION OF THE IMMUNE RESPONSE, IN PATIENTS WITH AUTOIMMUNE DISEASES. ALTERED EXPRESSION OF B55SS CONDITIONED RESISTANCE TO CYTOKINE WITHDRAWAL-INDUCED DEATH (CWID) IN PATIENTS WITH AUTOIMMUNE DISEASES. THE IMPAIRED UPREGULATION OF B55SS WAS CAUSED BY INFLAMMATION-DRIVEN HYPERMETHYLATION OF SPECIFIC CYTOSINES LOCATED WITHIN A REGULATORY ELEMENT OF PPP2R2B PREVENTING CTCF BINDING. THIS PHENOTYPE COULD BE INDUCED IN HEALTHY T CELLS BY EXPOSURE TO TNF-ALPHA. OUR RESULTS REVEAL A GENE WHOSE EXPRESSION IS AFFECTED BY AN ACQUIRED DEFECT, THROUGH AN EPIGENETIC MECHANISM, IN THE SETTING OF SYSTEMIC AUTOIMMUNITY. BECAUSE FAILURE TO REMOVE ACTIVATED T CELLS THROUGH CWID COULD CONTRIBUTE TO AUTOIMMUNE PATHOLOGY, THIS MECHANISM ILLUSTRATES A VICIOUS CYCLE THROUGH WHICH AUTOIMMUNE INFLAMMATION CONTRIBUTES TO ITS OWN PERPETUATION. 2019 17 102 23 A REGULATORY ROLE FOR CHD2 IN MYELOPOIESIS. THE TRANSCRIPTIONAL PROGRAM THAT DICTATES HAEMATOPOIETIC CELL FATE AND DIFFERENTIATION REQUIRES AN EPIGENETIC REGULATORY AND MEMORY FUNCTION, PROVIDED BY A NETWORK OF EPIGENETIC FACTORS THAT REGULATE DNA METHYLATION, POST-TRANSLATIONAL HISTONE MODIFICATIONS AND CHROMATIN STRUCTURE. DISTURBED EPIGENETIC REGULATION CAUSES PERTURBATIONS IN THE BLOOD CELL DIFFERENTIATION PROGRAM THAT RESULTS IN VARIOUS TYPES OF HAEMATOPOIETIC DISORDERS. THUS, ACCURATE EPIGENETIC REGULATION IS ESSENTIAL FOR FUNCTIONAL HAEMATOPOIESIS. IN THIS STUDY, WE USED A CRISPR-CAS9 SCREENING APPROACH TO IDENTIFY NEW EPIGENETIC REGULATORS IN MYELOID DIFFERENTIATION. WE DESIGNED A CHROMATIN-UMI CRISPR GUIDE LIBRARY TARGETING 1092 EPIGENETIC REGULATORS. PHORBOL 12-MYRISTATE 13-ACETATE (PMA) TREATMENT OF THE CHRONIC MYELOID LEUKAEMIA CELL LINE K-562 WAS USED AS A MEGAKARYOCYTIC MYELOID DIFFERENTIATION MODEL. BOTH PREVIOUSLY DESCRIBED DEVELOPMENTAL EPIGENETIC REGULATORS AND NOVEL FACTORS WERE IDENTIFIED IN OUR SCREEN. IN THIS STUDY, WE VALIDATED AND CHARACTERIZED A ROLE FOR THE CHROMATIN REMODELLER CHD2 IN MYELOID PROLIFERATION AND MEGAKARYOCYTIC DIFFERENTIATION. 2020 18 5059 29 PHENOTYPIC AND IMMUNOMETABOLIC ASPECTS ON STEM CELL MEMORY AND RESIDENT MEMORY CD8(+) T CELLS. THE IMMUNE SYSTEM, SMARTLY AND SURPRISINGLY, SAVES THE EXPOSURE OF A PARTICULAR PATHOGEN IN ITS MEMORY AND REACTS TO THE PATHOGEN VERY RAPIDLY, PREVENTING SERIOUS DISEASES. IMMUNOLOGISTS HAVE LONG BEEN FASCINATED BY UNDERSTANDING THE ABILITY TO RECALL AND RESPOND FASTER AND MORE VIGOROUSLY TO A PATHOGEN, KNOWN AS "MEMORY". T-CELL POPULATIONS CAN BE BETTER DESCRIBED BY USING MORE SOPHISTICATED TECHNIQUES TO DEFINE PHENOTYPE, TRANSCRIPTIONAL AND EPIGENETIC SIGNATURES AND METABOLIC PATHWAYS (SINGLE-CELL RESOLUTION), WHICH UNCOVERED THE HETEROGENEITY OF THE MEMORY T-COMPARTMENT. PHENOTYPE, EFFECTOR FUNCTIONS, MAINTENANCE, AND METABOLIC PATHWAYS HELP IDENTIFY THESE DIFFERENT SUBSETS. HERE, WE EXAMINE RECENT DEVELOPMENTS IN THE CHARACTERIZATION OF THE HETEROGENEITY OF THE MEMORY T CELL COMPARTMENT. IN PARTICULAR, WE FOCUS ON THE EMERGING ROLE OF CD8(+) T(RM) AND T(SCM) CELLS, PROVIDING EVIDENCE ON HOW THEIR IMMUNOMETABOLISM OR MODULATION CAN PLAY A VITAL ROLE IN THEIR GENERATION AND MAINTENANCE IN CHRONIC CONDITIONS SUCH AS INFECTIONS OR AUTOIMMUNE DISEASES. 2022 19 2446 17 EPIGENETIC STRATEGIES SYNERGIZE WITH PD-L1/PD-1 TARGETED CANCER IMMUNOTHERAPIES TO ENHANCE ANTITUMOR RESPONSES. IMMUNOTHERAPY STRATEGIES TARGETING THE PROGRAMMED CELL DEATH LIGAND 1 (PD-L1)/PROGRAMMED CELL DEATH 1 (PD-1) PATHWAY IN CLINICAL TREATMENTS HAVE ACHIEVED REMARKABLE SUCCESS IN TREATING MULTIPLE TYPES OF CANCER. HOWEVER, OWING TO THE HETEROGENEITY OF TUMORS AND INDIVIDUAL IMMUNE SYSTEMS, PD-L1/PD-1 BLOCKADE STILL SHOWS SLOW RESPONSE RATES IN CONTROLLING MALIGNANCIES IN MANY PATIENTS. ACCUMULATING EVIDENCE HAS SHOWN THAT AN EFFECTIVE RESPONSE TO ANTI-PD-L1/ANTI-PD-1 THERAPY REQUIRES ESTABLISHING AN INTEGRATED IMMUNE CYCLE. DAMAGE IN ANY STEP OF THE IMMUNE CYCLE IS ONE OF THE MOST IMPORTANT CAUSES OF IMMUNOTHERAPY FAILURE. IMPAIRMENTS IN THE IMMUNE CYCLE CAN BE RESTORED BY EPIGENETIC MODIFICATION, INCLUDING REPROGRAMMING THE ENVIRONMENT OF TUMOR-ASSOCIATED IMMUNITY, ELICITING AN IMMUNE RESPONSE BY INCREASING THE PRESENTATION OF TUMOR ANTIGENS, AND BY REGULATING T CELL TRAFFICKING AND REACTIVATION. THUS, A RATIONAL COMBINATION OF PD-L1/PD-1 BLOCKADE AND EPIGENETIC AGENTS MAY OFFER GREAT POTENTIAL TO RETRAIN THE IMMUNE SYSTEM AND TO IMPROVE CLINICAL OUTCOMES OF CHECKPOINT BLOCKADE THERAPY. 2020 20 2146 29 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