1 2650 94 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 2 2421 30 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 3 5058 30 PHENOTYPIC ALTERATION OF CD8+ T CELLS IN CHRONIC LYMPHOCYTIC LEUKEMIA IS ASSOCIATED WITH EPIGENETIC REPROGRAMMING. IMMUNOSUPPRESSION IS A PREVALENT CLINICAL FEATURE IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) PATIENTS, WITH MANY PATIENTS DEMONSTRATING INCREASED SUSCEPTIBILITY TO INFECTIONS AS WELL AS INCREASED FAILURE OF AN ANTITUMOR IMMUNE RESPONSE. HOWEVER, MUCH IS CURRENTLY NOT UNDERSTOOD REGARDING THE PRECISE MECHANISMS THAT ATTRIBUTE TO THIS IMMUNOSUPPRESSIVE PHENOTYPE IN CLL. TO PROVIDE FURTHER CLARITY TO THIS PARTICULAR PHENOMENON, WE ANALYZED THE T-CELL PROFILE OF CLL PATIENT SAMPLES WITHIN A LARGE COHORT AND OBSERVED THAT PATIENTS WITH AN INVERTED CD4/CD8 RATIO HAD A SHORTER TIME TO FIRST TREATMENT AS WELL AS OVERALL SURVIVAL. THESE OBSERVATIONS COINCIDED WITH HIGHER EXPRESSION OF THE IMMUNE CHECKPOINT RECEPTOR PD-1 IN CLL PATIENT CD8+ T CELLS WHEN COMPARED TO AGE-MATCHED HEALTHY DONORS. INTERESTINGLY, WE DISCOVERED THAT INCREASED PD-1 EXPRESSION IN CD8+ T CELLS CORRESPONDS WITH DECREASED DNA METHYLATION LEVELS IN A DISTAL UPSTREAM LOCUS OF THE PD-1 GENE PDCD1. FURTHER ANALYSIS USING LUCIFERASE REPORTER ASSAYS SUGGESTS THAT THE IDENTIFIED PDCD1 DISTAL UPSTREAM REGION ACTS AS AN ENHANCER FOR PDCD1 TRANSCRIPTION AND THIS REGION BECOMES DEMETHYLATED DURING ACTIVATION OF NAIVE CD8+ T CELLS BY ANTI-CD3/ANTI-CD28 ANTIBODIES AND IL2. FINALLY, WE CONDUCTED A GENOME-WIDE DNA METHYLATION ANALYSIS COMPARING CD8+ T CELLS FROM CLL PATIENTS AGAINST HEALTHY DONORS AND IDENTIFIED ADDITIONAL DIFFERENTIALLY METHYLATED GENES WITH KNOWN IMMUNE REGULATORY FUNCTIONS INCLUDING CCR6 AND KLRG1. TAKEN TOGETHER, OUR FINDINGS REVEAL THE OCCURRENCE OF EPIGENETIC REPROGRAMMING TAKING PLACE WITHIN CLL PATIENT CD8+ T CELLS AND HIGHLIGHT THE POTENTIAL MECHANISM OF HOW IMMUNOSUPPRESSION IS ACCOMPLISHED IN CLL. 2016 4 1379 31 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 5 6481 39 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 1759 31 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 7 5704 29 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 8 5671 34 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 9 5243 22 PROGNOSTIC IMPACT OF EPIGENETIC CLASSIFICATION IN CHRONIC LYMPHOCYTIC LEUKEMIA: THE CASE OF SUBSET #2. BASED ON THE METHYLATION STATUS OF 5 SINGLE CPG SITES, A NOVEL EPIGENETIC CLASSIFICATION OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) WAS RECENTLY PROPOSED, CLASSIFYING CLL PATIENTS INTO 3 CLINICO-BIOLOGICAL SUBGROUPS WITH DIFFERENT OUTCOME, TERMED MEMORY LIKE CLL (M-CLL), NAIVE LIKE CLL (N-CLL), AND A THIRD INTERMEDIATE CLL SUBGROUP (I-CLL). WHILE M-CLL AND N-CLL PATIENTS AT LARGE CORRESPONDED TO PATIENTS CARRYING MUTATED AND UNMUTATED IGHV GENES, RESPECTIVELY, LIMITED INFORMATION EXISTS REGARDING THE LESS DEFINED I-CLL GROUP. USING PYROSEQUENCING, WE INVESTIGATED THE PROGNOSTIC IMPACT OF THE PROPOSED 5 CPG SIGNATURE IN A WELL-CHARACTERIZED CLL COHORT (135 CASES), INCLUDING IGHV-MUTATED AND UNMUTATED PATIENTS AS WELL AS CLINICALLY AGGRESSIVE STEREOTYPED SUBSET #2 PATIENTS. OVERALL, WE CONFIRMED THE SIGNATURE'S ASSOCIATION WITH ESTABLISHED PROGNOSTIC MARKERS. MOREOVER, IN THE PRESENCE OF THE IGHV MUTATIONAL STATUS, THE EPIGENETIC SIGNATURE REMAINED INDEPENDENTLY ASSOCIATED WITH BOTH TIME-TO-FIRST-TREATMENT AND OVERALL SURVIVAL IN MULTIVARIATE ANALYSES. AS A PRIME FINDING, WE OBSERVED THAT SUBSET #2 PATIENTS WERE PREDOMINANTLY CLASSIFIED AS I-CLL, PROBABLY REFLECTING THEIR BORDERLINE IGHV MUTATIONAL STATUS (97-99% GERMLINE IDENTITY), THOUGH HAVING A SIMILARLY POOR PROGNOSIS AS N-CLL PATIENTS. IN SUMMARY, WE VALIDATED THE EPIGENETIC CLASSIFIER AS AN INDEPENDENT FACTOR IN CLL PROGNOSTICATION AND PROVIDE FURTHER EVIDENCE THAT SUBSET #2 IS A MEMBER OF THE I-CLL GROUP, HENCE SUPPORTING THE EXISTENCE OF A THIRD, INTERMEDIATE EPIGENETIC SUBGROUP. 2016 10 2392 28 EPIGENETIC REPRESSION OF INTERLEUKIN 2 EXPRESSION IN SENESCENT CD4+ T CELLS DURING CHRONIC HIV TYPE 1 INFECTION. THE MOLECULAR MECHANISMS FOR IL2 GENE-SPECIFIC DYSREGULATION DURING CHRONIC HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1) INFECTION ARE UNKNOWN. HERE, WE INVESTIGATED THE ROLE OF DNA METHYLATION IN SUPPRESSING INTERLEUKIN 2 (IL-2) EXPRESSION IN MEMORY CD4(+) T CELLS DURING CHRONIC HIV-1 INFECTION. WE OBSERVED THAT CPG SITES IN THE IL2 PROMOTER OF CD4(+) T CELLS WERE FULLY METHYLATED IN NAIVE CD4(+) T CELLS AND SIGNIFICANTLY DEMETHYLATED IN THE MEMORY POPULATIONS. INTERESTINGLY, WE FOUND THAT THE MEMORY CELLS THAT HAD A TERMINALLY DIFFERENTIATED PHENOTYPE AND EXPRESSED CD57 HAD INCREASED IL2 PROMOTER METHYLATION RELATIVE TO LESS DIFFERENTIATED MEMORY CELLS IN HEALTHY INDIVIDUALS. IMPORTANTLY, EARLY EFFECTOR MEMORY SUBSETS FROM HIV-1-INFECTED SUBJECTS EXPRESSED HIGH LEVELS OF CD57 AND WERE HIGHLY METHYLATED AT THE IL2 LOCUS. FURTHERMORE, THE INCREASED CD57 EXPRESSION ON MEMORY CD4(+) T CELLS WAS INVERSELY CORRELATED WITH IL-2 PRODUCTION. THESE DATA SUGGEST THAT DNA METHYLATION AT THE IL2 LOCUS IN CD4(+) T CELLS IS COUPLED TO IMMUNOSENESCENCE AND PLAYS A CRITICAL ROLE IN THE BROAD DYSFUNCTION THAT OCCURS IN POLYCLONAL T CELLS DURING HIV-1 INFECTION. 2015 11 1007 27 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 12 2764 31 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 13 590 31 BET BROMODOMAIN PROTEIN INHIBITION REVERSES CHIMERIC ANTIGEN RECEPTOR EXTINCTION AND REINVIGORATES EXHAUSTED T CELLS IN CHRONIC LYMPHOCYTIC LEUKEMIA. CHIMERIC ANTIGEN RECEPTOR (CAR) T CELLS HAVE INDUCED REMARKABLE ANTITUMOR RESPONSES IN B CELL MALIGNANCIES. SOME PATIENTS DO NOT RESPOND BECAUSE OF T CELL DEFICIENCIES THAT HAMPER THE EXPANSION, PERSISTENCE, AND EFFECTOR FUNCTION OF THESE CELLS. WE USED LONGITUDINAL IMMUNE PROFILING TO IDENTIFY PHENOTYPIC AND PHARMACODYNAMIC CHANGES IN CD19-DIRECTED CAR T CELLS IN PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). CAR EXPRESSION MAINTENANCE WAS ALSO INVESTIGATED BECAUSE THIS CAN AFFECT RESPONSE DURABILITY. CAR T CELL FAILURE WAS ACCOMPANIED BY PREEXISTING T CELL-INTRINSIC DEFECTS OR DYSFUNCTION ACQUIRED AFTER INFUSION. IN A SMALL SUBSET OF PATIENTS, CAR SILENCING WAS OBSERVED COINCIDENT WITH LEUKEMIA RELAPSE. USING A SMALL MOLECULE INHIBITOR, WE DEMONSTRATED THAT THE BROMODOMAIN AND EXTRA-TERMINAL (BET) FAMILY OF CHROMATIN ADAPTERS PLAYS A ROLE IN DOWNREGULATING CAR EXPRESSION. BET PROTEIN BLOCKADE ALSO AMELIORATED CAR T CELL EXHAUSTION AS MANIFESTED BY INHIBITORY RECEPTOR REDUCTION, ENHANCED METABOLIC FITNESS, INCREASED PROLIFERATIVE CAPACITY, AND ENRICHED TRANSCRIPTOMIC SIGNATURES OF T CELL REINVIGORATION. BET INHIBITION DECREASED LEVELS OF THE TET2 METHYLCYTOSINE DIOXYGENASE, AND FORCED EXPRESSION OF THE TET2 CATALYTIC DOMAIN ELIMINATED THE POTENCY-ENHANCING EFFECTS OF BET PROTEIN TARGETING IN CAR T CELLS, PROVIDING A MECHANISM LINKING BET PROTEINS AND T CELL DYSFUNCTION. THUS, MODULATING BET EPIGENETIC READERS MAY IMPROVE THE EFFICACY OF CELL-BASED IMMUNOTHERAPIES. 2021 14 6121 25 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 15 3309 28 HIGHER GENE EXPRESSION VARIABILITY IN THE MORE AGGRESSIVE SUBTYPE OF CHRONIC LYMPHOCYTIC LEUKEMIA. BACKGROUND: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) PRESENTS TWO SUBTYPES WHICH HAVE DRASTICALLY DIFFERENT CLINICAL OUTCOMES, IGVH MUTATED (M-CLL) AND IGVH UNMUTATED (U-CLL). SO FAR, THESE TWO SUBTYPES ARE NOT ASSOCIATED TO CLEAR DIFFERENCES IN GENE EXPRESSION PROFILES. INTERESTINGLY, RECENT RESULTS HAVE HIGHLIGHTED IMPORTANT ROLES FOR HETEROGENEITY, BOTH AT THE GENETIC AND AT THE EPIGENETIC LEVEL IN CLL PROGRESSION. METHODS: WE ANALYZED GENE EXPRESSION DATA OF TWO LARGE COHORTS OF CLL PATIENTS AND QUANTIFIED EXPRESSION VARIABILITY ACROSS INDIVIDUALS TO INVESTIGATE DIFFERENCES BETWEEN THE TWO SUBTYPES USING DIFFERENT MEASURES AND STATISTICAL TESTS. FUNCTIONAL SIGNIFICANCE WAS EXPLORED BY PATHWAY ENRICHMENT AND NETWORK ANALYSES. FURTHERMORE, WE IMPLEMENTED A RANDOM FOREST APPROACH BASED ON EXPRESSION VARIABILITY TO CLASSIFY PATIENTS INTO DISEASE SUBTYPES. RESULTS: WE FOUND THAT U-CLL, THE MORE AGGRESSIVE TYPE OF THE DISEASE, SHOWS SIGNIFICANTLY INCREASED VARIABILITY OF GENE EXPRESSION ACROSS PATIENTS AND THAT, OVERALL, GENES THAT SHOW HIGHER VARIABILITY IN THE AGGRESSIVE SUBTYPE ARE RELATED TO CELL CYCLE, DEVELOPMENT AND INTER-CELLULAR COMMUNICATION. THESE FUNCTIONS INDICATE A POTENTIAL RELATION BETWEEN GENE EXPRESSION VARIABILITY AND THE FASTER PROGRESSION OF THIS CLL SUBTYPE. FINALLY, A CLASSIFIER BASED ON GENE EXPRESSION VARIABILITY WAS ABLE TO CORRECTLY PREDICT THE DISEASE SUBTYPE OF CLL PATIENTS. CONCLUSIONS: THERE ARE STRONG RELATIONS BETWEEN GENE EXPRESSION VARIABILITY AND DISEASE SUBTYPE LINKING SIGNIFICANTLY INCREASED EXPRESSION VARIABILITY TO PHENOTYPES SUCH AS AGGRESSIVENESS AND RESISTANCE TO THERAPY IN CLL. 2015 16 1319 26 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 17 437 24 ANTIGEN RECEPTOR STEREOTYPY IN CHRONIC LYMPHOCYTIC LEUKEMIA. THE DISCOVERY OF ALMOST IDENTICAL OR 'STEREOTYPED' B-CELL RECEPTOR IMMUNOGLOBULINS (BCR IG) AMONG UNRELATED PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) CEMENTED THE IDEA OF ANTIGEN SELECTION IN DISEASE ONTOGENY AND EVOLUTION. THE SYSTEMATIC ANALYSIS OF THE STEREOTYPY PHENOMENON IN CLL REVEALED THAT AROUND ONE-THIRD OF CLL PATIENTS MAY BE GROUPED INTO SUBSETS BASED ON SHARED SEQUENCE MOTIFS WITHIN THE VARIABLE HEAVY COMPLEMENTARITY DETERMINING REGION 3. STEREOTYPED SUBSETS DISPLAY A STRIKINGLY SIMILAR BIOLOGY OF THE LEUKEMIC CLONES, REFERRING TO MANY DIFFERENT LEVELS, FROM THE IMMUNOGENETIC AND GENETIC AND EXTENDING TO THE EPIGENETIC AND FUNCTIONAL LEVELS. EVEN MORE IMPORTANTLY, THE HOMOGENEITY OF STEREOTYPED SUBSETS HAS CLINICAL CONSEQUENCES AS PATIENTS ASSIGNED TO THE SAME STEREOTYPED SUBSET GENERALLY EXHIBIT AN OVERALL SIMILAR DISEASE COURSE AND OUTCOME. IN OTHER WORDS, STEREOTYPY-BASED PATIENT CLASSIFICATION OF CLL HAS ALREADY PROVIDED A MORE COMPARTMENTALIZED VIEW OF THIS OTHERWISE HETEROGENEOUS DISEASE AND CAN ASSIST IN REFINING PROGNOSTICATION MODELS. WHILE THIS IS RELEVANT ONLY FOR THE ONE-THIRD OF CASES EXPRESSING STEREOTYPED BCR IG; IN PRINCIPLE, HOWEVER, THE FINDINGS FROM FURTHER ANALYSIS OF THE STEREOTYPED SUBSETS MAY ALSO CONTRIBUTE TOWARDS IMPROVED UNDERSTANDING OF THE REMAINING NON-STEREOTYPED FRACTION OF CLL PATIENTS. 2017 18 1464 29 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 19 1533 28 DNA METHYLATION DYNAMICS DURING B CELL MATURATION UNDERLIE A CONTINUUM OF DISEASE PHENOTYPES IN CHRONIC LYMPHOCYTIC LEUKEMIA. CHARTING DIFFERENCES BETWEEN TUMORS AND NORMAL TISSUE IS A MAINSTAY OF CANCER RESEARCH. HOWEVER, CLONAL TUMOR EXPANSION FROM COMPLEX NORMAL TISSUE ARCHITECTURES POTENTIALLY OBSCURES CANCER-SPECIFIC EVENTS, INCLUDING DIVERGENT EPIGENETIC PATTERNS. USING WHOLE-GENOME BISULFITE SEQUENCING OF NORMAL B CELL SUBSETS, WE OBSERVED BROAD EPIGENETIC PROGRAMMING OF SELECTIVE TRANSCRIPTION FACTOR BINDING SITES COINCIDENT WITH THE DEGREE OF B CELL MATURATION. BY COMPARING NORMAL B CELLS TO MALIGNANT B CELLS FROM 268 PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), WE SHOWED THAT TUMORS DERIVE LARGELY FROM A CONTINUUM OF MATURATION STATES REFLECTED IN NORMAL DEVELOPMENTAL STAGES. EPIGENETIC MATURATION IN CLL WAS ASSOCIATED WITH AN INDOLENT GENE EXPRESSION PATTERN AND INCREASINGLY FAVORABLE CLINICAL OUTCOMES. WE FURTHER UNCOVERED THAT MOST PREVIOUSLY REPORTED TUMOR-SPECIFIC METHYLATION EVENTS ARE NORMALLY PRESENT IN NON-MALIGNANT B CELLS. INSTEAD, WE IDENTIFIED A POTENTIAL PATHOGENIC ROLE FOR TRANSCRIPTION FACTOR DYSREGULATION IN CLL, WHERE EXCESS PROGRAMMING BY EGR AND NFAT WITH REDUCED EBF AND AP-1 PROGRAMMING IMBALANCES THE NORMAL B CELL EPIGENETIC PROGRAM. 2016 20 5393 38 REDUCED CHROMATIN ACCESSIBILITY TO CD4 T CELL SUPER-ENHANCERS ENCOMPASSING SUSCEPTIBILITY LOCI OF RHEUMATOID ARTHRITIS. BACKGROUND: RHEUMATOID ARTHRITIS (RA) IS AN INFLAMMATORY DISEASE THAT MANIFESTS AS A PRECLINICAL STAGE OF SYSTEMIC AUTOIMMUNITY FOLLOWED BY CHRONIC PROGRESSIVE SYNOVITIS. DISEASE-ASSOCIATED GENETIC SNP VARIANTS PREDOMINANTLY MAP TO NON-CODING, REGULATORY REGIONS OF FUNCTIONAL IMPORTANCE IN CD4 T CELLS, IMPLICATING THESE CELLS AS KEY REGULATORS. A BETTER UNDERSTANDING OF THE EPIGENOME OF CD4 T CELLS HOLDS THE PROMISE OF PROVIDING INFORMATION ON THE INTERACTION BETWEEN GENETIC SUSCEPTIBILITY AND EXOGENOUS FACTORS. METHODS: WE MAPPED REGIONS OF CHROMATIN ACCESSIBILITY USING ATAC-SEQ IN PERIPHERAL CD4 T CELL SUBSETS OF PATIENTS WITH RA (N=18) AND COMPARED THEM TO T CELLS FROM PATIENTS WITH PSORIATIC ARTHRITIS (N=11) AND AGE-MATCHED HEALTHY CONTROLS (N=10). TRANSCRIPTS OF SELECTED GENES WERE QUANTIFIED USING QPCR. FINDINGS: RA-ASSOCIATED EPIGENETIC SIGNATURES WERE IDENTIFIED THAT IN PART OVERLAPPED BETWEEN CENTRAL AND EFFECTOR MEMORY CD4 T CELLS AND THAT WERE TO A LESSER EXTENT ALREADY PRESENT IN NAIVE CELLS. SITES MORE ACCESSIBLE IN RA WERE HIGHLY ENRICHED FOR THE MOTIF OF THE TRANSCRIPTION FACTOR (TF) CTCF SUGGESTING DIFFERENCES IN THE THREE-DIMENSIONAL CHROMATIN STRUCTURE. UNEXPECTEDLY, SITES WITH REDUCED CHROMATIN ACCESSIBILITY WERE ENRICHED FOR MOTIFS OF TFS PERTINENT FOR T CELL FUNCTION. MOST STRIKINGLY, SUPER-ENHANCERS ENCOMPASSING RA-ASSOCIATED SNPS WERE LESS ACCESSIBLE. ANALYSIS OF SELECTED TRANSCRIPTS AND PUBLISHED DNA METHYLATION PATTERNS WERE CONSISTENT WITH THIS FINDING. THE PREFERENTIAL LOSS IN ACCESSIBILITY AT THESE SUPER-ENHANCERS WAS SEEN IN PATIENTS WITH HIGH AND LOW DISEASE ACTIVITY AND ON A VARIETY OF IMMUNOSUPPRESSIVE TREATMENT MODALITIES. INTERPRETATION: DISEASE-ASSOCIATED GENES ARE EPIGENETICALLY LESS POISED TO RESPOND IN CD4 T CELLS FROM PATIENTS WITH ESTABLISHED RA. FUNDING: THIS WORK WAS SUPPORTED BY I01 BX001669 FROM THE VETERANS ADMINISTRATION. 2022