1 1886 160 ENDOGENOUS BIOLOGICAL DRIVERS IN DIABETIC LOWER LIMB WOUNDS RECURRENCE: HYPOTHETICAL REFLECTIONS. AN IMPAIRED HEALING RESPONSE UNDERLIES DIABETIC FOOT WOUND CHRONICITY, FREQUENTLY TRANSLATING TO AMPUTATION, DISABILITY, AND MORTALITY. DIABETICS SUFFER FROM UNDERAPPRECIATED EPISODES OF POST-EPITHELIZATION ULCER RECURRENCE. RECURRENCE EPIDEMIOLOGICAL DATA ARE ALARMINGLY HIGH, SO THE ULCER IS CONSIDERED IN "REMISSION" AND NOT HEALED FROM THE TIME IT REMAINS EPITHELIALIZED. RECURRENCE MAY RESULT FROM THE COMBINED EFFECTS OF BEHAVIORAL AND ENDOGENOUS BIOLOGICAL FACTORS. ALTHOUGH THE DAMAGING ROLE OF BEHAVIORAL, CLINICAL PREDISPOSING FACTORS IS UNDEBATABLE, IT STILL REMAINS ELUSIVE IN THE IDENTIFICATION OF ENDOGENOUS BIOLOGICAL CULPRITS THAT MAY PRIME THE RESIDUAL SCAR TISSUE FOR RECURRENCE. FURTHERMORE, THE EVENT OF ULCER RECURRENCE STILL WAITS FOR THE IDENTIFICATION OF A MOLECULAR PREDICTOR. WE PROPOSE THAT ULCER RECURRENCE IS DEEPLY IMPINGED BY CHRONIC HYPERGLYCEMIA AND ITS DOWNSTREAM BIOLOGICAL EFFECTORS, WHICH ORIGINATE EPIGENETIC DRIVERS THAT ENFORCE ABNORMAL PATHOLOGIC PHENOTYPES TO DERMAL FIBROBLASTS AND KERATINOCYTES AS MEMORY CELLS. HYPERGLYCEMIA-DERIVED CYTOTOXIC REACTANTS ACCUMULATE AND MODIFY DERMAL PROTEINS, REDUCE SCAR TISSUE MECHANICAL TOLERANCE, AND DISRUPT FIBROBLAST-SECRETORY ACTIVITY. ACCORDINGLY, THE COMBINATION OF EPIGENETIC AND LOCAL AND SYSTEMIC CYTOTOXIC SIGNALERS INDUCE THE ONSET OF "AT-RISK PHENOTYPES" SUCH AS PREMATURE SKIN CELL AGING, DYSMETABOLISM, INFLAMMATORY, PRO-DEGRADATIVE, AND OXIDATIVE PROGRAMS THAT MAY ULTIMATELY CONVERGE TO SCAR CELL DEMISE. POST-EPITHELIALIZATION RECURRENCE RATE DATA ARE MISSING IN CLINICAL STUDIES OF REPUTED ULCER HEALING THERAPIES DURING FOLLOW-UP PERIODS. INTRA-ULCER INFILTRATION OF EPIDERMAL GROWTH FACTOR EXHIBITS THE MOST CONSISTENT REMISSION DATA WITH THE LOWEST RECURRENCES DURING 12-MONTH FOLLOW-UP. RECURRENCE DATA SHOULD BE REGARDED AS A VALUABLE CLINICAL ENDPOINT DURING THE INVESTIGATIONAL PERIOD FOR EACH EMERGENT HEALING CANDIDATE. 2023 2 6186 26 THE IMPACT OF HIV INFECTION ON THE FREQUENCIES, FUNCTION, SPATIAL LOCALIZATION AND HETEROGENEITY OF T FOLLICULAR REGULATORY CELLS (TFRS) WITHIN HUMAN LYMPH NODES. BACKGROUND: HIV ERADICATION EFFORTS HAVE BEEN UNSUCCESSFUL PARTLY DUE TO VIRUS PERSISTENCE IN IMMUNE SANCTUARY SITES SUCH AS GERMINAL CENTRES WITHIN LYMPH NODE (LN) TISSUES. RECENT EVIDENCE SUGGESTS THAT LNS HARBOUR A NOVEL SUBSET OF REGULATORY T CELLS, TERMED FOLLICULAR REGULATORY T CELLS (TFRS), BUT THEIR ROLE IN HIV PATHOGENESIS IS NOT FULLY ELUCIDATED. RESULTS: PAIRED EXCISIONAL LN AND PERIPHERAL BLOOD SAMPLES OBTAINED FROM 20 HIV-UNINFECTED AND 31 HIV-INFECTED TREATED AND 7 CHRONIC UNTREATED, WERE USED TO DETERMINE IF AND HOW HIV INFECTION MODULATE FREQUENCIES, FUNCTION AND SPATIAL LOCALIZATION OF TFRS WITHIN LN TISSUES. IMAGING STUDIES SHOWED THAT MOST TFRS ARE LOCALIZED IN EXTRA-FOLLICULAR REGIONS. CO-CULTURE ASSAYS SHOWED TFRS SUPPRESSION OF TFH HELP TO B CELLS. IMPORTANTLY, EPIGENETIC AND TRANSCRIPTIONAL STUDIES IDENTIFIED DPP4 AND FCRL3 AS NOVEL PHENOTYPIC MARKERS THAT DEFINE FOUR FUNCTIONALLY DISTINCT TFR SUBPOPULATIONS IN HUMAN LNS REGARDLESS OF HIV STATUS. IMAGING STUDIES CONFIRMED THE REGULATORY PHENOTYPE OF DPP4(+)TFRS. CONCLUSION: TOGETHER THESE STUDIES DESCRIBE TFRS DYNAMIC CHANGES DURING HIV INFECTION AND REVEAL PREVIOUSLY UNDERAPPRECIATED TFR HETEROGENEITY WITHIN HUMAN LNS. 2022 3 4517 28 MULTI-OMICS FACTOR ANALYSIS-A FRAMEWORK FOR UNSUPERVISED INTEGRATION OF MULTI-OMICS DATA SETS. MULTI-OMICS STUDIES PROMISE THE IMPROVED CHARACTERIZATION OF BIOLOGICAL PROCESSES ACROSS MOLECULAR LAYERS. HOWEVER, METHODS FOR THE UNSUPERVISED INTEGRATION OF THE RESULTING HETEROGENEOUS DATA SETS ARE LACKING. WE PRESENT MULTI-OMICS FACTOR ANALYSIS (MOFA), A COMPUTATIONAL METHOD FOR DISCOVERING THE PRINCIPAL SOURCES OF VARIATION IN MULTI-OMICS DATA SETS. MOFA INFERS A SET OF (HIDDEN) FACTORS THAT CAPTURE BIOLOGICAL AND TECHNICAL SOURCES OF VARIABILITY. IT DISENTANGLES AXES OF HETEROGENEITY THAT ARE SHARED ACROSS MULTIPLE MODALITIES AND THOSE SPECIFIC TO INDIVIDUAL DATA MODALITIES. THE LEARNT FACTORS ENABLE A VARIETY OF DOWNSTREAM ANALYSES, INCLUDING IDENTIFICATION OF SAMPLE SUBGROUPS, DATA IMPUTATION AND THE DETECTION OF OUTLIER SAMPLES. WE APPLIED MOFA TO A COHORT OF 200 PATIENT SAMPLES OF CHRONIC LYMPHOCYTIC LEUKAEMIA, PROFILED FOR SOMATIC MUTATIONS, RNA EXPRESSION, DNA METHYLATION AND EX VIVO DRUG RESPONSES. MOFA IDENTIFIED MAJOR DIMENSIONS OF DISEASE HETEROGENEITY, INCLUDING IMMUNOGLOBULIN HEAVY-CHAIN VARIABLE REGION STATUS, TRISOMY OF CHROMOSOME 12 AND PREVIOUSLY UNDERAPPRECIATED DRIVERS, SUCH AS RESPONSE TO OXIDATIVE STRESS. IN A SECOND APPLICATION, WE USED MOFA TO ANALYSE SINGLE-CELL MULTI-OMICS DATA, IDENTIFYING COORDINATED TRANSCRIPTIONAL AND EPIGENETIC CHANGES ALONG CELL DIFFERENTIATION. 2018 4 2490 23 EPIGENETICALLY REGULATED INFLAMMATION IN VASCULAR SENESCENCE AND RENAL PROGRESSION OF CHRONIC KIDNEY DISEASE. CHRONIC KIDNEY DISEASE (CKD) AND ITS COMPLICATIONS, INCLUDING VASCULAR SENESCENCE AND PROGRESSIVE RENAL FIBROSIS, ARE ASSOCIATED WITH INFLAMMATION. VASCULAR SENESCENCE, IN PARTICULAR, HAS EMERGED AS AN INSTRUMENTAL MEDIATOR OF VASCULAR INFLAMMATION THAT POTENTIALLY WORSENS RENAL FUNCTION. EPIGENETICALLY REGULATED INFLAMMATION INVOLVING HISTONE MODIFICATION, DNA METHYLATION, ACTIONS OF MICRORNAS AND OTHER NON-CODING RNAS, AND THEIR RECIPROCAL REACTIONS DURING VASCULAR SENESCENCE AND INFLAMMAGING ARE UNDERAPPRECIATED. THEIR SYNERGISTIC EFFECTS CAN CONTRIBUTE TO CKD PROGRESSION. VASCULAR SENOTHERAPEUTICS OR PHARMACOLOGICAL ANTI-SENESCENT THERAPIES BASED ON EPIGENETIC MACHINERIES CAN THEREFORE BE PLAUSIBLE OPTIONS FOR AMELIORATING VASCULAR AGING AND EVEN HALTING THE WORSENING OF RENAL FIBROSIS. THESE INCLUDE HISTONE DEACETYLASE MODULATORS, HISTONE METHYLTRANSFERASE MODULATORS, OTHER HISTONE MODIFICATION EFFECTORS, DNA METHYLTRANSFERASE INHIBITORS, TELOMERASE REVERSE TRANSCRIPTASE ENHANCERS, MICRORNA MIMIC DELIVERY, AND SMALL MOLECULES WITH MICRORNA-REGULATING POTENTIALS. SOME OF THESE MOLECULES HAVE ALREADY BEEN TESTED AND HAVE SHOWN ANECDOTAL EVIDENCE FOR TREATING UREMIC VASCULOPATHY AND RENAL FIBROSIS, SUPPORTING THE FEASIBILITY OF THIS APPROACH. 2022 5 1896 24 ENDOTHELIAL-TO-MESENCHYMAL TRANSITION: AN UNDERAPPRECIATED MEDIATOR OF DIABETIC COMPLICATIONS. DIABETES AND ITS COMPLICATIONS REPRESENT A GREAT BURDEN ON THE GLOBAL HEALTHCARE SYSTEM. DIABETIC COMPLICATIONS ARE FUNDAMENTALLY DISEASES OF THE VASCULATURE, WITH ENDOTHELIAL CELLS BEING THE CENTERPIECE OF EARLY HYPERGLYCEMIA-INDUCED CHANGES. ENDOTHELIAL-TO-MESENCHYMAL TRANSITION IS A TIGHTLY REGULATED PROCESS THAT RESULTS IN ENDOTHELIAL CELLS LOSING ENDOTHELIAL CHARACTERISTICS AND DEVELOPING MESENCHYMAL TRAITS. ALTHOUGH ENDOTHELIAL-TO-MESENCHYMAL TRANSITION HAS BEEN FOUND TO OCCUR WITHIN MOST OF THE MAJOR COMPLICATIONS OF DIABETES, IT HAS NOT BEEN A MAJOR FOCUS OF STUDY OR A COMMON TARGET IN THE TREATMENT OR PREVENTION OF DIABETIC COMPLICATIONS. IN THIS REVIEW WE SUMMARIZE THE IMPORTANCE OF ENDOTHELIAL-TO-MESENCHYMAL TRANSITION IN EACH MAJOR DIABETIC COMPLICATION, EXAMINE SPECIFIC MECHANISMS AT PLAY, AND HIGHLIGHT POTENTIAL MECHANISMS TO PREVENT ENDOTHELIAL-TO-MESENCHYMAL TRANSITION IN EACH OF THE MAJOR CHRONIC COMPLICATIONS OF DIABETES. 2023 6 568 26 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 7 3281 24 HETEROGENEOUS TFH CELL POPULATIONS THAT DEVELOP DURING ENTERIC HELMINTH INFECTION PREDICT THE QUALITY OF TYPE 2 PROTECTIVE RESPONSE. T FOLLICULAR HELPER (TFH) CELLS ARE AN IMPORTANT COMPONENT OF GERMINAL CENTER (GC)-MEDIATED HUMORAL IMMUNITY. YET, HOW A CHRONIC TYPE 1 VERSUS PROTECTIVE TYPE 2 HELMINTH INFECTION MODULATES TFH-GC RESPONSES REMAINS POORLY UNDERSTOOD. HERE, WE EMPLOY THE HELMINTH TRICHURIS MURIS MODEL AND DEMONSTRATE THAT TFH CELL PHENOTYPES AND GC ARE DIFFERENTIALLY REGULATED IN ACUTE VERSUS CHRONIC INFECTION. THE LATTER FAILED TO INDUCE TFH-GC B CELL RESPONSES, WITH TFH CELLS EXPRESSING TAU-BET AND INTERFERON-GAMMA. IN CONTRAST, INTERLEUKIN-4-PRODUCING TFH CELLS DOMINATE RESPONSES TO AN ACUTE, RESOLVING INFECTION. HEIGHTENED EXPRESSION AND INCREASED CHROMATIN ACCESSIBILITY OF T HELPER (TH)1- AND TH2 CELL-ASSOCIATED GENES ARE OBSERVED IN CHRONIC AND ACUTE INDUCED TFH CELLS, RESPECTIVELY. BLOCKADE OF THE TH1 CELL RESPONSE BY T-CELL-INTRINSIC T-BET DELETION PROMOTED TFH CELL EXPANSION DURING CHRONIC INFECTION, POINTING TO A CORRELATION BETWEEN A ROBUST TFH CELL RESPONSE AND PROTECTIVE IMMUNITY TO PARASITES. FINALLY, BLOCKADE OF TFH-GC INTERACTIONS IMPAIRED TYPE 2 IMMUNITY, REVEALING THE CRITICAL PROTECTIVE ROLE OF GC-DEPENDENT TH2-LIKE TFH CELL RESPONSES DURING ACUTE INFECTION. COLLECTIVELY, THESE RESULTS PROVIDE NEW INSIGHTS INTO THE PROTECTIVE ROLES OF TFH-GC RESPONSES AND IDENTIFY DISTINCT TRANSCRIPTIONAL AND EPIGENETIC FEATURES OF TFH CELLS THAT EMERGE DURING RESOLVING OR CHRONIC T. MURIS INFECTION. 2023 8 5853 25 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 9 1943 48 EPIDERMAL GROWTH FACTOR IN HEALING DIABETIC FOOT ULCERS: FROM GENE EXPRESSION TO TISSUE HEALING AND SYSTEMIC BIOMARKER CIRCULATION. LOWER-EXTREMITY DIABETIC ULCERS ARE RESPONSIBLE FOR 80% OF ANNUAL WORLDWIDE NONTRAUMATIC AMPUTATIONS. EPIDERMAL GROWTH FACTOR (EGF) REDUCTION IS ONE OF THE MOLECULAR PILLARS OF DIABETIC ULCER CHRONICITY, THUS EGF ADMINISTRATION MAY BE CONSIDERED A TYPE OF REPLACEMENT THERAPY. TOPICAL EGF AD-MINISTRATION TO IMPROVE AND SPEED WOUND HEALING BEGAN IN 1989 ON BURN PATIENTS AS PART OF AN ACUTE-HEALING THERAPY. FURTHER CLINICAL STUDIES BASED ON TOPICALLY ADMINISTERING EGF TO DIFFERENT CHRONIC WOUNDS RESULTED IN DISAPPOINTING OUT-COMES. AN ANALYSIS OF THE LITERATURE ON UNSUCCESSFUL CLINICAL TRIALS IDENTIFI ED A LACK OF KNOWLEDGE CONCERNING: (I) MOLECULAR AND CELLULAR FOUNDATIONS OF WOUND CHRONICITY AND (II) THE PHAR-MACODYNAMIC REQUISITES GOVERNING EGF INTERACTION WITH ITS RECEPTOR TO PROMOTE CELL RESPONSE. YET, EGF INTRA- AND PERILE-SIONAL INFI LTRATION WERE SHOWN TO CIRCUMVENT THE PHARMACODY-NAMIC LIMITATIONS OF TOPICAL APPLICATION. SINCE THE FI RST STUDIES, THE FOLLOWING DECADES OF BASIC AND CLINICAL RESEARCH ON EGF THERAPY FOR PROBLEM WOUNDS HAVE SHED LIGHT ON POTENTIAL USES OF GROWTH FACTORS IN REGENERATIVE MEDICINE. EGF'S MOLECULAR AND BIOCHEMICAL EFFECTS AT BOTH LOCAL AND SYSTEMIC LEVELS ARE DIVERSE: (1) DOWNREGULATION OF GENES ENCODING INFL AMMATION MEDIATORS AND INCREASED EXPRESSION OF GENES INVOLVED IN CELL PROLIFERATION, ANGIOGENESIS AND MATRIX SECRETION; (2) EGF IN-TERVENTION POSITIVELY IMPACTS BOTH MESENCHYMAL AND EPITHELIAL CELLS, REDUCING INFL AMMATION AND STIMULATING THE RECRUITMENT OF PRECURSOR CIRCULATING CELLS THAT PROMOTE THE FORMATION OF NEW BLOOD VESSELS; (3) AT THE SUBCELLULAR LEVEL, UPREGULATION OF THE EGF RECEPTOR WITH SUBSEQUENT INTRACELLULAR TRAFFI CKING, INCLUD-ING MITOCHONDRIAL ALLOCATION ALONG WITH RESTORED MORPHOLOGY OF MULTIPLE ORGANELLES; AND (4) LOCAL EGF INFI LTRATION RESULTING IN A SYSTEMIC, ORGANISMAL REPERCUSSION, THUS CONTRIBUTING TO ATTENUATION OF CIRCULATING INFL AMMATORY AND CATABOLIC REAC-TANTS, RESTORED REDUCTION-OXIDATION BALANCE, AND DECREASED TOXIC GLYCATION PRODUCTS AND SOLUBLE APOPTOGENIC EFFECTORS. IT IS LIKELY THAT EGF TREATMENT MAY REARRANGE CRITICAL EPIGENETIC DRIVERS OF DIABETIC METABOLIC MEMORY. KEYWORDS EPIDERMAL GROWTH FACTOR, DIABETES, DIABETES COMPLICATIONS, WOUND HEALING, DIABETIC FOOT, AMPUTATION, ULCER, CUBA. 2020 10 769 27 CD8 T CELL EXHAUSTION DURING CHRONIC VIRAL INFECTION AND CANCER. EXHAUSTED CD8 T (TEX) CELLS ARE A DISTINCT CELL LINEAGE THAT ARISE DURING CHRONIC INFECTIONS AND CANCERS IN ANIMAL MODELS AND HUMANS. TEX CELLS ARE CHARACTERIZED BY PROGRESSIVE LOSS OF EFFECTOR FUNCTIONS, HIGH AND SUSTAINED INHIBITORY RECEPTOR EXPRESSION, METABOLIC DYSREGULATION, POOR MEMORY RECALL AND HOMEOSTATIC SELF-RENEWAL, AND DISTINCT TRANSCRIPTIONAL AND EPIGENETIC PROGRAMS. THE ABILITY TO REINVIGORATE TEX CELLS THROUGH INHIBITORY RECEPTOR BLOCKADE, SUCH AS ALPHAPD-1, HIGHLIGHTS THE THERAPEUTIC POTENTIAL OF TARGETING THIS POPULATION. EMERGING INSIGHTS INTO THE MECHANISMS OF EXHAUSTION ARE INFORMING IMMUNOTHERAPIES FOR CANCER AND CHRONIC INFECTIONS. HOWEVER, LIKE OTHER IMMUNE CELLS, TEX CELLS ARE HETEROGENEOUS AND INCLUDE PROGENITOR AND TERMINAL SUBSETS WITH UNIQUE CHARACTERISTICS AND RESPONSES TO CHECKPOINT BLOCKADE. HERE, WE REVIEW OUR CURRENT UNDERSTANDING OF TEX CELL BIOLOGY, INCLUDING THE DEVELOPMENTAL PATHS, TRANSCRIPTIONAL AND EPIGENETIC FEATURES, AND CELL INTRINSIC AND EXTRINSIC FACTORS CONTRIBUTING TO EXHAUSTION AND HOW THIS KNOWLEDGE MAY INFORM THERAPEUTIC TARGETING OF TEX CELLS IN CHRONIC INFECTIONS, AUTOIMMUNITY, AND CANCER. 2019 11 6319 30 THE ROAD LESS TAKEN: LESS APPRECIATED PATHWAYS FOR MANIPULATING CD8(+) T CELL EXHAUSTION. EXHAUSTED CD8(+) T (TEX) CELLS ARE A DISTINCT CELL POPULATION THAT ARISE DURING PERSISTENT ANTIGEN EXPOSURE IN THE CONTEXT OF CHRONIC INFECTIONS AND CANCERS. ALTHOUGH CHARACTERIZED BY PROGRESSIVE LOSS OF EFFECTOR FUNCTIONS, HIGH AND SUSTAINED INHIBITORY RECEPTOR EXPRESSION AND DISTINCT TRANSCRIPTIONAL AND EPIGENETIC PROGRAMS, TEX CELLS ARE HETEROGENEOUS. AMONG THESE, A SELF-RENEWING TCF-1(+) TEX POPULATION, HAVING UNIQUE CHARACTERISTICS AND THE ABILITY TO RESPOND TO IMMUNE-CHECKPOINT BLOCKADE, GIVES RISE TO TCF-1(-) TERMINALLY TEX CELLS. THESE TCF-1(+) CELLS HAVE STEM CELL-LIKE PROPERTIES SIMILAR TO MEMORY T CELL POPULATIONS, BUT THE SIGNALS THAT REGULATE THE DEVELOPMENTAL PATHWAYS AND RELATIONSHIPS AMONG EXHAUSTED CELL POPULATIONS ARE STILL UNCLEAR. HERE, WE REVIEW OUR CURRENT UNDERSTANDING OF TEX CELL BIOLOGY, AND DISCUSS SOME LESS APPRECIATED MOLECULES AND PATHWAYS AFFECTING T CELL EXHAUSTION. WE HIGHLIGHT TWO CO-STIMULATORY RECEPTORS, CD226 AND CD137, AND THEIR ROLE IN INDUCING OR RESTRAINING T CELL EXHAUSTION, AS WELL AS SIGNALING PATHWAYS THAT MAY BE AMENABLE TO PHARMACOLOGICAL INHIBITION WITH A FOCUS ON PHOSPHOINOSITIDE-3 KINASE AND IL-2 PARTIAL AGONISTS. FINALLY, WE DISCUSS NOVEL METHODS THAT MAY INCREASE TCF-1(+) POPULATIONS AND THEREFORE IMPROVE IMMUNOTHERAPY RESPONSIVENESS. UNDERSTANDING FEATURES OF AND PATHWAYS TO EXHAUSTION HAS IMPORTANT IMPLICATIONS FOR THE SUCCESS OF IMMUNOTHERAPY, INCLUDING CHECKPOINT BLOCKADE AND ADOPTIVE T-CELL TRANSFER THERAPIES. 2022 12 5806 32 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 13 1379 24 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 14 1278 20 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 15 1108 15 COMMENTARY ON SOME RECENT THESES RELEVANT TO COMBATING AGING: JUNE 2021. THESES REVIEWED IN THIS ISSUE INCLUDE "ENGINEERING PROTEIN DISAGGREGASES TO COUNTER ALPHA-SYNUCLEIN AND AMYLOID-BETA NEUROTOXICITY," "HYPERGLYCAEMIA INDUCED IMMUNOMODULATION OF MACROPHAGES IN DIABETIC VASCULAR DISEASE," "MICROVASCULATURE-ON-A-CHIP SYSTEMS FOR HUMAN DISEASE MODELING," "SENESCENCE SURVEILLANCE: THE INTERPLAY BETWEEN THE IMMUNE SYSTEM AND SENESCENT CELLS," "THE HMG TRANSCRIPTION FACTOR TOX INDUCES A TRANSCRIPTIONAL AND EPIGENETIC PROGRAM OF CD8(+) T CELL EXHAUSTION IN CHRONIC INFECTION AND CANCER," AND "ZERO TO ONE-TRANSLATIONAL ADVANCEMENTS IN THE FIELD OF XENOTRANSPLANTATION." 2021 16 4177 33 MEMORY T CELL, EXHAUSTION, AND TUMOR IMMUNITY. CD8(+)T CELLS ARE IMPORTANT IN PROTECTIVE IMMUNITY AGAINST INTRACELLULAR PATHOGENS AND TUMORS. IN CHRONIC INFECTIONS OR CANCER, CD8(+)T CELLS ARE CONSTANTLY EXPOSED TO ANTIGENS AND INFLAMMATORY SIGNALS. SUCH EXCESSIVE AND CONSTITUTIVE SIGNALS LEAD TO THE DETERIORATION OF T CELL FUNCTION, CALLED 'EXHAUSTION'. EXHAUSTED T CELLS ARE CHARACTERIZED BY LOW PROLIFERATION IN RESPONSE TO ANTIGEN STIMULATION, PROGRESSIVE LOSS OF EFFECTOR FUNCTION (CYTOKINE PRODUCTION AND KILLING FUNCTION), EXPRESSION OF MULTIPLE INHIBITORY RECEPTORS SUCH AS PD-1, TIM3, AND LAG3, AND METABOLIC ALTERATIONS FROM OXIDATIVE PHOSPHORYLATION TO GLYCOLYSIS. THESE DYSFUNCTIONS ARE ASSOCIATED WITH ALTERED TRANSCRIPTIONAL PROGRAMS AND EPIGENETIC REGULATIONS AND RECENT STUDIES SUGGESTED THAT NR4A AND TOX TRANSCRIPTION FACTORS ARE DEEPLY INVOLVED IN EXHAUSTION PHENOTYPES. HOWEVER, AN INCREASE THE EARLY MEMORY T CELLS INCLUDING STEM CELL MEMORY T (T(SCM)) CELLS IS CRITICAL FOR T CELL PERSISTENCE AND EFFICIENT TUMOR KILLING ESPECIALLY FOR ADOPTIVE CANCER IMMUNOTHERAPY SUCH AS CAR-T CELL THERAPY. AN INCREASING AMOUNT OF EVIDENCE SUPPORTS THE THERAPEUTIC POTENTIAL OF TARGETING EXHAUSTED T CELLS AND T(SCM) CELLS. WE HAVE BEGUN TO UNDERSTAND THE MOLECULAR MECHANISMS OF T CELL EXHAUSTION AND EARLY MEMORY FORMATION, AND THE CLINICAL APPLICATION OF CONVERTING EXHAUSTED T CELLS TO REJUVENATED EARLY MEMORY T CELLS IS THE GOAL OF OUR STUDY. 2020 17 4057 27 MAPPING THE LINEAGE RELATIONSHIP BETWEEN CXCR5(+) AND CXCR5(-) CD4(+) T CELLS IN HIV-INFECTED HUMAN LYMPH NODES. CXCR5 IS A KEY MARKER OF FOLLICULAR HELPER T (T(FH)) CELLS. USING PRIMARY LYMPH NODES (LNS) FROM HIV-INFECTED PATIENTS, WE IDENTIFIED A POPULATION OF CXCR5(-) CD4(+) T CELLS WITH T(FH)-CELL-LIKE FEATURES. THIS CXCR5(-) SUBSET BECOMES EXPANDED IN SEVERE HIV INFECTION AND IS CHARACTERIZED BY THE UPREGULATION OF ACTIVATION MARKERS AND HIGH PD-1 AND ICOS SURFACE EXPRESSION. INTEGRATED ANALYSES ON THE PHENOTYPIC HETEROGENEITY, FUNCTIONAL CAPACITY, T CELL RECEPTOR (TCR) REPERTOIRE, TRANSCRIPTIONAL PROFILE, AND EPIGENETIC STATE OF CXCR5(-)PD-1(+)ICOS(+) T CELLS REVEALED A SHARED CLONAL RELATIONSHIP WITH T(FH) CELLS. CXCR5(-)PD-1(+)ICOS(+) T CELLS RETAINED A POISED STATE FOR CXCR5 EXPRESSION AND EXHIBITED A MIGRATORY TRANSCRIPTIONAL PROGRAM. TCR SEQUENCE OVERLAP REVEALED A CONTRIBUTION OF LN-DERIVED CXCR5(-)PD-1(+)ICOS(+) T CELLS TO CIRCULATING CXCR5(-) CD4(+) T CELLS WITH B CELL HELP FUNCTION. THESE DATA LINK LN PATHOLOGY TO CIRCULATING T CELLS AND EXPAND THE CURRENT UNDERSTANDING ON THE DIVERSITY OF T CELLS THAT REGULATE B CELL RESPONSES DURING CHRONIC INFLAMMATION. 2019 18 2367 20 EPIGENETIC REGULATION OF T CELL EXHAUSTION. CHRONIC ANTIGEN STIMULATION DURING VIRAL INFECTIONS AND CANCER CAN LEAD TO T CELL EXHAUSTION, WHICH IS CHARACTERIZED BY REDUCED EFFECTOR FUNCTION AND PROLIFERATION, AND THE EXPRESSION OF INHIBITORY IMMUNE CHECKPOINT RECEPTORS. RECENT STUDIES HAVE DEMONSTRATED THAT T CELL EXHAUSTION RESULTS IN WHOLESCALE EPIGENETIC REMODELING THAT CONFERS PHENOTYPIC STABILITY TO THESE CELLS AND PREVENTS T CELL REINVIGORATION BY CHECKPOINT BLOCKADE. HERE, WE REVIEW FOUNDATIONAL TECHNOLOGIES TO PROFILE THE EPIGENOME AT MULTIPLE SCALES, INCLUDING MAPPING THE LOCATIONS OF TRANSCRIPTION FACTORS AND HISTONE MODIFICATIONS, DNA METHYLATION AND THREE-DIMENSIONAL GENOME CONFORMATION. WE DISCUSS HOW THESE TECHNOLOGIES HAVE ELUCIDATED THE DEVELOPMENT AND EPIGENETIC REGULATION OF EXHAUSTED T CELLS AND FUNCTIONAL IMPLICATIONS ACROSS VIRAL INFECTION, CANCER, AUTOIMMUNITY AND ENGINEERED T CELL THERAPIES. FINALLY, WE COVER EMERGING MULTI-OMIC AND GENOME ENGINEERING TECHNOLOGIES, CURRENT AND UPCOMING OPPORTUNITIES TO APPLY THESE TO T CELL EXHAUSTION, AND THERAPEUTIC OPPORTUNITIES FOR T CELL ENGINEERING IN THE CLINIC. 2022 19 1763 29 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 20 4178 16 MEMORY T-CELL HETEROGENEITY AND TERMINOLOGY. IMMUNOLOGICAL MEMORY AND EXHAUSTION ARE FUNDAMENTAL FEATURES OF ADAPTIVE IMMUNITY. RECENT ADVANCES REVEAL INCREASING HETEROGENEITY AND DIVERSITY AMONG CD8 T-CELL SUBSETS, RESULTING IN NEW SUBSETS TO ANNOTATE AND UNDERSTAND. HERE, WE REVIEW OUR CURRENT KNOWLEDGE OF DIFFERENTIATION AND MAINTENANCE OF MEMORY AND EXHAUSTED CD8 T CELLS, INCLUDING PHENOTYPIC CLASSIFICATION, DEVELOPMENTAL PATHS, TRANSCRIPTIONAL AND EPIGENETIC FEATURES, AND CELL INTRINSIC AND EXTRINSIC FACTORS. ADDITIONALLY, WE USE THIS OUTLINE TO DISCUSS THE NOMENCLATURE OF EFFECTOR, MEMORY, AND EXHAUSTED CD8 T CELLS. FINALLY, WE DISCUSS HOW NEW FINDINGS ABOUT THESE CELL TYPES MAY IMPACT THE THERAPEUTIC EFFICACY AND DEVELOPMENT OF IMMUNOTHERAPIES TARGETING EFFECTOR, MEMORY, AND/OR EXHAUSTED CD8 T CELLS IN CHRONIC INFECTIONS AND CANCER. 2021