1 6677 107 USING EPIGENETICS TO DEFINE VACCINE-INDUCED MEMORY T CELLS. MEMORY T CELLS GENERATED FROM ACUTE INFECTION OR VACCINATION HAVE THE POTENTIAL TO PROVIDE THE HOST WITH LIFE-LONG IMMUNITY AGAINST RE-INFECTION. PROTECTION BY MEMORY T CELLS IS ACHIEVED THROUGH THEIR ACQUIRED ABILITY TO PERSIST AT ANATOMICAL SITES OF THE PRIMARY INFECTION AS WELL AS MAINTAINING A HEIGHTENED ABILITY TO RECALL EFFECTOR FUNCTIONS. THE MAINTENANCE OF CD8 AND CD4 T CELL FUNCTION IN A STATE OF READINESS IS KEY TO LIFE-LONG IMMUNITY AND MANIFEST THROUGH CHANGES IN TRANSCRIPTIONAL REGULATION. YET, THE ABILITY TO IDENTIFY POISED TRANSCRIPTIONAL PROGRAMS AT THE MAINTENANCE STAGE OF THE RESPONSE IS LACKING FROM MOST TRANSCRIPTIONAL PROFILING STUDIES OF MEMORY T CELLS. EPIGENETIC PROFILING ALLOWS FOR THE ASSESSMENT OF TRANSCRIPTIONALLY POISED (PROMOTERS THAT ARE READILY ACCESSIBLE FOR TRANSCRIPTION) STATES OF ANTIGEN-SPECIFIC T CELLS WITHOUT MANIPULATION OF THE ACTIVATION STATE OF THE CELL. HERE WE REVIEW RECENT STUDIES THAT HAVE EXAMINED EPIGENETIC PROGRAMS OF EFFECTOR AND MEMORY T CELL SUBSETS. THESE REPORTS DEMONSTRATE THAT ACQUISITION OF EPIGENETIC PROGRAMS DURING MEMORY T CELL DIFFERENTIATION TO ACUTE AND CHRONIC INFECTIONS IS COUPLED TO, AND POTENTIALLY REGULATE, THE CELL'S RECALL RESPONSE. WE DISCUSS THE USEFULNESS OF EPIGENETIC PROFILING IN CHARACTERIZING T CELL DIFFERENTIATION STATE AND FUNCTION FOR PRECLINICAL EVALUATION OF VACCINES AND THE CURRENT METHODOLOGIES FOR SINGLE LOCUS VERSUS GENOME-WIDE EPIGENETIC PROFILING. 2013 2 3380 28 HIV-1 INFECTION OF GENETICALLY ENGINEERED IPSC-DERIVED CENTRAL NERVOUS SYSTEM-ENGRAFTED MICROGLIA IN A HUMANIZED MOUSE MODEL. THE CENTRAL NERVOUS SYSTEM (CNS) IS A MAJOR HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 RESERVOIR. MICROGLIA ARE THE PRIMARY TARGET CELL OF HIV-1 INFECTION IN THE CNS. CURRENT MODELS HAVE NOT ALLOWED THE PRECISE MOLECULAR PATHWAYS OF ACUTE AND CHRONIC CNS MICROGLIAL INFECTION TO BE TESTED WITH IN VIVO GENETIC METHODS. HERE, WE DESCRIBE A NOVEL HUMANIZED MOUSE MODEL UTILIZING HUMAN-INDUCED PLURIPOTENT STEM CELL-DERIVED MICROGLIA TO XENOGRAFT INTO MURINE HOSTS. THESE MICE ARE ADDITIONALLY ENGRAFTED WITH HUMAN PERIPHERAL BLOOD MONONUCLEAR CELLS THAT SERVED AS A MEDIUM TO ESTABLISH A PERIPHERAL INFECTION THAT THEN SPREAD TO THE CNS MICROGLIA XENOGRAFT, MODELING A TRANS-BLOOD-BRAIN BARRIER ROUTE OF ACUTE CNS HIV-1 INFECTION WITH HUMAN TARGET CELLS. THE APPROACH IS COMPATIBLE WITH IPSC GENETIC ENGINEERING, INCLUDING INSERTING TARGETED TRANSGENIC REPORTER CASSETTES TO TRACK THE XENOGRAFTED HUMAN CELLS, ENABLING THE TESTING OF NOVEL TREATMENT AND VIRAL TRACKING STRATEGIES IN A COMPARATIVELY SIMPLE AND COST-EFFECTIVE WAY VIVO MODEL FOR NEUROHIV. IMPORTANCE: OUR MOUSE MODEL IS A POWERFUL TOOL FOR INVESTIGATING THE GENETIC MECHANISMS GOVERNING CNS HIV-1 INFECTION AND LATENCY IN THE CNS AT A SINGLE-CELL LEVEL. A MAJOR ADVANTAGE OF OUR MODEL IS THAT IT USES IPSC-DERIVED MICROGLIA, WHICH ENABLES HUMAN GENETICS, INCLUDING GENE FUNCTION AND THERAPEUTIC GENE MANIPULATION, TO BE EXPLORED IN VIVO , WHICH IS MORE CHALLENGING TO STUDY WITH CURRENT HEMATOPOIETIC STEM CELL-BASED MODELS FOR NEUROHIV. OUR TRANSGENIC TRACING OF XENOGRAFTED HUMAN CELLS WILL PROVIDE A QUANTITATIVE MEDIUM TO DEVELOP NEW MOLECULAR AND EPIGENETIC STRATEGIES FOR REDUCING THE HIV-1 LATENT RESERVOIR AND TO TEST THE IMPACT OF THERAPEUTIC INFLAMMATION-TARGETING DRUG INTERVENTIONS ON CNS HIV-1 LATENCY. 2023 3 5497 34 REVIEW: ANIMAL MODELS OF ACQUIRED EPILEPSY: INSIGHTS INTO MECHANISMS OF HUMAN EPILEPTOGENESIS. IN MANY PATIENTS WHO SUFFER FROM EPILEPSIES, RECURRENT EPILEPTIC SEIZURES DO NOT START AT BIRTH BUT DEVELOP LATER IN LIFE. THIS HOLDS PARTICULARLY TRUE FOR EPILEPSIES WITH A FOCAL SEIZURE ORIGIN INCLUDING FOCAL CORTICAL DYSPLASIAS AND TEMPORAL LOBE EPILEPSY (TLE). TLE MOST FREQUENTLY HAS ITS SEIZURE ONSET IN THE HIPPOCAMPAL FORMATION. HIPPOCAMPAL BIOPSIES OF PHARMACORESISTANT TLE PATIENTS UNDERGOING EPILEPSY SURGERY FOR SEIZURE CONTROL MOST FREQUENTLY REVEAL THE DAMAGE PATTERN OF HIPPOCAMPAL SCLEROSIS, THAT IS, SEGMENTAL NEURONAL CELL LOSS AND CONCOMITANT ASTROGLIOSIS. MANY TLE PATIENTS REPORT ON TRANSIENT BRAIN INSULTS EARLY IN LIFE, WHICH IS FOLLOWED BY A 'LATENCY' PERIOD LACKING SEIZURE ACTIVITY OF MONTHS OR EVEN YEARS BEFORE CHRONIC RECURRENT SEIZURES START. THE PLETHORA OF STRUCTURAL AND CELLULAR MECHANISMS THAT CONVERT THE HIPPOCAMPAL FORMATION TO BECOME CHRONICALLY HYPEREXCITABLE AFTER A TRANSIENT INSULT TO THE BRAIN ARE SUMMARIZED UNDER THE TERM EPILEPTOGENESIS. IN CONTRAST TO THE OBSTACLES ARISING FOR EXPERIMENTAL STUDIES OF EPILEPTOGENESIS ASPECTS IN HUMAN SURGICAL HIPPOCAMPAL TISSUE, RECENT ANIMAL MODEL APPROACHES ALLOW INSIGHTS INTO MECHANISMS OF EPILEPTOGENESIS. RELEVANT MODELS OF TRANSIENT BRAIN INSULTS IN THIS CONTEXT COMPRISE SEVERAL DISTINCT TYPES OF LESIONS INCLUDING EXCITOXIC STATUS EPILEPTICUS (SE), ELECTRICAL SEIZURE INDUCTION, TRAUMATIC BRAIN INJURY, INDUCTION OF INFLAMMATORY PROCESSES BY HYPERTHERMIA AND VIRAL INFLAMMATION AND OTHERS. IN PATHOGENETIC TERMS, ABERRANT TRANSCRIPTIONAL AND EPIGENETIC REPROGRAMMING, ACQUIRED CHANNEL- AND SYNAPTOPATHIES, NEURONAL NETWORK AND BLOOD-BRAIN BARRIER DYSFUNCTION AS WELL AS INNATE AND ADAPTIVE IMMUNITY-MEDIATED DAMAGE PLAY MAJOR ROLES. IN SUBSEQUENT STEPS, RESPECTIVE ANIMAL MODELS HAVE BEEN USED IN ORDER TO TEST WHETHER THIS DYNAMIC PROCESS CAN BE EITHER RETARDED OR EVEN ABOLISHED BY INTERFERING WITH EPILEPTOGENIC MECHANISMS. WELL-CONTROLLED SUBSEQUENT ANALYSES OF EPILEPTOGENIC CASCADES CHARACTERIZED IN ANIMAL MODELS USING CAREFULLY STRATIFIED HUMAN HIPPOCAMPAL BIOPSIES TO EXPLOIT THE UNIQUE OPPORTUNITIES GIVEN BY THESE RARE AND PRECIOUS BRAIN TISSUE SAMPLES AIM TO TRANSLATE INTO NOVEL ANTIEPILEPTOGENIC APPROACHES. RESPECTIVE PRECLINICAL TESTS CAN OPEN ENTIRELY NEW PERSPECTIVES FOR TAILOR-MADE TREATMENTS IN PATIENTS WITH THE POTENTIAL TO AVOID THE EMERGENCE OF CHRONIC FOCAL SEIZURE EVENTS. 2018 4 3064 24 GENOME-WIDE DNA METHYLATION ENCODES CARDIAC TRANSCRIPTIONAL REPROGRAMMING IN HUMAN ISCHEMIC HEART FAILURE. ISCHEMIC CARDIOMYOPATHY (ICM) IS THE CLINICAL ENDPOINT OF CORONARY HEART DISEASE AND A LEADING CAUSE OF HEART FAILURE. DESPITE GROWING DEMANDS TO DEVELOP PERSONALIZED APPROACHES TO TREAT ICM, PROGRESS IS LIMITED BY INADEQUATE KNOWLEDGE OF ITS PATHOGENESIS. SINCE EPIGENETICS HAS BEEN IMPLICATED IN THE DEVELOPMENT OF OTHER CHRONIC DISEASES, THE CURRENT STUDY WAS DESIGNED TO DETERMINE WHETHER TRANSCRIPTIONAL AND/OR EPIGENETIC CHANGES ARE SUFFICIENT TO DISTINGUISH ICM FROM OTHER ETIOLOGIES OF HEART FAILURE. SPECIFICALLY, WE HYPOTHESIZE THAT GENOME-WIDE DNA METHYLATION ENCODES TRANSCRIPTIONAL REPROGRAMMING IN ICM. RNA-SEQUENCING ANALYSIS WAS PERFORMED ON HUMAN ISCHEMIC LEFT VENTRICULAR TISSUE OBTAINED FROM PATIENTS WITH END-STAGE HEART FAILURE, WHICH ENRICHED KNOWN TARGETS OF THE POLYCOMB METHYLTRANSFERASE EZH2 COMPARED TO NON-ISCHEMIC HEARTS. COMBINED RNA SEQUENCING AND GENOME-WIDE DNA METHYLATION ANALYSIS REVEALED A ROBUST GENE EXPRESSION PATTERN CONSISTENT WITH SUPPRESSION OF OXIDATIVE METABOLISM, INDUCED ANAEROBIC GLYCOLYSIS, AND ALTERED CELLULAR REMODELING. LASTLY, KLF15 WAS IDENTIFIED AS A PUTATIVE UPSTREAM REGULATOR OF METABOLIC GENE EXPRESSION THAT WAS ITSELF REGULATED BY EZH2 IN A SET DOMAIN-DEPENDENT MANNER. OUR OBSERVATIONS THEREFORE DEFINE A NOVEL ROLE OF DNA METHYLATION IN THE METABOLIC REPROGRAMMING OF ICM. FURTHERMORE, WE IDENTIFY EZH2 AS AN EPIGENETIC REGULATOR OF KLF15 ALONG WITH DNA HYPERMETHYLATION, AND WE PROPOSE A NOVEL MECHANISM THROUGH WHICH CORONARY HEART DISEASE REPROGRAMS THE EXPRESSION OF BOTH INTERMEDIATE ENZYMES AND UPSTREAM REGULATORS OF CARDIAC METABOLISM SUCH AS KLF15. 2019 5 4856 31 OPTIMIZING RETROVIRAL GENE EXPRESSION FOR EFFECTIVE THERAPIES. WITH THEIR ABILITY TO INTEGRATE THEIR GENETIC MATERIAL INTO THE TARGET CELL GENOME, RETROVIRAL VECTORS (RV) OF BOTH THE GAMMA-RETROVIRAL (GAMMA-RV) AND LENTIVIRAL VECTOR (LV) CLASSES CURRENTLY REMAIN THE MOST EFFICIENT AND THUS THE SYSTEM OF CHOICE FOR ACHIEVING TRANSGENE RETENTION AND THEREFORE POTENTIALLY LONG-TERM EXPRESSION AND THERAPEUTIC BENEFIT. HOWEVER, GAMMA-RV AND LV INTEGRATION COMES AT A COST IN THAT TRANSCRIPTION UNITS WILL BE PRESENT WITHIN A NATIVE CHROMATIN ENVIRONMENT AND THUS BE SUBJECT TO EPIGENETIC EFFECTS (DNA METHYLATION, HISTONE MODIFICATIONS) THAT CAN NEGATIVELY IMPACT ON THEIR FUNCTION. INDEED, HIGHLY VARIABLE EXPRESSION AND SILENCING OF GAMMA-RV AND LV TRANSGENES ESPECIALLY RESULTING FROM PROMOTER DNA METHYLATION IS WELL DOCUMENTED AND WAS THE CAUSE OF THE FAILURE OF GENE THERAPY IN A CLINICAL TRIAL FOR X-LINKED CHRONIC GRANULOMATOUS DISEASE. THIS REVIEW WILL CRITICALLY EXPLORE THE USE OF DIFFERENT CLASSES OF GENETIC CONTROL ELEMENTS THAT CAN IN PRINCIPLE REDUCE VECTOR INSERTION SITE POSITION EFFECTS AND EPIGENETIC-MEDIATED SILENCING. THESE TRANSCRIPTIONAL REGULATORY ELEMENTS BROADLY DIVIDE THEMSELVES INTO EITHER THOSE WITH A CHROMATIN BOUNDARY OR BORDER FUNCTION (SCAFFOLD/MATRIX ATTACHMENT REGIONS, INSULATORS) OR THOSE WITH A DOMINANT CHROMATIN REMODELING AND TRANSCRIPTIONAL ACTIVATING CAPABILITY (LOCUS CONTROL REGIONS,, UBIQUITOUS CHROMATIN OPENING ELEMENTS). ALL THESE TYPES OF ELEMENTS HAVE THEIR STRENGTHS AND WEAKNESSES WITHIN THE CONSTRAINTS OF A GAMMA-RV AND LV BACKBONE, SHOWING VARYING DEGREES OF EFFICACY IN IMPROVING REPRODUCIBILITY AND STABILITY OF TRANSGENE FUNCTION. COMBINATIONS OF BOUNDARY AND CHROMATIN REMODELING; TRANSCRIPTIONAL ACTIVATING ELEMENTS, WHICH DO NOT IMPEDE VECTOR PRODUCTION; TRANSDUCTION EFFICIENCY; AND STABILITY ARE MOST LIKELY TO MEET THE REQUIREMENTS WITHIN A GENE THERAPY CONTEXT ESPECIALLY WHEN TARGETING A STEM CELL POPULATION. 2013 6 5702 26 SINGLE-CELL GENOMICS FOR INVESTIGATING PATHOGENESIS OF INFLAMMATORY DISEASES. RECENT TECHNICAL ADVANCES HAVE ENABLED UNBIASED TRANSCRIPTOMIC AND EPIGENETIC ANALYSIS OF EACH CELL, KNOWN AS "SINGLE-CELL ANALYSIS". SINGLE-CELL ANALYSIS HAS A VARIETY OF TECHNICAL APPROACHES TO INVESTIGATE THE STATE OF EACH CELL, INCLUDING MRNA LEVELS (TRANSCRIPTOME), THE IMMUNE REPERTOIRE (IMMUNE REPERTOIRE ANALYSIS), CELL SURFACE PROTEINS (SURFACE PROTEOME ANALYSIS), CHROMATIN ACCESSIBILITY (EPIGENOME), AND ACCORDANCE WITH GENOME VARIANTS (EQTLS; EXPRESSION QUANTITATIVE TRAIT LOCI). AS AN EFFECTIVE TOOL FOR INVESTIGATING ROBUST IMMUNE RESPONSES IN CORONAVIRUS DISEASE 2019 (COVID-19), MANY RESEARCHERS PERFORMED SINGLE-CELL ANALYSIS TO CAPTURE THE DIVERSE, UNBIASED IMMUNE CELL ACTIVATION AND DIFFERENTIATION. DESPITE CHALLENGES ELUCIDATING THE COMPLICATED IMMUNE MICROENVIRONMENTS OF CHRONIC INFLAMMATORY DISEASES USING EXISTING EXPERIMENTAL METHODS, IT IS NOW POSSIBLE TO CAPTURE THE SIMULTANEOUS IMMUNE FEATURES OF DIFFERENT CELL TYPES ACROSS INFLAMED TISSUES USING VARIOUS SINGLE-CELL TOOLS. IN THIS REVIEW, WE INTRODUCE PATIENT-BASED AND EXPERIMENTAL MOUSE MODEL RESEARCH UTILIZING SINGLE-CELL ANALYSES IN THE FIELD OF CHRONIC INFLAMMATORY DISEASES, AS WELL AS MULTI-ORGAN ATLAS TARGETING IMMUNE CELLS. 2023 7 3086 24 GENOME-WIDE TRANSCRIPTOMICS OF THE AMYGDALA REVEALS SIMILAR OLIGODENDROCYTE-RELATED RESPONSES TO ACUTE AND CHRONIC ALCOHOL DRINKING IN FEMALE MICE. REPEATED EXCESSIVE ALCOHOL CONSUMPTION IS A RISK FACTOR FOR ALCOHOL USE DISORDER (AUD). ALTHOUGH AUD HAS BEEN MORE COMMON IN MEN THAN WOMEN, WOMEN DEVELOP MORE SEVERE BEHAVIORAL AND PHYSICAL IMPAIRMENTS. HOWEVER, RELATIVELY FEW NEW THERAPEUTICS TARGETING DEVELOPMENT OF AUD, PARTICULARLY IN WOMEN, HAVE BEEN VALIDATED. TO GAIN A BETTER UNDERSTANDING OF MOLECULAR MECHANISMS UNDERLYING ALCOHOL INTAKE, WE CONDUCTED A GENOME-WIDE RNA-SEQUENCING ANALYSIS IN FEMALE MICE EXPOSED TO DIFFERENT MODES (ACUTE VS CHRONIC) OF ETHANOL DRINKING. WE FOCUSED ON TRANSCRIPTIONAL PROFILES IN THE AMYGDALA INCLUDING THE CENTRAL AND BASOLATERAL SUBNUCLEI, BRAIN AREAS PREVIOUSLY IMPLICATED IN ALCOHOL DRINKING AND SEEKING. SURPRISINGLY, WE FOUND THAT BOTH DRINKING MODES TRIGGERED SIMILAR CHANGES IN GENE EXPRESSION AND CANONICAL PATHWAYS, INCLUDING UPREGULATION OF RIBOSOME-RELATED/TRANSLATIONAL PATHWAYS AND MYELINATION PATHWAYS, AND DOWNREGULATION OF CHROMATIN BINDING AND HISTONE MODIFICATION. IN ADDITION, ANALYSES OF HUB GENES AND UPSTREAM REGULATORY PATHWAYS REVEALED THAT VOLUNTARY ETHANOL CONSUMPTION AFFECTS EPIGENETIC CHANGES VIA HISTONE DEACETYLATION PATHWAYS, OLIGODENDROCYTE AND MYELIN FUNCTION, AND THE OLIGODENDROCYTE-RELATED TRANSCRIPTION FACTOR, SOX17. FURTHERMORE, A VIRAL VECTOR-ASSISTED KNOCKDOWN OF SOX17 GENE EXPRESSION IN THE AMYGDALA PREVENTED A GRADUAL INCREASE IN ALCOHOL CONSUMPTION DURING REPEATED ACCESSES. OVERALL, THESE RESULTS SUGGEST THAT THE EXPRESSION OF OLIGODENDROCYTE-RELATED GENES IN THE AMYGDALA IS SENSITIVE TO VOLUNTARY ALCOHOL DRINKING IN FEMALE MICE. THESE FINDINGS SUGGEST POTENTIAL MOLECULAR TARGETS FOR FUTURE THERAPEUTIC APPROACHES TO PREVENT THE DEVELOPMENT OF AUD, DUE TO REPEATED EXCESSIVE ALCOHOL CONSUMPTION, PARTICULARLY IN WOMEN. 2022 8 3322 25 HISTONE ACETYLTRANSFERASE P300 INDUCES DE NOVO SUPER-ENHANCERS TO DRIVE CELLULAR SENESCENCE. ACCUMULATION OF SENESCENT CELLS DURING AGING CONTRIBUTES TO CHRONIC INFLAMMATION AND AGE-RELATED DISEASES. WHILE SENESCENCE IS ASSOCIATED WITH PROFOUND ALTERATIONS OF THE EPIGENOME, A SYSTEMATIC VIEW OF EPIGENETIC FACTORS IN REGULATING SENESCENCE IS LACKING. HERE, WE CURATED A LIBRARY OF SHORT HAIRPIN RNAS FOR TARGETED SILENCING OF ALL KNOWN EPIGENETIC PROTEINS AND PERFORMED A HIGH-THROUGHPUT SCREEN TO IDENTIFY KEY CANDIDATES WHOSE DOWNREGULATION CAN DELAY REPLICATIVE SENESCENCE OF PRIMARY HUMAN CELLS. THIS SCREEN IDENTIFIED MULTIPLE NEW PLAYERS INCLUDING THE HISTONE ACETYLTRANSFERASE P300 THAT WAS FOUND TO BE A PRIMARY DRIVER OF THE SENESCENT PHENOTYPE. P300, BUT NOT THE PARALOGOUS CBP, INDUCES A DYNAMIC HYPER-ACETYLATED CHROMATIN STATE AND PROMOTES THE FORMATION OF ACTIVE ENHANCER ELEMENTS IN THE NON-CODING GENOME, LEADING TO A SENESCENCE-SPECIFIC GENE EXPRESSION PROGRAM. OUR WORK ILLUSTRATES A CAUSAL ROLE OF HISTONE ACETYLTRANSFERASES AND ACETYLATION IN SENESCENCE AND SUGGESTS P300 AS A POTENTIAL THERAPEUTIC TARGET FOR SENESCENCE AND AGE-RELATED DISEASES. 2019 9 1336 25 DESCRIBING A TRANSCRIPTION FACTOR DEPENDENT REGULATION OF THE MICRORNA TRANSCRIPTOME. WHILE THE TRANSCRIPTION REGULATION OF PROTEIN CODING GENES WAS EXTENSIVELY STUDIED, LITTLE IS KNOWN ON HOW TRANSCRIPTION FACTORS ARE INVOLVED IN TRANSCRIPTION OF NON-CODING RNAS, SPECIFICALLY OF MICRORNAS. HERE, WE PROPOSE A STRATEGY TO STUDY THE POTENTIAL ROLE OF TRANSCRIPTION FACTOR IN REGULATING TRANSCRIPTION OF MICRORNAS USING PUBLICALLY AVAILABLE DATA, COMPUTATIONAL RESOURCES AND HIGH THROUGHPUT DATA. WE USE THE H3K4ME3 EPIGENETIC SIGNATURE TO IDENTIFY MICRORNA PROMOTERS AND CHROMATIN IMMUNOPRECIPITATION (CHIP)-SEQUENCING DATA FROM THE ENCODE PROJECT TO IDENTIFY MICRORNA PROMOTERS THAT ARE ENRICHED WITH TRANSCRIPTION FACTOR BINDING SITES. BY TRANSFECTING CELLS OF INTEREST WITH SHRNA TARGETING A TRANSCRIPTION FACTOR OF INTEREST AND SUBJECTING THE CELLS TO MICRORNA ARRAY, WE STUDY THE EFFECT OF THIS TRANSCRIPTION FACTOR ON THE MICRORNA TRANSCRIPTOME. AS AN ILLUSTRATIVE EXAMPLE WE USE OUR STUDY ON THE EFFECT OF STAT3 ON THE MICRORNA TRANSCRIPTOME OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) CELLS. 2016 10 3375 23 HISTONE POSTTRANSLATIONAL MODIFICATIONS PREDICT SPECIFIC ALTERNATIVE EXON SUBTYPES IN MAMMALIAN BRAIN. A COMPELLING BODY OF LITERATURE, BASED ON NEXT GENERATION CHROMATIN IMMUNOPRECIPITATION AND RNA SEQUENCING OF REWARD BRAIN REGIONS INDICATES THAT THE REGULATION OF THE EPIGENETIC LANDSCAPE LIKELY UNDERLIES CHRONIC DRUG ABUSE AND ADDICTION. IT IS NOW CRITICAL TO DEVELOP HIGHLY INNOVATIVE COMPUTATIONAL STRATEGIES TO REVEAL THE RELEVANT REGULATORY TRANSCRIPTIONAL MECHANISMS THAT MAY UNDERLIE NEUROPSYCHIATRIC DISEASE. WE HAVE ANALYZED CHROMATIN REGULATION OF ALTERNATIVE SPLICING, WHICH IS IMPLICATED IN COCAINE EXPOSURE IN MICE. RECENT LITERATURE HAS DESCRIBED CHROMATIN-REGULATED ALTERNATIVE SPLICING, SUGGESTING A NOVEL FUNCTION FOR DRUG-INDUCED NEUROEPIGENETIC REMODELING. HOWEVER, THE EXTENT OF THE GENOME-WIDE ASSOCIATION BETWEEN PARTICULAR HISTONE MODIFICATIONS AND ALTERNATIVE SPLICING REMAINS UNEXPLORED. TO ADDRESS THIS, WE HAVE DEVELOPED NOVEL COMPUTATIONAL APPROACHES TO MODEL THE ASSOCIATION BETWEEN ALTERNATIVE SPLICING AND HISTONE POSTTRANSLATIONAL MODIFICATIONS IN THE NUCLEUS ACCUMBENS (NAC), A BRAIN REWARD REGION. USING CLASSICAL STATISTICAL METHODS AND MACHINE LEARNING TO COMBINE CHIP-SEQ AND RNA-SEQ DATA, WE FOUND THAT SPECIFIC HISTONE MODIFICATIONS ARE STRONGLY ASSOCIATED WITH VARIOUS ASPECTS OF DIFFERENTIAL SPLICING. H3K36ME3 AND H3K4ME1 HAVE THE STRONGEST ASSOCIATION WITH SPLICING INDICATING THEY PLAY A SIGNIFICANT ROLE IN ALTERNATIVE SPLICING IN BRAIN REWARD TISSUE. 2017 11 1687 25 DRUGS OF ABUSE: EPIGENETIC MECHANISMS IN TOXICITY AND ADDICTION. THE ABUSE OF SUBSTANCES SUCH AS ETHANOL, COCAINE, AMPHETAMINES AND HEROIN IS ASSOCIATED WITH TOXIC EFFECTS ON ALMOST EVERY SYSTEM OF THE ORGANISM. FURTHERMORE, THE TRANSITION FROM OCCASIONAL-RECREATIONAL USE TO CHRONIC ABUSE AND ADDICTION IS A SERIOUS PSYCHIATRIC DISORDER WITH ONLY FEW CHANCES FOR EFFECTIVE AND DEFINITIVE TREATMENT SINCE MOST INDIVIDUALS RELAPSE, EVEN AFTER LONG PERIODS OF ABSTINENCE. IT IS THEREFORE OF UTMOST IMPORTANCE TO ELUCIDATE THE MECHANISMS BY WHICH THESE SUBSTANCES EXERT THEIR TOXICITY AND MEDIATE ADDICTION, IN ORDER TO DEVELOP NEW, EFFICIENT THERAPEUTIC STRATEGIES WITH A LONG-TERM OUTCOME, WHICH ARE CURRENTLY LACKING. WE ALREADY KNOW THAT IN A GREAT NUMBER OF THESE MECHANISMS, ALTERED GENE FUNCTION IS INVOLVED. BUT, WITH THE NEW FIELD OF EPIGENETICS, THERE IS INCREASING EVIDENCE THAT CHANGES IN THE EPIGENOME ARE RESPONSIBLE FOR THE ALTERED GENE FUNCTION. THE ADVANCES IN THE FIELD OF EPIGENETICS TOWARDS ELUCIDATION OF THE MECHANISMS UNDERLYING TOXICITY AND ADDICTION FOR ETHANOL, COCAINE, AMPHETAMINES AND HEROIN ARE CURRENTLY PRESENTED AND DISCUSSED IN THIS REVIEW. 2011 12 2697 22 EX VIVO MODELS OF CHRONIC GRANULOMATOUS DISEASE. INDUCED PLURIPOTENT STEM CELLS (IPSCS) ARE PLURIPOTENT STEM CELLS THAT CAN BE ESTABLISHED FROM DEDIFFERENTIATION OF ALL SOMATIC CELL TYPES BY EPIGENETIC PHENOMENA. IPSCS CAN BE DIFFERENTIATED INTO ANY MATURE CELLS LIKE NEURONS, HEPATOCYTES, OR PANCREATIC CELLS THAT HAVE NOT BEEN EASILY AVAILABLE TO DATE. THUS, IPSCS ARE WIDELY USED FOR DISEASE MODELING, DRUG DISCOVERY, AND CELL THERAPY DEVELOPMENT. HERE, WE DESCRIBE A PROTOCOL TO OBTAIN HUMAN MATURE AND FUNCTIONAL NEUTROPHILS AND MACROPHAGES AS EX VIVO MODELS OF X-LINKED CHRONIC GRANULOMATOUS DISEASE (X-CGD). THIS METHOD CAN BE APPLIED TO MODEL THE OTHER GENETIC FORMS OF CGD. WE ALSO DESCRIBE METHODS FOR TESTING THE CHARACTERISTICS AND FUNCTIONS OF NEUTROPHILS AND MACROPHAGES BY MORPHOLOGY, PHAGOCYTOSIS ASSAY, RELEASE OF GRANULE MARKERS OR CYTOKINES, CELL SURFACE MARKERS, AND NADPH OXIDASE ACTIVITY. 2019 13 661 26 BLOOD MIR-144-3P: A NOVEL DIAGNOSTIC AND THERAPEUTIC TOOL FOR DEPRESSION. MAJOR DEPRESSIVE DISORDER (MDD) IS THE LEADING CAUSE OF DISABILITY WORLDWIDE. THERE IS AN URGENT NEED FOR OBJECTIVE BIOMARKERS TO DIAGNOSE THIS HIGHLY HETEROGENEOUS SYNDROME, ASSIGN TREATMENT, AND EVALUATE TREATMENT RESPONSE AND PROGNOSIS. MICRORNAS (MIRNAS) ARE SHORT NON-CODING RNAS, WHICH ARE DETECTED IN BODY FLUIDS THAT HAVE EMERGED AS POTENTIAL BIOMARKERS OF MANY DISEASE CONDITIONS. THE PRESENT STUDY EXPLORED THE POTENTIAL USE OF MIRNAS AS BIOMARKERS FOR MDD AND ITS TREATMENT. WE PROFILED THE EXPRESSION LEVELS OF CIRCULATING BLOOD MIRNAS FROM MICE THAT WERE COLLECTED BEFORE AND AFTER EXPOSURE TO CHRONIC SOCIAL DEFEAT STRESS (CSDS), AN EXTENSIVELY VALIDATED MOUSE MODEL USED TO STUDY DEPRESSION, AS WELL AS AFTER EITHER REPEATED IMIPRAMINE OR SINGLE-DOSE KETAMINE TREATMENT. WE OBSERVED ROBUST DIFFERENCES IN BLOOD MIRNA SIGNATURES BETWEEN STRESS-RESILIENT AND STRESS-SUSCEPTIBLE MICE AFTER AN INCUBATION PERIOD, BUT NOT IMMEDIATELY AFTER EXPOSURE TO THE STRESS. FURTHERMORE, KETAMINE TREATMENT WAS MORE EFFECTIVE THAN IMIPRAMINE AT RE-ESTABLISHING BASELINE MIRNA EXPRESSION LEVELS, BUT ONLY IN MICE THAT RESPONDED BEHAVIORALLY TO THE DRUG. WE IDENTIFIED THE RED BLOOD CELL-SPECIFIC MIR-144-3P AS A CANDIDATE BIOMARKER TO AID DEPRESSION DIAGNOSIS AND PREDICT KETAMINE TREATMENT RESPONSE IN STRESS-SUSCEPTIBLE MICE AND MDD PATIENTS. LASTLY, WE DEMONSTRATE THAT SYSTEMIC KNOCKDOWN OF MIR-144-3P, VIA SUBCUTANEOUS ADMINISTRATION OF A SPECIFIC ANTAGOMIR, IS SUFFICIENT TO REDUCE THE DEPRESSION-RELATED PHENOTYPE IN STRESS-SUSCEPTIBLE MICE. RNA-SEQUENCING ANALYSIS OF BLOOD AFTER SUCH MIR-144-3P KNOCKDOWN REVEALED A BLUNTED TRANSCRIPTIONAL STRESS SIGNATURE AS WELL. THESE FINDINGS IDENTIFY MIR-144-3P AS A NOVEL TARGET FOR DIAGNOSIS OF MDD AS WELL AS FOR ANTIDEPRESSANT TREATMENT, AND ENHANCE OUR UNDERSTANDING OF EPIGENETIC PROCESSES ASSOCIATED WITH DEPRESSION. 2022 14 6540 32 TRANSCRIPTIONAL, EPIGENETIC, AND FUNCTIONAL REPROGRAMMING OF MONOCYTES FROM NON-HUMAN PRIMATES FOLLOWING CHRONIC ALCOHOL DRINKING. CHRONIC HEAVY DRINKING (CHD) OF ALCOHOL IS A KNOWN RISK FACTOR FOR INCREASED SUSCEPTIBILITY TO BACTERIAL AND VIRAL INFECTION AS WELL AS IMPAIRED WOUND HEALING. EVIDENCE SUGGESTS THAT THESE DEFECTS ARE MEDIATED BY A DYSREGULATED INFLAMMATORY RESPONSE ORIGINATING FROM MYELOID CELLS, NOTABLY MONOCYTES AND MACROPHAGES, BUT THE MECHANISMS REMAIN POORLY UNDERSTOOD. OUR ABILITY TO STUDY CHD IS IMPACTED BY THE COMPLEXITIES OF HUMAN DRINKING PATTERNS AND BEHAVIOR AS WELL AS COMORBIDITIES AND CONFOUNDING RISK FACTORS FOR PATIENTS WITH ALCOHOL USE DISORDERS. TO OVERCOME THESE CHALLENGES, WE UTILIZED A TRANSLATIONAL RHESUS MACAQUE MODEL OF VOLUNTARY ETHANOL SELF-ADMINISTRATION THAT CLOSELY RECAPITULATES HUMAN DRINKING PATTERNS AND CHRONICITY. IN THIS STUDY, WE EXAMINED THE EFFECTS OF CHD ON BLOOD MONOCYTES IN CONTROL AND CHD FEMALE MACAQUES AFTER 12 MONTHS OF DAILY ETHANOL CONSUMPTION. WHILE MONOCYTES FROM CHD FEMALE MACAQUES GENERATED A HYPER-INFLAMMATORY RESPONSE TO EX VIVO LPS STIMULATION, THEIR RESPONSE TO E. COLI WAS DAMPENED. IN DEPTH SCRNA-SEQ ANALYSIS OF PURIFIED MONOCYTES REVEALED SIGNIFICANT SHIFTS IN CLASSICAL MONOCYTE SUBSETS WITH ACCUMULATION OF CELLS EXPRESSING MARKERS OF HYPOXIA (HIF1A) AND INFLAMMATION (NFKB SIGNALING PATHWAY) IN CHD MACAQUES. THE INCREASED PRESENCE OF MONOCYTE SUBSETS SKEWED TOWARDS INFLAMMATORY PHENOTYPES WAS COMPLEMENTED BY EPIGENETIC ANALYSIS, WHICH REVEALED HIGHER ACCESSIBILITY OF PROMOTER REGIONS THAT REGULATE GENES INVOLVED IN CYTOKINE SIGNALING PATHWAYS. COLLECTIVELY, DATA PRESENTED IN THIS MANUSCRIPT DEMONSTRATE THAT CHD SHIFTS CLASSICAL MONOCYTE SUBSET COMPOSITION AND PRIMES THE MONOCYTES TOWARDS A MORE HYPER-INFLAMMATORY RESPONSE TO LPS, BUT COMPROMISED PATHOGEN RESPONSE. 2021 15 976 24 CHRONIC OPIOID USE IS ASSOCIATED WITH INCREASED DNA METHYLATION CORRELATING WITH INCREASED CLINICAL PAIN. ENVIRONMENTALLY CAUSED CHANGES IN CHROMOSOMES THAT DO NOT ALTER THE DNA SEQUENCE BUT CAUSE PHENOTYPIC CHANGES BY ALTERING GENE TRANSCRIPTION ARE SUMMARIZED AS EPIGENETICS. A MAJOR EPIGENETIC MECHANISM IS METHYLATION OR DEMETHYLATION AT CPG-RICH DNA ISLANDS. DNA METHYLATION TRIGGERED BY DRUGS HAS LARGELY UNEXPLORED THERAPEUTIC CONSEQUENCES. HERE WE REPORT INCREASED METHYLATION AT A CPG RICH ISLAND IN THE OPRM1 GENE CODING FOR MU-OPIOID RECEPTORS AND AT A GLOBAL METHYLATION SITE (LINE-1) IN LEUKOCYTES OF METHADONE-SUBSTITUTED FORMER OPIATE ADDICTS COMPARED WITH MATCHED HEALTHY CONTROLS. HIGHER DNA METHYLATION ASSOCIATED WITH CHRONIC OPIOID EXPOSURE WAS REPRODUCED IN AN INDEPENDENT COHORT OF OPIOID-TREATED AS COMPARED TO NON-OPIOID-TREATED PAIN PATIENTS. THIS SUGGESTS THAT OPIOIDS MAY STIMULATE DNA METHYLATION. THE OPRM1 METHYLATION HAD NO IMMEDIATE EFFECT ON MU-OPIOID RECEPTOR TRANSCRIPTION AND WAS NOT ASSOCIATED WITH OPIOID DOSING REQUIREMENTS. HOWEVER, THE GLOBAL DNA METHYLATION AT LINE-1 WAS SIGNIFICANTLY CORRELATED WITH INCREASED CHRONIC PAIN. THIS SUGGESTS INHIBITORY EFFECTS ON THE TRANSCRIPTION OF STILL UNSPECIFIED NOCIFENSIVE GENE PRODUCTS. IT FURTHER IMPLIES THAT OPIOIDS MAY BE CAUSALLY ASSOCIATED WITH INCREASED GENOME-WIDE DNA METHYLATION, ALTHOUGH CURRENTLY THERE IS NO DIRECT EVIDENCE OF THIS. THIS HAS PHENOTYPIC CONSEQUENCES FOR PAIN AND MAY PROVIDE A NEW, EPIGENETICS-ASSOCIATED MECHANISM OF OPIOID-INDUCED HYPERALGESIA. THE RESULTS INDICATE A POTENTIAL INFLUENCE OF OPIOID ANALGESICS ON THE PATIENTS' EPIGENOME. THEY EMPHASIZE THE NEED FOR RELIABLE AND COST-EFFECTIVE SCREENING TOOLS AND MAY IMPLY THAT HIGH-THROUGHPUT SCREENING FOR LEAD COMPOUNDS IN ARTIFICIAL EXPRESSION SYSTEMS MAY NOT PROVIDE THE BEST TOOLS FOR IDENTIFYING NEW PAIN MEDICATIONS. 2013 16 1314 28 DELINEATING CONDITIONS AND SUBTYPES IN CHRONIC PAIN USING NEUROIMAGING. DIFFERENTIATING SUBTYPES OF CHRONIC PAIN STILL REMAINS A CHALLENGE-BOTH FROM A SUBJECTIVE AND OBJECTIVE POINT OF VIEW. PERSONALIZED MEDICINE IS THE CURRENT GOAL OF MODERN MEDICAL CARE AND IS LIMITED BY THE SUBJECTIVE NATURE OF PATIENT SELF-REPORTING OF SYMPTOMS AND BEHAVIORAL EVALUATION. PHYSIOLOGY-FOCUSED TECHNIQUES SUCH AS GENOME AND EPIGENETIC ANALYSES INFORM THE DELINEATION OF PAIN GROUPS; HOWEVER, EXCEPT UNDER RARE CIRCUMSTANCES, THEY HAVE DILUTED EFFECTS THAT AGAIN, SHARE A COMMON RELIANCE ON BEHAVIORAL EVALUATION. THE APPLICATION OF STRUCTURAL NEUROIMAGING TOWARDS DISTINGUISHING PAIN SUBTYPES IS A GROWING FIELD AND MAY INFORM PAIN-GROUP CLASSIFICATION THROUGH THE ANALYSIS OF BRAIN REGIONS SHOWING HYPERTROPHIC AND ATROPHIC CHANGES IN THE PRESENCE OF PAIN. ANALYTICAL TECHNIQUES SUCH AS MACHINE-LEARNING CLASSIFIERS HAVE THE CAPACITY TO PROCESS LARGE VOLUMES OF DATA AND DELINEATE DIAGNOSTICALLY RELEVANT INFORMATION FROM NEUROIMAGING ANALYSIS. THE ISSUE OF DEFINING A "BRAIN TYPE" IS AN EMERGING FIELD AIMED AT INTERPRETING OBSERVED BRAIN CHANGES AND DELINEATING THEIR CLINICAL IDENTITY/SIGNIFICANCE. IN THIS REVIEW, 2 CHRONIC PAIN CONDITIONS (MIGRAINE AND IRRITABLE BOWEL SYNDROME) WITH SIMILAR CLINICAL PHENOTYPES ARE COMPARED IN TERMS OF THEIR STRUCTURAL NEUROIMAGING FINDINGS. INDEPENDENT INVESTIGATIONS ARE COMPARED WITH FINDINGS FROM APPLICATION OF MACHINE-LEARNING ALGORITHMS. FINDINGS ARE DISCUSSED IN TERMS OF DIFFERENTIATING PATIENT SUBGROUPS USING NEUROIMAGING DATA IN PATIENTS WITH CHRONIC PAIN AND HOW THEY MAY BE APPLIED TOWARDS DEFINING A PERSONALIZED PAIN SIGNATURE THAT HELPS SEGREGATE PATIENT SUBGROUPS (EG, MIGRAINE WITH AND WITHOUT AURA, WITH OR WITHOUT NAUSEA; IRRITABLE BOWEL SYNDROME VS OTHER FUNCTIONAL GASTROINTESTINAL DISORDERS). 2019 17 883 32 CHRONIC COCAINE-REGULATED EPIGENOMIC CHANGES IN MOUSE NUCLEUS ACCUMBENS. BACKGROUND: INCREASING EVIDENCE SUPPORTS A ROLE FOR ALTERED GENE EXPRESSION IN MEDIATING THE LASTING EFFECTS OF COCAINE ON THE BRAIN, AND RECENT WORK HAS DEMONSTRATED THE INVOLVEMENT OF CHROMATIN MODIFICATIONS IN THESE ALTERATIONS. HOWEVER, ALL SUCH STUDIES TO DATE HAVE BEEN RESTRICTED BY THEIR RELIANCE ON MICROARRAY TECHNOLOGIES THAT HAVE INTRINSIC LIMITATIONS. RESULTS: WE USE NEXT GENERATION SEQUENCING METHODS, RNA-SEQ AND CHIP-SEQ FOR RNA POLYMERASE II AND SEVERAL HISTONE METHYLATION MARKS, TO OBTAIN A MORE COMPLETE VIEW OF COCAINE-INDUCED CHANGES IN GENE EXPRESSION AND ASSOCIATED ADAPTATIONS IN NUMEROUS MODES OF CHROMATIN REGULATION IN THE MOUSE NUCLEUS ACCUMBENS, A KEY BRAIN REWARD REGION. WE DEMONSTRATE AN UNEXPECTEDLY LARGE NUMBER OF PRE-MRNA SPLICING ALTERATIONS IN RESPONSE TO REPEATED COCAINE TREATMENT. IN ADDITION, WE IDENTIFY COMBINATIONS OF CHROMATIN CHANGES, OR SIGNATURES, THAT CORRELATE WITH COCAINE-DEPENDENT REGULATION OF GENE EXPRESSION, INCLUDING THOSE INVOLVING PRE-MRNA ALTERNATIVE SPLICING. THROUGH BIOINFORMATIC PREDICTION AND BIOLOGICAL VALIDATION, WE IDENTIFY ONE PARTICULAR SPLICING FACTOR, A2BP1(RBFOX1/FOX-1), WHICH IS ENRICHED AT GENES THAT DISPLAY CERTAIN CHROMATIN SIGNATURES AND CONTRIBUTES TO DRUG-INDUCED BEHAVIORAL ABNORMALITIES. TOGETHER, THIS DELINEATION OF THE COCAINE-INDUCED EPIGENOME IN THE NUCLEUS ACCUMBENS REVEALS SEVERAL NOVEL MODES OF REGULATION BY WHICH COCAINE ALTERS THE BRAIN. CONCLUSIONS: WE ESTABLISH COMBINATORIAL CHROMATIN AND TRANSCRIPTIONAL PROFILES IN MOUSE NUCLEUS ACCUMBENS AFTER REPEATED COCAINE TREATMENT. THESE RESULTS SERVE AS AN IMPORTANT RESOURCE FOR THE FIELD AND PROVIDE A TEMPLATE FOR THE ANALYSIS OF OTHER SYSTEMS TO REVEAL NEW TRANSCRIPTIONAL AND EPIGENETIC MECHANISMS OF NEURONAL REGULATION. 2014 18 5058 37 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 19 2303 27 EPIGENETIC REGULATION OF CANNABINOID-MEDIATED ATTENUATION OF INFLAMMATION AND ITS IMPACT ON THE USE OF CANNABINOIDS TO TREAT AUTOIMMUNE DISEASES. CHRONIC INFLAMMATION IS CONSIDERED TO BE A SILENT KILLER BECAUSE IT IS THE UNDERLYING CAUSE OF A WIDE RANGE OF CLINICAL DISORDERS, FROM CARDIOVASCULAR TO NEUROLOGICAL DISEASES, AND FROM CANCER TO OBESITY. IN ADDITION, THERE ARE OVER 80 DIFFERENT TYPES OF DEBILITATING AUTOIMMUNE DISEASES FOR WHICH THERE ARE NO CURE. CURRENTLY, THE DRUGS THAT ARE AVAILABLE TO SUPPRESS CHRONIC INFLAMMATION ARE EITHER INEFFECTIVE OR OVERTLY SUPPRESS THE INFLAMMATION, THEREBY CAUSING INCREASED SUSCEPTIBILITY TO INFECTIONS AND CANCER. THUS, THE DEVELOPMENT OF A NEW CLASS OF DRUGS THAT CAN SUPPRESS CHRONIC INFLAMMATION IS IMPERATIVE. CANNABINOIDS ARE A GROUP OF COMPOUNDS PRODUCED IN THE BODY (ENDOCANNABINOIDS) OR FOUND IN CANNABIS (PHYTOCANNABINOIDS) THAT ACT THROUGH CANNABINOID RECEPTORS AND VARIOUS OTHER RECEPTORS EXPRESSED WIDELY IN THE BRAIN AND IMMUNE SYSTEM. IN THE LAST DECADE, CANNABINOIDS HAVE BEEN WELL ESTABLISHED EXPERIMENTALLY TO MEDIATE ANTI-INFLAMMATORY PROPERTIES. RESEARCH HAS SHOWN THAT THEY SUPPRESS INFLAMMATION THROUGH MULTIPLE PATHWAYS, INCLUDING APOPTOSIS AND INDUCING IMMUNOSUPPRESSIVE T REGULATORY CELLS (TREGS) AND MYELOID-DERIVED SUPPRESSOR CELLS (MDSCS). INTERESTINGLY, CANNABINOIDS ALSO MEDIATE EPIGENETIC ALTERATIONS IN GENES THAT REGULATE INFLAMMATION. IN THE CURRENT REVIEW, WE HIGHLIGHT HOW THE EPIGENETIC MODULATIONS CAUSED BY CANNABINOIDS LEAD TO THE SUPPRESSION OF INFLAMMATION AND HELP IDENTIFY NOVEL PATHWAYS THAT CAN BE USED TO TARGET AUTOIMMUNE DISEASES. 2021 20 1301 23 DEEP SEQUENCING REVEALS INCREASED DNA METHYLATION IN CHRONIC RAT EPILEPSY. EPILEPSY IS A FREQUENT NEUROLOGICAL DISORDER, ALTHOUGH ONSET AND PROGRESSION OF SEIZURES REMAIN DIFFICULT TO PREDICT IN AFFECTED PATIENTS, IRRESPECTIVE OF THEIR EPILEPTOGENIC CONDITION. PREVIOUS STUDIES IN ANIMAL MODELS AS WELL AS HUMAN EPILEPTIC BRAIN TISSUE REVEALED A REMARKABLY DIVERSE PATTERN OF GENE EXPRESSION IMPLICATING EPIGENETIC CHANGES TO CONTRIBUTE TO DISEASE PROGRESSION. HERE WE MAPPED FOR THE FIRST TIME GLOBAL DNA METHYLATION PATTERNS IN CHRONIC EPILEPTIC RATS AND CONTROLS. USING METHYL-CPG CAPTURE ASSOCIATED WITH MASSIVE PARALLEL SEQUENCING (METHYL-SEQ) WE REPORT THE GENOMIC METHYLATION SIGNATURE OF THE CHRONIC EPILEPTIC STATE. WE OBSERVED A PREDOMINANT INCREASE, RATHER THAN LOSS OF DNA METHYLATION IN CHRONIC RAT EPILEPSY. ABERRANT METHYLATION PATTERNS WERE INVERSELY CORRELATED WITH GENE EXPRESSION CHANGES USING MRNA SEQUENCING FROM SAME ANIMALS AND TISSUE SPECIMENS. ADMINISTRATION OF A KETOGENIC, HIGH-FAT, LOW-CARBOHYDRATE DIET ATTENUATED SEIZURE PROGRESSION AND AMELIORATED DNA METHYLATION MEDIATED CHANGES IN GENE EXPRESSION. THIS IS THE FIRST REPORT OF UNSUPERVISED CLUSTERING OF AN EPIGENETIC MARK BEING USED IN EPILEPSY RESEARCH TO SEPARATE EPILEPTIC FROM NON-EPILEPTIC ANIMALS AS WELL AS FROM ANIMALS RECEIVING ANTI-CONVULSIVE DIETARY TREATMENT. WE FURTHER DISCUSS THE POTENTIAL IMPACT OF EPIGENETIC CHANGES AS A PATHOGENIC MECHANISM OF EPILEPTOGENESIS. 2013