1 124 157 A SYSTEMS APPROACH DELIVERS A FUNCTIONAL MICRORNA CATALOG AND EXPANDED TARGETS FOR SEIZURE SUPPRESSION IN TEMPORAL LOBE EPILEPSY. TEMPORAL LOBE EPILEPSY IS THE MOST COMMON DRUG-RESISTANT FORM OF EPILEPSY IN ADULTS. THE REORGANIZATION OF NEURAL NETWORKS AND THE GENE EXPRESSION LANDSCAPE UNDERLYING PATHOPHYSIOLOGIC NETWORK BEHAVIOR IN BRAIN STRUCTURES SUCH AS THE HIPPOCAMPUS HAS BEEN SUGGESTED TO BE CONTROLLED, IN PART, BY MICRORNAS. TO SYSTEMATICALLY ASSESS THEIR SIGNIFICANCE, WE SEQUENCED ARGONAUTE-LOADED MICRORNAS TO DEFINE FUNCTIONALLY ENGAGED MICRORNAS IN THE HIPPOCAMPUS OF THREE DIFFERENT ANIMAL MODELS IN TWO SPECIES AND AT SIX TIME POINTS BETWEEN THE INITIAL PRECIPITATING INSULT THROUGH TO THE ESTABLISHMENT OF CHRONIC EPILEPSY. WE THEN SELECTED COMMONLY UP-REGULATED MICRORNAS FOR A FUNCTIONAL IN VIVO THERAPEUTIC SCREEN USING OLIGONUCLEOTIDE INHIBITORS. ARGONAUTE SEQUENCING GENERATED 1.44 BILLION SMALL RNA READS OF WHICH UP TO 82% WERE MICRORNAS, WITH OVER 400 UNIQUE MICRORNAS DETECTED PER MODEL. APPROXIMATELY HALF OF THE DETECTED MICRORNAS WERE DYSREGULATED IN EACH EPILEPSY MODEL. WE PRIORITIZED COMMONLY UP-REGULATED MICRORNAS THAT WERE FULLY CONSERVED IN HUMANS AND DESIGNED CUSTOM ANTISENSE OLIGONUCLEOTIDES FOR THESE CANDIDATE TARGETS. ANTISEIZURE PHENOTYPES WERE OBSERVED UPON KNOCKDOWN OF MIR-10A-5P, MIR-21A-5P, AND MIR-142A-5P AND ELECTROPHYSIOLOGICAL ANALYSES INDICATED BROAD SAFETY OF THIS APPROACH. COMBINED INHIBITION OF THESE THREE MICRORNAS REDUCED SPONTANEOUS SEIZURES IN EPILEPTIC MICE. PROTEOMIC DATA, RNA SEQUENCING, AND PATHWAY ANALYSIS ON PREDICTED AND VALIDATED TARGETS OF THESE MICRORNAS IMPLICATED DEREPRESSED TGF-BETA SIGNALING AS A SHARED SEIZURE-MODIFYING MECHANISM. CORRESPONDINGLY, INHIBITION OF TGF-BETA SIGNALING OCCLUDED THE ANTISEIZURE EFFECTS OF THE ANTAGOMIRS. TOGETHER, THESE RESULTS IDENTIFY SHARED, DYSREGULATED, AND FUNCTIONALLY ACTIVE MICRORNAS DURING THE PATHOGENESIS OF EPILEPSY WHICH REPRESENT THERAPEUTIC ANTISEIZURE TARGETS. 2020 2 2455 27 EPIGENETIC TARGETS FOR NOVEL THERAPIES OF LUNG DISEASES. IN SPITE OF SUBSTANTIAL ADVANCES IN DEFINING THE IMMUNOBIOLOGY AND FUNCTION OF STRUCTURAL CELLS IN LUNG DISEASES THERE IS STILL INSUFFICIENT KNOWLEDGE TO DEVELOP FUNDAMENTALLY NEW CLASSES OF DRUGS TO TREAT MANY LUNG DISEASES. FOR EXAMPLE, THERE IS A COMPELLING NEED FOR NEW THERAPEUTIC APPROACHES TO ADDRESS SEVERE PERSISTENT ASTHMA THAT IS INSENSITIVE TO INHALED CORTICOSTEROIDS. ALTHOUGH THE PREVALENCE OF STEROID-RESISTANT ASTHMA IS 5-10%, SEVERE ASTHMATICS REQUIRE A DISPROPORTIONATE LEVEL OF HEALTH CARE SPENDING AND CONSTITUTE A MAJORITY OF FATAL ASTHMA EPISODES. NONE OF THE ESTABLISHED DRUG THERAPIES INCLUDING LONG-ACTING BETA AGONISTS OR INHALED CORTICOSTEROIDS REVERSE ESTABLISHED AIRWAY REMODELING. OBSTRUCTIVE AIRWAYS REMODELING IN PATIENTS WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD), RESTRICTIVE REMODELING IN IDIOPATHIC PULMONARY FIBROSIS (IPF) AND OCCLUSIVE VASCULAR REMODELING IN PULMONARY HYPERTENSION ARE SIMILARLY UNRESPONSIVE TO CURRENT DRUG THERAPY. THEREFORE, DRUGS ARE NEEDED TO ACHIEVE LONG-ACTING SUPPRESSION AND REVERSAL OF PATHOLOGICAL AIRWAY AND VASCULAR REMODELING. NOVEL DRUG CLASSES ARE EMERGING FROM ADVANCES IN EPIGENETICS. NOVEL MECHANISMS ARE EMERGING BY WHICH CELLS ADAPT TO ENVIRONMENTAL CUES, WHICH INCLUDE CHANGES IN DNA METHYLATION, HISTONE MODIFICATIONS AND REGULATION OF TRANSCRIPTION AND TRANSLATION BY NONCODING RNAS. IN THIS REVIEW WE WILL SUMMARIZE CURRENT EPIGENETIC APPROACHES BEING APPLIED TO PRECLINICAL DRUG DEVELOPMENT ADDRESSING IMPORTANT THERAPEUTIC CHALLENGES IN LUNG DISEASES. THESE CHALLENGES ARE BEING ADDRESSED BY ADVANCES IN LUNG DELIVERY OF OLIGONUCLEOTIDES AND SMALL MOLECULES THAT MODIFY THE HISTONE CODE, DNA METHYLATION PATTERNS AND MIRNA FUNCTION. 2015 3 3493 40 IDENTIFICATION OF KEY GENES, PATHWAYS, AND MIRNA/MRNA REGULATORY NETWORKS OF CUMS-INDUCED DEPRESSION IN NUCLEUS ACCUMBENS BY INTEGRATED BIOINFORMATICS ANALYSIS. INTRODUCTION: MAJOR DEPRESSIVE DISORDER (MDD) IS A RECURRENT, DEVASTATING MENTAL DISORDER, WHICH AFFECTS >350 MILLION PEOPLE WORLDWIDE, AND EXERTS SUBSTANTIAL PUBLIC HEALTH AND FINANCIAL COSTS TO SOCIETY. THUS, THERE IS A SIGNIFICANT NEED TO DISCOVER INNOVATIVE THERAPEUTICS TO TREAT DEPRESSION EFFICIENTLY. STRESS-INDUCED DYSFUNCTION IN THE SUBTYPE OF NEURONAL CELLS AND THE CHANGE OF SYNAPTIC PLASTICITY AND STRUCTURAL PLASTICITY OF NUCLEUS ACCUMBENS (NAC) ARE IMPLICATED IN DEPRESSION SYMPTOMOLOGY. HOWEVER, THE MOLECULAR AND EPIGENETIC MECHANISMS AND STRESSES TO THE NAC PATHOLOGICAL CHANGES IN DEPRESSION REMAIN ELUSIVE. MATERIALS AND METHODS: IN THIS STUDY, TREATMENT GROUP MICE WERE TREATED CONTINUALLY WITH THE CHRONIC UNPREDICTABLE MILD STRESS (CUMS) UNTIL EXPRESSION OF DEPRESSION-LIKE BEHAVIORS WERE FOUND. DEPRESSION WAS CONFIRMED WITH SUCROSE PREFERENCE, NOVELTY-SUPPRESSED FEEDING, FORCED SWIMMING, AND TAIL SUSPENSION TESTS. WE APPLIED HIGH-THROUGHPUT RNA SEQUENCING TO ASSESS MICRORNA EXPRESSION AND TRANSCRIPTIONAL PROFILES IN THE NAC TISSUE FROM DEPRESSION-LIKE BEHAVIORS MICE AND CONTROL MICE. THE REGULATORY NETWORK OF MIRNAS/MRNAS WAS CONSTRUCTED BASED ON THE HIGH-THROUGHPUT RNA SEQUENCE AND BIOINFORMATICS SOFTWARE PREDICTIONS. RESULTS: A TOTAL OF 17 MIRNAS AND 10 MRNAS WERE SIGNIFICANTLY UPREGULATED IN THE NAC OF CUMS-INDUCED MICE WITH DEPRESSION-LIKE BEHAVIORS, AND 12 MIRNAS AND 29 MRNAS WERE DOWNREGULATED. A SERIES OF BIOINFORMATICS ANALYSES SHOWED THAT THESE ALTERED MIRNAS PREDICTED TARGET MRNA AND DIFFERENTIALLY EXPRESSED MRNAS WERE SIGNIFICANTLY ENRICHED IN THE MAPK SIGNALING PATHWAY, GABAERGIC SYNAPSE, DOPAMINERGIC SYNAPSE, CYTOKINE-CYTOKINE RECEPTOR INTERACTION, AXON GUIDANCE, REGULATION OF AUTOPHAGY, AND SO ON. FURTHERMORE, DUAL LUCIFERASE REPORT ASSAY AND QRT-PCR RESULTS VALIDATED THE MIRNA/MRNA REGULATORY NETWORK. CONCLUSION: THE DETERIORATIONS OF GABAERGIC SYNAPSES, DOPAMINERGIC SYNAPSES, NEUROTRANSMITTER SYNTHESIS, AS WELL AS AUTOPHAGY-ASSOCIATED APOPTOTIC PATHWAY ARE ASSOCIATED WITH THE MOLECULAR PATHOLOGICAL MECHANISM OF CUMS-INDUCED DEPRESSION. 2019 4 4015 41 LOW-DOSE EXPOSURE TO BISPHENOLS A, F AND S OF HUMAN PRIMARY ADIPOCYTE IMPACTS CODING AND NON-CODING RNA PROFILES. BISPHENOL A (BPA) EXPOSURE HAS BEEN SUSPECTED TO BE ASSOCIATED WITH DELETERIOUS EFFECTS ON HEALTH INCLUDING OBESITY AND METABOLICALLY-LINKED DISEASES. ALTHOUGH BISPHENOLS F (BPF) AND S (BPS) ARE BPA STRUCTURAL ANALOGS COMMONLY USED IN MANY MARKETED PRODUCTS AS A REPLACEMENT FOR BPA, ONLY SPARSE TOXICOLOGICAL DATA ARE AVAILABLE YET. OUR OBJECTIVE WAS TO COMPREHENSIVELY CHARACTERIZE BISPHENOLS GENE TARGETS IN A HUMAN PRIMARY ADIPOCYTE MODEL, IN ORDER TO DETERMINE WHETHER THEY MAY INDUCE CELLULAR DYSFUNCTION, USING CHRONIC EXPOSURE AT TWO CONCENTRATIONS: A "LOW-DOSE" SIMILAR TO THE DOSE USUALLY ENCOUNTERED IN HUMAN BIOLOGICAL FLUIDS AND A HIGHER DOSE. THEREFORE, BPA, BPF AND BPS HAVE BEEN ADDED AT 10 NM OR 10 MUM DURING THE DIFFERENTIATION OF HUMAN PRIMARY ADIPOCYTES FROM SUBCUTANEOUS FAT OF THREE NON-DIABETIC CAUCASIAN FEMALE PATIENTS. GENE EXPRESSION (MRNA/LNCRNA) ARRAYS AND MICRORNA ARRAYS, HAVE BEEN USED TO ASSESS CODING AND NON-CODING RNA CHANGES. WE DETECTED SIGNIFICANTLY DEREGULATED MRNA/LNCRNA AND MIRNA AT LOW AND HIGH DOSES. ENRICHMENT IN "CANCER" AND "ORGANISMAL INJURY AND ABNORMALITIES" RELATED PATHWAYS WAS FOUND IN RESPONSE TO THE THREE PRODUCTS. SOME LONG INTERGENIC NON-CODING RNAS AND SMALL NUCLEOLAR RNAS WERE DIFFERENTIALLY EXPRESSED SUGGESTING THAT BISPHENOLS MAY ALSO ACTIVATE MULTIPLE CELLULAR PROCESSES AND EPIGENETIC MODIFICATIONS. THE ANALYSIS OF UPSTREAM REGULATORS OF DEREGULATED GENES HIGHLIGHTED HORMONES OR HORMONE-LIKE CHEMICALS SUGGESTING THAT BPS AND BPF CAN BE SUSPECTED TO INTERFERE, JUST LIKE BPA, WITH HORMONAL REGULATION AND HAVE TO BE CONSIDERED AS ENDOCRINE DISRUPTORS. ALL THESE RESULTS SUGGEST THAT AS BPA, ITS SUBSTITUTES BPS AND BPF SHOULD BE USED WITH THE SAME RESTRICTIONS. 2017 5 6449 34 THERAPEUTIC TARGETING OF TELOMERASE. TELOMERE LENGTH AND CELL FUNCTION CAN BE PRESERVED BY THE HUMAN REVERSE TRANSCRIPTASE TELOMERASE (HTERT), WHICH SYNTHESIZES THE NEW TELOMERIC DNA FROM A RNA TEMPLATE, BUT IS NORMALLY RESTRICTED TO CELLS NEEDING A HIGH PROLIFERATIVE CAPACITY, SUCH AS STEM CELLS. CONSEQUENTLY, TELOMERASE-BASED THERAPIES TO ELONGATE SHORT TELOMERES ARE DEVELOPED, SOME OF WHICH HAVE SUCCESSFULLY REACHED THE STAGE I IN CLINICAL TRIALS. TELOMERASE IS ALSO PERMISSIVE FOR TUMORIGENESIS AND 90% OF ALL MALIGNANT TUMORS USE TELOMERASE TO OBTAIN IMMORTALITY. THUS, REVERSAL OF TELOMERASE UPREGULATION IN TUMOR CELLS IS A POTENTIAL STRATEGY TO TREAT CANCER. NATURAL AND SMALL-MOLECULE TELOMERASE INHIBITORS, IMMUNOTHERAPEUTIC APPROACHES, OLIGONUCLEOTIDE INHIBITORS, AND TELOMERASE-DIRECTED GENE THERAPY ARE USEFUL TREATMENT STRATEGIES. TELOMERASE IS MORE WIDELY EXPRESSED THAN ANY OTHER TUMOR MARKER. THE LOW EXPRESSION IN NORMAL TISSUES, TOGETHER WITH THE LONGER TELOMERES IN NORMAL STEM CELLS VERSUS CANCER CELLS, PROVIDES SOME DEGREE OF SPECIFICITY WITH LOW RISK OF TOXICITY. HOWEVER, LONG TERM TELOMERASE INHIBITION MAY ELICIT NEGATIVE EFFECTS IN HIGHLY-PROLIFERATIVE CELLS WHICH NEED TELOMERASE FOR SURVIVAL, AND IT MAY INTERFERE WITH TELOMERE-INDEPENDENT PHYSIOLOGICAL FUNCTIONS. MOREOVER, ONLY A FEW HTERT MOLECULES ARE REQUIRED TO OVERCOME SENESCENCE IN CANCER CELLS, AND TELOMERASE INHIBITION REQUIRES PROLIFERATING CELLS OVER A SUFFICIENT NUMBER OF POPULATION DOUBLINGS TO INDUCE TUMOR SUPPRESSIVE SENESCENCE. THESE LIMITATIONS MAY EXPLAIN THE MODERATE SUCCESS RATES IN MANY CLINICAL STUDIES. DESPITE EXTENSIVE STUDIES, ONLY ONE VACCINE AND ONE TELOMERASE ANTAGONIST ARE ROUTINELY USED IN CLINICAL WORK. FOR COMPLETE ERADICATION OF ALL SUBPOPULATIONS OF CANCER CELLS A SIMULTANEOUS TARGETING OF SEVERAL MECHANISMS WILL LIKELY BE NEEDED. POSSIBLE TECHNICAL IMPROVEMENTS HAVE BEEN PROPOSED INCLUDING THE DEVELOPMENT OF MORE SPECIFIC INHIBITORS, METHODS TO INCREASE THE EFFICACY OF VACCINATION METHODS, AND PERSONALIZED APPROACHES. TELOMERASE ACTIVATION AND CELL REJUVENATION IS SUCCESSFULLY USED IN REGENERATIVE MEDICINE FOR TISSUE ENGINEERING AND RECONSTRUCTIVE SURGERY. HOWEVER, THERE ARE ALSO A NUMBER OF PITFALLS IN THE TREATMENT WITH TELOMERASE ACTIVATING PROCEDURES FOR THE WHOLE ORGANISM AND FOR LONGER PERIODS OF TIME. EXTENDED CELL LIFESPAN MAY ACCUMULATE RARE GENETIC AND EPIGENETIC ABERRATIONS THAT CAN CONTRIBUTE TO MALIGNANT TRANSFORMATION. THEREFORE, NOVEL VECTOR SYSTEMS HAVE BEEN DEVELOPED FOR A 'MILD' INTEGRATION OF TELOMERASE INTO THE HOST GENOME AND LOSS OF THE VECTOR IN RAPIDLY-PROLIFERATING CELLS. IT IS CURRENTLY UNCLEAR IF THIS TECHNIQUE CAN ALSO BE USED IN HUMAN BEINGS TO TREAT CHRONIC DISEASES, SUCH AS ATHEROSCLEROSIS. 2016 6 1102 30 COMBINED CHEMOSENSITIVITY AND CHROMATIN PROFILING PRIORITIZES DRUG COMBINATIONS IN CLL. THE BRUTON TYROSINE KINASE (BTK) INHIBITOR IBRUTINIB HAS SUBSTANTIALLY IMPROVED THERAPEUTIC OPTIONS FOR CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). ALTHOUGH IBRUTINIB IS NOT CURATIVE, IT HAS A PROFOUND EFFECT ON CLL CELLS AND MAY CREATE NEW PHARMACOLOGICALLY EXPLOITABLE VULNERABILITIES. TO IDENTIFY SUCH VULNERABILITIES, WE DEVELOPED A SYSTEMATIC APPROACH THAT COMBINES EPIGENOME PROFILING (CHARTING THE GENE-REGULATORY BASIS OF CELL STATE) WITH SINGLE-CELL CHEMOSENSITIVITY PROFILING (QUANTIFYING CELL-TYPE-SPECIFIC DRUG RESPONSE) AND BIOINFORMATIC DATA INTEGRATION. BY APPLYING OUR METHOD TO A COHORT OF MATCHED PATIENT SAMPLES COLLECTED BEFORE AND DURING IBRUTINIB THERAPY, WE IDENTIFIED CHARACTERISTIC IBRUTINIB-INDUCED CHANGES THAT PROVIDE A STARTING POINT FOR THE RATIONAL DESIGN OF IBRUTINIB COMBINATION THERAPIES. SPECIFICALLY, WE OBSERVED AND VALIDATED PREFERENTIAL SENSITIVITY TO PROTEASOME, PLK1, AND MTOR INHIBITORS DURING IBRUTINIB TREATMENT. MORE GENERALLY, OUR STUDY ESTABLISHES A BROADLY APPLICABLE METHOD FOR INVESTIGATING TREATMENT-SPECIFIC VULNERABILITIES BY INTEGRATING THE COMPLEMENTARY PERSPECTIVES OF EPIGENETIC CELL STATES AND PHENOTYPIC DRUG RESPONSES IN PRIMARY PATIENT SAMPLES. 2019 7 6069 32 THE DIOXIN RECEPTOR IS SILENCED BY PROMOTER HYPERMETHYLATION IN HUMAN ACUTE LYMPHOBLASTIC LEUKEMIA THROUGH INHIBITION OF SP1 BINDING. THE TRANSCRIPTION FACTOR ARYL HYDROCARBON RECEPTOR (AHR) HAS RELEVANT FUNCTIONS IN CELL PROLIFERATION. INTERESTINGLY, THE AHR CAN EITHER PROMOTE OR INHIBIT PROLIFERATION DEPENDING ON THE CELL PHENOTYPE. ALTHOUGH RECENT DATA REVEAL POTENTIAL PATHWAYS FOR AHR SIGNALING IN CELL PROLIFERATION, THE MECHANISMS THAT REGULATE ITS ACTIVITY IN TUMOR CELLS REMAIN UNKNOWN. HERE, WE HAVE ANALYZED PROMOTER HYPERMETHYLATION AS A POTENTIAL MECHANISM CONTROLLING AHR EXPRESSION IN HUMAN TUMOR CELLS. AHR PROMOTER CPG METHYLATION WAS SPORADIC IN A PANEL OF 19 TUMOR CELL LINES EXCEPT FOR THE CHRONIC MYELOID LEUKEMIA (CML) K562 AND THE ACUTE LYMPHOBLASTIC LEUKEMIA (ALL) REH. WHEN COMPARED WITH NORMAL LYMPHOCYTES, REH HAD VERY LOW CONSTITUTIVE AHR EXPRESSION THAT COULD BE ATTRIBUTED TO PROMOTER HYPERMETHYLATION SINCE TREATMENT WITH THE DNA DEMETHYLATING AGENT 5-AZA-2'-DEOXYCITIDINE (AZA) SIGNIFICANTLY INCREASED AHR MRNA AND PROTEIN. THESE RESULTS IN LEUKEMIA-DERIVED CELL LINES WERE FURTHER CONFIRMED IN PRIMARY ALL, WHERE 33% OF THE PATIENTS (7/21) HAD AHR PROMOTER HYPERMETHYLATION. CHROMATIN IMMUNOPRECIPITATION (CHIP) SHOWED THAT METHYLATION IMPAIRED BINDING OF THE TRANSCRIPTION FACTOR SP1 TO THE AHR PROMOTER, THUS PROVIDING A MECHANISM FOR AHR DOWNREGULATION IN REH CELLS. THEREFORE, PROMOTER HYPERMETHYLATION REPRESENTS A NOVEL EPIGENETIC MECHANISM DOWNREGULATING AHR ACTIVITY IN HEMATOLOGICAL MALIGNANCIES SUCH AS ALL. 2006 8 661 35 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 9 6076 37 THE DYNAMICS OF NUCLEAR RECEPTORS AND NUCLEAR RECEPTOR COREGULATORS IN THE PATHOGENESIS OF ENDOMETRIOSIS. BACKGROUND: ENDOMETRIOSIS IS DEFINED AS THE COLONIZATION AND GROWTH OF ENDOMETRIAL TISSUE AT ANATOMIC SITES OUTSIDE THE UTERINE CAVITY. UP TO 15% OF REPRODUCTIVE-AGED WOMEN IN THE USA SUFFER FROM PAINFUL SYMPTOMS OF ENDOMETRIOSIS, SUCH AS INFERTILITY, PELVIC PAIN, MENSTRUAL CYCLE ABNORMALITIES AND INCREASED RISK OF CERTAIN CANCERS. HOWEVER, MANY OF THE CURRENT CLINICAL TREATMENTS FOR ENDOMETRIOSIS ARE NOT SUFFICIENTLY EFFECTIVE AND YIELD UNACCEPTABLE SIDE EFFECTS. THERE IS CLEARLY AN URGENT NEED TO IDENTIFY NEW MOLECULAR MECHANISMS THAT CRITICALLY UNDERPIN THE INITIATION AND PROGRESSION OF ENDOMETRIOSIS IN ORDER TO DEVELOP MORE SPECIFIC AND EFFECTIVE THERAPEUTICS WHICH LACK THE SIDE EFFECTS OF CURRENT THERAPIES. THE AIM OF THIS REVIEW IS TO DISCUSS HOW NUCLEAR RECEPTORS (NRS) AND THEIR COREGULATORS PROMOTE THE PROGRESSION OF ENDOMETRIOSIS. UNDERSTANDING THE PATHOGENIC MOLECULAR MECHANISMS FOR THE GENESIS AND MAINTENANCE OF ENDOMETRIOSIS AS MODULATED BY NRS AND COREGULATORS CAN REVEAL NEW THERAPEUTIC TARGETS FOR ALTERNATIVE ENDOMETRIOSIS TREATMENTS. METHODS: THIS REVIEW WAS PREPARED USING PUBLISHED GENE EXPRESSION MICROARRAY DATA SETS OBTAINED FROM PATIENTS WITH ENDOMETRIOSIS AND PUBLISHED LITERATURE ON NRS AND THEIR COREGULATORS THAT DEAL WITH ENDOMETRIOSIS PROGRESSION. USING THE ABOVE OBSERVATIONS, OUR CURRENT UNDERSTANDING OF HOW NRS AND NR COREGULATORS ARE INVOLVED IN THE PROGRESSION OF ENDOMETRIOSIS IS SUMMARIZED. RESULTS: ABERRANT LEVELS OF NRS AND NR COREGULATORS IN ECTOPIC ENDOMETRIOSIS LESIONS ARE ASSOCIATED WITH THE PROGRESSION OF ENDOMETRIOSIS. AS AN EXAMPLE, ENDOMETRIOTIC CELL-SPECIFIC ALTERATIONS IN GENE EXPRESSION ARE CORRELATED WITH A DIFFERENTIAL METHYLATION STATUS OF THE GENOME COMPARED WITH THE NORMAL ENDOMETRIUM. THESE DIFFERENTIAL EPIGENETIC REGULATIONS CAN GENERATE FAVORABLE CELL-SPECIFIC NR AND COREGULATOR MILIEUS FOR ENDOMETRIOSIS PROGRESSION. GENETIC ALTERATIONS, SUCH AS SINGLE NUCLEOTIDE POLYMORPHISMS AND INSERTION/DELETION POLYMORPHISMS OF NR AND COREGULATOR GENES, ARE FREQUENTLY DETECTED IN ECTOPIC LESIONS COMPARED WITH THE NORMAL ENDOMETRIUM. THESE GENETIC VARIATIONS IMPART NEW MOLECULAR PROPERTIES TO NRS AND COREGULATORS TO INCREASE THEIR CAPACITY TO STIMULATE PROGRESSION OF ENDOMETRIOSIS. FINALLY, POST-TRANSLATIONAL MODIFICATIONS OF NR COREGULATORS, SUCH AS PROTEOLYTIC PROCESSING, GENERATE ENDOMETRIOSIS-SPECIFIC ISOFORMS. COMPARED WITH THE UNMODIFIED COREGULATORS, THESE COREGULATOR ISOFORMS HAVE UNIQUE FUNCTIONS THAT ENHANCE THE PATHOGENESIS OF ENDOMETRIOSIS. CONCLUSIONS: EPIGENETIC/GENETIC VARIATIONS AND POSTTRANSLATIONAL MODIFICATIONS OF NRS AND COREGULATORS ALTER THEIR ORIGINAL FUNCTION SO THAT THEY BECOME POTENT 'DRIVERS' OF ENDOMETRIOSIS PROGRESSION. 2014 10 1212 27 CPG ISLAND METHYLATION OF THE HTERT PROMOTER IS ASSOCIATED WITH LOWER TELOMERASE ACTIVITY IN B-CELL LYMPHOCYTIC LEUKEMIA. OBJECTIVE: EXPRESSION OF THE CATALYTIC SUBUNIT OF THE TELOMERASE ENZYME HTERT IS ESSENTIAL FOR PROLONGING THE REPLICATIVE LIFESPAN AND IS THE RATE-LIMITING STEP IN CELLULAR IMMORTALIZATION AND CARCINOGENESIS. BECAUSE HTERT EXPRESSION IS POSITIVELY CORRELATED WITH TELOMERASE ACTIVITY, ITS REGULATION IS SUGGESTED AS THE MAJOR DETERMINANT OF ENZYMATIC ACTIVITY. THE HTERT PROMOTER REGION CONTAINS TWO CPG ISLANDS, WHICH ARE KNOWN TO BE TARGET SITES FOR DE NOVO DNA METHYLATION. TO ELUCIDATE THE IMPACT OF THIS EPIGENETIC MECHANISM ON TELOMERASE ACTIVITY, WE ANALYZED THE DEGREE OF HTERT PROMOTER METHYLATION IN 30 PATIENTS WITH B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA. MATERIALS AND METHODS: HTERT PROMOTER METHYLATION WAS ASSESSED USING A METHYLATION-SPECIFIC COMPETITIVE POLYMERASE CHAIN REACTION ASSAY. THE ASSAY IS BASED ON DIGESTION OF GENOMIC DNA WITH A METHYLATION-SENSITIVE RESTRICTION ENZYME BEFORE AMPLIFICATION WITH AN INTERNAL STANDARD. RESULTS: PATIENTS EXHIBITING HIGH TELOMERASE ACTIVITY SHOWED SIGNIFICANTLY LESS METHYLATION OF THE HTERT PROMOTER CORE DOMAIN THAN PATIENTS WITH LOW ENZYME ACTIVITY. IN ADDITION, TELOMERASE ACTIVITY WAS SIGNIFICANTLY ASSOCIATED WITH TELOMERE LENGTH AND OVERALL SURVIVAL. CONCLUSIONS: OUR DATA SHOW THAT THE DEGREE OF CPG ISLAND METHYLATION OF THE HTERT PROMOTER EXHIBITS AN IMPACT ON TELOMERASE ACTIVITY IN A SUBGROUP OF PATIENTS WITH B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA AND THEREFORE IS ASSUMED TO PLAY A ROLE IN REGULATING HTERT GENE EXPRESSION IN THESE PATIENTS. 2002 11 2123 34 EPIGENETIC IMPACTS OF STRESS PRIMING OF THE NEUROINFLAMMATORY RESPONSE TO SARIN SURROGATE IN MICE: A MODEL OF GULF WAR ILLNESS. BACKGROUND: GULF WAR ILLNESS (GWI) IS AN ARCHETYPAL, MEDICALLY UNEXPLAINED, CHRONIC CONDITION CHARACTERISED BY PERSISTENT SICKNESS BEHAVIOUR AND NEUROIMMUNE AND NEUROINFLAMMATORY COMPONENTS. AN ESTIMATED 25-32% OF THE OVER 900,000 VETERANS OF THE 1991 GULF WAR FULFIL THE REQUIREMENTS OF A GWI DIAGNOSIS. IT HAS BEEN HYPOTHESISED THAT THE HIGH PHYSICAL AND PSYCHOLOGICAL STRESS OF COMBAT MAY HAVE INCREASED VULNERABILITY TO IRREVERSIBLE ACETYLCHOLINESTERASE (ACHE) INHIBITORS LEADING TO A PRIMING OF THE NEUROIMMUNE SYSTEM. A NUMBER OF STUDIES HAVE LINKED HIGH LEVELS OF PSYCHOPHYSIOLOGICAL STRESS AND TOXICANT EXPOSURES TO EPIGENETIC MODIFICATIONS THAT REGULATE GENE EXPRESSION. RECENT RESEARCH IN A MOUSE MODEL OF GWI HAS SHOWN THAT PRE-EXPOSURE WITH THE STRESS HORMONE CORTICOSTERONE (CORT) CAUSES AN INCREASE IN EXPRESSION OF SPECIFIC CHEMOKINES AND CYTOKINES IN RESPONSE TO DIISOPROPYL FLUOROPHOSPHATE (DFP), A SARIN SURROGATE AND IRREVERSIBLE ACHE INHIBITOR. METHODS: C57BL/6J MICE WERE EXPOSED TO CORT FOR 4 DAYS, AND EXPOSED TO DFP ON DAY 5, BEFORE SACRIFICE 6 H LATER. THE TRANSCRIPTOME WAS EXAMINED USING RNA-SEQ, AND THE EPIGENOME WAS EXAMINED USING REDUCED REPRESENTATION BISULFITE SEQUENCING AND H3K27AC CHIP-SEQ. RESULTS: WE SHOW TRANSCRIPTIONAL, HISTONE MODIFICATION (H3K27AC) AND DNA METHYLATION CHANGES IN GENES RELATED TO THE IMMUNE AND NEURONAL SYSTEM, POTENTIALLY RELEVANT TO NEUROINFLAMMATORY AND COGNITIVE SYMPTOMS OF GWI. FURTHER EVIDENCE SUGGESTS ALTERED PROPORTIONS OF MYELINATING OLIGODENDROCYTES IN THE FRONTAL CORTEX, PERHAPS CONNECTED TO WHITE MATTER DEFICITS SEEN IN GWI SUFFERERS. CONCLUSIONS: OUR FINDINGS MAY REFLECT THE EARLY CHANGES WHICH OCCURRED IN GWI VETERANS, AND WE OBSERVE ALTERATIONS IN SEVERAL PATHWAYS ALTERED IN GWI SUFFERERS. THESE CLOSE LINKS TO CHANGES SEEN IN VETERANS WITH GWI INDICATES THAT THIS MODEL REFLECTS THE ENVIRONMENTAL EXPOSURES RELATED TO GWI AND MAY PROVIDE A MODEL FOR BIOMARKER DEVELOPMENT AND TESTING FUTURE TREATMENTS. 2018 12 244 34 ADOLESCENT IDIOPATHIC SCOLIOSIS (AIS), ENVIRONMENT, EXPOSOME AND EPIGENETICS: A MOLECULAR PERSPECTIVE OF POSTNATAL NORMAL SPINAL GROWTH AND THE ETIOPATHOGENESIS OF AIS WITH CONSIDERATION OF A NETWORK APPROACH AND POSSIBLE IMPLICATIONS FOR MEDICAL THERAPY. GENETIC FACTORS ARE BELIEVED TO PLAY AN IMPORTANT ROLE IN THE ETIOLOGY OF ADOLESCENT IDIOPATHIC SCOLIOSIS (AIS). DISCORDANT FINDINGS FOR MONOZYGOTIC (MZ) TWINS WITH AIS SHOW THAT ENVIRONMENTAL FACTORS INCLUDING DIFFERENT INTRAUTERINE ENVIRONMENTS ARE IMPORTANT IN ETIOLOGY, BUT WHAT THESE ENVIRONMENTAL FACTORS MAY BE IS UNKNOWN. RECENT EVIDENCE FOR COMMON CHRONIC NON-COMMUNICABLE DISEASES SUGGESTS EPIGENETIC DIFFERENCES MAY UNDERLIE MZ TWIN DISCORDANCE, AND BE THE LINK BETWEEN ENVIRONMENTAL FACTORS AND PHENOTYPIC DIFFERENCES. DNA METHYLATION IS ONE IMPORTANT EPIGENETIC MECHANISM OPERATING AT THE INTERFACE BETWEEN GENOME AND ENVIRONMENT TO REGULATE PHENOTYPIC PLASTICITY WITH A COMPLEX REGULATION ACROSS THE GENOME DURING THE FIRST DECADE OF LIFE. THE WORD EXPOSOME REFERS TO THE TOTALITY OF ENVIRONMENTAL EXPOSURES FROM CONCEPTION ONWARDS, COMPRISING FACTORS IN EXTERNAL AND INTERNAL ENVIRONMENTS. THE WORD EXPOSOME IS USED HERE ALSO IN RELATION TO PHYSIOLOGIC AND ETIOPATHOGENETIC FACTORS THAT AFFECT NORMAL SPINAL GROWTH AND MAY INDUCE THE DEFORMITY OF AIS. IN NORMAL POSTNATAL SPINAL GROWTH WE PROPOSE A NEW TERM AND CONCEPT, PHYSIOLOGIC GROWTH-PLATE EXPOSOME FOR THE NORMAL PROCESSES PARTICULARLY OF THE INTERNAL ENVIRONMENTS THAT MAY HAVE EPIGENETIC EFFECTS ON GROWTH PLATES OF VERTEBRAE. IN AIS, WE PROPOSE A NEW TERM AND CONCEPT PATHOPHYSIOLOGIC SCOLIOGENIC EXPOSOME FOR THE ABNORMAL PROCESSES IN MOLECULAR PATHWAYS PARTICULARLY OF THE INTERNAL ENVIRONMENT CURRENTLY EXPRESSED AS ETIOPATHOGENETIC HYPOTHESES; THESE ARE SUGGESTED TO HAVE DEFORMING EFFECTS ON THE GROWTH PLATES OF VERTEBRAE AT CELL, TISSUE, STRUCTURE AND/OR ORGAN LEVELS THAT ARE CONSIDERED TO BE EPIGENETIC. NEW RESEARCH IS REQUIRED FOR CHROMATIN MODIFICATIONS INCLUDING DNA METHYLATION IN AIS SUBJECTS AND VERTEBRAL GROWTH PLATES EXCISED AT SURGERY. IN ADDITION, CONSIDERATION IS NEEDED FOR A POSSIBLE NETWORK APPROACH TO ETIOPATHOGENESIS BY CONSTRUCTING AIS DISEASOMES. THESE APPROACHES MAY LEAD THROUGH SCREENING, GENETIC, EPIGENETIC, BIOCHEMICAL, METABOLIC PHENOTYPES AND PHARMACOGENOMIC RESEARCH TO IDENTIFY SUSCEPTIBLE INDIVIDUALS AT RISK AND MODULATE ABNORMAL MOLECULAR PATHWAYS OF AIS. THE POTENTIAL OF EPIGENETIC-BASED MEDICAL THERAPY FOR AIS CANNOT BE ASSESSED AT PRESENT, AND MUST AWAIT NEW RESEARCH DERIVED FROM THE EVALUATION OF EPIGENETIC CONCEPTS OF SPINAL GROWTH IN HEALTH AND DEFORMITY. THE TENETS OUTLINED HERE FOR AIS ARE APPLICABLE TO OTHER MUSCULOSKELETAL GROWTH DISORDERS INCLUDING INFANTILE AND JUVENILE IDIOPATHIC SCOLIOSIS. 2011 13 4828 35 OLANZAPINE INDUCED DNA METHYLATION CHANGES SUPPORT THE DOPAMINE HYPOTHESIS OF PSYCHOSIS. BACKGROUND: THE DOPAMINE (DA) HYPOTHESIS OF SCHIZOPHRENIA PROPOSES THE MENTAL ILLNESS IS CAUSED BY EXCESSIVE TRANSMISSION OF DOPAMINE IN SELECTED BRAIN REGIONS. MULTIPLE LINES OF EVIDENCE, INCLUDING BLOCKAGE OF DOPAMINE RECEPTORS BY ANTIPSYCHOTIC DRUGS THAT ARE USED TO TREAT SCHIZOPHRENIA, SUPPORT THE HYPOTHESIS. HOWEVER, THE DOPAMINE D2 RECEPTOR (DRD2) BLOCKADE CANNOT EXPLAIN SOME IMPORTANT ASPECTS OF THE THERAPEUTIC EFFECT OF ANTIPSYCHOTIC DRUGS. IN THIS STUDY, WE HYPOTHESIZED THAT ANTIPSYCHOTIC DRUGS COULD AFFECT THE TRANSCRIPTION OF GENES IN THE DA PATHWAY BY ALTERING THEIR EPIGENETIC PROFILE. METHODS: TO TEST THIS HYPOTHESIS, WE EXAMINED THE EFFECT OF OLANZAPINE, A COMMONLY USED ATYPICAL ANTIPSYCHOTIC DRUG, ON THE DNA METHYLATION STATUS OF GENES FROM DA NEUROTRANSMISSION IN THE BRAIN AND LIVER OF RATS. GENOMIC DNA ISOLATED FROM HIPPOCAMPUS, CEREBELLUM, AND LIVER OF OLANZAPINE TREATED (N = 2) AND CONTROL (N = 2) RATS WERE ANALYZED USING RAT SPECIFIC METHYLATION ARRAYS. RESULTS: OUR RESULTS SHOW THAT OLANZAPINE CAUSES METHYLATION CHANGES IN GENES ENCODING FOR DA RECEPTORS (DOPAMINE D1 RECEPTOR, DOPAMINE D2 RECEPTOR AND DOPAMINE D5 RECEPTOR), A DA TRANSPORTER (SOLUTE CARRIER FAMILY 18 MEMBER 2), A DA SYNTHESIS (DIFFERENTIAL DISPLAY CLONE 8), AND A DA METABOLISM (CATECHOL-O-METHYLTRANSFERASE). WE ASSESSED A TOTAL OF 40 GENES IN THE DA PATHWAY AND FOUND 19 TO BE DIFFERENTIALLY METHYLATED BETWEEN OLANZAPINE TREATED AND CONTROL RATS. MOST (17/19) GENES SHOWED AN INCREASE IN METHYLATION, IN THEIR PROMOTER REGIONS WITH IN SILICO ANALYSIS STRONGLY INDICATING A FUNCTIONAL POTENTIAL TO SUPPRESS TRANSCRIPTION IN THE BRAIN. CONCLUSION: OUR RESULTS SUGGEST THAT CHRONIC OLANZAPINE MAY REDUCE DA ACTIVITY BY ALTERING GENE METHYLATION. IT MAY ALSO EXPLAIN THE DELAYED THERAPEUTIC EFFECT OF ANTIPSYCHOTICS, WHICH OCCURS DESPITE RAPID DOPAMINE BLOCKADE. FURTHERMORE, GIVEN THE COMMON NATURE OF EPIGENETIC VARIATION, THIS LENDS INSIGHT INTO THE DIFFERENTIAL THERAPEUTIC RESPONSE OF PSYCHOTIC PATIENTS WHO DISPLAY ADEQUATE BLOCKAGE OF DOPAMINE RECEPTORS. 2013 14 2207 35 EPIGENETIC MODIFICATIONS AND GLUCOCORTICOID SENSITIVITY IN MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS). BACKGROUND: MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A DEBILITATING IDIOPATHIC DISEASE CHARACTERIZED BY UNEXPLAINED FATIGUE THAT FAILS TO RESOLVE WITH SUFFICIENT REST. DIAGNOSIS IS BASED ON A LIST OF SYMPTOMS AND EXCLUSION OF OTHER FATIGUE-RELATED HEALTH CONDITIONS. DESPITE A HETEROGENEOUS PATIENT POPULATION, IMMUNE AND HYPOTHALAMIC-PITUITARY-ADRENAL (HPA) AXIS FUNCTION DIFFERENCES, SUCH AS ENHANCED NEGATIVE FEEDBACK TO GLUCOCORTICOIDS, ARE RECURRING FINDINGS IN ME/CFS STUDIES. EPIGENETIC MODIFICATIONS, SUCH AS CPG METHYLATION, ARE KNOWN TO REGULATE LONG-TERM PHENOTYPIC DIFFERENCES AND PREVIOUS WORK BY OUR GROUP FOUND DNA METHYLOME DIFFERENCES IN ME/CFS, HOWEVER THE RELATIONSHIP BETWEEN DNA METHYLOME MODIFICATIONS, CLINICAL AND FUNCTIONAL CHARACTERISTICS ASSOCIATED WITH ME/CFS HAS NOT BEEN EXAMINED. METHODS: WE EXAMINED THE DNA METHYLOME IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) OF A LARGER COHORT OF FEMALE ME/CFS PATIENTS USING THE ILLUMINA HUMANMETHYLATION450 BEADCHIP ARRAY. IN PARALLEL TO THE DNA METHYLOME ANALYSIS, WE INVESTIGATED IN VITRO GLUCOCORTICOID SENSITIVITY DIFFERENCES BY STIMULATING PBMCS WITH PHYTOHAEMAGGLUTININ AND SUPPRESSED GROWTH WITH DEXAMETHASONE. WE EXPLORED DNA METHYLATION DIFFERENCES USING BISULFITE PYROSEQUENCING AND STATISTICAL PERMUTATION. LINEAR REGRESSION WAS IMPLEMENTED TO DISCOVER EPIGENOMIC REGIONS ASSOCIATED WITH SELF-REPORTED QUALITY OF LIFE AND NETWORK ANALYSIS OF GENE ONTOLOGY TERMS TO BIOLOGICALLY CONTEXTUALIZE RESULTS. RESULTS: WE DETECTED 12,608 DIFFERENTIALLY METHYLATED SITES BETWEEN ME/CFS PATIENTS AND HEALTHY CONTROLS PREDOMINANTLY LOCALIZED TO CELLULAR METABOLISM GENES, SOME OF WHICH WERE ALSO RELATED TO SELF-REPORTED QUALITY OF LIFE HEALTH SCORES. AMONG ME/CFS PATIENTS, GLUCOCORTICOID SENSITIVITY WAS ASSOCIATED WITH DIFFERENTIAL METHYLATION AT 13 LOCI. CONCLUSIONS: OUR RESULTS INDICATE DNA METHYLATION MODIFICATIONS IN CELLULAR METABOLISM IN ME/CFS DESPITE A HETEROGENEOUS PATIENT POPULATION, IMPLICATING THESE PROCESSES IN IMMUNE AND HPA AXIS DYSFUNCTION IN ME/CFS. MODIFICATIONS TO EPIGENETIC LOCI ASSOCIATED WITH DIFFERENCES IN GLUCOCORTICOID SENSITIVITY MAY BE IMPORTANT AS BIOMARKERS FOR FUTURE CLINICAL TESTING. OVERALL, THESE FINDINGS ALIGN WITH RECENT ME/CFS WORK THAT POINT TOWARDS IMPAIRMENT IN CELLULAR ENERGY PRODUCTION IN THIS PATIENT POPULATION. 2017 15 5497 42 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 16 3034 37 GENETICS/EPIGENETICS/ALLERGY: THE GUN IS LOADED ... BUT WHAT PULLS THE TRIGGER? BACKGROUND: THE ALLERGIC DISEASES COMPRISE A GROUP OF CHRONIC INFLAMMATORY CONDITIONS THAT DISPLAY A BROAD SPECTRUM OF CLINICAL MANIFESTATIONS PRIMARILY MEDIATED BY IMMUNOGLOBULIN E (IGE). THE PREVALENCE AND SEVERITY OF THESE IGE-MEDIATED ALLERGIC DISORDERS HAVE INCREASED DRAMATICALLY OVER THE PAST FEW DECADES AND ARE BECOMING A GLOBAL HEALTH PROBLEM. ALTHOUGH GENETICS PLAYS AN IMPORTANT ROLE IN DETERMINING WHO DEVELOPS THESE ATOPIC DISORDERS, GENETICS ALONE CANNOT FULLY EXPLAIN THIS RAPID GROWTH. RESULTS OF NUMEROUS STUDIES HAVE INDICATED THAT EPIGENETICS PLAYS A MAJOR PATHOGENETIC ROLE BY SUPERIMPOSING ITS EFFECTS ABOVE THE DNA PRIMAL GENETIC MOLECULE THROUGH INTERACTIONS WITH AND BETWEEN VARIOUS SUSCEPTIBILITY GENES, IMMUNOLOGIC INFLUENCES, AND ENVIRONMENTAL FACTORS. OBJECTIVE: IN THIS ARTICLE, THE IMPORTANCE AND RELATIONSHIPS OF GENETICS AND EPIGENETICS TO AN UNDERSTANDING OF THE IMMUNE SYSTEM IN HEALTH AND IN DISEASE WERE REVIEWED TOGETHER WITH THE PRINCIPLES AND MECHANISMS THAT UNDERLIE THESE ENTITIES AND WHICH RELATE TO CLINICAL ALLERGY PRACTICE. A SPECIFIC FOCUS OF THE ARTICLE WAS DIRECTED TO THE RECENT RECOGNITION THAT THE IGE-DRIVEN ATOPIC DISORDERS ARE DRIVEN BY ABERRANT IMMUNE RESPONSES IN WHICH CD25(+) FORKHEAD BOX P3(+) (FOXP3(+)) T-REGULATORY (TREG) CELLS THAT NORMALLY SUPPRESS INFLAMMATORY EVENTS ARE OFTEN POORLY FUNCTIONING. METHODS: BASED ON OUR PREVIOUS PUBLISHED FINDINGS THAT METHYLATED DNA CPG (CYTOSINE [C], PHOSPHATE [P], GUANINE [G]) OLIGONUCLEOTIDE (ODN) BUT NOT UNMETHYLATED CPG ODN SEQUENCE WAS SHOWN TO PROMOTE FOXP3 EXPRESSION IN HUMAN CD4(+) T CELLS, THE ARTICLE REVIEWED THE APPLICATION OF DNA METHYLATION AND TREG INDUCTION TO CANCER, AUTOIMMUNE DISEASES, AND THE ALLERGIC DISORDERS. RESULTS: THE CENTRAL UNIFYING THEME OF DNA METHYLATION EPIGENETIC MECHANISM IS ITS COMPARATIVE DESCRIPTION TO AN ELECTRONIC "SWITCH," WHICH, WHEN IN THE METHYLATED STATE FUNCTIONS IN THE "CLOSED" POSITION WITH GENE SILENCING, GENOME STABILITY, AND DECREASED GENE EXPRESSION, WHEREAS DNA HYPOMETHYLATION IS ANALOGOUS TO THE "OPENED" POSITION OF THE SWITCH, WHICH LEADS TO ACTIVE TRANSCRIPTION AND INCREASED GENE EXPRESSION. CONCLUSION: OF THE THREE EPIGENETIC MECHANISMS THAT INCLUDE DNA METHYLATION, COVALENT POSTTRANSLATIONAL HISTONE MODIFICATIONS, AND MICRO-RNA-MEDIATED GENE SILENCING, DNA METHYLATION PLAYS THE MAJOR ROLE IN UNDERSTANDING MECHANISMS INVOLVED IN ALLERGY AND IMMUNOTHERAPY. EPIGENETICS HOLDS THE KEY TO UNRAVELING THE COMPLEX ASSOCIATIONS BETWEEN DISEASE PHENOTYPES AND ENDOTYPES, IDENTIFYING SAFER AND EFFECTIVE THERAPIES, AND CREATING A BETTER DIAGNOSIS AND TREATMENT OF ALLERGIC DISEASES. GENETICS LOADS THE GUN AND EPIGENETICS PULLS THE TRIGGER. 2019 17 1683 29 DRUG-RESISTANT EPILEPSY: DRUG TARGET HYPOTHESIS AND BEYOND THE RECEPTORS. EPILEPSY IS A CHRONIC NEUROLOGICAL DISORDER THAT AFFECTS MORE THAN 50 MILLION PEOPLE WORLDWIDE. DESPITE A RECENT INTRODUCTION OF ANTISEIZURE DRUGS FOR THE TREATMENT OF EPILEPTIC SEIZURES, ONE-THIRD OF THESE PATIENTS SUFFER FROM DRUG-RESISTANT EPILEPSY (DRE). THE THERAPEUTIC TARGET HYPOTHESIS IS A CITED THEORY TO EXPLAIN DRE. ACCORDING TO THE TARGET HYPOTHESIS, THE FAILURE TO ACHIEVE SEIZURE FREEDOM LEADS TO ALTERATION OF THE STRUCTURE AND/OR FUNCTION OF THE ANTISEIZURE MEDICATION (ASM) TARGET. HOWEVER, THIS HYPOTHESIS FAILS TO EXPLAIN WHY PATIENTS WITH DRE DO NOT RESPOND TO ANTISEIZURE MEDICATIONS OF DIFFERENT TARGETS. THIS REVIEW PRESENTS DIFFERENT CONDITIONS, SUCH AS EPIGENETIC MECHANISMS AND PROTEIN-PROTEIN INTERACTIONS THAT MAY RESULT IN ALTERATIONS OF DIVERSE DRUG TARGETS USING DIFFERENT MECHANISMS. THESE NOVEL CONDITIONS REPRESENT NEW TARGETS TO CONTROL DRE. 2022 18 4885 25 OVERVIEW ON MOLECULAR BIOMARKERS FOR LARYNGEAL CANCER: LOOKING FOR NEW ANSWERS TO AN OLD PROBLEM. LARYNGEAL SQUAMOUS CELL CANCER (LSCC) ACCOUNTS FOR ALMOST 25-30% OF ALL HEAD AND NECK SQUAMOUS CELL CANCERS AND IS CLUSTERED ACCORDING TO THE AFFECTED DISTRICTS, AS THIS DETERMINES DISTINCT TENDENCY TO RECUR AND METASTASIZE. A MAJOR ROLE FOR NUMEROUS GENETIC ALTERATIONS IN DRIVING THE ONSET AND PROGRESSION OF THIS NEOPLASM IS EMERGING. HOWEVER, MAJOR EFFORTS ARE STILL REQUIRED FOR THE IDENTIFICATION OF MOLECULAR MARKERS USEFUL FOR BOTH EARLY DIAGNOSIS AND PROGNOSTIC DEFINITION OF LSCC THAT IS STILL CHARACTERIZED BY SIGNIFICANT MORBIDITY AND MORTALITY. NON-CODING RNAS APPEAR THE MOST PROMISING AS THEY CIRCULATE IN ALL THE BIOLOGICAL FLUIDS ALLOWING LIQUID BIOPSY DETERMINATION, AS WELL AS DUE TO THEIR QUICK AND CHARACTERISTIC MODULATION USEFUL FOR NON-INVASIVE DETECTION AND MONITORING OF CANCER. OTHER CRITICAL ASPECTS ARE RELATED TO RECENT PROGRESS IN CIRCULATING TUMOR CELLS AND DNA DETECTION, IN METASTATIC STATUS AND CHEMO-REFRACTORINESS PREDICTION, AND IN THE FUNCTIONAL INTERACTION OF LSCC WITH CHRONIC INFLAMMATION AND INNATE IMMUNITY. WE REVIEW ALL THESE ASPECTS TAKING INTO ACCOUNT THE PROGRESS OF THE TECHNOLOGIES IN THE FIELD OF NEXT GENERATION SEQUENCING. 2022 19 22 23 5-HYDROXYMETHYLCYTOSINE AS A CLINICAL BIOMARKER: FLUORESCENCE-BASED ASSAY FOR HIGH-THROUGHPUT EPIGENETIC QUANTIFICATION IN HUMAN TISSUES. EPIGENETIC TRANSFORMATIONS MAY PROVIDE EARLY INDICATORS FOR CANCER AND OTHER DISEASE. SPECIFICALLY, THE AMOUNT OF GENOMIC 5-HYDROXYMETHYLCYTOSINE (5-HMC) WAS SHOWN TO BE GLOBALLY REDUCED IN A WIDE RANGE OF CANCERS. THE INTEGRATION OF THIS GLOBAL BIOMARKER INTO DIAGNOSTIC WORKFLOWS IS HAMPERED BY THE LIMITATIONS OF CURRENT 5-HMC QUANTIFICATION METHODS. HERE WE PRESENT AND VALIDATE A FLUORESCENCE-BASED PLATFORM FOR HIGH-THROUGHPUT AND COST-EFFECTIVE QUANTIFICATION OF GLOBAL GENOMIC 5-HMC LEVELS. WE UTILIZED THE ASSAY TO CHARACTERIZE CANCEROUS TISSUES BASED ON THEIR 5-HMC CONTENT, AND OBSERVED A PRONOUNCED REDUCTION IN 5-HMC LEVEL IN VARIOUS CANCER TYPES. WE PRESENT DATA FOR GLIOBLASTOMA, COLORECTAL CANCER, MULTIPLE MYELOMA, CHRONIC LYMPHOCYTIC LEUKEMIA AND PANCREATIC CANCER, COMPARED TO CORRESPONDING CONTROLS. POTENTIALLY, THE TECHNIQUE COULD ALSO BE USED TO FOLLOW RESPONSE TO TREATMENT FOR PERSONALIZED TREATMENT SELECTION. WE PRESENT INITIAL PROOF-OF-CONCEPT DATA FOR TREATMENT OF FAMILIAL ADENOMATOUS POLYPOSIS. 2020 20 2106 31 EPIGENETIC EVOLUTION AND LINEAGE HISTORIES OF CHRONIC LYMPHOCYTIC LEUKAEMIA. GENETIC AND EPIGENETIC INTRA-TUMORAL HETEROGENEITY COOPERATE TO SHAPE THE EVOLUTIONARY COURSE OF CANCER(1). CHRONIC LYMPHOCYTIC LEUKAEMIA (CLL) IS A HIGHLY INFORMATIVE MODEL FOR CANCER EVOLUTION AS IT UNDERGOES SUBSTANTIAL GENETIC DIVERSIFICATION AND EVOLUTION AFTER THERAPY(2,3). THE CLL EPIGENOME IS ALSO AN IMPORTANT DISEASE-DEFINING FEATURE(4,5), AND GROWING POPULATIONS OF CELLS IN CLL DIVERSIFY BY STOCHASTIC CHANGES IN DNA METHYLATION KNOWN AS EPIMUTATIONS(6). HOWEVER, PREVIOUS STUDIES USING BULK SEQUENCING METHODS TO ANALYSE THE PATTERNS OF DNA METHYLATION WERE UNABLE TO DETERMINE WHETHER EPIMUTATIONS AFFECT CLL POPULATIONS HOMOGENEOUSLY. HERE, TO MEASURE THE EPIMUTATION RATE AT SINGLE-CELL RESOLUTION, WE APPLIED MULTIPLEXED SINGLE-CELL REDUCED-REPRESENTATION BISULFITE SEQUENCING TO B CELLS FROM HEALTHY DONORS AND PATIENTS WITH CLL. WE OBSERVED THAT THE COMMON CLONAL ORIGIN OF CLL RESULTS IN A CONSISTENTLY INCREASED EPIMUTATION RATE, WITH LOW VARIABILITY IN THE CELL-TO-CELL EPIMUTATION RATE. BY CONTRAST, VARIABLE EPIMUTATION RATES ACROSS HEALTHY B CELLS REFLECT DIVERSE EVOLUTIONARY AGES ACROSS THE TRAJECTORY OF B CELL DIFFERENTIATION, CONSISTENT WITH EPIMUTATIONS SERVING AS A MOLECULAR CLOCK. HERITABLE EPIMUTATION INFORMATION ALLOWED US TO RECONSTRUCT LINEAGES AT HIGH-RESOLUTION WITH SINGLE-CELL DATA, AND TO APPLY THIS DIRECTLY TO PATIENT SAMPLES. THE CLL LINEAGE TREE SHAPE REVEALED EARLIER BRANCHING AND LONGER BRANCH LENGTHS THAN IN NORMAL B CELLS, REFLECTING RAPID DRIFT AFTER THE INITIAL MALIGNANT TRANSFORMATION AND A GREATER PROLIFERATIVE HISTORY. INTEGRATION OF SINGLE-CELL BISULFITE SEQUENCING ANALYSIS WITH SINGLE-CELL TRANSCRIPTOMES AND GENOTYPING CONFIRMED THAT GENETIC SUBCLONES MAPPED TO DISTINCT CLADES, AS INFERRED SOLELY ON THE BASIS OF EPIMUTATION INFORMATION. FINALLY, TO EXAMINE POTENTIAL LINEAGE BIASES DURING THERAPY, WE PROFILED SERIAL SAMPLES DURING IBRUTINIB-ASSOCIATED LYMPHOCYTOSIS, AND IDENTIFIED CLADES OF CELLS THAT WERE PREFERENTIALLY EXPELLED FROM THE LYMPH NODE AFTER TREATMENT, MARKED BY DISTINCT TRANSCRIPTIONAL PROFILES. THE SINGLE-CELL INTEGRATION OF GENETIC, EPIGENETIC AND TRANSCRIPTIONAL INFORMATION THUS CHARTS THE LINEAGE HISTORY OF CLL AND ITS EVOLUTION WITH THERAPY. 2019