1 3106 133 GENOMICS AND THE RESPIRATORY EFFECTS OF AIR POLLUTION EXPOSURE. ADVERSE HEALTH EFFECTS FROM AIR POLLUTANTS REMAIN IMPORTANT, DESPITE IMPROVEMENT IN AIR QUALITY IN THE PAST FEW DECADES. THE EXACT MECHANISMS OF LUNG INJURY FROM EXPOSURE TO AIR POLLUTANTS ARE NOT YET FULLY UNDERSTOOD. STUDYING THE GENOME (E.G. SINGLE-NUCLEOTIDE POLYMORPHISMS (SNP) ), EPIGENOME (E.G. METHYLATION OF GENES), TRANSCRIPTOME (MRNA EXPRESSION) AND MICRORNAOME (MICRORNA EXPRESSION) HAS THE POTENTIAL TO IMPROVE OUR UNDERSTANDING OF THE ADVERSE EFFECTS OF AIR POLLUTANTS. GENOME-WIDE ASSOCIATION STUDIES OF SNP HAVE DETECTED SNP ASSOCIATED WITH RESPIRATORY PHENOTYPES; HOWEVER, TO DATE, ONLY CANDIDATE GENE STUDIES OF AIR POLLUTION EXPOSURE HAVE BEEN PERFORMED. CHANGES IN EPIGENETIC PROCESSES, SUCH DNA METHYLATION THAT LEADS TO GENE SILENCING WITHOUT ALTERING THE DNA SEQUENCE, OCCUR WITH AIR POLLUTANT EXPOSURE, ESPECIALLY GLOBAL AND GENE-SPECIFIC METHYLATION CHANGES. RESPIRATORY CELL LINE AND ANIMAL MODELS DEMONSTRATE DISTINCT GENE EXPRESSION SIGNATURES IN THE TRANSCRIPTOME, ARISING FROM EXPOSURE TO PARTICULATE MATTER OR OZONE. PARTICULATE MATTER AND OTHER ENVIRONMENTAL TOXINS ALTER EXPRESSION OF MICRORNA, WHICH ARE SHORT NON-CODING RNA THAT REGULATE GENE EXPRESSION. WHILE IT IS CLEARLY IMPORTANT TO CONTAIN RISING LEVELS OF AIR POLLUTION, STRATEGIES ALSO NEED TO BE DEVELOPED TO MINIMIZE THE DAMAGING EFFECTS OF AIR POLLUTANT EXPOSURE ON THE LUNG, ESPECIALLY FOR PATIENTS WITH CHRONIC LUNG DISEASE AND FOR PEOPLE AT RISK OF FUTURE LUNG DISEASE. CAREFUL STUDY OF GENOMIC RESPONSES WILL IMPROVE OUR UNDERSTANDING OF MECHANISMS OF LUNG INJURY FROM AIR POLLUTION AND ENABLE FUTURE CLINICAL TESTING OF INTERVENTIONS AGAINST THE TOXIC EFFECTS OF AIR POLLUTANTS. 2012 2 528 44 ASTHMA EPIGENETICS. ASTHMA IS THE MOST COMMON CHRONIC DISEASE OF CHILDHOOD, AND A GROWING BODY OF EVIDENCE INDICATES THAT EPIGENETIC VARIATIONS MAY MEDIATE THE EFFECTS OF ENVIRONMENTAL EXPOSURES ON THE DEVELOPMENT AND NATURAL HISTORY OF ASTHMA. EPIGENETICS IS THE STUDY OF MITOTICALLY OR MEIOTICALLY HERITABLE CHANGES IN GENE EXPRESSION THAT OCCUR WITHOUT DIRECTLY ALTERING THE DNA SEQUENCE. DNA METHYLATION, HISTONE MODIFICATIONS AND MICRORNAS ARE MAJOR EPIGENETIC VARIATIONS IN HUMANS THAT ARE CURRENTLY BEING INVESTIGATED FOR ASTHMA ETIOLOGY AND NATURAL HISTORY. DNA METHYLATION RESULTS FROM ADDITION OF A METHYL GROUP TO THE 5 POSITION OF A CYTOSINE RING AND OCCURS ALMOST EXCLUSIVELY ON A CYTOSINE IN A CPG DINUCLEOTIDE. HISTONE MODIFICATIONS INVOLVE POSTTRANSLATIONAL MODIFICATIONS SUCH AS ACETYLATION, METHYLATION, PHOSPHORYLATION AND UBIQUITINATION ON THE TAILS OF CORE HISTONES. MICRORNAS ARE SHORT ~22 NUCLEOTIDE LONG, NON-CODING, SINGLE-STRANDED RNAS THAT BINDS TO COMPLEMENTARY SEQUENCES IN THE TARGET MRNAS, USUALLY RESULTING IN GENE SILENCING. WHILE MANY STUDIES HAVE DOCUMENTED RELATIONSHIPS OF ENVIRONMENTAL EXPOSURES THAT HAVE BEEN IMPLICATED IN ASTHMA ETIOLOGY WITH EPIGENETIC ALTERATIONS, TO DATE, FEW STUDIES HAVE DIRECTLY LINKED EPIGENETIC VARIATIONS WITH ASTHMA DEVELOPMENT. THERE ARE SEVERAL METHODOLOGICAL CHALLENGES IN STUDYING THE EPIGENETICS OF ASTHMA. IN THIS CHAPTER, THE INFLUENCE OF EPIGENETIC VARIATIONS ON ASTHMA PATHOPHYSIOLOGY, METHODOLOGICAL CONCERNS IN CONDUCTING EPIGENETIC RESEARCH AND FUTURE DIRECTION OF ASTHMA EPIGENETICS RESEARCH ARE DISCUSSED. 2014 3 4460 37 MOLECULAR MECHANISMS OF ENVIRONMENTAL EXPOSURES AND HUMAN DISEASE. A SUBSTANTIAL PROPORTION OF DISEASE RISK FOR COMMON COMPLEX DISORDERS IS ATTRIBUTABLE TO ENVIRONMENTAL EXPOSURES AND POLLUTANTS. AN APPRECIATION OF HOW ENVIRONMENTAL POLLUTANTS ACT ON OUR CELLS TO PRODUCE DELETERIOUS HEALTH EFFECTS HAS LED TO ADVANCES IN OUR UNDERSTANDING OF THE MOLECULAR MECHANISMS UNDERLYING THE PATHOGENESIS OF CHRONIC DISEASES, INCLUDING CANCER AND CARDIOVASCULAR, NEURODEGENERATIVE AND RESPIRATORY DISEASES. HERE, WE DISCUSS EMERGING RESEARCH ON THE INTERPLAY OF ENVIRONMENTAL POLLUTANTS WITH THE HUMAN GENOME AND EPIGENOME. WE REVIEW EVIDENCE SHOWING THE ENVIRONMENTAL IMPACT ON GENE EXPRESSION THROUGH EPIGENETIC MODIFICATIONS, INCLUDING DNA METHYLATION, HISTONE MODIFICATION AND NON-CODING RNAS. WE ALSO HIGHLIGHT RECENT STUDIES THAT EVALUATE RECENTLY DISCOVERED MOLECULAR PROCESSES THROUGH WHICH THE ENVIRONMENT CAN EXERT ITS EFFECTS, INCLUDING EXTRACELLULAR VESICLES, THE EPITRANSCRIPTOME AND THE MITOCHONDRIAL GENOME. FINALLY, WE DISCUSS CURRENT CHALLENGES WHEN STUDYING THE EXPOSOME - THE CUMULATIVE MEASURE OF ENVIRONMENTAL INFLUENCES OVER THE LIFESPAN - AND ITS INTEGRATION INTO FUTURE ENVIRONMENTAL HEALTH RESEARCH. 2023 4 6054 33 THE CURRENT STATE AND FUTURE OF T-CELL EXHAUSTION RESEARCH. 'EXHAUSTION' IS A TERM USED TO DESCRIBE A STATE OF NATIVE AND REDIRECTED T-CELL HYPO-RESPONSIVENESS RESULTING FROM PERSISTENT ANTIGEN EXPOSURE DURING CHRONIC VIRAL INFECTIONS OR CANCER. ALTHOUGH A WELL-ESTABLISHED PHENOTYPE ACROSS MICE AND HUMANS, EXHAUSTION AT THE MOLECULAR LEVEL REMAINS POORLY DEFINED AND INCONSISTENT ACROSS THE LITERATURE. THIS IS, IN PART, DUE TO AN OVERRELIANCE ON SURFACE RECEPTORS TO DEFINE THESE CELLS AND EXPLAIN EXHAUSTIVE BEHAVIOURS, AN INCOMPLETE UNDERSTANDING OF HOW EXHAUSTION ARISES, AND A LACK OF CLARITY OVER WHETHER EXHAUSTION IS THE SAME ACROSS CONTEXTS, E.G. CHRONIC VIRAL INFECTIONS VERSUS CANCER. WITH THE DEVELOPMENT OF SYSTEMS-BASED GENETIC APPROACHES SUCH AS SINGLE-CELL RNA-SEQ AND CRISPR SCREENS APPLIED TO IN VIVO DATA, WE ARE MOVING CLOSER TO A CONSENSUS VIEW OF EXHAUSTION, ALTHOUGH UNDERSTANDING HOW IT ARISES REMAINS CHALLENGING GIVEN THE DIFFICULTY IN MANIPULATING THE IN VIVO SETTING. ACCORDINGLY, PRODUCING AND STUDYING EXHAUSTED T-CELLS EX VIVO ARE BURGEONING, ALLOWING EXPERIMENTS TO BE CONDUCTED AT SCALE UP AND WITH HIGH THROUGHPUT. HERE, WE FIRST REVIEW WHAT IS CURRENTLY KNOWN ABOUT T-CELL EXHAUSTION AND HOW IT'S BEING STUDIED. WE THEN DISCUSS HOW IMPROVEMENTS IN THEIR METHOD OF ISOLATION/PRODUCTION AND EXAMINING THE IMPACT OF DIFFERENT MICROENVIRONMENTAL SIGNALS AND CELL INTERACTIONS HAVE NOW BECOME AN ACTIVE AREA OF RESEARCH. FINALLY, WE DISCUSS WHAT THE FUTURE HOLDS FOR THE ANALYSIS OF THIS PHYSIOLOGICAL CONDITION AND, GIVEN THE DIVERSITY OF WAYS IN WHICH EXHAUSTED CELLS ARE NOW BEING GENERATED, PROPOSE THE ADOPTION OF A UNIFIED APPROACH TO CLEARLY DEFINING EXHAUSTION USING A SET OF METABOLIC-, EPIGENETIC-, TRANSCRIPTIONAL-, AND ACTIVATION-BASED PHENOTYPIC MARKERS, THAT WE CALL 'M.E.T.A'. 2023 5 4389 41 MODELING EPIGENETIC MODIFICATIONS IN RENAL DEVELOPMENT AND DISEASE WITH ORGANOIDS AND GENOME EDITING. UNDERSTANDING EPIGENETIC MECHANISMS IS CRUCIAL TO OUR COMPREHENSION OF GENE REGULATION IN DEVELOPMENT AND DISEASE. IN THE PAST DECADES, DIFFERENT STUDIES HAVE SHOWN THE ROLE OF EPIGENETIC MODIFICATIONS AND MODIFIERS IN RENAL DISEASE, ESPECIALLY DURING ITS PROGRESSION TOWARDS CHRONIC AND END-STAGE RENAL DISEASE. THUS, THE IDENTIFICATION OF GENETIC VARIATION ASSOCIATED WITH CHRONIC KIDNEY DISEASE HAS RESULTED IN BETTER CLINICAL MANAGEMENT OF PATIENTS. DESPITE THE IMPORTANCE OF THESE FINDINGS, THE TRANSLATION OF GENOTYPE-PHENOTYPE DATA INTO GENE-BASED MEDICINE IN CHRONIC KIDNEY DISEASE POPULATIONS STILL LACKS FAITHFUL CELLULAR OR ANIMAL MODELS THAT RECAPITULATE THE KEY ASPECTS OF THE HUMAN KIDNEY. THE LATEST ADVANCES IN THE FIELD OF STEM CELLS HAVE SHOWN THAT IT IS POSSIBLE TO EMULATE KIDNEY DEVELOPMENT AND FUNCTION WITH ORGANOIDS DERIVED FROM HUMAN PLURIPOTENT STEM CELLS. THESE HAVE SUCCESSFULLY RECAPITULATED NOT ONLY KIDNEY DIFFERENTIATION, BUT ALSO THE SPECIFIC PHENOTYPICAL TRAITS RELATED TO KIDNEY FUNCTION. THE COMBINATION OF THIS METHODOLOGY WITH CRISPR/CAS9 GENOME EDITING HAS ALREADY HELPED RESEARCHERS TO MODEL DIFFERENT GENETIC KIDNEY DISORDERS. NOWADAYS, CRISPR/CAS9-BASED APPROACHES ALSO ALLOW EPIGENETIC MODIFICATIONS, AND THUS REPRESENT AN UNPRECEDENTED TOOL FOR THE SCREENING OF GENETIC VARIANTS, EPIGENETIC MODIFICATIONS OR EVEN CHANGES IN CHROMATIN STRUCTURE THAT ARE ALTERED IN RENAL DISEASE. IN THIS REVIEW, WE DISCUSS THESE TECHNICAL ADVANCES IN KIDNEY MODELING, AND OFFER AN OVERVIEW OF THE ROLE OF EPIGENETIC REGULATION IN KIDNEY DEVELOPMENT AND DISEASE. 2018 6 228 45 ADAPTATION OF THE HUMAN POPULATION TO THE ENVIRONMENT: CURRENT KNOWLEDGE, CLUES FROM CZECH CYTOGENETIC AND "OMICS" BIOMONITORING STUDIES AND POSSIBLE MECHANISMS. THE HUMAN POPULATION IS CONTINUALLY EXPOSED TO NUMEROUS HARMFUL ENVIRONMENTAL STRESSORS, CAUSING NEGATIVE HEALTH EFFECTS AND/OR DEREGULATION OF BIOMARKER LEVELS. HOWEVER, STUDIES REPORTING NO OR EVEN POSITIVE IMPACTS OF SOME STRESSORS ON HUMANS ARE ALSO SOMETIMES PUBLISHED. THE MAIN AIM OF THIS REVIEW IS TO PROVIDE A COMPREHENSIVE OVERVIEW OF THE LAST DECADE OF CZECH BIOMONITORING RESEARCH, CONCERNING THE EFFECT OF VARIOUS LEVELS OF AIR POLLUTION (BENZO[A]PYRENE) AND RADIATION (URANIUM, X-RAY EXAMINATION AND NATURAL RADON BACKGROUND), ON THE DIFFERENTLY EXPOSED POPULATION GROUPS. BECAUSE SOME RESULTS OBTAINED FROM CYTOGENETIC STUDIES WERE OPPOSITE THAN HYPOTHESIZED, WE HAVE SEARCHED FOR A MEANINGFUL INTERPRETATION IN GENOMIC/EPIGENETIC STUDIES. A DETAILED ANALYSIS OF OUR DATA SUPPORTED BY THE STUDIES OF OTHERS AND CURRENT EPIGENETIC KNOWLEDGE, LEADS TO A HYPOTHESIS OF THE VERSATILE MECHANISM OF ADAPTATION TO ENVIRONMENTAL STRESSORS VIA DNA METHYLATION SETTINGS WHICH MAY EVEN ORIGINATE IN PRENATAL DEVELOPMENT, AND HELP TO REDUCE THE RESULTING DNA DAMAGE LEVELS. THIS HYPOTHESIS IS FULLY IN AGREEMENT WITH UNEXPECTED DATA FROM OUR STUDIES (E.G. LOWER LEVELS OF DNA DAMAGE IN SUBJECTS FROM HIGHLY POLLUTED REGIONS THAN IN CONTROLS OR IN SUBJECTS EXPOSED REPEATEDLY TO A POLLUTANT THAN IN THOSE WITHOUT PREVIOUS EXPOSURE), AND IS ALSO SUPPORTED BY DIFFERENCES IN DNA METHYLATION PATTERNS IN GROUPS FROM REGIONS WITH VARIOUS LEVELS OF POLLUTION. IN LIGHT OF THE ADAPTATION HYPOTHESIS, THE FOLLOWING POINTS MAY BE SUGGESTED FOR FUTURE RESEARCH: (I) THE CHRONIC AND ACUTE EXPOSURE OF STUDY SUBJECTS SHOULD BE DISTINGUISHED; (II) THE EXPOSURE HISTORY SHOULD BE MAPPED INCLUDING PLACE OF RESIDENCE DURING THE LIFE AND PRENATAL DEVELOPMENT; (III) CHANGES OF EPIGENETIC MARKERS SHOULD BE MONITORED OVER TIME. IN SUMMARY, INVESTIGATION OF HUMAN ADAPTATION TO THE ENVIRONMENT, ONE OF THE MOST IMPORTANT PROCESSES OF SURVIVAL, IS A NEW CHALLENGE FOR FUTURE RESEARCH IN THE FIELD OF HUMAN BIOMONITORING THAT MAY CHANGE OUR VIEW ON THE RESULTS OF BIOMARKER ANALYSES AND POTENTIAL NEGATIVE HEALTH IMPACTS OF THE ENVIRONMENT. 2017 7 6703 36 VERSATILE WORKFLOW FOR CELL TYPE-RESOLVED TRANSCRIPTIONAL AND EPIGENETIC PROFILES FROM CRYOPRESERVED HUMAN LUNG. COMPLEXITY OF LUNG MICROENVIRONMENT AND CHANGES IN CELLULAR COMPOSITION DURING DISEASE MAKE IT EXCEPTIONALLY HARD TO UNDERSTAND MOLECULAR MECHANISMS DRIVING DEVELOPMENT OF CHRONIC LUNG DISEASES. ALTHOUGH RECENT ADVANCES IN CELL TYPE-RESOLVED APPROACHES HOLD GREAT PROMISE FOR STUDYING COMPLEX DISEASES, THEIR IMPLEMENTATION RELIES ON LOCAL ACCESS TO FRESH TISSUE, AS TRADITIONAL TISSUE STORAGE METHODS DO NOT ALLOW VIABLE CELL ISOLATION. TO OVERCOME THESE HURDLES, WE DEVELOPED A VERSATILE WORKFLOW THAT ALLOWS STORAGE OF LUNG TISSUE WITH HIGH VIABILITY, PERMITS THOROUGH SAMPLE QUALITY CHECK BEFORE CELL ISOLATION, AND BEFITS SEQUENCING-BASED PROFILING. WE DEMONSTRATE THAT CRYOPRESERVATION ENABLES ISOLATION OF MULTIPLE CELL TYPES FROM BOTH HEALTHY AND DISEASED LUNGS. BASAL CELLS FROM CRYOPRESERVED AIRWAYS RETAIN THEIR DIFFERENTIATION ABILITY, INDICATING THAT CELLULAR IDENTITY IS NOT ALTERED BY CRYOPRESERVATION. IMPORTANTLY, USING RNA SEQUENCING AND EPIC ARRAY, WE SHOW THAT GENE EXPRESSION AND DNA METHYLATION SIGNATURES ARE PRESERVED UPON CRYOPRESERVATION, EMPHASIZING THE SUITABILITY OF OUR WORKFLOW FOR OMICS PROFILING OF LUNG CELLS. MOREOVER, WE OBTAINED HIGH-QUALITY SINGLE-CELL RNA-SEQUENCING DATA OF CELLS FROM CRYOPRESERVED HUMAN LUNGS, DEMONSTRATING THAT CRYOPRESERVATION EMPOWERS SINGLE-CELL APPROACHES. OVERALL, THANKS TO ITS SIMPLICITY, OUR WORKFLOW IS WELL SUITED FOR PROSPECTIVE TISSUE COLLECTION BY ACADEMIC COLLABORATORS AND BIOBANKS, OPENING WORLDWIDE ACCESS TO VIABLE HUMAN TISSUE. 2021 8 357 35 ALTERNATIVE MODELS FOR TRANSGENERATIONAL EPIGENETIC INHERITANCE: MOLECULAR PSYCHIATRY BEYOND MICE AND MAN. MENTAL ILLNESS REMAINS THE GREATEST CHRONIC HEALTH BURDEN GLOBALLY WITH FEW IN-ROADS HAVING BEEN MADE DESPITE SIGNIFICANT ADVANCES IN GENOMIC KNOWLEDGE IN RECENT DECADES. THE FIELD OF PSYCHIATRY IS CONSTANTLY CHALLENGED TO BRING NEW APPROACHES AND TOOLS TO ADDRESS AND TREAT THE NEEDS OF VULNERABLE INDIVIDUALS AND SUBPOPULATIONS, AND THAT HAS TO BE SUPPORTED BY A CONTINUOUS GROWTH IN KNOWLEDGE. THE MAJORITY OF NEUROPSYCHIATRIC SYMPTOMS REFLECT COMPLEX GENE-ENVIRONMENT INTERACTIONS, WITH EPIGENETICS BRIDGING THE GAP BETWEEN GENETIC SUSCEPTIBILITY AND ENVIRONMENTAL STRESSORS THAT TRIGGER DISEASE ONSET AND DRIVE THE ADVANCEMENT OF SYMPTOMS. IT HAS MORE RECENTLY BEEN DEMONSTRATED IN PRECLINICAL MODELS THAT EPIGENETICS UNDERPINS THE TRANSGENERATIONAL INHERITANCE OF STRESS-RELATED BEHAVIOURAL PHENOTYPES IN BOTH PATERNAL AND MATERNAL LINEAGES, PROVIDING FURTHER SUPPORTING EVIDENCE FOR HERITABILITY IN HUMANS. HOWEVER, UNBIASED PROSPECTIVE STUDIES OF THIS NATURE ARE PRACTICALLY IMPOSSIBLE TO CONDUCT IN HUMANS SO PRECLINICAL MODELS REMAIN OUR BEST OPTION FOR RESEARCHING THE MOLECULAR PATHOPHYSIOLOGIES UNDERLYING MANY NEUROPSYCHIATRIC CONDITIONS. WHILE RODENTS WILL REMAIN THE DOMINANT MODEL SYSTEM FOR PRECLINICAL STUDIES (ESPECIALLY FOR ADDRESSING COMPLEX BEHAVIOURAL PHENOTYPES), THERE IS SCOPE TO EXPAND CURRENT RESEARCH OF THE MOLECULAR AND EPIGENETIC PATHOLOGIES BY USING INVERTEBRATE MODELS. HERE, WE WILL DISCUSS THE UTILITY AND ADVANTAGES OF TWO ALTERNATIVE MODEL ORGANISMS-CAENORHABDITIS ELEGANS AND DROSOPHILA MELANOGASTER-AND SUMMARISE THE COMPELLING INSIGHTS OF THE EPIGENETIC REGULATION OF TRANSGENERATIONAL INHERITANCE THAT ARE POTENTIALLY RELEVANT TO HUMAN PSYCHIATRY. 2021 9 6155 37 THE GENETIC EPIDEMIOLOGY OF SUBSTANCE USE DISORDER: A REVIEW. BACKGROUND: SUBSTANCE USE DISORDER (SUD) REMAINS A SIGNIFICANT PUBLIC HEALTH ISSUE. A GREATER UNDERSTANDING OF HOW GENES AND ENVIRONMENT INTERACT TO REGULATE PHENOTYPES COMPRISING SUD WILL FACILITATE DIRECTED TREATMENTS AND PREVENTION. METHODS: THE LITERATURE STUDYING THE NEUROBIOLOGICAL CORRELATES OF SUD WITH A FOCUS ON THE GENETIC AND ENVIRONMENTAL INFLUENCES UNDERLYING THESE MECHANISMS WAS REVIEWED. RESULTS FROM TWIN/FAMILY, HUMAN GENETIC ASSOCIATION, GENE-ENVIRONMENT INTERACTION, EPIGENETIC LITERATURE, PHENOME-WIDE ASSOCIATION STUDIES ARE SUMMARIZED FOR ALCOHOL, NICOTINE, CANNABINOIDS, COCAINE, AND OPIOIDS. RESULTS: THERE ARE SUBSTANTIAL GENETIC INFLUENCES ON SUD THAT ARE EXPECTED TO INFLUENCE MULTIPLE NEUROTRANSMISSION PATHWAYS, AND THESE INFLUENCES ARE PARTICULARLY IMPORTANT WITHIN THE DOPAMINERGIC SYSTEM. GENETIC INFLUENCES INVOLVED IN OTHER ASPECTS OF SUD ETIOLOGY INCLUDING DRUG PROCESSING AND METABOLISM ARE ALSO IDENTIFIED. STUDIES OF GENE-ENVIRONMENT INTERACTION EMPHASIZE THE IMPORTANCE OF ENVIRONMENTAL CONTEXT IN SUD. EPIGENETIC STUDIES INDICATE DRUG-SPECIFIC CHANGES IN GENE EXPRESSION AS WELL AS DIFFERENCES IN GENE EXPRESSION RELATED TO THE USE OF MULTIPLE SUBSTANCES. FURTHER, GENE EXPRESSION IS EXPECTED TO DIFFER BY STAGE OF SUD SUCH AS SUBSTANCE INITIATION VERSUS CHRONIC SUBSTANCE USE. WHILE A SUBSTANTIAL LITERATURE HAS DEVELOPED FOR ALCOHOL AND NICOTINE USE DISORDERS, THERE IS COMPARATIVELY LESS INFORMATION FOR OTHER COMMONLY ABUSED SUBSTANCES. CONCLUSIONS: A BETTER UNDERSTANDING OF GENETICALLY-MEDIATED MECHANISMS INVOLVED IN THE NEUROBIOLOGY OF SUD PROVIDES INCREASED OPPORTUNITY TO DEVELOP BEHAVIORAL AND BIOLOGICALLY BASED TREATMENT AND PREVENTION OF SUD. 2017 10 5182 37 PREMALIGNANT LESIONS OF SQUAMOUS CELL CARCINOMA OF THE LUNG: THE MOLECULAR MAKE-UP AND FACTORS AFFECTING THEIR PROGRESSION. SQUAMOUS CELL CARCINOMA (SCC), ONE OF THE MOST COMMON FORMS OF LUNG CANCER, SHOWS ACCELERATED PROGRESSION AND AGGRESSIVE GROWTH AND USUALLY IS OBSERVED AT ADVANCED STAGES. SCC ORIGINATES FROM MORPHOLOGICAL CHANGES IN THE BRONCHIAL EPITHELIUM THAT OCCUR DURING CHRONIC INFLAMMATION: BASAL CELL HYPERPLASIA, SQUAMOUS METAPLASIA, AND DYSPLASIA I-III. HOWEVER, THE PROCESS IS NOT INEVITABLE; IT CAN BE STOPPED AT ANY STAGE, REMAIN IN THE STABLE STATE INDEFINITELY AND EITHER PROGRESS OR REGRESS. THE REASONS AND MECHANISMS OF DIFFERENT SCENARIOS OF THE EVOLUTION OF PREMALIGNANT LESIONS IN THE RESPIRATORY EPITHELIUM ARE NOT FULLY UNDERSTOOD. IN THIS REVIEW, WE SUMMARIZED THE LITERATURE DATA (INCLUDING OUR OWN DATA) REGARDING GENETIC, EPIGENETIC, TRANSCRIPTOMIC AND PROTEOMIC PROFILES OF THE PREMALIGNANT LESIONS AND HIGHLIGHTED FACTORS (ENVIRONMENTAL CAUSES, INFLAMMATION, AND GENE POLYMORPHISM) THAT MAY GOVERN THEIR PROGRESSION OR REGRESSION. IN CONCLUSION, WE REVIEWED STRATEGIES FOR LUNG CANCER PREVENTION AND PROPOSED NEW MODELS AND RESEARCH DIRECTIONS FOR STUDYING PREMALIGNANT LESIONS AND DEVELOPING NEW TOOLS TO PREDICT THE RISK OF THEIR MALIGNANT TRANSFORMATION. 2019 11 1546 25 DNA METHYLATION IN NASAL EPITHELIUM: STRENGTHS AND LIMITATIONS OF AN EMERGENT BIOMARKER FOR CHILDHOOD ASTHMA. ASTHMA IS ONE OF THE MOST WIDESPREAD CHRONIC RESPIRATORY CONDITIONS. THIS DISEASE PRIMARILY DEVELOPS IN CHILDHOOD AND IS INFLUENCED BY DIFFERENT FACTORS, MAINLY GENETICS AND ENVIRONMENTAL FACTORS. DNA METHYLATION IS AN EPIGENETIC MECHANISM WHICH MAY REPRESENT A BRIDGE BETWEEN THESE TWO FACTORS, PROVIDING A TOOL TO COMPREHEND THE INTERACTION BETWEEN GENETICS AND ENVIRONMENT. MOST EPIDEMIOLOGICAL STUDIES IN THIS FIELD HAVE BEEN CONDUCTED USING BLOOD SAMPLES, ALTHOUGH DNA METHYLATION MARKS IN BLOOD MAY NOT BE RELIABLE FOR DRAWING EXHAUSTIVE CONCLUSIONS ABOUT DNA METHYLATION IN THE AIRWAYS. BECAUSE OF THE ROLE OF NASAL EPITHELIUM IN ASTHMA AND THE TISSUE SPECIFICITY OF DNA METHYLATION, STUDYING THE RELATIONSHIP BETWEEN DNA METHYLATION AND CHILDHOOD ASTHMA MIGHT REVEAL CRUCIAL INFORMATION ABOUT THIS WIDESPREAD RESPIRATORY DISEASE. THE PURPOSE OF THIS REVIEW IS TO DESCRIBE CURRENT FINDINGS IN THIS FIELD OF RESEARCH. WE WILL PRESENT A VIEWPOINT OF SELECTED STUDIES, CONSIDER STRENGTHS AND LIMITATIONS, AND PROPOSE FUTURE RESEARCH IN THIS AREA. 2020 12 396 44 AN UPDATE ON EPIGENETICS AND CHILDHOOD RESPIRATORY DISEASES. EPIGENETIC MECHANISMS, DEFINED AS CHANGES IN PHENOTYPE OR GENE EXPRESSION CAUSED BY MECHANISMS OTHER THAN CHANGES IN THE UNDERLYING DNA SEQUENCE, HAVE BEEN PROPOSED TO CONSTITUTE A LINK BETWEEN GENETIC AND ENVIRONMENTAL FACTORS THAT AFFECT COMPLEX DISEASES. RECENT STUDIES SHOW THAT DNA METHYLATION, ONE OF THE KEY EPIGENETIC MECHANISMS, IS ALTERED IN CHILDREN EXPOSED TO AIR POLLUTANTS AND ENVIRONMENTAL TOBACCO SMOKE EARLY IN LIFE. SEVERAL CANDIDATE GENE STUDIES ON EPIGENETICS HAVE BEEN PUBLISHED TO DATE, BUT IT IS ONLY RECENTLY THAT GLOBAL METHYLATION ANALYSES HAVE BEEN PERFORMED FOR RESPIRATORY DISORDERS SUCH AS ASTHMA AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE. HOWEVER, LARGE-SCALE STUDIES WITH ADEQUATE POWER ARE YET TO BE PRESENTED IN CHILDREN, AND IMPLICATIONS FOR CLINICAL USE REMAIN TO BE EVALUATED. IN THIS REVIEW, WE SUMMARIZE THE RECENT ADVANCES IN EPIGENETICS AND RESPIRATORY DISORDERS IN CHILDREN, WITH A MAIN FOCUS ON METHODOLOGICAL CHALLENGES AND ANALYSES RELATED TO PHENOTYPE AND EXPOSURE USING GLOBAL METHYLATION APPROACHES. 2014 13 36 32 A CHROMATIN ASSAY FOR HUMAN BRAIN TISSUE. CHRONIC NEUROPSYCHIATRIC ILLNESSES SUCH AS SCHIZOPHRENIA, BIPOLAR DISEASE AND AUTISM ARE THOUGHT TO RESULT FROM A COMBINATION OF GENETIC AND ENVIRONMENTAL FACTORS THAT MIGHT RESULT IN EPIGENETIC ALTERATIONS OF GENE EXPRESSION AND OTHER MOLECULAR PATHOLOGY. TRADITIONALLY, HOWEVER, EXPRESSION STUDIES IN POSTMORTEM BRAIN WERE CONFINED TO QUANTIFICATION OF MRNA OR PROTEIN. THE LIMITATIONS ENCOUNTERED IN POSTMORTEM BRAIN RESEARCH SUCH AS VARIABILITIES IN AUTOLYSIS TIME AND TISSUE INTEGRITIES ARE ALSO LIKELY TO IMPACT ANY STUDIES OF HIGHER ORDER CHROMATIN STRUCTURES. HOWEVER, THE NUCLEOSOMAL ORGANIZATION OF GENOMIC DNA INCLUDING DNA:CORE HISTONE BINDING - APPEARS TO BE LARGELY PRESERVED IN REPRESENTATIVE SAMPLES PROVIDED BY VARIOUS BRAIN BANKS. THEREFORE, IT IS POSSIBLE TO STUDY THE METHYLATION PATTERN AND OTHER COVALENT MODIFICATIONS OF THE CORE HISTONES AT DEFINED GENOMIC LOCI IN POSTMORTEM BRAIN. HERE, WE PRESENT A SIMPLIFIED NATIVE CHROMATIN IMMUNOPRECIPITATION (NCHIP) PROTOCOL FOR FROZEN (NEVER-FIXED) HUMAN BRAIN SPECIMENS. STARTING WITH MICROCOCCAL NUCLEASE DIGESTION OF BRAIN HOMOGENATES, NCHIP FOLLOWED BY QPCR CAN BE COMPLETED WITHIN THREE DAYS. THE METHODOLOGY PRESENTED HERE SHOULD BE USEFUL TO ELUCIDATE EPIGENETIC MECHANISMS OF GENE EXPRESSION IN NORMAL AND DISEASED HUMAN BRAIN. 2008 14 1240 29 CURRENT ADVANCES OF EPIGENETICS IN PERIODONTOLOGY FROM ENCODE PROJECT: A REVIEW AND FUTURE PERSPECTIVES. BACKGROUND: THE ENCYCLOPEDIA OF DNA ELEMENTS (ENCODE) PROJECT HAS ADVANCED OUR KNOWLEDGE OF THE FUNCTIONAL ELEMENTS IN THE GENOME AND EPIGENOME. THE AIM OF THIS ARTICLE WAS TO PROVIDE THE COMPREHENSION ABOUT CURRENT RESEARCH TRENDS FROM ENCODE PROJECT AND ESTABLISH THE LINK BETWEEN EPIGENETICS AND PERIODONTAL DISEASES BASED ON EPIGENOME STUDIES AND SEEK THE FUTURE DIRECTION. MAIN BODY: GLOBAL EPIGENOME RESEARCH PROJECTS HAVE EMPHASIZED THE IMPORTANCE OF EPIGENETIC RESEARCH FOR UNDERSTANDING HUMAN HEALTH AND DISEASE, AND CURRENT INTERNATIONAL CONSORTIA SHOW AN IMPROVED INTEREST IN THE IMPORTANCE OF ORAL HEALTH WITH SYSTEMIC HEALTH. THE EPIGENETIC STUDIES IN DENTAL FIELD HAVE BEEN MAINLY CONDUCTED IN PERIODONTOLOGY AND HAVE FOCUSED ON DNA METHYLATION ANALYSIS. ADVANCES IN SEQUENCING TECHNOLOGY HAVE BROADENED THE TARGET FOR EPIGENETIC STUDIES FROM SPECIFIC GENES TO GENOME-WIDE ANALYSES. CONCLUSIONS: IN LINE WITH GLOBAL RESEARCH TRENDS, FURTHER EXTENDED AND ADVANCED EPIGENETIC STUDIES WOULD PROVIDE CRUCIAL INFORMATION FOR THE REALIZATION OF COMPREHENSIVE DENTAL MEDICINE AND EXPAND THE SCOPE OF ONGOING LARGE-SCALE RESEARCH PROJECTS. 2021 15 311 30 ALCOHOL AND THE METHYLOME: DESIGN AND ANALYSIS CONSIDERATIONS FOR RESEARCH USING HUMAN SAMPLES. BACKGROUND: A GROWING NUMBER OF STUDIES IN HUMAN SAMPLES HAVE SOUGHT TO DETERMINE WHETHER CHRONIC ALCOHOL USE AND ALCOHOL USE DISORDERS (AUDS) MAY BE ASSOCIATED WITH EPIGENETIC FACTORS, SUCH AS DNA METHYLATION. WE REVIEW THE EXTANT LITERATURE IN LIGHT OF SOME OF THE CHALLENGES THAT CURRENTLY AFFECT THE DESIGN AND INTERPRETATION OF EPIGENETIC RESEARCH IN HUMAN SAMPLES. METHOD: A LITERATURE SEARCH WAS USED TO IDENTIFY STUDIES THAT HAVE EXAMINED DNA METHYLATION IN RELATION TO ALCOHOL USE OR AUDS IN HUMAN SAMPLES (THROUGH JULY 2013). A TOTAL OF 22 STUDIES WERE IDENTIFIED. RESULTS: ASSOCIATIONS WITH QUANTITATIVE OR DIAGNOSTIC PHENOTYPES OF ALCOHOL USE OR AUDS HAVE BEEN REPORTED FOR SEVERAL GENES. HOWEVER, ALL STUDIES TO DATE HAVE RELIED ON RELATIVELY SMALL SAMPLES AND CROSS-SECTIONAL STUDY DESIGNS. ADDITIONALLY, ATTEMPTS TO REPLICATE RESULTS HAVE BEEN RARE. MORE GENERALLY, RESEARCH PROGRESS IS HAMPERED BY SEVERAL ISSUES, INCLUDING LIMITATIONS OF THE TECHNOLOGIES USED TO ASSESS DNA METHYLATION, TISSUE- AND CELL-SPECIFICITY OF METHYLATION PATTERNS, THE DIFFICULTIES OF RELATING OBSERVED METHYLATION DIFFERENCES AT A GIVEN LOCUS TO A FUNCTIONAL EFFECT, AND LIMITED KNOWLEDGE ABOUT THE MOLECULAR MECHANISMS UNDERLYING THE EFFECTS OF ALCOHOL ON DNA METHYLATION. CONCLUSIONS: ALTHOUGH WE SHARE THE OPTIMISM THAT EPIGENETICS MAY LEAD TO NEW INSIGHTS INTO THE ETIOLOGY AND PATHOPHYSIOLOGY OF AUDS, THE METHODOLOGICAL AND SCIENTIFIC CHALLENGES ASSOCIATED WITH CONDUCTING METHYLOMIC RESEARCH IN HUMAN SAMPLES NEED TO BE CAREFULLY CONSIDERED WHEN DESIGNING AND EVALUATING SUCH STUDIES. 2013 16 6676 33 USING EPIGENETIC TOOLS TO INVESTIGATE ANTIDEPRESSANT RESPONSE. MAJOR DEPRESSIVE DISORDER IS A CHRONIC AND DEBILITATING ILLNESS. IT IS MOST COMMONLY TREATED WITH ANTIDEPRESSANT DRUGS, HOWEVER, AS THE MAJORITY OF PATIENTS DO NOT RESPOND ON THEIR FIRST TRIAL OR FOLLOWING SEVERAL ADEQUATE TRIALS, THERE IS GREAT INTEREST IN IDENTIFYING BIOLOGICAL FACTORS THAT MAY HELP SELECT THE MOST APPROPRIATE TREATMENT FOR EACH PATIENT AND IN UNDERSTANDING BIOLOGICAL PROCESSES THAT MEDIATE TREATMENT RESPONSE. EPIGENETIC FACTORS, SUCH AS NON-CODING RNAS (NCRNAS), HOLD POTENTIAL AS BIOMARKERS OF ANTIDEPRESSANT RESPONSE. IN THIS CHAPTER, WE REVIEW KEY METHODOLOGICAL CONSIDERATIONS WHEN INVESTIGATING NCRNA BIOMARKERS, INCLUDING BIOLOGICAL SAMPLES AND TECHNOLOGIES WHICH HAVE BEEN USED IN THESE STUDIES. SECONDLY, WE SUMMARIZE FINDINGS FROM STUDIES INVESTIGATING NCRNAS IN ANTIDEPRESSANT TREATMENT RESPONSE. FINALLY, WE DISCUSS SOME OF THE FUTURE DIRECTIONS WHICH WILL BE NECESSARY FOR THE DEVELOPMENT OF CLINICALLY RELEVANT EPIGENETIC TOOLS. 2018 17 2107 30 EPIGENETIC FACTORS IN SCHIZOPHRENIA: MECHANISMS AND EXPERIMENTAL APPROACHES. SCHIZOPHRENIA IS A CHRONIC MENTAL DISORDER THAT IS STILL POORLY UNDERSTOOD DESPITE DECADES OF STUDY. MANY FACTORS HAVE BEEN FOUND TO CONTRIBUTE TO THE PATHOGENESIS, INCLUDING NEURODEVELOPMENTAL DISTURBANCE, GENETIC RISK, AND ENVIRONMENTAL INSULT, BUT NO SINGLE ROOT CAUSE HAS EMERGED. WHILE EVIDENCE FROM TWIN STUDIES SUGGESTS A STRONG HERITABLE COMPONENT, FEW INDIVIDUAL LOCI HAVE BEEN IDENTIFIED IN GENOMEWIDE SCREENS, SUGGESTING A ROLE FOR EPIGENETIC EFFECTS. RATHER, LARGE NUMBERS OF WEAKLY ACTING LOCI MAY CUMULATIVELY INCREASE DISEASE RISK, INCLUDING SEVERAL MAPPING TO EPIGENETIC PATHWAYS. IN THIS REVIEW, WE DISCUSS MECHANISMS OF EPIGENETIC REGULATION AND EVIDENCE FOR AN EPIGENETIC CONTRIBUTION TO DISEASE PHENOTYPE. WE FURTHER DESCRIBE THE RANGE OF EXPERIMENTAL TOOLS CURRENTLY AVAILABLE TO STUDY EPIGENETIC EFFECTS ASSOCIATED WITH THE DISEASE. 2019 18 6317 32 THE RELEVANCE OF INTER- AND INTRASTRAIN DIFFERENCES IN MICE AND RATS AND THEIR IMPLICATIONS FOR MODELS OF SEIZURES AND EPILEPSY. IT IS BECOMING INCREASINGLY CLEAR THAT THE GENETIC BACKGROUND OF MICE AND RATS, EVEN IN INBRED STRAINS, CAN HAVE A PROFOUND INFLUENCE ON MEASURES OF SEIZURE SUSCEPTIBILITY AND EPILEPSY. THESE DIFFERENCES CAN BE CAPITALIZED UPON THROUGH GENETIC MAPPING STUDIES TO REVEAL GENES IMPORTANT FOR SEIZURES AND EPILEPSY. HOWEVER, STRAIN BACKGROUND AND PARTICULARLY MIXED GENETIC BACKGROUNDS OF TRANSGENIC ANIMALS NEED CAREFUL CONSIDERATION IN BOTH THE SELECTION OF STRAINS AND IN THE INTERPRETATION OF RESULTS AND CONCLUSIONS. FOR INSTANCE, MICE WITH TARGETED DELETIONS OF GENES INVOLVED IN EPILEPSY CAN HAVE PROFOUNDLY DISPARATE PHENOTYPES DEPENDING ON THE BACKGROUND STRAIN. IN THIS REVIEW, WE DISCUSS FINDINGS RELATED TO HOW THIS GENETIC HETEROGENEITY HAS AND CAN BE UTILIZED IN THE EPILEPSY FIELD TO REVEAL NOVEL INSIGHTS INTO SEIZURES AND EPILEPSY. MOREOVER, WE DISCUSS HOW CAUTION IS NEEDED IN REGARDS TO RODENT STRAIN OR EVEN ANIMAL VENDOR CHOICE, AND HOW THIS CAN SIGNIFICANTLY INFLUENCE SEIZURE AND EPILEPSY PARAMETERS IN UNEXPECTED WAYS. THIS IS PARTICULARLY CRITICAL IN DECISIONS REGARDING THE STRAIN OF CHOICE USED IN GENERATING MICE WITH TARGETED DELETIONS OF GENES. FINALLY, WE DISCUSS THE ROLE OF ENVIRONMENT (AT VENDOR AND/OR LABORATORY) AND EPIGENETIC FACTORS FOR INTER- AND INTRASTRAIN DIFFERENCES AND HOW SUCH DIFFERENCES CAN AFFECT THE EXPRESSION OF SEIZURES AND THE ANIMALS' PERFORMANCE IN BEHAVIORAL TESTS THAT OFTEN ACCOMPANY ACUTE AND CHRONIC SEIZURE TESTING. 2017 19 4911 17 PAIN IMAGING: FUTURE APPLICATIONS TO INTEGRATIVE CLINICAL AND BASIC NEUROBIOLOGY. WE HAVE ENTERED A NEW ERA IN UNDERSTANDING CNS CIRCUITRY INVOLVED IN ACUTE AND CHRONIC PAIN. THE ABILITY TO OBJECTIVELY MEASURE A PAIN OR ANALGESIC STATE OF THE BRAIN USING NON-INVASIVE METHODS THAT DEFINE NEURAL ACTIVATION PROVIDES THE POSSIBILITY FOR TOP-DOWN APPROACHES TO DRUG DISCOVERY. THESE BRAIN MAPS REPRESENT THE SPECIFIC BRAIN STATE. IN THE FUTURE, CORRELATIONS WITH SUCH STATES AND BEHAVIORAL, GENETIC, EPIGENETIC OR OTHER CHEMICAL MARKERS MAY HELP DEFINE SPECIFIC DIAGNOSTIC TOOLS AND NOVEL APPROACHES TO DRUG DISCOVERY. 2003 20 2404 38 EPIGENETIC RESEARCH IN MULTIPLE SCLEROSIS: PROGRESS, CHALLENGES, AND OPPORTUNITIES. MULTIPLE SCLEROSIS (MS) IS A CHRONIC INFLAMMATORY AND DEMYELINATING DISEASE OF THE CENTRAL NERVOUS SYSTEM. MS LIKELY RESULTS FROM A COMPLEX INTERPLAY BETWEEN PREDISPOSING CAUSAL GENE VARIANTS (THE STRONGEST INFLUENCE COMING FROM HLA CLASS II LOCUS) AND ENVIRONMENTAL RISK FACTORS SUCH AS SMOKING, INFECTIOUS MONONUCLEOSIS, AND LACK OF SUN EXPOSURE/VITAMIN D. HOWEVER, LITTLE IS KNOWN ABOUT THE MECHANISMS UNDERLYING MS DEVELOPMENT AND PROGRESSION. MOREOVER, THE CLINICAL HETEROGENEITY AND VARIABLE RESPONSE TO TREATMENT REPRESENT ADDITIONAL CHALLENGES TO A COMPREHENSIVE UNDERSTANDING AND EFFICIENT TREATMENT OF DISEASE. EPIGENETIC PROCESSES, SUCH AS DNA METHYLATION AND HISTONE POSTTRANSLATIONAL MODIFICATIONS, INTEGRATE INFLUENCES FROM THE GENES AND THE ENVIRONMENT TO REGULATE GENE EXPRESSION ACCORDINGLY. STUDYING EPIGENETIC MODIFICATIONS, WHICH ARE STABLE AND REVERSIBLE, MAY PROVIDE AN ALTERNATIVE APPROACH TO BETTER UNDERSTAND AND MANAGE DISEASE. WE HERE AIM TO REVIEW FINDINGS FROM EPIGENETIC STUDIES IN MS AND FURTHER DISCUSS THE CHALLENGES AND CLINICAL OPPORTUNITIES ARISING FROM EPIGENETIC RESEARCH, MANY OF WHICH APPLY TO OTHER DISEASES WITH SIMILAR COMPLEX ETIOLOGY. A GROWING BODY OF EVIDENCE SUPPORTS A ROLE OF EPIGENETIC PROCESSES IN THE MECHANISMS UNDERLYING IMMUNE PATHOGENESIS AND NERVOUS SYSTEM DYSFUNCTION IN MS. HOWEVER, DISPARITIES BETWEEN STUDIES SHED LIGHT ON THE NEED TO CONSIDER POSSIBLE CONFOUNDERS AND METHODOLOGICAL LIMITATIONS FOR A BETTER INTERPRETATION OF THE DATA. NEVERTHELESS, TRANSLATIONAL USE OF EPIGENETICS MIGHT OFFER NEW OPPORTUNITIES IN EPIGENETIC-BASED DIAGNOSTICS AND THERAPEUTIC TOOLS FOR A PERSONALIZED CARE OF MS PATIENTS. 2017