1 1281 99 DECIPHERING NEURODEGENERATIVE DISEASES USING LONG-READ SEQUENCING. NEURODEGENERATIVE DISEASES EXHIBIT CHRONIC PROGRESSIVE LESIONS IN THE CENTRAL AND PERIPHERAL NERVOUS SYSTEMS WITH UNCLEAR CAUSES. THE SEARCH FOR PATHOGENIC MUTATIONS IN HUMAN NEURODEGENERATIVE DISEASES HAS BENEFITED FROM MASSIVELY PARALLEL SHORT-READ SEQUENCERS. HOWEVER, GENOMIC REGIONS, INCLUDING REPETITIVE ELEMENTS, ESPECIALLY WITH HIGH/LOW GC CONTENT, ARE FAR BEYOND THE CAPABILITY OF CONVENTIONAL APPROACHES. RECENTLY, LONG-READ SINGLE-MOLECULE DNA SEQUENCING TECHNOLOGIES HAVE EMERGED AND ENABLED RESEARCHERS TO STUDY GENOMES, TRANSCRIPTOMES, AND METAGENOMES AT UNPRECEDENTED RESOLUTIONS. THE IDENTIFICATION OF NOVEL MUTATIONS IN UNRESOLVED NEURODEGENERATIVE DISORDERS, THE CHARACTERIZATION OF CAUSATIVE REPEAT EXPANSIONS, AND THE DIRECT DETECTION OF EPIGENETIC MODIFICATIONS ON NAIVE DNA BY VIRTUE OF LONG-READ SEQUENCERS WILL FURTHER EXPAND OUR UNDERSTANDING OF NEURODEGENERATIVE DISEASES. IN THIS ARTICLE, WE REVIEW AND COMPARE 2 PREVAILING LONG-READ SEQUENCING TECHNOLOGIES, PACIFIC BIOSCIENCES AND OXFORD NANOPORE TECHNOLOGIES, AND DISCUSS THEIR APPLICATIONS IN NEURODEGENERATIVE DISEASES. 2021 2 4590 27 NANOPORE SEQUENCING IDENTIFIES DIFFERENTIALLY METHYLATED GENES IN THE CENTRAL NERVOUS SYSTEM IN EXPERIMENTAL AUTOIMMUNE ENCEPHALOMYELITIS. MULTIPLE SCLEROSIS (MS) IS A CHRONIC AUTOIMMUNE-MEDIATED DEMYELINATING DISEASE OF THE CENTRAL NERVOUS SYSTEM (CNS) THAT MIGHT BE TRIGGERED BY ABERRANT EPIGENETIC CHANGES IN THE GENOME. DNA METHYLATION IS THE MOST STUDIED EPIGENETIC MECHANISM THAT PARTICIPATES IN MS PATHOGENESIS. HOWEVER, THE OVERALL METHYLATION LEVEL IN THE CNS OF MS PATIENTS REMAINS ELUSIVE. WE USED DIRECT LONG-READ NANOPORE DNA SEQUENCING AND CHARACTERIZED THE DIFFERENTIALLY METHYLATED GENES IN THE BRAIN FROM MICE WITH EXPERIMENTAL AUTOIMMUNE ENCEPHALOMYELITIS (EAE), AN ANIMAL MODEL OF MS. WE IDENTIFIED 163 HYPOMETHYLATED PROMOTERS AND 327 HYPERMETHYLATED PROMOTERS. THESE GENOMIC ALTERATIONS WERE LINKED TO VARIOUS BIOLOGICAL PROCESSES INCLUDING METABOLISM, IMMUNE RESPONSES, NEURAL ACTIVITIES, AND MITOCHONDRIAL DYNAMICS, ALL OF WHICH ARE VITAL FOR EAE DEVELOPMENT. OUR RESULTS INDICATE A GREAT POTENTIAL OF NANOPORE SEQUENCING IN IDENTIFYING GENOMIC DNA METHYLATION IN EAE AND PROVIDE IMPORTANT GUIDANCE FOR FUTURE STUDIES INVESTIGATING THE MS/EAE PATHOLOGY. 2023 3 2404 26 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 4 2695 22 EVOLVING UNDERSTANDING OF THE CLL GENOME. OVER THE PAST FEW YEARS, MASSIVELY PARALLEL SEQUENCING TECHNOLOGIES HAVE REVEALED WITH HIGH RESOLUTION THE TREMENDOUS GENETIC AND EPIGENETIC HETEROGENEITY IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). WE HAVE LEARNED HOW THE MOLECULAR ARCHITECTURE DIFFERS NOT ONLY BETWEEN AFFECTED INDIVIDUALS BUT ALSO WITHIN SAMPLES AND OVER TIME. THESE INSIGHTS HAVE CATALYZED OUR UNDERSTANDING OF THE PATHOBIOLOGY OF CLL AND POINT TO CRITICAL SIGNALING PATHWAYS IN THE DEVELOPMENT AND PROGRESSION OF THE DISEASE. SEVERAL KEY DRIVER ALTERATIONS HAVE BEEN IDENTIFIED, WHICH SERVE TO REFINE PROGNOSTIC SCHEMATA BUT ALSO TO INSPIRE THE DEVELOPMENT OF NEW THERAPEUTIC STRATEGIES. ONGOING ADVANCES IN TECHNOLOGY PROMISE TO FURTHER ELUCIDATE THE MOLECULAR BASIS OF CLL, AND THIS KNOWLEDGE IS ANTICIPATED TO AID US IN UNDERSTANDING AND ADDRESSING THE CLINICAL CHALLENGE PRESENTED BY THE VAST VARIABILITY IN THE CLINICAL COURSE OF PATIENTS WITH CLL. 2014 5 3651 30 INCREASING COMPLEXITY OF MOLECULAR LANDSCAPES IN HUMAN HEMATOPOIETIC STEM AND PROGENITOR CELLS DURING DEVELOPMENT AND AGING. THE PAST FIVE DECADES HAVE SEEN SIGNIFICANT PROGRESS IN OUR UNDERSTANDING OF HUMAN HEMATOPOIESIS. THIS HAS IN PART BEEN DUE TO THE UNPRECEDENTED DEVELOPMENT OF ADVANCED TECHNOLOGIES, WHICH HAVE ALLOWED THE IDENTIFICATION AND CHARACTERIZATION OF RARE SUBSETS OF HUMAN HEMATOPOIETIC STEM AND PROGENITOR CELLS AND THEIR LINEAGE TRAJECTORIES FROM EMBRYONIC THROUGH TO ADULT LIFE. ADDITIONALLY, SURROGATE IN VITRO AND IN VIVO MODELS, ALTHOUGH NOT FULLY RECAPITULATING HUMAN HEMATOPOIESIS, HAVE SPURRED ON THESE SCIENTIFIC ADVANCES. THESE APPROACHES HAVE HEIGHTENED OUR KNOWLEDGE OF HEMATOLOGICAL DISORDERS AND DISEASES AND HAVE LED TO THEIR IMPROVED DIAGNOSIS AND THERAPIES. HERE, WE REVIEW HUMAN HEMATOPOIESIS AT EACH END OF THE AGE SPECTRUM, DURING EMBRYONIC AND FETAL DEVELOPMENT AND ON AGING, PROVIDING EXEMPLARS OF RECENT PROGRESS IN DECIPHERING THE INCREASINGLY COMPLEX CELLULAR AND MOLECULAR HEMATOPOIETIC LANDSCAPES IN HEALTH AND DISEASE. THIS REVIEW CONCLUDES BY HIGHLIGHTING LINKS BETWEEN CHRONIC INFLAMMATION AND METABOLIC AND EPIGENETIC CHANGES ASSOCIATED WITH AGING AND IN THE DEVELOPMENT OF CLONAL HEMATOPOIESIS. 2022 6 2139 26 EPIGENETIC INSIGHTS INTO MULTIPLE SCLEROSIS DISEASE PROGRESSION. MULTIPLE SCLEROSIS (MS), A CHRONIC INFLAMMATORY DEMYELINATING AND NEURODEGENERATIVE DISEASE OF THE CENTRAL NERVOUS SYSTEM, IS TODAY A LEADING CAUSE OF UNPREDICTABLE LIFELONG DISABILITY IN YOUNG ADULTS. THE TREATMENT OF PATIENTS IN PROGRESSIVE STAGES REMAINS HIGHLY CHALLENGING, ALLUDING TO OUR LIMITED UNDERSTANDING OF THE UNDERLYING PATHOLOGICAL PROCESSES. IN THIS REVIEW, WE PROVIDE INSIGHTS INTO THE MECHANISMS UNDERPINNING MS PROGRESSION FROM A PERSPECTIVE OF EPIGENETICS, THAT REFERS TO STABLE AND MITOTICALLY HERITABLE, YET REVERSIBLE, CHANGES IN THE GENOME ACTIVITY AND GENE EXPRESSION. WE FIRST RECAPITULATE FINDINGS FROM EPIGENETIC STUDIES EXAMINING THE BRAIN TISSUE OF PROGRESSIVE MS PATIENTS, WHICH SUPPORT A CONTRIBUTION OF DNA AND HISTONE MODIFICATIONS IN IMPAIRED OLIGODENDROCYTE DIFFERENTIATION, DEFECTIVE MYELINATION/REMYELINATION AND SUSTAINED NEURO-AXONAL VULNERABILITY. WE NEXT EXPLORE POSSIBILITIES FOR IDENTIFYING FACTORS AFFECTING PROGRESSION USING EASILY ACCESSIBLE TISSUES SUCH AS BLOOD BY COMPARING EPIGENETIC SIGNATURES IN PERIPHERAL IMMUNE CELLS AND BRAIN TISSUE. DESPITE MINOR OVERLAP AT INDIVIDUAL METHYLATION SITES, NEARLY 30% OF ALTERED GENES REPORTED IN PERIPHERAL IMMUNE CELLS OF PROGRESSIVE MS PATIENTS WERE FOUND IN BRAIN TISSUE, JOINTLY CONVERGING ON ALTERATIONS OF NEURONAL FUNCTIONS. WE FURTHER SPECULATE ABOUT THE MECHANISMS UNDERLYING SHARED EPIGENETIC PATTERNS BETWEEN BLOOD AND BRAIN, WHICH LIKELY IMPLY THE INFLUENCE OF INTERNAL (GENETIC CONTROL) AND/OR EXTERNAL (E.G. SMOKING AND AGEING) FACTORS IMPRINTING A COMMON SIGNATURE IN BOTH COMPARTMENTS. OVERALL, WE PROPOSE THAT EPIGENETICS MIGHT SHED LIGHT ON CLINICALLY RELEVANT MECHANISMS INVOLVED IN DISEASE PROGRESSION AND OPEN NEW AVENUES FOR THE TREATMENT OF PROGRESSIVE MS PATIENTS IN THE FUTURE. 2020 7 2447 28 EPIGENETIC STUDIES IN ALZHEIMER'S DISEASE: CURRENT FINDINGS, CAVEATS, AND CONSIDERATIONS FOR FUTURE STUDIES. ALZHEIMER'S DISEASE (AD) IS A SPORADIC, CHRONIC NEURODEGENERATIVE DISEASE, USUALLY OCCURRING LATE IN LIFE. THE LAST DECADE HAS WITNESSED TREMENDOUS ADVANCES IN OUR UNDERSTANDING ABOUT THE GENETIC BASIS OF AD, BUT A LARGE AMOUNT OF THE VARIANCE IN DISEASE RISK REMAINS TO BE EXPLAINED. EPIGENETIC MECHANISMS, WHICH DEVELOPMENTALLY REGULATE GENE EXPRESSION VIA MODIFICATIONS TO DNA, HISTONE PROTEINS, AND CHROMATIN, HAVE BEEN HYPOTHESIZED TO PLAY A ROLE IN OTHER COMPLEX NEUROBIOLOGICAL DISEASES, AND STUDIES TO IDENTIFY GENOME-WIDE EPIGENETIC CHANGES IN AD ARE CURRENTLY UNDER WAY. HOWEVER, THE SIMPLE BRUTE-FORCE APPROACH THAT HAS BEEN SUCCESSFULLY EMPLOYED IN GENOME-WIDE ASSOCIATION STUDIES IS UNLIKELY TO BE SUCCESSFUL IN EPIGENOME-WIDE ASSOCIATION STUDIES OF NEURODEGENERATION. A MORE ACADEMIC APPROACH TO UNDERSTANDING THE ROLE OF EPIGENETIC VARIATION IN AD IS REQUIRED, WITH CAREFUL CONSIDERATION OF STUDY DESIGN, METHODOLOGICAL APPROACHES, TISSUE-SPECIFICITY, AND CAUSAL INFERENCE. IN THIS ARTICLE, WE REVIEW THE EMPIRICAL LITERATURE SUPPORTING A ROLE FOR EPIGENETIC PROCESSES IN AD, AND DISCUSS IMPORTANT CONSIDERATIONS AND FUTURE DIRECTIONS FOR THIS NEW AND EMERGING FIELD OF RESEARCH. 2013 8 3089 20 GENOMIC AND EPIGENOMIC ALTERATIONS IN CHRONIC LYMPHOCYTIC LEUKEMIA. CHRONIC LYMPHOCYTIC LEUKEMIA IS A COMMON DISEASE IN WESTERN COUNTRIES AND HAS HETEROGENEOUS CLINICAL BEHAVIOR. THE RELEVANCE OF THE GENETIC BASIS OF THE DISEASE HAS COME TO THE FOREFRONT RECENTLY, WITH GENOME-WIDE STUDIES THAT HAVE PROVIDED A COMPREHENSIVE VIEW OF STRUCTURAL VARIANTS, SOMATIC MUTATIONS, AND DIFFERENT LAYERS OF EPIGENETIC CHANGES. THE MUTATIONAL LANDSCAPE IS CHARACTERIZED BY RELATIVELY COMMON COPY NUMBER ALTERATIONS, A FEW MUTATED GENES OCCURRING IN 10-15% OF CASES, AND A LARGE NUMBER OF GENES MUTATED IN A SMALL NUMBER OF CASES. THE EPIGENOMIC PROFILE HAS REVEALED A MARKED REPROGRAMMING OF REGULATORY REGIONS IN TUMOR CELLS COMPARED WITH NORMAL B CELLS. ALL OF THESE ALTERATIONS ARE DIFFERENTIALLY DISTRIBUTED IN CLINICAL AND BIOLOGICAL SUBSETS OF THE DISEASE, INDICATING THAT THEY MAY UNDERLIE THE HETEROGENEOUS EVOLUTION OF THE DISEASE. THESE GLOBAL STUDIES ARE REVEALING THE MOLECULAR COMPLEXITY OF CHRONIC LYMPHOCYTIC LEUKEMIA AND PROVIDE NEW PERSPECTIVES THAT HAVE HELPED TO UNDERSTAND ITS PATHOGENIC MECHANISMS AND IMPROVE THE CLINICAL MANAGEMENT OF PATIENTS. 2020 9 3038 24 GENOME ENGINEERING FOR OSTEOARTHRITIS: FROM DESIGNER CELLS TO DISEASE-MODIFYING DRUGS. BACKGROUND: OSTEOARTHRITIS (OA) IS A HIGHLY PREVALENT DEGENERATIVE JOINT DISEASE INVOLVING JOINT CARTILAGE AND ITS SURROUNDING TISSUES. OA IS THE LEADING CAUSE OF PAIN AND DISABILITY WORLDWIDE. AT PRESENT, THERE ARE NO DISEASE-MODIFYING OA DRUGS, AND THE PRIMARY THERAPIES INCLUDE EXERCISE AND NONSTEROIDAL ANTI-INFLAMMATORY DRUGS UNTIL TOTAL JOINT REPLACEMENT AT THE END-STAGE OF THE DISEASE. METHODS: IN THIS REVIEW, WE SUMMARIZED THE CURRENT STATE OF KNOWLEDGE IN GENETIC AND EPIGENETIC ASSOCIATIONS AND RISK FACTORS FOR OA AND THEIR POTENTIAL DIAGNOSTIC AND THERAPEUTIC APPLICATIONS. RESULTS: GENOME-WIDE ASSOCIATION STUDIES AND ANALYSIS OF EPIGENETIC MODIFICATIONS (SUCH AS MIRNA EXPRESSION, DNA METHYLATION AND HISTONE MODIFICATIONS) CONDUCTED ACROSS VARIOUS POPULATIONS SUPPORT THE NOTION THAT THERE IS A GENETIC BASIS FOR CERTAIN SUBSETS OF OA PATHOGENESIS. CONCLUSION: WITH RECENT ADVANCES IN THE DEVELOPMENT OF GENOME EDITING TECHNOLOGIES SUCH AS THE CRISPR-CAS9 SYSTEM, THESE GENETIC AND EPIGENETIC ALTERNATIONS IN OA CAN BE USED AS PLATFORMS FROM WHICH POTENTIAL BIOMARKERS FOR THE DIAGNOSIS, PROGNOSIS, DRUG RESPONSE, AND DEVELOPMENT OF POTENTIAL PERSONALIZED THERAPEUTIC TARGETS FOR OA CAN BE APPROACHED. FURTHERMORE, GENOME EDITING HAS ALLOWED THE DEVELOPMENT OF "DESIGNER" CELLS, WHEREBY THE RECEPTORS, GENE REGULATORY NETWORKS, OR TRANSGENES CAN BE MODIFIED AS A BASIS FOR NEW CELL-BASED THERAPIES. 2019 10 1518 26 DNA METHYLATION AS AN EPIGENETIC MECHANISM IN THE DEVELOPMENT OF MULTIPLE SCLEROSIS. THE EPIGENETIC MECHANISMS OF GENE EXPRESSION REGULATION ARE A GROUP OF THE KEY CELLULAR AND MOLECULAR PATHWAYS THAT LEAD TO INHERITED ALTERATIONS IN GENES' ACTIVITY WITHOUT CHANGING THEIR CODING SEQUENCE. DNA METHYLATION AT THE C5 POSITION OF CYTOSINE IN CPG DINUCLEOTIDES IS AMONGST THE CENTRAL EPIGENETIC MECHANISMS. CURRENTLY, THE NUMBER OF STUDIES THAT ARE DEVOTED TO THE IDENTIFICATION OF METHYLATION PATTERNS SPECIFIC TO MULTIPLE SCLEROSIS (MS), A SEVERE CHRONIC AUTOIMMUNE DISEASE OF THE CENTRAL NERVOUS SYSTEM, IS ON A RAPID RISE. HOWEVER, THE ISSUE OF THE CONTRIBUTION OF DNA METHYLATION TO THE DEVELOPMENT OF THE DIFFERENT CLINICAL PHENOTYPES OF THIS HIGHLY HETEROGENEOUS DISEASE HAS ONLY BEGUN TO ATTRACT THE ATTENTION OF RESEARCHERS. THIS REVIEW SUMMARIZES THE DATA ON THE MOLECULAR MECHANISMS UNDERLYING DNA METHYLATION AND THE MS RISK FACTORS THAT CAN AFFECT THE DNA METHYLATION PROFILE AND, THEREBY, MODULATE THE EXPRESSION OF THE GENES INVOLVED IN THE DISEASE'S PATHOGENESIS. THE FOCUS OF OUR ATTENTION IS CENTERED ON THE ANALYSIS OF THE PUBLISHED DATA ON THE DIFFERENTIAL METHYLATION OF DNA FROM VARIOUS BIOLOGICAL SAMPLES OF MS PATIENTS OBTAINED USING BOTH THE CANDIDATE GENE APPROACH AND HIGH-THROUGHPUT METHODS. 2021 11 3028 22 GENETICS OF COMPLEX AIRWAY DISEASE. THE PAST 3 YEARS HAVE SEEN HIGHLY SIGNIFICANT GENETIC EFFECTS IDENTIFIED FOR A WIDE VARIETY OF COMMON COMPLEX DISEASES, INCLUDING THE AIRWAY DISORDERS OF ASTHMA AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE. IT APPEARS THAT ONLY A PORTION OF THE GENETICALLY MEDIATED SUSCEPTIBILITY TO COMPLEX DISEASES HAS BEEN IDENTIFIED, AND THERE IS MUCH LEFT TO BE DISCOVERED. THIS REVIEW BRIEFLY DESCRIBES THE RESULTS OF THE GENOME-WIDE ASSOCIATION STUDIES OF ASTHMA AND GIVES AN OVERVIEW OF THE PARALLEL AND INCREASINGLY LARGE-SCALE STUDIES THAT ARE TAKING PLACE WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE. THE FUTURE IMPACT IS DISCUSSED OF TECHNOLOGICAL ADVANCES THAT ALLOW INCREASINGLY LARGE-SCALE GENE EXPRESSION STUDIES, NEXT-GENERATION SEQUENCING, AND GENOME-WIDE TESTING FOR EPIGENETIC EFFECTS. THE USE OF GENETIC TECHNOLOGY TO EXAMINE THE AIRWAY MICROBIOTA THAT INTERACT WITH THE MUCOSA IN HEALTH AND DISEASE IS DESCRIBED. 2011 12 3108 20 GENOMICS OF PAIN IN OSTEOARTHRITIS. OSTEOARTHRITIS (OA) ACCOUNTS FOR THE MAJORITY OF THE DISEASE BURDEN FOR MUSCULOSKELETAL DISORDERS AND IS ONE OF THE LEADING CAUSES OF DISABILITY WORLDWIDE. THIS DISABILITY IS THE RESULT NOT OF THE CARTILAGE LOSS THAT DEFINES OA RADIOGRAPHICALLY, BUT OF THE CHRONIC PAIN WHOSE PRESENCE DEFINES SYMPTOMATIC OA. IT IS BECOMING CLEAR THAT MANY GENES, EACH WITH A SMALL EFFECT SIZE, CONTRIBUTE TO THE RISK OF DEVELOPING OA. HOWEVER, THE GENETICS OF OA PAIN ARE ONLY JUST STARTING TO BE EXPLORED. THIS REVIEW WILL DESCRIBE THE FIRST GENES TO HAVE BEEN IDENTIFIED IN GENOMIC STUDIES OF OA PAIN, AS WELL AS THE POSSIBLE DUAL ROLES OF GENES PREVIOUSLY IDENTIFIED IN GENOMIC STUDIES OF OA IN THE CONTEXT OF PAIN. DIFFICULTIES ASSOCIATED WITH ATTEMPTING TO CHARACTERISE THE GENETICS OF OA PAIN WILL BE DISCUSSED AND PROMISING FUTURE AVENUES OF RESEARCH INTO GENETIC AND EPIGENETIC FACTORS AFFECTING OA PAIN DESCRIBED. 2013 13 5913 20 TARGETED THERAPY IN LEUKEMIA. RESEARCH CONDUCTED OVER THE LAST TWO DECADES HAS YIELDED A DETAILED UNDERSTANDING OF THE MOLECULAR LESIONS THAT CONTRIBUTE TO THE MALIGNANT TRANSFORMATION OF HEMATOPOIETIC STEM CELLS AND COMMITTED PROGENITORS INTO THE VARIOUS FORMS OF ACUTE AND CHRONIC LEUKEMIA. ALTHOUGH OUR UNDERSTANDING OF THE MOLECULAR PATHOLOGY OF LEUKEMIA REMAINS INCOMPLETE, THE INFORMATION GAINED TO DATE HAS HAD A PROFOUND IMPACT ON THE WAY THESE MALIGNANCIES ARE BOTH DIAGNOSED AND MONITORED DURING THERAPY. MORE RECENTLY, TARGETED THERAPIES HAVE BEEN DEVELOPED AGAINST SOME OF THE IDENTIFIED GENETIC LESIONS. THESE THERAPIES HAVE LED TO SIGNIFICANT IMPROVEMENTS IN PATIENT OUTCOMES WHILE SIMULTANEOUSLY DECREASING THERAPY-RELATED TOXICITY. WITH THE ADVENT OF GENOME-WIDE METHODS TO DEFINE THE TOTAL COMPLEMENT OF GENETIC AND EPIGENETIC LESIONS INVOLVED IN LEUKEMOGENESIS, NEW TARGETED THERAPIES CAN BE ANTICIPATED. THIS REVIEW HIGHLIGHTS SOME OF THE TARGETED THERAPIES THAT ARE PRESENTLY BEING USED TO TREAT HEMATOPOIETIC MALIGNANCIES AND DESCRIBES SOME OF THE RECENT ADVANCES THAT SHOULD HAVE A SIGNIFICANT IMPACT ON THE DEVELOPMENT OF FUTURE TARGET THERAPIES. 2008 14 4531 30 MULTILAYER-OMICS ANALYSES OF HUMAN CANCERS: EXPLORATION OF BIOMARKERS AND DRUG TARGETS BASED ON THE ACTIVITIES OF THE INTERNATIONAL HUMAN EPIGENOME CONSORTIUM. EPIGENETIC ALTERATIONS CONSISTING MAINLY OF DNA METHYLATION ALTERATIONS AND HISTONE MODIFICATION ALTERATIONS ARE FREQUENTLY OBSERVED IN CANCERS ASSOCIATED WITH CHRONIC INFLAMMATION AND/OR PERSISTENT INFECTION WITH VIRUSES OR OTHER PATHOGENIC MICROORGANISMS, OR WITH CIGARETTE SMOKING. ACCUMULATING EVIDENCE SUGGESTS THAT ALTERATIONS OF DNA METHYLATION ARE INVOLVED EVEN IN THE EARLY AND PRECANCEROUS STAGES. ON THE OTHER HAND, IN PATIENTS WITH CANCERS, ABERRANT DNA METHYLATION IS FREQUENTLY ASSOCIATED WITH TUMOR AGGRESSIVENESS AND POOR PATIENT OUTCOME. RECENTLY, EPIGENOME ALTERATIONS HAVE BEEN ATTRACTING A GREAT DEAL OF ATTENTION FROM RESEARCHERS WHO ARE FOCUSING ON NOT ONLY CANCERS BUT ALSO NEURONAL, IMMUNE AND METABOLIC DISORDERS. IN ORDER TO ACCURATELY IDENTIFY DISEASE-SPECIFIC EPIGENOME PROFILES THAT COULD BE POTENTIALLY APPLICABLE FOR DISEASE PREVENTION, DIAGNOSIS AND THERAPY, STRICT COMPARISON WITH STANDARD EPIGENOME PROFILES OF NORMAL TISSUES IS INDISPENSABLE. HOWEVER, EPIGENOME MECHANISMS SHOW HETEROGENEITY AMONG TISSUES AND CELL LINEAGES. THEREFORE, IT IS NOT EASY TO OBTAIN A COMPREHENSIVE PICTURE OF STANDARD EPIGENOME PROFILES OF NORMAL TISSUES. IN 2010, THE INTERNATIONAL HUMAN EPIGENOME CONSORTIUM (IHEC) WAS ESTABLISHED TO COORDINATE THE PRODUCTION OF REFERENCE MAPS OF HUMAN EPIGENOMES FOR KEY CELLULAR STATES. IN ORDER TO GAIN SUBSTANTIAL COVERAGE OF THE HUMAN EPIGENOME, THE IHEC HAS SET AN AMBITIOUS GOAL TO DECIPHER AT LEAST 1000 EPIGENOMES WITHIN THE NEXT 7-10 YEARS. WE CONSIDER THAT PATHWAY ANALYSIS USING GENES SHOWING MULTILAYER-OMICS ABNORMALITIES, INCLUDING GENOME, EPIGENOME, TRANSCRIPTOME, PROTEOME AND METABOLOME ABNORMALITIES, MAY BE USEFUL FOR ELUCIDATING THE MOLECULAR BACKGROUND OF PATHOGENESIS AND FOR EXPLORING POSSIBLE THERAPEUTIC TARGETS FOR EACH DISEASE. 2014 15 6843 22 [MEDICAL APPLICATIONS OF GENOME DISCOVERY]. THE DISCOVERY OF THE COMPLETE BASE SEQUENCE OF HUMAN GENOME UNVEILS SEVERAL PERSPECTIVES TO UNDERSTAND HUMAN DISEASES AND DEVELOP NEW THERAPIES. HUMAN GENOME CONTAINS APPROXIMATELY 39,000 GENES OF WHICH 26,000 CODE SPECIFIC PROTEINS THAT HAVE BEEN IDENTIFIED. THERE ARE APPROXIMATELY 1,500 DISEASES WITH IDENTIFIED MOLECULAR DISTURBANCES. GENES CAN MODIFY SIGNS AND SYMPTOMS OF COMMON DISEASES. THUS, THERE ARE NO PURE MONOGENIC DISEASES. CHRONIC DISEASES OF ADULTS ARE COMPLEX AND DEPENDENT ON MULTIPLE FACTORS. SEVERAL GENES THAT PREDISPOSE TO CHRONIC DEGENERATIVE DISEASES HAVE BEEN IDENTIFIED. THIS IS REVEALING THE COMPLEX NATURE AND THE INTERACTION OF THESE AILMENTS WITH THE ENVIRONMENT. THE DISCOVERY OF BACTERIAL AND VIRAL GENOMIC SEQUENCES WILL ALLOW THE MANUFACTURING OF NEW VACCINES AND SPECIFIC MOLECULAR ANTIMICROBIALS. THE NEW PHARMACOGENOMICS WILL DEVISE TREATMENTS FOR EACH SUBJECT ACCORDING TO HER SPECIFIC GENOMIC PROFILE. THE NEW APPLICATIONS OF GENOMIC TECHNOLOGY IS CREATING NEW PARADIGMS IN BIOMEDICAL RESEARCH SUCH AS FUNCTIONAL GENOMICS, PROTEONOMICS, EPIGENETIC REGULATION. GENE DIAGNOSIS AND THERAPY WILL CONSIDERABLY IMPROVE THE FUTURE OF MEDICINE. 2001 16 3015 22 GENETICS AND EPIGENETICS OF CLL. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) HAS A HETEROGENEOUS BIOLOGICAL BEHAVIOR, WHICH IS HIGHLY INFLUENCED BY ITS IMMUNOGENETIC, EPIGENETIC, AND GENOMIC PROPERTIES. THE REMARKABLY VARIABLE CLINICAL COURSE OF THE DISEASE HAS BEEN ASSOCIATED WITH GENETIC FEATURES SUCH AS CHROMOSOMAL ABNORMALITIES, THE PRESENCE OF EITHER HIGH OR LOW NUMBERS OF SOMATIC HYPERMUTATIONS (SHM) IN THE VARIABLE REGION OF THE IMMUNOGLOBULIN HEAVY CHAIN LOCUS (IGHV), AND SOMATIC MUTATIONS OF SEVERAL SPECIFIC DRIVER GENES. NEXT-GENERATION SEQUENCING (NGS) TECHNOLOGIES HAVE PROVIDED A COMPREHENSIVE CHARACTERIZATION OF THE GENOMIC AND EPIGENOMIC LANDSCAPE IN CLL, ELUCIDATING IMPORTANT UNDERLYING MECHANISMS OF THE DISEASE'S BIOLOGY. THE SCOPE OF THIS REVIEW IS TO SUMMARIZE THE MOST RECENT DISCOVERIES ABOUT NOVEL GENETIC AND EPIGENETIC ALTERATIONS, DISCUSSING THEIR IMPACT ON CLINICAL OUTCOMES AND RESPONSE TO CURRENTLY AVAILABLE THERAPY. 2023 17 3404 23 HOW EPIGENETICS IMPACTS ON HUMAN DISEASES. EPIGENETICS IS A RAPIDLY GROWING FIELD OF BIOLOGY THAT STUDIES THE CHANGES IN GENE EXPRESSION THAT ARE NOT DUE TO ALTERATIONS IN THE DNA SEQUENCE BUT RATHER THE CHEMICAL MODIFICATIONS OF DNA AND ITS ASSOCIATED PROTEINS. EPIGENETIC MECHANISMS CAN PROFOUNDLY INFLUENCE GENE EXPRESSION, CELL DIFFERENTIATION, TISSUE DEVELOPMENT, AND DISEASE SUSCEPTIBILITY. UNDERSTANDING EPIGENETIC CHANGES IS ESSENTIAL TO ELUCIDATE THE MECHANISMS UNDERLYING THE INCREASINGLY RECOGNIZED ROLE OF ENVIRONMENTAL AND LIFESTYLE FACTORS IN HEALTH AND DISEASE AND THE INTERGENERATIONAL TRANSMISSION OF PHENOTYPES. RECENT STUDIES SUGGEST EPIGENETICS MAY BE CRITICAL IN VARIOUS DISEASES, FROM CARDIOVASCULAR DISEASE AND CANCER TO NEURODEVELOPMENTAL AND NEURODEGENERATIVE DISORDERS. EPIGENETIC MODIFICATIONS ARE POTENTIALLY REVERSIBLE AND COULD PROVIDE NEW THERAPEUTIC AVENUES FOR TREATING THESE DISEASES USING EPIGENETIC MODULATORS. MOREOVER, EPIGENETICS PROVIDE INSIGHT INTO DISEASE PATHOGENESIS AND BIOMARKERS FOR DISEASE DIAGNOSIS AND RISK STRATIFICATION. NEVERTHELESS, EPIGENETIC INTERVENTIONS HAVE THE POTENTIAL FOR UNINTENDED CONSEQUENCES AND MAY POTENTIALLY LEAD TO INCREASED RISKS OF UNEXPECTED OUTCOMES, SUCH AS ADVERSE DRUG REACTIONS, DEVELOPMENTAL ABNORMALITIES, AND CANCER. THEREFORE, RIGOROUS STUDIES ARE ESSENTIAL TO MINIMIZE THE RISKS ASSOCIATED WITH EPIGENETIC THERAPIES AND TO DEVELOP SAFE AND EFFECTIVE INTERVENTIONS FOR IMPROVING HUMAN HEALTH. THIS ARTICLE PROVIDES A SYNTHETIC AND HISTORICAL VIEW OF THE ORIGIN OF EPIGENETICS AND SOME OF THE MOST RELEVANT ACHIEVEMENTS. 2023 18 1240 26 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 19 2333 30 EPIGENETIC REGULATION OF INFLAMMATION: THE METABOLOMICS CONNECTION. EPIGENETIC FACTORS ARE CONSIDERED THE REGULATOR OF COMPLEX MACHINERY BEHIND INFLAMMATORY DISORDERS AND SIGNIFICANTLY CONTRIBUTED TO THE EXPRESSION OF INFLAMMATION-ASSOCIATED GENES. EPIGENETIC MODIFICATIONS MODULATE VARIATION IN THE EXPRESSION PATTERN OF TARGET GENES WITHOUT AFFECTING THE DNA SEQUENCE. THE CURRENT KNOWLEDGE OF EPIGENETIC RESEARCH FOCUSED ON THEIR ROLE IN THE PATHOGENESIS OF VARIOUS INFLAMMATORY DISEASES THAT CAUSES MORBIDITY AND MORTALITY WORLDWIDE. INFLAMMATORY DISEASES ARE CATEGORIZED AS ACUTE AND CHRONIC BASED ON THE DISEASE SEVERITY AND ARE REGULATED BY THE EXPRESSION PATTERN OF VARIOUS GENES. HENCE, UNDERSTANDING THE ROLE OF EPIGENETIC MODIFICATIONS DURING INFLAMMATION PROGRESSION WILL CONTRIBUTE TO THE DISEASE OUTCOMES AND THERAPEUTIC APPROACHES. THIS REVIEW ALSO FOCUSES ON THE METABOLOMICS APPROACH ASSOCIATED WITH THE STUDY OF INFLAMMATORY DISORDERS. INFLAMMATORY RESPONSES AND METABOLIC REGULATION ARE HIGHLY INTEGRATED AND VARIOUS ADVANCED TECHNIQUES ARE ADOPTED TO STUDY THE METABOLIC SIGNATURE MOLECULES. HERE WE DISCUSS SEVERAL METABOLOMICS APPROACHES USED TO LINK INFLAMMATORY DISORDERS AND EPIGENETIC CHANGES. WE PROPOSED THAT DECIPHERING THE MECHANISM BEHIND THE INFLAMMATION-METABOLISM LOOP MAY HAVE IMMENSE IMPORTANCE IN BIOMARKERS RESEARCH AND MAY ACT AS A PRINCIPAL COMPONENT IN DRUG DISCOVERY AS WELL AS THERAPEUTIC APPLICATIONS. 2022 20 3016 22 GENETICS AND EPIGENETICS OF IBD. INFLAMMATORY BOWEL DISEASES (IBD) ARE CHRONIC INTERMITTENT INFLAMMATORY DISORDERS OF THE GASTROINTESTINAL TRACT OF UNKNOWN ETIOLOGY BUT A CLEAR GENETIC PREDISPOSITION. PROMPTED BY THE FIRST INVESTIGATIONS ON IBD FAMILIES AND TWINS, THE GENETIC AND EPIGENETIC STUDIES HAVE PRODUCED AN UNPRECEDENTED AMOUNT OF INFORMATION IN COMPARISON WITH OTHER IMMUNE-MEDIATED OR COMPLEX DISEASES. NEW INFLAMMATORY PATHWAYS AND POSSIBLE MECHANISMS OF ACTION HAVE BEEN DISCLOSED, POTENTIALLY LEADING TO NEW-TARGETED THERAPY. HOWEVER, THE IDENTIFICATION OF GENETIC MARKERS DUE TO THE GREAT DISEASE HETEROGENEITY AND THE OVERWHELMING CONTRIBUTION OF ENVIRONMENTAL RISK FACTORS HAS NOT MODIFIED YET THE DISEASE MANAGEMENT. THE POSSIBILITY FOR THE FUTURE OF A BETTER PREDICTION OF DISEASE COURSE, RESPONSE TO THERAPY AND THERAPY-RELATED ADVERSE EVENTS MAY ALLOW A MORE EFFICIENT AND PERSONALIZED STRATEGY. THIS REVIEW WILL FOCUS ON MORE RECENT DISCOVERIES THAT MAY POTENTIALLY BE OF RELEVANCE IN DAILY CLINICAL PRACTICE. 2020