1 4869 121 OSTEOARTHRITIS YEAR IN REVIEW: GENETICS, GENOMICS, EPIGENETICS. OBJECTIVE: IN THIS REVIEW, WE HAVE HIGHLIGHTED ADVANCES IN GENETICS, GENOMICS AND EPIGENETICS IN THE FIELD OF OSTEOARTHRITIS (OA) OVER THE PAST YEAR. METHODS: A LITERATURE SEARCH WAS PERFORMED USING PUBMED AND THE CRITERIA: "OSTEOARTHRITIS" AND ONE OF THE FOLLOWING TERMS "GENETIC(S), GENOMIC(S), EPIGENETIC(S), EPIGENOMIC(S), NONCODING RNA, MICRORNA, LONG NONCODING RNA, LNCRNA, CIRCULAR RNA, RNA SEQUENCING, SINGLE CELL SEQUENCING, OR DNA METHYLATION BETWEEN APRIL 1, 2019 AND APRIL 30, 2020. RESULTS: WE IDENTIFIED 653 UNIQUE PUBLICATIONS, MANY STUDIES SPANNED MULTIPLE SEARCH TERMS. WE SUMMARIZED ADVANCES RELATING TO EVOLUTIONARY GENETICS, PAIN, ETHNICITY SPECIFIC RISK FACTORS, FUNCTIONAL STUDIES OF GENE VARIANTS, AND INTERACTIONS BETWEEN CODING AND NON-CODING RNAS IN OA PATHOGENESIS. CONCLUSIONS: STUDIES HAVE IDENTIFIED VARIANTS CONTRIBUTING TO OA SUSCEPTIBILITY, CANDIDATE BIOMARKERS FOR DIAGNOSIS AND PROGNOSIS, AS WELL AS PROMISING THERAPEUTIC CANDIDATES. VALIDATION IN MULTIPLE COHORTS, MULTI-OMICS STRATEGIES, AND MACHINE LEARNING AIDED COMPUTATIONAL ANALYSES HAVE ALL CONTRIBUTED TO THE STRENGTH OF PUBLISHED LITERATURE. OPEN ACCESS DATA-SETS, GREATER SAMPLE SIZES TO CAPTURE BROADER POPULATIONS AND UNDERSTANDING DISEASE MECHANISMS BY INVESTIGATING THE INTERACTIONS BETWEEN MULTIPLE TISSUE TYPES WILL FURTHER AID IN PROGRESS TOWARDS UNDERSTANDING AND CURING OA. 2021 2 728 28 CAN WE IDENTIFY PATIENTS WITH HIGH RISK OF OSTEOARTHRITIS PROGRESSION WHO WILL RESPOND TO TREATMENT? A FOCUS ON BIOMARKERS AND FRAILTY. OSTEOARTHRITIS (OA), A DISEASE AFFECTING DIFFERENT PATIENT PHENOTYPES, APPEARS AS AN OPTIMAL CANDIDATE FOR PERSONALIZED HEALTHCARE. THE AIM OF THE DISCUSSIONS OF THE EUROPEAN SOCIETY FOR CLINICAL AND ECONOMIC ASPECTS OF OSTEOPOROSIS AND OSTEOARTHRITIS (ESCEO) WORKING GROUP WAS TO EXPLORE THE VALUE OF MARKERS OF DIFFERENT SOURCES IN DEFINING DIFFERENT PHENOTYPES OF PATIENTS WITH OA. THE ESCEO ORGANIZED A SERIES OF MEETINGS TO EXPLORE THE POSSIBILITY OF IDENTIFYING PATIENTS WHO WOULD MOST BENEFIT FROM TREATMENT FOR OA, ON THE BASIS OF RECENT DATA AND EXPERT OPINION. IN THE FIRST MEETING, PATIENT PHENOTYPES WERE IDENTIFIED ACCORDING TO THE NUMBER OF AFFECTED JOINTS, BIOMECHANICAL FACTORS, AND THE PRESENCE OF LESIONS IN THE SUBCHONDRAL BONE. IN THE SECOND MEETING, SUMMARIZED IN THE PRESENT ARTICLE, THE WORKING GROUP EXPLORED OTHER MARKERS INVOLVED IN OA. PROFILES OF PATIENTS MAY BE DEFINED ACCORDING TO THEIR LEVEL OF PAIN, FUNCTIONAL LIMITATION, AND PRESENCE OF COEXISTENT CHRONIC CONDITIONS INCLUDING FRAILTY STATUS. A CONSIDERABLE AMOUNT OF DATA SUGGESTS THAT MAGNETIC RESONANCE IMAGING MAY ALSO ASSIST IN DELINEATING DIFFERENT PHENOTYPES OF PATIENTS WITH OA. AMONG MULTIPLE BIOCHEMICAL BIOMARKERS IDENTIFIED, NONE IS SUFFICIENTLY VALIDATED AND RECOGNIZED TO IDENTIFY PATIENTS WHO SHOULD BE TREATED. CONSIDERABLE EFFORTS ARE ALSO BEING MADE TO IDENTIFY GENETIC AND EPIGENETIC FACTORS INVOLVED IN OA, BUT RESULTS ARE STILL LIMITED. THE MANY POTENTIAL BIOMARKERS THAT COULD BE USED AS POTENTIAL STRATIFIERS ARE PROMISING, BUT MORE RESEARCH IS NEEDED TO CHARACTERIZE AND QUALIFY THE EXISTING BIOMARKERS AND TO IDENTIFY NEW CANDIDATES. 2015 3 1240 27 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 4 5256 39 PROGRESSES IN EPIGENETIC STUDIES OF ASTHMA FROM THE PERSPECTIVE OF HIGH-THROUGHPUT ANALYSIS TECHNOLOGIES: A NARRATIVE REVIEW. BACKGROUND AND OBJECTIVE: ASTHMA IS THE MOST COMMON CHRONIC RESPIRATORY DISEASE IN THE WORLD WITH AN ESTIMATED HERITABILITY BETWEEN 50% AND 60%, AND RECENT STUDIES HAVE SHOWN THAT EPIGENETIC MECHANISMS PLAY AN IMPORTANT ROLE IN ITS DEVELOPMENT. MANY CUTTING-EDGE EPIGENETIC RESEARCH TECHNIQUES HAVE BEEN APPLIED TO THE STUDY OF THE PATHOGENESIS OF ASTHMA, WHICH HAS PROMOTED THE DEVELOPMENT OF ASTHMA ETIOLOGY AND BROUGHT NEW POSSIBILITIES FOR TREATMENT. WE SUMMARIZED RECENT ADVANCES IN EPIGENETIC RESEARCH OF THE PATHOGENESIS OF ASTHMA, ESPECIALLY FROM THE PERSPECTIVE OF HIGH-THROUGHPUT ANALYSIS TECHNIQUES, TO FIND POTENTIAL EPIGENETIC BIOMARKERS AND POSSIBLE MOLECULAR TARGETS FOR THE FUTURE INTERVENTION AND TREATMENT OF THE DISEASE. METHODS: WE REVIEWED AND SUMMARIZED RECENT PROGRESS IN EPIGENOMIC STUDIES OF ASTHMA ON A "PRE-TRANSCRIPTIONAL LEVEL", INCLUDING DNA METHYLATION, HISTONE MODIFICATION, AND CHROMATIN REMODELING, AND ON A "POST-TRANSCRIPTIONAL LEVEL" WITH A FOCUS ON NON-CODING RNA, FROM THE PERSPECTIVE OF HIGH-THROUGHPUT ANALYSIS TECHNOLOGIES. KEY CONTENT AND FINDINGS: WE HAVE SUMMARIZED THE PROGRESS OF DIFFERENT KINDS OF RECENT EPIGENETIC STUDIES IN ASTHMA, INCLUDING DNA METHYLATION STUDIES [CANDIDATE GENES METHYLATION STUDIES AND EPIGENOME-WIDE ASSOCIATION STUDY (EWAS)], HISTONE MODIFICATION STUDIES (HISTONE ACETYLATION/DEACETYLATION STUDIES AND HISTONE METHYLATION STUDIES), NON-CODING RNA STUDIES [MICRORNAS (MIRNAS), LONG NON-CODING RNAS (LNCRNAS) AND CIRCULAR RNAS (CIRCRNAS)], TO HELP THE READERS TO GAIN A COMPREHENSIVE INSIGHT INTO THE EPIGENETIC RESEARCH FIELDS FOR ASTHMA. THE APPLICATION OF HIGH-THROUGHPUT ANALYSIS TECHNIQUES IN ASTHMA RESEARCH, INCLUDING EWAS (DNA METHYLATION CHIPS), CHROMATIN IMMUNOPRECIPITATION SEQUENCING (CHIP-SEQ), MICRORNA SEQUENCING, WHOLE TRANSCRIPTOME SEQUENCING, CO-EXPRESSION NETWORK AND COMPETING ENDOGENOUS RNA (CERNA) ANALYSES, WERE INTRODUCED ACCOMPANY WITH THE MAIN FINDINGS. AND THE POTENTIAL EPIGENETIC BIOMARKERS AND POSSIBLE MOLECULAR TARGETS IDENTIFIED VIA HIGH-THROUGHPUT ANALYSES WERE ALSO DISCUSSED. CONCLUSIONS: EPIGENETIC RESEARCH HAS BECOME A HOTSPOT IN RESEARCH ON THE PATHOGENESIS OF ASTHMA. THE COMBINATION OF HIGH-THROUGHPUT EPIGENETIC ANALYSIS TECHNOLOGIES AND TRADITIONAL BIOLOGICAL FUNCTION AND CLINICAL STUDIES WILL BRING NEW BREAKTHROUGH IN THE PATHOGENESIS STUDY OF ASTHMA, WHICH WILL IMPROVE THE GENETIC INTERPRETATION OF THE DISEASE AND BRING MORE POSSIBILITIES FOR THE DEVELOPMENT OF PRECISION MEDICINE TO TREAT IT. 2022 5 1510 40 DNA METHYLATION AND NONCODING RNA IN OA: RECENT FINDINGS AND METHODOLOGICAL ADVANCES. INTRODUCTION: OSTEOARTHRITIS (OA) IS A CHRONIC MUSCULOSKELETAL DISEASE CHARACTERIZED BY PROGRESSIVE LOSS OF JOINT FUNCTION. HISTORICALLY, IT HAS BEEN CHARACTERIZED AS A DISEASE CAUSED BY MECHANICAL TRAUMA, SO-CALLED 'WEAR AND TEAR'. OVER THE PAST TWO DECADES, IT HAS COME TO BE UNDERSTOOD AS A COMPLEX SYSTEMIC DISORDER INVOLVING GENE-ENVIRONMENTAL INTERACTIONS. EPIGENETIC CHANGES HAVE BEEN INCREASINGLY IMPLICATED. RECENT IMPROVEMENTS IN MICROARRAY AND NEXT-GENERATION SEQUENCING (NGS) TECHNOLOGIES HAVE ALLOWED FOR EVER MORE COMPLEX EVALUATIONS OF EPIGENETIC ABERRATIONS ASSOCIATED WITH THE DEVELOPMENT AND PROGRESSION OF OA. METHODS: A SYSTEMATIC REVIEW WAS CONDUCTED IN THE PUBMED DATABASE. WE CURATED STUDIES THAT PRESENTED THE RESULTS OF DNA METHYLATION AND NONCODING RNA RESEARCH IN HUMAN OA AND OA ANIMAL MODELS SINCE 1985. RESULTS: HEREIN, WE DISCUSS RECENT FINDINGS AND METHODOLOGICAL ADVANCEMENTS IN OA EPIGENETICS, INCLUDING A DISCUSSION OF DNA METHYLATION, INCLUDING MICROARRAY AND NGS STUDIES, AND NONCODING RNAS. BEYOND CARTILAGE, WE ALSO HIGHLIGHT STUDIES IN SUBCHONDRAL BONE AND PERIPHERAL BLOOD MONONUCLEAR CELLS, WHICH HIGHLIGHT WIDESPREAD AND POTENTIALLY CLINICALLY IMPORTANT ALTERATIONS IN EPIGENETIC PATTERNS SEEN IN OA PATIENTS. FINALLY, WE DISCUSS EPIGENETIC EDITING APPROACHES IN THE CONTEXT OF OA. CONCLUSIONS: ALTHOUGH A SUBSTANTIAL BODY OF LITERATURE HAS ALREADY BEEN PUBLISHED IN OA, MUCH IS STILL UNKNOWN. FUTURE OA EPIGENETICS STUDIES WILL NO DOUBT CONTINUE TO BROADEN OUR UNDERSTANDING OF UNDERLYING PATHOPHYSIOLOGY AND PERHAPS OFFER NOVEL DIAGNOSTICS AND/OR TREATMENTS FOR HUMAN OA. 2021 6 3038 34 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 7 3108 27 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 8 1546 30 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 9 6458 32 TIME COURSE OF DNA METHYLATION IN PAIN CONDITIONS: FROM EXPERIMENTAL MODELS TO HUMANS. BACKGROUND AND OBJECTIVE: THROUGHOUT THE LAST DECADE, RESEARCH HAS UNCOVERED ASSOCIATIONS BETWEEN PAIN AND EPIGENETIC ALTERATIONS CAUSED BY ENVIRONMENTAL FACTORS. SPECIFICALLY, STUDIES HAVE DEMONSTRATED CORRELATIONS BETWEEN PAIN CONDITIONS AND ALTERED DNA METHYLATION PATTERNS. THUS, DNA METHYLATION HAS BEEN REVEALED AS A POSSIBLE MODULATOR OR CONTRIBUTOR TO PAIN CONDITIONS, PROVIDING A POTENTIAL THERAPEUTIC TARGET FOR TREATMENT BY DNA METHYLATION MODIFICATION. TO DEVELOP SUCH TREATMENTS, IT IS NECESSARY TO CLARIFY A WIDE NUMBER OF ASPECTS ON HOW DNA METHYLATION AFFECTS PAIN PERCEPTION; FIRST AND FOREMOST, THE TEMPORAL DYNAMICS. THE OBJECTIVE OF THE PRESENT REVIEW IS TO PROVIDE AN OVERVIEW OF CURRENT KNOWLEDGE ON TEMPORAL DYNAMICS OF DNA METHYLATION IN RESPONSE TO PAIN, AND TO INVESTIGATE IF A TIMEFRAME CAN BE ESTABLISHED BASED ON THE DATA OF CURRENTLY PUBLISHED STUDIES. DATABASES AND DATA TREATMENT: PUBMED, MEDLINE, GOOGLE SCHOLAR AND EMBASE WERE SEARCHED COMPREHENSIVELY FOR STUDIES OF DNA METHYLATION IN NEUROPATHIC, INFLAMMATORY AND ALTERNATIVE ANIMAL PAIN MODELS, AND IN CHRONIC PAIN PATIENTS INCLUDING COMPLEX REGIONAL PAIN SYNDROME, CHRONIC POSTSURGICAL PAIN, CHRONIC WIDESPREAD PAIN, FIBROMYALGIA AND CROHN'S DISEASE. RESULTS: WE IDENTIFIED 34 ARTICLES HIGHLIGHTING VARIATIONS IN TEMPORAL DYNAMICS OF DNA METHYLATION ACROSS SPECIES AND BETWEEN DIFFERENT TYPES OF PAIN. THESE STUDIES REPRESENT A STARTING POINT TO UNCOVER NEW INSIGHTS IN THE DNA METHYLATION TIME COURSE IN PAIN. CONCLUSIONS: NO TIMEFRAME CAN CURRENTLY BE MADE FOR THE DNA METHYLATION RESPONSE TO PAIN IN ANY OF THE REVIEWED CONDITIONS, HIGHLIGHTING AN IMPORTANT FOCUS AREA FOR FUTURE RESEARCH. 2021 10 2651 32 EPIGENOMICS AND TRANSCRIPTOMICS IN THE PREDICTION AND DIAGNOSIS OF CHILDHOOD ASTHMA: ARE WE THERE YET? ASTHMA IS THE MOST COMMON NON-COMMUNICABLE CHRONIC DISEASE OF CHILDHOOD. DESPITE ITS HIGH PREVALENCE, TO DATE WE LACK METHODS THAT ARE BOTH EFFICIENT AND ACCURATE IN DIAGNOSING ASTHMA. MOST TRADITIONAL APPROACHES HAVE BEEN BASED ON GARNERING CLINICAL EVIDENCE, SUCH AS RISK FACTORS AND EXPOSURES. GIVEN THE HIGH HERITABILITY OF ASTHMA, MORE RECENT APPROACHES HAVE LOOKED AT GENETIC POLYMORPHISMS AS POTENTIAL "RISK FACTORS." HOWEVER, GENETIC VARIANTS EXPLAIN ONLY A SMALL PROPORTION OF ASTHMA RISK, AND HAVE BEEN LESS THAN OPTIMAL AT PREDICTING RISK FOR INDIVIDUAL SUBJECTS. EPIGENOMIC STUDIES OFFER SIGNIFICANT ADVANTAGES OVER PREVIOUS APPROACHES. EPIGENETIC REGULATION IS HIGHLY TISSUE-SPECIFIC, AND CAN INDUCE BOTH SHORT- AND LONG-TERM CHANGES IN GENE EXPRESSION. SUCH CHANGES CAN START IN UTERO, CAN VARY THROUGHOUT THE LIFE SPAN, AND IN SOME INSTANCES CAN BE PASSED ON FROM ONE GENERATION TO ANOTHER. MOST IMPORTANTLY, THE EPIGENOME CAN BE MODIFIED BY ENVIRONMENTAL FACTORS AND EXPOSURES, AND THUS EPIGENETIC AND TRANSCRIPTOMIC PROFILING MAY YIELD THE MOST ACCURATE RISK ESTIMATES FOR A GIVEN PATIENT BY INCORPORATING ENVIRONMENTAL (AND TREATMENT) EFFECTS THROUGHOUT THE LIFESPAN. HERE WE WILL REVIEW THE MOST RECENT ADVANCES IN THE USE OF EPIGENETIC AND TRANSCRIPTOMIC ANALYSIS FOR THE EARLY DIAGNOSIS OF ASTHMA AND ATOPY, AS WELL AS CHALLENGES AND FUTURE DIRECTIONS IN THE FIELD AS IT MOVES FORWARD. WE WILL PARTICULARLY FOCUS ON DNA METHYLATION, THE MOST STUDIED MECHANISM OF EPIGENETIC REGULATION. 2019 11 6013 33 THE APPLICATIONS OF DNA METHYLATION AS A BIOMARKER IN KIDNEY TRANSPLANTATION: A SYSTEMATIC REVIEW. BACKGROUND: ALTHOUGH KIDNEY TRANSPLANTATION IMPROVES PATIENT SURVIVAL AND QUALITY OF LIFE, LONG-TERM RESULTS ARE HAMPERED BY BOTH IMMUNE- AND NON-IMMUNE-MEDIATED COMPLICATIONS. CURRENT BIOMARKERS OF POST-TRANSPLANT COMPLICATIONS, SUCH AS ALLOGRAFT REJECTION, CHRONIC RENAL ALLOGRAFT DYSFUNCTION, AND CUTANEOUS SQUAMOUS CELL CARCINOMA, HAVE A SUBOPTIMAL PREDICTIVE VALUE. DNA METHYLATION IS AN EPIGENETIC MODIFICATION THAT DIRECTLY AFFECTS GENE EXPRESSION AND PLAYS AN IMPORTANT ROLE IN PROCESSES SUCH AS ISCHEMIA/REPERFUSION INJURY, FIBROSIS, AND ALLOREACTIVE IMMUNE RESPONSE. NOVEL TECHNIQUES CAN QUICKLY ASSESS THE DNA METHYLATION STATUS OF MULTIPLE LOCI IN DIFFERENT CELL TYPES, ALLOWING A DEEP AND INTERESTING STUDY OF CELLS' ACTIVITY AND FUNCTION. THEREFORE, DNA METHYLATION HAS THE POTENTIAL TO BECOME AN IMPORTANT BIOMARKER FOR PREDICTION AND MONITORING IN KIDNEY TRANSPLANTATION. PURPOSE OF THE STUDY: THE AIM OF THIS STUDY WAS TO EVALUATE THE ROLE OF DNA METHYLATION AS A POTENTIAL BIOMARKER OF GRAFT SURVIVAL AND COMPLICATIONS DEVELOPMENT IN KIDNEY TRANSPLANTATION. MATERIAL AND METHODS: A SYSTEMATIC REVIEW OF SEVERAL DATABASES HAS BEEN CONDUCTED. THE NEWCASTLE-OTTAWA SCALE AND THE JADAD SCALE HAVE BEEN USED TO ASSESS THE RISK OF BIAS FOR OBSERVATIONAL AND RANDOMIZED STUDIES, RESPECTIVELY. RESULTS: TWENTY ARTICLES REPORTING ON DNA METHYLATION AS A BIOMARKER FOR KIDNEY TRANSPLANTATION WERE INCLUDED, ALL USING DNA METHYLATION FOR PREDICTION AND MONITORING. DNA METHYLATION PATTERN ALTERATIONS IN CELLS ISOLATED FROM DIFFERENT TISSUES, SUCH AS KIDNEY BIOPSIES, URINE, AND BLOOD, HAVE BEEN ASSOCIATED WITH ISCHEMIA-REPERFUSION INJURY AND CHRONIC RENAL ALLOGRAFT DYSFUNCTION. THESE ALTERATIONS OCCURRED IN DIFFERENT AND SPECIFIC LOCI. DNA METHYLATION STATUS HAS ALSO PROVED TO BE IMPORTANT FOR IMMUNE RESPONSE MODULATION, HAVING A CRUCIAL ROLE IN REGULATORY T CELL DEFINITION AND ACTIVITY. RESEARCH ALSO FOCUSED ON A BETTER UNDERSTANDING OF THE ROLE OF THIS EPIGENETIC MODIFICATION ASSESSMENT FOR REGULATORY T CELLS ISOLATION AND EXPANSION FOR FUTURE TOLERANCE INDUCTION-ORIENTED THERAPIES. CONCLUSIONS: STUDIES INCLUDED IN THIS REVIEW ARE HETEROGENEOUS IN STUDY DESIGN, BIOLOGICAL SAMPLES, AND OUTCOME. MORE COORDINATED INVESTIGATIONS ARE NEEDED TO AFFIRM DNA METHYLATION AS A CLINICALLY RELEVANT BIOMARKER IMPORTANT FOR PREVENTION, MONITORING, AND INTERVENTION. 2022 12 3020 32 GENETICS AND EPIGENETICS OF OSTEOARTHRITIS. OSTEOARTHRITIS (OA) IS A COMMON AGE-RELATED DISEASE THAT AFFECTS THE TISSUES OF THE SYNOVIAL JOINT, LEADING TO LOSS OF FUNCTION AND PAIN. IT IMPACTS ON BOTH PATIENT MORBIDITY AND MORTALITY. IT IS A COMPLEX, POLYGENIC DISEASE THAT LACKS ANY LARGE-EFFECT SUSCEPTIBILITY LOCI. INSTEAD, OA SUSCEPTIBILITY ALLELES INDIVIDUALLY CONTRIBUTE ONLY MODESTLY TO THE OVERALL DISEASE RISK, MAKING THEIR IDENTIFICATION CHALLENGING. DESPITE THIS, BREAKTHROUGHS HAVE OCCURRED WITH COMPELLING ASSOCIATIONS SO FAR REPORTED TO POLYMORPHISMS WITHIN THE GENES GDF5 AND MCF2L AND TO THE GENOMIC REGION 7Q22. THE LATTER TWO HAVE EMERGED FROM GENOME-WIDE ASSOCIATION SCANS, WHICH ARE LIKELY TO YIELD MORE HITS IN THE NEAR FUTURE. AS FOR MANY COMPLEX DISEASES, IT IS NOW APPARENT THAT EPIGENETIC EFFECTS ARE ALSO IMPORTANT MEDIATORS OF DISEASE BIOLOGY, WITH DNA METHYLATION, HISTONE MODIFICATIONS AND NON-CODING RNAS ALL HAVING A ROLE. AT PRESENT, MUCH OF THE EPIGENETIC FOCUS HAS BEEN ON CARTILAGE, THE TISSUE AT THE CENTER OF THE OA DISEASE PROCESS. IF WE ARE TO GET CLOSE TO A QUALITATIVE AND QUANTITATIVE UNDERSTANDING OF THE IMPACT OF EPIGENETICS ON OA, THEN IN FUTURE THE OTHER TISSUES OF THE JOINT WILL ALSO NEED TO BE INVESTIGATED. ONE OF THE MORE EXCITING INSIGHTS TO HAVE EMERGED RECENTLY IS THE FACT THAT EPIGENETIC EFFECTS CAN IMPACT ON OA GENETIC EFFECTS AND THIS MAY BE A PARTICULARLY FRUITFUL AVENUE FOR INTEGRATING BOTH AS WE MOVE TOWARD A CLEARER UNDERSTANDING OF THE PATHOPHYSIOLOGY OF THIS INTRIGUING DISEASE. 2012 13 777 28 CELL-FREE CIRCULATING EPIGENOMIC SIGNATURES: NON-INVASIVE BIOMARKER FOR CARDIOVASCULAR AND OTHER AGE-RELATED CHRONIC DISEASES. THE BURDEN OF CARDIO-VASCULAR AND OTHER AGE-RELATED NON-COMMUNICABLE DISEASES ARE RAPIDLY INCREASING WORLDWIDE. MAJORITY OF THESE CHRONIC AILMENTS ARE CURABLE, IF DIAGNOSED AT EARLY STAGES. CANDIDATE BIOMARKERS OF EARLY DETECTION ARE THEREFORE ESSENTIAL FOR IDENTIFICATION OF HIGH-RISK INDIVIDUALS, PROMPT AND ACCURATE DISEASE DIAGNOSIS, AND TO MONITOR THERAPEUTIC RESPONSE. THE FUNCTIONAL SIGNIFICANCE OF CIRCULATING NUCLEIC ACIDS THAT RECAPITULATE SPECIFIC DISEASE PROFILES IS NOW WELL ESTABLISHED. BUT SUBTLE CHANGES IN DNA SEQUENCE MAY NOT SOLELY REFLECT THE DIFFERENTIATION OF GENE EXPRESSION PATTERNS OBSERVED IN DIVERSE SET OF DISEASES AS EPIGENETIC PHENOMENA PLAY A LARGER ROLE IN AETIOLOGY AND PATHO-PHYSIOLOGY. UNLIKE GENETIC MARKERS, KNOWLEDGE ABOUT THE DIAGNOSTIC UTILITY OF CIRCULATING EPIGENETIC SIGNATURES: METHYLATED DNA; MICRO RNA AND MODIFIED HISTONES ARE DEFICIENT. CHARACTERIZATION OF THESE NOVEL ENTITIES THROUGH OMICS-BASED MOLECULAR TECHNOLOGIES MIGHT PROMPT DEVELOPMENT OF A RANGE OF LABORATORY-BASED STRATEGIES, THEREBY ACCELERATING THEIR BROADER TRANSLATIONAL PURPOSE FOR EARLY DISEASE DIAGNOSIS, MONITORING THERAPEUTIC RESPONSE AND DRUG RESISTANCE. HOWEVER, LARGEST OPPORTUNITY FOR INNOVATION LIES IN DEVELOPING POINT-OF-CARE TESTS WITH ACCURATE DIAGNOSTIC AND HIGHER PROGNOSTIC SCORE THAT IS APPLICABLE FOR SCREENING OF HIGH-RISK POPULATIONS. 2017 14 605 31 BEYOND ENDOMETRIOSIS GENOME-WIDE ASSOCIATION STUDY: FROM GENOMICS TO PHENOMICS TO THE PATIENT. ENDOMETRIOSIS IS A HERITABLE, COMPLEX CHRONIC INFLAMMATORY DISEASE, FOR WHICH MUCH OF THE CAUSAL PATHOGENIC MECHANISM REMAINS UNKNOWN. GENOME-WIDE ASSOCIATION STUDIES (GWAS) TO DATE HAVE IDENTIFIED 12 SINGLE NUCLEOTIDE POLYMORPHISMS AT 10 INDEPENDENT GENETIC LOCI ASSOCIATED WITH ENDOMETRIOSIS. MOST OF THESE WERE MORE STRONGLY ASSOCIATED WITH REVISED AMERICAN FERTILITY SOCIETY STAGE III/IV, RATHER THAN STAGE I/II. THE LOCI ARE ALMOST ALL LOCATED IN INTERGENIC REGIONS THAT ARE KNOWN TO PLAY A ROLE IN THE REGULATION OF EXPRESSION OF TARGET GENES YET TO BE IDENTIFIED. TO IDENTIFY THE TARGET GENES AND PATHWAYS PERTURBED BY THE IMPLICATED VARIANTS, STUDIES ARE REQUIRED INVOLVING FUNCTIONAL GENOMIC ANNOTATION OF THE SURROUNDING CHROMOSOMAL REGIONS, IN TERMS OF TRANSCRIPTION FACTOR BINDING, EPIGENETIC MODIFICATION (E.G., DNA METHYLATION AND HISTONE MODIFICATION) SITES, AS WELL AS THEIR CORRELATION WITH RNA TRANSCRIPTION. THESE STUDIES NEED TO BE CONDUCTED IN TISSUE TYPES RELEVANT TO ENDOMETRIOSIS-IN PARTICULAR, ENDOMETRIUM. IN ADDITION, TO ALLOW BIOLOGICALLY AND CLINICALLY RELEVANT INTERPRETATION OF MOLECULAR PROFILING DATA, THEY NEED TO BE COMBINED AND CORRELATED WITH DETAILED, SYSTEMATICALLY COLLECTED PHENOTYPIC INFORMATION (SURGICAL AND CLINICAL). THE WERF ENDOMETRIOSIS PHENOME AND BIOBANKING HARMONISATION PROJECT IS A GLOBAL STANDARDIZATION INITIATIVE THAT HAS PRODUCED CONSENSUS DATA AND SAMPLE COLLECTION PROTOCOLS FOR ENDOMETRIOSIS RESEARCH. THESE NOW PAVE THE WAY FOR COLLABORATIVE STUDIES INTEGRATING PHENOMIC WITH GENOMIC DATA, TO IDENTIFY INFORMATIVE SUBTYPES OF ENDOMETRIOSIS THAT WILL ENHANCE UNDERSTANDING OF THE PATHOGENIC MECHANISMS OF THE DISEASE AND DISCOVERY OF NOVEL, TARGETED TREATMENTS. 2016 15 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 16 2029 34 EPIGENETIC CHANGES IN HEADACHE. INTRODUCTION: MULTIPLE FACTORS, INCLUDING BOTH GENETIC AND ENVIRONMENTAL MECHANISMS, APPEAR TO PLAY A ROLE IN THE AETIOLOGY OF HEADACHE. AN INTERESTING AREA OF STUDY IS THE POSSIBLE INVOLVEMENT OF EPIGENETIC MECHANISMS IN HEADACHE DEVELOPMENT AND THE TRANSFORMATION TO CHRONIC HEADACHE, AND THE POTENTIAL ROLE OF THESE FACTORS AS A THERAPEUTIC TARGET. METHODS: WE PERFORMED A LITERATURE REVIEW OF THE INVOLVEMENT OF DIFFERENT EPIGENETIC MECHANISMS IN HEADACHE, MAINLY USING THE MEDLINE/PUBMED DATABASE. TO THIS END, WE USED THE FOLLOWING ENGLISH SEARCH TERMS: HEADACHE, MIGRAINE, EPIGENETICS, DNA METHYLATION, HISTONES, NON-CODING RNA, AND MIRNA. RESULTS: A TOTAL OF 15 ENGLISH-LANGUAGE PUBLICATIONS RELATED TO THE ABOVE TERMS WERE OBTAINED. CONCLUSION: THERE IS LIMITED BUT CONSISTENT EVIDENCE OF THE RELATIONSHIP BETWEEN EPIGENETICS AND HEADACHE; IT IS THEREFORE ESSENTIAL TO CONTINUE RESEARCH OF EPIGENETIC CHANGES IN HEADACHE. THIS MAY HELP TO UNDERSTAND THE PATHOPHYSIOLOGY OF HEADACHE AND EVEN TO IDENTIFY CANDIDATE BIOMARKERS AND NEW, MORE EFFECTIVE, THERAPEUTIC TARGETS. 2021 17 527 25 ASTHMA AND THE MISSING HERITABILITY PROBLEM: NECESSITY FOR MULTIOMICS APPROACHES IN DETERMINING ACCURATE RISK PROFILES. ASTHMA IS RANKED AMONG THE MOST COMMON CHRONIC CONDITIONS AND HAS BECOME A SIGNIFICANT PUBLIC HEALTH ISSUE DUE TO THE RECENT AND RAPID INCREASE IN ITS PREVALENCE. INVESTIGATIONS INTO THE UNDERLYING GENETIC FACTORS PREDICT A HERITABLE COMPONENT FOR ITS INCIDENCE, ESTIMATED BETWEEN 35% AND 90% OF CAUSATION. DESPITE THE APPLICATION OF LARGE-SCALE GENOME-WIDE ASSOCIATION STUDIES (GWAS) AND ADMIXTURE MAPPING APPROACHES, THE PROPORTION OF VARIANTS IDENTIFIED ACCOUNTS FOR LESS THAN 15% OF THE OBSERVED HERITABILITY OF THE DISEASE. THE DISCREPANCY BETWEEN THE PREDICTED HERITABLE COMPONENT OF DISEASE AND THE PROPORTION OF HERITABILITY MAPPED TO THE CURRENTLY IDENTIFIED SUSCEPTIBILITY LOCI HAS BEEN TERMED THE 'MISSING HERITABILITY PROBLEM.' HERE, WE EXAMINE RECENT STUDIES INVOLVING BOTH THE ANALYSIS OF GENETICALLY ENCODED FEATURES THAT CONTRIBUTE TO ASTHMA AND ALSO THE ROLE OF NON-ENCODED HERITABLE CHARACTERISTICS, INCLUDING EPIGENETIC, ENVIRONMENTAL, AND DEVELOPMENTAL ASPECTS OF DISEASE. THE IMPORTANCE OF VERTICAL MATERNAL MICROBIOME TRANSFER AND THE INFLUENCE OF MATERNAL IMMUNE FACTORS ON FETAL CONDITIONING IN THE INHERITANCE OF DISEASE ARE ALSO DISCUSSED. IN ORDER TO HIGHLIGHT THE BROAD ARRAY OF BIOLOGICAL INPUTS THAT CONTRIBUTE TO THE SUM OF HERITABLE RISK FACTORS ASSOCIATED WITH ALLERGIC DISEASE INCIDENCE THAT, TOGETHER, CONTRIBUTE TO THE INDUCTION OF A PRO-ATOPIC STATE. CURRENTLY, THERE IS A NEED TO DEVELOP IN-DEPTH MODELS OF ASTHMA RISK FACTORS TO OVERCOME THE LIMITATIONS ENCOUNTERED IN THE INTERPRETATION OF GWAS RESULTS IN ISOLATION, WHICH HAVE RESULTED IN THE MISSING HERITABILITY PROBLEM. HENCE, MULTIOMICS ANALYSES NEED TO BE ESTABLISHED CONSIDERING GENETIC, EPIGENETIC, AND FUNCTIONAL DATA TO CREATE A TRUE SYSTEMS BIOLOGY-BASED APPROACH FOR ANALYZING THE REGULATORY PATHWAYS THAT UNDERLIE THE INHERITANCE OF ASTHMA AND TO DEVELOP ACCURATE RISK PROFILES FOR DISEASE. 2022 18 396 31 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 19 2919 33 GENE-GENE AND GENE-ENVIRONMENT INTERACTIONS DEFINING LIPID-RELATED TRAITS. PURPOSE OF REVIEW: STEPS TOWARDS REDUCING CHRONIC DISEASE PROGRESSION ARE CONTINUOUSLY BEING TAKEN THROUGH THE FORM OF GENOMIC RESEARCH. STUDIES OVER THE LAST YEAR HAVE HIGHLIGHTED MORE AND MORE POLYMORPHISMS, PATHWAYS AND INTERACTIONS RESPONSIBLE FOR METABOLIC DISORDERS SUCH AS CARDIOVASCULAR DISEASE, OBESITY AND DYSLIPIDEMIA. RECENT FINDINGS: MANY OF THESE CHRONIC ILLNESSES CAN BE PARTIALLY BLAMED BY ALTERED LIPID METABOLISM, COMBINED WITH INDIVIDUAL GENETIC COMPONENTS. CRITICAL EVALUATION AND COMPARISON OF THESE RECENT STUDIES IS ESSENTIAL IN ORDER TO COMPREHEND THE RESULTS, CONCLUSIONS AND FUTURE PROSPECTS IN THE FIELD OF GENOMICS AS A WHOLE. RECENT LITERATURE ELUCIDATES SIGNIFICANT GENE--DIET AND GENE--ENVIRONMENT INTERACTIONS RESULTING IN ALTERED LIPID METABOLISM, INFLAMMATION AND OTHER METABOLIC IMBALANCES LEADING TO CARDIOVASCULAR DISEASE AND OBESITY. SUMMARY: EPIGENETIC AND EPISTATIC INTERACTIONS ARE NOW BECOMING MORE SIGNIFICANTLY ASSOCIATED WITH SUCH DISORDERS, AS GENOMIC RESEARCH DIGS DEEPER INTO THE COMPLEX NATURE OF GENETIC INDIVIDUALITY AND HERITABILITY. THE VAST ARRAY OF DATA COLLECTED FROM GENOME-WIDE ASSOCIATION STUDIES MUST NOW BE EMPOWERED AND EXPLORED THROUGH MORE COMPLEX INTERACTION STUDIES, USING STANDARDIZED METHODS AND LARGER SAMPLE SIZES. IN DOING SO THE ETIOLOGY OF CHRONIC DISEASE PROGRESSION WILL BE FURTHER UNDERSTOOD. 2011 20 4531 25 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