1 2920 136 GENE-SET ANALYSIS IS SEVERELY BIASED WHEN APPLIED TO GENOME-WIDE METHYLATION DATA. MOTIVATION: DNA METHYLATION IS AN EPIGENETIC MARK THAT CAN STABLY REPRESS GENE EXPRESSION. BECAUSE OF ITS BIOLOGICAL AND CLINICAL SIGNIFICANCE, SEVERAL METHODS HAVE BEEN DEVELOPED TO COMPARE GENOME-WIDE PATTERNS OF METHYLATION BETWEEN GROUPS OF SAMPLES. THE APPLICATION OF GENE SET ANALYSIS TO IDENTIFY RELEVANT GROUPS OF GENES THAT ARE ENRICHED FOR DIFFERENTIALLY METHYLATED GENES IS OFTEN A MAJOR COMPONENT OF THE ANALYSIS OF THESE DATA. THIS CAN BE USED, FOR EXAMPLE, TO IDENTIFY PROCESSES OR PATHWAYS THAT ARE PERTURBED IN DISEASE DEVELOPMENT. WE SHOW THAT GENE-SET ANALYSIS, AS IT IS TYPICALLY APPLIED TO GENOME-WIDE METHYLATION ASSAYS, IS SEVERELY BIASED AS A RESULT OF DIFFERENCES IN THE NUMBERS OF CPG SITES ASSOCIATED WITH DIFFERENT CLASSES OF GENES AND GENE PROMOTERS. RESULTS: WE DEMONSTRATE THIS BIAS USING PUBLISHED DATA FROM A STUDY OF DIFFERENTIAL CPG ISLAND METHYLATION IN LUNG CANCER AND A DATASET WE GENERATED TO STUDY METHYLATION CHANGES IN PATIENTS WITH LONG-STANDING ULCERATIVE COLITIS. WE SHOW THAT SEVERAL OF THE GENE SETS THAT SEEM ENRICHED WOULD ALSO BE IDENTIFIED WITH RANDOMIZED DATA. WE SUGGEST TWO EXISTING APPROACHES THAT CAN BE ADAPTED TO CORRECT THE BIAS. ACCOUNTING FOR THE BIAS IN THE LUNG CANCER AND ULCERATIVE COLITIS DATASETS PROVIDES NOVEL BIOLOGICAL INSIGHTS INTO THE ROLE OF METHYLATION IN CANCER DEVELOPMENT AND CHRONIC INFLAMMATION, RESPECTIVELY. OUR RESULTS HAVE SIGNIFICANT IMPLICATIONS FOR MANY PREVIOUS GENOME-WIDE METHYLATION STUDIES THAT HAVE DRAWN CONCLUSIONS ON THE BASIS OF SUCH STRONGLY BIASED ANALYSIS. CONTACT: CATHAL.SEOIGHE@NUIGALWAY.IE SUPPLEMENTARY INFORMATION: SUPPLEMENTARY DATA ARE AVAILABLE AT BIOINFORMATICS ONLINE. 2013 2 1585 45 DNA METHYLATION PROFILING IDENTIFIES EPIGENETIC DIFFERENCES BETWEEN DIABETES PATIENTS WITH ESRD AND DIABETES PATIENTS WITHOUT NEPHROPATHY. WE IDENTIFIED POTENTIAL EPIGENETIC BIOMARKERS FOR CHRONIC KIDNEY DISEASE PROGRESSION BY COMPARING SITE-SPECIFIC DNA METHYLATION LEVELS IN MORE THAN 14,000 GENES BETWEEN AFRICAN AMERICAN AND HISPANIC DIABETES PATIENTS WITH END STAGE RENAL DISEASE (ESRD) AND DIABETES PATIENTS WITHOUT NEPHROPATHY. WE IDENTIFIED 187 GENES THAT ARE DIFFERENTIALLY METHYLATED BETWEEN THE TWO GROUPS ON AT LEAST TWO CPG SITES IN EACH GENE IN DNA EXTRACTED FROM SALIVA. OF THE 187 GENES WHOSE MEAN METHYLATION LEVELS DIFFERED BETWEEN THE TWO GROUPS, 39 GENES, OR CLOSELY RELATED GENE FAMILY MEMBERS, HAVE BEEN REPORTED TO BE INVOLVED IN KIDNEY DEVELOPMENT OR DIABETIC NEPHROPATHY, PER SE, OR HAVE BEEN ASSOCIATED WITH DIALYSIS-INDUCED CHANGES IN GENE EXPRESSION IN PERIPHERAL BLOOD CELLS. THE FACT THAT SUCH A SUBSTANTIAL FRACTION (21%) OF THE 187 CANDIDATE GENES HAVE BEEN IMPLICATED PREVIOUSLY THROUGH GENOME ASSOCIATION OR TRANSCRIPTION PROFILING STUDIES SUGGESTS STRONGLY THAT THE DNA METHYLATION DIFFERENCES WE OBSERVE ARE ASSOCIATED WITH DISEASE PREDISPOSITION AND/OR TREATMENT. THE FACT THAT THESE NEPHROPATHY AND/OR DIALYSIS-ASSOCIATED DIFFERENCES BETWEEN PATIENTS WERE IDENTIFIED IN DNA EXTRACTED FROM SALIVA OFFERS PROOF-OF-PRINCIPLE THAT INTER-INDIVIDUAL EPIGENETIC DIFFERENCES MAY PROVE USEFUL AS PREDICTIVE BIOMARKERS OF DISEASE SUSCEPTIBILITY. 2011 3 1493 51 DNA HYPERMETHYLATION AND DNA HYPOMETHYLATION IS PRESENT AT DIFFERENT LOCI IN CHRONIC KIDNEY DISEASE. GENETIC RISK FACTORS FOR CHRONIC KIDNEY DISEASE (CKD) ARE BEING IDENTIFIED THROUGH INTERNATIONAL COLLABORATIONS. BY COMPARISON, EPIGENETIC RISK FACTORS FOR CKD HAVE ONLY RECENTLY BEEN CONSIDERED USING POPULATION-BASED APPROACHES. DNA METHYLATION IS A MAJOR EPIGENETIC MODIFICATION THAT IS ASSOCIATED WITH COMPLEX DISEASES, SO WE INVESTIGATED METHYLOME-WIDE LOCI FOR ASSOCIATION WITH CKD. A TOTAL OF 485,577 UNIQUE FEATURES WERE EVALUATED IN 255 INDIVIDUALS WITH CKD (CASES) AND 152 INDIVIDUALS WITHOUT EVIDENCE OF RENAL DISEASE (CONTROLS). FOLLOWING STRINGENT QUALITY CONTROL, RAW DATA WERE QUANTILE NORMALIZED AND BETA VALUES CALCULATED TO REFLECT THE METHYLATION STATUS AT EACH SITE. THE DIFFERENCE IN METHYLATION STATUS WAS EVALUATED BETWEEN CASES AND CONTROLS WITH RESULTANT P VALUES ADJUSTED FOR MULTIPLE TESTING. GENES WITH SIGNIFICANTLY INCREASED AND DECREASED LEVELS OF DNA METHYLATION WERE CONSIDERED FOR BIOLOGICAL RELEVANCE BY FUNCTIONAL ENRICHMENT ANALYSIS USING KEGG PATHWAYS IN PARTEK GENOMICS SUITE. TWENTY-THREE GENES, WHERE MORE THAN ONE CPG PER LOCI WAS IDENTIFIED WITH PADJUSTED<10(-8), DEMONSTRATED SIGNIFICANT METHYLATION CHANGES ASSOCIATED WITH CKD AND ADDITIONAL SUPPORT FOR THESE ASSOCIATED LOCI WAS SOUGHT FROM PUBLISHED LITERATURE. STRONG BIOLOGICAL CANDIDATES FOR CKD THAT SHOWED STATISTICALLY SIGNIFICANT DIFFERENTIAL METHYLATION INCLUDE CUX1, ELMO1, FKBP5, INHBA-AS1, PTPRN2, AND PRKAG2 GENES; SEVERAL GENES ARE DIFFERENTIALLY METHYLATED IN KIDNEY TISSUE AND RNA-SEQ SUPPORTS A FUNCTIONAL ROLE FOR DIFFERENTIAL METHYLATION IN ELMO1 AND PRKAG2 GENES. THIS STUDY REPORTS THE LARGEST, MOST COMPREHENSIVE, GENOME-WIDE QUANTITATIVE EVALUATION OF DNA METHYLATION FOR ASSOCIATION WITH CKD. EVIDENCE CONFIRMING METHYLATION SITES INFLUENCE DEVELOPMENT OF CKD WOULD STIMULATE RESEARCH TO IDENTIFY EPIGENETIC THERAPIES THAT MIGHT BE CLINICALLY USEFUL FOR CKD. 2014 4 3027 39 GENETICS OF CHRONIC OBSTRUCTIVE PULMONARY DISEASE. CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS A COMPLEX DISEASE WITH MULTIFACTORIAL BACKGROUND, BASED ON THE INTERACTION OF ENVIRONMENTAL AND GENETIC FACTORS. ENVIRONMENTAL FACTORS ARE CLEARLY RELATED TO THE DEVELOPMENT OF THE DISEASE. HOWEVER, FAMILY AND TWIN STUDIES SUGGESTED GENETICS FACTORS TO BE ONE OF THE IMPORTANT DETERMINANTS FOR THE DEVELOPMENT OF COPD. DIFFERENT APPROACHES HAVE BEEN USED TO IDENTIFY GENES OF INTEREST. GENOMEWIDE LINKAGE ANALYSIS FOUND AREAS OF INTEREST ON DIFFERENT CHROMOSOMES, WITH SOME GENES LOCATED IN THIS REGIONS BEING IDENTIFIED AND REPLICATED AS SUSCEPTIBILITY GENES. NUMEROUS OF CANDIDATE GENES THAT COULD BE LINKED TO DISEASE PATHOGENESIS HAVE BEEN IMPLICATED IN COPD GENETICS. HOWEVER, THE CANDIDATE GENE APPROACH IS OFTEN LIMITED BY INCONSISTENT RESULTS IN OTHER STUDY POPULATIONS. RECENTLY, A COMBINATION OF DIFFERENT METHODS IS USED GIVING MORE EVIDENCE FOR SOME CANDIDATE GENES, INCLUDING TGFBETA-1, SURFACTANT, SERPINE2 AND MICROSOMAL EPOXIDE HYDROLASE. IN THE FUTURE ONGOING EXACT PHENOTYPE DEFINITION, COMBINATION OF SEVERAL APPROACHES, GENOME-WIDE ASSOCIATION STUDIES AND ANIMAL MODEL GENETICS WILL LEAD TO NEW INSIGHTS INTO THE GENETICS OF COPD, WITH EPIGENETIC FACTORS NEEDS TO BE FURTHER INVESTIGATED AND CONSIDERED IN CONCERT WITH GENETIC FINDINGS. 2007 5 2622 49 EPIGENOME-WIDE ASSOCIATION STUDIES IN ASTHMA: A SYSTEMATIC REVIEW. OBJECTIVE: ASTHMA IS A COMMON CHRONIC RESPIRATORY AIRWAY DISEASE INFLUENCED BY ENVIRONMENTAL FACTORS AND POSSIBLY THEIR INTERACTION WITH THE HUMAN GENOME CAUSING EPIGENETIC CHANGES. EPIGENOME-WIDE ASSOCIATION STUDIES (EWAS) HAVE MAINLY INVESTIGATED DNA METHYLATION AND ITS ASSOCIATION WITH DISEASE OR TRAITS, EXPOSURE FACTORS OR GENE EXPRESSION. THIS SYSTEMATIC REVIEW AIMED TO IDENTIFY ALL EWAS ASSESSING DIFFERENTIALLY METHYLATED SITES ASSOCIATED WITH ASTHMA IN HUMANS. DESIGN: STRUCTURED SYSTEMATIC LITERATURE SEARCH FOLLOWING PRISMA GUIDELINES, NEWCASTLE-OTTAWA SCALE (NOS) FOR COHORT STUDIES WAS USED FOR BIAS ASSESSMENT. DATA SOURCES: WE SEARCHED PUBMED AND EMBASE DATABASES FROM 2005 TO 2019. ELIGIBILITY CRITERIA: EPIGENOME-WIDE ASSOCIATION STUDIES TESTING ASSOCIATION BETWEEN DIFFERENTIAL METHYLATION AND ASTHMA IN HUMANS. RESULTS: OVERALL, WE IDENTIFIED 16 EWAS STUDIES COMPLYING WITH OUR SEARCH CRITERIA. TWELVE STUDIES WERE CONDUCTED ON CHILDREN, AND 10 WERE CONDUCTED ON SAMPLE SIZES <150 SUBJECTS. FOUR HUNDRED AND NINETEEN CPGS WERE REPORTED IN CHILDREN STUDIES AFTER CORRECTION FOR MULTIPLE TESTING. IN THE ADULT STUDIES, THOUSANDS OF DIFFERENTIALLY METHYLATED SITES WERE IDENTIFIED. DIFFERENTIAL METHYLATION IN INFLAMMATORY-RELATED GENES CORRELATED WITH HIGHER LEVELS OF GENE EXPRESSIONS OF INFLAMMATORY MODULATORS IN ASTHMA. DIFFERENTIALLY METHYLATED GENES ASSOCIATED WITH ASTHMA INCLUDED SMAD3, SERPINC1, PROK1, IL13, RUNX3 AND TIGIT. FORTY-ONE CPGS WERE REPLICATED AT LEAST ONCE IN BLOOD SAMPLES, AND 28 CPGS WERE REPLICATED IN NASAL SAMPLES. CONCLUSION: ALTHOUGH MANY DIFFERENTIALLY METHYLATED CPGS IN GENES KNOWN TO BE INVOLVED IN ASTHMA HAVE BEEN IDENTIFIED IN EWAS TO DATE, WE CONCLUDE THAT FURTHER STUDIES OF LARGER SAMPLE SIZES AND ANALYSES OF DIFFERENTIAL METHYLATION BETWEEN DIFFERENT PHENOTYPES ARE NEEDED IN ORDER TO COMPREHENSIVELY EVALUATE THE ROLE OF EPIGENETIC FACTORS IN THE PATHOPHYSIOLOGY AND HETEROGENEITY OF ASTHMA, AND THE POTENTIAL CLINICAL UTILITY TO PREDICT OR CLASSIFY PATIENTS WITH ASTHMA. 2019 6 1705 47 DYNAMICS OF SMOKING-INDUCED GENOME-WIDE METHYLATION CHANGES WITH TIME SINCE SMOKING CESSATION. SEVERAL STUDIES HAVE RECENTLY IDENTIFIED STRONG EPIGENETIC SIGNALS RELATED TO TOBACCO SMOKING. HOWEVER, AN ASPECT THAT DID NOT RECEIVE MUCH ATTENTION IS THE EVOLUTION OF EPIGENETIC CHANGES WITH TIME SINCE SMOKING CESSATION. WE CONDUCTED A SERIES OF EPIGENOME-WIDE ASSOCIATION STUDIES TO CAPTURE THE DYNAMICS OF SMOKING-INDUCED EPIGENETIC CHANGES AFTER SMOKING CESSATION, USING GENOME-WIDE METHYLATION PROFILES OBTAINED FROM BLOOD SAMPLES IN 745 WOMEN FROM 2 EUROPEAN POPULATIONS. TWO DISTINCT CLASSES OF CPG SITES WERE IDENTIFIED: SITES WHOSE METHYLATION REVERTS TO LEVELS TYPICAL OF NEVER SMOKERS WITHIN DECADES AFTER SMOKING CESSATION, AND SITES REMAINING DIFFERENTIALLY METHYLATED, EVEN MORE THAN 35 YEARS AFTER SMOKING CESSATION. OUR RESULTS SUGGEST THAT THE DYNAMICS OF METHYLATION CHANGES FOLLOWING SMOKING CESSATION ARE DRIVEN BY A DIFFERENTIAL AND SITE-SPECIFIC MAGNITUDE OF THE SMOKING-INDUCED ALTERATIONS (WITH PERSISTENT SITES BEING MOST AFFECTED) IRRESPECTIVE OF THE INTENSITY AND DURATION OF SMOKING. ANALYSES OF THE LINK BETWEEN METHYLATION AND EXPRESSION LEVELS REVEALED THAT METHYLATION PREDOMINANTLY AND REMOTELY DOWN-REGULATES GENE EXPRESSION. AMONG GENES WHOSE EXPRESSION WAS ASSOCIATED WITH OUR CANDIDATE CPG SITES, LRRN3 APPEARED TO BE PARTICULARLY INTERESTING AS IT WAS ONE OF THE FEW GENES WHOSE METHYLATION AND EXPRESSION WERE DIRECTLY ASSOCIATED, AND THE ONLY GENE IN WHICH BOTH METHYLATION AND GENE EXPRESSION WERE FOUND ASSOCIATED WITH SMOKING. OUR STUDY HIGHLIGHTS PERSISTENT EPIGENETIC MARKERS OF SMOKING, WHICH CAN POTENTIALLY BE DETECTED DECADES AFTER CESSATION. SUCH HISTORICAL SIGNATURES ARE PROMISING BIOMARKERS TO REFINE INDIVIDUAL RISK PROFILING OF SMOKING-INDUCED CHRONIC DISEASE SUCH AS LUNG CANCER. 2015 7 938 38 CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) RISK IS MEDIATED BY MULTIPLE ENHANCER VARIANTS WITHIN CLL RISK LOCI. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS THE MOST COMMON ADULT LEUKEMIA IN WESTERN COUNTRIES. IT HAS A STRONG GENETIC BASIS, SHOWING A ~ 8-FOLD INCREASED RISK OF CLL IN FIRST-DEGREE RELATIVES. GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE IDENTIFIED 41 RISK VARIANTS ACROSS 41 LOCI. HOWEVER, FOR A MAJORITY OF THE LOCI, THE FUNCTIONAL VARIANTS AND THE MECHANISMS UNDERLYING THEIR CAUSAL ROLES REMAIN UNDEFINED. HERE, WE EXAMINED THE GENETIC AND EPIGENETIC FEATURES ASSOCIATED WITH 12 INDEX VARIANTS, ALONG WITH ANY CORRELATED (R2 >/= 0.5) VARIANTS, AT THE CLL RISK LOCI LOCATED OUTSIDE OF GENE PROMOTERS. BASED ON PUBLICLY AVAILABLE CHIP-SEQ AND CHROMATIN ACCESSIBILITY DATA AS WELL AS OUR OWN CHIP-SEQ DATA FROM CLL PATIENTS, WE IDENTIFIED SIX CANDIDATE FUNCTIONAL VARIANTS AT SIX LOCI AND AT LEAST TWO CANDIDATE FUNCTIONAL VARIANTS AT EACH OF THE REMAINING SIX LOCI. THE FUNCTIONAL VARIANTS ARE PREDOMINANTLY LOCATED WITHIN ENHANCERS OR SUPER-ENHANCERS, INCLUDING BI-DIRECTIONALLY TRANSCRIBED ENHANCERS, WHICH ARE OFTEN RESTRICTED TO IMMUNE CELL TYPES. FURTHERMORE, WE FOUND THAT, AT 78% OF THE FUNCTIONAL VARIANTS, THE ALTERNATIVE ALLELES ALTERED THE TRANSCRIPTION FACTOR BINDING MOTIFS OR HISTONE MODIFICATIONS, INDICATING THE INVOLVEMENT OF THESE VARIANTS IN THE CHANGE OF LOCAL CHROMATIN STATE. FINALLY, THE ENHANCERS CARRYING FUNCTIONAL VARIANTS PHYSICALLY INTERACTED WITH GENES ENRICHED IN THE TYPE I INTERFERON SIGNALING PATHWAY, APOPTOSIS, OR TP53 NETWORK THAT ARE KNOWN TO PLAY KEY ROLES IN CLL. THESE RESULTS SUPPORT THE REGULATORY ROLES FOR INHERITED NONCODING VARIANTS IN THE PATHOGENESIS OF CLL. 2020 8 70 42 A METHOD TO DETECT DIFFERENTIALLY METHYLATED LOCI WITH NEXT-GENERATION SEQUENCING. EPIGENETIC CHANGES, ESPECIALLY DNA METHYLATION AT CPG LOCI HAVE IMPORTANT IMPLICATIONS IN CANCER AND OTHER COMPLEX DISEASES. WITH THE DEVELOPMENT OF NEXT-GENERATION SEQUENCING (NGS), IT IS FEASIBLE TO GENERATE DATA TO INTERROGATE THE DIFFERENCE IN METHYLATION STATUS FOR GENOME-WIDE LOCI USING CASE-CONTROL DESIGN. HOWEVER, A PROPER AND EFFICIENT STATISTICAL TEST IS LACKING. THERE ARE SEVERAL CHALLENGES. FIRST, UNLIKE METHYLATION EXPERIMENTS USING MICROARRAYS, WHERE THERE IS ONE MEASURE OF METHYLATION FOR ONE INDIVIDUAL AT A PARTICULAR CPG SITE, HERE WE HAVE THE COUNTS OF METHYLATION ALLELE AND UNMETHYLATION ALLELE FOR EACH INDIVIDUAL. SECOND, DUE TO THE NATURE OF SAMPLE PREPARATION, THE MEASURED METHYLATION REFLECTS THE METHYLATION STATUS OF A MIXTURE OF CELLS INVOLVED IN SAMPLE PREPARATION. THEREFORE, THE UNDERLYING DISTRIBUTION OF THE MEASURED METHYLATION LEVEL IS UNKNOWN, AND A ROBUST TEST IS MORE DESIRABLE THAN PARAMETRIC APPROACH. THIRD, CURRENTLY NGS MEASURES METHYLATION AT OVER 2 MILLION CPG SITES. ANY STATISTICAL TESTS HAVE TO BE COMPUTATIONALLY EFFICIENT IN ORDER TO BE APPLIED TO THE NGS DATA. TAKING THESE CHALLENGES INTO ACCOUNT, WE PROPOSE A TEST FOR DIFFERENTIAL METHYLATION BASED ON CLUSTERED DATA ANALYSIS BY MODELING THE METHYLATION COUNTS. WE PERFORMED SIMULATIONS TO SHOW THAT IT IS ROBUST UNDER SEVERAL DISTRIBUTIONS FOR THE MEASURED METHYLATION LEVELS. IT HAS GOOD POWER AND IS COMPUTATIONALLY EFFICIENT. FINALLY, WE APPLY THE TEST TO OUR NGS DATA ON CHRONIC LYMPHOCYTIC LEUKEMIA. THE RESULTS INDICATE THAT IT IS A PROMISING AND PRACTICAL TEST. 2013 9 3503 38 IDENTIFICATION OF POTENTIAL DIFFERENTIALLY METHYLATED GENE-RELATED BIOMARKERS IN ENDOMETRIOSIS. AIM: TO IDENTIFY EPIGENETIC ALTERATIONS OF DIFFERENTIALLY EXPRESSED GENES AND SCREEN OUT TARGETED THERAPEUTIC DRUGS IN ENDOMETRIOSIS. METHODS: BASED ON THE GENE EXPRESSION OMNIBUS DATABASE AND A SERIES OF BIOLOGICAL INFORMATION ANALYSIS TOOLS, SUPPLEMENTED BY VALIDATION OF CLINICAL SAMPLES, ABERRANT DNA METHYLATION-DRIVEN GENES AND THEIR FUNCTIONS WERE EXPLORED, AS WELL AS POSSIBLE TARGETED DRUGS. RESULTS: THIS STUDY SCREENED OUT A RANGE OF DNA METHYLATION-DRIVEN GENES THAT WERE ASSOCIATED WITH POWERFUL PROPERTIES AND CORRESPONDING PATHWAYS. AMONG THEM, BDNF AND CCL2 WERE KEY GENES IN THE DEVELOPMENT OF ENDOMETRIOSIS. FOUR CHEMICAL AGENTS HAVE BEEN FLAGGED AS POTENTIAL TREATMENTS FOR ENDOMETRIOSIS. CONCLUSION: THESE CANDIDATE GENES AND SMALL-MOLECULE AGENTS MAY BE FURTHER EXPLORED AS POTENTIAL TARGETS AND DRUGS FOR ENDOMETRIOSIS DIAGNOSIS AND THERAPY, RESPECTIVELY. 2022 10 311 41 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 11 4869 27 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 12 3068 40 GENOME-WIDE DNA METHYLATION PROFILING IDENTIFIES DIFFERENTIAL METHYLATION IN UNINVOLVED PSORIATIC EPIDERMIS. PSORIASIS IS A CHRONIC INFLAMMATORY SKIN DISEASE WITH BOTH LOCAL AND SYSTEMIC COMPONENTS. GENOME-WIDE APPROACHES HAVE IDENTIFIED MORE THAN 60 PSORIASIS-SUSCEPTIBILITY LOCI, BUT GENES ARE ESTIMATED TO EXPLAIN ONLY ONE-THIRD OF THE HERITABILITY IN PSORIASIS, SUGGESTING ADDITIONAL, YET UNIDENTIFIED, SOURCES OF HERITABILITY. EPIGENETIC MODIFICATIONS HAVE BEEN LINKED TO PSORIASIS AND ALTERED DNA METHYLATION PATTERNS IN PSORIATIC VERSUS HEALTHY SKIN HAVE BEEN REPORTED IN WHOLE-SKIN BIOPSIES. IN THIS STUDY, FOCUSING ON EPIGENETIC MODIFICATIONS IN THE PSORIATIC UNINVOLVED SKIN, WE COMPARED THE LESIONAL AND NON-LESIONAL EPIDERMIS FROM PSORIASIS PATIENTS WITH EPIDERMIS FROM HEALTHY CONTROLS. WE PERFORMED AN EXHAUSTIVE GENOME-WIDE DNA METHYLATION PROFILING USING REDUCED REPRESENTATION BISULFITE SEQUENCING, WHICH INTERROGATES THE METHYLATION STATUS OF APPROXIMATELY 3-4 MILLION CPG SITES. MORE THAN 2,000 STRONGLY DIFFERENTIALLY METHYLATED SITES WERE IDENTIFIED AND A STRIKING OVERREPRESENTATION OF THE WNT AND CADHERIN PATHWAYS AMONG THE DIFFERENTIALLY METHYLATED SITES WAS FOUND. IN PARTICULAR, WE OBSERVE A STRONG DIFFERENTIAL METHYLATION IN SEVERAL PSORIASIS CANDIDATE GENES. A SUBSTANTIAL NUMBER OF DIFFERENTIALLY METHYLATED SITES PRESENT IN THE UNINVOLVED VERSUS HEALTHY EPIDERMIS SUGGESTS THE PRESENCE OF A PRE-PSORIATIC STATE IN THE CLINICALLY HEALTHY SKIN TYPE. OUR EXPLORATORY STUDY REPRESENTS A STARTING POINT FOR IDENTIFYING BIOMARKERS FOR PSORIASIS-PRONE SKIN BEFORE DISEASE ONSET. 2018 13 101 40 A RAT METHYL-SEQ PLATFORM TO IDENTIFY EPIGENETIC CHANGES ASSOCIATED WITH STRESS EXPOSURE. AS GENOMES OF A WIDER VARIETY OF ANIMALS BECOME AVAILABLE, THERE IS AN INCREASING NEED FOR TOOLS THAT CAN CAPTURE DYNAMIC EPIGENETIC CHANGES IN THESE ANIMAL MODELS. THE RAT IS ONE PARTICULAR MODEL ANIMAL WHERE AN EPIGENETIC TOOL CAN COMPLEMENT MANY PHARMACOLOGICAL AND BEHAVIORAL STUDIES TO PROVIDE INSIGHTFUL MECHANISTIC INFORMATION. TO THIS END, WE ADAPTED THE SURESELECT TARGET CAPTURE SYSTEM (REFERRED TO AS METHYL-SEQ) FOR THE RAT, WHICH CAN ASSESS DNA METHYLATION LEVELS ACROSS THE RAT GENOME. THE RAT DESIGN TARGETED PROMOTERS, CPG ISLANDS, ISLAND SHORES, AND GC-RICH REGIONS FROM ALL REFSEQ GENES. TO IMPLEMENT THE PLATFORM ON A RAT EXPERIMENT, MALE SPRAGUE DAWLEY RATS WERE EXPOSED TO CHRONIC VARIABLE STRESS FOR 3 WEEKS, AFTER WHICH BLOOD SAMPLES WERE COLLECTED FOR GENOMIC DNA EXTRACTION. METHYL-SEQ LIBRARIES WERE CONSTRUCTED FROM THE RAT DNA SAMPLES BY SHEARING, ADAPTER LIGATION, TARGET ENRICHMENT, BISULFITE CONVERSION, AND MULTIPLEXING. LIBRARIES WERE SEQUENCED ON A NEXT-GENERATION SEQUENCING PLATFORM AND THE SEQUENCED READS WERE ANALYZED TO IDENTIFY DMRS BETWEEN DNA OF STRESSED AND UNSTRESSED RATS. TOP CANDIDATE DMRS WERE INDEPENDENTLY VALIDATED BY BISULFITE PYROSEQUENCING TO CONFIRM THE ROBUSTNESS OF THE PLATFORM. RESULTS DEMONSTRATE THAT THE RAT METHYL-SEQ PLATFORM IS A USEFUL EPIGENETIC TOOL THAT CAN CAPTURE METHYLATION CHANGES INDUCED BY EXPOSURE TO STRESS. 2018 14 666 43 BLOOD-BASED DNA METHYLATION BIOMARKERS FOR TYPE 2 DIABETES: POTENTIAL FOR CLINICAL APPLICATIONS. TYPE 2 DIABETES (T2D) IS A LEADING CAUSE OF DEATH AND DISABILITY WORLDWIDE. IT IS A CHRONIC METABOLIC DISORDER THAT DEVELOPS DUE TO AN INTERPLAY OF GENETIC, LIFESTYLE, AND ENVIRONMENTAL FACTORS. THE BIOLOGICAL ONSET OF THE DISEASE OCCURS LONG BEFORE CLINICAL SYMPTOMS DEVELOP, THUS THE SEARCH FOR EARLY DIAGNOSTIC AND PROGNOSTIC BIOMARKERS, WHICH COULD FACILITATE INTERVENTION STRATEGIES TO PREVENT OR DELAY DISEASE PROGRESSION, HAS INCREASED CONSIDERABLY IN RECENT YEARS. EPIGENETIC MODIFICATIONS REPRESENT IMPORTANT LINKS BETWEEN GENETIC, ENVIRONMENTAL AND LIFESTYLE CUES AND INCREASING EVIDENCE IMPLICATE ALTERED EPIGENETIC MARKS SUCH AS DNA METHYLATION, THE MOST CHARACTERIZED AND WIDELY STUDIED EPIGENETIC MECHANISM, IN THE PATHOGENESIS OF T2D. THIS REVIEW PROVIDES AN UPDATE OF THE CURRENT STATUS OF DNA METHYLATION AS A BIOMARKER FOR T2D. FOUR DATABASES, SCOPUS, PUBMED, COCHRANE CENTRAL, AND GOOGLE SCHOLAR WERE SEARCHED FOR STUDIES INVESTIGATING DNA METHYLATION IN BLOOD. THIRTY-SEVEN STUDIES WERE IDENTIFIED, AND ARE SUMMARIZED WITH RESPECT TO POPULATION CHARACTERISTICS, BIOLOGICAL SOURCE, AND METHOD OF DNA METHYLATION QUANTIFICATION (GLOBAL, CANDIDATE GENE OR GENOME-WIDE). WE HIGHLIGHT THAT DIFFERENTIAL METHYLATION OF THE TCF7L2, KCNQ1, ABCG1, TXNIP, PHOSPHO1, SREBF1, SLC30A8, AND FTO GENES IN BLOOD ARE REPRODUCIBLY ASSOCIATED WITH T2D IN DIFFERENT POPULATION GROUPS. THESE GENES SHOULD BE PRIORITIZED AND REPLICATED IN LONGITUDINAL STUDIES ACROSS MORE POPULATIONS IN FUTURE STUDIES. FINALLY, WE DISCUSS THE LIMITATIONS FACED BY DNA METHYLATION STUDIES, WHICH INCLUDE INCLUDING INTERPATIENT VARIABILITY, CELLULAR HETEROGENEITY, AND LACK OF ACCOUNTING FOR STUDY CONFOUNDERS. THESE LIMITATIONS AND CHALLENGES MUST BE OVERCOME BEFORE THE IMPLEMENTATION OF BLOOD-BASED DNA METHYLATION BIOMARKERS INTO A CLINICAL SETTING. WE EMPHASIZE THE NEED FOR LONGITUDINAL PROSPECTIVE STUDIES TO SUPPORT THE ROBUSTNESS OF THE CURRENT FINDINGS OF THIS REVIEW. 2018 15 287 36 AGING AND CHRONIC SUN EXPOSURE CAUSE DISTINCT EPIGENETIC CHANGES IN HUMAN SKIN. EPIGENETIC CHANGES ARE WIDELY CONSIDERED TO PLAY AN IMPORTANT ROLE IN AGING, BUT EXPERIMENTAL EVIDENCE TO SUPPORT THIS HYPOTHESIS HAS BEEN SCARCE. WE HAVE USED ARRAY-BASED ANALYSIS TO DETERMINE GENOME-SCALE DNA METHYLATION PATTERNS FROM HUMAN SKIN SAMPLES AND TO INVESTIGATE THE EFFECTS OF AGING, CHRONIC SUN EXPOSURE, AND TISSUE VARIATION. OUR RESULTS REVEAL A HIGH DEGREE OF TISSUE SPECIFICITY IN THE METHYLATION PATTERNS AND ALSO SHOWED VERY LITTLE INTERINDIVIDUAL VARIATION WITHIN TISSUES. DATA STRATIFICATION BY AGE REVEALED THAT DNA FROM OLDER INDIVIDUALS WAS CHARACTERIZED BY A SPECIFIC HYPERMETHYLATION PATTERN AFFECTING LESS THAN 1% OF THE MARKERS ANALYZED. INTERESTINGLY, STRATIFICATION BY SUN EXPOSURE PRODUCED A FUNDAMENTALLY DIFFERENT PATTERN WITH A SIGNIFICANT TREND TOWARDS HYPOMETHYLATION. OUR RESULTS THUS IDENTIFY DEFINED AGE-RELATED DNA METHYLATION CHANGES AND SUGGEST THAT THESE ALTERATIONS MIGHT CONTRIBUTE TO THE PHENOTYPIC CHANGES ASSOCIATED WITH SKIN AGING. 2010 16 5882 40 SYSTEMATIC REVIEW OF LUNG FUNCTION AND COPD WITH PERIPHERAL BLOOD DNA METHYLATION IN POPULATION BASED STUDIES. BACKGROUND: EPIGENETIC VARIATIONS IN PERIPHERAL BLOOD HAVE POTENTIAL AS BIOMARKERS FOR DISEASE. THIS SYSTEMATIC REVIEW ASSESSES THE ASSOCIATION OF LUNG FUNCTION AND CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) WITH DNA METHYLATION PROFILES IN PERIPHERAL BLOOD FROM POPULATION-BASED STUDIES. METHODS: ONLINE DATABASES MEDLINE, EMBASE, AND WEB OF SCIENCE WERE SEARCHED. GOOGLE SCHOLAR WAS SEARCHED TO IDENTIFY GREY LITERATURE. AFTER REMOVING DUPLICATE ARTICLES, 1155 ARTICLES WERE INDEPENDENTLY SCREENED BY TWO INVESTIGATORS. PEER REVIEWED REPORTS ON POPULATION-BASED STUDIES THAT EXAMINED PERIPHERAL BLOOD DNA METHYLATION IN PARTICIPANTS WITH MEASURED LUNG FUNCTION (FEV1, FEV1/FVC RATIO) OR KNOWN COPD STATUS WERE SELECTED FOR FULL-TEXT REVIEW. SIX ARTICLES WERE SUITABLE FOR INCLUSION. INFORMATION REGARDING STUDY CHARACTERISTICS, DESIGNS, METHODOLOGIES AND CONCLUSIONS WAS EXTRACTED. A NARRATIVE SYNTHESIS WAS PERFORMED BASED ON PUBLISHED RESULTS. RESULTS: THREE OF THE SIX ARTICLES ASSESSED THE ASSOCIATION OF COPD WITH DNA METHYLATION, AND TWO OF THESE ALSO INCLUDED ASSOCIATIONS WITH LUNG FUNCTION. OVERALL, FIVE REPORTS EXAMINED THE ASSOCIATION OF LUNG FUNCTION WITH DNA METHYLATION PROFILES. FIVE OF THE SIX ARTICLES REPORTED 'SIGNIFICANT' RESULTS. HOWEVER, NO CONSISTENT CPG SITES WERE IDENTIFIED ACROSS STUDIES FOR COPD STATUS OR LUNG FUNCTION VALUES. CONCLUSIONS: DNA METHYLATION PATTERNS IN PERIPHERAL BLOOD FROM INDIVIDUALS WITH REDUCED LUNG FUNCTION OR COPD MAY BE DIFFERENT TO THOSE IN PEOPLE WITH NORMAL LUNG FUNCTION. HOWEVER, THIS SYSTEMATIC REVIEW DID NOT FIND ANY CONSISTENT ASSOCIATIONS OF LUNG FUNCTION OR COPD WITH DIFFERENTIALLY METHYLATED CPG SITES. LARGE STUDIES WITH A LONGITUDINAL DESIGN TO ADDRESS REVERSE CAUSALITY MAY PROVE A MORE FRUITFUL AREA OF RESEARCH. TRIAL REGISTRATION: PROSPERO 2016: CRD42016037352 . 2017 17 4287 38 MICRORNA EXPRESSION PROFILING IN BEHCET'S DISEASE. BACKGROUND: BEHCET'S DISEASE (BD) IS A CHRONIC INFLAMMATORY MULTISYSTEM DISEASE CHARACTERIZED BY ORAL AND GENITAL ULCERS, UVEITIS, AND SKIN LESIONS. MICRORNAS (MIRNAS) ARE KEY REGULATORS OF IMMUNE RESPONSES. DIFFERENTIAL EXPRESSION OF MIRNAS HAS BEEN REPORTED IN SEVERAL INFLAMMATORY AUTOIMMUNE DISEASES; HOWEVER, THEIR ROLE IN BD IS NOT FULLY ELUCIDATED. WE AIMED TO IDENTIFY MIRNA EXPRESSION SIGNATURES ASSOCIATED WITH BD AND TO INVESTIGATE THEIR POTENTIAL IMPLICATION IN THE DISEASE PATHOGENESIS. METHODS: MIRNA MICROARRAY ANALYSIS WAS PERFORMED IN BLOOD CELLS OF BD PATIENTS AND HEALTHY CONTROLS. MIRNA EXPRESSION PROFILES WERE ANALYZED USING AFFYMETRIX ARRAYS WITH A COMPREHENSIVE COVERAGE OF MIRNA SEQUENCES. PATHWAY ANALYSES WERE PERFORMED, AND THE GLOBAL MIRNA PROFILING WAS COMBINED WITH TRANSCRIPTOMA DATA IN BD. DEREGULATION OF SELECTED MIRNAS WAS VALIDATED BY REAL-TIME PCR. RESULTS: WE IDENTIFIED SPECIFIC MIRNA SIGNATURES ASSOCIATED WITH BD PATIENTS WITH ACTIVE DISEASE. THESE MIRNAS TARGET PATHWAYS RELEVANT IN BD, SUCH AS TNF, IFN GAMMA, AND VEGF-VEGFR SIGNALING CASCADES. NETWORK ANALYSIS REVEALED SEVERAL MIRNAS REGULATING HIGHLY CONNECTED GENES WITHIN THE BD TRANSCRIPTOMA. CONCLUSIONS: THE COMBINED ANALYSIS OF DEREGULATED MIRNAS AND BD TRANSCRIPTOME SHEDS LIGHT ON SOME EPIGENETIC ASPECTS OF BD IDENTIFYING SPECIFIC MIRNAS, WHICH MAY REPRESENT PROMISING CANDIDATES AS BIOMARKERS AND/OR FOR THE DESIGN OF NOVEL THERAPEUTIC STRATEGIES IN BD. 2018 18 4607 37 NEIGHBORHOOD ENVIRONMENT AND DNA METHYLATION: IMPLICATIONS FOR CARDIOVASCULAR DISEASE RISK. EXPOSURE TO CHRONIC STRESS SUCH AS LIVING IN DISADVANTAGED NEIGHBORHOODS HAS BEEN RELATED TO CARDIOVASCULAR DISEASE (CVD). CHRONIC STRESS MAY INCREASE THE RISK FOR CVD BY INCREASING LEVELS OF SYSTEMIC INFLAMMATION (E.G., HIGHER LEVELS OF PRO-INFLAMMATORY CYTOKINES). DIFFERENTIAL DNA METHYLATION OF INFLAMMATION-RELATED CANDIDATE GENES IS ALSO RELATED TO HIGHER RISK FOR CVD. THUS, THE PURPOSE OF THIS REVIEW WAS TO EXAMINE THE ASSOCIATION OF NEIGHBORHOOD DISADVANTAGE WITH DNA METHYLATION. A SEARCH OF LITERATURE WAS CONDUCTED USING SCOPUS, CINAHL, PUBMED, MEDLINE, AND EMBASE DATABASES. THE KEYWORDS NEIGHBORHOOD, NEIGHBORHOOD DISORDER, NEIGHBORHOOD CRIME, NEIGHBORHOOD VIOLENCE, NEIGHBORHOOD SAFETY, BUILT ENVIRONMENT, AND HOUSING VACANCY WERE COMBINED WITH THE KEYWORDS DNA METHYLATION AND EPIGENETICS. FIVE STUDIES WERE INCLUDED IN THIS REVIEW (N = 3 ADULT BLOOD SAMPLES AND N = 2 FETAL BLOOD SAMPLES). FOUR OF THE FIVE STUDIES REPORTED AN ASSOCIATION OF NEIGHBORHOOD SOCIOECONOMIC STATUS, SOCIAL ENVIRONMENT, AND CRIME WITH EITHER GLOBAL OR GENE-SPECIFIC DNA METHYLATION. ONLY TWO STUDIES EXAMINED THE ASSOCIATION OF NEIGHBORHOOD DISADVANTAGE WITH INFLAMMATION-RELATED CANDIDATE GENES. ONE OF THESE STUDIES FOUND A SIGNIFICANT ASSOCIATION OF NEIGHBORHOOD SOCIOECONOMIC DISADVANTAGE AND SOCIAL ENVIRONMENT WITH DNA METHYLATION IN INFLAMMATION-RELATED CANDIDATE GENES. THUS, DATA ARE LIMITED ON THE ASSOCIATION BETWEEN NEIGHBORHOOD DISADVANTAGE AND DNA METHYLATION OF INFLAMMATION-RELATED CANDIDATE GENES, AS WELL AS GENES IN OTHER POTENTIAL MECHANISTIC PATHWAYS INCLUDING PSYCHOSOCIAL STRESS, TOXIN RESPONSE, AND ADIPOSITY. FUTURE STUDIES SHOULD EXAMINE THESE ASSOCIATIONS AND THE POTENTIAL EPIGENETIC MECHANISMS BY WHICH NEIGHBORHOOD DISADVANTAGE INCREASES THE RISK FOR CVD. 2019 19 2418 42 EPIGENETIC SIGNATURE OF CHRONIC LOW BACK PAIN IN HUMAN T CELLS. OBJECTIVE: DETERMINE IF CHRONIC LOW BACK PAIN (LBP) IS ASSOCIATED WITH DNA METHYLATION SIGNATURES IN HUMAN T CELLS THAT WILL REVEAL NOVEL MECHANISMS AND POTENTIAL THERAPEUTIC TARGETS AND EXPLORE THE FEASIBILITY OF EPIGENETIC DIAGNOSTIC MARKERS FOR PAIN-RELATED PATHOPHYSIOLOGY. METHODS: GENOME-WIDE DNA METHYLATION ANALYSIS OF 850,000 CPG SITES IN WOMEN AND MEN WITH CHRONIC LBP AND PAIN-FREE CONTROLS WAS PERFORMED. T CELLS WERE ISOLATED (DISCOVERY COHORT, N = 32) AND USED TO IDENTIFY DIFFERENTIALLY METHYLATED CPG SITES, AND GENE ONTOLOGIES AND MOLECULAR PATHWAYS WERE IDENTIFIED. A POLYGENIC DNA METHYLATION SCORE FOR LBP WAS GENERATED IN BOTH WOMEN AND MEN. VALIDATION WAS PERFORMED IN AN INDEPENDENT COHORT (VALIDATION COHORT, N = 63) OF CHRONIC LBP AND HEALTHY CONTROLS. RESULTS: ANALYSIS WITH THE DISCOVERY COHORT REVEALED A TOTAL OF 2,496 AND 419 DIFFERENTIALLY METHYLATED CPGS IN WOMEN AND MEN, RESPECTIVELY. IN WOMEN, MOST OF THESE SITES WERE HYPOMETHYLATED AND ENRICHED IN GENES WITH FUNCTIONS IN THE EXTRACELLULAR MATRIX, IN THE IMMUNE SYSTEM (IE, CYTOKINES), OR IN EPIGENETIC PROCESSES. IN MEN, A UNIQUE CHRONIC LBP DNA METHYLATION SIGNATURE WAS IDENTIFIED CHARACTERIZED BY SIGNIFICANT ENRICHMENT FOR GENES FROM THE MAJOR HISTOCOMPATIBILITY COMPLEX. SEX-SPECIFIC POLYGENIC DNA METHYLATION SCORES WERE GENERATED TO ESTIMATE THE PAIN STATUS OF EACH INDIVIDUAL AND CONFIRMED IN THE VALIDATION COHORT USING PYROSEQUENCING. CONCLUSION: THIS STUDY REVEALS SEX-SPECIFIC DNA METHYLATION SIGNATURES IN HUMAN T CELLS THAT DISCRIMINATES CHRONIC LBP PARTICIPANTS FROM HEALTHY CONTROLS. 2021 20 5702 28 SINGLE-CELL GENOMICS FOR INVESTIGATING PATHOGENESIS OF INFLAMMATORY DISEASES. RECENT TECHNICAL ADVANCES HAVE ENABLED UNBIASED TRANSCRIPTOMIC AND EPIGENETIC ANALYSIS OF EACH CELL, KNOWN AS "SINGLE-CELL ANALYSIS". SINGLE-CELL ANALYSIS HAS A VARIETY OF TECHNICAL APPROACHES TO INVESTIGATE THE STATE OF EACH CELL, INCLUDING MRNA LEVELS (TRANSCRIPTOME), THE IMMUNE REPERTOIRE (IMMUNE REPERTOIRE ANALYSIS), CELL SURFACE PROTEINS (SURFACE PROTEOME ANALYSIS), CHROMATIN ACCESSIBILITY (EPIGENOME), AND ACCORDANCE WITH GENOME VARIANTS (EQTLS; EXPRESSION QUANTITATIVE TRAIT LOCI). AS AN EFFECTIVE TOOL FOR INVESTIGATING ROBUST IMMUNE RESPONSES IN CORONAVIRUS DISEASE 2019 (COVID-19), MANY RESEARCHERS PERFORMED SINGLE-CELL ANALYSIS TO CAPTURE THE DIVERSE, UNBIASED IMMUNE CELL ACTIVATION AND DIFFERENTIATION. DESPITE CHALLENGES ELUCIDATING THE COMPLICATED IMMUNE MICROENVIRONMENTS OF CHRONIC INFLAMMATORY DISEASES USING EXISTING EXPERIMENTAL METHODS, IT IS NOW POSSIBLE TO CAPTURE THE SIMULTANEOUS IMMUNE FEATURES OF DIFFERENT CELL TYPES ACROSS INFLAMED TISSUES USING VARIOUS SINGLE-CELL TOOLS. IN THIS REVIEW, WE INTRODUCE PATIENT-BASED AND EXPERIMENTAL MOUSE MODEL RESEARCH UTILIZING SINGLE-CELL ANALYSES IN THE FIELD OF CHRONIC INFLAMMATORY DISEASES, AS WELL AS MULTI-ORGAN ATLAS TARGETING IMMUNE CELLS. 2023