1  1132 128 COMPREHENSIVE DNA METHYLATION ANALYSIS USING A METHYL-CPG-BINDING DOMAIN CAPTURE-BASED METHOD IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS. THE ROLE OF LONG NONCODING RNAS (LNCRNAS) IN CANCER IS COMING TO THE FOREFRONT DUE TO GROWING INTEREST IN UNDERSTANDING THEIR MECHANISTIC FUNCTIONS DURING CANCER DEVELOPMENT AND PROGRESSION. DESPITE THIS, THE GLOBAL EPIGENETIC REGULATION OF LNCRNAS AND REPETITIVE SEQUENCES IN CANCER HAS NOT BEEN WELL INVESTIGATED, PARTICULARLY IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). THIS STUDY FOCUSES ON A UNIQUE APPROACH: THE IMMUNOPRECIPITATION-BASED CAPTURE OF DOUBLE-STRANDED, METHYLATED DNA FRAGMENTS USING METHYL-BINDING DOMAIN (MBD) PROTEINS, FOLLOWED BY NEXT-GENERATION SEQUENCING (MBD-SEQ). CLL PATIENT SAMPLES BELONGING TO TWO PROGNOSTIC SUBGROUPS (5 IGVH MUTATED SAMPLES + 5 IGVH UNMUTATED SAMPLES) WERE USED IN THIS STUDY. ANALYSIS REVEALED 5,800 HYPERMETHYLATED AND 12,570 HYPOMETHYLATED CLL-SPECIFIC DIFFERENTIALLY METHYLATED GENES (CLLDMGS) COMPARED TO NORMAL HEALTHY CONTROLS. IMPORTANTLY, THESE RESULTS IDENTIFIED SEVERAL CLL-SPECIFIC, DIFFERENTIALLY METHYLATED LNCRNAS, REPETITIVE ELEMENTS, AND PROTEIN-CODING GENES WITH POTENTIAL PROGNOSTIC VALUE. THIS WORK OUTLINES A DETAILED PROTOCOL FOR AN MBD-SEQ AND BIOINFORMATICS PIPELINE DEVELOPED FOR THE COMPREHENSIVE ANALYSIS OF GLOBAL METHYLATION PROFILES IN HIGHLY CPG-RICH REGIONS USING CLL PATIENT SAMPLES. FINALLY, A PROTEIN-CODING GENE AND AN LNCRNA WERE VALIDATED USING PYROSEQUENCING, WHICH IS A HIGHLY QUANTITATIVE METHOD TO ANALYZE CPG METHYLATION LEVELS TO FURTHER CORROBORATE THE FINDINGS FROM THE MBD-SEQ PROTOCOL.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
2   972  29 CHRONIC OBSTRUCTIVE PULMONARY DISEASE IS ASSOCIATED WITH EPIGENOME-WIDE DIFFERENTIAL METHYLATION IN BAL LUNG CELLS. DNA METHYLATION PATTERNS IN CHRONIC PULMONARY OBSTRUCTIVE DISEASE (COPD) MIGHT OFFER NEW INSIGHTS INTO DISEASE PATHOGENESIS. TO ASSESS METHYLATION PROFILES IN THE MAIN COPD TARGET ORGAN, WE PERFORMED AN EPIGENOME-WIDE ASSOCIATION STUDY ON BAL CELLS. BRONCHOSCOPIES WERE PERFORMED IN 18 SUBJECTS WITH COPD AND 15 CONTROL SUBJECTS (EX- AND CURRENT SMOKERS). DNA METHYLATION WAS MEASURED USING THE ILLUMINA METHYLATIONEPIC BEADCHIP KIT, COVERING MORE THAN 850,000 CPGS. DIFFERENTIALLY METHYLATED POSITIONS (DMPS) WERE EXAMINED FOR 1) ENRICHMENT IN PATHWAYS AND FUNCTIONAL GENE RELATIONSHIPS USING THE KYOTO ENCYCLOPEDIA OF GENES AND GENOMES AND GENE ONTOLOGY, 2) ACCELERATED AGING USING HORVATH'S EPIGENETIC CLOCK, 3) CORRELATION WITH GENE EXPRESSION, AND 4) COLOCALIZATION WITH GENETIC VARIATION. WE FOUND 1,155 BONFERRONI-SIGNIFICANT (P < 6.74 X 10(-8)) DMPS ASSOCIATED WITH COPD, MANY WITH LARGE EFFECT SIZES. FUNCTIONAL ANALYSIS IDENTIFIED BIOLOGICALLY PLAUSIBLE PATHWAYS AND GENE RELATIONSHIPS, INCLUDING ENRICHMENT FOR TRANSCRIPTION FACTOR ACTIVITY. STRONG CORRELATION WAS FOUND BETWEEN DNA METHYLATION AND CHRONOLOGICAL AGE BUT NOT BETWEEN COPD AND ACCELERATED AGING. FOR 79 UNIQUE DMPS, DNA METHYLATION CORRELATED SIGNIFICANTLY WITH GENE EXPRESSION IN BAL CELLS. THIRTY-NINE PERCENT OF DMPS WERE COLOCALIZED WITH COPD-ASSOCIATED SNPS. TO THE BEST OF OUR KNOWLEDGE, THIS IS THE FIRST EPIGENOME-WIDE ASSOCIATION STUDY OF COPD ON BAL CELLS, AND OUR ANALYSES REVEALED MANY DIFFERENTIAL METHYLATION SITES. INTEGRATION WITH MRNA DATA SHOWED A STRONG FUNCTIONAL READOUT FOR RELEVANT GENES, IDENTIFYING SITES WHERE DNA METHYLATION MIGHT DIRECTLY AFFECT EXPRESSION. ALMOST HALF OF DMPS WERE COLOCATED WITH SNPS IDENTIFIED IN PREVIOUS GENOME-WIDE ASSOCIATION STUDIES OF COPD, SUGGESTING JOINT GENETIC AND EPIGENETIC PATHWAYS RELATED TO DISEASE.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
3  2771  40 EXTENSIVE PROMOTER DNA HYPERMETHYLATION AND HYPOMETHYLATION IS ASSOCIATED WITH ABERRANT MICRORNA EXPRESSION IN CHRONIC LYMPHOCYTIC LEUKEMIA. DYSREGULATED MICRORNA (MIRNA) EXPRESSION CONTRIBUTES TO THE PATHOGENESIS OF HEMATOPOIETIC MALIGNANCIES, INCLUDING CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). HOWEVER, AN UNDERSTANDING OF THE MECHANISMS THAT CAUSE ABERRANT MIRNA TRANSCRIPTIONAL CONTROL IS LACKING. IN THIS STUDY, WE COMPREHENSIVELY INVESTIGATED THE ROLE AND EXTENT OF MIRNA EPIGENETIC REGULATION IN CLL. GENOME-WIDE PROFILING CONDUCTED ON 24 CLL AND 10 HEALTHY B CELL SAMPLES REVEALED GLOBAL DNA METHYLATION PATTERNS UPSTREAM OF MIRNA SEQUENCES THAT DISTINGUISHED MALIGNANT FROM HEALTHY CELLS AND IDENTIFIED PUTATIVE MIRNA PROMOTERS. INTEGRATION OF DNA METHYLATION AND MIRNA PROMOTER DATA LED TO THE IDENTIFICATION OF 128 RECURRENT MIRNA TARGETS FOR ABERRANT PROMOTER DNA METHYLATION. DNA HYPOMETHYLATION ACCOUNTED FOR MORE THAN 60% OF ALL ABERRANT PROMOTER-ASSOCIATED DNA METHYLATION IN CLL, AND PROMOTER DNA HYPOMETHYLATION WAS RESTRICTED TO WELL-DEFINED REGIONS. INDIVIDUAL HYPER- AND HYPOMETHYLATED PROMOTERS ALLOWED DISCRIMINATION OF CLL SAMPLES FROM HEALTHY CONTROLS. PROMOTER DNA METHYLATION PATTERNS WERE CONFIRMED IN AN INDEPENDENT PATIENT COHORT, WITH 11 MIRNAS CONSISTENTLY SHOWING AN INVERSE CORRELATION BETWEEN DNA METHYLATION STATUS AND EXPRESSION LEVEL. TOGETHER, OUR FINDINGS CHARACTERIZE THE ROLE OF EPIGENETIC CHANGES IN THE REGULATION OF MIRNA TRANSCRIPTION AND CREATE A REPOSITORY OF DISEASE-SPECIFIC PROMOTER REGIONS THAT MAY PROVIDE ADDITIONAL INSIGHTS INTO THE PATHOGENESIS OF CLL.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
4  2639  32 EPIGENOMIC ANALYSIS DETECTS WIDESPREAD GENE-BODY DNA HYPOMETHYLATION IN CHRONIC LYMPHOCYTIC LEUKEMIA. WE HAVE EXTENSIVELY CHARACTERIZED THE DNA METHYLOMES OF 139 PATIENTS WITH CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) WITH MUTATED OR UNMUTATED IGHV AND OF SEVERAL MATURE B-CELL SUBPOPULATIONS THROUGH THE USE OF WHOLE-GENOME BISULFITE SEQUENCING AND HIGH-DENSITY MICROARRAYS. THE TWO MOLECULAR SUBTYPES OF CLL HAVE DIFFERING DNA METHYLOMES THAT SEEM TO REPRESENT EPIGENETIC IMPRINTS FROM DISTINCT NORMAL B-CELL SUBPOPULATIONS. DNA HYPOMETHYLATION IN THE GENE BODY, TARGETING MOSTLY ENHANCER SITES, WAS THE MOST FREQUENT DIFFERENCE BETWEEN NAIVE AND MEMORY B CELLS AND BETWEEN THE TWO MOLECULAR SUBTYPES OF CLL AND NORMAL B CELLS. ALTHOUGH DNA METHYLATION AND GENE EXPRESSION WERE POORLY CORRELATED, WE IDENTIFIED GENE-BODY CPG DINUCLEOTIDES WHOSE METHYLATION WAS POSITIVELY OR NEGATIVELY ASSOCIATED WITH EXPRESSION. WE HAVE ALSO RECOGNIZED A DNA METHYLATION SIGNATURE THAT DISTINGUISHES NEW CLINICO-BIOLOGICAL SUBTYPES OF CLL. WE PROPOSE AN EPIGENOMIC SCENARIO IN WHICH DIFFERENTIAL METHYLATION IN THE GENE BODY MAY HAVE FUNCTIONAL AND CLINICAL IMPLICATIONS IN LEUKEMOGENESIS.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
5  1581  27 DNA METHYLATION PROFILES IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS TREATED WITH CHEMOIMMUNOTHERAPY. BACKGROUND: IN ORDER TO GAIN INSIGHT INTO THE CONTRIBUTION OF DNA METHYLATION TO DISEASE PROGRESSION OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), USING 450K ILLUMINA ARRAYS, WE DETERMINED THE DNA METHYLATION PROFILES IN PAIRED PRE-TREATMENT/RELAPSE SAMPLES FROM 34 CLL PATIENTS TREATED WITH CHEMOIMMUNOTHERAPY, MOSTLY (N = 31) WITH THE FLUDARABINE-CYCLOPHOSPHAMIDE-RITUXIMAB (FCR) REGIMEN. RESULTS: THE EXTENT OF IDENTIFIED CHANGES IN CLL CELLS VERSUS MEMORY B CELLS FROM HEALTHY DONORS WAS TERMED "EPIGENETIC BURDEN" (EB) WHEREAS THE NUMBER OF CHANGES BETWEEN THE PRE-TREATMENT VERSUS THE RELAPSE SAMPLE WAS TERMED "RELAPSE CHANGES" (RC). SIGNIFICANT (P < 0.05) ASSOCIATIONS WERE IDENTIFIED BETWEEN (I) HIGH EB AND SHORT TIME-TO-FIRST-TREATMENT (TTFT); AND, (II) FEW RCS AND SHORT TIME-TO-RELAPSE. BOTH THE EB AND THE RC CLUSTERED IN SPECIFIC GENOMIC REGIONS AND CHROMATIN STATES, INCLUDING REGULATORY REGIONS CONTAINING BINDING SITES OF TRANSCRIPTION FACTORS IMPLICATED IN B CELL AND CLL BIOLOGY. CONCLUSIONS: OVERALL, WE SHOW THAT DNA METHYLATION IN CLL FOLLOWS DIFFERENT DYNAMICS IN RESPONSE TO CHEMOIMMUNOTHERAPY. THESE EPIGENETIC ALTERATIONS WERE LINKED WITH SPECIFIC CLINICAL AND BIOLOGICAL FEATURES.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
6  3070  41 GENOME-WIDE DNA METHYLATION PROFILING IN CD8 T-CELLS AND GAMMA DELTA T-CELLS OF ASIAN INDIAN PATIENTS WITH TAKAYASU ARTERITIS. BACKGROUND: TAKAYASU'S ARTERITIS (TA) IS A CHRONIC INFLAMMATORY DISEASE THAT AFFECTS AORTA AND ITS MAIN BRANCHES AT THEIR ORIGIN. GENETIC, PATHOLOGICAL AND FUNCTIONAL STUDIES HAVE SHOWN THAT CD8 AND GAMMA DELTA (GAMMA/DELTA) T-LYMPHOCYTES ARE INVOLVED IN INFLAMMATORY PROCESSES IN AFFECTED REGIONS OF ARTERIES CAUSING VASCULAR DAMAGE. THE MOLECULAR FUNCTION OF THESE LYMPHOCYTES REMAINS UNCLEAR AND CURRENTLY NO EPIGENETIC STUDIES ARE AVAILABLE IN TA. WE PRIMARILY PERFORMED GENOME WIDE METHYLATION ANALYSIS IN CD8 T CELLS AND GAMMADELTA T CELLS OF PATIENTS WITH TA AND COMPARED WITH HEALTHY CONTROLS. METHODS: WE RECRUITED 12 SUBJECTS IN EACH GROUP NAMELY TA PATIENT AND HEALTHY CONTROLS. BLOOD SAMPLES WERE COLLECTED AFTER OBTAINING INFORMED WRITTEN CONSENT. CD8 T CELLS AND GAMMADELTA T CELLS WERE SEPARATED FROM WHOLE BLOOD. DNA EXTRACTED FROM THESE CELLS AND WERE SUBJECTED TO BISULFITE TREATMENT. FINALLY, BISULFITE TREATED DNA WAS LOADED IN INFINIUM METHYLATION EPIC ARRAY. BIOINFORMATICS ANALYSIS WAS USED TO IDENTIFY DIFFERENTIAL METHYLATION REGIONS WHICH WERE THEN MAPPED TO GENES. RESULTS: INTERLEUKIN (IL)-32 AND LYMPHOTOXIN-A WERE GENES SIGNIFICANTLY HYPOMETHYLATED IN CD8 T-CELLS. ANTI-INFLAMMATORY CYTOKINE GENES, IL-10, IL-1RN AND IL-27 WERE HYPOMETHYLATED IN GAMMADELTA T CELLS OF TA PATIENTS AS COMPARED TO HEALTHY CONTROLS. GENE ENRICHMENT ANALYSIS USING GENE ONTOLOGY (GO) DATABASE AND KYOTO ENCYCLOPAEDIA OF GENES AND GENOMES (KEGG) IDENTIFIED THAT GENES INVOLVED IN T-CELL RECEPTOR SIGNALLING PATHWAYS WERE HYPOMETHYLATED IN CD8 T-CELLS AND HYPERMETHYLATED IN GAMMADELTA T CELLS OF TA PATIENTS. CONCLUSION: CD8 T-CELLS MIGHT PLAY A MAJOR ROLE IN IMMUNOPATHOGENESIS OF INFLAMMATION IN TA, WHEREAS GAMMADELTA T CELLS MAY PLAY A REGULATORY ROLE.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
7  1571  42 DNA METHYLATION PATTERNS IN CD8(+) T CELLS DISCERN PSORIASIS FROM PSORIATIC ARTHRITIS AND CORRELATE WITH CUTANEOUS DISEASE ACTIVITY. BACKGROUND: PSORIASIS IS A T CELL-MEDIATED CHRONIC AUTOIMMUNE/INFLAMMATORY DISEASE. WHILE SOME PATIENTS EXPERIENCE DISEASE LIMITED TO THE SKIN (SKIN PSORIASIS), OTHERS DEVELOP JOINT INVOLVEMENT (PSORIATIC ARTHRITIS; PSA). IN THE ABSENCE OF DISEASE- AND/OR OUTCOME-SPECIFIC BIOMARKERS, AND AS ARTHRITIS CAN PRECEDE SKIN MANIFESTATIONS, DIAGNOSTIC AND THERAPEUTIC DELAYS ARE COMMON AND CONTRIBUTE TO DISEASE BURDEN AND DAMAGE ACCRUAL. OBJECTIVE: ALTERED EPIGENETIC MARKS, INCLUDING DNA METHYLATION, CONTRIBUTE TO EFFECTOR T CELL PHENOTYPES AND ALTERED CYTOKINE EXPRESSION IN AUTOIMMUNE/INFLAMMATORY DISEASES. THIS PROJECT AIMED AT THE IDENTIFICATION OF DISEASE-/OUTCOME-SPECIFIC DNA METHYLATION SIGNATURES IN CD8(+) T CELLS FROM PATIENTS WITH PSORIASIS AND PSA AS COMPARED TO HEALTHY CONTROLS. METHOD: PERIPHERAL BLOOD CD8(+) T CELLS FROM NINE HEALTHY CONTROLS, 10 PSORIASIS, AND SEVEN PSA PATIENTS WERE COLLECTED TO ANALYZE DNA METHYLATION MARKS USING ILLUMINA HUMAN METHYLATION EPIC BEADCHIPS (>850,000 CPGS PER SAMPLE). BIOINFORMATIC ANALYSIS WAS PERFORMED USING R (MINFI, LIMMA, CHAMP, AND DMRCATE PACKAGES). RESULTS: DNA METHYLATION PROFILES IN CD8(+) T CELLS DIFFERENTIATE HEALTHY CONTROLS FROM PSORIASIS PATIENTS [397 DIFFERENTIALLY METHYLATED POSITIONS (DMPS); 9 DIFFERENTIALLY METHYLATED REGIONS (DMRS) WHEN >/=CPGS PER DMR WERE CONSIDERED; 2 DMRS FOR >/=10 CPGS]. FURTHERMORE, PATIENTS WITH SKIN PSORIASIS CAN BE DISCRIMINATED FROM PSA PATIENTS [1,861 DMPS, 20 DMRS (>/=5 CPGS PER REGION), 4 DMRS (>/=10 CPGS PER REGION)]. GENE ONTOLOGY (GO) ANALYSES CONSIDERING GENES WITH >/=1 DMP IN THEIR PROMOTER DELIVERED METHYLATION DEFECTS IN SKIN PSORIASIS AND PSA PRIMARILY AFFECTING THE BMP SIGNALING PATHWAY AND ENDOPEPTIDASE REGULATOR ACTIVITY, RESPECTIVELY. GO ANALYSIS OF GENES ASSOCIATED WITH DMRS BETWEEN SKIN PSORIASIS AND PSA DEMONSTRATED AN ENRICHMENT OF GABAERGIC NEURON AND CORTEX NEURON DEVELOPMENT PATHWAYS. TREATMENT WITH CYTOKINE BLOCKERS ASSOCIATED WITH DNA METHYLATION CHANGES [2,372 DMPS; 1,907 DMPS WITHIN PROMOTERS, 7 DMRS (>/=5 CPG PER REGIONS)] AFFECTING TRANSFORMING GROWTH FACTOR BETA RECEPTOR AND TRANSMEMBRANE RECEPTOR PROTEIN SERINE/THREONINE KINASE SIGNALING PATHWAYS. LASTLY, A METHYLATION SCORE INCLUDING TNF AND IL-17 PATHWAY ASSOCIATED DMPS INVERSE CORRELATES WITH SKIN DISEASE ACTIVITY SCORES (PASI). CONCLUSION: PATIENTS WITH SKIN PSORIASIS EXHIBIT DNA METHYLATION PATTERNS IN CD8(+) T CELLS THAT ALLOW DIFFERENTIATION FROM PSA PATIENTS AND HEALTHY INDIVIDUALS, AND REFLECT CLINICAL ACTIVITY OF SKIN DISEASE. THUS, DNA METHYLATION PROFILING PROMISES POTENTIAL AS DIAGNOSTIC AND PROGNOSTIC TOOL TO BE USED FOR MOLECULAR PATIENT STRATIFICATION TOWARD INDIVIDUALIZED TREATMENT.	2021	

8  3501  43 IDENTIFICATION OF POTENTIAL BIOMARKERS FOR SYSTEMIC LUPUS ERYTHEMATOSUS BY INTEGRATED ANALYSIS OF GENE EXPRESSION AND METHYLATION DATA. INTRODUCTION: SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A HETEROGENEOUS AND CHRONIC AUTOIMMUNE DISEASE. ABERRANT DNA METHYLATION OCCURS DURING VARIOUS PROCESSES OF SLE DEVELOPMENT REGULATING THE MRNA EXPRESSION OF INTERRELATED GENES. THIS STUDY AIMS TO SCREEN POTENTIAL DNA METHYLATION MARKERS FOR SLE. METHODS: GENE EXPRESSION AND METHYLATION DATASETS WERE DOWNLOADED FROM THE GENE EXPRESSION OMNIBUS (GEO) DATABASE. DIFFERENTIALLY EXPRESSED GENES (DEGS) BETWEEN SLE PATIENTS AND HEALTHY CONTROLS WERE SCREENED USING THE LIMMA R PACKAGE, AND DIFFERENTIALLY METHYLATED POSITIONS (DMPS) AND REGIONS (DMRS) WERE IDENTIFIED USING DMPFINDER AND BUMPHUNTER (MINFI). ADDITIONALLY, THE DNA METHYLATION MARKERS TO DISTINGUISH SLE PATIENTS FROM HEALTHY CONTROLS WERE EXPLORED THROUGH RECEIVER OPERATING CHARACTERISTIC (ROC) CURVES AND LOGISTIC REGRESSION ANALYSES. FINALLY, WE VALIDATED THE RESULTS OF THE BIOINFORMATIC ANALYSIS BY PYROSEQUENCING. RESULTS: IN TOTAL, 91 DEGS, 90,092 DMPS, 15 DMRS, AND 13 DMR-ASSOCIATED GENES WERE IDENTIFIED. THROUGH THE INTEGRATIVE ANALYSIS OF DEG- AND DMR-ASSOCIATED GENES, WE IDENTIFIED FIVE TYPE I INTERFERON (IFN)-RELATED GENES AS KEY EPIGENETIC-DRIVEN GENES IN SLE. GO ENRICHMENT ANALYSIS SHOWED THAT THE FIVE SLE-ASSOCIATED EPIGENETIC-DRIVEN GENES WERE MAINLY ENRICHED IN THE TYPE I IFN SIGNALING PATHWAY INVOLVED IN IMMUNE RESPONSE AND DEFENSE RESPONSE TO VIRUS. MOREOVER, WE IDENTIFIED TWO SLE-SPECIFIC DNA METHYLATION MARKERS, THREE SLE WITHOUT LUPUS NEPHRITIS (SLE-LN(-))-SPECIFIC DNA METHYLATION MARKERS, AND TWO SLE WITH LUPUS NEPHRITIS (SLE-LN(+))-SPECIFIC DNA METHYLATION MARKERS BY STEPWISE LOGISTIC REGRESSION. CONCLUSIONS: OVERALL, OUR STUDY DEMONSTRATES POTENTIAL DNA METHYLATION MARKERS OF SLE, SLE-LN(-), AND SLE-LN(+), WHICH MAY HELP THE DIAGNOSIS, BOOST THE DEVELOPMENT OF NEW EPIGENETIC THERAPY, AND CONTRIBUTE TO INDIVIDUALIZED TREATMENT. KEY POINTS * THIS STUDY IDENTIFIED FIVE TYPE I IFN-RELATED GENES AS KEY EPIGENETIC-DRIVEN GENES IN SLE, WHICH SUPPORT THE IMPORTANCE OF THE TYPE I IFN PATHWAY IN THE PATHOGENESIS OF SLE * WE IDENTIFIED NOVEL DNA METHYLATION BIOMARKERS IN SLE, SLE-LN-, AND SLE-LN+ BY A COMPREHENSIVE ANALYSIS OF BIOINFORMATICS METHODS AND EXECUTED EXPERIMENTAL VALIDATION, AND BINARY LOGISTIC REGRESSION ANALYSIS SHOWED THAT THEY HAVE EXCELLENT POTENTIAL * THESE RESULTS MAY PROVIDE NEW INSIGHTS INTO THE BIOLOGICAL MECHANISMS OF SLE, AND IDENTIFY RELIABLE BIOMARKERS FOR SLE, SLE-LN-, AND SLE-LN+, WHICH MAY CONTRIBUTE TO DIAGNOSIS AND INDIVIDUALIZED TREATMENT.	2023	
                                                                                                                                                                                 
9  1433  47 DIFFERENTIAL GENOME-WIDE ARRAY-BASED METHYLATION PROFILES IN PROGNOSTIC SUBSETS OF CHRONIC LYMPHOCYTIC LEUKEMIA. GLOBAL HYPOMETHYLATION AND REGIONAL HYPERMETHYLATION ARE WELL-KNOWN EPIGENETIC FEATURES OF CANCER; HOWEVER, IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), STUDIES ON GENOME-WIDE EPIGENETIC MODIFICATIONS ARE LIMITED. HERE, WE ANALYZED THE GLOBAL METHYLATION PROFILES IN CLL, BY APPLYING HIGH-RESOLUTION METHYLATION MICROARRAYS (27,578 CPG SITES) TO 23 CLL SAMPLES, BELONGING TO THE IMMUNOGLOBULIN HEAVY-CHAIN VARIABLE (IGHV) MUTATED (FAVORABLE) AND IGHV UNMUTATED/IGHV3-21 (POOR-PROGNOSTIC) SUBSETS. OVERALL, RESULTS DEMONSTRATED SIGNIFICANT DIFFERENCES IN METHYLATION PATTERNS BETWEEN THESE SUBGROUPS. SPECIFICALLY, IN IGHV UNMUTATED CLL, WE IDENTIFIED METHYLATION OF 7 KNOWN OR CANDIDATE TUMOR SUPPRESSOR GENES (EG, VHL, ABI3, AND IGSF4) AS WELL AS 8 UNMETHYLATED GENES INVOLVED IN CELL PROLIFERATION AND TUMOR PROGRESSION (EG, ADORA3 AND PRF1 ENHANCING THE NUCLEAR FACTOR-KAPPAB AND MITOGEN-ACTIVATED PROTEIN KINASE PATHWAYS, RESPECTIVELY). IN CONTRAST, THESE LATTER GENES WERE SILENCED BY METHYLATION IN IGHV MUTATED PATIENTS. THE ARRAY DATA WERE VALIDATED FOR SELECTED GENES USING METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION, QUANTITATIVE REVERSE TRANSCRIPTASE-POLYMERASE CHAIN REACTION, AND BISULFITE SEQUENCING. FINALLY, THE SIGNIFICANCE OF DNA METHYLATION IN REGULATING GENE PROMOTERS WAS SHOWN BY REINDUCING 4 METHYLATED TUMOR SUPPRESSOR GENES (EG, VHL AND ABI3) IN IGHV UNMUTATED SAMPLES USING THE METHYL-INHIBITOR 5-AZA-2'-DEOXYCYTIDINE. TAKEN TOGETHER, OUR DATA FOR THE FIRST TIME REVEAL DIFFERENCES IN GLOBAL METHYLATION PROFILES BETWEEN PROGNOSTIC SUBSETS OF CLL, WHICH MAY UNFOLD EPIGENETIC SILENCING MECHANISMS INVOLVED IN CLL PATHOGENESIS.	2010	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
10  3132  50 GLOBAL DISTRIBUTION OF DNA HYDROXYMETHYLATION AND DNA METHYLATION IN CHRONIC LYMPHOCYTIC LEUKEMIA. BACKGROUND: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) HAS BEEN A GOOD MODEL SYSTEM TO UNDERSTAND THE FUNCTIONAL ROLE OF 5-METHYLCYTOSINE (5-MC) IN CANCER PROGRESSION. MORE RECENTLY, AN OXIDIZED FORM OF 5-MC, 5-HYDROXYMETHYLCYTOSINE (5-HMC) HAS GAINED LOT OF ATTENTION AS A REGULATORY EPIGENETIC MODIFICATION WITH PROGNOSTIC AND DIAGNOSTIC IMPLICATIONS FOR SEVERAL CANCERS. HOWEVER, THERE IS NO GLOBAL STUDY EXPLORING THE ROLE OF 5-HYDROXYMETHYLCYTOSINE (5-HMC) LEVELS IN CLL. HEREIN, USING MASS SPECTROMETRY AND HMEDIP-SEQUENCING, WE ANALYSED THE DYNAMICS OF 5-HMC DURING B CELL MATURATION AND CLL PATHOGENESIS. RESULTS: WE SHOW THAT NAIVE B-CELLS HAD HIGHER LEVELS OF 5-HMC AND 5-MC COMPARED TO NON-CLASS SWITCHED AND CLASS-SWITCHED MEMORY B-CELLS. WE FOUND A SIGNIFICANT DECREASE IN GLOBAL 5-MC LEVELS IN CLL PATIENTS (N = 15) COMPARED TO NAIVE AND MEMORY B CELLS, WITH NO CHANGES DETECTED BETWEEN THE CLL PROGNOSTIC GROUPS. ON THE OTHER HAND, GLOBAL 5-HMC LEVELS OF CLL PATIENTS WERE SIMILAR TO MEMORY B CELLS AND REDUCED COMPARED TO NAIVE B CELLS. INTERESTINGLY, 5-HMC LEVELS WERE INCREASED AT REGULATORY REGIONS SUCH AS GENE-BODY, CPG ISLAND SHORES AND SHELVES AND 5-HMC DISTRIBUTION OVER THE GENE-BODY POSITIVELY CORRELATED WITH DEGREE OF TRANSCRIPTIONAL ACTIVITY. IMPORTANTLY, CLL SAMPLES SHOWED ABERRANT 5-HMC AND 5-MC PATTERN OVER GENE-BODY COMPARED TO WELL-DEFINED PATTERNS IN NORMAL B-CELLS. INTEGRATED ANALYSIS OF 5-HMC AND RNA-SEQUENCING FROM CLL DATASETS IDENTIFIED THREE NOVEL ONCOGENIC DRIVERS THAT COULD HAVE POTENTIAL ROLES IN CLL DEVELOPMENT AND PROGRESSION. CONCLUSIONS: THUS, OUR STUDY SUGGESTS THAT THE GLOBAL LOSS OF 5-HMC, ACCOMPANIED BY ITS SIGNIFICANT INCREASE AT THE GENE REGULATORY REGIONS, CONSTITUTE A NOVEL HALLMARK OF CLL PATHOGENESIS. OUR COMBINED ANALYSIS OF 5-MC AND 5-HMC SEQUENCING PROVIDED INSIGHTS INTO THE POTENTIAL ROLE OF 5-HMC IN MODULATING GENE EXPRESSION CHANGES DURING CLL PATHOGENESIS.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
11  1577  32 DNA METHYLATION PROFILE IN CHRONIC MYELOMONOCYTIC LEUKEMIA ASSOCIATES WITH DISTINCT CLINICAL, BIOLOGICAL AND GENETIC FEATURES. CHROMOSOMAL ABNORMALITIES ARE DETECTED IN 20-30% OF PATIENTS WITH CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML) AND CORRELATE WITH PROGNOSIS. ON THE MUTATION LEVEL, DISRUPTIVE ALTERATIONS ARE PARTICULARLY FREQUENT IN CHROMATIN REGULATORY GENES. HOWEVER, LITTLE IS KNOWN ABOUT THE CONSEQUENTIAL ALTERATIONS IN THE EPIGENETIC MARKING OF THE GENOME. HERE, WE REPORT THE ANALYSIS OF GENOMIC DNA METHYLATION PATTERNS OF 64 CMML PATIENTS AND 10 HEALTHY CONTROLS, USING A DNA METHYLATION MICROARRAY FOCUSED ON PROMOTER REGIONS. DIFFERENTIAL METHYLATION ANALYSIS BETWEEN PATIENTS AND CONTROLS ALLOWED US TO IDENTIFY ABNORMALITIES IN DNA METHYLATION, INCLUDING HYPERMETHYLATION OF SPECIFIC GENES AND LARGE GENOME REGIONS WITH ABERRANT DNA METHYLATION. UNSUPERVISED HIERARCHICAL CLUSTER ANALYSIS IDENTIFIED TWO MAIN CLUSTERS THAT ASSOCIATED WITH THE CLINICAL, BIOLOGICAL, AND GENETIC FEATURES OF PATIENTS. GROUP 1 WAS ENRICHED IN PATIENTS WITH ADVERSE CLINICAL AND BIOLOGICAL CHARACTERISTICS AND POORER OVERALL AND PROGRESSION-FREE SURVIVAL. IN ADDITION, SIGNIFICANT DIFFERENCES IN DNA METHYLATION WERE OBSERVED BETWEEN PATIENTS WITH LOW RISK AND INTERMEDIATE/HIGH RISK KARYOTYPES AND BETWEEN TET2 MUTANT AND WILD TYPE PATIENTS. TAKEN TOGETHER, OUR RESULTS DEMONSTRATE THAT ALTERED DNA METHYLATION PATTERNS REFLECT THE CMML DISEASE STATE AND ALLOW TO IDENTIFY PATIENT GROUPS WITH DISTINCT CLINICAL FEATURES.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
12  3056  39 GENOME-WIDE DNA METHYLATION ANALYSIS IMPLICATES ENRICHMENT OF INTERFERON PATHWAY IN AFRICAN AMERICAN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS AND EUROPEAN AMERICANS WITH LUPUS NEPHRITIS. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS A CHRONIC, MULTISYSTEM, INFLAMMATORY AUTOIMMUNE DISEASE THAT DISPROPORTIONATELY AFFECTS WOMEN. TRENDS IN SLE PREVALENCE AND CLINICAL COURSE DIFFER BY ANCESTRY, WITH THOSE OF AFRICAN AMERICAN ANCESTRY PRESENTING WITH MORE ACTIVE, SEVERE AND RAPIDLY PROGRESSIVE DISEASE THAN EUROPEAN AMERICANS. PREVIOUS RESEARCH ESTABLISHED ALTERED EPIGENETIC SIGNATURES IN SLE PATIENTS COMPARED TO CONTROLS. HOWEVER, THE CONTRIBUTION OF ABERRANT DNA METHYLATION (DNAM) TO THE RISK OF SLE BY ANCESTRY AND DIFFERENCES AMONG PATIENTS WITH SLE-ASSOCIATED LUPUS NEPHRITIS (LN) HAS NOT BEEN WELL DESCRIBED. WE EVALUATED THE DNA METHYLOMES OF 87 INDIVIDUALS INCLUDING 41 SLE PATIENTS, WITH AND WITHOUT LN, AND 46 CONTROLS ENROLLED IN AN ANCESTRY DIVERSE, WELL-CHARACTERIZED COHORT STUDY OF ESTABLISHED SLE (41 SLE PATIENTS [20 SLE-LN+, 21 SLE-LN-] AND 46 SEX-, RACE- AND AGE-MATCHED CONTROLS; 55% AFRICAN AMERICAN, 45% EUROPEAN AMERICAN). PARTICIPANTS WERE GENOTYPED USING THE INFINIUM GLOBAL DIVERSITY ARRAY (GDA), AND GENETIC ANCESTRY WAS ESTIMATED USING PRINCIPAL COMPONENTS. GENOME-WIDE DNA METHYLATION WAS INITIALLY MEASURED USING THE ILLUMINA METHYLATIONEPIC 850K BEADCHIP ARRAY FOLLOWED BY METHYLATION-SPECIFIC QPCR TO VALIDATE THE METHYLATION STATUS AT PUTATIVE LOCI. DIFFERENTIALLY METHYLATED POSITIONS (DMP) WERE IDENTIFIED USING A CASE-CONTROL APPROACH ADJUSTED FOR ANCESTRY. WE IDENTIFIED A TOTAL OF 51 DMPS IN CPGS AMONG SLE PATIENTS COMPARED TO CONTROLS. GENES PROXIMAL TO THESE CPGS WERE HIGHLY ENRICHED FOR INVOLVEMENT IN TYPE I INTERFERON SIGNALING. DMPS AMONG EUROPEAN AMERICAN SLE PATIENTS WITH LN WERE SIMILAR TO AFRICAN AMERICAN SLE PATIENTS WITH AND WITHOUT LN. OUR FINDINGS WERE VALIDATED USING AN ORTHOGONAL, METHYL-SPECIFIC PCR FOR THREE SLE-ASSOCIATED DMPS NEAR OR PROXIMAL TO MX1, USP18, AND IFITM1. OUR STUDY CONFIRMS PREVIOUS REPORTS THAT DMPS IN CPGS ASSOCIATED WITH SLE ARE ENRICHED IN TYPE I INTERFERON GENES. HOWEVER, WE SHOW THAT EUROPEAN AMERICAN SLE PATIENTS WITH LN HAVE SIMILAR DNAM PATTERNS TO AFRICAN AMERICAN SLE PATIENTS IRRESPECTIVE OF LN, SUGGESTING THAT ABERRANT DNAM ALTERS ACTIVITY OF TYPE I INTERFERON PATHWAY LEADING TO MORE SEVERE DISEASE INDEPENDENT OF ANCESTRY.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                          
13  5979  30 TET2 MUTATIONS ARE ASSOCIATED WITH SPECIFIC 5-METHYLCYTOSINE AND 5-HYDROXYMETHYLCYTOSINE PROFILES IN PATIENTS WITH CHRONIC MYELOMONOCYTIC LEUKEMIA. CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML) HAS RECENTLY BEEN ASSOCIATED WITH A HIGH INCIDENCE OF DIVERSE MUTATIONS IN GENES SUCH AS TET2 OR EZH2 THAT ARE IMPLICATED IN EPIGENETIC MECHANISMS. WE HAVE PERFORMED GENOME-WIDE DNA METHYLATION ARRAYS AND MUTATIONAL ANALYSIS OF TET2, IDH1, IDH2, EZH2 AND JAK2 IN A GROUP OF 24 PATIENTS WITH CMML. 249 GENES WERE DIFFERENTIALLY METHYLATED BETWEEN CMML PATIENTS AND CONTROLS. USING INGENUITY PATHWAY ANALYSIS, WE IDENTIFIED ENRICHMENT IN A GENE NETWORK CENTERED AROUND PLC, JNK AND ERK SUGGESTING THAT THESE PATHWAYS, WHOSE DEREGULATION HAS BEEN RECENTLY DESCRIBED IN CMML, ARE AFFECTED BY EPIGENETIC MECHANISMS. MUTATIONS OF TET2, JAK2 AND EZH2 WERE FOUND IN 15 PATIENTS (65%), 4 PATIENTS (17%) AND 1 PATIENT (4%) RESPECTIVELY WHILE NO MUTATIONS IN THE IDH1 AND IDH2 GENES WERE IDENTIFIED. INTERESTINGLY, PATIENTS WITH WILD TYPE TET2 CLUSTERED SEPARATELY FROM PATIENTS WITH TET2 MUTATIONS, SHOWED A HIGHER DEGREE OF HYPERMETHYLATION AND WERE ASSOCIATED WITH HIGHER RISK KARYOTYPES. OUR RESULTS DEMONSTRATE THE PRESENCE OF ABERRANT DNA METHYLATION IN CMML AND IDENTIFIES TET2 MUTANT CMML AS A BIOLOGICALLY DISTINCT DISEASE SUBTYPE WITH A DIFFERENT EPIGENETIC PROFILE.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
14   812  45 CHANGES IN DNA METHYLATION PROFILES OF MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME PATIENTS REFLECT SYSTEMIC DYSFUNCTIONS. BACKGROUND: MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A LIFELONG DEBILITATING DISEASE WITH A COMPLEX PATHOLOGY NOT YET CLEARLY DEFINED. SUSCEPTIBILITY TO ME/CFS INVOLVES GENETIC PREDISPOSITION AND EXPOSURE TO ENVIRONMENTAL FACTORS, SUGGESTING AN EPIGENETIC ASSOCIATION. EPIGENETIC STUDIES WITH OTHER ME/CFS COHORTS HAVE USED ARRAY-BASED TECHNOLOGY TO IDENTIFY DIFFERENTIALLY METHYLATED INDIVIDUAL SITES. CHANGES IN RNA QUANTITIES AND PROTEIN ABUNDANCE HAVE BEEN DOCUMENTED IN OUR PREVIOUS INVESTIGATIONS WITH THE SAME ME/CFS COHORT USED FOR THIS STUDY. RESULTS: DNA FROM A WELL-CHARACTERISED NEW ZEALAND COHORT OF 10 ME/CFS PATIENTS AND 10 AGE-/SEX-MATCHED HEALTHY CONTROLS WAS ISOLATED FROM PERIPHERAL BLOOD MONONUCLEAR (PBMC) CELLS, AND USED TO GENERATE REDUCED GENOME-SCALE DNA METHYLATION MAPS USING REDUCED REPRESENTATION BISULPHITE SEQUENCING (RRBS). THE SEQUENCING DATA WERE ANALYSED UTILISING THE DMAP ANALYSIS PIPELINE TO IDENTIFY DIFFERENTIALLY METHYLATED FRAGMENTS, AND THE METHYLKIT PIPELINE WAS USED TO QUANTIFY METHYLATION DIFFERENCES AT INDIVIDUAL CPG SITES. DMAP IDENTIFIED 76 DIFFERENTIALLY METHYLATED FRAGMENTS AND METHYLKIT IDENTIFIED 394 DIFFERENTIALLY METHYLATED CYTOSINES THAT INCLUDED BOTH HYPER- AND HYPO-METHYLATION. FOUR CLUSTERS WERE IDENTIFIED WHERE DIFFERENTIALLY METHYLATED DNA FRAGMENTS OVERLAPPED WITH OR WERE WITHIN CLOSE PROXIMITY TO MULTIPLE DIFFERENTIALLY METHYLATED INDIVIDUAL CYTOSINES. THESE CLUSTERS IDENTIFIED REGULATORY REGIONS FOR 17 PROTEIN ENCODING GENES RELATED TO METABOLIC AND IMMUNE ACTIVITY. ANALYSIS OF DIFFERENTIALLY METHYLATED GENE BODIES (EXONS/INTRONS) IDENTIFIED 122 UNIQUE GENES. COMPARISON WITH OTHER STUDIES ON PBMCS FROM ME/CFS PATIENTS AND CONTROLS WITH ARRAY TECHNOLOGY SHOWED 59% OF THE GENES IDENTIFIED IN THIS STUDY WERE ALSO FOUND IN ONE OR MORE OF THESE STUDIES. FUNCTIONAL PATHWAY ENRICHMENT ANALYSIS IDENTIFIED 30 ASSOCIATED PATHWAYS. THESE INCLUDED IMMUNE, METABOLIC AND NEUROLOGICAL-RELATED FUNCTIONS DIFFERENTIALLY REGULATED IN ME/CFS PATIENTS COMPARED TO THE MATCHED HEALTHY CONTROLS. CONCLUSIONS: MAJOR DIFFERENCES WERE IDENTIFIED IN THE DNA METHYLATION PATTERNS OF ME/CFS PATIENTS THAT CLEARLY DISTINGUISHED THEM FROM THE HEALTHY CONTROLS. OVER HALF FOUND IN GENE BODIES WITH RRBS IN THIS STUDY HAD BEEN IDENTIFIED IN OTHER ME/CFS STUDIES USING THE SAME CELLS BUT WITH ARRAY TECHNOLOGY. WITHIN THE ENRICHED FUNCTIONAL IMMUNE, METABOLIC AND NEUROLOGICAL PATHWAYS, A NUMBER OF ENRICHED NEUROTRANSMITTER AND NEUROPEPTIDE REACTOME PATHWAYS HIGHLIGHTED A DISTURBED NEUROLOGICAL PATHOPHYSIOLOGY WITHIN THE PATIENT GROUP.	2020	
                                                                                                      
15  2418  40 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
16  1620  33 DNA METHYLTRANSFERASE-MEDIATED TRANSCRIPTIONAL SILENCING IN MALIGNANT GLIOMA: A COMBINED WHOLE-GENOME MICROARRAY AND PROMOTER ARRAY ANALYSIS. EPIGENETIC INACTIVATION OF TUMOR SUPPRESSOR GENES IS A COMMON FEATURE IN HUMAN CANCER. PROMOTER HYPERMETHYLATION AND HISTONE DEACETYLATION ARE REVERSIBLE EPIGENETIC MECHANISMS ASSOCIATED WITH TRANSCRIPTIONAL REGULATION. DNA METHYLTRANSFERASES (DNMT1 AND DNMT3B) REGULATE AND MAINTAIN PROMOTER METHYLATION AND ARE OVEREXPRESSED IN HUMAN CANCER. WE PERFORMED WHOLE-GENOME MICROARRAY ANALYSIS TO IDENTIFY GENES WITH ALTERED EXPRESSION AFTER RNAI-INDUCED SUPPRESSION OF DNMT IN A GLIOBLASTOMA MULTIFORME (GBM) CELL LINE. WE THEN IDENTIFIED GENES WITH BOTH DECREASED EXPRESSION AND EVIDENCE OF PROMOTER CPG ISLAND HYPERMETHYLATION IN GBM TISSUE SAMPLES USING A COMBINED WHOLE-GENOME MICROARRAY TRANSCRIPTOME ANALYSIS IN CONJUNCTION WITH A PROMOTER ARRAY ANALYSIS AFTER DNA IMMUNOPRECIPITATION WITH ANTI-5-METHYLCYTIDINE. DNMT1 AND 3B KNOCKDOWN RESULTED IN THE RESTORED EXPRESSION OF 308 GENES THAT ALSO CONTAINED PROMOTER REGION HYPERMETHYLATION. OF THESE, 43 WERE ALSO FOUND TO BE DOWNREGULATED IN GBM TISSUE SAMPLES. THREE DOWNREGULATED GENES WITH HYPERMETHYLATED PROMOTERS AND RESTORED EXPRESSION IN RESPONSE TO ACUTE DNMT SUPPRESSION WERE ASSAYED FOR METHYLATION CHANGES USING BISULFITE SEQUENCE ANALYSIS OF THE PROMOTER REGION AFTER CHRONIC DNMT SUPPRESSION. RESTORATION OF GENE EXPRESSION WAS NOT ASSOCIATED WITH CHANGES IN PROMOTER REGION METHYLATION, BUT RATHER WITH CHANGES IN HISTONE METHYLATION AND CHROMATIN CONFORMATION. TWO OF THE IDENTIFIED GENES EXHIBITED GROWTH SUPPRESSIVE ACTIVITY IN IN VITRO ASSAYS. COMBINING TARGETED GENETIC MANIPULATIONS WITH COMPREHENSIVE GENOMIC AND EXPRESSION ANALYSES PROVIDES A POTENTIALLY POWERFUL NEW APPROACH FOR IDENTIFYING EPIGENETICALLY REGULATED GENES IN GBM.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
17  3068  34 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
18  3309  39 HIGHER GENE EXPRESSION VARIABILITY IN THE MORE AGGRESSIVE SUBTYPE OF CHRONIC LYMPHOCYTIC LEUKEMIA. BACKGROUND: CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) PRESENTS TWO SUBTYPES WHICH HAVE DRASTICALLY DIFFERENT CLINICAL OUTCOMES, IGVH MUTATED (M-CLL) AND IGVH UNMUTATED (U-CLL). SO FAR, THESE TWO SUBTYPES ARE NOT ASSOCIATED TO CLEAR DIFFERENCES IN GENE EXPRESSION PROFILES. INTERESTINGLY, RECENT RESULTS HAVE HIGHLIGHTED IMPORTANT ROLES FOR HETEROGENEITY, BOTH AT THE GENETIC AND AT THE EPIGENETIC LEVEL IN CLL PROGRESSION. METHODS: WE ANALYZED GENE EXPRESSION DATA OF TWO LARGE COHORTS OF CLL PATIENTS AND QUANTIFIED EXPRESSION VARIABILITY ACROSS INDIVIDUALS TO INVESTIGATE DIFFERENCES BETWEEN THE TWO SUBTYPES USING DIFFERENT MEASURES AND STATISTICAL TESTS. FUNCTIONAL SIGNIFICANCE WAS EXPLORED BY PATHWAY ENRICHMENT AND NETWORK ANALYSES. FURTHERMORE, WE IMPLEMENTED A RANDOM FOREST APPROACH BASED ON EXPRESSION VARIABILITY TO CLASSIFY PATIENTS INTO DISEASE SUBTYPES. RESULTS: WE FOUND THAT U-CLL, THE MORE AGGRESSIVE TYPE OF THE DISEASE, SHOWS SIGNIFICANTLY INCREASED VARIABILITY OF GENE EXPRESSION ACROSS PATIENTS AND THAT, OVERALL, GENES THAT SHOW HIGHER VARIABILITY IN THE AGGRESSIVE SUBTYPE ARE RELATED TO CELL CYCLE, DEVELOPMENT AND INTER-CELLULAR COMMUNICATION. THESE FUNCTIONS INDICATE A POTENTIAL RELATION BETWEEN GENE EXPRESSION VARIABILITY AND THE FASTER PROGRESSION OF THIS CLL SUBTYPE. FINALLY, A CLASSIFIER BASED ON GENE EXPRESSION VARIABILITY WAS ABLE TO CORRECTLY PREDICT THE DISEASE SUBTYPE OF CLL PATIENTS. CONCLUSIONS: THERE ARE STRONG RELATIONS BETWEEN GENE EXPRESSION VARIABILITY AND DISEASE SUBTYPE LINKING SIGNIFICANTLY INCREASED EXPRESSION VARIABILITY TO PHENOTYPES SUCH AS AGGRESSIVENESS AND RESISTANCE TO THERAPY IN CLL.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
19   408  38 ANALYSIS OF GENE EXPRESSION AND METHYLATION DATASETS IDENTIFIED ADAMTS9, FKBP5, AND PFKBF3 AS BIOMARKERS FOR OSTEOARTHRITIS. BACKGROUND: OSTEOARTHRITIS (OA) IS A KIND OF CHRONIC OSTEOARTHROPATHY AND DEGENERATIVE JOINT DISEASE. EPIGENETIC REGULATION IN THE GENE EXPRESSION DYNAMICS HAS BECOME INCREASINGLY IMPORTANT IN OA. WE PERFORMED A COMBINED ANALYSIS OF TWO TYPES OF MICROARRAY DATASETS (GENE EXPRESSION AND DNA METHYLATION) TO IDENTIFY METHYLATION-BASED KEY BIOMARKERS TO PROVIDE A BETTER UNDERSTANDING OF MOLECULAR BIOLOGICAL MECHANISMS OF OA. METHODS: WE OBTAINED TWO EXPRESSION PROFILING DATASETS (GSE55235, GSE55457) AND ONE DNA METHYLATION PROFILING DATA SET (GSE63695) FROM THE GENE EXPRESSION OMNIBUS. FIRST, DIFFERENTIALLY EXPRESSED GENES (DEGS) BETWEEN PATIENTS WITH OA AND CONTROLS WERE IDENTIFIED USING THE LIMMA PACKAGE IN R(V3.4.4). THEN, FUNCTION ENRICHMENT ANALYSIS OF DEGS WAS PERFORMED USING A DAVID DATABASE. FOR DNA METHYLATION DATASETS, CHAMP METHYLATION ANALYSIS PACKAGE WAS USED TO IDENTIFY DIFFERENTIAL METHYLATION GENES (DMGS). FINALLY, A COMPREHENSIVE ANALYSIS OF DEGS AND DMGS WAS CONDUCTED TO IDENTIFY GENES THAT EXHIBITED DIFFERENTIAL EXPRESSION AND METHYLATION SIMULTANEOUSLY. RESULTS: WE IDENTIFIED 112 DEGS AND 2,896 DMGS IN PATIENTS WITH OA COMPARED WITH CONTROLS. FUNCTIONAL ANALYSIS OF DEGS OBTAINED THAT INFLAMMATORY RESPONSES, IMMUNE RESPONSES, AND POSITIVE REGULATION OF APOPTOSIS, TUMOR NECROSIS FACTOR (TNF) SIGNALING PATHWAY, AND OSTEOCLAST DIFFERENTIATION MAY BE INVOLVED IN THE PATHOGENESIS OF OA. CROSS-ANALYSIS REVEALED 26 GENES THAT EXHIBITED DIFFERENTIAL EXPRESSION AND METHYLATION IN OA. AMONG THEM, ADAMTS9, FKBP5, AND PFKBF3 WERE IDENTIFIED AS VALUABLE METHYLATION-BASED BIOMARKERS FOR OA. CONCLUSION: IN SUMMARY, OUR STUDY IDENTIFIED DIFFERENT MOLECULAR FEATURES BETWEEN PATIENTS WITH OA AND CONTROLS. THIS MAY PROVIDE NEW CLUES FOR CLARIFYING THE PATHOGENETIC MECHANISMS OF OA.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
20  3138  68 GLOBAL DNA METHYLATION PROFILING REVEALS NEW INSIGHTS INTO EPIGENETICALLY DEREGULATED PROTEIN CODING AND LONG NONCODING RNAS IN CLL. BACKGROUND: METHYL-CPG-BINDING DOMAIN PROTEIN ENRICHED GENOME-WIDE SEQUENCING (MBD-SEQ) IS A ROBUST AND POWERFUL METHOD FOR ANALYZING METHYLATED CPG-RICH REGIONS WITH COMPLETE GENOME-WIDE COVERAGE. IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), THE ROLE OF CPG METHYLATED REGIONS ASSOCIATED WITH TRANSCRIBED LONG NONCODING RNAS (LNCRNA) AND REPETITIVE GENOMIC ELEMENTS ARE POORLY UNDERSTOOD. BASED ON MBD-SEQ, WE CHARACTERIZED THE GLOBAL METHYLATION PROFILE OF HIGH CPG-RICH REGIONS IN DIFFERENT CLL PROGNOSTIC SUBGROUPS BASED ON IGHV MUTATIONAL STATUS. RESULTS: OUR STUDY IDENTIFIED 5800 HYPERMETHYLATED AND 12,570 HYPOMETHYLATED CLL-SPECIFIC DIFFERENTIALLY METHYLATED GENES (CLLDMGS) COMPARED TO NORMAL CONTROLS. FROM CLLDMGS, 40 % OF HYPERMETHYLATED AND 60 % OF HYPOMETHYLATED GENES WERE MAPPED TO NONCODING RNAS. IN ADDITION, WE FOUND THAT THE MAJOR REPETITIVE ELEMENTS SUCH AS SHORT INTERSPERSED ELEMENTS (SINE) AND LONG INTERSPERSED ELEMENTS (LINE) HAVE A HIGH PERCENTAGE OF CLLDMRS (DIFFERENTIALLY METHYLATED REGIONS) IN IGHV SUBGROUPS COMPARED TO NORMAL CONTROLS. FINALLY, TWO NOVEL LNCRNAS (HYPERMETHYLATED CRNDE AND HYPOMETHYLATED AC012065.7) WERE VALIDATED IN AN INDEPENDENT CLL SAMPLE COHORT (48 SAMPLES) COMPARED WITH 6 NORMAL SORTED B CELL SAMPLES USING QUANTITATIVE PYROSEQUENCING ANALYSIS. THE METHYLATION LEVELS SHOWED AN INVERSE CORRELATION TO GENE EXPRESSION LEVELS ANALYZED BY REAL-TIME QUANTITATIVE PCR. NOTABLY, SURVIVAL ANALYSIS REVEALED THAT HYPERMETHYLATION OF CRNDE AND HYPOMETHYLATION OF AC012065.7 CORRELATED WITH AN INFERIOR OUTCOME. CONCLUSIONS: THUS, OUR COMPREHENSIVE METHYLATION ANALYSIS BY MBD-SEQ PROVIDED NOVEL HYPER AND HYPOMETHYLATED LONG NONCODING RNAS, REPETITIVE ELEMENTS, ALONG WITH PROTEIN CODING GENES AS POTENTIAL EPIGENETIC-BASED CLL-SIGNATURE GENES INVOLVED IN DISEASE PATHOGENESIS AND PROGNOSIS.	2016