1  112 145 A ROLE FOR GLOBAL DNA METHYLATION LEVEL AND IL2 EXPRESSION IN THE TRANSITION FROM ACUTE TO CHRONIC LOW BACK PAIN. OBJECTIVES: THE TRANSITION FROM ACUTE LOW BACK PAIN (ALBP) TO CHRONIC LBP (CLBP) RESULTS FROM A VARIETY OF FACTORS, INCLUDING EPIGENETIC MODIFICATIONS OF DNA. THE AIM OF THIS STUDY WAS TO (1) COMPARE GLOBAL DNA (GDNA) METHYLATION AND HISTONE ACETYLATION AT LBP ONSET BETWEEN THE ALBP AND CLBP PARTICIPANTS, (2) COMPARE MRNA EXPRESSION OF GENES WITH KNOWN ROLES IN THE TRANSDUCTION, MAINTENANCE, AND/OR MODULATION OF PAIN BETWEEN THE ALBP AND CLBP PARTICIPANTS, (3) COMPARE SOMATOSENSORY FUNCTION AND PAIN RATINGS IN OUR PARTICIPANTS, AND (4) DETERMINE IF THE AFOREMENTIONED MEASUREMENTS WERE ASSOCIATED. METHODS: A TOTAL OF 220 PARTICIPANTS WERE RECRUITED FOR THIS PROSPECTIVE OBSERVATIONAL STUDY FOLLOWING RECENT ONSET OF AN EPISODE OF LBP. WE RETAINED 45 INDIVIDUALS WHOSE GDNA WAS OF SUFFICIENT QUALITY FOR ANALYSIS. THE FINAL SAMPLE INCLUDED 14 PARTICIPANTS WHOSE PAIN RESOLVED WITHIN 6 WEEKS OF ONSET (ALBP),15 PARTICIPANTS THAT REPORTED PAIN FOR 6 MONTHS (CLBP), AND 16 HEALTHY CONTROLS. PARTICIPANTS WERE SUBJECTED TO QUANTITATIVE SENSORY TESTING (QST), BLOOD WAS DRAWN VIA VENIPUNCTURE, GDNA ISOLATED, AND GLOBAL DNA METHYLATION AND HISTONE ACETYLATION, AS WELL AS MRNA EXPRESSION OF 84 CANDIDATE GENES, WERE MEASURED. RESULTS: INDIVIDUALS THAT DEVELOP CLBP DISPLAY MULTIMODAL SOMATOSENSORY HYPERSENSITIVITY RELATIVE TO ALBP PARTICIPANTS. CLBP PARTICIPANTS ALSO HAD SIGNIFICANTLY LOWER GLOBAL DNA METHYLATION, WHICH WAS NEGATIVELY CORRELATED WITH INTERLEUKIN-2 (IL2) MRNA EXPRESSION. DISCUSSION: CLBP IS CHARACTERIZED BY SOMATOSENSORY HYPERSENSITIVITY, LOWER GLOBAL DNA METHYLATION, AND HIGHER IL2 EXPRESSION LEVEL COMPARED TO THOSE WHOSE PAIN WILL RESOLVE QUICKLY (ALBP). THESE RESULTS SUGGEST POTENTIAL DIAGNOSTIC AND THERAPEUTIC RELEVANCE FOR GLOBAL DNA METHYLATION AND IL2 EXPRESSION IN THE PATHOLOGY UNDERLYING THE TRANSITION FROM ACUTE TO CHRONIC LBP.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
2 3488  31 IDENTIFICATION OF DNA METHYLATION ASSOCIATED ENRICHMENT PATHWAYS IN ADULTS WITH NON-SPECIFIC CHRONIC LOW BACK PAIN. CHRONIC LOW BACK PAIN (CLBP) THAT CANNOT BE ATTRIBUTABLE TO A SPECIFIC PATHOANATOMICAL CHANGE IS ASSOCIATED WITH HIGH PERSONAL AND SOCIETAL COSTS. STILL, THE UNDERLYING MECHANISM THAT CAUSES AND SUSTAINS SUCH A PHENOTYPE IS LARGELY UNKNOWN. EMERGING EVIDENCE SUGGESTS THAT EPIGENETIC CHANGES PLAY A ROLE IN CHRONIC PAIN CONDITIONS. USING REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS), WE EVALUATED DNA METHYLATION PROFILES OF ADULTS WITH NON-SPECIFIC CLBP (N = 50) AND PAIN-FREE CONTROLS (N = 48). WE IDENTIFIED 28,325 HYPERMETHYLATED AND 36,936 HYPOMETHYLATED CPG SITES (P < 0.05). AFTER CORRECTING FOR MULTIPLE TESTING, WE IDENTIFIED 159 DMRS (Q < 0.01AND METHYLATION DIFFERENCE > 10%), THE MAJORITY OF WHICH WERE LOCATED IN CPG ISLAND (50%) AND PROMOTER REGIONS (48%) ON THE ASSOCIATED GENES. THE GENES ASSOCIATED WITH THE DIFFERENTIALLY METHYLATED REGIONS WERE HIGHLY ENRICHED IN BIOLOGICAL PROCESSES THAT HAVE PREVIOUSLY BEEN IMPLICATED IN IMMUNE SIGNALING, ENDOCHONDRAL OSSIFICATION, AND G-PROTEIN COUPLED TRANSMISSIONS. OUR FINDINGS SUPPORT INFLAMMATORY ALTERATIONS AND THE ROLE OF BONE MATURATION IN CLBP. THIS STUDY SUGGESTS THAT EPIGENETIC REGULATION HAS AN IMPORTANT ROLE IN THE PATHOPHYSIOLOGY OF NON-SPECIFIC CLBP AND A BASIS FOR FUTURE STUDIES IN BIOMARKER DEVELOPMENT AND TARGETED INTERVENTIONS.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
3 3076  42 GENOME-WIDE EPIGENOMIC ANALYSES IN PATIENTS WITH NOCICEPTIVE AND NEUROPATHIC CHRONIC PAIN SUBTYPES REVEALS ALTERATIONS IN METHYLATION OF GENES INVOLVED IN THE NEURO-MUSCULOSKELETAL SYSTEM. NOCICEPTIVE PAIN INVOLVES THE ACTIVATION OF NOCICEPTORS WITHOUT DAMAGE TO THE NERVOUS SYSTEM, WHEREAS NEUROPATHIC PAIN IS RELATED TO AN ALTERATION IN THE CENTRAL OR PERIPHERAL NERVOUS SYSTEM. CHRONIC PAIN ITSELF AND THE TRANSITION FROM ACUTE TO CHRONIC PAIN MAY BE EPIGENETICALLY CONTROLLED. IN THIS CROSS-SECTIONAL STUDY, A GENOME-WIDE DNA METHYLATION ANALYSIS WAS PERFORMED USING THE BLOOD DNA REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS) TECHNIQUE. THREE PROSPECTIVE COHORTS INCLUDING 20 HEALTHY CONTROLS (CTL), 18 PATIENTS WITH CHRONIC NOCICEPTIVE PAIN (NOCI), AND 19 PATIENTS WITH CHRONIC NEUROPATHIC PAIN (NEURO) WERE COMPARED AT BOTH THE SINGLE CPG AND DIFFERENTIALLY METHYLATED REGION (DMR) LEVELS. GENES WITH DMRS WERE SEEN IN THE NOCI AND NEURO GROUPS BELONGED TO THE NEURO-MUSCULOSKELETAL SYSTEM AND DIFFERED BETWEEN NOCI AND NEURO PATIENTS. OUR RESULTS DEMONSTRATE THAT THE EPIGENETIC DISTURBANCES ACCOMPANYING NOCICEPTIVE PAIN ARE VERY DIFFERENT FROM THOSE ACCOMPANYING NEUROPATHIC PAIN. IN THE FORMER, AMONG OTHERS, THE EPIGENETIC DISTURBANCE OBSERVED WOULD AFFECT THE FUNCTION OF THE OPIOID ANALGESIC SYSTEM, WHEREAS IN THE LATTER IT WOULD AFFECT THAT OF THE GABAERGIC REWARD SYSTEM. THIS STUDY PRESENTS BIOLOGICAL FINDINGS THAT HELP TO CHARACTERIZE NOCI- AND NEURO-AFFECTED PATHWAYS AND OPENS THE POSSIBILITY OF DEVELOPING EPIGENETIC DIAGNOSTIC ASSAYS. PERSPECTIVE: OUR RESULTS HELP TO EXPLAIN THE VARIOUS BIOLOGICAL PATHWAYS MODIFICATIONS UNDERLYING THE DIFFERENT CLINICAL MANIFESTATIONS OF NOCICEPTIVE AND NEUROPATHIC PAINS. FURTHERMORE, THE NEW TARGETS IDENTIFIED IN OUR STUDY MIGHT HELP TO DISCOVER MORE SPECIFIC TREATMENTS FOR NOCICEPTIVE OR NEUROPATHIC PAINS.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
4 1909  37 ENRICHMENT OF GENOMIC PATHWAYS BASED ON DIFFERENTIAL DNA METHYLATION PROFILES ASSOCIATED WITH CHRONIC MUSCULOSKELETAL PAIN IN OLDER ADULTS: AN EXPLORATORY STUDY. OUR STUDY AIMED TO IDENTIFY DIFFERENTIALLY METHYLATED CPGS/REGIONS AND THEIR ENRICHED GENOMIC PATHWAYS ASSOCIATED WITH UNDERLYING CHRONIC MUSCULOSKELETAL PAIN IN OLDER INDIVIDUALS. WE RECRUITED COGNITIVELY HEALTHY OLDER ADULTS WITH (N = 20) AND WITHOUT (N = 9) SELF-REPORTED MUSCULOSKELETAL PAIN AND COLLECTED DNA FROM PERIPHERAL BLOOD THAT WAS ANALYZED USING METHYLATIONEPIC ARRAYS. WE IDENTIFIED 31,739 HYPERMETHYLATED CPG AND 10,811 HYPOMETHYLATED CPG PROBES (PS </= 0.05). ALL CPG PROBES WERE CLUSTERED INTO 5966 REGIONS, AMONG WHICH 600 REGIONS WERE DIFFERENTIALLY METHYLATED AT P </= 0.05 LEVEL, INCLUDING 294 HYPERMETHYLATED REGIONS AND 306 HYPOMETHYLATED REGIONS (DIFFERENTIALLY METHYLATED REGIONS). INGENUITY PATHWAY ENRICHMENT ANALYSIS REVEALED THAT THE PAIN-RELATED DIFFERENTIALLY METHYLATED REGIONS WERE ENRICHED ACROSS MULTIPLE PATHWAYS. THE TOP 10 CANONICAL PATHWAYS WERE LINKED TO CELLULAR SIGNALING PROCESSES RELATED TO IMMUNE RESPONSES (I.E. ANTIGEN PRESENTATION, PROGRAMED CELL DEATH 1 RECEPTOR/PD-1 LIGAND 1, INTERLEUKIN-4, OX40 SIGNALING, T CELL EXHAUSTION, AND APOPTOSIS) AND GAMMA-AMINOBUTYRIC ACID RECEPTOR SIGNALING. FURTHER, WEIGHTED GENE CORRELATION NETWORK ANALYSIS REVEALED A COMETHYLATION NETWORK MODULE IN THE PAIN GROUP THAT WAS NOT PRESERVED IN THE CONTROL GROUP, WHERE THE HUB GENE WAS THE CYCLIC ADENOSINE MONOPHOSPHATE-DEPENDENT TRANSCRIPTION FACTOR ATF-2. OUR PRELIMINARY FINDINGS PROVIDE NEW EPIGENETIC INSIGHTS INTO THE ROLE OF ABERRANT IMMUNE SIGNALING IN MUSCULOSKELETAL PAIN IN OLDER ADULTS WHILE FURTHER SUPPORTING INVOLVEMENT OF DYSFUNCTIONAL GABAERGIC SIGNALING MECHANISMS IN CHRONIC PAIN. OUR FINDINGS NEED TO BE URGENTLY REPLICATED IN LARGER COHORTS AS THEY MAY SERVE AS A BASIS FOR DEVELOPING AND TARGETING FUTURE INTERVENTIONS.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
5 5273  39 PROMOTER METHYLATION AND BDNF AND DAT1 GENE EXPRESSION PROFILES IN PATIENTS WITH DRUG ADDICTION. BACKGROUND: DRUG ADDICTION IS A BRAIN DISORDER THAT HAS NEGATIVE CONSEQUENCES FOR INDIVIDUALS AND SOCIETY. ADDICTIONS ARE CHRONIC RELAPSING DISEASES OF THE BRAIN THAT ARE CAUSED BY DIRECT DRUG-INDUCED EFFECTS AND PERSEVERING NEUROADAPTATIONS AT THE EPIGENETIC, NEUROPEPTIDE AND NEUROTRANSMITTER LEVELS. BECAUSE THE DOPAMINERGIC SYSTEM HAS A SIGNIFICANT ROLE IN DRUG ABUSE, THE PURPOSE OF THIS STUDY WAS TO ANALYZE THE METHYLATION AND EXPRESSION PROFILE OF BRAIN-DERIVED NEUROTROPHIC FACTOR (BDNF) AND DOPAMINE TRANSPORTER (DAT1) GENES IN INDIVIDUALS WITH DRUG ADDICTION. MATERIALS AND METHODS: BDNF AND DAT1 PROMOTER METHYLATION WERE INVESTIGATED WITH A METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (PCR) TECHNIQUE IN BLOOD SAMPLES FROM 75 INDIVIDUALS WITH DRUG ADDICTION AND 65 HEALTHY CONTROLS. THE EXPRESSION LEVELS OF BDNF AND DAT1 WERE ASSESSED IN 12 MRNA SAMPLES FROM THE BLOOD OF PATIENTS AND COMPARED TO THE SAMPLES OF HEALTHY CONTROLS (N = 12) WITH REAL-TIME QUANTITATIVE REVERSE TRANSCRIPTION PCR. RESULTS: NO SIGNIFICANT DIFFERENCES WERE FOUND IN THE METHYLATION OF BDNF AND DAT1 BETWEEN PATIENTS AND CONTROLS, BUT THE RELATIVE LEVELS OF EXPRESSION OF BDNF AND DAT1 MRNA DIFFERED SIGNIFICANTLY IN THE PATIENTS COMPARED TO CONTROLS (P < 0.0001). CONCLUSION: THESE RESULTS SHOWED THAT THE METHYLATION STATUS OF THE BDNF AND DAT1 GENES HAD NO SIGNIFICANT FUNCTION IN THE PROCESSES OF DRUG ADDICTION.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
6  686  38 BRAIN-SPECIFIC GENES CONTRIBUTE TO CHRONIC BUT NOT TO ACUTE BACK PAIN. INTRODUCTION: BACK PAIN IS THE LEADING CAUSE OF DISABILITY WORLDWIDE. ALTHOUGH MOST BACK PAIN CASES ARE ACUTE, 20% OF ACUTE PAIN PATIENTS EXPERIENCE CHRONIC BACK PAIN SYMPTOMS. IT IS UNCLEAR WHETHER ACUTE PAIN AND CHRONIC PAIN HAVE SIMILAR OR DISTINCT UNDERLYING GENETIC MECHANISMS. OBJECTIVES: TO CHARACTERIZE THE MOLECULAR AND CELLULAR PATHWAYS CONTRIBUTING TO ACUTE AND CHRONIC PAIN STATES. METHODS: CROSS-SECTIONAL OBSERVATIONAL GENOME-WIDE ASSOCIATION STUDY. RESULTS: A TOTAL OF 375,158 INDIVIDUALS FROM THE UK BIOBANK COHORT WERE INCLUDED IN THE DISCOVERY OF GENOME-WIDE ASSOCIATION STUDY. OF THOSE, 70,633 (19%) AND 32,209 (9%) INDIVIDUALS MET THE DEFINITION OF CHRONIC AND ACUTE BACK PAIN, RESPECTIVELY. A TOTAL OF 355 SINGLE NUCLEOTIDE POLYMORPHISM GROUPED INTO 13 LOCI REACHED THE GENOME-WIDE SIGNIFICANCE THRESHOLD (5X10(-8)) FOR CHRONIC BACK PAIN, BUT NONE FOR ACUTE. OF THESE, 7 LOCI WERE REPLICATED IN THE NORD-TRONDELAG HEALTH STUDY (HUNT) COHORT (19,760 CHRONIC LOW BACK PAIN CASES AND 28,674 PAIN-FREE CONTROLS). SINGLE NUCLEOTIDE POLYMORPHISM HERITABILITY WAS 4.6% (P=1.4X10(-78)) FOR CHRONIC BACK PAIN AND 0.81% (P=1.4X10-8) FOR ACUTE BACK PAIN. SIMILAR DIFFERENCES IN HERITABILITY ESTIMATES BETWEEN ACUTE AND CHRONIC BACK PAIN WERE FOUND IN THE HUNT COHORT: 3.4% (P=0.0011) AND 0.6% (P=0.851), RESPECTIVELY. PATHWAY ANALYSES, TISSUE-SPECIFIC HERITABILITY ENRICHMENT ANALYSES, AND EPIGENETIC CHARACTERIZATION SUGGEST A SUBSTANTIAL GENETIC CONTRIBUTION TO CHRONIC BUT NOT ACUTE BACK PAIN FROM THE LOCI PREDOMINANTLY EXPRESSED IN THE CENTRAL NERVOUS SYSTEM. CONCLUSION: CHRONIC BACK PAIN IS SUBSTANTIALLY MORE HERITABLE THAN ACUTE BACK PAIN. THIS HERITABILITY IS MOSTLY ATTRIBUTED TO GENES EXPRESSED IN THE BRAIN.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
7 1739  41 EARLY DNA METHYLATION CHANGES IN CHILDREN DEVELOPING BETA CELL AUTOIMMUNITY AT A YOUNG AGE. AIMS/HYPOTHESIS: TYPE 1 DIABETES IS A CHRONIC AUTOIMMUNE DISEASE OF COMPLEX AETIOLOGY, INCLUDING A POTENTIAL ROLE FOR EPIGENETIC REGULATION. PREVIOUS EPIGENOMIC STUDIES FOCUSED MAINLY ON CLINICALLY DIAGNOSED INDIVIDUALS. THE AIM OF THE STUDY WAS TO ASSESS EARLY DNA METHYLATION CHANGES ASSOCIATED WITH TYPE 1 DIABETES ALREADY BEFORE THE DIAGNOSIS OR EVEN BEFORE THE APPEARANCE OF AUTOANTIBODIES. METHODS: REDUCED REPRESENTATION BISULPHITE SEQUENCING (RRBS) WAS APPLIED TO STUDY DNA METHYLATION IN PURIFIED CD4(+) T CELL, CD8(+) T CELL AND CD4(-)CD8(-) CELL FRACTIONS OF 226 PERIPHERAL BLOOD MONONUCLEAR CELL SAMPLES LONGITUDINALLY COLLECTED FROM SEVEN TYPE 1 DIABETES-SPECIFIC AUTOANTIBODY-POSITIVE INDIVIDUALS AND CONTROL INDIVIDUALS MATCHED FOR AGE, SEX, HLA RISK AND PLACE OF BIRTH. WE ALSO EXPLORED CORRELATIONS BETWEEN DNA METHYLATION AND GENE EXPRESSION USING RNA SEQUENCING DATA FROM THE SAME SAMPLES. TECHNICAL VALIDATION OF RRBS RESULTS WAS PERFORMED USING PYROSEQUENCING. RESULTS: WE IDENTIFIED 79, 56 AND 45 DIFFERENTIALLY METHYLATED REGIONS IN CD4(+) T CELLS, CD8(+) T CELLS AND CD4(-)CD8(-) CELL FRACTIONS, RESPECTIVELY, BETWEEN TYPE 1 DIABETES-SPECIFIC AUTOANTIBODY-POSITIVE INDIVIDUALS AND CONTROL PARTICIPANTS. THE ANALYSIS OF PRE-SEROCONVERSION SAMPLES IDENTIFIED DNA METHYLATION SIGNATURES AT THE VERY EARLY STAGE OF DISEASE, INCLUDING DIFFERENTIAL METHYLATION AT THE PROMOTER OF IRF5 IN CD4(+) T CELLS. FURTHER, WE VALIDATED RRBS RESULTS USING PYROSEQUENCING AT THE FOLLOWING CPG SITES: CHR19:18118304 IN THE PROMOTER OF ARRDC2; CHR21:47307815 IN THE INTRON OF PCBP3; AND CHR14:81128398 IN THE INTERGENIC REGION NEAR TRAF3 IN CD4(+) T CELLS. CONCLUSIONS/INTERPRETATION: THESE PRELIMINARY RESULTS PROVIDE NOVEL INSIGHTS INTO CELL TYPE-SPECIFIC DIFFERENTIAL EPIGENETIC REGULATION OF GENES, WHICH MAY CONTRIBUTE TO TYPE 1 DIABETES PATHOGENESIS AT THE VERY EARLY STAGE OF DISEASE DEVELOPMENT. SHOULD THESE FINDINGS BE VALIDATED, THEY MAY SERVE AS A POTENTIAL SIGNATURE USEFUL FOR DISEASE PREDICTION AND MANAGEMENT.	2022	
                                                                                                                                                                                                                                                                                                                                                                                    
8 1607  29 DNA METHYLATION, COLON CANCER AND MEDITERRANEAN DIET: RESULTS FROM THE EPIC-ITALY COHORT. THE BIOLOGICAL MECHANISMS THROUGH WHICH ADHERENCE TO MEDITERRANEAN DIET (MD) PROTECTS AGAINST COLON CANCER (CC) ARE POORLY UNDERSTOOD. EVIDENCE SUGGESTS THAT CHRONIC INFLAMMATION MAY BE IMPLICATED IN THE PATHWAY. BOTH DIET AND CC ARE RELATED TO EPIGENETIC REGULATION. WE PERFORMED A NESTED CASE-CONTROL STUDY ON 161 PAIRS FROM THE ITALIAN COMPONENT OF THE EUROPEAN PROSPECTIVE INVESTIGATION INTO CANCER AND NUTRITION (EPIC) COHORT, IN WHICH WE LOOKED FOR THE METHYLATION SIGNALS IN DNA EXTRACTED FROM LEUCOCYTES ASSOCIATED WITH BOTH CC AND MD IN 995 CPGS LOCATED IN 48 INFLAMMATION GENES. THE DNA METHYLATION SIGNALS DETECTED IN THIS ANALYSIS WERE VALIDATED IN A SUBGROUP OF 47 CASE-CONTROL PAIRS AND FURTHER REPLICATED (WHERE VALIDATED) IN 95 NEW PAIRS BY MEANS OF PYROSEQUENCING. AMONG THE CPG SITES SELECTED A-PRIORI IN INFLAMMATION-RELATED GENES, SEVEN CPG SITES WERE FOUND TO BE ASSOCIATED WITH CC STATUS AND WITH MD, IN LINE WITH ITS PROTECTIVE EFFECT. ONLY TWO CPG SITES (CG17968347-SERPINE1 AND CG20674490-RUNX3) WERE VALIDATED USING BISULPHITE PYROSEQUENCING AND, AFTER REPLICATION, WE FOUND THAT DNA METHYLATION OF CG20674490-RUNX3 MAY BE A POTENTIAL MOLECULAR MEDIATOR EXPLAINING THE PROTECTIVE EFFECT OF MD ON CC ONSET. THE USE OF A 'MEET-IN-THE-MIDDLE' APPROACH TO IDENTIFY THE OVERLAP BETWEEN EXPOSURE AND PREDICTIVE MARKERS OF DISEASE IS INNOVATIVE IN STUDIES ON THE RELATIONSHIP BETWEEN DIET AND CANCER, IN WHICH EXPOSURE ASSESSMENT IS DIFFICULT AND THE MECHANISMS THROUGH WHICH THE NUTRIENTS EXERT THEIR PROTECTIVE EFFECT IS LARGELY UNKNOWN.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
9 2653  39 EPIGENOTYPING IN PERIPHERAL BLOOD CELL DNA AND BREAST CANCER RISK: A PROOF OF PRINCIPLE STUDY. BACKGROUND: EPIGENETIC CHANGES ARE EMERGING AS ONE OF THE MOST IMPORTANT EVENTS IN CARCINOGENESIS. TWO ALTERATIONS IN THE PATTERN OF DNA METHYLATION IN BREAST CANCER (BC) HAVE BEEN PREVIOUSLY REPORTED; ACTIVE ESTROGEN RECEPTOR-ALPHA (ER-ALPHA) IS ASSOCIATED WITH DECREASED METHYLATION OF ER-ALPHA TARGET (ERT) GENES, AND POLYCOMB GROUP TARGET (PCGT) GENES ARE MORE LIKELY THAN OTHER GENES TO HAVE PROMOTER DNA HYPERMETHYLATION IN CANCER. HOWEVER, WHETHER DNA METHYLATION IN NORMAL UNRELATED CELLS IS ASSOCIATED WITH BC RISK AND WHETHER THESE IMPRINTS CAN BE RELATED TO FACTORS WHICH CAN BE MODIFIED BY THE ENVIRONMENT, IS UNCLEAR. METHODOLOGY/PRINCIPAL FINDINGS: USING QUANTITATIVE METHYLATION ANALYSIS IN A CASE-CONTROL STUDY (N = 1,083) WE FOUND THAT DNA METHYLATION OF PERIPHERAL BLOOD CELL DNA PROVIDES GOOD PREDICTION OF BC RISK. WE ALSO REPORT THAT INVASIVE DUCTAL AND INVASIVE LOBULAR BC IS CHARACTERIZED BY TWO DIFFERENT SETS OF GENES, THE LATTER PARTICULAR BY GENES INVOLVED IN THE DIFFERENTIATION OF THE MESENCHYME (PITX2, TITF1, GDNF AND MYOD1). FINALLY WE DEMONSTRATE THAT ONLY ERT GENES PREDICT ER POSITIVE BC; LACK OF PERIPHERAL BLOOD CELL DNA METHYLATION OF ZNF217 PREDICTED BC INDEPENDENT OF AGE AND FAMILY HISTORY (ODDS RATIO 1.49; 95% CONFIDENCE INTERVAL 1.12-1.97; P = 0.006) AND WAS ASSOCIATED WITH ER-ALPHA BIOACTIVITY IN THE CORRESPONDING SERUM. CONCLUSION/SIGNIFICANCE: THIS FIRST LARGE-SCALE EPIGENOTYPING STUDY DEMONSTRATES THAT DNA METHYLATION MAY SERVE AS A LINK BETWEEN THE ENVIRONMENT AND THE GENOME. FACTORS THAT CAN BE MODULATED BY THE ENVIRONMENT (LIKE ESTROGENS) LEAVE AN IMPRINT IN THE DNA OF CELLS THAT ARE UNRELATED TO THE TARGET ORGAN AND INDICATE THE PREDISPOSITION TO DEVELOP A CANCER. FURTHER RESEARCH WILL NEED TO DEMONSTRATE WHETHER DNA METHYLATION PROFILES WILL BE ABLE TO SERVE AS A NEW TOOL TO PREDICT THE RISK OF DEVELOPING CHRONIC DISEASES WITH SUFFICIENT ACCURACY TO GUIDE PREVENTIVE MEASURES.	2008	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
10 2297  30 EPIGENETIC REGULATION OF ACUTE INFLAMMATORY PAIN. ACUTE PAIN IS ASSOCIATED WITH TISSUE DAMAGE, WHICH RESULTS IN THE RELEASE OF INFLAMMATORY MEDIATORS. RECENT STUDIES POINT TO THE INVOLVEMENT OF EPIGENETIC MECHANISMS (DNA METHYLATION) IN THE DEVELOPMENT OF PAIN. WE HAVE FOUND THAT DURING ACUTE INFLAMMATORY PAIN INDUCED BY THE APPLICATION OF 10% MUSTARD OIL ON THE TONGUES OF RATS, LEVELS OF DNMT3A AND 3B WERE ELEVATED MARKEDLY (36 AND 42 % RESPECTIVELY), WHEREAS THE LEVEL OF DNMT1 WAS NOT CHANGED SIGNIFICANTLY. PREVIOUS INJECTION OF XEFOCAM WITH 0,4 MG/KG DOSE DECREASED LEVELS OF DNMT3A AND 3B (25 AND 24% RESPECTIVELY). THE LEVEL OF DNMT1 WAS NOT CHANGED SIGNIFICANTLY COMPARED TO THE CONTROL GROUP. THE FINDINGS SUPPORT THE IDEA THAT INHIBITORS OF DNA-METHYLTRANSFERASES COULD BE USEFUL FOR PAIN MANAGEMENT. OUR DATA SUGGEST THAT NSAIDS (ALONE OR IN COMBINATION WITH DNMT INHIBITORS) MAY BE PROPOSED AS POSSIBLE EPIGENETIC REGULATORY AGENTS, WHICH MAY PLAY A ROLE IN EPIGENETIC MECHANISMS INDIRECTLY THROUGH ALTERING THE ACTIVITY OF INFLAMMATORY MEDIATORS INVOLVED IN PAIN DEVELOPMENT.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
11 1584  34 DNA METHYLATION PROFILES OF SELECTED PRO-INFLAMMATORY CYTOKINES IN ALZHEIMER DISEASE. BY MEANS OF FUNCTIONAL GENOMICS ANALYSIS, WE RECENTLY DESCRIBED THE MRNA EXPRESSION PROFILES OF VARIOUS GENES INVOLVED IN THE NEUROINFLAMMATORY RESPONSE IN THE BRAINS OF SUBJECTS WITH LATE-ONSET ALZHEIMER DISEASE (LOAD). SOME OF THESE GENES, NAMELY INTERLEUKIN (IL)-1BETA AND IL-6, SHOWED DISTINCT EXPRESSION PROFILES WITH PEAK EXPRESSION DURING THE FIRST STAGES OF THE DISEASE AND CONTROL-LIKE LEVELS AT LATER STAGES. IL-1BETA AND IL-6 GENES ARE MODULATED BY DNA METHYLATION IN DIFFERENT CHRONIC AND DEGENERATIVE DISEASES; IT IS ALSO WELL KNOWN THAT LOAD MAY HAVE AN EPIGENETIC BASIS. INDEED, WE AND OTHERS HAVE PREVIOUSLY REPORTED GENE-SPECIFIC DNA METHYLATION ALTERATIONS IN LOAD AND IN RELATED ANIMAL MODELS. BASED ON THESE DATA, WE STUDIED THE DNA METHYLATION PROFILES, AT SINGLE CYTOSINE RESOLUTION, OF IL-1BETA AND IL-6 5'-FLANKING REGION BY BISULPHITE MODIFICATION IN THE CORTEX OF HEALTHY CONTROLS AND LOAD PATIENTS AT 2 DIFFERENT DISEASE STAGES: BRAAK I-II/A AND BRAAK V-VI/C. OUR ANALYSIS PROVIDES EVIDENCE THAT NEUROINFLAMMATION IN LOAD IS ASSOCIATED WITH (AND POSSIBLY MEDIATED BY) EPIGENETIC MODIFICATIONS.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
12 2634  45 EPIGENOME-WIDE DNA METHYLATION PROFILING OF CONDITIONED PAIN MODULATION IN INDIVIDUALS WITH NON-SPECIFIC CHRONIC LOW BACK PAIN. BACKGROUND: THE PATHOANATOMIC CAUSE OF CHRONIC LOW BACK PAIN (CLBP) CANNOT BE IDENTIFIED FOR UP TO 90% OF INDIVIDUALS. HOWEVER, DYSFUNCTIONAL PROCESSING OF ENDOGENOUS NOCICEPTIVE INPUT, MEASURED AS CONDITIONED PAIN MODULATION (CPM), HAS BEEN ASSOCIATED WITH CLBP AND MAY INVOLVE CHANGES IN NEURONAL GENE EXPRESSION. EPIGENETIC-INDUCED CHANGES SUCH AS DNA METHYLATION (DNAM) HAVE BEEN ASSOCIATED WITH CLBP. METHODS: IN THE PRESENT STUDY, THE RELATIONSHIP BETWEEN CPM AND DNAM CHANGES IN A SAMPLE OF COMMUNITY-DWELLING ADULTS WITH NONSPECIFIC CLBP (N = 48) AND PAIN-FREE CONTROLS (PFC; N = 50) WAS EXAMINED USING REDUCED REPRESENTATION BISULFITE SEQUENCING. GENE ONTOLOGY (GO) TERM ENRICHMENT AND KYOTO ENCYCLOPEDIA OF GENES AND GENOMES (KEGG) PATHWAY ANALYSIS WERE APPLIED TO IDENTIFY KEY PATHWAYS INVOLVED IN EFFICIENT VERSUS DEFICIENT CPM. RESULTS: BASED ON CPM EFFICIENCY, WE IDENTIFIED 6006 AND 18,305 DIFFERENTIALLY METHYLATED CPG SITES (DMCS) WITH Q VALUES < 0.01 AMONG INDIVIDUALS WITH CLBP AND PFCS, RESPECTIVELY. MOST OF THE DMCS WERE HYPOMETHYLATED AND ANNOTATED TO GENES OF RELEVANCE TO PAIN, INCLUDING OPRM1, ADRB2, CACNA2D3, GNA12, LPL, NAXD, AND ASPHD1. IN BOTH CLBP AND PFC GROUPS, THE DMCS ANNOTATED GENES ENRICHED MANY GO TERMS RELEVANT TO PAIN PROCESSING, INCLUDING TRANSCRIPTION REGULATION BY RNA POLYMERASE II, NERVOUS SYSTEM DEVELOPMENT, GENERATION OF NEURONS, NEURON DIFFERENTIATION, AND NEUROGENESIS. BOTH GROUPS ALSO ENRICHED THE PATHWAYS INVOLVED IN RAP1-SIGNALING, CANCER, AND DOPAMINERGIC NEUROGENESIS. HOWEVER, MAPK-RAS SIGNALING PATHWAYS WERE ENRICHED IN THE CLBP, NOT THE PFC GROUP. CONCLUSIONS: THIS IS THE FIRST STUDY TO INVESTIGATE THE GENOME-SCALE DNA METHYLATION PROFILES OF CPM PHENOTYPE IN ADULTS WITH CLBP AND PFCS. BASED ON CPM EFFICIENCY, FEWER DMC ENRICHMENT PATHWAYS WERE UNIQUE TO THE CLBP THAN THE PFCS GROUP. OUR RESULTS SUGGEST THAT EPIGENETICALLY INDUCED MODIFICATION OF NEURONAL DEVELOPMENT/DIFFERENTIATION PATHWAYS MAY AFFECT CPM EFFICIENCY, SUGGESTING NOVEL POTENTIAL THERAPEUTIC TARGETS FOR CENTRAL SENSITIZATION. HOWEVER, CPM EFFICIENCY AND THE EXPERIENCE OF NONSPECIFIC CLBP MAY BE INDEPENDENT. FURTHER MECHANISTIC STUDIES ARE REQUIRED TO CONFIRM THE RELATIONSHIP BETWEEN CPM, CENTRAL SENSITIZATION, AND NONSPECIFIC CLBP.	2022	
                                                                                           
13 1434  41 DIFFERENTIAL METHYLATION AND EXPRESSION OF GENES IN THE HYPOXIA-INDUCIBLE FACTOR 1 SIGNALING PATHWAY ARE ASSOCIATED WITH PACLITAXEL-INDUCED PERIPHERAL NEUROPATHY IN BREAST CANCER SURVIVORS AND WITH PRECLINICAL MODELS OF CHEMOTHERAPY-INDUCED NEUROPATHIC PAIN. BACKGROUND: PACLITAXEL IS AN IMPORTANT CHEMOTHERAPEUTIC AGENT FOR THE TREATMENT OF BREAST CANCER. PACLITAXEL-INDUCED PERIPHERAL NEUROPATHY (PIPN) IS A MAJOR DOSE-LIMITING TOXICITY THAT CAN PERSIST INTO SURVIVORSHIP. WHILE NOT ALL SURVIVORS DEVELOP PIPN, FOR THOSE WHO DO, IT HAS A SUBSTANTIAL NEGATIVE IMPACT ON THEIR FUNCTIONAL STATUS AND QUALITY OF LIFE. NO INTERVENTIONS ARE AVAILABLE TO TREAT PIPN. IN OUR PREVIOUS STUDIES, WE IDENTIFIED THAT THE HIF-1 SIGNALING PATHWAY (H1SP) WAS PERTURBED BETWEEN BREAST CANCER SURVIVORS WITH AND WITHOUT PIPN. PRECLINICAL STUDIES SUGGEST THAT THE H1SP IS INVOLVED IN THE DEVELOPMENT OF BORTEZOMIB-INDUCED AND DIABETIC PERIPHERAL NEUROPATHY, AND SCIATIC NERVE INJURY. THE PURPOSE OF THIS STUDY WAS TO IDENTIFY H1SP GENES THAT HAVE BOTH DIFFERENTIAL METHYLATION AND DIFFERENTIAL GENE EXPRESSION BETWEEN BREAST CANCER SURVIVORS WITH AND WITHOUT PIPN. METHODS: A MULTI-STAGED INTEGRATED ANALYSIS WAS PERFORMED. IN PERIPHERAL BLOOD, METHYLATION WAS ASSAYED USING MICROARRAY AND GENE EXPRESSION WAS ASSAYED USING RNA-SEQ. CANDIDATE GENES IN THE H1SP HAVING BOTH DIFFERENTIALLY METHYLATION AND DIFFERENTIAL EXPRESSION WERE IDENTIFIED BETWEEN SURVIVORS WHO RECEIVED PACLITAXEL AND DID (N = 25) AND DID NOT (N = 25) DEVELOP PIPN. THEN, CANDIDATE GENES WERE EVALUATED FOR DIFFERENTIAL METHYLATION AND DIFFERENTIAL EXPRESSION IN PUBLIC DATA SETS OF PRECLINICAL MODELS OF PIPN AND SCIATIC NERVE INJURY. RESULTS: EIGHT CANDIDATE GENES WERE IDENTIFIED AS BOTH DIFFERENTIAL METHYLATION AND DIFFERENTIAL EXPRESSION IN SURVIVORS. OF THE EIGHT HOMOLOGS IDENTIFIED, ONE WAS FOUND TO BE DIFFERENTIAL EXPRESSION IN BOTH PIPN AND "NORMAL" MICE DORSAL ROOT GANGLIA; THREE WERE DIFFERENTIAL METHYLATION IN SCIATIC NERVE INJURY VERSUS SHAM RATS IN BOTH PRE-FRONTAL CORTEX AND T-CELLS; AND TWO WERE DIFFERENTIAL METHYLATION IN SCIATIC NERVE INJURY VERSUS SHAM RATS IN THE PRE-FRONTAL CORTEX. CONCLUSIONS: THIS STUDY IS THE FIRST TO EVALUATE FOR METHYLATION IN CANCER SURVIVORS WITH CHRONIC PIPN. THE FINDINGS PROVIDE EVIDENCE THAT THE EXPRESSION OF H1SP GENES ASSOCIATED WITH CHRONIC PIPN IN CANCER SURVIVORS MAY BE REGULATED BY EPIGENETIC MECHANISMS AND SUGGESTS GENES FOR VALIDATION AS POTENTIAL THERAPEUTIC TARGETS.	2020	

14 1537  31 DNA METHYLATION IN ADOLESCENTS WITH ANXIETY DISORDER: A LONGITUDINAL STUDY. ANXIETY DISORDERS (AD) TYPICALLY MANIFEST IN CHILDREN AND ADOLESCENTS AND MIGHT PERSIST INTO ADULTHOOD. HOWEVER, THERE ARE STILL FEW DATA CONCERNING EPIGENETIC MECHANISMS ASSOCIATED WITH ONSET, PERSISTENCE OR REMISSION OF AD OVER TIME. WE INVESTIGATED A COHORT OF ADOLESCENTS AND YOUNG ADULTS AT BASELINE (AGE; 13.19 +/- 2.38) AND AFTER 5 YEARS AND CLASSIFIED THEM ACCORDING TO THE AD DIAGNOSIS AND THEIR LONGITUDINAL TRAJECTORIES INTO 4 GROUPS: (1) TYPICALLY DEVELOPING COMPARISONS (TDC; CONTROL GROUP, N = 14); (2) INCIDENT (AD IN THE SECOND EVALUATION ONLY, N = 11); (3) PERSISTENT (AD IN BOTH EVALUATIONS, N = 14) AND (4) REMITTENT (AD IN THE FIRST EVALUATION ONLY, N = 8). DNA METHYLATION WAS EVALUATED WITH THE INFINIUM HUMANMETHYLATION450 BEADCHIP FROM SALIVA SAMPLES COLLECTED AT BOTH EVALUATIONS. GENE SET ENRICHMENT ANALYSIS WAS APPLIED TO CONSIDER BIOLOGICAL PATHWAYS. WE FOUND DECREASED DNA METHYLATION IN TDC GROUP WHILE THE CHRONIC CASES OF AD PRESENTED HYPERMETHYLATION IN CENTRAL NERVOUS SYSTEM DEVELOPMENT PATHWAYS. MOREOVER, WE SHOWED THAT THIS PERSISTENT GROUP ALSO PRESENTED HYPERMETHYLATION WHILE THE OTHER THREE GROUPS WERE ASSOCIATED WITH HYPOMETHYLATION IN NERVOUS SYSTEM DEVELOPMENT PATHWAY. INCIDENCE AND REMISSION GROUPS WERE ASSOCIATED WITH INCREASED AND DECREASED METHYLATION IN NEURON DEVELOPMENT PATHWAYS, RESPECTIVELY. LARGER STUDIES ARE LIKELY TO DETECT SPECIFIC GENES RELEVANT TO AD.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
15  277  38 AGE-RELATED EPIGENOME-WIDE DNA METHYLATION AND HYDROXYMETHYLATION IN LONGITUDINAL MOUSE BLOOD. DNA METHYLATION AT CYTOSINE-PHOSPHATE-GUANINE (CPG) DINUCLEOTIDES CHANGES AS A FUNCTION OF AGE IN HUMANS AND ANIMAL MODELS, A PROCESS THAT MAY CONTRIBUTE TO CHRONIC DISEASE DEVELOPMENT. RECENT STUDIES HAVE INVESTIGATED THE ROLE OF AN OXIDIZED FORM OF DNA METHYLATION - 5-HYDROXYMETHYLCYTOSINE (5HMC) - IN THE EPIGENOME, BUT ITS CONTRIBUTION TO AGE-RELATED DNA METHYLATION REMAINS UNCLEAR. WE TESTED THE HYPOTHESIS THAT 5HMC CHANGES WITH AGE, BUT IN A DIRECTION OPPOSITE TO 5-METHYLCYTOSINE (5MC), POTENTIALLY PLAYING A DISTINCT ROLE IN AGING. TO CHARACTERIZE EPIGENETIC AGING, GENOME-WIDE 5MC AND 5HMC WERE MEASURED IN LONGITUDINAL BLOOD SAMPLES (2, 4, AND 10 MONTHS OF AGE) FROM ISOGENIC MICE USING TWO SEQUENCING METHODS - ENHANCED REDUCED REPRESENTATION BISULFITE SEQUENCING AND HYDROXYMETHYLATED DNA IMMUNOPRECIPITATION SEQUENCING. EXAMINING THE EPIGENOME BY AGE, WE IDENTIFIED 28,196 UNIQUE DIFFERENTIALLY METHYLATED CPGS (DMCS) AND 8,613 DIFFERENTIALLY HYDROXYMETHYLATED REGIONS (DHMRS). MOUSE BLOOD SHOWED A GENERAL PATTERN OF EPIGENOME-WIDE HYPERMETHYLATION AND HYPO-HYDROXYMETHYLATION WITH AGE. COMPARING AGE-RELATED DMCS AND DHMRS, 1,854 ANNOTATED GENES SHOWED BOTH DIFFERENTIAL 5MC AND 5HMC, INCLUDING ONE GENE - NFIC - AT FIVE CPGS IN THE SAME 250 BP CHROMOSOMAL REGION. AT THIS REGION, 5MC AND 5HMC LEVELS BOTH DECREASED WITH AGE. REFLECTING THESE AGE-RELATED EPIGENETIC CHANGES, NFIC RNA EXPRESSION IN BLOOD DECREASED WITH AGE, SUGGESTING THAT AGE-RELATED REGULATION OF THIS GENE MAY BE DRIVEN BY 5HMC, NOT CANONICAL DNA METHYLATION. COMBINED, OUR GENOME-WIDE RESULTS SHOW AGE-RELATED DIFFERENTIAL 5MC AND 5HMC, AS WELL AS SOME EVIDENCE THAT CHANGES IN 5HMC MAY DRIVE AGE-RELATED DNA METHYLATION AND GENE EXPRESSION.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
16  658  33 BLOOD DNA METHYLATION PREDICTS DIABETIC KIDNEY DISEASE PROGRESSION IN HIGH FAT DIET-FED MICE. DIABETIC KIDNEY DISEASE (DKD) PROGRESSES AT DIFFERENT RATES AMONG PATIENTS WITH TYPE 2 DIABETES MELLITUS (T2D). EARLY IDENTIFICATION OF PATIENTS WITH A HIGHER RISK OF DKD PROGRESSION IS ESSENTIAL TO IMPROVE PROGNOSIS. EPIGENETIC MODIFICATIONS, PARTICULARLY DNA METHYLATION, HAVE BEEN INDEPENDENTLY IMPLICATED IN T2D AND CHRONIC KIDNEY DISEASE. THE CURRENT STUDY AIMED TO DETERMINE CHANGES IN BLOOD DNA METHYLATION THAT REFLECTS AND PREDICTS DKD PROGRESSION. C57BL/6 MICE WERE FED A HIGH-FAT DIET (HFD) FROM WEANING AND SUBCLASSIFIED INTO TWO GROUPS, HFD-1 AND HFD-2, ACCORDING TO URINARY KIDNEY INJURY MARKER KIM-1/CREATININE RATIOS (LOW VS. HIGH) AND HISTOLOGICAL ABNORMALITIES (MILD-MODERATE VS. ADVANCED). DNA METHYLATION PROFILES WERE DETERMINED BY REDUCED REPRESENTATIVE BISULFIDE SEQUENCING (RRBS). OUR RESULTS CONFIRMED EARLY AND ESTABLISHED DKD AT WEEK 9 AND WEEK 32, RESPECTIVELY. AT WEEK 32, ADVANCED KIDNEY INJURY WAS ASSOCIATED WITH DYSREGULATION OF METHYLATION AND DEMETHYLATION ENZYMES IN THE KIDNEY. BLOOD RRBS REVEALED 579 AND 203 DIFFERENTIALLY METHYLATED SITES (DMS) BETWEEN HFD-1 AND HFD-2 ANIMALS AT WEEK 32 AND WEEK 9, RESPECTIVELY, AMONG WHICH 11 WERE COMMON. THE DMS IN BLOOD AND KIDNEY AT WEEK 32 WERE BOTH RELATED TO ORGAN DEVELOPMENT, NEUROGENESIS, CELL JUNCTION, AND WNT SIGNALLING, WHILE THE DMS IN BLOOD AT WEEK 9 SUGGESTED A SPECIFIC ENRICHMENT OF KIDNEY DEVELOPMENT PROCESSES. IN CONCLUSION, OUR DATA STRONGLY SUPPORT THE IMPLICATION OF EARLY BLOOD DNA METHYLATION MODIFICATIONS AND DKD PROGRESSION IN T2D THAT COULD BE USED TO IMPROVE THE DISEASE'S PROGNOSTICATION.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
17 1436  29 DIFFERENTIAL METHYLATION OF THE TRPA1 PROMOTER IN PAIN SENSITIVITY. CHRONIC PAIN IS A GLOBAL PUBLIC HEALTH PROBLEM, BUT THE UNDERLYING MOLECULAR MECHANISMS ARE NOT FULLY UNDERSTOOD. HERE WE EXAMINE GENOME-WIDE DNA METHYLATION, FIRST IN 50 IDENTICAL TWINS DISCORDANT FOR HEAT PAIN SENSITIVITY AND THEN IN 50 FURTHER UNRELATED INDIVIDUALS. WHOLE-BLOOD DNA METHYLATION WAS CHARACTERIZED AT 5.2 MILLION LOCI BY MEDIP SEQUENCING AND ASSESSED LONGITUDINALLY TO IDENTIFY DIFFERENTIALLY METHYLATED REGIONS ASSOCIATED WITH HIGH OR LOW PAIN SENSITIVITY (PAIN DMRS). NINE META-ANALYSIS PAIN DMRS SHOW ROBUST EVIDENCE FOR ASSOCIATION (FALSE DISCOVERY RATE 5%) WITH THE STRONGEST SIGNAL IN THE PAIN GENE TRPA1 (P=1.2 X 10(-13)). SEVERAL PAIN DMRS SHOW LONGITUDINAL STABILITY CONSISTENT WITH SUSCEPTIBILITY EFFECTS, HAVE SIMILAR METHYLATION LEVELS IN THE BRAIN AND ALTERED EXPRESSION IN THE SKIN. OUR APPROACH IDENTIFIES EPIGENETIC CHANGES IN BOTH NOVEL AND ESTABLISHED CANDIDATE GENES THAT PROVIDE MOLECULAR INSIGHTS INTO PAIN AND MAY GENERALIZE TO OTHER COMPLEX TRAITS.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
18 3045  30 GENOME-WIDE ANALYSIS OF ABERRANT METHYLATION OF ENHANCER DNA IN HUMAN OSTEOARTHRITIS. BACKGROUND: OSTEOARTHRITIS IS A CHRONIC MUSCULOSKELETAL DISEASE CHARACTERIZED BY AGE-RELATED GRADUAL THINNING AND A HIGH RISK IN FEMALES. RECENT STUDIES HAVE SHOWN THAT DNA METHYLATION PLAYS IMPORTANT ROLES IN OSTEOARTHRITIS. HOWEVER, THE GENOME-WIDE PATTERN OF METHYLATION IN ENHANCERS IN OSTEOARTHRITIS REMAINS UNCLEAR. METHODS: TO EXPLORE THE FUNCTION OF ENHANCERS IN OSTEOARTHRITIS, WE QUANTIFIED CPG METHYLATION IN HUMAN ENHANCERS BASED ON A PUBLIC DATASET THAT INCLUDED METHYLATION PROFILES OF 470,870 CPG PROBES IN 108 SAMPLES FROM PATIENTS WITH HIP AND KNEE OSTEOARTHRITIS AND HIP TISSUES FROM HEALTHY INDIVIDUALS. COMBINING VARIOUS BIOINFORMATICS ANALYSIS TOOLS, WE SYSTEMATICALLY ANALYZED ABERRANT DNA METHYLATION OF THE ENHANCERS THROUGHOUT THE GENOME IN KNEE OSTEOARTHRITIS AND HIP OSTEOARTHRITIS. RESULTS: WE IDENTIFIED 16,816 DIFFERENTIALLY METHYLATED CPGS, AND NEARLY HALF (8111) OF THEM WERE FROM ENHANCERS, SUGGESTING MAJOR DNA METHYLATION CHANGES IN BOTH TYPES OF OSTEOARTHRITIS IN THE ENHANCER REGIONS. A DETAILED ANALYSIS OF HIP OSTEOARTHRITIS IDENTIFIED 2426 DIFFERENTIALLY METHYLATED CPGS IN ENHANCERS BETWEEN MALE AND FEMALE PATIENTS, AND 84.5% OF THEM WERE HYPOMETHYLATED IN FEMALE PATIENTS AND ENRICHED IN PHENOTYPES RELATED TO HIP OSTEOARTHRITIS IN FEMALES. NEXT, WE EXPLORED THE ENHANCER METHYLATION DYNAMICS AMONG PATIENTS WITH KNEE OSTEOARTHRITIS AND IDENTIFIED 280 DIFFERENTIALLY METHYLATED ENHANCER CPGS THAT WERE ENRICHED IN THE HUMAN PHENOTYPES AND DISEASE ONTOLOGIES RELATED TO OSTEOARTHRITIS. FINALLY, A COMPARISON OF ENHANCER METHYLATION BETWEEN KNEE OSTEOARTHRITIS AND HIP OSTEOARTHRITIS REVEALED ORGAN SOURCE-DEPENDENT DIFFERENCES IN ENHANCER METHYLATION. CONCLUSION: OUR FINDINGS INDICATE THAT ABERRANT METHYLATION OF ENHANCERS IS RELATED TO OSTEOARTHRITIS PHENOTYPES, AND A COMPREHENSIVE ATLAS OF ENHANCER METHYLATION IS USEFUL FOR FURTHER ANALYSIS OF THE EPIGENETIC REGULATION OF OSTEOARTHRITIS AND THE DEVELOPMENT OF CLINICAL DRUGS FOR TREATMENT OF OSTEOARTHRITIS.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                
19 5269  38 PROMOTER DNA METHYLATION CONTRIBUTES TO HUMAN BETA-DEFENSIN-1 DEFICIENCY IN ATOPIC DERMATITIS. ATOPIC DERMATITIS (AD) IS A CHRONIC INFLAMMATORY SKIN DISEASE CAUSED BY EPIDERMAL BARRIER DYSFUNCTION AND DYSREGULATION OF INNATE AND ADAPTIVE IMMUNITY. EPIGENETIC REGULATION OF HUMAN BETA-DEFENSIN-1 (HBD-1) MIGHT BE ASSOCIATED WITH A VARIETY OF DEFECTS IN THE INNATE IMMUNE SYSTEM DURING AD PATHOGENESIS. WE INVESTIGATED THE POSSIBLE MECHANISM OF DECREASED HBD-1 GENE EXPRESSION IN AD AND DEMONSTRATED THE RESTORATION OF HBD-1 TRANSCRIPTION IN UNDIFFERENTIATED NORMAL HUMAN EPIDERMAL KERATINOCYTE CELLS AFTER TREATMENT WITH A DNA METHYLTRANSFERASE INHIBITOR. WE ALSO CONDUCTED AN IN VITRO METHYLATED REPORTER ASSAY USING A REPORTER CONTAINING 14 CPG SITES. METHYLATION OF THE 14 CPG SITES WITHIN THE HBD-1 5' REGION RESULTED IN AN APPROXIMATELY 86% REDUCTION IN PROMOTER ACTIVITY AND AFFECTED HBD-1 TRANSCRIPTIONAL REGULATION. WE THEN COMPARED METHYLATION FREQUENCIES AT CPG 3 AND CPG 4 BETWEEN NON-LESIONAL AND LESIONAL EPIDERMIS SAMPLES OF PATIENTS WITH SEVERE AD AND BETWEEN THESE PAIRED TISSUES AND HEALTHY CONTROL EPIDERMIS FROM NORMAL VOLUNTEERS WITHOUT AD HISTORY. BISULFITE PYROSEQUENCING DATA SHOWED SIGNIFICANTLY HIGHER METHYLATION FREQUENCIES AT THE CPG 3 AND 4 SITES IN AD LESIONAL SAMPLES THAN IN NON-LESIONAL AD SKIN AND NORMAL SKIN SAMPLES (P < 0.05). THESE RESULTS SUGGEST THAT THE DNA METHYLATION SIGNATURE OF HBD-1 IS A NOVEL DIAGNOSTIC/PROGNOSTIC MARKER AND A PROMISING THERAPEUTIC TARGET FOR THE COMPROMISED STRATUM CORNEUM BARRIER ATTRIBUTED TO HBD-1 DEFICIENCY.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
20 2418  48 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