1  5236 177 PROFILING NON-CODING RNA LEVELS WITH CLINICAL CLASSIFIERS IN PEDIATRIC CROHN'S DISEASE. BACKGROUND: CROHN'S DISEASE (CD) IS A HERITABLE CHRONIC INFLAMMATORY DISORDER. NON-CODING RNAS (NCRNAS) PLAY AN IMPORTANT ROLE IN EPIGENETIC REGULATION BY AFFECTING GENE EXPRESSION, BUT CAN ALSO DIRECTLY AFFECT PROTEIN FUNCTION, THUS HAVING A SUBSTANTIAL IMPACT ON BIOLOGICAL PROCESSES. WE INVESTIGATED WHETHER NON-CODING RNAS (NCRNA) AT DIAGNOSIS ARE DYSREGULATED DURING CD AT DIFFERENT CD LOCATIONS AND FUTURE DISEASE BEHAVIORS TO DETERMINE IF NCRNA SIGNATURES CAN SERVE AS AN INDEX TO OUTCOMES. METHODS: USING SUBJECTS BELONGING TO THE RISK COHORT, WE ANALYZED NCRNA FROM THE ILEAL BIOPSIES OF 345 CD AND 71 NON-IBD CONTROLS, AND NCRNA FROM RECTAL BIOPSIES OF 329 CD AND 61 NON-IBD CONTROLS. SEQUENCE ALIGNMENT WAS DONE (STAR PACKAGE) USING HUMAN GENOME VERSION 38 (HG38) AS REFERENCE PANEL. THE DIFFERENTIAL EXPRESSION (DE) ANALYSIS WAS PERFORMED WITH EDGER PACKAGE AND DE NCRNAS WERE IDENTIFIED WITH A THRESHOLD OF FOLD CHANGE (FC) > 2 AND FDR < 0.05 AFTER MULTIPLE TEST CORRECTIONS. RESULTS: IN TOTAL, WE IDENTIFIED 130 CD SPECIFIC DE NCRNAS (89 IN ILEUM AND 41 IN RECTUM) WHEN COMPARED TO NON-IBD CONTROLS. SIMILARLY, 35 DE NCRNAS WERE IDENTIFIED BETWEEN B1 AND B2 IN ILEUM, WHEREAS NO DIFFERENCES AMONG CD DISEASE BEHAVIORS WERE NOTICED IN RECTUM. WE ALSO FOUND INFLAMMATION SPECIFIC NCRNAS BETWEEN INFLAMED AND NON-INFLAMED GROUPS IN ILEAL BIOPSIES. OVERALL, WE OBSERVED THAT EXPRESSION OF MIR1244-2, MIR1244-3, MIR1244-4, AND RN7SL2 WERE INCREASED DURING CD, REGARDLESS OF DISEASE BEHAVIOR, LOCATION, OR INFLAMMATORY STATUS. LASTLY, WE TESTED NCRNA EXPRESSION AT BASELINE AS POTENTIAL TOOL TO PREDICT THE DISEASE STATUS, DISEASE BEHAVIORS AND DISEASE INFLAMMATION AT 3-YEAR FOLLOW UP. CONCLUSIONS: WE HAVE IDENTIFIED NCRNAS THAT ARE SPECIFIC TO DISEASE LOCATION, DISEASE BEHAVIOR, AND DISEASE INFLAMMATION IN CD. BOTH ILEAL AND RECTAL SPECIFIC NCRNA ARE CHANGING OVER THE COURSE OF CD, SPECIFICALLY DURING THE DISEASE PROGRESSION IN THE INTESTINAL MUCOSA. COLLECTIVELY, OUR FINDINGS SHOW CHANGES IN NCRNA DURING CD AND MAY HAVE A CLINICAL UTILITY IN EARLY IDENTIFICATION AND CHARACTERIZATION OF DISEASE PROGRESSION.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
2  4594  40 NATURAL HISTORY AND LONG-TERM CLINICAL COURSE OF CROHN'S DISEASE. CROHN'S DISEASE IS A CHRONIC INFLAMMATORY DISEASE PROCESS INVOLVING DIFFERENT SITES IN THE GASTROINTESTINAL TRACT. OCCASIONALLY, SO-CALLED METASTATIC DISEASE OCCURS IN EXTRA-INTESTINAL SITES. GRANULOMATOUS INFLAMMATION MAY BE DETECTED IN ENDOSCOPIC BIOPSIES OR RESECTED TISSUES. GENETIC, EPIGENETIC AND ENVIRONMENTAL FACTORS APPEAR TO PLAY A ROLE. MULTIPLE SUSCEPTIBILITY GENES HAVE BEEN DESCRIBED IN BOTH FAMILIAL AND NON-FAMILIAL FORMS WHILE THE DISEASE IS PHENOTYPICALLY HETEROGENEOUS WITH A FEMALE PREDOMINANCE. THE DISORDER OCCURS OVER A BROAD AGE SPECTRUM, FROM EARLY CHILDHOOD TO LATE ADULTHOOD. MORE THAN 80% ARE DIAGNOSED BEFORE AGE 40 YEARS USUALLY WITH TERMINAL ILEAL AND COLONIC INVOLVEMENT. PEDIATRIC-ONSET DISEASE IS MORE SEVERE AND MORE EXTENSIVE, USUALLY WITH A HIGHER CHANCE OF UPPER GASTROINTESTINAL TRACT DISEASE, COMPARED TO ADULT-ONSET DISEASE. LONG-TERM STUDIES HAVE SHOWN THAT THE DISORDER MAY EVOLVE WITH TIME INTO MORE COMPLEX DISEASE WITH STRICTURE FORMATION AND PENETRATING DISEASE COMPLICATIONS (I.E., FISTULA, ABSCESS). ALTHOUGH PROLONGED REMISSION MAY OCCUR, DISCRETE PERIODS OF SYMPTOMATIC DISEASE MAY RE-APPEAR OVER MANY DECADES SUGGESTING RECURRENCE OR RE-ACTIVATION OF THIS INFLAMMATORY PROCESS. EVENTUAL DEVELOPMENT OF A CURE WILL LIKELY DEPEND ON IDENTIFICATION OF AN ETIOLOGIC CAUSE AND A FUNDAMENTAL UNDERSTANDING OF ITS PATHOGENESIS. UNTIL NOW, TREATMENT HAS FOCUSED ON REMOVING RISK FACTORS, PARTICULARLY CIGARETTE SMOKING, AND IMPROVING SYMPTOMS. IN CLINICAL TRIALS, CLINICAL REMISSION IS LARGELY DEFINED AS IMPROVED NUMERICAL AND ENDOSCOPIC INDICES FOR "MUCOSAL HEALING". "DEEP REMISSION" IS A CONCEPTUAL, MORE "EXTENDED" GOAL THAT MAY OR MAY NOT ALTER THE LONG-TERM NATURAL HISTORY OF THE DISEASE IN SELECTED PATIENTS, ALBEIT AT A SIGNIFICANT RISK FOR TREATMENT COMPLICATIONS, INCLUDING SERIOUS AND UNUSUAL OPPORTUNISTIC INFECTIONS.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
3    51  46 A DISTINCT EPIGENETIC PROFILE DISTINGUISHES STENOTIC FROM NON-INFLAMED FIBROBLASTS IN THE ILEAL MUCOSA OF CROHN'S DISEASE PATIENTS. BACKGROUND: THE CHRONIC REMITTING AND RELAPSING INTESTINAL INFLAMMATION CHARACTERISTIC OF CROHN'S DISEASE FREQUENTLY LEADS TO FIBROSIS AND SUBSEQUENT STENOSIS OF THE INFLAMED REGION. APPROXIMATELY A THIRD OF ALL CROHN'S DISEASE PATIENTS REQUIRE RESECTION AT SOME STAGE IN THEIR DISEASE COURSE. AS THE PATHOGENESIS OF CROHN'S DISEASE ASSOCIATED FIBROSIS IS LARGELY UNKNOWN, A STRONG NECESSITY EXISTS TO BETTER UNDERSTAND THE PATHOPHYSIOLOGY THEREOF. METHODS: IN THIS STUDY, WE INVESTIGATED CHANGES OF THE DNA METHYLOME AND TRANSCRIPTOME OF ILEUM-DERIVED FIBROBLASTS ASSOCIATED TO THE OCCURRENCE OF CROHN'S DISEASE ASSOCIATED FIBROSIS. EIGHTEEN SAMPLES WERE INCLUDED IN A DNA METHYLATION ARRAY AND TWENTY-ONE SAMPLES WERE USED FOR RNA SEQUENCING. RESULTS: MOST DIFFERENTIALLY METHYLATED REGIONS AND DIFFERENTIALLY EXPRESSED GENES WERE OBSERVED WHEN COMPARING STENOTIC WITH NON-INFLAMED SAMPLES. BY CONTRAST, FEW DIFFERENCES WERE OBSERVED WHEN COMPARING CROHN'S DISEASE WITH NON-CROHN'S DISEASE, OR INFLAMED WITH NON-INFLAMED TISSUE. INTEGRATIVE METHYLATION AND GENE EXPRESSION ANALYSES REVEALED DYSREGULATION OF GENES ASSOCIATED TO THE PRKACA AND E2F1 NETWORK, WHICH IS INVOLVED IN CELL CYCLE PROGRESSION, ANGIOGENESIS, EPITHELIAL TO MESENCHYMAL TRANSITION, AND BILE METABOLISM. CONCLUSION: OUR RESEARCH PROVIDES EVIDENCE THAT THE METHYLOME AND THE TRANSCRIPTOME ARE SYSTEMATICALLY DYSREGULATED IN STENOSIS-ASSOCIATED FIBROBLASTS.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
4  3413  44 HSA-MIR-29C AND HSA-MIR-135B DIFFERENTIAL EXPRESSION AS POTENTIAL BIOMARKER OF GASTRIC CARCINOGENESIS. AIM: TO INVESTIGATE THE EXPRESSION PROFILES OF HSA-MIR-29C AND HSA-MIR-135B IN GASTRIC MUCOSAL SAMPLES AND THEIR VALUES AS GASTRIC CARCINOGENESIS BIOMARKERS. METHODS: THE EXPRESSION LEVELS OF HSA-MIR-29C AND HSA-MIR-135B IN NORMAL GASTRIC MUCOSA, NON-ATROPHIC CHRONIC GASTRITIS, INTESTINAL METAPLASIA AND INTESTINAL-TYPE GASTRIC ADENOCARCINOMA WERE ANALYSED USING QUANTITATIVE REAL-TIME PCR. THE DIFFERENCE BETWEEN HSA-MIR-29C AND HSA-MIR-135B EXPRESSION PROFILES IN THE GROUPED SAMPLES WAS EVALUATED BY ANOVA AND STUDENT'S T-TEST TESTS. THE RESULTS WERE ADJUSTED FOR MULTIPLE TESTING BY USING BONFERRONI'S CORRECTION. P VALUES </= 0.05 WERE CONSIDERED STATISTICALLY SIGNIFICANT. TO EVALUATE HSA-MIR-29C AND HSA-MIR-135B EXPRESSIONS AS POTENTIAL BIOMARKERS OF GASTRIC CARCINOGENESIS, WE PERFORMED A RECEIVER OPERATING CHARACTERISTIC CURVE ANALYSIS AND THE DERIVED AREA UNDER THE CURVE, AND A CATEGORICAL PRINCIPAL COMPONENTS ANALYSIS. IN SILICO IDENTIFICATION OF THE GENETIC TARGETS OF HSA-MIR-29C AND HSA-MIR-135B WAS PERFORMED USING DIFFERENT PREDICTION TOOLS, IN ORDER TO IDENTIFY POSSIBLE GENES INVOLVED IN GASTRIC CARCINOGENESIS. RESULTS: THE EXPRESSION LEVELS OF HSA-MIR-29C WERE HIGHER IN NORMAL GASTRIC MUCOSAL SAMPLES, AND DECREASED PROGRESSIVELY IN NON-ATROPHIC CHRONIC GASTRITIS SAMPLES, INTESTINAL METAPLASIA SAMPLES AND INTESTINAL-TYPE GASTRIC ADENOCARCINOMA SAMPLES. THE EXPRESSION OF HSA-MIR-29C IN THE GASTRIC LESIONS SHOWED THAT NON-ATROPHIC GASTRITIS HAVE AN INTERMEDIATE PROFILE TO GASTRIC NORMAL MUCOSA AND INTESTINAL-TYPE GASTRIC ADENOCARCINOMA, AND THAT INTESTINAL METAPLASIA SAMPLES PRESENTED AN EXPRESSION PATTERN SIMILAR TO THAT IN INTESTINAL-TYPE GASTRIC ADENOCARCINOMA. THIS MICRORNA (MIRNA) HAS A GOOD DISCRIMINATORY ACCURACY BETWEEN NORMAL GASTRIC SAMPLES AND (1) INTESTINAL-TYPE GASTRIC ADENOCARCINOMA; AND (2) INTESTINAL METAPLASIA, AND REGULATES THE DMNT3A ONCOGENE. HSA-MIR-135B IS UP-REGULATED IN NON-ATROPHIC CHRONIC GASTRITIS AND INTESTINAL METAPLASIA SAMPLES AND DOWN-REGULATED IN NORMAL GASTRIC MUCOSA AND INTESTINAL-TYPE GASTRIC ADENOCARCINOMA SAMPLES. NON-ATROPHIC CHRONIC GASTRITIS AND INTESTINAL METAPLASIA ARE SIGNIFICANTLY DIFFERENT FROM NORMAL GASTRIC MUCOSA SAMPLES. HSA-MIR-135B EXPRESSION PRESENTED A GREATER DISCRIMINATORY ACCURACY BETWEEN NORMAL SAMPLES AND GASTRIC LESIONS. THIS MIRNA WAS ASSOCIATED WITH HELICOBACTER PYLORI PRESENCE IN NON-ATROPHIC CHRONIC GASTRITIS SAMPLES AND REGULATES THE APC AND KLF4 TUMOUR SUPPRESSOR GENES. CONCLUSION: OUR RESULTS PROVIDE EVIDENCE OF EPIGENETIC ALTERATIONS IN NON-ATROPHIC CHRONIC GASTRITIS AND INTESTINAL METAPLASIA AND SUGGEST THAT HSA-MIR-29C AND HSA-MIR-135B ARE PROMISING BIOMARKERS OF GASTRIC CARCINOGENESIS.	2016	
                                                                                                                                                                                                                                                                                                                     
5  1194  49 CORRELATION OF EPIGENETIC CHANGE AND IDENTIFICATION OF RISK FACTORS FOR ORAL SUBMUCOUS FIBROSIS. BACKGROUND: DNA METHYLATION OF CERTAIN GENES IS AN EPIGENETIC CHANGE THAT IS ESSENTIAL FOR TUMORIGENESIS. ORAL SUBMUCOUS FIBROSIS (OSF) IS A PRECANCEROUS CONDITION OF ORAL MUCOSA WITH INFLAMMATION AND PROGRESSIVE FIBROSIS OF THE LAMINA PROPRIA AND DEEPER CONNECTIVE TISSUE. THE HYPERMETHYLATION OF E-CADHERIN AND CYCLOOXYGENASE 2 (COX-2) IN CHRONIC INFLAMMATION MAY DEMONSTRATE A MILD LESION/MUTATION AT EPIGENETIC LEVELS. THIS STUDY COMPARES THE HYPERMETHYLATION STATUS OF E-CADHERIN AND COX-2 GENES IN PATIENTS WITH ORAL CANCER AND PATIENTS WITH OSF AND ALSO AIMS TO IDENTIFY RISK FACTORS FOR THE DEVELOPMENT OF OSF. METHODS: DNA WAS EXTRACTED FROM BLOOD SAMPLES OF 50 HEALTHY SUBJECTS, 50 PATIENTS WITH OSF AND 60 PATIENTS WITH ORAL CANCER. METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION FOR E-CADHERIN AND COX-2 WAS PERFORMED ON THESE SAMPLES AND THE PRODUCTS WERE ANALYZED ON 2% AGAROSE GEL. SURVEYS ABOUT ORAL HEALTH HABITS AND CLINICAL PERIODONTAL EXAMINATIONS IN PATIENTS WITH OSF AND HEALTHY SUBJECTS WERE ALSO CONDUCTED BY WELL-TRAINED DENTISTS, AND LOGISTIC REGRESSION WAS PERFORMED TO IDENTIFY RISK FACTORS FOR OSF. RESULTS: HYPERMETHYLATION OF E-CADHERIN AND COX-2 WAS OBSERVED IN 36% AND 22% OF ORAL CANCER SAMPLES, RESPECTIVELY. IN PATIENTS WITH OSF, THE RATES WERE 52% AND 30%, AND IN HEALTHY CONTROLS THE RATES WERE 4% AND 6%. HYPERMETHYLATION WAS SHOWN TO BE CORRELATED BETWEEN THE 3 GROUPS WITH STATISTICAL SIGNIFICANCE (P<0.01). METHYLATION OF CPG ISLANDS IN E-CADHERIN AND COX-2 OCCURRED MORE FREQUENTLY IN PATIENTS WITH OSF THAN IN THE CONTROL GROUP, BUT LESS FREQUENTLY THAN IN PATIENTS WITH ORAL CANCER. IN THE LOGISTIC REGRESSION ANALYSIS, SMOKING, BRUSHING MORE THAN TWICE DAILY, PERIODONTAL PROBING DEPTH AND PLAQUE INDEX WERE IDENTIFIED AS 4 MAJOR RISK FACTORS FOR OSF. CONCLUSIONS: THESE DATA CONFIRM THAT E-CADHERIN AND COX-2 EXPRESSIONS ARE RELATED TO OSF. THE EPIGENETIC CHANGES PRESENTED IN PATIENTS WITH CHRONIC INFLAMMATION MIGHT DEMONSTRATE AN IRREVERSIBLE DESTRUCTION IN THE TISSUES OR ORGANS SIMILAR TO THE EFFECTS OF CANCER. CHRONIC OSF WAS SIGNIFICANTLY ASSOCIATED WITH HYPERMETHYLATION, A CANCER RISK FACTOR.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
6  4724  34 NONINVASIVE MULTIMODAL METHODS TO DIFFERENTIATE INFLAMED VS FIBROTIC STRICTURES IN PATIENTS WITH CROHN'S DISEASE. FIBROTIC STRICTURES OCCUR IN 30% OF PATIENTS WITH CROHN'S DISEASE (CD). HOWEVER, THERE ARE NO THERAPEUTIC AGENTS THAT PREVENT OR REVERSE FIBROTIC STRICTURES. STRICTURES ARE TREATED BY ENDOSCOPIC DILATATION PROCEDURES AND SURGICAL PROCEDURES, BUT THERE ARE HIGH RATES OF RECURRENCE. TWO ANTIFIBROTIC AGENTS (NINTEDANIB AND PIRFENIDONE) RECENTLY WERE APPROVED FOR THE TREATMENT OF IDIOPATHIC PULMONARY FIBROSIS AND INHIBITORS OF RHO-ASSOCIATED PROTEIN KINASES 1 AND 2 REVERSED FIBROSIS IN MICE WITH CHRONIC INTESTINAL INFLAMMATION. CROSS-SECTIONAL IMAGING TECHNIQUES, SUCH AS MAGNETIC RESONANCE (MR) ENTEROGRAPHY, COMPUTED TOMOGRAPHY ENTEROGRAPHY, AND BOWEL ULTRASOUND, ARE USED TO ASSESS SMALL-BOWEL AND CD-RELATED COMPLICATIONS, INCLUDING STRICTURES. IT IS IMPORTANT TO BE ABLE TO DETERMINE THE DEGREE OF INFLAMMATION AND FIBROSIS IN STRICTURES TO SELECT THE BEST THERAPY; THIS CAN BE A CHALLENGE BECAUSE INFLAMMATION AND FIBROSIS CO-EXIST TO VARYING DEGREES IN A DAMAGED BOWEL SEGMENT. DELAYED GADOLINIUM ENHANCEMENT, MAGNETIZATION TRANSFER MR IMAGING, AND ULTRASOUND ELASTOGRAPHY SEEM TO BE PROMISING TOOLS FOR ASSESSING FIBROSIS IN PATIENTS WITH CD. WE REVIEW NONINVASIVE TECHNIQUES FOR FIBROSIS ASSESSMENT, INCLUDING ANALYSES OF GENETIC, EPIGENETIC, AND PROTEIN MARKERS. WE DISCUSS THE POTENTIAL OF IMAGING TECHNIQUES SUCH AS DIFFUSION-WEIGHTED AND MAGNETIZATION TRANSFER MR IMAGING, STRAIN ELASTOGRAPHY, SHEAR-WAVE IMAGING, AND POSITRON EMISSION TOMOGRAPHY TO GUIDE THERAPEUTIC DECISIONS FOR PATIENTS WITH STRICTURING CD.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
7  3056  42 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
8  5744  32 SMOKING-INDUCED EXPRESSION OF THE GPR15 GENE INDICATES ITS POTENTIAL ROLE IN CHRONIC INFLAMMATORY PATHOLOGIES. DESPITE THE DESCRIBED CLEAR EPIGENETIC EFFECTS OF SMOKING, THE EFFECT OF SMOKING ON GENOME-WIDE GENE EXPRESSION IN THE BLOOD IS OBSCURE. WE THEREFORE STUDIED THE SMOKING-INDUCED CHANGES IN THE GENE-EXPRESSION PROFILE OF THE PERIPHERAL BLOOD. RNA WAS EXTRACTED FROM THE WHOLE BLOOD OF 48 INDIVIDUALS WITH A DETAILED SMOKING HISTORY (24 NEVER-SMOKERS, 16 SMOKERS, AND 8 EX-SMOKERS). GENE-EXPRESSION PROFILES WERE EVALUATED WITH RNA SEQUENCING, AND RESULTS WERE ANALYZED SEPARATELY IN 24 MEN AND 24 WOMEN. IN THE MALE SMOKERS, 13 GENES WERE STATISTICALLY SIGNIFICANTLY (FALSE-DISCOVERY RATE <0.1) DIFFERENTIALLY EXPRESSED; IN FEMALE SMOKERS, 5 GENES. ALTHOUGH MOST OF THE DIFFERENTIALLY EXPRESSED GENES WERE DIFFERENT BETWEEN THE MALE AND FEMALE SMOKERS, THE G-PROTEIN-COUPLED RECEPTOR 15 GENE (GPR15) WAS DIFFERENTIALLY EXPRESSED IN BOTH MALE AND FEMALE SMOKERS COMPARED WITH NEVER-SMOKERS. ANALYSIS OF GPR15 METHYLATION IDENTIFIED SIGNIFICANTLY GREATER HYPOMETHYLATION IN SMOKERS COMPARED WITH THAT IN NEVER-SMOKERS. GPR15 IS THE CHEMOATTRACTANT RECEPTOR THAT REGULATES T-CELL MIGRATION AND IMMUNITY. UP-REGULATION OF GPR15 COULD EXPLAIN TO SOME EXTENT THE HEALTH HAZARDS OF SMOKING WITH REGARD TO CHRONIC INFLAMMATORY DISEASES.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
9  1064  47 CLINICAL SIGNIFICANCE OF PROMOTER METHYLATION STATUS OF TUMOR SUPPRESSOR GENES IN CIRCULATING DNA OF PANCREATIC CANCER PATIENTS. INTRODUCTION: PANCREATIC DUCTAL ADENOCARCINOMA (PDAC) IS A VERY AGGRESSIVE CANCER. THERE ARE VARIOUS SUB-CELLULAR EVENTS (BOTH GENETIC AND EPIGENETIC) THAT GET DYSREGULATED LEADING TO TUMORIGENESIS. METHYLATION IN PROMOTERS OF TUMOR SUPPRESSOR GENES IS ONE OF THESE EPIGENETIC PHENOMENA CONTRIBUTING TO THE PATHOGENESIS OF CANCER. GENES ANALYZED FOR PROMOTER METHYLATION STATUS IN THIS STUDY NAMELY SPARC (SECRETED PROTEIN ACIDIC AND RICH IN CYSTEINE, UCHL1 (UBIQUITIN CARBOXY-TERMINAL HYDROLASE L1), NPTX2 (NEURONAL PENTRAXIN 2), PENK (PROENKEPHALIN) HAD BEEN STUDIED IN PANCREATIC CANCER, BUT THERE IS A NEED TO CHECK METHYLATION IN THESE GENES AS CIRCULATORY NON-INVASIVE MARKERS. THIS STUDY ANALYZED THE ABSOLUTE QUANTIFICATION OF METHYLATION LEVELS OF SPARC, UCHL1, PENK, AND NPTX2 GENES PROMOTERS IN PDAC PATIENTS AS WELL AS IN CHRONIC PANCREATITIS (CP) PATIENTS AND HEALTHY SUBJECTS (HC) AND EVALUATED ITS CLINICAL SIGNIFICANCE IN PDAC. MATERIALS AND METHODS: THE STUDY INCLUDED 65 PDAC PATIENTS, 25 CP PATIENTS, AND 25 HEALTHY CONTROLS. DNA WAS EXTRACTED FROM THEIR PLASMA SAMPLES AND SUBSEQUENTLY GIVEN BISULFITE TREATMENT. ABSOLUTE QUANTIZATION OF METHYLATED AND UNMETHYLATED COPIES OF GENE PROMOTERS OF ALL THE FOUR GENES WAS PERFORMED USING REAL-TIME PCR (SYBR GREEN) BY THE STANDARD CURVE METHOD. METHYLATION LEVELS WERE EXPRESSED AS METHYLATION INDEX (MI) FOR EACH GENE IN EACH PATIENT. MI WAS CALCULATED FROM ABSOLUTE COPY NUMBERS AS FOLLOWS: MI-METHYLATED COPY NUMBER/METHYLATED COPY NUMBER + UNMETHYLATED COPY NUMBER). THESE INDICES WERE USED TO COMPARE GENE METHYLATION LEVELS WITHIN DIFFERENT GROUPS AND TO CORRELATE WITH CLINICOPATHOLOGICAL FEATURES AND SURVIVAL OF PANCREATIC CANCER PATIENTS. AN APPROPRIATE STATISTICAL ANALYSIS WAS APPLIED. RESULTS: METHYLATION INDICES FOR ALL THE FOUR GENES IN PDAC CASES WERE FOUND TO BE SIGNIFICANTLY HIGHER AS COMPARED TO THAT IN HEALTHY INDIVIDUALS. SPARC MI VALUES WERE FOUND TO DIFFERENTIATE EARLY-STAGE PDAC PATIENTS FROM CP PATIENTS. PDAC PATIENTS WITH THE METASTASIZED DISEASE AND STAGE IV DISEASE WERE FOUND TO HAVE HIGH MI FOR THE SPARC GENE AS WELL AS FOR THE NPTX2 GENE, WHILE A HIGHER UCHL1 METHYLATION INDEX WAS FOUND TO CORRELATE WITH AN ADVANCED STAGE OF THE DISEASE. HIGHER MI VALUES FOR SPARC AND NPTX2 GENES WERE FOUND TO ASSOCIATE WITH POOR SURVIVAL IN PATIENTS WITH PDAC. CONCLUSION: METHYLATION LOAD IN THE FORM OF MI FOR EACH OF THE FOUR GENES ASSESSED IN PLASMA MAY EMERGE AS A NON-INVASIVE BIOMARKER TO DIFFERENTIATE PANCREATIC CANCER FROM HEALTHY INDIVIDUALS. BUT ONLY SPARC AND NPTX2 HYPERMETHYLATION WERE ABLE TO DISTINGUISH PANCREATIC CANCER FROM CHRONIC PANCREATITIS. ASSOCIATION OF ABERRANT METHYLATION IN SPARC AND NPTX2 GENE WITH METASTASIS AND POOR SURVIVAL OF PATIENTS SUGGEST THE ROLE OF METHYLATION IN THESE GENES AS PROGNOSTIC MARKERS.	2020	
                                                                                                                                                               
10  2622  49 EPIGENOME-WIDE ASSOCIATION STUDIES IN ASTHMA: A SYSTEMATIC REVIEW. OBJECTIVE: ASTHMA IS A COMMON CHRONIC RESPIRATORY AIRWAY DISEASE INFLUENCED BY ENVIRONMENTAL FACTORS AND POSSIBLY THEIR INTERACTION WITH THE HUMAN GENOME CAUSING EPIGENETIC CHANGES. EPIGENOME-WIDE ASSOCIATION STUDIES (EWAS) HAVE MAINLY INVESTIGATED DNA METHYLATION AND ITS ASSOCIATION WITH DISEASE OR TRAITS, EXPOSURE FACTORS OR GENE EXPRESSION. THIS SYSTEMATIC REVIEW AIMED TO IDENTIFY ALL EWAS ASSESSING DIFFERENTIALLY METHYLATED SITES ASSOCIATED WITH ASTHMA IN HUMANS. DESIGN: STRUCTURED SYSTEMATIC LITERATURE SEARCH FOLLOWING PRISMA GUIDELINES, NEWCASTLE-OTTAWA SCALE (NOS) FOR COHORT STUDIES WAS USED FOR BIAS ASSESSMENT. DATA SOURCES: WE SEARCHED PUBMED AND EMBASE DATABASES FROM 2005 TO 2019. ELIGIBILITY CRITERIA: EPIGENOME-WIDE ASSOCIATION STUDIES TESTING ASSOCIATION BETWEEN DIFFERENTIAL METHYLATION AND ASTHMA IN HUMANS. RESULTS: OVERALL, WE IDENTIFIED 16 EWAS STUDIES COMPLYING WITH OUR SEARCH CRITERIA. TWELVE STUDIES WERE CONDUCTED ON CHILDREN, AND 10 WERE CONDUCTED ON SAMPLE SIZES <150 SUBJECTS. FOUR HUNDRED AND NINETEEN CPGS WERE REPORTED IN CHILDREN STUDIES AFTER CORRECTION FOR MULTIPLE TESTING. IN THE ADULT STUDIES, THOUSANDS OF DIFFERENTIALLY METHYLATED SITES WERE IDENTIFIED. DIFFERENTIAL METHYLATION IN INFLAMMATORY-RELATED GENES CORRELATED WITH HIGHER LEVELS OF GENE EXPRESSIONS OF INFLAMMATORY MODULATORS IN ASTHMA. DIFFERENTIALLY METHYLATED GENES ASSOCIATED WITH ASTHMA INCLUDED SMAD3, SERPINC1, PROK1, IL13, RUNX3 AND TIGIT. FORTY-ONE CPGS WERE REPLICATED AT LEAST ONCE IN BLOOD SAMPLES, AND 28 CPGS WERE REPLICATED IN NASAL SAMPLES. CONCLUSION: ALTHOUGH MANY DIFFERENTIALLY METHYLATED CPGS IN GENES KNOWN TO BE INVOLVED IN ASTHMA HAVE BEEN IDENTIFIED IN EWAS TO DATE, WE CONCLUDE THAT FURTHER STUDIES OF LARGER SAMPLE SIZES AND ANALYSES OF DIFFERENTIAL METHYLATION BETWEEN DIFFERENT PHENOTYPES ARE NEEDED IN ORDER TO COMPREHENSIVELY EVALUATE THE ROLE OF EPIGENETIC FACTORS IN THE PATHOPHYSIOLOGY AND HETEROGENEITY OF ASTHMA, AND THE POTENTIAL CLINICAL UTILITY TO PREDICT OR CLASSIFY PATIENTS WITH ASTHMA.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
11   401  49 ANALYSIS OF ABERRANT METHYLATION ON PROMOTER SEQUENCES OF TUMOR SUPPRESSOR GENES AND TOTAL DNA IN SPUTUM SAMPLES: A PROMISING TOOL FOR EARLY DETECTION OF COPD AND LUNG CANCER IN SMOKERS. BACKGROUND: CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS A DISORDER ASSOCIATED TO CIGARETTE SMOKE AND LUNG CANCER (LC). SINCE EPIGENETIC CHANGES IN ONCOGENES AND TUMOR SUPPRESSOR GENES (TSGS) ARE CLEARLY IMPORTANT IN THE DEVELOPMENT OF LC. IN THIS STUDY, WE HYPOTHESIZE THAT TOBACCO SMOKERS ARE SUSCEPTIBLE FOR METHYLATION IN THE PROMOTER REGION OF TSGS IN AIRWAY EPITHELIAL CELLS WHEN COMPARED WITH NON-SMOKER SUBJECTS. THE PURPOSE OF THIS STUDY WAS TO INVESTIGATE THE USEFULNESS OF DETECTION OF GENES PROMOTER METHYLATION IN SPUTUM SPECIMENS, AS A COMPLEMENTARY TOOL TO IDENTIFY LC BIOMARKERS AMONG SMOKERS WITH EARLY COPD. METHODS: WE DETERMINED THE AMOUNT OF DNA IN INDUCED SPUTUM FROM PATIENTS WITH COPD (N = 23), LC (N = 26), AS WELL AS IN HEALTHY SUBJECTS (CTR) (N = 33), USING A COMMERCIAL KIT FOR DNA PURIFICATION, FOLLOWED BY ABSORBANCE MEASUREMENT AT 260 NM. THE FREQUENCY OF CDKN2A, CDH1 AND MGMT PROMOTER METHYLATION IN THE SAME GROUPS WAS DETERMINED BY METHYLATION-SPECIFIC POLYMERASE CHAIN REACTION (MSP). THE FISHER'S EXACT TEST WAS EMPLOYED TO COMPARE FREQUENCY OF RESULTS BETWEEN DIFFERENT GROUPS. RESULTS: DNA CONCENTRATION WAS 7.4 AND 5.8 TIMES HIGHER IN LC AND COPD COMPARED TO THE (CTR) (P < 0.0001), RESPECTIVELY. METHYLATION STATUS OF CDKN2A AND MGMT WAS SIGNIFICANTLY HIGHER IN COPD AND LC PATIENTS COMPARED WITH CTR GROUP (P < 0.0001). FREQUENCY OF CDH1 METHYLATION ONLY SHOWED A STATISTICALLY SIGNIFICANT DIFFERENCE BETWEEN LC PATIENTS AND CTR GROUP (P < 0.05). CONCLUSIONS: WE PROVIDE EVIDENCE THAT ABERRANT METHYLATION OF TSGS IN SAMPLES OF INDUCED SPUTUM IS A USEFUL TOOL FOR EARLY DIAGNOSTIC OF LUNG DISEASES (LC AND COPD) IN SMOKER SUBJECTS. VIRTUAL SLIDES: THE ABSTRACT MUST FINISH WITH THE FOLLOWING TEXT: VIRTUAL SLIDES THE VIRTUAL SLIDE(S) FOR THIS ARTICLE CAN BE FOUND HERE: HTTP://WWW.DIAGNOSTICPATHOLOGY.DIAGNOMX.EU/VS/1127865005664160.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
12   713  40 CADMIUM EXPOSURE AND AGE-ASSOCIATED DNA METHYLATION CHANGES IN NON-SMOKING WOMEN FROM NORTHERN THAILAND. DNA METHYLATION CHANGES WITH AGE, AND MAY SERVE AS A BIOMARKER OF AGING. CADMIUM (CD) MODIFIES CELLULAR PROCESSES THAT PROMOTE AGING AND DISRUPTS METHYLATION GLOBALLY. WHETHER CD MODIFIES AGING PROCESSES BY INFLUENCING ESTABLISHMENT OF AGE-ASSOCIATED METHYLATION MARKS IS CURRENTLY UNKNOWN. IN THIS PILOT STUDY, WE CHARACTERIZED METHYLATION PROFILES IN > 450 000 CPG SITES IN 40 NON-SMOKING WOMEN (AGE 40-80) DIFFERENTIALLY EXPOSED TO ENVIRONMENTAL CD FROM THAILAND. BASED ON SPECIFIC GRAVITY ADJUSTED URINARY CD, WE CLASSIFIED THEM AS HIGH (HE) AND LOW (LE) EXPOSED AND AGE-MATCHED WITHIN 5 YEARS. URINARY CD WAS DEFINED AS BELOW 2 MICROG/L IN THE LE GROUP. WE PREDICTED EPIGENETIC AGE (DNAM-AGE) USING TWO PUBLISHED METHODS BY HORVATH AND HANNUM AND EXAMINED THE DIFFERENCE BETWEEN EPIGENETIC AGE AND CHRONOLOGIC AGE (DELTAAGE). WE ASSESSED DIFFERENCES BY CD EXPOSURE USING LINEAR MIXED MODELS ADJUSTED FOR ESTIMATED WHITE BLOOD CELL PROPORTIONS, BMI, AND URINARY CREATININE. WE IDENTIFIED 213 AGE-ASSOCIATED CPG SITES IN OUR POPULATION (P < 10(-4)). COUNTERINTUITIVELY, THE MEAN DELTAAGE WAS SMALLER IN HE VS. LE (HANNUM: 3.6 VS. 7.6 YEARS, P = 0.0093; HORVATH: 2.4 VS. 4.5 YEARS, P = 0.1308). THE CD EXPOSED GROUP WAS ASSOCIATED WITH CHANGES IN METHYLATION (P < 0.05) AT 12, 8, AND 20 AGE-ASSOCIATED SITES IDENTIFIED IN OUR POPULATION, HANNUM, AND HORVATH. FROM THE RESULTS OF THIS PILOT STUDY, ELEVATED CD EXPOSURE IS ASSOCIATED WITH METHYLATION CHANGES AT AGE-ASSOCIATED SITES AND SMALLER DIFFERENCES BETWEEN DNAM-AGE AND CHRONOLOGIC AGE, IN CONTRAST TO EXPECTED AGE-ACCELERATING EFFECTS. CD MAY MODIFY EPIGENETIC AGING, AND BIOMARKERS OF AGING WARRANT FURTHER INVESTIGATION WHEN EXAMINING CD AND ITS RELATIONSHIP WITH CHRONIC DISEASE AND MORTALITY.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
13  6386  35 THE ROLE OF QUANTITATIVE NPTX2 HYPERMETHYLATION AS A NOVEL SERUM DIAGNOSTIC MARKER IN PANCREATIC CANCER. OBJECTIVES: THE MAJORITY OF PANCREATIC CANCERS ARE FOUND TO BE UNRESECTABLE, AND THE ONLY CHANCE FOR CURE LIES ON EARLY DETECTION AND COMPLETE RESECTION. SEVERAL GENES HAVE BEEN DISCOVERED TO BE ABERRANTLY METHYLATED IN PRIMARY PANCREATIC CANCER TISSUE, AND THIS CANCER DNA CAN BE DETECTED IN THE PLASMA. THE AIMS OF THIS STUDY WERE TO DEVELOP A NOVEL DIAGNOSTIC MARKER BASED ON EPIGENETIC CHARACTERISTICS OF PANCREATIC CANCER. METHODS: WE ENROLLED 104 PATIENTS WITH PANCREATIC CANCER, 60 WITH CHRONIC PANCREATITIS, AND 5 WITH BENIGN BILIARY STONE DISEASES. THE BLOOD SAMPLES WERE COLLECTED BEFORE SURGERY OR ANY KINDS OF TREATMENT MODALITIES. DNA WAS EXTRACTED FROM THE PLASMA OF EACH PATIENT, AND NPTX2 (NEURONAL PENTRAXIN II) CPG ISLAND HYPERMETHYLATION WAS EXAMINED QUANTITATIVELY BY REAL-TIME POLYMERASE CHAIN REACTION. RESULTS: NPTX2 HYPERMETHYLATION LEVELS WERE SIGNIFICANTLY HIGHER COMPARED WITH CHRONIC PANCREATITIS (P = 0.016). THE SENSITIVITY AND SPECIFICITY WERE 80% AND 76%, RESPECTIVELY (CUTOFF = 0.015). NPTX2 GENE HYPERMETHYLATION LEVEL WAS SIGNIFICANTLY ELEVATED IN CORRELATION WITH HIGHER AMERICAN JOINT COMMITTEE ON CANCER STAGES. CONCLUSIONS: THE ABERRANTLY METHYLATED NPTX2 GENE MAY HELP TO DISTINGUISH BETWEEN CHRONIC PANCREATITIS AND PANCREATIC CANCER WITH CONVENTIONAL DIAGNOSTIC TOOLS AND COULD BECOME A VALUABLE DIAGNOSTIC MARKER.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
14  3850  38 IS GENDER A FACTOR AFFECTING LONG-TERM HETEROTOPIC OSSIFICATION INCIDENCE AFTER SINGLE-LEVEL CERVICAL DISC ARTHROPLASTY? BACKGROUND: CERVICAL DISC DISEASES HAVE BEEN TREATED BY CERVICAL DISC ARTHROPLASTY (CDA). NEVERTHELESS, SOME PATIENTS WILL EXPERIENCE A MOBILITY FAILURE IN THEIR CERVICAL PROSTHESES OVER TIME BECAUSE OF HETEROTOPIC OSSIFICATION. THE AIM OF THIS STUDY WAS TO INVESTIGATE THE ROLE OF GENDER IN LONG-TERM OUTCOMES AFTER CDA. METHODS: A RETROSPECTIVE, SINGLE-CENTER STUDY OF PATIENTS WHO UNDERWENT SINGLE-LEVEL CDA WITH A BRYAN CERVICAL DISC PROSTHESIS WAS PERFORMED, INCLUDING A NARRATIVE REVIEW ABOUT GENDER DIFFERENCES IN BOTH STRUCTURAL AND BIOMECHANICAL FEATURES OF THE CERVICAL SPINE. RESULTS: STUDY PATIENTS (14 MEN, 30 WOMEN) HAD AN AVERAGE FOLLOW-UP OF 9.8 +/- 3.2 YEARS. SIGNIFICANT DIFFERENCES EMERGED BETWEEN GENDERS FOR SPECIFIC ITEMS IN NECK DISABILITY INDEX PREOPERATIVE EVALUATION, WITH WOMEN REPORTING WORSE PAIN SCORES (P = 0.05). AFTER STRATIFICATION BY AGE, WE FOUND A HIGHER PREOPERATIVE OVERALL NECK DISABILITY INDEX SCORE FOR FEMALE PATIENTS <36 YEARS OF AGE (P = 0.03). IN AN INTERGENDER, BODY MASS INDEX-SPECIFIC COMPARISON, WE ALSO FOUND A SIGNIFICANT DIFFERENCE IN NECK DISABILITY INDEX PREOPERATIVE SCORE WITH NORMAL-WEIGHT MALE PATIENTS FARING WORSE THAN OVERWEIGHT MALE PATIENTS (P = 0.05). AT A RADIOLOGICAL LEVEL, WE FOUND A TENDENCY TOWARD A HIGHER HETEROTOPIC OSSIFICATION INCIDENCE IN MALE PATIENTS (62% IN MEN, 17% IN WOMEN, P = 0.06). THE FEMALE CERVICAL SPINE HAS DISTINCTIVE FEATURES, INCLUDING BONE STRUCTURE, MUSCULAR ACTION, SOFT TISSUE RESPONSE, AND GENETIC AND EPIGENETIC RESPONSE TO OSTEOARTHRITIS. CONCLUSIONS: THE INCIDENCE OF MOBILITY FAILURE IN OUR SERIES OF SINGLE-LEVEL CDA WAS LOWER IN FEMALE PATIENTS. SEVERAL GENDER-SPECIFIC FACTORS BOTH IN STATIC AND IN DYNAMIC FEATURES MAY PLAY A SIGNIFICANT ROLE IN SPINAL PATHOLOGY AND CDA LONG-TERM RADIOLOGICAL OUTCOME.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
15  4293  38 MICRORNA PROFILING IN MUC2 KNOCKOUT MICE OF COLITIS-ASSOCIATED CANCER MODEL REVEALS EPIGENETIC ALTERATIONS DURING CHRONIC COLITIS MALIGNANT TRANSFORMATION. OUR PREVIOUS STUDIES HAVE DEMONSTRATED THAT GENETIC DELETION OF THE MUC2 GENE CAUSES COLORECTAL CANCERS IN MICE. THE CURRENT STUDY FURTHER SHOWED THAT AT THE EARLY STAGE (<3 MONTHS) THE MUC2 KNOCKOUT MICE SPONTANEOUSLY DEVELOPED CHRONIC INFLAMMATION IN COLON AND RECTUM, SIMILAR PATHOLOGICAL FEATURES AS HUMAN COLITIS; AND AT THE LATE STAGE (>3 MONTHS) THE MICE EXHIBITED COLORECTAL CANCER, INCLUDING A UNIQUE PHENOTYPE OF RECTAL PROLAPSED (RECTAL SEVERE INFLAMMATION AND ADENOCARCINOMA). THUS, THE AGE OF 3 MONTHS MIGHT BE THE KEY POINT OF THE TRANSITION FROM CHRONIC INFLAMMATION TO CANCER. TO DETERMINE THE MECHANISMS OF THE MALIGNANT TRANSFORMATION, WE CONDUCTED MIRNA ARRAY ON THE COLONIC EPITHELIAL CELLS FROM THE 3-MONTH MUC2-/- AND +/+ MICE. MICRORNA PROFILING SHOWED DIFFERENTIAL EXPRESSION OF MIRNAS (I.E. LOWER OR HIGHER EXPRESSION ENRICHMENTS) IN MUC2-/- MICE. 15 OF THEM WERE VALIDATED BY QUANTITATIVE PCR. BASED ON RELEVANCE TO CYTOKINE AND CANCER, 4 MIRNAS (MIR-138, MIR-145, MIR-146A, AND MIR-150) WERE VALIDATE AND WERE FOUND SIGNIFICANTLY DOWNREGULATED IN HUMAN COLITIS AND COLORECTAL CANCER TISSUES. THE NETWORK OF THE TARGETS OF THESE MIRNAS WAS CHARACTERIZED, AND INTERESTEDLY, MIRNA-ASSOCIATED CYTOKINES WERE SIGNIFICANTLY INCREASED IN MUC2-/-MICE. THIS IS THE FIRST TO REVEAL THE IMPORTANCE OF ABERRANT EXPRESSION OF MIRNAS IN DYNAMICALLY TRANSFORMATION FROM CHRONIC COLITIS TO COLITIS-ASSOCIATED CANCER. THESE FINDINGS SHED LIGHT ON REVEALING THE MECHANISMS OF CHRONIC COLITIS MALIGNANT TRANSFORMATION.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
16  2643  41 EPIGENOMIC ASSOCIATION ANALYSIS IDENTIFIES SMOKING-RELATED DNA METHYLATION SITES IN AFRICAN AMERICANS. CIGARETTE SMOKING IS AN ENVIRONMENTAL RISK FACTOR FOR MANY CHRONIC DISEASES, AND DISEASE RISK CAN OFTEN BE MANAGED BY SMOKING CONTROL. SMOKING CAN INDUCE CELLULAR AND MOLECULAR CHANGES, INCLUDING EPIGENETIC MODIFICATION, BUT THE SHORT- AND LONG-TERM EPIGENETIC MODIFICATIONS CAUSED BY CIGARETTE SMOKING AT THE GENE LEVEL HAVE NOT BEEN WELL UNDERSTOOD. RECENT STUDIES HAVE IDENTIFIED SMOKING-RELATED DNA METHYLATION (DNAM) SITES IN CAUCASIANS. TO DETERMINE WHETHER THE SAME DNAM SITES ASSOCIATE WITH SMOKING IN AFRICAN AMERICANS, AND TO IDENTIFY NOVEL SMOKING-RELATED DNAM SITES, WE CONDUCTED A METHYLOME-WIDE ASSOCIATION STUDY OF CIGARETTE SMOKING USING A DISCOVERY SAMPLE OF 972 AFRICAN AMERICANS, AND A REPLICATION SAMPLE OF 239 AFRICAN AMERICANS WITH TWO ARRAY-BASED METHODS. AMONG 15 DNAM SITES SIGNIFICANTLY ASSOCIATED WITH SMOKING AFTER CORRECTION FOR MULTIPLE TESTING IN OUR DISCOVERY SAMPLE, 5 DNAM SITES ARE REPLICATED IN AN INDEPENDENT COHORT, AND 14 SITES IN THE REPLICATION SAMPLE HAVE EFFECTS IN THE SAME DIRECTION AS IN THE DISCOVERY SAMPLE. THE TOP TWO SMOKING-RELATED DNAM SITES IN F2RL3 (FACTOR II RECEPTOR-LIKE 3) AND GPR15 (G-PROTEIN-COUPLED RECEPTOR 15) OBSERVED IN AFRICAN AMERICANS ARE CONSISTENT WITH PREVIOUS FINDINGS IN CAUCASIANS. THE ASSOCIATIONS BETWEEN THE REPLICATED DNAM SITES AND SMOKING REMAIN SIGNIFICANT AFTER ADJUSTING FOR GENETIC BACKGROUND. DESPITE THE DISTINCT GENETIC BACKGROUND BETWEEN AFRICAN AMERICANS AND CAUCASIANS, THE DNAM FROM THE TWO ETHNIC GROUPS SHARES COMMON ASSOCIATIONS WITH CIGARETTE SMOKING, WHICH SUGGESTS A COMMON MOLECULAR MECHANISM OF EPIGENETIC MODIFICATION INFLUENCED BY ENVIRONMENTAL EXPOSURE.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
17   526  31 ASSOCIATIONS OF HELICOBACTER PYLORI INFECTION AND CHRONIC ATROPHIC GASTRITIS WITH ACCELERATED EPIGENETIC AGEING IN OLDER ADULTS. BACKGROUND: HELICOBACTER PYLORI (HP) INFECTION AND CHRONIC ATROPHIC GASTRITIS (CAG) HAVE SHOWN STRONG ASSOCIATIONS WITH THE DEVELOPMENT OF GASTRIC CANCER. THIS STUDY AIMED TO EXAMINE WHETHER BOTH RISK FACTORS ARE ASSOCIATED WITH ACCELERATED EPIGENETIC AGEING, AS DETERMINED BY THE 'DNA METHYLATION AGE', IN A POPULATION-BASED STUDY OF OLDER ADULTS (N=1477). METHODS: SEROLOGICAL MEASUREMENTS OF HP ANTIBODIES AND PEPSINOGEN I AND II FOR CAG DEFINITION WERE OBTAINED BY ELISA KITS. WHOLE BLOOD DNA METHYLATION PROFILES WERE MEASURED BY ILLUMINA HUMAN METHYLATION450K BEADCHIP. DNA METHYLATION AGES WERE CALCULATED BY TWO ALGORITHMS PROPOSED BY HORVATH AND HANNUM ET AL. RESULTS: AFTER ADJUSTING FOR POTENTIAL COVARIATES IN LINEAR REGRESSION MODELS, WE FOUND THAT HP INFECTION, INFECTION WITH VIRULENT HP STRAINS (CAGA+) AND SEVERE CAG WERE SIGNIFICANTLY ASSOCIATED WITH AN INCREASE IN DNA METHYLATION AGE BY APPROXIMATELY 0.4, 0.6 AND 1 YEAR (ALL P-VALUES <0.05), RESPECTIVELY. CONCLUSIONS: OUR STUDY INDICATES THAT BOTH CAGA+ HP INFECTION AND CAG GO ALONG WITH ACCELERATED EPIGENETIC AGEING.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
18  1061  42 CLINICAL REMISSION OF SIGHT-THREATENING NON-INFECTIOUS UVEITIS IS CHARACTERIZED BY AN UPREGULATION OF PERIPHERAL T-REGULATORY CELL POLARIZED TOWARDS T-BET AND TIGIT. BACKGROUND: NON-INFECTIOUS UVEITIS CAN CAUSE CHRONIC RELAPSING AND REMITTING OCULAR INFLAMMATION, WHICH MAY REQUIRE HIGH DOSE SYSTEMIC IMMUNOSUPPRESSION TO PREVENT SEVERE SIGHT LOSS. IT HAS BEEN CLASSICALLY DESCRIBED AS AN AUTOIMMUNE DISEASE, MEDIATED BY PRO-INFLAMMATORY TH1 AND TH17 T-CELL SUBSETS. STUDIES SUGGEST THAT NATURAL IMMUNOSUPPRESSIVE CD4(+)CD25(+)FOXP3(+) T-REGULATORY CELLS (TREGS) ARE INVOLVED IN RESOLUTION OF INFLAMMATION AND MAY BE INVOLVED IN THE MAINTENANCE OF CLINICAL REMISSION. OBJECTIVE: TO INVESTIGATE WHETHER THERE IS A PERIPHERAL BLOOD IMMUNOREGULATORY PHENOTYPE ASSOCIATED WITH CLINICAL REMISSION OF SIGHT-THREATENING NON-INFECTIOUS UVEITIS BY COMPARING PERIPHERAL BLOOD LEVELS OF TREG, TH1, AND TH17, AND ASSOCIATED DNA METHYLATION AND CYTOKINE LEVELS IN PATIENTS WITH ACTIVE UVEITIC DISEASE, CONTROL SUBJECTS AND PATIENTS (WITH PREVIOUSLY ACTIVE DISEASE) IN CLINICAL REMISSION INDUCED BY IMMUNOSUPPRESSIVE DRUGS. METHODS: ISOLATED PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMC) FROM PERIPHERAL BLOOD SAMPLES FROM PROSPECTIVELY RECRUITED SUBJECTS WERE ANALYZED BY FLOW CYTOMETRY FOR CD3, CD4, FOXP3, TIGIT, T-BET, AND RELATED ORPHAN RECEPTOR GAMMAT. EPIGENETIC DNA METHYLATION LEVELS OF FOXP3 TREG-SPECIFIC DEMETHYLATED REGION (TSDR), FOXP3 PROMOTER, TBX21, RORC2, AND TIGIT LOCI WERE DETERMINED IN CRYOPRESERVED PBMC USING A NEXT-GENERATION SEQUENCING APPROACH. RELATED CYTOKINES WERE MEASURED IN BLOOD SERA. FUNCTIONAL SUPPRESSIVE CAPACITY OF TREG WAS ASSESSED USING T-CELL PROLIFERATION ASSAYS. RESULTS: FIFTY PATIENTS WITH UVEITIS (INTERMEDIATE, POSTERIOR, AND PANUVEITIS) AND 10 CONTROL SUBJECTS WERE RECRUITED. THE FREQUENCY OF CD4(+)CD25(+)FOXP3(+) TREG, TIGIT(+) TREG, AND T-BET(+) TREG AND THE RATIO OF TREG TO TH1 WERE SIGNIFICANTLY HIGHER IN REMISSION PATIENTS COMPARED WITH PATIENTS WITH ACTIVE UVEITIC DISEASE; AND TIGIT(+) TREGS WERE A SIGNIFICANT PREDICTOR OF CLINICAL REMISSION. TREG FROM PATIENTS IN CLINICAL REMISSION DEMONSTRATED A HIGH LEVEL OF IN VITRO SUPPRESSIVE FUNCTION COMPARED WITH TREG FROM CONTROL SUBJECTS AND FROM PATIENTS WITH UNTREATED ACTIVE DISEASE. PBMC FROM PATIENTS IN CLINICAL REMISSION HAD SIGNIFICANTLY LOWER METHYLATION LEVELS AT THE FOXP3 TSDR, FOXP3 PROMOTER, AND TIGIT LOCI AND HIGHER LEVELS AT RORC LOCI THAN THOSE WITH ACTIVE DISEASE. CLINICAL REMISSION WAS ALSO ASSOCIATED WITH SIGNIFICANTLY HIGHER SERUM LEVELS OF TRANSFORMING GROWTH FACTOR BETA AND IL-10, WHICH POSITIVELY CORRELATED WITH TREG LEVELS, AND LOWER SERUM LEVELS OF IFNGAMMA, IL-17A, AND IL-22 COMPARED WITH PATIENTS WITH ACTIVE DISEASE. CONCLUSION: CLINICAL REMISSION OF SIGHT-THREATENING NON-INFECTIOUS UVEITIS HAS AN IMMUNOREGULATORY PHENOTYPE CHARACTERIZED BY UPREGULATION OF PERIPHERAL TREG, POLARIZED TOWARD T-BET AND TIGIT. THESE FINDINGS MAY ASSIST WITH INDIVIDUALIZED THERAPY OF UVEITIS, BY INFORMING WHETHER DRUG THERAPY HAS INDUCED PHENOTYPICALLY STABLE TREG ASSOCIATED WITH LONG-TERM CLINICAL REMISSION.	2018	

19  3445  41 HYPERMETHYLATION OF ITGA4, TFPI2 AND VIMENTIN PROMOTERS IS INCREASED IN INFLAMED COLON TISSUE: PUTATIVE RISK MARKERS FOR COLITIS-ASSOCIATED CANCER. PURPOSE: EPIGENETIC SILENCING OF TUMOR SUPPRESSOR GENES IS INVOLVED IN EARLY TRANSFORMING EVENTS AND HAS A HIGH IMPACT ON COLORECTAL CARCINOGENESIS. LIKEWISE, COLON CANCERS THAT DERIVE FROM CHRONICALLY INFLAMED BOWEL DISEASES FREQUENTLY EXHIBIT EPIGENETIC CHANGES. BUT THERE IS LITTLE DATA ABOUT EPIGENETIC ABERRATIONS CAUSING COLORECTAL CANCER IN CHRONICALLY INFLAMED TISSUE. THE AIM OF THE PRESENT STUDY WAS TO EVALUATE THE ABERRANT GAIN OF METHYLATION IN THE GENE PROMOTERS OF VIM, TFPI2 AND ITGA4 AS PUTATIVE EARLY MARKERS IN THE DEVELOPMENT FROM INFLAMED TISSUE VIA PRECANCEROUS LESIONS TOWARD COLORECTAL CANCER. METHODS: INITIAL SCREENING OF DIFFERENT CANCER CELL LINES BY USING METHYLATION-SPECIFIC PCR REVEALED A PUTATIVE COLON CANCER-SPECIFIC METHYLATION PATTERN. ADDITIONALLY, A DEMETHYLATION ASSAY WAS PERFORMED TO INVESTIGATE THE METHYLATION-DEPENDENT GENE SILENCING OF ITGA4. THE CANDIDATE MARKERS WERE ANALYZED IN COLONIC TISSUE SPECIMENS FROM PATIENTS WITH COLORECTAL CANCER (N = 15), ADENOMAS (N = 76), SERRATED LESIONS (N = 13), CHRONIC INFLAMMATION (N = 10) AND NORMAL MUCOSAL SAMPLES (N = 9). RESULTS: A HIGH METHYLATION FREQUENCY OF VIM (55.6 %) WAS OBSERVED IN NORMAL COLON TISSUE, WHEREAS ITGA4 AND TFPI2 WERE COMPLETELY UNMETHYLATED IN CONTROLS. A SIGNIFICANT GAIN OF METHYLATION FREQUENCY WITH PROGRESSION OF DISEASE AS WELL AS AN AGE-DEPENDENT EFFECT WAS DETECTABLE FOR TFPI2. ITGA4 METHYLATION FREQUENCY WAS HIGH IN PRECANCEROUS AND CANCEROUS TISSUES AS WELL AS IN INFLAMMATORY BOWEL DISEASES (IBD). CONCLUSION: THE ALREADY ESTABLISHED METHYLATION MARKER VIM DOES NOT PERMIT A SPECIFIC AND SENSITIVE DISCRIMINATION OF HEALTHY AND NEOPLASTIC TISSUE. THE METHYLATION MARKERS ITGA4 AND TFPI2 SEEM TO BE SUITABLE RISK MARKERS FOR INFLAMMATION-ASSOCIATED COLON CANCER.	2015	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
20  5395  40 REDUCED EPIGENETIC AGE IN OLDER ADULTS WITH HIGH SENSE OF PURPOSE IN LIFE. PSYCHOSOCIAL RISK FACTORS HAVE BEEN LINKED WITH ACCELERATED EPIGENETIC AGING, BUT LITTLE IS KNOWN ABOUT WHETHER PSYCHOSOCIAL RESILIENCE FACTORS (EG, SENSE OF PURPOSE IN LIFE) MIGHT REDUCE EPIGENETIC AGE ACCELERATION. IN THIS STUDY, WE TESTED IF OLDER ADULTS WHO EXPERIENCE HIGH LEVELS OF PURPOSE MIGHT SHOW REDUCED EPIGENETIC AGE ACCELERATION. WE EVALUATED THE RELATIONSHIP BETWEEN PURPOSE AND EPIGENETIC AGE ACCELERATION AS MEASURED BY 13 DNA METHYLATION (DNAM) "EPIGENETIC CLOCKS" ASSESSED IN 1 572 OLDER ADULTS FROM THE HEALTH AND RETIREMENT STUDY (MEAN AGE 70 YEARS). WE QUANTIFIED THE TOTAL ASSOCIATION BETWEEN PURPOSE AND DNAM AGE ACCELERATION AS WELL AS THE EXTENT TO WHICH THAT TOTAL ASSOCIATION MIGHT BE ATTRIBUTABLE TO DEMOGRAPHIC FACTORS, CHRONIC DISEASE, OTHER PSYCHOSOCIAL VARIABLES (EG, POSITIVE AFFECT), AND HEALTH-RELATED BEHAVIORS (HEAVY DRINKING, SMOKING, PHYSICAL ACTIVITY, AND BODY MASS INDEX [BMI]). PURPOSE IN LIFE WAS ASSOCIATED WITH REDUCED EPIGENETIC AGE ACCELERATION ACROSS 4 "SECOND-GENERATION" DNAM CLOCKS OPTIMIZED FOR PREDICTING HEALTH AND LONGEVITY (FALSE DISCOVERY RATE [FDR] Q < 0.0001: PHENOAGE, GRIMAGE, ZHANG EPIGENETIC MORTALITY INDEX; FDR Q < 0.05: DUNEDINPOAM). THESE ASSOCIATIONS WERE INDEPENDENT OF DEMOGRAPHIC AND PSYCHOSOCIAL FACTORS, BUT SUBSTANTIALLY ATTENUATED AFTER ADJUSTING FOR HEALTH-RELATED BEHAVIORS (DRINKING, SMOKING, PHYSICAL ACTIVITY, AND BMI). PURPOSE SHOWED NO SIGNIFICANT ASSOCIATION WITH 9 "FIRST-GENERATION" DNAM EPIGENETIC CLOCKS TRAINED ON CHRONOLOGICAL AGE. OLDER ADULTS WITH GREATER PURPOSE IN LIFE SHOW "YOUNGER" DNAM EPIGENETIC AGE ACCELERATION. THESE RESULTS MAY BE DUE IN PART TO ASSOCIATED DIFFERENCES IN HEALTH-RELATED BEHAVIORS. RESULTS SUGGEST NEW OPPORTUNITIES TO REDUCE BIOLOGICAL AGE ACCELERATION BY ENHANCING PURPOSE AND ITS BEHAVIORAL SEQUELAE IN LATE ADULTHOOD.	2023