1  1129 131 COMPREHENSIVE ANALYSIS OF MRNA-LNCRNA CO-EXPRESSION PROFILES IN MOUSE BRAIN DURING INFECTION WITH TOXOPLASMA GONDII. TOXOPLASMA GONDII IS AN OBLIGATE INTRACELLULAR PROTOZOAN PARASITE WHICH SERIOUSLY THREATENS THE HEALTH OF DOMESTIC ANIMALS AND HUMANS. LONG NON-CODING RNAS (LNCRNAS) ARE NON-PROTEIN-CODING TRANSCRIPTS GREATER THAN 200 NUCLEOTIDES, WHICH ARE WIDELY INVOLVED IN TRANSCRIPTIONAL AND EPIGENETIC REGULATIONS. HOWEVER, LITTLE IS KNOWN ABOUT THE ROLES OF HOST LNCRNAS IN THE RESPONSE TO T. GONDII INFECTIONS. IN THIS STUDY, USING ILLUMINA SEQUENCING TECHNOLOGY, WE ANALYZED THE EXPRESSION PROFILES OF MRNAS AND LNCRNAS IN BALB/C MOUSE BRAIN FOLLOWING INFECTION BY T. GONDII PRU STRAIN (TYPE II GENOTYPE) CYSTS. THE IDENTIFIED DIFFERENTIALLY EXPRESSED (DE) RNAS WERE SUBJECTED TO BIOINFORMATICS ANALYSIS. A TOTAL OF 2,090 ANNOTATED LNCRNAS ALONG WITH 3,577 NOVEL LNCRNAS WERE IDENTIFIED. IN THE ACUTELY INFECTED MOUSE BRAIN, A TOTAL OF 330 MRNAS AND 19 LNCRNAS WERE DYS-REGULATED, WHEREAS 136 DE MRNAS AND 9 DE LNCRNAS WERE IDENTIFIED IN CHRONICALLY INFECTED MOUSE BRAIN. GO ANALYSIS REVEALED THAT THESE DE MRNAS IDENTIFIED AT ACUTE INFECTION STAGE WERE INVOLVED IN IMMUNE RESPONSE, WHEREAS DE MRNAS FOUND AT CHRONIC INFECTION STAGE WERE MOSTLY ENRICHED IN RESPONSE TO PROTOZOAN. KEGG ANALYSIS SHOWED THAT DE MRNAS WERE SIGNIFICANTLY ENRICHED IN DISEASE RELATED PATHWAYS. IN ADDITION, THE PUTATIVE MRNA-LNCRNA CO-EXPRESSION NETWORK WAS CONSTRUCTED, AND SEVERAL HUB REGULATORY RNAS WERE IDENTIFIED BASED ON THE TRANSCRIPTOME DATA. THIS STUDY FIRSTLY CHARACTERIZED THE CO-EXPRESSION PROFILE OF MRNAS AND LNCRNAS IN MOUSE BRAIN INFECTED WITH T. GONDII AND PROVIDED A FRAMEWORK FOR FURTHER STUDIES OF THE ROLES OF LNCRNAS IN HOST NEUROPATHOLOGY DURING TOXOPLASMOSIS PROGRESSION.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
2  1132  36 COMPREHENSIVE DNA METHYLATION ANALYSIS USING A METHYL-CPG-BINDING DOMAIN CAPTURE-BASED METHOD IN CHRONIC LYMPHOCYTIC LEUKEMIA PATIENTS. THE ROLE OF LONG NONCODING RNAS (LNCRNAS) IN CANCER IS COMING TO THE FOREFRONT DUE TO GROWING INTEREST IN UNDERSTANDING THEIR MECHANISTIC FUNCTIONS DURING CANCER DEVELOPMENT AND PROGRESSION. DESPITE THIS, THE GLOBAL EPIGENETIC REGULATION OF LNCRNAS AND REPETITIVE SEQUENCES IN CANCER HAS NOT BEEN WELL INVESTIGATED, PARTICULARLY IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). THIS STUDY FOCUSES ON A UNIQUE APPROACH: THE IMMUNOPRECIPITATION-BASED CAPTURE OF DOUBLE-STRANDED, METHYLATED DNA FRAGMENTS USING METHYL-BINDING DOMAIN (MBD) PROTEINS, FOLLOWED BY NEXT-GENERATION SEQUENCING (MBD-SEQ). CLL PATIENT SAMPLES BELONGING TO TWO PROGNOSTIC SUBGROUPS (5 IGVH MUTATED SAMPLES + 5 IGVH UNMUTATED SAMPLES) WERE USED IN THIS STUDY. ANALYSIS REVEALED 5,800 HYPERMETHYLATED AND 12,570 HYPOMETHYLATED CLL-SPECIFIC DIFFERENTIALLY METHYLATED GENES (CLLDMGS) COMPARED TO NORMAL HEALTHY CONTROLS. IMPORTANTLY, THESE RESULTS IDENTIFIED SEVERAL CLL-SPECIFIC, DIFFERENTIALLY METHYLATED LNCRNAS, REPETITIVE ELEMENTS, AND PROTEIN-CODING GENES WITH POTENTIAL PROGNOSTIC VALUE. THIS WORK OUTLINES A DETAILED PROTOCOL FOR AN MBD-SEQ AND BIOINFORMATICS PIPELINE DEVELOPED FOR THE COMPREHENSIVE ANALYSIS OF GLOBAL METHYLATION PROFILES IN HIGHLY CPG-RICH REGIONS USING CLL PATIENT SAMPLES. FINALLY, A PROTEIN-CODING GENE AND AN LNCRNA WERE VALIDATED USING PYROSEQUENCING, WHICH IS A HIGHLY QUANTITATIVE METHOD TO ANALYZE CPG METHYLATION LEVELS TO FURTHER CORROBORATE THE FINDINGS FROM THE MBD-SEQ PROTOCOL.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
3  2481  39 EPIGENETIC UPREGULATION OF LNCRNAS AT 13Q14.3 IN LEUKEMIA IS LINKED TO THE IN CIS DOWNREGULATION OF A GENE CLUSTER THAT TARGETS NF-KB. NON-CODING RNAS ARE MUCH MORE COMMON THAN PREVIOUSLY THOUGHT. HOWEVER, FOR THE VAST MAJORITY OF NON-CODING RNAS, THE CELLULAR FUNCTION REMAINS ENIGMATIC. THE TWO LONG NON-CODING RNA (LNCRNA) GENES DLEU1 AND DLEU2 MAP TO A CRITICAL REGION AT CHROMOSOMAL BAND 13Q14.3 THAT IS RECURRENTLY DELETED IN SOLID TUMORS AND HEMATOPOIETIC MALIGNANCIES LIKE CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). WHILE NO POINT MUTATIONS HAVE BEEN FOUND IN THE PROTEIN CODING CANDIDATE GENES AT 13Q14.3, THEY ARE DEREGULATED IN MALIGNANT CELLS, SUGGESTING AN EPIGENETIC TUMOR SUPPRESSOR MECHANISM. WE THEREFORE CHARACTERIZED THE EPIGENETIC MAKEUP OF 13Q14.3 IN CLL CELLS AND FOUND HISTONE MODIFICATIONS BY CHROMATIN-IMMUNOPRECIPITATION (CHIP) THAT ARE ASSOCIATED WITH ACTIVATED TRANSCRIPTION AND SIGNIFICANT DNA-DEMETHYLATION AT THE TRANSCRIPTIONAL START SITES OF DLEU1 AND DLEU2 USING 5 DIFFERENT SEMI-QUANTITATIVE AND QUANTITATIVE METHODS (APRIMES, BIOCOBRA, MCIP, MASSARRAY, AND BISULFITE SEQUENCING). THESE EPIGENETIC ABERRATIONS WERE CORRELATED WITH TRANSCRIPTIONAL DEREGULATION OF THE NEIGHBORING CANDIDATE TUMOR SUPPRESSOR GENES, SUGGESTING A COREGULATION IN CIS OF THIS GENE CLUSTER. WE FOUND THAT THE 13Q14.3 GENES IN ADDITION TO THEIR PREVIOUSLY KNOWN FUNCTIONS REGULATE NF-KB ACTIVITY, WHICH WE COULD SHOW AFTER OVEREXPRESSION, SIRNA-MEDIATED KNOCKDOWN, AND DOMINANT-NEGATIVE MUTANT GENES BY USING WESTERN BLOTS WITH PREVIOUSLY UNDESCRIBED ANTIBODIES, BY A CUSTOMIZED ELISA AS WELL AS BY REPORTER ASSAYS. IN ADDITION, WE PERFORMED AN UNBIASED SCREEN OF 810 HUMAN MIRNAS AND IDENTIFIED THE MIR-15/16 FAMILY OF GENES AT 13Q14.3 AS THE STRONGEST INDUCERS OF NF-KB ACTIVITY. IN SUMMARY, THE TUMOR SUPPRESSOR MECHANISM AT 13Q14.3 IS A CLUSTER OF GENES CONTROLLED BY TWO LNCRNA GENES THAT ARE REGULATED BY DNA-METHYLATION AND HISTONE MODIFICATIONS AND WHOSE MEMBERS ALL REGULATE NF-KB. THEREFORE, THE TUMOR SUPPRESSOR MECHANISM IN 13Q14.3 UNDERLINES THE ROLE BOTH OF EPIGENETIC ABERRATIONS AND OF LNCRNA GENES IN HUMAN TUMORIGENESIS AND IS AN EXAMPLE OF COLOCALIZATION OF A FUNCTIONALLY RELATED GENE CLUSTER.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
4   812  38 CHANGES IN DNA METHYLATION PROFILES OF MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME PATIENTS REFLECT SYSTEMIC DYSFUNCTIONS. BACKGROUND: MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A LIFELONG DEBILITATING DISEASE WITH A COMPLEX PATHOLOGY NOT YET CLEARLY DEFINED. SUSCEPTIBILITY TO ME/CFS INVOLVES GENETIC PREDISPOSITION AND EXPOSURE TO ENVIRONMENTAL FACTORS, SUGGESTING AN EPIGENETIC ASSOCIATION. EPIGENETIC STUDIES WITH OTHER ME/CFS COHORTS HAVE USED ARRAY-BASED TECHNOLOGY TO IDENTIFY DIFFERENTIALLY METHYLATED INDIVIDUAL SITES. CHANGES IN RNA QUANTITIES AND PROTEIN ABUNDANCE HAVE BEEN DOCUMENTED IN OUR PREVIOUS INVESTIGATIONS WITH THE SAME ME/CFS COHORT USED FOR THIS STUDY. RESULTS: DNA FROM A WELL-CHARACTERISED NEW ZEALAND COHORT OF 10 ME/CFS PATIENTS AND 10 AGE-/SEX-MATCHED HEALTHY CONTROLS WAS ISOLATED FROM PERIPHERAL BLOOD MONONUCLEAR (PBMC) CELLS, AND USED TO GENERATE REDUCED GENOME-SCALE DNA METHYLATION MAPS USING REDUCED REPRESENTATION BISULPHITE SEQUENCING (RRBS). THE SEQUENCING DATA WERE ANALYSED UTILISING THE DMAP ANALYSIS PIPELINE TO IDENTIFY DIFFERENTIALLY METHYLATED FRAGMENTS, AND THE METHYLKIT PIPELINE WAS USED TO QUANTIFY METHYLATION DIFFERENCES AT INDIVIDUAL CPG SITES. DMAP IDENTIFIED 76 DIFFERENTIALLY METHYLATED FRAGMENTS AND METHYLKIT IDENTIFIED 394 DIFFERENTIALLY METHYLATED CYTOSINES THAT INCLUDED BOTH HYPER- AND HYPO-METHYLATION. FOUR CLUSTERS WERE IDENTIFIED WHERE DIFFERENTIALLY METHYLATED DNA FRAGMENTS OVERLAPPED WITH OR WERE WITHIN CLOSE PROXIMITY TO MULTIPLE DIFFERENTIALLY METHYLATED INDIVIDUAL CYTOSINES. THESE CLUSTERS IDENTIFIED REGULATORY REGIONS FOR 17 PROTEIN ENCODING GENES RELATED TO METABOLIC AND IMMUNE ACTIVITY. ANALYSIS OF DIFFERENTIALLY METHYLATED GENE BODIES (EXONS/INTRONS) IDENTIFIED 122 UNIQUE GENES. COMPARISON WITH OTHER STUDIES ON PBMCS FROM ME/CFS PATIENTS AND CONTROLS WITH ARRAY TECHNOLOGY SHOWED 59% OF THE GENES IDENTIFIED IN THIS STUDY WERE ALSO FOUND IN ONE OR MORE OF THESE STUDIES. FUNCTIONAL PATHWAY ENRICHMENT ANALYSIS IDENTIFIED 30 ASSOCIATED PATHWAYS. THESE INCLUDED IMMUNE, METABOLIC AND NEUROLOGICAL-RELATED FUNCTIONS DIFFERENTIALLY REGULATED IN ME/CFS PATIENTS COMPARED TO THE MATCHED HEALTHY CONTROLS. CONCLUSIONS: MAJOR DIFFERENCES WERE IDENTIFIED IN THE DNA METHYLATION PATTERNS OF ME/CFS PATIENTS THAT CLEARLY DISTINGUISHED THEM FROM THE HEALTHY CONTROLS. OVER HALF FOUND IN GENE BODIES WITH RRBS IN THIS STUDY HAD BEEN IDENTIFIED IN OTHER ME/CFS STUDIES USING THE SAME CELLS BUT WITH ARRAY TECHNOLOGY. WITHIN THE ENRICHED FUNCTIONAL IMMUNE, METABOLIC AND NEUROLOGICAL PATHWAYS, A NUMBER OF ENRICHED NEUROTRANSMITTER AND NEUROPEPTIDE REACTOME PATHWAYS HIGHLIGHTED A DISTURBED NEUROLOGICAL PATHOPHYSIOLOGY WITHIN THE PATIENT GROUP.	2020	

5  2771  32 EXTENSIVE PROMOTER DNA HYPERMETHYLATION AND HYPOMETHYLATION IS ASSOCIATED WITH ABERRANT MICRORNA EXPRESSION IN CHRONIC LYMPHOCYTIC LEUKEMIA. DYSREGULATED MICRORNA (MIRNA) EXPRESSION CONTRIBUTES TO THE PATHOGENESIS OF HEMATOPOIETIC MALIGNANCIES, INCLUDING CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). HOWEVER, AN UNDERSTANDING OF THE MECHANISMS THAT CAUSE ABERRANT MIRNA TRANSCRIPTIONAL CONTROL IS LACKING. IN THIS STUDY, WE COMPREHENSIVELY INVESTIGATED THE ROLE AND EXTENT OF MIRNA EPIGENETIC REGULATION IN CLL. GENOME-WIDE PROFILING CONDUCTED ON 24 CLL AND 10 HEALTHY B CELL SAMPLES REVEALED GLOBAL DNA METHYLATION PATTERNS UPSTREAM OF MIRNA SEQUENCES THAT DISTINGUISHED MALIGNANT FROM HEALTHY CELLS AND IDENTIFIED PUTATIVE MIRNA PROMOTERS. INTEGRATION OF DNA METHYLATION AND MIRNA PROMOTER DATA LED TO THE IDENTIFICATION OF 128 RECURRENT MIRNA TARGETS FOR ABERRANT PROMOTER DNA METHYLATION. DNA HYPOMETHYLATION ACCOUNTED FOR MORE THAN 60% OF ALL ABERRANT PROMOTER-ASSOCIATED DNA METHYLATION IN CLL, AND PROMOTER DNA HYPOMETHYLATION WAS RESTRICTED TO WELL-DEFINED REGIONS. INDIVIDUAL HYPER- AND HYPOMETHYLATED PROMOTERS ALLOWED DISCRIMINATION OF CLL SAMPLES FROM HEALTHY CONTROLS. PROMOTER DNA METHYLATION PATTERNS WERE CONFIRMED IN AN INDEPENDENT PATIENT COHORT, WITH 11 MIRNAS CONSISTENTLY SHOWING AN INVERSE CORRELATION BETWEEN DNA METHYLATION STATUS AND EXPRESSION LEVEL. TOGETHER, OUR FINDINGS CHARACTERIZE THE ROLE OF EPIGENETIC CHANGES IN THE REGULATION OF MIRNA TRANSCRIPTION AND CREATE A REPOSITORY OF DISEASE-SPECIFIC PROMOTER REGIONS THAT MAY PROVIDE ADDITIONAL INSIGHTS INTO THE PATHOGENESIS OF CLL.	2012	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
6  3496  35 IDENTIFICATION OF MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME-ASSOCIATED DNA METHYLATION PATTERNS. BACKGROUND: MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A COMPLEX CONDITION INVOLVING MULTIPLE ORGAN SYSTEMS AND CHARACTERIZED BY PERSISTENT/RELAPSING DEBILITATING FATIGUE, IMMUNE DYSFUNCTION, NEUROLOGICAL PROBLEMS, AND OTHER SYMPTOMS NOT CURABLE FOR AT LEAST 6 MONTHS. DISRUPTION OF DNA METHYLATION PATTERNS HAS BEEN TIED TO VARIOUS IMMUNE AND NEUROLOGICAL DISEASES; HOWEVER, ITS STATUS IN ME/CFS REMAINS UNCERTAIN. OUR STUDY AIMED AT IDENTIFYING CHANGES IN THE DNA METHYLATION PATTERNS THAT ASSOCIATE WITH ME/CFS. METHODS: WE EXTRACTED GENOMIC DNA FROM PERIPHERAL BLOOD MONONUCLEAR CELLS FROM 13 ME/CFS STUDY SUBJECTS AND 12 HEALTHY CONTROLS AND MEASURED GLOBAL DNA METHYLATION BY ELISA-LIKE METHOD AND SITE-SPECIFIC METHYLATION STATUS USING ILLUMINA METHYLATIONEPIC MICROARRAYS. PYROSEQUENCING VALIDATION INCLUDED 33 ME/CFS CASES AND 31 CONTROLS FROM TWO GEOGRAPHICALLY DISTANT COHORTS. RESULTS: GLOBAL DNA METHYLATION LEVELS OF ME/CFS CASES WERE SIMILAR TO THOSE OF CONTROLS. HOWEVER, MICROARRAY-BASED APPROACH ALLOWED DETECTION OF 17,296 DIFFERENTIALLY METHYLATED CPG SITES IN 6,368 GENES ACROSS REGULATORY ELEMENTS AND WITHIN CODING REGIONS OF GENES. ANALYSIS OF DNA METHYLATION IN PROMOTER REGIONS REVEALED 307 DIFFERENTIALLY METHYLATED PROMOTERS. INGENUITY PATHWAY ANALYSIS INDICATED THAT GENES ASSOCIATED WITH DIFFERENTIALLY METHYLATED PROMOTERS PARTICIPATED IN AT LEAST 15 DIFFERENT PATHWAYS MOSTLY RELATED TO CELL SIGNALING WITH A STRONG IMMUNE COMPONENT. CONCLUSIONS: THIS IS THE FIRST STUDY THAT HAS EXPLORED GENOME-WIDE EPIGENETIC CHANGES ASSOCIATED WITH ME/CFS USING THE ADVANCED ILLUMINA METHYLATIONEPIC MICROARRAYS COVERING ABOUT 850,000 CPG SITES IN TWO GEOGRAPHICALLY DISTANT COHORTS OF ME/CFS CASES AND MATCHED CONTROLS. OUR RESULTS ARE ALIGNED WITH PREVIOUS STUDIES THAT INDICATE A DYSREGULATION OF THE IMMUNE SYSTEM IN ME/CFS. THEY ALSO SUGGEST A POTENTIAL ROLE OF EPIGENETIC DE-REGULATION IN THE PATHOBIOLOGY OF ME/CFS. WE PROPOSE SCREENING OF LARGER COHORTS OF ME/CFS CASES TO DETERMINE THE EXTERNAL VALIDITY OF THESE EPIGENETIC CHANGES IN ORDER TO IMPLEMENT THEM AS POSSIBLE DIAGNOSTIC MARKERS IN CLINICAL SETTING.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
7  1620  28 DNA METHYLTRANSFERASE-MEDIATED TRANSCRIPTIONAL SILENCING IN MALIGNANT GLIOMA: A COMBINED WHOLE-GENOME MICROARRAY AND PROMOTER ARRAY ANALYSIS. EPIGENETIC INACTIVATION OF TUMOR SUPPRESSOR GENES IS A COMMON FEATURE IN HUMAN CANCER. PROMOTER HYPERMETHYLATION AND HISTONE DEACETYLATION ARE REVERSIBLE EPIGENETIC MECHANISMS ASSOCIATED WITH TRANSCRIPTIONAL REGULATION. DNA METHYLTRANSFERASES (DNMT1 AND DNMT3B) REGULATE AND MAINTAIN PROMOTER METHYLATION AND ARE OVEREXPRESSED IN HUMAN CANCER. WE PERFORMED WHOLE-GENOME MICROARRAY ANALYSIS TO IDENTIFY GENES WITH ALTERED EXPRESSION AFTER RNAI-INDUCED SUPPRESSION OF DNMT IN A GLIOBLASTOMA MULTIFORME (GBM) CELL LINE. WE THEN IDENTIFIED GENES WITH BOTH DECREASED EXPRESSION AND EVIDENCE OF PROMOTER CPG ISLAND HYPERMETHYLATION IN GBM TISSUE SAMPLES USING A COMBINED WHOLE-GENOME MICROARRAY TRANSCRIPTOME ANALYSIS IN CONJUNCTION WITH A PROMOTER ARRAY ANALYSIS AFTER DNA IMMUNOPRECIPITATION WITH ANTI-5-METHYLCYTIDINE. DNMT1 AND 3B KNOCKDOWN RESULTED IN THE RESTORED EXPRESSION OF 308 GENES THAT ALSO CONTAINED PROMOTER REGION HYPERMETHYLATION. OF THESE, 43 WERE ALSO FOUND TO BE DOWNREGULATED IN GBM TISSUE SAMPLES. THREE DOWNREGULATED GENES WITH HYPERMETHYLATED PROMOTERS AND RESTORED EXPRESSION IN RESPONSE TO ACUTE DNMT SUPPRESSION WERE ASSAYED FOR METHYLATION CHANGES USING BISULFITE SEQUENCE ANALYSIS OF THE PROMOTER REGION AFTER CHRONIC DNMT SUPPRESSION. RESTORATION OF GENE EXPRESSION WAS NOT ASSOCIATED WITH CHANGES IN PROMOTER REGION METHYLATION, BUT RATHER WITH CHANGES IN HISTONE METHYLATION AND CHROMATIN CONFORMATION. TWO OF THE IDENTIFIED GENES EXHIBITED GROWTH SUPPRESSIVE ACTIVITY IN IN VITRO ASSAYS. COMBINING TARGETED GENETIC MANIPULATIONS WITH COMPREHENSIVE GENOMIC AND EXPRESSION ANALYSES PROVIDES A POTENTIALLY POWERFUL NEW APPROACH FOR IDENTIFYING EPIGENETICALLY REGULATED GENES IN GBM.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
8  5120  32 POSSIBLE EPIGENETIC REGULATORY EFFECT OF DYSREGULATED CIRCULAR RNAS IN EPILEPSY. CIRCULAR RNAS (CIRCRNAS) INVOLVE IN THE EPIGENETIC REGULATION AND ITS MAJOR MECHANISM IS THE SEQUESTRATION OF THE TARGET MICRO RNAS (MIRNAS). WE HYPOTHESIZED THAT CIRCRNAS MIGHT BE RELATED WITH THE PATHOPHYSIOLOGY OF CHRONIC EPILEPSY AND EVALUATED THE ALTERED CIRCRNA EXPRESSIONS AND THEIR POSSIBLE REGULATORY EFFECTS ON THEIR TARGET MIRNAS AND MRNAS IN A MOUSE EPILEPSY MODEL. THE CIRCRNA EXPRESSION PROFILE IN THE HIPPOCAMPUS OF THE PILOCARPINE MICE WAS ANALYZED AND COMPARED WITH CONTROL. THE CORRELATION BETWEEN THE EXPRESSION OF MIRNA BINDING SITES (MIRNA RESPONSE ELEMENTS, MRE) IN THE DYSREGULATED CIRCRNAS AND THE EXPRESSION OF THEIR TARGET MIRNAS WAS EVALUATED. AS MIRNAS ALSO INHIBIT THEIR TARGET MRNAS, CIRCRNA-MIRNA-MRNA REGULATORY NETWORK, COMPRISED OF DYSREGULATED RNAS THAT TARGETS ONE ANOTHER WERE SEARCHED. FOR THE IDENTIFIED NETWORKS, BIOINFORMATICS ANALYSES WERE PERFORMED. AS THE RESULT, FORTY-THREE CIRCRNAS WERE DYSREGULATED IN THE HIPPOCAMPUS (UP-REGULATED, 26; DOWN-REGULATED, 17). THE CHANGE IN THE EXPRESSION OF MRE IN THOSE CIRCRNAS NEGATIVELY CORRELATED WITH THE CHANGE IN THE RELEVANT TARGET MIRNA EXPRESSION (R = -0.461, P<0.001), SUPPORTING THAT CIRCRNAS INHIBIT THEIR TARGET MIRNA. 333 DYSREGULATED CIRCRNA-MIRNA-MRNA NETWORKS WERE IDENTIFIED. GENE ONTOLOGY AND PATHWAY ANALYSES DEMONSTRATED THAT THE UP-REGULATED MRNAS IN THOSE NETWORKS WERE CLOSELY RELATED TO THE MAJOR PROCESSES IN EPILEPSY. AMONG THEM, STRING ANALYSIS IDENTIFIED 37 KEY MRNAS WITH ABUNDANT (>/=4) INTERACTIONS WITH OTHER DYSREGULATED TARGET MRNAS. THE DYSREGULATION OF THE CIRCRNAS WHICH HAD MULTIPLE INTERACTIONS WITH KEY MRNAS WERE VALIDATED BY PCR. WE CONCLUDED THAT DYSREGULATED CIRCRNAS MIGHT HAVE A PATHOPHYSIOLOGIC ROLE IN CHRONIC EPILEPSY BY REGULATING MULTIPLE DISEASE RELEVANT MRNAS VIA CIRCRNA-MIRNA-MRNA INTERACTIONS.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
9  6752  36 WIDESPREAD EXONIZATION OF TRANSPOSABLE ELEMENTS IN HUMAN CODING SEQUENCES IS ASSOCIATED WITH EPIGENETIC REGULATION OF TRANSCRIPTION. TRANSPOSABLE ELEMENTS (TES) HAVE LONG BEEN REGARDED AS SELFISH OR JUNK DNA HAVING LITTLE OR NO ROLE IN THE REGULATION OR FUNCTIONING OF THE HUMAN GENOME. HOWEVER, OVER THE PAST SEVERAL YEARS THIS VIEW CAME TO BE CHALLENGED AS SEVERAL STUDIES PROVIDED ANECDOTAL AS WELL AS GLOBAL EVIDENCE FOR THE CONTRIBUTION OF TES TO THE REGULATORY AND CODING NEEDS OF HUMAN GENES. IN THIS STUDY, WE EXPLORED THE INCORPORATION AND EPIGENETIC REGULATION OF CODING SEQUENCES DONATED BY TES USING GENE EXPRESSION AND OTHER ANCILLARY GENOMICS DATA FROM TWO HUMAN HEMATOPOIETIC CELL-LINES: GM12878 (A LYMPHOBLASTOID CELL LINE) AND K562 (A CHRONIC MYELOGENOUS LEUKEMIA CELL LINE). IN EACH CELL LINE, WE FOUND SEVERAL THOUSAND INSTANCES OF TES DONATING CODING SEQUENCES TO HUMAN GENES. WE COMPARED THE TRANSCRIPTOME ASSEMBLY OF THE RNA SEQUENCING (RNA-SEQ) READS WITH AND WITHOUT THE AID OF A REFERENCE TRANSCRIPTOME AND FOUND THAT THE PERCENTAGE OF GENES THAT INCORPORATE TES IN THEIR CODING SEQUENCES IS SIGNIFICANTLY GREATER THAN THAT OBTAINED FROM THE REFERENCE TRANSCRIPTOME ASSEMBLIES USING REFSEQ AND GENCODE GENE MODELS. WE ALSO USED HISTONE MODIFICATIONS CHROMATIN IMMUNOPRECIPITATION SEQUENCING (CHIP-SEQ) DATA, CAP ANALYSIS OF GENE EXPRESSION (CAGE) DATA AND DNASEI HYPERSENSITIVITY SITE (DHS) DATA TO DEMONSTRATE THE EPIGENETIC REGULATION OF THE TE DERIVED CODING SEQUENCES. OUR RESULTS SUGGEST THAT TES FORM A SIGNIFICANTLY HIGHER PERCENTAGE OF CODING SEQUENCES THAN REPRESENTED IN GENE ANNOTATION DATABASES AND THESE TE DERIVED SEQUENCES ARE EPIGENETICALLY REGULATED IN ACCORDANCE WITH THEIR EXPRESSION IN THE TWO CELL TYPES.	2013	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
10  2418  32 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
11   336  31 ALTERATIONS IN DNA METHYLATION STATUS ASSOCIATED WITH GULF WAR ILLNESS. GULF WAR ILLNESS (GWI) AFFECTS ABOUT 25% OF PERSIAN GULF VETERANS WITH A CLUSTER OF CHRONIC SYMPTOMS, INCLUDING IMMUNE DYSFUNCTION AND NEUROLOGICAL ISSUES. RECENT STUDIES IMPLICATE GENE EXPRESSION CHANGES IN IMMUNE FUNCTION TO BE ASSOCIATED WITH GWI. SINCE DNA METHYLATION CAN REGULATE SUCH CHANGES IN GENE EXPRESSION, AND DISRUPTION OF DNA METHYLATION PATTERN IS IMPLICATED IN VARIOUS IMMUNE AND NEUROLOGICAL DISEASES, WE AIMED TO STUDY THE DNA METHYLATION PATTERNS IN PERIPHERAL BLOOD MONONUCLEAR CELLS FROM GWI PATIENTS. GLOBAL DNA METHYLATION LEVELS WERE SIMILAR IN GWI PATIENTS AND CONTROLS. HOWEVER, THE GENOME-WIDE MICROARRAY TECHNOLOGY DETECTED 10,767 DIFFERENTIALLY METHYLATED CPG SITES ACROSS GENE REGULATORY ELEMENTS AND WITHIN CODING REGIONS. APPROXIMATELY 88% OF THEM WERE HYPERMETHYLATED IN GWI PATIENTS. THE SEPARATE ANALYSIS FOUND 776 DIFFERENTIALLY METHYLATED GENE PROMOTERS (DMP), WHICH WERE PREDOMINANTLY HYPERMETHYLATED. PYROSEQUENCING VALIDATION CONFIRMED MICROARRAY RESULTS. FUNCTIONAL ANALYSIS REVEALED THAT MAJORITY OF THE DMPS BELONGED TO GENES RESPONSIBLE FOR METABOLISM AND IMMUNE SYSTEM. THIS IS THE FIRST PILOT HUMAN STUDY CHARACTERIZING GENOME-WIDE EPIGENETIC CHANGES ASSOCIATED WITH GWI. IT SUGGESTS A SIGNIFICANT CONTRIBUTION OF EPIGENETIC DYSFUNCTION IN GWI. MOREOVER, IT SUPPORTS THE DYSREGULATION OF IMMUNE FUNCTION IN GWI. LASTLY, IT SUGGESTS STUDIES WITH THE LARGER COHORT TO VALIDATE OUR FINDINGS.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
12  3410  37 HOXA5 UNDERGOES DYNAMIC DNA METHYLATION AND TRANSCRIPTIONAL REPRESSION IN THE ADIPOSE TISSUE OF MICE EXPOSED TO HIGH-FAT DIET. BACKGROUND/OBJECTIVES: THE GENOMIC BASES OF THE ADIPOSE TISSUE ABNORMALITIES INDUCED BY CHRONIC POSITIVE CALORIE EXCESS HAVE BEEN ONLY PARTIALLY ELUCIDATED. WE ADOPTED A GENOME-WIDE APPROACH TO DIRECTLY TEST WHETHER LONG-TERM HIGH-FAT DIET (HFD) EXPOSURE AFFECTS THE DNA METHYLATION PROFILE OF THE MOUSE ADIPOSE TISSUE AND TO IDENTIFY THE FUNCTIONAL CONSEQUENCES OF THESE CHANGES. SUBJECTS/METHODS: WE HAVE USED EPIDIDYMAL FAT OF MICE FED EITHER HIGH-FAT (HFD) OR REGULAR CHOW (STD) DIET FOR 5 MONTHS AND PERFORMED GENOME-WIDE DNA METHYLATION ANALYSES BY METHYLATED DNA IMMUNOPRECIPITATION SEQUENCING (MEDIP-SEQ). MOUSE HOMEOBOX (HOX) GENE DNA METHYLATION PCR, RT-QPCR AND BISULPHITE SEQUENCING ANALYSES WERE THEN PERFORMED. RESULTS: MICE FED THE HFD PROGRESSIVELY EXPANDED THEIR ADIPOSE MASS ACCOMPANIED BY A SIGNIFICANT DECREASE IN GLUCOSE TOLERANCE (P<0.001) AND INSULIN SENSITIVITY (P<0.05). MEDIP-SEQ DATA ANALYSIS REVEALED A UNIFORM DISTRIBUTION OF DIFFERENTIALLY METHYLATED REGIONS (DMR) THROUGH THE ENTIRE ADIPOCYTE GENOME, WITH A HIGHER NUMBER OF HYPERMETHYLATED REGIONS IN HFD MICE (P<0.005). THIS DIFFERENT METHYLATION PROFILE WAS ACCOMPANIED BY INCREASED EXPRESSION OF THE DNMT3A DNA METHYLTRANSFERASE (DNMT; P<0.05) AND THE METHYL-CPG-BINDING DOMAIN PROTEIN MBD3 (P<0.05) GENES IN HFD MICE. GENE ONTOLOGY ANALYSIS REVEALED THAT, IN THE HFD-TREATED MICE, THE HOX FAMILY OF DEVELOPMENT GENES WAS HIGHLY ENRICHED IN DIFFERENTIALLY METHYLATED GENES (P=0.008). TO VALIDATE THIS FINDING, HOXA5, WHICH IS IMPLICATED IN FAT TISSUE DIFFERENTIATION AND REMODELING, HAS BEEN SELECTED AND ANALYZED BY BISULPHITE SEQUENCING, CONFIRMING HYPERMETHYLATION IN THE ADIPOSE TISSUE FROM THE HFD MICE. HOXA5 HYPERMETHYLATION WAS ASSOCIATED WITH DOWNREGULATION OF HOXA5 MRNA AND PROTEIN EXPRESSION. FEEDING ANIMALS PREVIOUSLY EXPOSED TO THE HFD WITH A STANDARD CHOW DIET FOR TWO FURTHER MONTHS IMPROVED THE METABOLIC PHENOTYPE OF THE ANIMALS, ACCOMPANIED BY RETURN OF HOXA5 METHYLATION AND EXPRESSION LEVELS (P<0.05) TO VALUES SIMILAR TO THOSE OF THE CONTROL MICE MAINTAINED UNDER STANDARD CHOW. CONCLUSIONS: HFD INDUCES ADIPOSE TISSUE ABNORMALITIES ACCOMPANIED BY EPIGENETIC CHANGES AT THE HOXA5 ADIPOSE TISSUE REMODELING GENE.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                         
13   101  27 A RAT METHYL-SEQ PLATFORM TO IDENTIFY EPIGENETIC CHANGES ASSOCIATED WITH STRESS EXPOSURE. AS GENOMES OF A WIDER VARIETY OF ANIMALS BECOME AVAILABLE, THERE IS AN INCREASING NEED FOR TOOLS THAT CAN CAPTURE DYNAMIC EPIGENETIC CHANGES IN THESE ANIMAL MODELS. THE RAT IS ONE PARTICULAR MODEL ANIMAL WHERE AN EPIGENETIC TOOL CAN COMPLEMENT MANY PHARMACOLOGICAL AND BEHAVIORAL STUDIES TO PROVIDE INSIGHTFUL MECHANISTIC INFORMATION. TO THIS END, WE ADAPTED THE SURESELECT TARGET CAPTURE SYSTEM (REFERRED TO AS METHYL-SEQ) FOR THE RAT, WHICH CAN ASSESS DNA METHYLATION LEVELS ACROSS THE RAT GENOME. THE RAT DESIGN TARGETED PROMOTERS, CPG ISLANDS, ISLAND SHORES, AND GC-RICH REGIONS FROM ALL REFSEQ GENES. TO IMPLEMENT THE PLATFORM ON A RAT EXPERIMENT, MALE SPRAGUE DAWLEY RATS WERE EXPOSED TO CHRONIC VARIABLE STRESS FOR 3 WEEKS, AFTER WHICH BLOOD SAMPLES WERE COLLECTED FOR GENOMIC DNA EXTRACTION. METHYL-SEQ LIBRARIES WERE CONSTRUCTED FROM THE RAT DNA SAMPLES BY SHEARING, ADAPTER LIGATION, TARGET ENRICHMENT, BISULFITE CONVERSION, AND MULTIPLEXING. LIBRARIES WERE SEQUENCED ON A NEXT-GENERATION SEQUENCING PLATFORM AND THE SEQUENCED READS WERE ANALYZED TO IDENTIFY DMRS BETWEEN DNA OF STRESSED AND UNSTRESSED RATS. TOP CANDIDATE DMRS WERE INDEPENDENTLY VALIDATED BY BISULFITE PYROSEQUENCING TO CONFIRM THE ROBUSTNESS OF THE PLATFORM. RESULTS DEMONSTRATE THAT THE RAT METHYL-SEQ PLATFORM IS A USEFUL EPIGENETIC TOOL THAT CAN CAPTURE METHYLATION CHANGES INDUCED BY EXPOSURE TO STRESS.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
14   972  37 CHRONIC OBSTRUCTIVE PULMONARY DISEASE IS ASSOCIATED WITH EPIGENOME-WIDE DIFFERENTIAL METHYLATION IN BAL LUNG CELLS. DNA METHYLATION PATTERNS IN CHRONIC PULMONARY OBSTRUCTIVE DISEASE (COPD) MIGHT OFFER NEW INSIGHTS INTO DISEASE PATHOGENESIS. TO ASSESS METHYLATION PROFILES IN THE MAIN COPD TARGET ORGAN, WE PERFORMED AN EPIGENOME-WIDE ASSOCIATION STUDY ON BAL CELLS. BRONCHOSCOPIES WERE PERFORMED IN 18 SUBJECTS WITH COPD AND 15 CONTROL SUBJECTS (EX- AND CURRENT SMOKERS). DNA METHYLATION WAS MEASURED USING THE ILLUMINA METHYLATIONEPIC BEADCHIP KIT, COVERING MORE THAN 850,000 CPGS. DIFFERENTIALLY METHYLATED POSITIONS (DMPS) WERE EXAMINED FOR 1) ENRICHMENT IN PATHWAYS AND FUNCTIONAL GENE RELATIONSHIPS USING THE KYOTO ENCYCLOPEDIA OF GENES AND GENOMES AND GENE ONTOLOGY, 2) ACCELERATED AGING USING HORVATH'S EPIGENETIC CLOCK, 3) CORRELATION WITH GENE EXPRESSION, AND 4) COLOCALIZATION WITH GENETIC VARIATION. WE FOUND 1,155 BONFERRONI-SIGNIFICANT (P < 6.74 X 10(-8)) DMPS ASSOCIATED WITH COPD, MANY WITH LARGE EFFECT SIZES. FUNCTIONAL ANALYSIS IDENTIFIED BIOLOGICALLY PLAUSIBLE PATHWAYS AND GENE RELATIONSHIPS, INCLUDING ENRICHMENT FOR TRANSCRIPTION FACTOR ACTIVITY. STRONG CORRELATION WAS FOUND BETWEEN DNA METHYLATION AND CHRONOLOGICAL AGE BUT NOT BETWEEN COPD AND ACCELERATED AGING. FOR 79 UNIQUE DMPS, DNA METHYLATION CORRELATED SIGNIFICANTLY WITH GENE EXPRESSION IN BAL CELLS. THIRTY-NINE PERCENT OF DMPS WERE COLOCALIZED WITH COPD-ASSOCIATED SNPS. TO THE BEST OF OUR KNOWLEDGE, THIS IS THE FIRST EPIGENOME-WIDE ASSOCIATION STUDY OF COPD ON BAL CELLS, AND OUR ANALYSES REVEALED MANY DIFFERENTIAL METHYLATION SITES. INTEGRATION WITH MRNA DATA SHOWED A STRONG FUNCTIONAL READOUT FOR RELEVANT GENES, IDENTIFYING SITES WHERE DNA METHYLATION MIGHT DIRECTLY AFFECT EXPRESSION. ALMOST HALF OF DMPS WERE COLOCATED WITH SNPS IDENTIFIED IN PREVIOUS GENOME-WIDE ASSOCIATION STUDIES OF COPD, SUGGESTING JOINT GENETIC AND EPIGENETIC PATHWAYS RELATED TO DISEASE.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
15  1577  33 DNA METHYLATION PROFILE IN CHRONIC MYELOMONOCYTIC LEUKEMIA ASSOCIATES WITH DISTINCT CLINICAL, BIOLOGICAL AND GENETIC FEATURES. CHROMOSOMAL ABNORMALITIES ARE DETECTED IN 20-30% OF PATIENTS WITH CHRONIC MYELOMONOCYTIC LEUKEMIA (CMML) AND CORRELATE WITH PROGNOSIS. ON THE MUTATION LEVEL, DISRUPTIVE ALTERATIONS ARE PARTICULARLY FREQUENT IN CHROMATIN REGULATORY GENES. HOWEVER, LITTLE IS KNOWN ABOUT THE CONSEQUENTIAL ALTERATIONS IN THE EPIGENETIC MARKING OF THE GENOME. HERE, WE REPORT THE ANALYSIS OF GENOMIC DNA METHYLATION PATTERNS OF 64 CMML PATIENTS AND 10 HEALTHY CONTROLS, USING A DNA METHYLATION MICROARRAY FOCUSED ON PROMOTER REGIONS. DIFFERENTIAL METHYLATION ANALYSIS BETWEEN PATIENTS AND CONTROLS ALLOWED US TO IDENTIFY ABNORMALITIES IN DNA METHYLATION, INCLUDING HYPERMETHYLATION OF SPECIFIC GENES AND LARGE GENOME REGIONS WITH ABERRANT DNA METHYLATION. UNSUPERVISED HIERARCHICAL CLUSTER ANALYSIS IDENTIFIED TWO MAIN CLUSTERS THAT ASSOCIATED WITH THE CLINICAL, BIOLOGICAL, AND GENETIC FEATURES OF PATIENTS. GROUP 1 WAS ENRICHED IN PATIENTS WITH ADVERSE CLINICAL AND BIOLOGICAL CHARACTERISTICS AND POORER OVERALL AND PROGRESSION-FREE SURVIVAL. IN ADDITION, SIGNIFICANT DIFFERENCES IN DNA METHYLATION WERE OBSERVED BETWEEN PATIENTS WITH LOW RISK AND INTERMEDIATE/HIGH RISK KARYOTYPES AND BETWEEN TET2 MUTANT AND WILD TYPE PATIENTS. TAKEN TOGETHER, OUR RESULTS DEMONSTRATE THAT ALTERED DNA METHYLATION PATTERNS REFLECT THE CMML DISEASE STATE AND ALLOW TO IDENTIFY PATIENT GROUPS WITH DISTINCT CLINICAL FEATURES.	2018	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
16  6418  34 THE TEMPORAL EXPRESSION OF CIRCULATING MICRORNAS AFTER ACUTE EXPERIMENTAL PAIN IN HUMANS. BACKGROUND: MICRORNAS (MIRNAS) CAN MODULATE SEVERAL BIOLOGICAL SYSTEMS, INCLUDING THE PAIN SYSTEM. THIS STUDY AIMED TO EVALUATE THE TEMPORAL EXPRESSION OF CIRCULATING MIRNAS IN THE PLASMA OF HEALTHY VOLUNTEERS AS A MARKER FOR EPIGENETIC CHANGES BEFORE AND AFTER AN ACUTE, EXPERIMENTAL, PAIN PROVOCATION BY INTRAMUSCULAR HYPERTONIC SALINE INJECTION. METHODS: TWENTY VOLUNTEERS WERE RANDOMLY ALLOCATED INTO TWO GROUPS AND RECEIVED EITHER HYPERTONIC (PAIN) OR ISOTONIC (CONTROL) SALINE INJECTION IN THE FIRST DORSAL INTEROSSEOUS MUSCLE OF THEIR DOMINANT HAND. PAIN INTENSITY WAS CONTINUOUSLY RECORDED FOR 20 MINUTES AFTER INJECTION ON A VAS SCALE FROM 0 TO 100 (0 INDICATES NO PAIN AND 100 THE WORST IMAGINABLE PAIN). BLOOD SAMPLES WERE TAKEN AT BASELINE, 30 MINUTES, 3 HOURS, AND 24 HOURS POST-INJECTION, AND PLASMA WAS SEPARATED. MIRNA EXTRACTS WERE USED FOR RNA SEQUENCING WITH THE ILLUMINA NEXTSEQ PLATFORM. MIRNA TRANSCRIPTS WERE COMPARED BETWEEN THE PAIN AND THE NO-PAIN, CONTROL GROUP AT EVERY TIME POINT. SIGNIFICANT DIFFERENCES WERE CONSIDERED WHEN FOLDS WERE >2 AND THE FALSE DISCOVERY RATE WAS P < 0.05. RESULTS: AFTER 30 MINUTES, 4 MIRNAS WERE SIGNIFICANTLY ALTERED IN THE PAIN GROUP COMPARED TO CONTROLS, WHICH INCREASED TO 24 AFTER 3 HOURS AND TO 42 AFTER 24 HOURS FROM BASELINE (P < 0.0001). TWO MIRNAS WERE CONSISTENTLY UPREGULATED THROUGHOUT THE EXPERIMENT. ENRICHMENT ANALYSIS SHOWED SIGNIFICANT MIRNAS INVOLVED IN BRAIN PERCEPTION OF PAIN, BRAIN SIGNALLING AND RESPONSE TO STIMULI. CONCLUSIONS: THIS EXPLORATORY STUDY IS THE FIRST TO REPORT ON THE TEMPORAL EXPRESSION OF CIRCULATING MIRNAS AFTER AN ACUTE, HUMAN EXPERIMENTAL MUSCLE PAIN MODEL. SIGNIFICANCE: THIS EXPLORATORY STUDY EVALUATED THE TEMPORAL PROFILE OF CIRCULATING MIRNAS IN THE PLASMA OF HEALTHY SUBJECTS AFTER ACUTE EXPERIMENTAL PAIN. SEVERAL MIRNAS WERE ALTERED IN SUBJECTS AT THE TIMES OF FOLLOW-UP AFTER THE ACUTE PAIN MODEL WHEN COMPARED TO CONTROLS. MIRNAS PREVIOUSLY ASSOCIATED WITH PAIN PROCESSES WERE ALTERED IN THE PAIN GROUP. OUR RESULTS, BY SHOWING THE FAST AND PROLONGED MODIFICATIONS OF MIRNA ELICITED BY THE ACUTE EXPERIMENTAL PAIN MODEL, ADD NEW PERSPECTIVES TO THE TOPIC OF EPIGENETICS AND PAIN.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
17  1336  31 DESCRIBING A TRANSCRIPTION FACTOR DEPENDENT REGULATION OF THE MICRORNA TRANSCRIPTOME. WHILE THE TRANSCRIPTION REGULATION OF PROTEIN CODING GENES WAS EXTENSIVELY STUDIED, LITTLE IS KNOWN ON HOW TRANSCRIPTION FACTORS ARE INVOLVED IN TRANSCRIPTION OF NON-CODING RNAS, SPECIFICALLY OF MICRORNAS. HERE, WE PROPOSE A STRATEGY TO STUDY THE POTENTIAL ROLE OF TRANSCRIPTION FACTOR IN REGULATING TRANSCRIPTION OF MICRORNAS USING PUBLICALLY AVAILABLE DATA, COMPUTATIONAL RESOURCES AND HIGH THROUGHPUT DATA. WE USE THE H3K4ME3 EPIGENETIC SIGNATURE TO IDENTIFY MICRORNA PROMOTERS AND CHROMATIN IMMUNOPRECIPITATION (CHIP)-SEQUENCING DATA FROM THE ENCODE PROJECT TO IDENTIFY MICRORNA PROMOTERS THAT ARE ENRICHED WITH TRANSCRIPTION FACTOR BINDING SITES. BY TRANSFECTING CELLS OF INTEREST WITH SHRNA TARGETING A TRANSCRIPTION FACTOR OF INTEREST AND SUBJECTING THE CELLS TO MICRORNA ARRAY, WE STUDY THE EFFECT OF THIS TRANSCRIPTION FACTOR ON THE MICRORNA TRANSCRIPTOME. AS AN ILLUSTRATIVE EXAMPLE WE USE OUR STUDY ON THE EFFECT OF STAT3 ON THE MICRORNA TRANSCRIPTOME OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) CELLS.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
18   938  35 CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) RISK IS MEDIATED BY MULTIPLE ENHANCER VARIANTS WITHIN CLL RISK LOCI. CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) IS THE MOST COMMON ADULT LEUKEMIA IN WESTERN COUNTRIES. IT HAS A STRONG GENETIC BASIS, SHOWING A ~ 8-FOLD INCREASED RISK OF CLL IN FIRST-DEGREE RELATIVES. GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE IDENTIFIED 41 RISK VARIANTS ACROSS 41 LOCI. HOWEVER, FOR A MAJORITY OF THE LOCI, THE FUNCTIONAL VARIANTS AND THE MECHANISMS UNDERLYING THEIR CAUSAL ROLES REMAIN UNDEFINED. HERE, WE EXAMINED THE GENETIC AND EPIGENETIC FEATURES ASSOCIATED WITH 12 INDEX VARIANTS, ALONG WITH ANY CORRELATED (R2 >/= 0.5) VARIANTS, AT THE CLL RISK LOCI LOCATED OUTSIDE OF GENE PROMOTERS. BASED ON PUBLICLY AVAILABLE CHIP-SEQ AND CHROMATIN ACCESSIBILITY DATA AS WELL AS OUR OWN CHIP-SEQ DATA FROM CLL PATIENTS, WE IDENTIFIED SIX CANDIDATE FUNCTIONAL VARIANTS AT SIX LOCI AND AT LEAST TWO CANDIDATE FUNCTIONAL VARIANTS AT EACH OF THE REMAINING SIX LOCI. THE FUNCTIONAL VARIANTS ARE PREDOMINANTLY LOCATED WITHIN ENHANCERS OR SUPER-ENHANCERS, INCLUDING BI-DIRECTIONALLY TRANSCRIBED ENHANCERS, WHICH ARE OFTEN RESTRICTED TO IMMUNE CELL TYPES. FURTHERMORE, WE FOUND THAT, AT 78% OF THE FUNCTIONAL VARIANTS, THE ALTERNATIVE ALLELES ALTERED THE TRANSCRIPTION FACTOR BINDING MOTIFS OR HISTONE MODIFICATIONS, INDICATING THE INVOLVEMENT OF THESE VARIANTS IN THE CHANGE OF LOCAL CHROMATIN STATE. FINALLY, THE ENHANCERS CARRYING FUNCTIONAL VARIANTS PHYSICALLY INTERACTED WITH GENES ENRICHED IN THE TYPE I INTERFERON SIGNALING PATHWAY, APOPTOSIS, OR TP53 NETWORK THAT ARE KNOWN TO PLAY KEY ROLES IN CLL. THESE RESULTS SUPPORT THE REGULATORY ROLES FOR INHERITED NONCODING VARIANTS IN THE PATHOGENESIS OF CLL.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
19  5144  33 POTENTIAL ROLE OF LNCRNA-TSIX, MIR-548-A-3P, AND SOGA1 MRNA IN THE DIAGNOSIS OF HEPATOCELLULAR CARCINOMA. RECENT TRENDS ARE MOVING TOWARDS THE USE OF THE CIRCULATING TRANSCRIPTOME AS A POTENTIAL DIAGNOSTIC AND THERAPEUTIC TOOL FOR HEPATOCELLULAR CARCINOMA (HCC). THE AIM OF THIS STUDY IS TO IDENTIFY CIRCULATORY RNA BASED BIOMARKER PANEL, IN ADDITION TO THEIR RELATIONSHIP TO THE OUTCOME IN HCC. FIRST, UTILIZING BIOINFORMATICS TOOLS, WE SELECTED AN HCC-SPECIFIC RNA-BASED BIOMARKER PANEL THAT DEPENDED ON THE INTEGRATION OF SUPPRESSOR OF GLUCOSE AUTOPHAGY-ASSOCIATED (SOGA1) GENE EXPRESSION WITH THE CHOSEN PANEL OF EPIGENETIC REGULATORS OF THIS GENE [LONG NON-CODING RNA ANTISENSE FOR X-INACTIVE-SPECIFIC TRANSCRIPT (LNCRNA-TSIX) AND MICRORNA-548-A-3P (MIR-548-A-3P)]. SECOND, WE ATTEMPTED TO VALIDATE THESE BIOMARKERS USING THE SERA OF 65 PATIENTS WITH HCC, 34 PATIENTS WITH CHRONIC HEPATITIS C VIRUS (CHC) INFECTION AND 32 HEALTHY VOLUNTEERS. FINALLY, THE EXPRESSION LEVELS OF THE CHOSEN RNA-BASED BIOMARKER PANEL WERE ASSESSED IN THE SERUM SAMPLES USING QRT-PCR ASSAYS. THE PANEL OF 3 RNA-BASED BIOMARKERS (LNCRNA-TSIX, MIR-548-A-3P, AND SOGA1) EXHIBITED HIGH SENSITIVITY AND SPECIFICITY IN DIFFERENTIATING HCC PATIENTS FROM CHC PATIENTS AND HEALTHY CONTROLS. AMONG THESE 3 RNAS, SERUM LNCRNA-TSIX AND SOGA1 WERE INDEPENDENT PROGNOSTIC FACTOR. THE CHOSEN CIRCULATORY RNA-BASED BIOMARKER PANEL MAY SERVE AS A DIAGNOSTIC AND PROGNOSTIC BIOMARKER FOR HCC.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
20  3138  44 GLOBAL DNA METHYLATION PROFILING REVEALS NEW INSIGHTS INTO EPIGENETICALLY DEREGULATED PROTEIN CODING AND LONG NONCODING RNAS IN CLL. BACKGROUND: METHYL-CPG-BINDING DOMAIN PROTEIN ENRICHED GENOME-WIDE SEQUENCING (MBD-SEQ) IS A ROBUST AND POWERFUL METHOD FOR ANALYZING METHYLATED CPG-RICH REGIONS WITH COMPLETE GENOME-WIDE COVERAGE. IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), THE ROLE OF CPG METHYLATED REGIONS ASSOCIATED WITH TRANSCRIBED LONG NONCODING RNAS (LNCRNA) AND REPETITIVE GENOMIC ELEMENTS ARE POORLY UNDERSTOOD. BASED ON MBD-SEQ, WE CHARACTERIZED THE GLOBAL METHYLATION PROFILE OF HIGH CPG-RICH REGIONS IN DIFFERENT CLL PROGNOSTIC SUBGROUPS BASED ON IGHV MUTATIONAL STATUS. RESULTS: OUR STUDY IDENTIFIED 5800 HYPERMETHYLATED AND 12,570 HYPOMETHYLATED CLL-SPECIFIC DIFFERENTIALLY METHYLATED GENES (CLLDMGS) COMPARED TO NORMAL CONTROLS. FROM CLLDMGS, 40 % OF HYPERMETHYLATED AND 60 % OF HYPOMETHYLATED GENES WERE MAPPED TO NONCODING RNAS. IN ADDITION, WE FOUND THAT THE MAJOR REPETITIVE ELEMENTS SUCH AS SHORT INTERSPERSED ELEMENTS (SINE) AND LONG INTERSPERSED ELEMENTS (LINE) HAVE A HIGH PERCENTAGE OF CLLDMRS (DIFFERENTIALLY METHYLATED REGIONS) IN IGHV SUBGROUPS COMPARED TO NORMAL CONTROLS. FINALLY, TWO NOVEL LNCRNAS (HYPERMETHYLATED CRNDE AND HYPOMETHYLATED AC012065.7) WERE VALIDATED IN AN INDEPENDENT CLL SAMPLE COHORT (48 SAMPLES) COMPARED WITH 6 NORMAL SORTED B CELL SAMPLES USING QUANTITATIVE PYROSEQUENCING ANALYSIS. THE METHYLATION LEVELS SHOWED AN INVERSE CORRELATION TO GENE EXPRESSION LEVELS ANALYZED BY REAL-TIME QUANTITATIVE PCR. NOTABLY, SURVIVAL ANALYSIS REVEALED THAT HYPERMETHYLATION OF CRNDE AND HYPOMETHYLATION OF AC012065.7 CORRELATED WITH AN INFERIOR OUTCOME. CONCLUSIONS: THUS, OUR COMPREHENSIVE METHYLATION ANALYSIS BY MBD-SEQ PROVIDED NOVEL HYPER AND HYPOMETHYLATED LONG NONCODING RNAS, REPETITIVE ELEMENTS, ALONG WITH PROTEIN CODING GENES AS POTENTIAL EPIGENETIC-BASED CLL-SIGNATURE GENES INVOLVED IN DISEASE PATHOGENESIS AND PROGNOSIS.	2016