1 5723 113 SJOGREN'S SYNDROME X-CHROMOSOME DOSE EFFECT: AN EPIGENETIC PERSPECTIVE. SJOGREN'S SYNDROME (SS) IS A CHRONIC AUTOIMMUNE DISEASE AFFECTING EXOCRINE GLANDS LEADING TO MOUTH AND EYES DRYNESS. THE EXTENT TO WHICH EPIGENETIC DNA METHYLATION CHANGES ARE RESPONSIBLE FOR AN X-CHROMOSOME DOSE EFFECT HAS YET TO BE DETERMINED. OUR OBJECTIVES WERE TO (I) DESCRIBE HOW EPIGENETIC DNA METHYLATION CHANGES COULD EXPLAIN AN X-CHROMOSOME DOSE EFFECT IN SS FOR WOMEN WITH NORMAL 46,XX GENOTYPE AND (II) DETERMINE THE RELEVANT RELATIONSHIPS TO THIS DOSE EFFECT, BETWEEN X-LINKED GENES, GENES CONTROLLING X-CHROMOSOME INACTIVATION (XCI) AND GENES ENCODING ASSOCIATED TRANSCRIPTION FACTORS, ALL OF WHICH ARE DIFFERENTIALLY EXPRESSED AND/OR DIFFERENTIALLY METHYLATED IN THE SALIVARY GLANDS OF PATIENTS WITH SS. WE IDENTIFIED 58 UPREGULATED X-CHROMOSOME GENES, INCLUDING 22 GENES PREVIOUSLY SHOWN TO ESCAPE XCI, BASED ON THE ANALYSIS OF SS PATIENT SALIVARY GLAND GEO2R GENE EXPRESSION DATASETS. MOREOVER, WE FOUND XIST AND ITS CIS REGULATORS RLIM, FTX, AND CHIC1, AND POLYCOMB REPRESSOR GENES OF THE PRC1/2 COMPLEXES TO BE UPREGULATED. MANY OF THE X-CHROMOSOME GENES IMPLICATED IN SS PATHOGENESIS CAN BE REGULATED BY TRANSCRIPTION FACTORS WHICH WE FOUND TO BE OVEREXPRESSED AND/OR DIFFERENTIALLY METHYLATED IN PATIENTS WITH SS. DETERMINATION OF THE MECHANISMS UNDERLYING METHYLATION-DEPENDENT GENE EXPRESSION AND IMPAIRED XCI IS NEEDED TO FURTHER ELUCIDATE THE ETIOPATHOGENESIS OF SS. 2019 2 3959 35 LONG NON-CODING RNAS TARGET PATHOGENETICALLY RELEVANT GENES AND PATHWAYS IN RHEUMATOID ARTHRITIS. RHEUMATOID ARTHRITIS (RA) IS A CHRONIC INFLAMMATORY AUTOIMMUNE DISEASE DRIVEN BY GENETIC, ENVIRONMENTAL AND EPIGENETIC FACTORS. LONG NON-CODING RNAS (LNCRNAS) ARE A KEY COMPONENT OF THE EPIGENETIC MECHANISMS AND ARE KNOWN TO BE INVOLVED IN THE DEVELOPMENT OF AUTOIMMUNE DISEASES. IN THIS WORK WE AIMED TO IDENTIFY SIGNIFICANTLY DIFFERENTIALLY EXPRESSED LNCRNAS (DE-LNCRNAS) THAT ARE FUNCTIONALLY CONNECTED TO MODULATED GENES STRICTLY ASSOCIATED WITH RA. IN TOTAL, 542,500 TRANSCRIPTS HAVE BEEN PROFILED IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) FROM FOUR PATIENTS WITH EARLY ONSET RA PRIOR ANY TREATMENT AND FOUR HEALTHY DONORS USING CLARIOM D ARRAYS. RESULTS WERE CONFIRMED BY REAL-TIME PCR IN 20 PATIENTS AND 20 CONTROLS. SIX DE-LNCRNAS TARGET EXPERIMENTALLY VALIDATED MIRNAS ABLE TO REGULATE DIFFERENTIALLY EXPRESSED GENES (DEGS) IN RA; AMONG THEM, ONLY FTX, HNRNPU-AS1 AND RP11-498C9.15 TARGETED A LARGE NUMBER OF DEGS. MOST IMPORTANTLY, RP11-498C9.15 TARGETED THE LARGEST NUMBER OF SIGNALLING PATHWAYS THAT WERE FOUND TO BE ENRICHED BY THE GLOBAL AMOUNT OF RA-DEGS AND THAT HAVE ALREADY BEEN ASSOCIATED WITH RA AND RA-SYNOVIOCYTES. MOREOVER, RP11-498C9.15 TARGETED THE MOST HIGHLY CONNECTED GENES IN THE RA INTERACTOME, THUS SUGGESTING ITS INVOLVEMENT IN CRUCIAL GENE REGULATION. THESE RESULTS INDICATE THAT, BY MODULATING BOTH MICRORNAS AND GENE EXPRESSION, RP11-498C9.15 MAY PLAY A PIVOTAL ROLE IN RA PATHOGENESIS. 2019 3 4573 21 MYOCARDIAL INFARCTION-ASSOCIATED TRANSCRIPT, A LONG NONCODING RNA, IS OVEREXPRESSED DURING DILATED CARDIOMYOPATHY DUE TO CHRONIC CHAGAS DISEASE. LONG NONCODING RNAS (LNCRNAS) MODULATE GENE EXPRESSION AT THE EPIGENETIC, TRANSCRIPTIONAL, AND POSTTRANSCRIPTIONAL LEVELS. DYSREGULATION OF THE LNCRNA KNOWN AS MYOCARDIAL INFARCTION-ASSOCIATED TRANSCRIPT (MIAT) HAS BEEN ASSOCIATED WITH MYOCARDIAL INFARCTION. CHAGAS DISEASE CAUSES A SEVERE INFLAMMATORY DILATED CHRONIC CARDIOMYOPATHY (CCC). WE INVESTIGATED THE ROLE OF MIAT IN CCC. A WHOLE-TRANSCRIPTOME ANALYSIS OF HEART BIOPSY SPECIMENS AND FORMALIN-FIXED, PARAFFIN-EMBEDDED SAMPLES REVEALED THAT MIAT WAS OVEREXPRESSED IN PATIENTS WITH CCC, COMPARED WITH SUBJECTS WITH NONINFLAMMATORY DILATED CARDIOMYOPATHY AND CONTROLS. THESE RESULTS WERE CONFIRMED IN A MOUSE MODEL. RESULTS SUGGEST THAT MIAT IS A SPECIFIC BIOMARKER OF CCC. 2016 4 4868 35 OSTEOARTHRITIS RELATED EPIGENETIC VARIATIONS IN MIRNA EXPRESSION AND DNA METHYLATION. OSTEOARTHRITIS (OA) IS CHRONIC ARTHRITIS CHARACTERIZED BY ARTICULAR CARTILAGE DEGRADATION. HOWEVER, A COMPREHENSIVE REGULATORY NETWORK FOR OA-RELATED MICRORNAS AND DNA METHYLATION MODIFICATIONS HAS YET TO BE ESTABLISHED. THUS, WE AIMED TO IDENTIFY EPIGENETIC CHANGES IN MICRORNAS AND DNA METHYLATION AND ESTABLISH THE REGULATORY NETWORK BETWEEN MIRNAS AND DNA METHYLATION. THE MRNA, MIRNA, AND DNA METHYLATION EXPRESSION PROFILES OF HEALTHY OR OSTEOARTHRITIS ARTICULAR CARTILAGE SAMPLES WERE DOWNLOADED FROM GENE EXPRESSION OMNIBUS (GEO) DATABASE, INCLUDING GSE169077, GSE175961, AND GSE162484. THE DIFFERENTIALLY EXPRESSED GENES (DEGS), DIFFERENTIALLY EXPRESSED MIRNAS (DEMS), AND DIFFERENTIALLY METHYLATED GENES (DMGS) WERE ANALYZED BY THE ONLINE TOOL GEO2R. DAVID AND STRING DATABASES WERE APPLIED FOR FUNCTIONAL ENRICHMENT ANALYSIS AND PROTEIN-PROTEIN INTERACTION (PPI) NETWORK. POTENTIAL THERAPEUTIC COMPOUNDS FOR THE TREATMENT OF OA WERE IDENTIFIED BY CONNECTIVITY MAP (CMAP) ANALYSIS. A TOTAL OF 1424 UP-REGULATED DEGS, 1558 DOWN-REGULATED DEGS, 5 DEMS WITH HIGH EXPRESSION, 6 DEMS WITH LOW EXPRESSION, 1436 HYPERMETHYLATED GENES, AND 455 HYPOMETHYLATED GENES WERE SELECTED. A TOTAL OF 136 UP-REGULATED AND 65 DOWNREGULATED GENES WERE IDENTIFIED BY OVERLAPPING DEGS AND DEMS PREDICTED TARGET GENES WHICH WERE ENRICHED IN APOPTOSIS AND CIRCADIAN RHYTHM. A TOTAL OF 39 HYPOMETHYLATED AND 117 HYPERMETHYLATED GENES WERE OBTAINED BY OVERLAPPING DEGS AND DMGS, WHICH WERE ASSOCIATED WITH ECM RECEPTOR INTERACTIONS AND CELLULAR METABOLIC PROCESSES, CELL CONNECTIVITY, AND TRANSCRIPTION. MOREOVER, THE PPI NETWORK SHOWED COL5A1, COL6A1, LAMA4, T3GAL6A, AND TP53 WERE THE MOST CONNECTIVE PROTEINS. AFTER OVERLAPPING OF DEGS, DMGS AND DEMS PREDICTED TARGETED GENES, 4 UP-REGULATED GENES AND 11 DOWN-REGULATED GENES WERE ENRICHED IN THE AXON GUIDANCE PATHWAY. THE TOP TEN GENES RANKED BY PPI NETWORK CONNECTIVITY DEGREE IN THE UP-REGULATED AND DOWNREGULATED OVERLAPPING GENES OF DEGS AND DMGS WERE FURTHER ANALYZED BY THE CMAP DATABASE, AND NINE CHEMICALS WERE PREDICTED AS POTENTIAL DRUGS FOR THE TREATMENT OF OA. IN CONCLUSION, TP53, COL5A1, COL6A1, LAMA4, AND ST3GAL6 MAY PLAY IMPORTANT ROLES IN OA GENESIS AND DEVELOPMENT. 2023 5 3752 29 INTEGRATED ANALYSIS OF CIRCRNAS AND MRNAS EXPRESSION PROFILE REVEALED THE INVOLVEMENT OF HSA_CIRC_0007919 IN THE PATHOGENESIS OF ULCERATIVE COLITIS. BACKGROUND: ULCERATIVE COLITIS (UC) IS CHARACTERIZED BY CHRONIC INFLAMMATION IN THE COLON AND EPIGENETIC FACTORS UNDERLYING THE OCCURRENCE. CIRCULAR RNAS (CIRCRNAS) HAVE BEEN UNDER INTENSIVE FOCUS DUE TO THE CIRCULAR CONSTRUCT AND GENE-REGULATING FUNCTIONS. HOWEVER, THE CHANGES AND ROLES OF CIRCRNAS IN UC REMAIN UNKNOWN. METHODS: MICROARRAYS WERE USED TO DETECT THE DIFFERENTIALLY EXPRESSED GENES, AND QUANTITATIVE REAL-TIME PCR WAS USED TO IDENTIFY THE CHANGES IN UC. IN SILICO ANALYSES WERE PERFORMED TO PREDICT THE FUNCTIONS OF CIRCRNAS AND MRNAS. IN VITRO, EPITHELIAL CELL LINES WERE STIMULATED BY PRO-INFLAMMATION EFFECTORS TO TEST THE ALTERATIONS IN CIRCRNAS. CIRCRNAS-MICRORNAS-MRNAS NETWORK CLARIFIED THE POTENTIAL MECHANISMS UNDERLYING CIRCRNAS IN UC. THE BINDING SITE BETWEEN HSA_CIRC_0007919 AND MIR-138 OR LET-7A WAS VERIFIED USING DUAL-LUCIFERASE ASSAY. RESULTS: A TOTAL OF 264 SIGNIFICANTLY DYSREGULATED CIRCRNAS AND 1869 DIFFERENTIALLY EXPRESSED MRNAS IN INFLAMED MUCOSA WERE COMPARED WITH THE NON-INFLAMED MUCOSA IN UC. HSA_CIRC_0004662 AND HSA_CIRC_0007919 WERE ALTERED LARGELY IN UC TISSUES. HSA_CIRC_0007919 WAS REDUCED PERSISTENTLY AFTER INFLAMMATORY TREATMENTS, AND IT WAS RELEVANT TO MAYO ENDOSCOPIC SUBSCORES AND THE EXPRESSION OF TIGHT JUNCTION MOLECULES. FINALLY, HSA_CIRC_0007919 COULD HARBOR MIR-138, AND LET-7A TO REGULATE THE TARGETED MRNAS EPC1 AND VIPR1. CONCLUSIONS: SEVERAL CIRCRNAS WERE DIFFERENTIALLY EXPRESSED IN UC. HSA_CIRC_0007919 IS RELATED TO CLINICAL CHARACTERISTICS AND EPITHELIAL INTEGRITY BY BINDING TO HSA-LET-7A, HSA-MIR-138 TO REGULATE THE TARGET GENES. CIRCRNAS, ESPECIALLY HSA_CIRC_0007919, ARE ASSOCIATED WITH THE PATHOGENESIS AND DEVELOPMENT OF UC, WITH POTENTIAL DIAGNOSTIC AND THERAPEUTIC IMPLICATIONS. 2019 6 1227 35 CRITICAL ROLE OF MICRORNAS IN CHRONIC LYMPHOCYTIC LEUKEMIA: OVEREXPRESSION OF THE ONCOGENE PLAG1 BY DEREGULATED MIRNAS. MICRORNAS (MIRNAS) ARE SMALL, GENE ENCODED RNAS WHICH ARE ABLE TO INFLUENCE GENE EXPRESSION IN BINDING TO THE 3'UTR OF MRNAS. COMPARED TO HEALTHY TISSUES, THE GLOBAL EXPRESSION OF MIRNAS IN CANCEROUS TISSUE IS FREQUENTLY DOWN-REGULATED. LIKEWISE IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), DOWN-REGULATION OF SEVERAL MIRNAS HAS BEEN REPORTED. ANALYSIS OF MIRNA PROMOTERS FOR EPIGENETIC MODIFICATIONS REVEALED A STRONGER METHYLATION OF DOWN-REGULATED MIRNAS IN CLL. TO DATE, SEVERAL TARGET GENES AFFECTED BY DEREGULATED MIRNAS HAVE BEEN IDENTIFIED THAT HAVE IMPACT ON CLL PATHOGENESIS. THE BEST-DESCRIBED CONSEQUENCE OF MIRNA DEREGULATION IS FOR MIRNA-15/16 CLUSTER DELETION, WHICH IS FREQUENTLY DOWN-REGULATED IN A SUBGROUP OF PATIENTS WITH CLL CARRYING 13Q14 DELETION. SO FAR, MODELS FOR MIRNA DEREGULATION HAVE ADDRESSED JUST SINGLE MIRNAS. FOR ASSESSMENT OF COMPLETE MIRNA DEREGULATION, FURTHER EVALUATION OF THE RESULTS FROM MICROARRAY STUDIES IS NEEDED. PREVIOUSLY WE IDENTIFIED THE ONCOGENE PLAG1, WHOSE EXPRESSION IS AFFECTED BY VARIOUS MIRNAS DEREGULATED IN CLL. THE INVOLVEMENT OF MIRNAS IN PLAG1 EXPRESSION WAS SHOWN TO BE RELEVANT IN PLEOMORPHIC ADENOMAS OF THE SALIVARY GLAND, TOO. AS PLAG1 IS HIGHLY OVEREXPRESSED, AND ITS TARGET GENES APPEAR TO BE DEREGULATED IN CLL, E.G. BCL-2, PLAG1 IS A PUTATIVE NEW RELEVANT ONCOGENE INVOLVED IN THE PATHOGENESIS OF CLL. 2010 7 6657 27 UPREGULATED KAT7 IN SYNOVIAL FIBROBLASTS PROMOTES TH17 CELL DIFFERENTIATION AND INFILTRATION IN RHEUMATOID ARTHRITIS. RHEUMATOID ARTHRITIS (RA) IS A CHRONIC AUTOIMMUNE DISEASE INVOLVING MULTIPLE CELLULAR PARTICIPANTS, OF WHICH SYNOVIAL FIBROBLASTS (SFS) ARE TIGHTLY CONNECTED WITH THE DEVELOPMENT AND PROGRESSION OF RA. HERE, WE PROVIDE EVIDENCE CONFIRMING THAT KAT7, AN H4-SPECIFIC HISTONE ACETYLASE, IS UPREGULATED IN SFS OF RA PATIENTS, WHICH IS AT LEAST ATTRIBUTED TO THE STIMULATION BY RA-ASSOCIATED PROINFLAMMATORY CYTOKINES, SUCH AS TNF-ALPHA, IL-1BETA OR IFN-GAMMA. IN ADDITION, KAT7 OVEREXPRESSION IN CULTURED HUMAN FIBROBLAST-LIKE SYNOVIOCYTES (HFLSS) INDUCES IL-6 AND TGF-BETA EXPRESSION THROUGH AN EPIGENETIC MECHANISM, AND IN VITRO T HELPER 17 (TH17) CELL POLARIZATION CULTURED IN THESE SUPERNATANTS SHOWS PROMOTED CELL DIFFERENTIATION. MOREOVER, KAT7 OVEREXPRESSION IN HFLSS INDUCES CCL20 EXPRESSION VIA P44/42 MAPK PATHWAY, WHEREBY PROMOTING TH17 CELL MIGRATION. THESE TWO ACTIVITIES OF KAT7 IN RA SFS INDICATE ITS POTENTIAL ROLES IN ACCELERATING RA PATHOLOGY. OVERALL, THESE RESULTS DEMONSTRATE SOME CONNECTIONS BETWEEN KAT7 UPREGULATED IN RA SFS AND RA PROGRESSION AND PRESENT THE INHIBITION OF KAT7 ACTIVITY AS A NOVEL THERAPEUTIC TARGET FOR INTERFERING RA DISEASE. 2017 8 1989 30 EPIGENETIC ANALYSIS IN RHEUMATOID ARTHRITIS SYNOVIOCYTES. RHEUMATOID ARTHRITIS (RA) IS A COMPLEX CHRONIC SYSTEMATIC DISEASE WITH PROGRESSIVE DESTRUCTION OF THE JOINTS BY INVASIVE SYNOVIOCYTES. TO CHARACTERIZE THE KEY REGULATORS INVOLVED IN THE DEVELOPMENT OF RA, WE OBTAINED MULTILAYER EPIGENOMICS DATA INCLUDING DNA METHYLATION BY WHOLE-GENOME BISULFITE SEQUENCING, MIRNA PROFILES, GENETIC VARIATIONS BY WHOLE-EXOME SEQUENCING, AND MRNA PROFILES FROM SYNOVIOCYTES OF RA AND OSTEOARTHRITIS (OA) PATIENTS. THE OVERALL DNA METHYLATION PATTERNS WERE NOT MUCH DIFFERENT BETWEEN RA AND OA, BUT 523 LOW-METHYLATED REGIONS (LMRS) WERE SPECIFIC TO RA. THE LMRS WERE PREFERENTIALLY LOCALIZED AT THE 5' INTRONS AND OVERLAPPED WITH TRANSCRIPTION FACTOR BINDING MOTIFS FOR GLI1, RUNX2, AND TFAP2A/C. SINGLE BASE-SCALE DIFFERENTIALLY METHYLATED CPGS WERE LINKED WITH SEVERAL NETWORKS RELATED TO WOUND RESPONSE, TISSUE DEVELOPMENT, COLLAGEN FIBRIL ORGANIZATION, AND THE TGF-BETA RECEPTOR SIGNALING PATHWAY. FURTHER, THE DNA METHYLATION OF 201 CPGS WAS SIGNIFICANTLY CORRELATED WITH 27 EXPRESSED MIRNA GENES. OUR INTERPRETATION OF EPIGENOMIC DATA OF THE SYNOVIOCYTES FROM RA AND OA PATIENTS IS AN INFORMATIVE RESOURCE TO FURTHER INVESTIGATE REGULATORY ELEMENTS AND BIOMARKERS RESPONSIBLE FOR THE PATHOPHYSIOLOGY OF RA AND OA. 2019 9 4305 21 MICRORNA-27A-3P ENHANCES THE INFLAMMATORY PHENOTYPE OF JUVENILE IDIOPATHIC ARTHRITIS FIBROBLAST-LIKE SYNOVIOCYTES. BACKGROUND: JUVENILE IDIOPATHIC ARTHRITIS (JIA) IS THE MOST PREVALENT CHRONIC PEDIATRIC RHEUMATIC DISORDER. IN JOINTS OF JIA PATIENTS, AGGRESSIVE PHENOTYPIC CHANGES IN FIBROBLAST-LIKE SYNOVIOCYTES (FLS) OF THE SYNOVIAL LINING PLAY A KEY ROLE IN INFLAMMATION. MICRORNAS ARE DYSREGULATED IN RHEUMATOID ARTHRITIS AND JIA, INCLUDING MIR-27A-3P. HOWEVER, IT IS NOT UNDERSTOOD IF MIR-27A-3P, ENRICHED IN JIA SYNOVIAL FLUID (SF) AND LEUKOCYTES, ALTERS FLS FUNCTION. METHODS: PRIMARY JIA FLS CELLS WERE TRANSFECTED WITH A MIR-27A-3P MIMIC OR A NEGATIVE CONTROL MICRORNA (MIR-NC) AND STIMULATED WITH POOLED JIA SF OR INFLAMMATORY CYTOKINES. VIABILITY AND APOPTOSIS WERE ANALYZED BY FLOW CYTOMETRY. PROLIFERATION WAS EVALUATED USING A (3)H-THYMIDINE INCORPORATION ASSAY. CYTOKINE PRODUCTION WAS ASSESSED BY QPCR AND ELISA. EXPRESSION OF TGF-BETA PATHWAY GENES WAS DETERMINED USING A QPCR ARRAY. RESULTS: MIR-27A-3P WAS CONSTITUTIVELY EXPRESSED IN FLS. OVEREXPRESSION OF MIR-27A-3P CAUSED INCREASED INTERLEUKIN-8 SECRETION IN RESTING FLS, AND INTERLEUKIN-6 WAS ELEVATED IN SF-ACTIVATED FLS COMPARED TO MIR-NC. FURTHERMORE, STIMULATION WITH PRO-INFLAMMATORY CYTOKINES AUGMENTED FLS PROLIFERATION IN MIR-27A-3P-TRANSFECTED FLS RELATIVE TO MIR-NC. EXPRESSION OF MULTIPLE TGF-BETA PATHWAY GENES WAS MODULATED BY OVEREXPRESSION OF MIR-27A-3P. CONCLUSIONS: MIR-27A-3P SIGNIFICANTLY CONTRIBUTES TO FLS PROLIFERATION AND CYTOKINE PRODUCTION, MAKING IT A POTENTIAL CANDIDATE FOR EPIGENETIC THERAPY THAT TARGETS FLS IN ARTHRITIS. 2023 10 2684 28 EVALUATION OF X CHROMOSOME INACTIVATION WITH RESPECT TO HLA GENETIC SUSCEPTIBILITY IN RHEUMATOID ARTHRITIS AND SYSTEMIC SCLEROSIS. BACKGROUND: AUTOIMMUNE DISEASES, INCLUDING RHEUMATOID ARTHRITIS (RA) AND SYSTEMIC SCLEROSIS (SSC) ARE CHARACTERIZED BY A STRONG GENETIC SUSCEPTIBILITY FROM THE HUMAN LEUCOCYTE ANTIGEN (HLA) LOCUS. ADDITIONALLY, DISORDERS OF EPIGENETIC PROCESSES, IN PARTICULAR NON-RANDOM X CHROMOSOME INACTIVATION (XCI), HAVE BEEN REPORTED IN MANY FEMALE-PREDOMINANT AUTOIMMUNE DISEASES. HERE WE TEST THE HYPOTHESIS THAT WOMEN WITH RA OR SSC WHO ARE STRONGLY GENETICALLY PREDISPOSED ARE LESS SUSCEPTIBLE TO XCI BIAS. METHODS: USING METHYLATION SENSITIVE GENOTYPING OF THE ANDROGEN RECEPTOR (AR) GENE, XCI PROFILES WERE PERFORMED IN PERIPHERAL BLOOD MONONUCLEAR CELLS FROM 161 WOMEN WITH RA, 96 WOMEN WITH SSC AND 100 HEALTHY WOMEN. HLA-DRB1 AND DQB1 WERE GENOTYPED. PRESENCE OF SPECIFIC AUTOANTIBODIES WAS DOCUMENTED FOR PATIENTS. XCI SKEWING WAS DEFINED AS HAVING A RATIO >/= 80:20 OF CELLS INACTIVATING THE SAME X CHROMOSOME. RESULTS: 110 WOMEN WITH RA, 68 WOMEN WITH SSC, AND 69 CONTROLS WERE INFORMATIVE FOR THE AR POLYMORPHISM. AMONG THEM 40.9% OF RA PATIENTS AND 36.8% OF SSC PATIENTS HAD SKEWED XCI COMPARED TO 17.4% OF HEALTHY WOMEN (P = 0.002 AND 0.018, RESPECTIVELY). PRESENCE OF RA-SUSCEPTIBILITY ALLELES CODING FOR THE "SHARED EPITOPE" CORRELATED WITH HIGHER SKEWING AMONG RA PATIENTS (P = 0.002) AND SUCH CORRELATION WAS NOT OBSERVED IN OTHER WOMEN, HEALTHY OR WITH SSC. PRESENCE OF SSC-SUSCEPTIBILITY ALLELES DID NOT CORRELATE WITH XCI PATTERNS AMONG SSC PATIENTS. CONCLUSION: DATA DEMONSTRATE XCI SKEWING IN BOTH RA AND SSC COMPARED TO HEALTHY WOMEN. UNEXPECTEDLY, SKEWED XCI OCCURS MORE OFTEN IN WOMEN WITH RA CARRYING THE SHARED EPITOPE, WHICH USUALLY REFLECTS SEVERE DISEASE. THIS REINFORCES THE VIEW THAT LOSS OF MOSAICISM IN PERIPHERAL BLOOD MAY BE A CONSEQUENCE OF CHRONIC AUTOIMMUNITY. 2016 11 408 33 ANALYSIS OF GENE EXPRESSION AND METHYLATION DATASETS IDENTIFIED ADAMTS9, FKBP5, AND PFKBF3 AS BIOMARKERS FOR OSTEOARTHRITIS. BACKGROUND: OSTEOARTHRITIS (OA) IS A KIND OF CHRONIC OSTEOARTHROPATHY AND DEGENERATIVE JOINT DISEASE. EPIGENETIC REGULATION IN THE GENE EXPRESSION DYNAMICS HAS BECOME INCREASINGLY IMPORTANT IN OA. WE PERFORMED A COMBINED ANALYSIS OF TWO TYPES OF MICROARRAY DATASETS (GENE EXPRESSION AND DNA METHYLATION) TO IDENTIFY METHYLATION-BASED KEY BIOMARKERS TO PROVIDE A BETTER UNDERSTANDING OF MOLECULAR BIOLOGICAL MECHANISMS OF OA. METHODS: WE OBTAINED TWO EXPRESSION PROFILING DATASETS (GSE55235, GSE55457) AND ONE DNA METHYLATION PROFILING DATA SET (GSE63695) FROM THE GENE EXPRESSION OMNIBUS. FIRST, DIFFERENTIALLY EXPRESSED GENES (DEGS) BETWEEN PATIENTS WITH OA AND CONTROLS WERE IDENTIFIED USING THE LIMMA PACKAGE IN R(V3.4.4). THEN, FUNCTION ENRICHMENT ANALYSIS OF DEGS WAS PERFORMED USING A DAVID DATABASE. FOR DNA METHYLATION DATASETS, CHAMP METHYLATION ANALYSIS PACKAGE WAS USED TO IDENTIFY DIFFERENTIAL METHYLATION GENES (DMGS). FINALLY, A COMPREHENSIVE ANALYSIS OF DEGS AND DMGS WAS CONDUCTED TO IDENTIFY GENES THAT EXHIBITED DIFFERENTIAL EXPRESSION AND METHYLATION SIMULTANEOUSLY. RESULTS: WE IDENTIFIED 112 DEGS AND 2,896 DMGS IN PATIENTS WITH OA COMPARED WITH CONTROLS. FUNCTIONAL ANALYSIS OF DEGS OBTAINED THAT INFLAMMATORY RESPONSES, IMMUNE RESPONSES, AND POSITIVE REGULATION OF APOPTOSIS, TUMOR NECROSIS FACTOR (TNF) SIGNALING PATHWAY, AND OSTEOCLAST DIFFERENTIATION MAY BE INVOLVED IN THE PATHOGENESIS OF OA. CROSS-ANALYSIS REVEALED 26 GENES THAT EXHIBITED DIFFERENTIAL EXPRESSION AND METHYLATION IN OA. AMONG THEM, ADAMTS9, FKBP5, AND PFKBF3 WERE IDENTIFIED AS VALUABLE METHYLATION-BASED BIOMARKERS FOR OA. CONCLUSION: IN SUMMARY, OUR STUDY IDENTIFIED DIFFERENT MOLECULAR FEATURES BETWEEN PATIENTS WITH OA AND CONTROLS. THIS MAY PROVIDE NEW CLUES FOR CLARIFYING THE PATHOGENETIC MECHANISMS OF OA. 2019 12 3947 28 LNCRNA UCA1 INDUCES AUTOPHAGIC GENE EXPRESSION VIA EPIGENETIC REGULATION MEDIATED BY ATG16L1 AND MIR-132-3P IN SH-SY5Y CELLS TREATED WITH RETINOIC ACID. OBJECTIVE: EPILEPSY IS A CHRONIC BRAIN DISEASE WITH RECURRENT SEIZURES. AUTOPHAGY PLAYS A CRUCIAL ROLE IN THE PROGRESSION OF EPILEPSY. THIS STUDY AIMED TO EXPLORE THE FUNCTION AND INTRINSIC MECHANISM OF THE LONG NON-CODING RNA (LNCRNA) UCA1/MIR-132-3P/ATG16L1 AXIS IN EPILEPSY VIA REGULATION OF AUTOPHAGY. METHODS: THE EXPRESSION OF LNCRNA UCA1, MIR-132-3P AND ATG16L1 WAS MEASURED IN SERUM FROM EPILEPTIC PATIENTS BY QUANTITATIVE RT-PCR. A SH-SY5Y CELL MODEL WAS FURTHER CONSTRUCTED USING RETINOIC ACID TO INVESTIGATE THE UCA1/ MIR-132-3P/ATG16L1 AXIS BY QUANTITATIVE RT-PCR, WESTERN BLOTTING, FLUORESCENCE IN SITU HYBRIDISATION, RNA IMMUNOPRECIPITATION, CHROMATIN IMMUNOPRECIPITATION, AND A DUAL-LUCIFERASE REPORTER GENE ASSAY. RESULTS: IN THE SERUM OF EPILEPTIC PATIENTS, THE LEVEL OF LNCRNA UCA1 AND ATG16L1 WAS REDUCED AND MIR-132-3P ELEVATED, COMPARED TO CONTROLS. SIMILARLY, IN THE SH-SY5Y CELL MODEL, THE LEVEL OF LNCRNA UCA1 AND ATG16L1 WAS REDUCED AND MIR-132-3P ELEVATED IN RETINOIC ACID-TREATED CELLS; LNCRNA UCA1 WAS MAINLY LOCATED IN THE CYTOPLASM. LNCRNA UCA1 OVEREXPRESSION WAS SHOWN TO PROMOTE AUTOPHAGIC GENE EXPRESSION, WHICH WAS REVERSED BY MIR-132-3P OVEREXPRESSION. MOREOVER, AUTOPHAGIC GENE EXPRESSION INDUCED BY MIR-132-3P KNOCKDOWN WAS REVERSED BY ATG16L1 KNOCKDOWN. BASED ON PRECIPITATION ASSAYS, LNCRNA UCA1 AND MIR-132-3P WERE SHOWN TO FORM A COMPLEX WITH THE TRANSCRIPTION FACTOR, EZH2, AND MIR-132-3P WAS SHOWN TO INTERACT WITH ATG16L1 BASED ON A LUCIFERASE ASSAY. FINALLY, LNCRNA UCA1 WAS SHOWN TO NEGATIVELY REGULATE MIR-132-3P EXPRESSION, AND MIR-132-3P WAS SHOWN TO NEGATIVELY REGULATE ATG16L1. SIGNIFICANCE: IN THIS CELL MODEL, LNCRNA UCA1 PROMOTES AUTOPHAGIC GENE EXPRESSION VIA EPIGENETIC REGULATION MEDIATED BY ATG16L1 AND MIR-132-3P. 2022 13 207 41 ACTIVATION OF THE TYPE I INTERFERON PATHWAY IN PRIMARY SJOGREN'S SYNDROME. SJOGREN'S SYNDROME (SS), A CHRONIC AUTOIMMUNE SYSTEMIC DISEASE AFFECTING MIDDLE AGED WOMEN, IS CHARACTERIZED BY LYMPHOCYTIC INFILTRATION OF THE SALIVARY AND LACHRYMAL GLANDS RESULTING IN DRY EYES AND DRY MOUTH. RECENT ADVANCES HAVE REVEALED A MAJOR ROLE FOR ACTIVATION OF THE TYPE I INTERFERON (IFN) PATHWAY IN THE PATHOGENESIS OF THE SYNDROME, AS EVIDENCED BY THE INCREASED CIRCULATING TYPE I IFN ACTIVITY AND AN IFN "SIGNATURE" IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMC) AND MINOR SALIVARY GLAND (MSG) BIOPSIES FROM THESE PATIENTS. POLYMORPHISMS IN GENES INVOLVED IN THE IFNALPHA PATHWAY, SUCH AS IRF5 AND STAT4, HAVE BEEN FOUND TO BE ASSOCIATED WITH DISEASE SUSCEPTIBILITY. WHILE THE INITIAL TRIGGERS OF THE INNATE IMMUNE RESPONSE IN SS REMAIN ELUSIVE, PRELIMINARY EVIDENCE SUPPORTS THE ROLE OF INAPPROPRIATELY EXPRESSED ENDOGENOUS LINE-1 (L1) RETROELEMENTS AS POTENTIAL TRIGGERS OF TYPE I IFN ACTIVATION IN SS, POSSIBLY THROUGH TOLL-LIKE RECEPTOR (TLR) DEPENDENT OR INDEPENDENT PATHWAYS. PROTEINS OF THE METHYLATION MACHINERY AND THE APOBEC FAMILY OF CYTIDINE DEAMINASES ARE COORDINATELY OVEREXPRESSED, SUGGESTING THAT THOSE PROTEINS MIGHT CONTRIBUTE TO REGULATION OF THE INAPPROPRIATELY EXPRESSED L1 ENDOGENOUS RETROELEMENTS IN SS. GIVEN THE APPARENT CENTRAL ROLE OF IFNALPHA IN THE PATHOGENESIS OF SS, BLOCKADE OF THIS CYTOKINE MAY BE A RATIONAL THERAPEUTIC APPROACH. IN THE CURRENT REVIEW WE SUMMARIZE THE CURRENT EVIDENCE REGARDING THE POTENTIAL TRIGGERS OF TYPE I IFN ACTIVATION AS WELL AS THE DATA SUPPORTING GENETIC AND EPIGENETIC REGULATION OF THE TYPE I IFN SYSTEM IN SS. 2010 14 4350 30 MIR-181A-5P IS A POTENTIAL CANDIDATE EPIGENETIC BIOMARKER IN MULTIPLE SCLEROSIS. MULTIPLE SCLEROSIS (MS) IS A CHRONIC INFLAMMATORY DISEASE OF THE CENTRAL NERVOUS SYSTEM (CNS) CHARACTERIZED BY DEMYELINATION AND AXONAL DEGENERATION. ABNORMAL EXPRESSION OF MICRORNAS (MIRNAS) PLAYS AN IMPORTANT ROLE IN MS PATHOLOGY. IN THIS COHORT STUDY, DIFFERENTIAL EXPRESSION OF THE FOUR MIRNAS (HSA-MIR-155-5P, HSA-MIR-9-5P, HSA-MIR-181A-5P, AND HSA-MIR-125B-5P) WAS INVESTIGATED IN 69 INDIVIDUALS, INCLUDING 39 MS PATIENTS (RELAPSING-REMITTING MS (RRMS), N = 27; SECONDARY PROGRESSIVE MS (SPMS), N = 12) AND 30 HEALTHY CONTROLS. IN SILICO ANALYSES REVEALED POSSIBLE GENES AND PATHWAYS SPECIFIC TO MIRNAS. PERIPHERAL BLOOD MIRNA EXPRESSIONS WERE DETECTED BY QUANTITATIVE REAL-TIME PCR (QPCR). HSA-MIR-181A-5P WAS DOWNREGULATED AND ASSOCIATED WITH INCREASED MS RISK (P = 0.012). THE OTHER THREE MIRNAS WERE UPREGULATED AND NOT ASSOCIATED WITH MS (P < 0.05). THE AREA UNDER THE CURVE (AUC) IS 0.779. IN SILICO ANALYSES SHOWED THAT HSA-MIR-181A-5P MAY PARTICIPATE IN MS PATHOLOGY BY TARGETING MAP2K1, CREB1, ATXN1, AND ATXN3 GENES IN INFLAMMATION AND NEURODEGENERATION PATHWAYS. THE CIRCULATORY HSA-MIR-181A-5P CAN REGULATE TARGET GENES, REVERSING THE MECHANISMS INVOLVED IN MS PATHOLOGIES SUCH AS PROTEIN UPTAKE AND PROCESSING, CELL PROLIFERATION AND SURVIVAL, INFLAMMATION, AND NEURODEGENERATION. THUS, THIS MIRNA COULD BE USED AS AN EPIGENOMIC-GUIDED DIAGNOSTIC TOOL AND FOR THERAPEUTIC PURPOSE. 2022 15 1726 25 DYSREGULATION OF LNCRNAS IN RHEUMATOID ARTHRITIS: BIOMARKERS, PATHOGENESIS AND POTENTIAL THERAPEUTIC TARGETS. RHEUMATOID ARTHRITIS (RA) IS A CHRONIC AUTOIMMUNE DISEASE OF UNKNOWN ETIOLOGY, MAINLY MANIFESTED BY PERSISTENT ABNORMAL PROLIFERATION OF FIBROBLAST-LIKE SYNOVIOCYTES (FLSS), INFLAMMATION, SYNOVIAL HYPERPLASIA AND CARTILAGE EROSION, ACCOMPANIED BY JOINT SWELLING AND JOINT DESTRUCTION. ABNORMAL EXPRESSION OR FUNCTION OF LONG NONCODING RNAS (LNCRNAS) ARE CLOSELY RELATED TO HUMAN DISEASES, INCLUDING CANCERS, MENTAL DISEASES, AUTOIMMUNE DISEASES AND OTHERS. THE ABNORMAL SEQUENCE AND SPATIAL STRUCTURE OF LNCRNAS, THE DISORDER EXPRESSION AND THE ABNORMAL INTERACTION WITH THE BINDING PROTEIN WILL LEAD TO THE CHANGE OF GENE EXPRESSION IN THE WAY OF EPIGENETIC MODIFICATION. INCREASING EVIDENCE DEMONSTRATED THAT LNCRNAS WERE INVOLVED IN THE ACTIVATION OF FLSS, WHICH PLAYED A KEY ROLE IN THE PATHOGENESIS OF RA. IN THIS REVIEW, THE RESEARCH PROGRESS OF LNCRNAS IN THE PATHOGENESIS OF RA WAS SYSTEMATICALLY SUMMARIZED, INCLUDING THE ROLE OF LNCRNAS IN THE DIAGNOSIS OF RA, THE REGULATORY MECHANISM OF LNCRNAS IN THE PATHOGENESIS OF RA, AND THE INTERVENTION ROLE OF LNCRNAS IN THE TREATMENT OF RA. FURTHERMORE, THE ACTIVATED SIGNAL PATHWAYS, THE ROLE OF DNA METHYLATION AND OTHER MECHANISM HAVE ALSO BEEN OVERVIEW IN THIS REVIEW. 2021 16 5225 33 PRMT1 MODULATES PROCESSING OF ASTHMA-RELATED PRIMARY MICRORNAS (PRI-MIRNAS) INTO MATURE MIRNAS IN LUNG EPITHELIAL CELLS. PROTEIN ARGININE METHYLTRANSFERASE-1 (PRMT1) IS AN IMPORTANT EPIGENETIC REGULATOR OF CELL FUNCTION AND CONTRIBUTES TO INFLAMMATION AND REMODELING IN ASTHMA IN A CELL TYPE-SPECIFIC MANNER. DISEASE-SPECIFIC EXPRESSION PATTERNS OF MICRORNAS (MIRNA) ARE ASSOCIATED WITH CHRONIC INFLAMMATORY LUNG DISEASES, INCLUDING ASTHMA. THE DE NOVO SYNTHESIS OF MIRNA DEPENDS ON THE TRANSCRIPTION OF PRIMARY MIRNA (PRI-MIRNA) TRANSCRIPT. THIS STUDY ASSESSED THE ROLE OF PRMT1 ON PRI-MIRNA TO MATURE MIRNA PROCESS IN LUNG EPITHELIAL CELLS. HUMAN AIRWAY EPITHELIAL CELLS, BEAS-2B, WERE TRANSFECTED WITH THE PRMT1 EXPRESSION PLASMID PCDNA3.1-PRMT1 FOR 48 H. EXPRESSION PROFILES OF MIRNA WERE DETERMINED BY SMALL RNA DEEP SEQUENCING. COMPARING THESE MIRNAS WITH DATASETS OF MICROARRAYS FROM FIVE ASTHMA PATIENTS (GENE EXPRESSION OMNIBUS DATASET), 12 MIRNAS WERE IDENTIFIED THAT RELATED TO PRMT1 OVEREXPRESSION AND TO ASTHMA. THE OVEREXPRESSION OR KNOCKDOWN OF PRMT1 MODULATED THE EXPRESSION OF THE ASTHMA-RELATED MIRNAS AND THEIR PRI-MIRNAS. COIMMUNOPRECIPITATION SHOWED THAT PRMT1 FORMED A COMPLEX WITH STAT1 OR RUNX1 AND THUS ACTED AS A COACTIVATOR, STIMULATING THE TRANSCRIPTION OF PRI-MIRNAS. STIMULATION WITH TGF-BETA1 PROMOTED THE INTERACTION OF PRMT1 WITH STAT1 OR RUNX1, THEREBY UPREGULATING THE TRANSCRIPTION OF TWO MIRNAS: LET-7I AND MIR-423. SUBSEQUENT CHROMATIN IMMUNOPRECIPITATION ASSAYS REVEALED THAT THE BINDING OF THE PRMT1/STAT1 OR PRMT1/RUNX1 COACTIVATORS TO PRIMARY LET-7I (PRI-LET-7I) AND PRIMARY MIR (PRI-MIR) 423 PROMOTER WAS CRITICAL FOR PRI-LET-7I AND PRI-MIR-423 TRANSCRIPTION. THIS STUDY DESCRIBES A NOVEL ROLE OF PRMT1 AS A COACTIVATOR FOR STAT1 OR RUNX1, WHICH IS ESSENTIAL FOR THE TRANSCRIPTION OF PRI-LET-7I AND PRI-MIR-423 IN EPITHELIAL CELLS AND MIGHT BE RELEVANT TO EPITHELIUM DYSFUNCTION IN ASTHMA. 2021 17 1691 33 DUCTAL CELLS OF MINOR SALIVARY GLANDS IN SJOGREN'S SYNDROME EXPRESS LINE-1 ORF2P AND APOBEC3B. BACKGROUND: TYPE I INTERFERON ACTIVATION IS A HALLMARK EVENT IN SJOGREN'S SYNDROME. L1 RETROELEMENTS STIMULATE PLASMACYTOID DENDRITIC CELLS, ACTIVATING THE TYPE I INTERFERONS, AND ARE REGULATED BY VARIOUS MECHANISMS, INCLUDING THE APOBEC3 DEAMINASES. AS L1S ARE POTENTIAL TRIGGER FACTORS IN AUTOIMMUNITY, WE AIMED TO INVESTIGATE THE IMMUNOHISTOCHEMICAL LOCALIZATION OF L1 ORF2P AND ITS INHIBITOR APOBEC3B PROTEIN IN MINOR SALIVARY GLANDS OF SJOGREN'S SYNDROME PATIENTS. METHODS: TWENTY MINOR SALIVARY GLAND-TISSUE SAMPLES FROM 20 SJOGREN'S SYNDROME PATIENTS, CLASSIFIED ACCORDING TO TARPLEY'S HISTOLOGICAL CRITERIA, AND 10 CONTROLS WERE EVALUATED FOR L1 ORF2P AND APOBEC3B EXPRESSION VIA IMMUNOHISTOCHEMISTRY. RESULTS: L1 ORF2P WAS EXPRESSED IN 17/20 SS PATIENTS AND ALL CONTROLS. APOBEC3B EXPRESSION WAS OBSERVED IN 15/20 SJOGREN'S SYNDROME PATIENTS, 5/5 CHRONIC SIALADENITIS, AND 3/5 NORMAL MINOR SALIVARY GLANDS. BOTH ANTIBODIES STAINED THE CYTOPLASM OF THE DUCTAL EPITHELIAL CELLS. NEGATIVE STAINING WAS OBSERVED IN THE ACINAR CELLS. L1 ORF2P-POSITIVE IMMUNOSTAINING WAS SIGNIFICANTLY LOWER IN TARPLEY IV SJOGREN'S SYNDROME PATIENTS THAN CONTROLS (P = .039), AND APOBEC3B-POSITIVE STAINING WAS SIGNIFICANTLY LOWER IN TARPLEY I COMPARED TO TARPLEY II SJOGREN'S SYNDROME PATIENTS (P = .008) AND CONTROLS (P = .035). CONCLUSIONS: L1 ORF2P AND APOBEC3B ARE EXPRESSED IN THE DUCTAL EPITHELIAL CELLS OF MINOR SALIVARY GLANDS THAT ARE AMONG THE KEY TARGETS IN SJOGREN'S SYNDROME. L1 ORF2P EXPRESSION MAY PROMOTE THE L1 ABILITY TO ACT AS AN INTRINSIC ANTIGEN IN SJOGREN'S SYNDROME. THE POTENTIAL FUTURE USE OF L1 ORF2-REVERSE TRANSCRIPTASE INHIBITORS IN AUTOIMMUNITY SUPPORTS FURTHER INVESTIGATION OF L1 EPIGENETIC REGULATION BY APOBEC3 ENZYMES. 2018 18 4059 29 MASSIVE ANALYSIS OF CDNA ENDS (MACE) AND MIRNA EXPRESSION PROFILING IDENTIFIES PROATHEROGENIC PATHWAYS IN CHRONIC KIDNEY DISEASE. EPIGENETIC DYSREGULATION CONTRIBUTES TO THE HIGH CARDIOVASCULAR DISEASE BURDEN IN CHRONIC KIDNEY DISEASE (CKD) PATIENTS. ALTHOUGH MICRORNAS (MIRNAS) ARE CENTRAL EPIGENETIC REGULATORS, WHICH SUBSTANTIALLY AFFECT THE DEVELOPMENT AND PROGRESSION OF CARDIOVASCULAR DISEASE (CVD), NO DATA ON MIRNA DYSREGULATION IN CKD-ASSOCIATED CVD ARE AVAILABLE UNTIL NOW. WE NOW PERFORMED HIGH-THROUGHPUT MIRNA SEQUENCING OF PERIPHERAL BLOOD MONONUCLEAR CELLS FROM TEN CLINICALLY STABLE HEMODIALYSIS (HD) PATIENTS AND TEN HEALTHY CONTROLS, WHICH ALLOWED US TO IDENTIFY 182 DIFFERENTIALLY EXPRESSED MIRNAS (E.G., MIR-21, MIR-26B, MIR-146B, MIR-155). TO TEST BIOLOGICAL RELEVANCE, WE AIMED TO CONNECT MIRNA DYSREGULATION TO DIFFERENTIAL GENE EXPRESSION. GENOME-WIDE GENE EXPRESSION PROFILING BY MACE (MASSIVE ANALYSIS OF CDNA ENDS) IDENTIFIED 80 GENES TO BE DIFFERENTIALLY EXPRESSED BETWEEN HD PATIENTS AND CONTROLS, WHICH COULD BE LINKED TO CARDIOVASCULAR DISEASE (E.G., KLF6, DUSP6, KLF4), TO INFECTION / IMMUNE DISEASE (E.G., ZFP36, SOCS3, JUND), AND TO DISTINCT PROATHEROGENIC PATHWAYS SUCH AS THE TOLL-LIKE RECEPTOR SIGNALING PATHWAY (E.G., IL1B, MYD88, TICAM2), THE MAPK SIGNALING PATHWAY (E.G., DUSP1, FOS, HSPA1A), AND THE CHEMOKINE SIGNALING PATHWAY (E.G., RHOA, PAK1, CXCL5). FORMAL INTERACTION NETWORK ANALYSIS PROVED BIOLOGICAL RELEVANCE OF MIRNA DYSREGULATION, AS 68 DIFFERENTIALLY EXPRESSED MIRNAS COULD BE CONNECTED TO 47 RECIPROCALLY EXPRESSED TARGET GENES. OUR STUDY IS THE FIRST COMPREHENSIVE MIRNA ANALYSIS IN CKD THAT LINKS DYSREGULATED MIRNA EXPRESSION WITH DIFFERENTIAL EXPRESSION OF GENES CONNECTED TO INFLAMMATION AND CVD. AFTER RECENT ANIMAL DATA SUGGESTED THAT TARGETING MIRNAS IS BENEFICIAL IN EXPERIMENTAL CVD, OUR DATA MAY NOW SPUR FURTHER RESEARCH IN THE FIELD OF CKD-ASSOCIATED HUMAN CVD. 2014 19 3477 31 IDENTIFICATION OF ABNORMALLY METHYLATED DIFFERENTIALLY EXPRESSED GENES IN CHRONIC PERIODONTITIS BY INTEGRATED BIOINFORMATICS ANALYSIS. BACKGROUND: DNA METHYLATION PLAYS A VITAL ROLE AS AN EPIGENETIC CHANGE THAT CONTRIBUTES TO CHRONIC PERIODONTITIS. OBJECTIVE: THIS STUDY AIMED TO INTEGRATE TWO METHYLATION DATASETS (GSE173081 AND GSE59962) AND TWO GENE EXPRESSION DATASETS (GSE10334 AND GES16134) TO IDENTIFY ABNORMALLY METHYLATED DIFFERENTIALLY EXPRESSED GENES RELATED TO CHRONIC PERIODONTITIS. METHODS: DIFFERENTIALLY METHYLATED GENES WERE OBTAINED. FUNCTIONAL ENRICHMENT ANALYSIS OF DMGS WAS PERFORMED. THE PROTEIN-PROTEIN INTERACTION (PPI) NETWORK WAS CONSTRUCTED USING STRING AND CYTOSCAPE SOFTWARE. FINALLY, THE HUB GENES WERE SELECTED FROM THE PPI NETWORK BY USING CYTOHUBBA. RESULTS: IN TOTAL, 122 HYPOMETHYLATED AND HIGHLY EXPRESSED GENES WERE ENRICHED IN THE BIOLOGICAL MECHANISMS THAT ARE INVOLVED IN THE DIFFERENTIATION OF EXTRACELLULAR MATRIX ORGANIZATION, EXTRACELLULAR STRUCTURE ORGANIZATION, AND CELL CHEMOTAXIS. THE THREE SELECTED HUB GENES OF THE PPI NETWORK WERE IL1B, KDR, AND MMP9. A TOTAL OF 122 HYPERMETHYLATED AND LOWLY EXPRESSED GENES WERE IDENTIFIED, AND BIOLOGICAL PROCESSES, SUCH AS CORNIFICATION, EPIDERMIS DEVELOPMENT, SKIN DEVELOPMENT, AND KERATINOCYTE DIFFERENTIATION WERE ENRICHED. CDSN DSG1, AND KRT2 WERE IDENTIFIED AS THE TOP 3 HUB GENES OF THE PPI NETWORK. CONCLUSION: BASED ON THE COMPREHENSIVE BIOINFORMATICS ANALYSIS, SIX HUB GENES (IL1B, KDR, MMP9, CDSN DSG1, AND KRT2) WERE ASSOCIATED WITH CHRONIC PERIODONTITIS. OUR FINDINGS PROVIDE NOVEL INSIGHTS INTO THE MECHANISMS UNDERLYING EPIGENETIC CHANGES IN CHRONIC PERIODONTITIS. 2023 20 4364 27 MIRNA DEREGULATION BY EPIGENETIC SILENCING DISRUPTS SUPPRESSION OF THE ONCOGENE PLAG1 IN CHRONIC LYMPHOCYTIC LEUKEMIA. MICRORNAS (MIRNA) PLAY A KEY ROLE IN CELLULAR REGULATION AND, IF DEREGULATED, IN THE DEVELOPMENT OF NEOPLASTIC DISORDERS INCLUDING CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). RNAS FROM PRIMARY CELLS OF 50 TREATMENT-NAIVE CLL PATIENTS AND PERIPHERAL B CELLS OF 14 HEALTHY DONORS WERE APPLIED TO MIRNA EXPRESSION PROFILING USING BEAD CHIP TECHNOLOGY. IN CLL CELLS, A SET OF 7 UP- AND 19 DOWN-REGULATED MIRNAS WAS IDENTIFIED. AMONG THE MIRNAS DOWN-REGULATED IN CLL CELLS, 6 OF 10 MIRNA PROMOTERS EXAMINED SHOWED GAIN OF METHYLATION COMPARED WITH NORMAL B-CELL CONTROLS. SUBSEQUENT TARGET PREDICTION OF DEREGULATED MIRNAS REVEALED A HIGHLY SIGNIFICANT BINDING PREDICTION AT THE 3' UNTRANSLATED REGION OF THE PLEOMORPHIC ADENOMA GENE 1 (PLAG1) ONCOGENE. LUCIFERASE REPORTER ASSAYS INCLUDING SITE-DIRECTED MUTAGENESIS OF BINDING SITES REVEALED A SIGNIFICANT REGULATION OF PLAG1 BY MIR-181A, MIR-181B, MIR-107, AND MIR-424. ALTHOUGH EXPRESSION OF PLAG1 MRNA WAS NOT AFFECTED, PLAG1 PROTEIN EXPRESSION WAS SHOWN TO BE SIGNIFICANTLY ELEVATED IN CLL CELLS COMPARED WITH THE LEVELS IN HEALTHY DONOR B CELLS. IN SUMMARY, WE COULD DEMONSTRATE DISRUPTION OF MIRNA-MEDIATED TRANSLATIONAL CONTROL, PARTLY DUE TO EPIGENETIC TRANSCRIPTIONAL SILENCING OF MIRNAS, WITH SUBSEQUENT OVEREXPRESSION OF THE ONCOGENIC TRANSCRIPTION FACTOR PLAG1 AS A PUTATIVE NOVEL MECHANISM OF CLL PATHOGENESIS. 2009