1 2856 149 FROM METHYLATION TO MYELINATION: EPIGENOMIC AND TRANSCRIPTOMIC PROFILING OF CHRONIC INACTIVE DEMYELINATED MULTIPLE SCLEROSIS LESIONS. IN THE PROGRESSIVE PHASE OF MULTIPLE SCLEROSIS (MS), THE HAMPERED DIFFERENTIATION CAPACITY OF OLIGODENDROCYTE PRECURSOR CELLS (OPCS) EVENTUALLY RESULTS IN REMYELINATION FAILURE. WE HAVE PREVIOUSLY SHOWN THAT DNA METHYLATION OF ID2/ID4 IS HIGHLY INVOLVED IN OPC DIFFERENTIATION AND REMYELINATION. IN THIS STUDY, WE TOOK AN UNBIASED APPROACH BY DETERMINING GENOME-WIDE DNA METHYLATION PATTERNS WITHIN CHRONICALLY DEMYELINATED MS LESIONS AND INVESTIGATED HOW CERTAIN EPIGENETIC SIGNATURES RELATE TO OPC DIFFERENTIATION CAPACITY. WE COMPARED GENOME-WIDE DNA METHYLATION AND TRANSCRIPTIONAL PROFILES BETWEEN CHRONICALLY DEMYELINATED MS LESIONS AND MATCHED NORMAL-APPEARING WHITE MATTER (NAWM), MAKING USE OF POST-MORTEM BRAIN TISSUE (N = 9/GROUP). DNA METHYLATION DIFFERENCES THAT INVERSELY CORRELATED WITH MRNA EXPRESSION OF THEIR CORRESPONDING GENES WERE VALIDATED FOR THEIR CELL-TYPE SPECIFICITY IN LASER-CAPTURED OPCS USING PYROSEQUENCING. THE CRISPR-DCAS9-DNMT3A/TET1 SYSTEM WAS USED TO EPIGENETICALLY EDIT HUMAN-IPSC-DERIVED OLIGODENDROCYTES TO ASSESS THE EFFECT ON CELLULAR DIFFERENTIATION. OUR DATA SHOW HYPERMETHYLATION OF CPGS WITHIN GENES THAT CLUSTER IN GENE ONTOLOGIES RELATED TO MYELINATION AND AXON ENSHEATHMENT. CELL TYPE-SPECIFIC VALIDATION INDICATES A REGION-DEPENDENT HYPERMETHYLATION OF MBP, ENCODING FOR MYELIN BASIC PROTEIN, IN OPCS OBTAINED FROM WHITE MATTER LESIONS COMPARED TO NAWM-DERIVED OPCS. BY ALTERING THE DNA METHYLATION STATE OF SPECIFIC CPGS WITHIN THE PROMOTOR REGION OF MBP, USING EPIGENETIC EDITING, WE SHOW THAT CELLULAR DIFFERENTIATION AND MYELINATION CAN BE BIDIRECTIONALLY MANIPULATED USING THE CRISPR-DCAS9-DNMT3A/TET1 SYSTEM IN VITRO. OUR DATA INDICATE THAT OPCS WITHIN CHRONICALLY DEMYELINATED MS LESIONS ACQUIRE AN INHIBITORY PHENOTYPE, WHICH TRANSLATES INTO HYPERMETHYLATION OF CRUCIAL MYELINATION-RELATED GENES. ALTERING THE EPIGENETIC STATUS OF MBP CAN RESTORE THE DIFFERENTIATION CAPACITY OF OPCS AND POSSIBLY BOOST (RE)MYELINATION.	2023	
                                                                                                                                                                                                                                                                   
2 1526  46 DNA METHYLATION CHANGES IN GLIAL CELLS OF THE NORMAL-APPEARING WHITE MATTER IN MULTIPLE SCLEROSIS PATIENTS. MULTIPLE SCLEROSIS (MS), THE LEADING CAUSE OF NON-TRAUMATIC NEUROLOGICAL DISABILITY IN YOUNG ADULTS, IS A CHRONIC INFLAMMATORY AND NEURODEGENERATIVE DISEASE OF THE CENTRAL NERVOUS SYSTEM (CNS). DUE TO THE POOR ACCESSIBILITY TO THE TARGET ORGAN, CNS-CONFINED PROCESSES UNDERPINNING THE LATER PROGRESSIVE FORM OF MS REMAIN ELUSIVE THEREBY LIMITING TREATMENT OPTIONS. WE AIMED TO EXAMINE DNA METHYLATION, A STABLE EPIGENETIC MARK OF GENOME ACTIVITY, IN GLIAL CELLS TO CAPTURE RELEVANT MOLECULAR CHANGES UNDERLYING MS NEUROPATHOLOGY. WE PROFILED DNA METHYLATION IN NUCLEI OF NON-NEURONAL CELLS, ISOLATED FROM 38 POST-MORTEM NORMAL-APPEARING WHITE MATTER (NAWM) SPECIMENS OF MS PATIENTS (N = 8) IN COMPARISON TO WHITE MATTER OF CONTROL INDIVIDUALS (N = 14), USING INFINIUM METHYLATIONEPIC BEADCHIP. WE IDENTIFIED 1,226 SIGNIFICANT (GENOME-WIDE ADJUSTED P-VALUE < 0.05) DIFFERENTIALLY METHYLATED POSITIONS (DMPS) BETWEEN MS PATIENTS AND CONTROLS. FUNCTIONAL ANNOTATION OF THE ALTERED DMP-GENES UNCOVERED ALTERATIONS OF PROCESSES RELATED TO CELLULAR MOTILITY, CYTOSKELETON DYNAMICS, METABOLIC PROCESSES, SYNAPTIC SUPPORT, NEUROINFLAMMATION AND SIGNALING, SUCH AS WNT AND TGF-BETA PATHWAYS. A FRACTION OF THE AFFECTED GENES DISPLAYED TRANSCRIPTIONAL DIFFERENCES IN THE BRAIN OF MS PATIENTS, AS REPORTED BY PUBLICALLY AVAILABLE TRANSCRIPTOMIC DATA. CELL TYPE-RESTRICTED ANNOTATION OF DMP-GENES ATTRIBUTED ALTERATIONS OF CYTOSKELETON REARRANGEMENT AND EXTRACELLULAR MATRIX REMODELLING TO ALL GLIAL CELL TYPES, WHILE SOME PROCESSES, INCLUDING ION TRANSPORT, WNT/TGF-BETA SIGNALING AND IMMUNE PROCESSES WERE MORE SPECIFICALLY LINKED TO OLIGODENDROCYTES, ASTROCYTES AND MICROGLIAL CELLS, RESPECTIVELY. OUR FINDINGS STRONGLY SUGGEST THAT NAWM GLIAL CELLS ARE HIGHLY ALTERED, EVEN IN THE ABSENCE OF LESIONAL INSULT, COLLECTIVELY EXHIBITING A MULTICELLULAR REACTION IN RESPONSE TO DIFFUSE INFLAMMATION.	2022	
                                                                                                                                                                                                                                                                                                                                                                                       
3  808  38 CHANGED HISTONE ACETYLATION PATTERNS IN NORMAL-APPEARING WHITE MATTER AND EARLY MULTIPLE SCLEROSIS LESIONS. THE EPIGENETIC IDENTITY OF OLIGODENDROCYTES IS MODULATED BY POSTTRANSLATIONAL MODIFICATIONS OF HISTONES. ACETYLATION OF HISTONE H3 RESULTS FROM THE BALANCE BETWEEN THE ACTIVITY OF HISTONE ACETYLTRANSFERASES (HATS) AND HISTONE DEACETYLASES AND MODULATES TRANSCRIPTIONAL ACTIVATION. WE HAVE PREVIOUSLY SHOWN THAT, IN RODENTS, HISTONE DEACETYLATION FAVORS OLIGODENDROCYTE DIFFERENTIATION, WHEREAS ACETYLATION IS ASSOCIATED WITH INCREASED LEVELS OF TRANSCRIPTIONAL INHIBITORS OF OLIGODENDROCYTE DIFFERENTIATION. HERE, WE REPORT, IN HUMANS BRAINS, A SHIFT TOWARD HISTONE ACETYLATION IN THE WHITE MATTER OF THE FRONTAL LOBES OF AGED SUBJECTS AND IN PATIENTS WITH CHRONIC MULTIPLE SCLEROSIS (MS). INCREASED IMMUNOREACTIVITY FOR ACETYLATED HISTONE H3 WAS OBSERVED IN THE NUCLEI OF NOGOA+ OLIGODENDROCYTES IN A SUBSET OF MS SAMPLES. THESE CHANGES WERE ASSOCIATED WITH HIGH LEVELS OF TRANSCRIPTIONAL INHIBITORS OF OLIGODENDROCYTE DIFFERENTIATION (I.E., TCF7L2, ID2, AND SOX2) AND HIGHER HAT TRANSCRIPT LEVELS (I.E., CBP, P300) IN FEMALE MS PATIENTS COMPARED WITH NON-NEUROLOGICAL CONTROLS AND CORRELATED WITH DISEASE DURATION. CHROMATIN IMMUNOPRECIPITATION FROM SAMPLES OF MS PATIENTS REVEALED ENRICHMENT OF ACETYL-HISTONE H3 AT THE PROMOTER OF THE INCREASED TARGET GENES (I.E., TCF7L2). THE DATA IN CHRONIC LESIONS CONTRASTED WITH FINDINGS IN EARLY MS LESIONS, WHERE A MARKED OLIGODENDROGLIAL HISTONE DEACETYLATION WAS OBSERVED. TOGETHER, THESE DATA SUGGEST THAT HISTONE DEACETYLATION IS A PROCESS THAT OCCURS AT THE EARLY STAGES OF THE DISEASE AND WHOSE EFFICIENCY DECREASES WITH DISEASE DURATION.	2011	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
4 1611  39 DNA METHYLATION: A NEW PLAYER IN MULTIPLE SCLEROSIS. MULTIPLE SCLEROSIS (MS) IS A NEUROLOGICAL AND CHRONIC INFLAMMATORY DISEASE THAT IS MEDIATED BY DEMYELINATION AND AXONAL DEGENERATION IN THE CENTRAL NERVOUS SYSTEM (CNS). STUDIES HAVE SHOWN THAT IMMUNE SYSTEM COMPONENTS SUCH AS CD4+, CD8+, CD44+ T CELLS, B LYMPHATIC CELLS, AND INFLAMMATORY CYTOKINES PLAY A CRITICAL ROLE IN INFLAMMATORY PROCESSES AND MYELIN DAMAGE ASSOCIATED WITH MS. NEVERTHELESS, THE PATHOGENESIS OF MS REMAINS POORLY DEFINED. DNA METHYLATION, A SIGNIFICANT EPIGENETIC MODIFICATION, IS REPORTED TO BE EXTENSIVELY INVOLVED IN MS PATHOGENESIS THROUGH THE REGULATION OF GENE EXPRESSION. THIS REVIEW FOCUSES ON DNA METHYLATION INVOLVED IN MS PATHOGENESIS. EVIDENCE SHOWED THE HYPERMETHYLATION OF HUMAN LEUKOCYTE ANTIGEN-DRB1 (HLA-DRB1) IN CD4+ T CELLS, THE GENOME-WIDE DNA METHYLATION IN CD8+ T CELLS, THE HYPERMETHYLATION OF INTERLEUKIN-4 (IL-4)/FORKHEAD WINGED HELIX TRANSCRIPTION FACTOR 3 (FOXP3), AND THE DEMETHYLATION OF INTERFERON-GAMMA (IFN-GAMMA)/IL-17A IN CD44+ ENCEPHALITOGENIC T CELLS. STUDIES ALSO SHOWED THE HYPERMETHYLATION OF SH2-CONTAINING PROTEIN TYROSINE PHOSPHATASE-1 (SHP-1) IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) AND METHYLATED CHANGES OF GENES REGULATING OLIGODENDROCYTE AND NEURONAL FUNCTION IN NORMAL-APPEARING WHITE MATTER. CLARIFYING THE MECHANISM OF ABERRANT METHYLATION ON MS MAY EXPLAIN PART OF THE PATHOLOGY AND WILL LEAD TO THE DEVELOPMENT OF A NEW THERAPEUTIC TARGET FOR THE TREATMENT OF MS IN THE FUTURE.	2017	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
5 3069  41 GENOME-WIDE DNA METHYLATION PROFILING IDENTIFIES EPIGENETIC CHANGES IN CD4+ AND CD14+ CELLS OF MULTIPLE SCLEROSIS PATIENTS. MULTIPLE SCLEROSIS (MS) IS A CHRONIC AUTOIMMUNE AND DEGENERATIVE DISEASE OF THE CENTRAL NERVOUS SYSTEM, WHICH DEVELOPS IN GENETICALLY PREDISPOSED INDIVIDUALS UPON EXPOSURE TO ENVIRONMENTAL INFLUENCES. ENVIRONMENTAL TRIGGERS OF MS, SUCH AS VIRAL INFECTIONS OR SMOKING, WERE DEMONSTRATED TO AFFECT DNA METHYLATION, AND THUS TO INVOLVE THIS IMPORTANT EPIGENETIC MECHANISM IN THE DEVELOPMENT OF PATHOLOGICAL PROCESS. TO IDENTIFY MS-ASSOCIATED DNA METHYLATION HALLMARKS, WE PERFORMED GENOME-WIDE DNA METHYLATION PROFILING OF TWO CELL POPULATIONS (CD4+ T-LYMPHOCYTES AND CD14+ MONOCYTES), COLLECTED FROM THE SAME TREATMENT-NAIVE RELAPSING-REMITTING MS PATIENTS AND HEALTHY SUBJECTS, USING ILLUMINA 450 K METHYLATION ARRAYS. WE REVEALED SIGNIFICANT CHANGES IN DNA METHYLATION FOR BOTH CELL POPULATIONS IN MS. IN CD4+ CELLS OF MS PATIENTS THE MAJORITY OF DIFFERENTIALLY METHYLATED POSITIONS (DMPS) WERE SHOWN TO BE HYPOMETHYLATED, WHILE IN CD14+ CELLS - HYPERMETHYLATED. DIFFERENTIAL METHYLATION OF HLA-DRB1 GENE IN CD4+ AND CD14+ CELLS WAS ASSOCIATED WITH CARRIAGE OF DRB1*15 ALLELE INDEPENDENTLY FROM THE DISEASE STATUS. BESIDES, ABOUT 20% OF IDENTIFIED DMPS WERE SHARED BETWEEN TWO CELL POPULATIONS AND HAD THE SAME DIRECTION OF METHYLATION CHANGES; THEY MAY BE INVOLVED IN BASIC EPIGENETIC PROCESSES OCCURING IN MS. THESE FINDINGS SUGGEST THAT THE EPIGENETIC MECHANISM OF DNA METHYLATION IN IMMUNE CELLS CONTRIBUTES TO MS; FURTHER STUDIES ARE NOW REQUIRED TO VALIDATE THESE RESULTS AND UNDERSTAND THEIR FUNCTIONAL SIGNIFICANCE.	2022	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
6 5426  47 REGULATION OF SIRTUIN EXPRESSION IN AUTOIMMUNE NEUROINFLAMMATION: INDUCTION OF SIRT1 IN OLIGODENDROCYTE PROGENITOR CELLS. IN MULTIPLE SCLEROSIS (MS) REGENERATION OF OLIGODENDROCYTES FOLLOWING INFLAMMATORY DEMYELINATION IS LIMITED BY THE COMPROMISED ABILITY OF PROGENITORS TO REPOPULATE LESIONED AREAS AND TRANSITION TO FUNCTIONALLY COMPETENT OLIGODENDROCYTES. REGARDING UNDERLYING MECHANISMS, THE INVOLVEMENT OF EPIGENETIC PROCESSES HAS BEEN SUGGESTED, E.G. THE CONTRIBUTION OF HISTONE DEACETYLASES (HDAC) KNOWN TO REGULATE OLIGODENDROCYTE PROGENITOR CELL (OPC) DIFFERENTIATION. HOWEVER, THEIR PRECISE EXPRESSION PATTERNS, PARTICULAR OF REDOX-SENSITIVE NAD(+) HDACS, REMAINS LARGELY UNKNOWN. IN THIS STUDY, WE DETERMINED THE EXPRESSION AND ACTIVITY OF SIRTUINS, MEMBERS OF THE HDAC CLASS III FAMILY WITH A SPECIFIC FOCUS ON SIRT1, PREVIOUSLY ASSOCIATED WITH NEURODEGENERATIVE, INFLAMMATORY AND DEMYELINATING DISORDERS OF THE CENTRAL NERVOUS SYSTEM (CNS). BY INVESTIGATING MOUSE EXPERIMENTAL AUTOIMMUNE ENCEPHALOMYELITIS (EAE), A MODEL FOR MS, WE FOUND THAT TRANSCRIPTION OF SIRT1, SIRT2 AND SIRT6 WAS SIGNIFICANTLY INCREASED IN THE CNS DURING CHRONIC DISEASE STAGES. WE CONFIRMED THIS FINDING FOR SIRT1 PROTEIN EXPRESSION AND WERE ABLE TO LOCALIZE UPREGULATED SIRT1 IN NUCLEI OF NG2(+) OR PDGFRALPHA(+) OPCS IN DEMYELINATED BRAIN LESIONS. IN CULTURED MOUSE A2B5(+) OPCS BLOCKADE OF SIRT1 ACTIVITY BY THE SMALL MOLECULE COMPOUND EX527 ENHANCED MITOTIC ACTIVITY BUT DID NOT AFFECT THE CAPACITY TO DIFFERENTIATE. A SIMILAR PATTERN WAS DETECTABLE IN OPCS DERIVED FROM SIRT1-DEFICIENT ANIMALS. TAKEN TOGETHER, OUR DATA SUGGEST THAT SIRT1 INHIBITION MAY HELP TO EXPAND THE ENDOGENOUS POOL OF OPCS WITHOUT AFFECTING THEIR DIFFERENTIATION.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
7 4590  35 NANOPORE SEQUENCING IDENTIFIES DIFFERENTIALLY METHYLATED GENES IN THE CENTRAL NERVOUS SYSTEM IN EXPERIMENTAL AUTOIMMUNE ENCEPHALOMYELITIS. MULTIPLE SCLEROSIS (MS) IS A CHRONIC AUTOIMMUNE-MEDIATED DEMYELINATING DISEASE OF THE CENTRAL NERVOUS SYSTEM (CNS) THAT MIGHT BE TRIGGERED BY ABERRANT EPIGENETIC CHANGES IN THE GENOME. DNA METHYLATION IS THE MOST STUDIED EPIGENETIC MECHANISM THAT PARTICIPATES IN MS PATHOGENESIS. HOWEVER, THE OVERALL METHYLATION LEVEL IN THE CNS OF MS PATIENTS REMAINS ELUSIVE. WE USED DIRECT LONG-READ NANOPORE DNA SEQUENCING AND CHARACTERIZED THE DIFFERENTIALLY METHYLATED GENES IN THE BRAIN FROM MICE WITH EXPERIMENTAL AUTOIMMUNE ENCEPHALOMYELITIS (EAE), AN ANIMAL MODEL OF MS. WE IDENTIFIED 163 HYPOMETHYLATED PROMOTERS AND 327 HYPERMETHYLATED PROMOTERS. THESE GENOMIC ALTERATIONS WERE LINKED TO VARIOUS BIOLOGICAL PROCESSES INCLUDING METABOLISM, IMMUNE RESPONSES, NEURAL ACTIVITIES, AND MITOCHONDRIAL DYNAMICS, ALL OF WHICH ARE VITAL FOR EAE DEVELOPMENT. OUR RESULTS INDICATE A GREAT POTENTIAL OF NANOPORE SEQUENCING IN IDENTIFYING GENOMIC DNA METHYLATION IN EAE AND PROVIDE IMPORTANT GUIDANCE FOR FUTURE STUDIES INVESTIGATING THE MS/EAE PATHOLOGY.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
8 2139  44 EPIGENETIC INSIGHTS INTO MULTIPLE SCLEROSIS DISEASE PROGRESSION. MULTIPLE SCLEROSIS (MS), A CHRONIC INFLAMMATORY DEMYELINATING AND NEURODEGENERATIVE DISEASE OF THE CENTRAL NERVOUS SYSTEM, IS TODAY A LEADING CAUSE OF UNPREDICTABLE LIFELONG DISABILITY IN YOUNG ADULTS. THE TREATMENT OF PATIENTS IN PROGRESSIVE STAGES REMAINS HIGHLY CHALLENGING, ALLUDING TO OUR LIMITED UNDERSTANDING OF THE UNDERLYING PATHOLOGICAL PROCESSES. IN THIS REVIEW, WE PROVIDE INSIGHTS INTO THE MECHANISMS UNDERPINNING MS PROGRESSION FROM A PERSPECTIVE OF EPIGENETICS, THAT REFERS TO STABLE AND MITOTICALLY HERITABLE, YET REVERSIBLE, CHANGES IN THE GENOME ACTIVITY AND GENE EXPRESSION. WE FIRST RECAPITULATE FINDINGS FROM EPIGENETIC STUDIES EXAMINING THE BRAIN TISSUE OF PROGRESSIVE MS PATIENTS, WHICH SUPPORT A CONTRIBUTION OF DNA AND HISTONE MODIFICATIONS IN IMPAIRED OLIGODENDROCYTE DIFFERENTIATION, DEFECTIVE MYELINATION/REMYELINATION AND SUSTAINED NEURO-AXONAL VULNERABILITY. WE NEXT EXPLORE POSSIBILITIES FOR IDENTIFYING FACTORS AFFECTING PROGRESSION USING EASILY ACCESSIBLE TISSUES SUCH AS BLOOD BY COMPARING EPIGENETIC SIGNATURES IN PERIPHERAL IMMUNE CELLS AND BRAIN TISSUE. DESPITE MINOR OVERLAP AT INDIVIDUAL METHYLATION SITES, NEARLY 30% OF ALTERED GENES REPORTED IN PERIPHERAL IMMUNE CELLS OF PROGRESSIVE MS PATIENTS WERE FOUND IN BRAIN TISSUE, JOINTLY CONVERGING ON ALTERATIONS OF NEURONAL FUNCTIONS. WE FURTHER SPECULATE ABOUT THE MECHANISMS UNDERLYING SHARED EPIGENETIC PATTERNS BETWEEN BLOOD AND BRAIN, WHICH LIKELY IMPLY THE INFLUENCE OF INTERNAL (GENETIC CONTROL) AND/OR EXTERNAL (E.G. SMOKING AND AGEING) FACTORS IMPRINTING A COMMON SIGNATURE IN BOTH COMPARTMENTS. OVERALL, WE PROPOSE THAT EPIGENETICS MIGHT SHED LIGHT ON CLINICALLY RELEVANT MECHANISMS INVOLVED IN DISEASE PROGRESSION AND OPEN NEW AVENUES FOR THE TREATMENT OF PROGRESSIVE MS PATIENTS IN THE FUTURE.	2020	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
9 1500  45 DNA METHYLATION ANALYSIS OF CD4+ T CELLS IN PATIENTS WITH PSORIASIS. PSORIASIS IS A CHRONIC INFLAMMATORY SKIN DISEASE THAT IS CHARACTERIZED BY ABERRANT CROSS-TALK BETWEEN KERATINOCYTES AND IMMUNE CELLS SUCH AS CD4+ T CELLS, RESULTING IN KERATINOCYTE HYPERPROLIFERATION IN THE EPIDERMIS. DNA METHYLATION, ONE OF SEVERAL EPIGENETIC MECHANISMS, PLAYS AN IMPORTANT ROLE IN GENE EXPRESSION WITHOUT CHANGING THE DNA SEQUENCE. SEVERAL STUDIES HAVE SUGGESTED THE INVOLVEMENT OF EPIGENETIC REGULATION IN SKIN LESIONS FROM PATIENTS WITH PSORIASIS. IN THIS STUDY, WE INVESTIGATED THE GENOME-WIDE DNA METHYLATION STATUS OF CD4+ T CELLS IN PATIENTS WITH PSORIASIS COMPARED WITH HEALTHY SUBJECTS USING METHYLATED DNA IMMUNOPRECIPITATION SEQUENCING (MEDIP-SEQ). THE RESULTS OF MEDIP-SEQ SHOWED THAT THE GLOBAL METHYLATION VALUES OF CD4+ T CELLS ARE HIGHER IN PATIENTS WITH PSORIASIS THAN IN HEALTHY CONTROLS, PARTICULARLY IN THE PROMOTER REGIONS. AMONG THE MOST HYPERMETHYLATED GENES IN THE PROMOTER REGIONS, WE SELECTED THE GENES WHOSE EXPRESSION IS SIGNIFICANTLY REDUCED IN THE CD4+ T CELLS OF PSORIASIS PATIENTS. STUDIES USING THE METHYLATION INHIBITOR 5-AZACYTIDINE IN VITRO METHYLATION ASSAYS HAVE SHOWN THAT THE DIFFERENTIAL EXPRESSION LEVELS WERE ASSOCIATED WITH THE METHYLATION STATUS OF EACH GENE. BISULFITE SEQUENCING OF THE TRANSCRIPTION START REGION OF PHOSPHATIDIC ACID PHOSPHATASE TYPE 2 DOMAIN CONTAINING 3 (PPAPDC3), ONE OF THE SELECTED GENES, SHOWED HYPERMETHYLATION IN THE CD4+ T CELLS OF PSORIASIS PATIENTS. THESE RESULTS SUGGESTED THAT THE METHYLATION STATUS, WHICH IS IDENTIFIED BY MEDIP-SEQ OF THE GENES, WAS CORRELATED WITH THE MRNA EXPRESSION LEVEL OF THE GENES. COLLECTIVELY, THE DNA METHYLATION STATUS IN CD4+ T CELLS MIGHT BE ASSOCIATED WITH THE PATHOGENESIS OF PSORIASIS.	2014	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
10 3422  40 HUMAN MONOCYTE-TO-MACROPHAGE DIFFERENTIATION INVOLVES HIGHLY LOCALIZED GAIN AND LOSS OF DNA METHYLATION AT TRANSCRIPTION FACTOR BINDING SITES. BACKGROUND: MACROPHAGES AND THEIR PRECURSORS MONOCYTES PLAY A KEY ROLE IN INFLAMMATION AND CHRONIC INFLAMMATORY DISORDERS. MONOCYTE-TO-MACROPHAGE DIFFERENTIATION AND ACTIVATION PROGRAMS ARE ACCOMPANIED BY SIGNIFICANT EPIGENETIC REMODELING WHERE DNA METHYLATION ASSOCIATES WITH CELL IDENTITY. HERE WE SHOW THAT DNA METHYLATION CHANGES CHARACTERISTIC FOR MONOCYTE-TO-MACROPHAGE DIFFERENTIATION OCCUR AT TRANSCRIPTION FACTOR BINDING SITES, AND, IN CONTRAST TO WHAT WAS PREVIOUSLY DESCRIBED, ARE GENERALLY HIGHLY LOCALIZED AND ENCOMPASS BOTH LOSSES AND GAINS OF DNA METHYLATION. RESULTS: WE COMPARED GENOME-WIDE DNA METHYLATION ACROSS 440,292 CPG SITES BETWEEN HUMAN MONOCYTES, NAIVE MACROPHAGES AND MACROPHAGES FURTHER ACTIVATED TOWARD A PRO-INFLAMMATORY STATE (USING LPS/IFNGAMMA), AN ANTI-INFLAMMATORY STATE (IL-4) OR FOAM CELLS (OXLDL AND ACLDL). MOREOVER, WE INTEGRATED THESE DATA WITH PUBLIC WHOLE-GENOME SEQUENCING DATA ON MONOCYTES AND MACROPHAGES TO DEMARCATE DIFFERENTIALLY METHYLATED REGIONS. OUR ANALYSIS SHOWED THAT DIFFERENTIAL DNA METHYLATION WAS MOST PRONOUNCED DURING MONOCYTE-TO-MACROPHAGE DIFFERENTIATION, WAS TYPICALLY RESTRICTED TO SINGLE CPGS OR VERY SHORT REGIONS, AND CO-LOCALIZED WITH LINEAGE-SPECIFIC ENHANCERS IRRESPECTIVE OF WHETHER IT CONCERNS GAIN OR LOSS OF METHYLATION. FURTHERMORE, DIFFERENTIALLY METHYLATED CPGS WERE LOCATED AT SITES CHARACTERIZED BY INCREASED BINDING OF TRANSCRIPTION FACTORS KNOWN TO BE INVOLVED IN MONOCYTE-TO-MACROPHAGE DIFFERENTIATION INCLUDING C/EBP AND ETS FOR GAIN AND AP-1 FOR LOSS OF METHYLATION. CONCLUSION: OUR STUDY HIGHLIGHTS THE INVOLVEMENT OF SUBTLE, YET HIGHLY LOCALIZED REMODELING OF DNA METHYLATION AT REGULATORY REGIONS IN CELL DIFFERENTIATION.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
11 3135  34 GLOBAL DNA METHYLATION AND HYDROXYMETHYLATION LEVELS IN PBMCS ARE ALTERED IN RRMS PATIENTS TREATED WITH IFN-BETA AND GA-A PRELIMINARY STUDY. MULTIPLE SCLEROSIS (MS) IS A CHRONIC DISEASE AFFECTING THE CENTRAL NERVOUS SYSTEM (CNS) DUE TO AN AUTOIMMUNE ATTACK ON AXONAL MYELIN SHEATHS. EPIGENETICS IS AN OPEN RESEARCH TOPIC ON MS, WHICH HAS BEEN INVESTIGATED IN SEARCH OF BIOMARKERS AND TREATMENT TARGETS FOR THIS HETEROGENEOUS DISEASE. IN THIS STUDY, WE QUANTIFIED GLOBAL LEVELS OF EPIGENETIC MARKS USING AN ELISA-LIKE APPROACH IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) FROM 52 PATIENTS WITH MS, TREATED WITH INTERFERON BETA (IFN-BETA) AND GLATIRAMER ACETATE (GA) OR UNTREATED, AND 30 HEALTHY CONTROLS. WE PERFORMED MEDIA COMPARISONS AND CORRELATION ANALYSES OF THESE EPIGENETIC MARKERS WITH CLINICAL VARIABLES IN SUBGROUPS OF PATIENTS AND CONTROLS. WE OBSERVED THAT DNA METHYLATION (5-MC) DECREASED IN TREATED PATIENTS COMPARED WITH UNTREATED AND HEALTHY CONTROLS. MOREOVER, 5-MC AND HYDROXYMETHYLATION (5-HMC) CORRELATED WITH CLINICAL VARIABLES. IN CONTRAST, HISTONE H3 AND H4 ACETYLATION DID NOT CORRELATE WITH THE DISEASE VARIABLES CONSIDERED. GLOBALLY QUANTIFIED EPIGENETIC DNA MARKS 5-MC AND 5-HMC CORRELATE WITH DISEASE AND WERE ALTERED WITH TREATMENT. HOWEVER, TO DATE, NO BIOMARKER HAS BEEN IDENTIFIED THAT CAN PREDICT THE POTENTIAL RESPONSE TO THERAPY BEFORE TREATMENT INITIATION.	2023	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
12 6531  35 TRANSCRIPTIONAL REGULATION OF BRAIN-DERIVED NEUROTROPHIC FACTOR (BDNF) BY METHYL CPG BINDING PROTEIN 2 (MECP2): A NOVEL MECHANISM FOR RE-MYELINATION AND/OR MYELIN REPAIR INVOLVED IN THE TREATMENT OF MULTIPLE SCLEROSIS (MS). MULTIPLE SCLEROSIS (MS) IS A CHRONIC PROGRESSIVE, NEUROLOGICAL DISEASE CHARACTERIZED BY THE TARGETED IMMUNE SYSTEM-MEDIATED DESTRUCTION OF CENTRAL NERVOUS SYSTEM (CNS) MYELIN. AUTOREACTIVE CD4+ T HELPER CELLS HAVE A KEY ROLE IN ORCHESTRATING MS-INDUCED MYELIN DAMAGE. ONCE ACTIVATED, CIRCULATING TH1-CELLS SECRETE A VARIETY OF INFLAMMATORY CYTOKINES THAT FOSTER THE BREAKDOWN OF BLOOD-BRAIN BARRIER (BBB) EVENTUALLY INFILTRATING INTO THE CNS. INSIDE THE CNS, THEY BECOME REACTIVATED UPON EXPOSURE TO THE MYELIN STRUCTURAL PROTEINS AND CONTINUE TO PRODUCE INFLAMMATORY CYTOKINES SUCH AS TUMOR NECROSIS FACTOR ALPHA (TNFALPHA) THAT LEADS TO DIRECT ACTIVATION OF ANTIBODIES AND MACROPHAGES THAT ARE INVOLVED IN THE PHAGOCYTOSIS OF MYELIN. PROLIFERATING OLIGODENDROCYTE PRECURSORS (OPS) MIGRATING TO THE LESION SITES ARE CAPABLE OF ACUTE REMYELINATION BUT UNABLE TO COMPLETELY REPAIR OR RESTORE THE IMMUNE SYSTEM-MEDIATED MYELIN DAMAGE. THIS RESULTS IN VARIOUS PERMANENT CLINICAL NEUROLOGICAL DISABILITIES SUCH AS COGNITIVE DYSFUNCTION, FATIGUE, BOWEL/BLADDER ABNORMALITIES, AND NEUROPATHIC PAIN. AT PRESENT, THERE IS NO CURE FOR MS. RECENT REMYELINATION AND/OR MYELIN REPAIR STRATEGIES HAVE FOCUSED ON THE ROLE OF THE NEUROTROPHIN BRAIN-DERIVED NEUROTROPHIC FACTOR (BDNF) AND ITS UPSTREAM TRANSCRIPTIONAL REPRESSOR METHYL CPG BINDING PROTEIN (MECP2). RESEARCH IN THE FIELD OF EPIGENETIC THERAPEUTICS INVOLVING HISTONE DEACETYLASE (HDAC) INHIBITORS AND LYSINE ACETYL TRANSFERASE (KAT) INHIBITORS IS BEING EXPLORED TO REPRESS THE DETRIMENTAL EFFECTS OF MECP2. THIS REVIEW WILL ADDRESS THE ROLE OF MECP2 AND BDNF IN REMYELINATION AND/OR MYELIN REPAIR AND THE POTENTIAL OF HDAC AND KAT INHIBITORS AS NOVEL THERAPEUTIC INTERVENTIONS FOR MS.	2016	
                                                                                                                                                                                                                                                                                                                                                                                                                            
13 1336  33 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	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
14 1307  36 DEFINING A METHYLATION SIGNATURE ASSOCIATED WITH OPERATIONAL TOLERANCE IN KIDNEY TRANSPLANT RECIPIENTS. OPERATIONAL TOLERANCE AFTER KIDNEY TRANSPLANTATION IS DEFINED AS STABLE GRAFT ACCEPTANCE WITHOUT THE NEED FOR IMMUNOSUPPRESSION THERAPY. HOWEVER, IT IS NOT CLEAR WHICH CELLULAR AND MOLECULAR PATHWAYS ARE DRIVING TOLERANCE IN THESE PATIENTS. WE PERFORMED GENOME-WIDE ANALYSIS OF DNA METHYLATION IN PERIPHERAL BLOOD MONONUCLEAR CELLS FROM KIDNEY TRANSPLANT RECIPIENTS WITH CHRONIC REJECTION AND OPERATIONAL TOLERANCE FROM THE GENETIC ANALYSIS OF MOLECULAR BIOMARKERS OF IMMUNOLOGICAL TOLERANCE (GAMBIT) STUDY. OUR RESULTS SHOWED THAT BOTH CLINICAL STAGES DIVERGE IN 2737 GENES, INDICATING THAT EACH ONE HAS A SPECIFIC METHYLATION SIGNATURE ASSOCIATED WITH TRANSPLANT OUTCOME. WE ALSO OBSERVED THAT TOLERANCE IS ASSOCIATED WITH DEMETHYLATION IN GENES INVOLVED IN IMMUNE FUNCTION, INCLUDING B AND T CELL ACTIVATION AND TH17 DIFFERENTIATION, WHILE IN CHRONIC REJECTION IT IS ASSOCIATED WITH INTRACELLULAR SIGNALING AND UBIQUITINATION PATHWAYS. USING CO-EXPRESSION NETWORK ANALYSIS, WE SELECTED 12 GENOMIC REGIONS THAT ARE SPECIFICALLY HYPOMETHYLATED OR HYPERMETHYLATED IN TOLERANT PATIENTS. ANALYSIS OF THESE GENES IN TRANSPLANTED PATIENTS WITH LOW DOSE OF STEROIDS SHOWED THAT THESE HAVE A SIMILAR METHYLATION SIGNATURE TO THAT OF TOLERANT RECIPIENTS. OVERALL, THESE RESULTS DEMONSTRATE THAT METHYLATION ANALYSIS CAN MIRROR THE IMMUNE STATUS ASSOCIATED WITH TRANSPLANT OUTCOME AND PROVIDES A STARTING POINT FOR UNDERSTANDING THE EPIGENETIC MECHANISMS ASSOCIATED WITH TOLERANCE.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
15 6684  33 VALIDATION OF AN LC-MS BASED APPROACH FOR PROFILING HISTONES IN CHRONIC LYMPHOCYTIC LEUKEMIA. THE IN VITRO EVALUATION OF HISTONES AND THEIR PTMS HAS DRAWN SUBSTANTIAL INTEREST IN THE DEVELOPMENT OF EPIGENETIC THERAPIES. THE DIFFERENTIAL EXPRESSION OF HISTONE ISOFORMS MAY SERVE AS A POTENTIAL MARKER IN THE CLASSIFICATION OF DISEASES AFFECTED BY CHROMATIN ABNORMALITIES. IN THIS STUDY, PROTEIN PROFILING BY LC AND MS WAS USED TO EXPLORE DIFFERENCES IN HISTONE COMPOSITION IN PRIMARY CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) CELLS. EXTENSIVE METHOD VALIDATIONS WERE PERFORMED TO DETERMINE THE EXPERIMENTAL VARIANCES THAT WOULD IMPACT HISTONE RELATIVE ABUNDANCE. THE RESULTING DATA DEMONSTRATED THAT THE PROPOSED METHODOLOGY WAS SUITABLE FOR THE ANALYSIS OF HISTONE PROFILES. IN 4 NORMAL INDIVIDUALS AND 40 CLL PATIENTS, A SIGNIFICANT DECREASE IN THE RELATIVE ABUNDANCE OF HISTONE H2A VARIANTS (H2AFL AND H2AFA/M*) WAS OBSERVED IN PRIMARY CLL CELLS AS COMPARED TO NORMAL B CELLS. PROTEIN IDENTITIES WERE DETERMINED USING HIGH MASS ACCURACY MS AND SHOTGUN PROTEOMICS.	2009	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
16 1562  29 DNA METHYLATION OF ENHANCER ELEMENTS IN MYELOID NEOPLASMS: THINK OUTSIDE THE PROMOTERS? GENE REGULATION THROUGH DNA METHYLATION IS A WELL DESCRIBED PHENOMENON THAT HAS A PROMINENT ROLE IN PHYSIOLOGICAL AND PATHOLOGICAL CELL-STATES. THIS EPIGENETIC MODIFICATION IS USUALLY GROUPED IN REGIONS DENOMINATED CPG ISLANDS, WHICH FREQUENTLY CO-LOCALIZE WITH GENE PROMOTERS, SILENCING THE TRANSCRIPTION OF THOSE GENES. RECENT GENOME-WIDE DNA METHYLATION STUDIES HAVE CHALLENGED THIS PARADIGM, DEMONSTRATING THAT DNA METHYLATION OF REGULATORY REGIONS OUTSIDE PROMOTERS IS ABLE TO INFLUENCE CELL-TYPE SPECIFIC GENE EXPRESSION PROGRAMS UNDER PHYSIOLOGIC OR PATHOLOGIC CONDITIONS. COUPLING GENOME-WIDE DNA METHYLATION ASSAYS WITH HISTONE MARK ANNOTATION HAS ALLOWED FOR THE IDENTIFICATION OF SPECIFIC EPIGENOMIC CHANGES THAT AFFECT ENHANCER REGULATORY REGIONS, REVEALING AN ADDITIONAL LAYER OF COMPLEXITY TO THE EPIGENETIC REGULATION OF GENE EXPRESSION. IN THIS REVIEW, WE SUMMARIZE THE NOVEL EVIDENCE FOR THE MOLECULAR AND BIOLOGICAL REGULATION OF DNA METHYLATION IN ENHANCER REGIONS AND THE DYNAMISM OF THESE CHANGES CONTRIBUTING TO THE FINE-TUNING OF GENE EXPRESSION. WE ALSO ANALYZE THE CONTRIBUTION OF ENHANCER DNA METHYLATION ON THE EXPRESSION OF RELEVANT GENES IN ACUTE MYELOID LEUKEMIA AND CHRONIC MYELOPROLIFERATIVE NEOPLASMS. THE CHARACTERIZATION OF THE ABERRANT ENHANCER DNA METHYLATION PROVIDES NOT ONLY A NOVEL PATHOGENIC MECHANISM FOR DIFFERENT TUMORS BUT ALSO HIGHLIGHTS NOVEL POTENTIAL THERAPEUTIC TARGETS FOR MYELOID DERIVED NEOPLASMS.	2019	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
17 4261  38 MGMT-METHYLATION IN NON-NEOPLASTIC DISEASES OF THE CENTRAL NERVOUS SYSTEM. QUANTIFYING O(6)-METHYLGUANINE-DNA METHYLTRANSFERASE (MGMT) PROMOTER METHYLATION PLAYS AN ESSENTIAL ROLE IN ASSESSING THE POTENTIAL EFFICACY OF ALKYLATING AGENTS IN THE CHEMOTHERAPY OF MALIGNANT GLIOMAS. MGMT PROMOTER METHYLATION IS CONSIDERED TO BE A CHARACTERISTIC OF SUBGROUPS OF CERTAIN MALIGNANCIES BUT HAS ALSO BEEN DESCRIBED IN VARIOUS PERIPHERAL INFLAMMATORY DISEASES. HOWEVER, MGMT PROMOTER METHYLATION LEVELS HAVE NOT YET BEEN INVESTIGATED IN NON-NEOPLASTIC BRAIN DISEASES. THIS STUDY DEMONSTRATES FOR THE FIRST TIME THAT ONE CAN INDEED DETECT SLIGHTLY ENHANCED MGMT PROMOTER METHYLATION IN INDIVIDUAL CASES OF INFLAMMATORY DEMYELINATING CNS DISEASES SUCH AS MULTIPLE SCLEROSIS AND PROGRESSIVE MULTIFOCAL LEUCENCEPHALOPATHY (PML), AS WELL AS IN OTHER DEMYELINATING DISEASES SUCH AS CENTRAL PONTINE AND EXPTRAPONTINE MYELINOLYSIS, AND DISEASES WITH MYELIN DAMAGE SUCH AS WALLERIAN DEGENERATION. IN THIS CONTEXT, WE IDENTIFIED A REDUCTION IN THE EXPRESSION OF THE DEMETHYLASE TET1 AS A POSSIBLE CAUSE FOR THE ENHANCED MGMT PROMOTER METHYLATION. HENCE, WE SHOW FOR THE FIRST TIME THAT MGMT HYPERMETHYLATION OCCURS IN CHRONIC DISEASES THAT ARE NOT STRICTLY ASSOCIATED TO DISTINCT PATHOGENS, ONCOGENIC VIRUSES OR NEOPLASMS BUT THAT LEAD TO DAMAGE OF THE MYELIN SHEATH IN VARIOUS WAYS. WHILE THIS GIVES NEW INSIGHTS INTO EPIGENETIC AND PATHOPHYSIOLOGICAL PROCESSES INVOLVED IN DE- AND REMYELINATION, WHICH MIGHT OFFER NEW THERAPEUTIC OPPORTUNITIES FOR DEMYELINATING DISEASES IN THE FUTURE, IT ALSO REDUCES THE SPECIFICITY OF MGMT HYPERMETHYLATION AS A TUMOR BIOMARKER.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
18 1518  37 DNA METHYLATION AS AN EPIGENETIC MECHANISM IN THE DEVELOPMENT OF MULTIPLE SCLEROSIS. THE EPIGENETIC MECHANISMS OF GENE EXPRESSION REGULATION ARE A GROUP OF THE KEY CELLULAR AND MOLECULAR PATHWAYS THAT LEAD TO INHERITED ALTERATIONS IN GENES' ACTIVITY WITHOUT CHANGING THEIR CODING SEQUENCE. DNA METHYLATION AT THE C5 POSITION OF CYTOSINE IN CPG DINUCLEOTIDES IS AMONGST THE CENTRAL EPIGENETIC MECHANISMS. CURRENTLY, THE NUMBER OF STUDIES THAT ARE DEVOTED TO THE IDENTIFICATION OF METHYLATION PATTERNS SPECIFIC TO MULTIPLE SCLEROSIS (MS), A SEVERE CHRONIC AUTOIMMUNE DISEASE OF THE CENTRAL NERVOUS SYSTEM, IS ON A RAPID RISE. HOWEVER, THE ISSUE OF THE CONTRIBUTION OF DNA METHYLATION TO THE DEVELOPMENT OF THE DIFFERENT CLINICAL PHENOTYPES OF THIS HIGHLY HETEROGENEOUS DISEASE HAS ONLY BEGUN TO ATTRACT THE ATTENTION OF RESEARCHERS. THIS REVIEW SUMMARIZES THE DATA ON THE MOLECULAR MECHANISMS UNDERLYING DNA METHYLATION AND THE MS RISK FACTORS THAT CAN AFFECT THE DNA METHYLATION PROFILE AND, THEREBY, MODULATE THE EXPRESSION OF THE GENES INVOLVED IN THE DISEASE'S PATHOGENESIS. THE FOCUS OF OUR ATTENTION IS CENTERED ON THE ANALYSIS OF THE PUBLISHED DATA ON THE DIFFERENTIAL METHYLATION OF DNA FROM VARIOUS BIOLOGICAL SAMPLES OF MS PATIENTS OBTAINED USING BOTH THE CANDIDATE GENE APPROACH AND HIGH-THROUGHPUT METHODS.	2021	
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
19  665  38 BLOOD TRANSCRIPTOMICS OF DRUG-NAIVE SPORADIC PARKINSON'S DISEASE PATIENTS. BACKGROUND: PARKINSON'S DISEASE (PD) IS A CHRONIC PROGRESSIVE NEURODEGENERATIVE DISORDER THAT IS CLINICALLY DEFINED IN TERMS OF MOTOR SYMPTOMS. THESE ARE PRECEDED BY PRODROMAL NON-MOTOR MANIFESTATIONS THAT PROVE THE SYSTEMIC NATURE OF THE DISEASE. IDENTIFYING GENES AND PATHWAYS ALTERED IN LIVING PATIENTS PROVIDE NEW INFORMATION ON THE DIAGNOSIS AND PATHOGENESIS OF SPORADIC PD. METHODS: CHANGES IN GENE EXPRESSION IN THE BLOOD OF 40 SPORADIC PD PATIENTS AND 20 HEALTHY CONTROLS ("DISCOVERY SET") WERE ANALYZED BY TAKING ADVANTAGE OF THE AFFYMETRIX PLATFORM. PATIENTS WERE AT THE ONSET OF MOTOR SYMPTOMS AND BEFORE INITIATING ANY PHARMACOLOGICAL TREATMENT. DATA ANALYSIS WAS PERFORMED BY APPLYING RANKING-PRINCIPAL COMPONENT ANALYSIS, PUMA AND SIGNIFICANCE ANALYSIS OF MICROARRAYS. FUNCTIONAL ANNOTATIONS WERE ASSIGNED USING GO, DAVID, GSEA TO UNVEIL SIGNIFICANT ENRICHED BIOLOGICAL PROCESSES IN THE DIFFERENTIALLY EXPRESSED GENES. THE EXPRESSIONS OF SELECTED GENES WERE VALIDATED USING RT-QPCR AND SAMPLES FROM AN INDEPENDENT COHORT OF 12 PATIENTS AND CONTROLS ("VALIDATION SET"). RESULTS: GENE EXPRESSION PROFILING OF BLOOD SAMPLES DISCRIMINATES PD PATIENTS FROM HEALTHY CONTROLS AND IDENTIFIES DIFFERENTIALLY EXPRESSED GENES IN BLOOD. THE MAJORITY OF THESE ARE ALSO PRESENT IN DOPAMINERGIC NEURONS OF THE SUBSTANTIA NIGRA, THE KEY SITE OF NEURODEGENERATION. TOGETHER WITH NEURONAL APOPTOSIS, LYMPHOCYTE ACTIVATION AND MITOCHONDRIAL DYSFUNCTION, ALREADY FOUND IN PREVIOUS ANALYSIS OF PD BLOOD AND POST-MORTEM BRAINS, WE UNVEILED TRANSCRIPTOME CHANGES ENRICHED IN BIOLOGICAL TERMS RELATED TO EPIGENETIC MODIFICATIONS INCLUDING CHROMATIN REMODELING AND METHYLATION. CANDIDATE TRANSCRIPTS AS CBX5, TCF3, MAN1C1 AND DOCK10 WERE VALIDATED BY RT-QPCR. CONCLUSIONS: OUR DATA SUPPORT THE USE OF BLOOD TRANSCRIPTOMICS TO STUDY NEURODEGENERATIVE DISEASES. IT IDENTIFIES CHANGES IN CRUCIAL COMPONENTS OF CHROMATIN REMODELING AND METHYLATION MACHINERIES AS EARLY EVENTS IN SPORADIC PD SUGGESTING EPIGENETICS AS TARGET FOR THERAPEUTIC INTERVENTION.	2015	
                                                                                                                                                                                                                                                               
20 1508  42 DNA METHYLATION AND MRNA AND MICRORNA EXPRESSION OF SLE CD4+ T CELLS CORRELATE WITH DISEASE PHENOTYPE. SYSTEMIC LUPUS ERYTHEMATOSUS (SLE) IS AN AUTOIMMUNE DISEASE WELL KNOWN FOR ITS CLINICAL HETEROGENEITY, AND ITS ETIOLOGY SECONDARY TO A CROSS-TALK INVOLVING GENETIC PREDISPOSITION AND ENVIRONMENTAL STIMULI. ALTHOUGH GENOME-WIDE ANALYSIS HAS CONTRIBUTED GREATLY TO OUR UNDERSTANDING OF THE GENETIC BASIS OF SLE, THERE IS INCREASING EVIDENCE FOR A ROLE OF EPIGENETICS. INDEED, RECENT DATA HAVE DEMONSTRATED THAT IN PATIENTS WITH SLE, THERE ARE STRIKING ALTERATIONS OF DNA METHYLATION, HISTONE MODIFICATIONS, AND DEREGULATED MICRORNA EXPRESSION, THE SUM OF WHICH CONTRIBUTE TO OVER-EXPRESSION OF SELECT AUTOIMMUNE-RELATED GENES AND LOSS OF TOLERANCE. TO ADDRESS THIS ISSUE AT THE LEVEL OF CLINICAL PHENOTYPE, WE PERFORMED DNA METHYLATION, MRNA AND MICRORNA EXPRESSION SCREENING USING HIGH-THROUGHPUT SEQUENCING OF PURIFIED CD4+ T CELLS FROM PATIENTS WITH SLE, COMPARED TO AGE AND SEX MATCHED CONTROLS. IN PARTICULAR, WE STUDIED 42 PATIENTS WITH SLE AND DIVIDED THIS GROUP INTO THREE CLINICAL PHENOTYPES: A) THE PRESENCE OF SKIN LESIONS WITHOUT SIGNS OF SYSTEMIC PATHOLOGY; B) SKIN LESIONS BUT ALSO CHRONIC RENAL PATHOLOGY; AND C) SKIN LESIONS, CHRONIC RENAL PATHOLOGY AND POLYARTICULAR DISEASE. INTERESTINGLY, AND AS EXPECTED, SEQUENCING DATA REVEALED CHANGES IN DNA METHYLATION IN SLE COMPARED TO CONTROLS. HOWEVER, AND MORE IMPORTANTLY, ALTHOUGH THERE WERE COMMON METHYLATION CHANGES FOUND IN ALL GROUPS OF SLE COMPARED TO CONTROLS, THERE WAS SPECIFIC DNA METHYLATION CHANGES THAT CORRELATED WITH CLINICAL PHENOTYPE. THESE INCLUDED CHANGES IN THE NOVEL KEY TARGET GENES NLRP2, CD300LB AND S1PR3, AS WELL AS CHANGES IN THE CRITICAL PATHWAYS, INCLUDING THE ADHERENS JUNCTION AND LEUKOCYTE TRANSENDOTHELIAL MIGRATION. WE ALSO NOTED THAT A SIGNIFICANT PROPORTION OF GENES UNDERGOING DNA METHYLATION CHANGES WERE INVERSELY CORRELATED WITH GENE EXPRESSION AND THAT MIRNA SCREENING REVEALED THE EXISTENCE OF SUBSETS WITH CHANGES IN EXPRESSION. INTEGRATED ANALYSIS OF THIS DATA HIGHLIGHTS SPECIFIC SETS OF MIRNAS CONTROLLED BY DNA METHYLATION, AND GENES THAT ARE ALTERED BY METHYLATION AND TARGETED BY MIRNAS. IN CONCLUSION, OUR FINDINGS SUGGEST SELECT EPIGENETIC MECHANISMS THAT CONTRIBUTE TO CLINICAL PHENOTYPES AND FURTHER SHED LIGHT ON A NEW VENUE FOR BASIC SLE RESEARCH.	2014