1 351 149 ALTERED ENDOTHELIAL DYSFUNCTION-RELATED MIRS IN PLASMA FROM ME/CFS PATIENTS. MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A COMPLEX DISEASE CHARACTERIZED BY UNEXPLAINED DEBILITATING FATIGUE. ALTHOUGH THE ETIOLOGY IS UNKNOWN, EVIDENCE SUPPORTS IMMUNOLOGICAL ABNORMALITIES, SUCH AS PERSISTENT INFLAMMATION AND IMMUNE-CELL ACTIVATION, IN A SUBSET OF PATIENTS. SINCE THE INTERPLAY BETWEEN INFLAMMATION AND VASCULAR ALTERATIONS IS WELL-ESTABLISHED IN OTHER DISEASES, ENDOTHELIAL DYSFUNCTION HAS EMERGED AS ANOTHER PLAYER IN ME/CFS PATHOGENESIS. ENDOTHELIAL NITRIC OXIDE SYNTHASE (ENOS) GENERATES NITRIC OXIDE (NO) THAT MAINTAINS ENDOTHELIAL HOMEOSTASIS. ENOS IS ACTIVATED BY SILENT INFORMATION REGULATOR 1 (SIRT1), AN ANTI-INFLAMMATORY PROTEIN. DESPITE ITS RELEVANCE, NO STUDY HAS ADDRESSED THE SIRT1/ENOS AXIS IN ME/CFS. THE INTEREST IN CIRCULATING MICRORNAS (MIRS) AS POTENTIAL BIOMARKERS IN ME/CFS HAS INCREASED IN RECENT YEARS. ACCORDINGLY, WE ANALYZE A SET OF MIRS REPORTED TO MODULATE THE SIRT1/ENOS AXIS USING PLASMA FROM ME/CFS PATIENTS. OUR RESULTS SHOW THAT MIR-21, MIR-34A, MIR-92A, MIR-126, AND MIR-200C ARE JOINTLY INCREASED IN ME/CFS PATIENTS COMPARED TO HEALTHY CONTROLS. A SIMILAR FINDING WAS OBTAINED WHEN ANALYZING PUBLIC MIR DATA ON PERIPHERAL BLOOD MONONUCLEAR CELLS. BIOINFORMATICS ANALYSIS SHOWS THAT ENDOTHELIAL FUNCTION-RELATED SIGNALING PATHWAYS ARE ASSOCIATED WITH THESE MIRS, INCLUDING OXIDATIVE STRESS AND OXYGEN REGULATION. INTERESTINGLY, HISTONE DEACETYLASE 1, A PROTEIN RESPONSIBLE FOR EPIGENETIC REGULATIONS, REPRESENTED THE MOST RELEVANT NODE WITHIN THE NETWORK. IN CONCLUSION, OUR STUDY PROVIDES A BASIS TO FIND ENDOTHELIAL DYSFUNCTION-RELATED BIOMARKERS AND EXPLORE NOVEL TARGETS IN ME/CFS. 2021 2 1026 48 CIRCULATING MIRNAS EXPRESSION IN MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME. MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A COMPLEX MULTIFACTORIAL DISEASE THAT CAUSES INCREASING MORBIDITY WORLDWIDE, AND MANY INDIVIDUALS WITH ME/CFS SYMPTOMS REMAIN UNDIAGNOSED DUE TO THE LACK OF DIAGNOSTIC BIOMARKERS. ITS ETIOLOGY IS STILL UNKNOWN, BUT INCREASING EVIDENCE SUPPORTS A ROLE OF HERPESVIRUSES (INCLUDING HHV-6A AND HHV-6B) AS POTENTIAL TRIGGERS. INTERESTINGLY, THE INFECTION BY THESE VIRUSES HAS BEEN REPORTED TO IMPACT THE EXPRESSION OF MICRORNAS (MIRNAS), SHORT NON-CODING RNA SEQUENCES WHICH HAVE BEEN SUGGESTED TO BE EPIGENETIC FACTORS MODULATING ME/CFS PATHOGENIC MECHANISMS. NOTABLY, THE PRESENCE OF CIRCULATING MIRNAS IN PLASMA HAS RAISED THE POSSIBILITY TO USE THEM AS VALUABLE BIOMARKERS FOR DISTINGUISHING ME/CFS PATIENTS FROM HEALTHY CONTROLS. THUS, THIS STUDY AIMED AT DETERMINING THE ROLE OF EIGHT MIRNAS, WHICH WERE SELECTED FOR THEIR PREVIOUS ASSOCIATION WITH ME/CFS, AS POTENTIAL CIRCULATING BIOMARKERS OF THE DISEASE. THEIR PRESENCE WAS QUANTITATIVELY EVALUATED IN PLASMA FROM 40 ME/CFS PATIENTS AND 20 HEALTHY CONTROLS BY SPECIFIC TAQMAN ASSAYS, AND THE RESULTS SHOWED THAT SIX OUT OF THE EIGHT OF THE SELECTED MIRNAS WERE DIFFERENTLY EXPRESSED IN PATIENTS COMPARED TO CONTROLS; MORE SPECIFICALLY, FIVE MIRNAS WERE SIGNIFICANTLY UPREGULATED (MIR-127-3P, MIR-142-5P, MIR-143-3P, MIR-150-5P, AND MIR-448), AND ONE WAS DOWNMODULATED (MIR-140-5P). MIRNA LEVELS DIRECTLY CORRELATED WITH DISEASE SEVERITY, WHEREAS NO SIGNIFICANT CORRELATIONS WERE OBSERVED WITH THE PLASMA LEVELS OF SEVEN PRO-INFLAMMATORY CYTOKINES OR WITH THE PRESENCE/LOAD OF HHV-6A/6B GENOME, AS JUDGED BY SPECIFIC PCR AMPLIFICATION. THE RESULTS MAY OPEN THE WAY FOR FURTHER VALIDATION OF MIRNAS AS NEW POTENTIAL BIOMARKERS IN ME/CFS AND INCREASE THE KNOWLEDGE OF THE COMPLEX PATHWAYS INVOLVED IN THE ME/CFS DEVELOPMENT. 2023 3 3041 35 GENOME-EPIGENOME INTERACTIONS ASSOCIATED WITH MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME. MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A COMPLEX DISEASE OF UNKNOWN ETIOLOGY. MULTIPLE STUDIES POINT TO DISRUPTIONS IN IMMUNE FUNCTIONING IN ME/CFS PATIENTS AS WELL AS SPECIFIC GENETIC POLYMORPHISMS AND ALTERATIONS OF THE DNA METHYLOME IN LYMPHOCYTES. HOWEVER, POTENTIAL INTERACTIONS BETWEEN DNA METHYLATION AND GENETIC BACKGROUND IN RELATION TO ME/CFS HAVE NOT BEEN EXAMINED. IN THIS STUDY WE EXPLORED THIS ASSOCIATION BY CHARACTERIZING THE EPIGENETIC (~480 THOUSAND CPG LOCI) AND GENETIC (~4.3 MILLION SNPS) VARIATION BETWEEN COHORTS OF ME/CFS PATIENTS AND HEALTHY CONTROLS. WE FOUND SIGNIFICANT ASSOCIATIONS OF DNA METHYLATION STATES IN T-LYMPHOCYTES AT SEVERAL CPG LOCI AND REGIONS WITH ME/CFS PHENOTYPE. THESE METHYLATION ANOMALIES ARE IN CLOSE PROXIMITY TO GENES INVOLVED WITH IMMUNE FUNCTION AND CELLULAR METABOLISM. FINALLY, WE FOUND SIGNIFICANT CORRELATIONS OF GENOTYPES WITH METHYLATION MODIFICATIONS ASSOCIATED WITH ME/CFS. THE FINDINGS FROM THIS STUDY HIGHLIGHT THE ROLE OF EPIGENETIC AND GENETIC INTERACTIONS IN COMPLEX DISEASES, AND SUGGEST SEVERAL GENETIC AND EPIGENETIC ELEMENTS POTENTIALLY INVOLVED IN THE MECHANISMS OF DISEASE IN ME/CFS. 2018 4 2207 52 EPIGENETIC MODIFICATIONS AND GLUCOCORTICOID SENSITIVITY IN MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS). BACKGROUND: MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A DEBILITATING IDIOPATHIC DISEASE CHARACTERIZED BY UNEXPLAINED FATIGUE THAT FAILS TO RESOLVE WITH SUFFICIENT REST. DIAGNOSIS IS BASED ON A LIST OF SYMPTOMS AND EXCLUSION OF OTHER FATIGUE-RELATED HEALTH CONDITIONS. DESPITE A HETEROGENEOUS PATIENT POPULATION, IMMUNE AND HYPOTHALAMIC-PITUITARY-ADRENAL (HPA) AXIS FUNCTION DIFFERENCES, SUCH AS ENHANCED NEGATIVE FEEDBACK TO GLUCOCORTICOIDS, ARE RECURRING FINDINGS IN ME/CFS STUDIES. EPIGENETIC MODIFICATIONS, SUCH AS CPG METHYLATION, ARE KNOWN TO REGULATE LONG-TERM PHENOTYPIC DIFFERENCES AND PREVIOUS WORK BY OUR GROUP FOUND DNA METHYLOME DIFFERENCES IN ME/CFS, HOWEVER THE RELATIONSHIP BETWEEN DNA METHYLOME MODIFICATIONS, CLINICAL AND FUNCTIONAL CHARACTERISTICS ASSOCIATED WITH ME/CFS HAS NOT BEEN EXAMINED. METHODS: WE EXAMINED THE DNA METHYLOME IN PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) OF A LARGER COHORT OF FEMALE ME/CFS PATIENTS USING THE ILLUMINA HUMANMETHYLATION450 BEADCHIP ARRAY. IN PARALLEL TO THE DNA METHYLOME ANALYSIS, WE INVESTIGATED IN VITRO GLUCOCORTICOID SENSITIVITY DIFFERENCES BY STIMULATING PBMCS WITH PHYTOHAEMAGGLUTININ AND SUPPRESSED GROWTH WITH DEXAMETHASONE. WE EXPLORED DNA METHYLATION DIFFERENCES USING BISULFITE PYROSEQUENCING AND STATISTICAL PERMUTATION. LINEAR REGRESSION WAS IMPLEMENTED TO DISCOVER EPIGENOMIC REGIONS ASSOCIATED WITH SELF-REPORTED QUALITY OF LIFE AND NETWORK ANALYSIS OF GENE ONTOLOGY TERMS TO BIOLOGICALLY CONTEXTUALIZE RESULTS. RESULTS: WE DETECTED 12,608 DIFFERENTIALLY METHYLATED SITES BETWEEN ME/CFS PATIENTS AND HEALTHY CONTROLS PREDOMINANTLY LOCALIZED TO CELLULAR METABOLISM GENES, SOME OF WHICH WERE ALSO RELATED TO SELF-REPORTED QUALITY OF LIFE HEALTH SCORES. AMONG ME/CFS PATIENTS, GLUCOCORTICOID SENSITIVITY WAS ASSOCIATED WITH DIFFERENTIAL METHYLATION AT 13 LOCI. CONCLUSIONS: OUR RESULTS INDICATE DNA METHYLATION MODIFICATIONS IN CELLULAR METABOLISM IN ME/CFS DESPITE A HETEROGENEOUS PATIENT POPULATION, IMPLICATING THESE PROCESSES IN IMMUNE AND HPA AXIS DYSFUNCTION IN ME/CFS. MODIFICATIONS TO EPIGENETIC LOCI ASSOCIATED WITH DIFFERENCES IN GLUCOCORTICOID SENSITIVITY MAY BE IMPORTANT AS BIOMARKERS FOR FUTURE CLINICAL TESTING. OVERALL, THESE FINDINGS ALIGN WITH RECENT ME/CFS WORK THAT POINT TOWARDS IMPAIRMENT IN CELLULAR ENERGY PRODUCTION IN THIS PATIENT POPULATION. 2017 5 2050 37 EPIGENETIC COMPONENTS OF MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME UNCOVER POTENTIAL TRANSPOSABLE ELEMENT ACTIVATION. PURPOSE: STUDIES TO DETERMINE EPIGENETIC CHANGES ASSOCIATED WITH MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) REMAIN SCARCE; HOWEVER, CURRENT EVIDENCE CLEARLY SHOWS THAT METHYLATION PATTERNS OF GENOMIC DNA AND NONCODING RNA PROFILES OF IMMUNE CELLS DIFFER BETWEEN PATIENTS AND HEALTHY SUBJECTS, SUGGESTING AN ACTIVE ROLE OF THESE EPIGENETIC MECHANISMS IN THE DISEASE. THE PRESENT STUDY COMPARES AND CONTRASTS THE AVAILABLE ME/CFS EPIGENETIC DATA IN AN EFFORT TO EVIDENCE OVERLAPPING PATHWAYS CAPABLE OF EXPLAINING AT LEAST SOME OF THE DYSFUNCTIONAL IMMUNE PARAMETERS LINKED TO THIS DISEASE. METHODS: A SYSTEMATIC SEARCH OF THE LITERATURE EVALUATING THE ME/CFS EPIGENOME LANDSCAPE WAS PERFORMED FOLLOWING THE PREFERRED REPORTING ITEMS FOR SYSTEMATIC REVIEWS AND META-ANALYSES CRITERIA. DIFFERENTIAL DNA METHYLATION AND NONCODING RNA DIFFERENTIAL EXPRESSION PATTERNS ASSOCIATED WITH ME/CFS WERE USED TO SCREEN FOR THE PRESENCE OF TRANSPOSABLE ELEMENTS USING THE DFAM BROWSER, A SEARCH PROGRAM NURTURED WITH THE REPBASE REPETITIVE SEQUENCE DATABASE AND THE REPEATMASKER ANNOTATION TOOL. FINDINGS: UNEXPECTEDLY, PARTICULAR ASSOCIATIONS OF TRANSPOSABLE ELEMENTS AND ME/CFS EPIGENETIC HALLMARKS WERE UNCOVERED. A MODEL FOR THE DISEASE EMERGED INVOLVING TRANSCRIPTIONAL INDUCTION OF ENDOGENOUS DORMANT TRANSPOSONS AND STRUCTURED CELLULAR RNA INTERACTIONS, TRIGGERING THE ACTIVATION OF THE INNATE IMMUNE SYSTEM WITHOUT A CONCOMITANT ACTIVE INFECTION. IMPLICATIONS: REPETITIVE SEQUENCE FILTERS (IE, REPEATMASKER) SHOULD BE AVOIDED WHEN ANALYZING TRANSCRIPTOMIC DATA TO ASSESS THE POTENTIAL PARTICIPATION OF REPETITIVE SEQUENCES ("JUNK REPETITIVE DNA"), REPRESENTING >45% OF THE HUMAN GENOME, IN THE ONSET AND EVOLUTION OF ME/CFS. IN ADDITION, TRANSPOSABLE ELEMENT SCREENINGS AIMED AT DESIGNING COST-EFFECTIVE, FOCUSED EMPIRICAL ASSAYS THAT CAN CONFIRM OR DISPROVE THE SUSPECTED INVOLVEMENT OF TRANSPOSON TRANSCRIPTIONAL ACTIVATION IN THIS DISEASE, FOLLOWING THE PILOT STRATEGY PRESENTED HERE, WILL REQUIRE DATABASES GATHERING LARGE ME/CFS EPIGENETIC DATASETS. 2019 6 1699 35 DYNAMIC EPIGENETIC CHANGES DURING A RELAPSE AND RECOVERY CYCLE IN MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME. MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) IS A COMPLEX DISEASE WITH VARIABLE SEVERITY. PATIENTS EXPERIENCE FREQUENT RELAPSES WHERE SYMPTOMS INCREASE IN SEVERITY, LEAVING THEM WITH A MARKED REDUCTION IN QUALITY OF LIFE. PREVIOUS WORK HAS INVESTIGATED MOLECULAR DIFFERENCES BETWEEN ME/CFS PATIENTS AND HEALTHY CONTROLS, BUT NOT THE DYNAMIC CHANGES SPECIFIC TO EACH INDIVIDUAL PATIENT. WE APPLIED PRECISION MEDICINE HERE TO MAP GENOMIC CHANGES IN TWO SELECTED ME/CFS PATIENTS THROUGH A PERIOD THAT CONTAINED A RELAPSE RECOVERY CYCLE. DNA WAS ISOLATED FROM TWO PATIENTS AND A HEALTHY AGE/GENDER MATCHED CONTROL AT REGULAR INTERVALS AND CAPTURED THE PATIENT RELAPSE IN EACH CASE. REDUCED REPRESENTATION DNA METHYLATION SEQUENCING PROFILES WERE OBTAINED SPANNING THE RELAPSE RECOVERY CYCLE. BOTH PATIENTS SHOWED A SIGNIFICANTLY LARGER METHYLOME VARIABILITY (10-20-FOLD) THROUGH THE PERIOD OF SAMPLING COMPARED WITH THE CONTROL. DURING THE RELAPSE, CHANGES IN THE METHYLOME PROFILES OF THE TWO PATIENTS WERE DETECTED IN REGULATORY-ACTIVE REGIONS OF THE GENOME THAT WERE ASSOCIATED, RESPECTIVELY, WITH 157 AND 127 DOWNSTREAM GENES, INDICATING DISTURBED METABOLIC, IMMUNE AND INFLAMMATORY FUNCTIONS. SEVERE HEALTH RELAPSES IN THE ME/CFS PATIENTS RESULTED IN FUNCTIONALLY IMPORTANT CHANGES IN THEIR DNA METHYLOMES THAT, WHILE DIFFERING BETWEEN THE TWO PATIENTS, LED TO VERY SIMILAR COMPROMISED PHYSIOLOGY. DNA METHYLATION AS A SIGNATURE OF DISEASE VARIABILITY IN ONGOING ME/CFS MAY HAVE PRACTICAL APPLICATIONS FOR STRATEGIES TO DECREASE RELAPSE FREQUENCY. 2022 7 1556 54 DNA METHYLATION MODIFICATIONS ASSOCIATED WITH CHRONIC FATIGUE SYNDROME. CHRONIC FATIGUE SYNDROME (CFS), ALSO KNOWN AS MYALGIC ENCEPHALOMYELITIS, IS A COMPLEX MULTIFACTORIAL DISEASE THAT IS CHARACTERIZED BY THE PERSISTENT PRESENCE OF FATIGUE AND OTHER PARTICULAR SYMPTOMS FOR A MINIMUM OF 6 MONTHS. SYMPTOMS FAIL TO DISSIPATE AFTER SUFFICIENT REST AND HAVE MAJOR EFFECTS ON THE DAILY FUNCTIONING OF CFS SUFFERERS. CFS IS A MULTI-SYSTEM DISEASE WITH A HETEROGENEOUS PATIENT POPULATION SHOWING A WIDE VARIETY OF FUNCTIONAL DISABILITIES AND ITS BIOLOGICAL BASIS REMAINS POORLY UNDERSTOOD. STABLE ALTERATIONS IN GENE FUNCTION IN THE IMMUNE SYSTEM HAVE BEEN REPORTED IN SEVERAL STUDIES OF CFS. EPIGENETIC MODIFICATIONS HAVE BEEN IMPLICATED IN LONG-TERM EFFECTS ON GENE FUNCTION, HOWEVER, TO OUR KNOWLEDGE, GENOME-WIDE EPIGENETIC MODIFICATIONS ASSOCIATED WITH CFS HAVE NOT BEEN EXPLORED. WE EXAMINED THE DNA METHYLOME IN PERIPHERAL BLOOD MONONUCLEAR CELLS ISOLATED FROM CFS PATIENTS AND HEALTHY CONTROLS USING THE ILLUMINA HUMANMETHYLATION450 BEADCHIP ARRAY, CONTROLLING FOR INVARIANT PROBES AND PROBES OVERLAPPING POLYMORPHIC SEQUENCES. GENE ONTOLOGY (GO) AND NETWORK ANALYSIS OF DIFFERENTIALLY METHYLATED GENES WAS PERFORMED TO DETERMINE POTENTIAL BIOLOGICAL PATHWAYS SHOWING CHANGES IN DNA METHYLATION IN CFS. WE FOUND AN INCREASED ABUNDANCE OF DIFFERENTIALLY METHYLATED GENES RELATED TO THE IMMUNE RESPONSE, CELLULAR METABOLISM, AND KINASE ACTIVITY. GENES ASSOCIATED WITH IMMUNE CELL REGULATION, THE LARGEST COORDINATED ENRICHMENT OF DIFFERENTIALLY METHYLATED PATHWAYS, SHOWED HYPOMETHYLATION WITHIN PROMOTERS AND OTHER GENE REGULATORY ELEMENTS IN CFS. THESE DATA ARE CONSISTENT WITH EVIDENCE OF MULTISYSTEM DYSREGULATION IN CFS AND IMPLICATE THE INVOLVEMENT OF DNA MODIFICATIONS IN CFS PATHOLOGY. 2014 8 6405 48 THE SARS-COV-2 RECEPTOR ANGIOTENSIN-CONVERTING ENZYME 2 (ACE2) IN MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME: ANALYSIS OF HIGH-THROUGHPUT EPIGENETIC AND GENE EXPRESSION STUDIES. PATIENTS AFFECTED BY MYALGIC ENCEPHALOMYELITIS/CHRONIC FATIGUE SYNDROME (ME/CFS) SHOW SPECIFIC EPIGENETIC AND GENE EXPRESSION SIGNATURES OF THE DISEASE. HOWEVER, IT IS UNKNOWN WHETHER THESE SIGNATURES INCLUDE ABNORMAL LEVELS OF THE HUMAN ANGIOTENSIN-CONVERTING ENZYMES, ACE AND ACE2, THE LATTER BEING THE MAIN RECEPTOR DESCRIBED FOR THE HOST-CELL INVASION BY SARS-COV-2. TO INVESTIGATE THAT, WE FIRST RE-ANALYZED AVAILABLE CASE-CONTROL EPIGENOME-WIDE ASSOCIATION STUDIES BASED ON DNA METHYLATION DATA, AND CASE-CONTROL GENE EXPRESSION STUDIES BASED ON MICROARRAY DATA. FROM THESE PUBLISHED STUDIES, WE FOUND AN ASSOCIATION BETWEEN ME/CFS AND 4 POTENTIALLY HYPOMETHYLATED PROBES LOCATED IN THE ACE LOCUS. WE ALSO FOUND ANOTHER DISEASE ASSOCIATION WITH ONE HYPOMETHYLATED PROBE LOCATED IN THE TRANSCRIPTION START SITE OF ACE2. THE SAME DISEASE ASSOCIATIONS WERE OBTAINED FOR WOMEN BUT NOT FOR MEN AFTER PERFORMING SEX-SPECIFIC ANALYSES. IN CONTRAST, A META-ANALYSIS OF GENE EXPRESSION LEVELS COULD NOT PROVIDE EVIDENCE FOR A DIFFERENTIALLY EXPRESSION OF ACE AND ACE2 IN AFFECTED PATIENTS WHEN COMPARED TO HEALTHY CONTROLS. IN LINE WITH THIS NEGATIVE FINDING, THE ANALYSIS OF A NEW DATA SET ON THE GENE EXPRESSION OF ACE AND ACE2 IN PERIPHERAL BLOOD MONONUCLEAR CELLS DID NOT FIND ANY DIFFERENCES BETWEEN A FEMALE COHORT OF 37 PATIENTS AND 34 AGE-MATCHED HEALTHY CONTROLS. FUTURE STUDIES SHOULD BE CONDUCTED TO EXTEND THIS INVESTIGATION TO OTHER POTENTIAL RECEPTORS USED BY SARS-COV-2. THESE STUDIES WILL HELP RESEARCHERS AND CLINICIANS TO IMPROVE THE UNDERSTANDING OF THE HEALTH RISK IMPOSED BY THIS VIRUS WHEN INFECTING PATIENTS AFFECTED BY THIS DEBILITATING DISEASE. 2021 9 4348 43 MIR-146A DYSREGULATES ENERGY METABOLISM DURING NEUROINFLAMMATION. ALZHEIMER'S DISEASE (AD) AND OTHER NEURODEGENERATIVE DISEASES ARE CHARACTERIZED BY CHRONIC NEUROINFLAMMATION AND A REDUCTION IN BRAIN ENERGY METABOLISM. AN IMPORTANT ROLE HAS EMERGED FOR SMALL, NON-CODING RNA MOLECULES KNOWN AS MICRORNAS (MIRNAS) IN THE PATHOPHYSIOLOGY OF MANY NEURODEGENERATIVE DISORDERS. AS EPIGENETIC REGULATORS, MIRNAS POSSESS THE CAPACITY TO REGULATE AND FINE TUNE PROTEIN PRODUCTION BY INHIBITING TRANSLATION. SEVERAL MIRNAS, WHICH INCLUDE MIR-146A, ARE ELEVATED IN THE BRAIN, CSF, AND PLASMA OF AD PATIENTS. MIR-146A PARTICIPATES IN PATHWAYS THAT REGULATE IMMUNE ACTIVATION AND HAS SEVERAL MRNA TARGETS WHICH ENCODE FOR PROTEINS INVOLVED IN CELLULAR ENERGY METABOLISM. AN ADDITIONAL ROLE FOR EXTRACELLULAR VESICLES (EVS) HAS ALSO EMERGED IN THE PROGRESSION AD, AS EVS CAN TRANSFER FUNCTIONALLY ACTIVE PROTEINS AND RNAS FROM DISEASED TO HEALTHY CELLS. IN THE CURRENT STUDY, WE EXPOSED VARIOUS CELL TYPES PRESENT WITHIN THE CNS TO IMMUNOMODULATORY MOLECULES AND OBSERVED SIGNIFICANT UPREGULATION OF MIR-146A EXPRESSION, BOTH WITHIN CELLS AND WITHIN THEIR SECRETED EVS. FURTHER, WE ASSESSED THE EFFECTS OF MIR-146A OVEREXPRESSION ON BIOENERGETIC FUNCTION IN PRIMARY RAT GLIAL CELLS AND FOUND SIGNIFICANT REDUCTIONS IN OXIDATIVE PHOSPHORYLATION AND GLYCOLYSIS. LASTLY, WE CORRELATED MIR-146A EXPRESSION LEVELS WITHIN VARIOUS REGIONS OF THE AD BRAIN TO DISEASE STAGING AND FOUND SIGNIFICANT, POSITIVE CORRELATIONS. THESE NOVEL RESULTS DEMONSTRATE THAT THE MODULATION OF MIR-146A IN RESPONSE TO NEUROINFLAMMATORY STIMULI MAY MEDIATE THE LOSS OF MITOCHONDRIAL INTEGRITY AND FUNCTION IN CELLS, THEREBY CONTRIBUTING TO THE PROGRESSION OF BETA-AMYLOID AND TAU PATHOLOGY IN THE AD BRAIN. MULTIPLE INFLAMMATORY STIMULI CAN UPREGULATE MIRNA-146A EXPRESSION WITHIN NEURONS, MIXED GLIAL CELLS, AND BRAIN ENDOTHELIAL CELLS, WHICH IS EITHER RETAINED WITHIN THESE CELLS OR RELEASED FROM THEM AS EXTRACELLULAR VESICLE CARGO. THE UPREGULATION OF MIR-146A DISRUPTS CELLULAR BIOENERGETICS IN MIXED GLIAL CELLS. THIS MECHANISM MAY PLAY A CRITICAL ROLE IN THE NEUROINFLAMMATORY RESPONSE OBSERVED DURING ALZHEIMER'S DISEASE. 2022 10 3496 50 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 11 822 32 CHARACTERIZATION OF BLOOD SURROGATE IMMUNE-METHYLATION BIOMARKERS FOR IMMUNE CELL INFILTRATION IN CHRONIC INFLAMMAGING DISORDERS. ALZHEIMER'S DISEASE (AD) AND ATHEROSCLEROSIS ARE BOTH CHRONIC AGE- AND INFLAMMATION-DEPENDENT DISEASES. IN ADDITION, ATHEROSCLEROSIS IS FREQUENTLY OBSERVED IN AD PATIENTS INDICATING COMMON INVOLVEMENT OF VASCULAR COMPONENTS IN BOTH DISEASE ETIOLOGIES. RECENTLY, EPIGENOME-WIDE ASSOCIATION STUDIES HAVE IDENTIFIED EPIGENETIC ALTERATIONS, AND IN PARTICULARLY DNA METHYLATION CHANGES FOR BOTH DISORDERS. WE HYPOTHESIZED THE EXISTENCE OF A COMMON DNA METHYLATION PROFILE IN ATHEROSCLEROSIS AND AD WHICH MAY BE VALUABLE AS A BLOOD-BASED DNA METHYLATION INFLAMMAGING BIOMARKER. USING PUBLICLY AVAILABLE 450K ILLUMINA METHYLATION DATASETS, WE IDENTIFIED A CO-METHYLATION NETWORK ASSOCIATED WITH BOTH ATHEROSCLEROSIS AND AD IN WHOLE BLOOD SAMPLES. THIS METHYLATION PROFILE APPEARED TO INDICATE SHIFTS IN BLOOD IMMUNE CELL TYPE DISTRIBUTION. REMARKABLY, SIMILAR METHYLATION CHANGES WERE ALSO DETECTED IN DISEASE TISSUES, INCLUDING AD BRAIN TISSUES, ATHEROSCLEROTIC PLAQUES, AND TUMORS AND WERE FOUND TO CORRELATE WITH IMMUNE CELL INFILTRATION. IN ADDITION, THIS IMMUNE-RELATED METHYLATION PROFILE COULD ALSO BE DETECTED IN OTHER INFLAMMAGING DISEASES, INCLUDING PARKINSON'S DISEASE AND OBESITY, BUT NOT IN MULTIPLE SCLEROSIS, SCHIZOPHRENIA, AND OSTEOPOROSIS. IN CONCLUSION, WE IDENTIFIED A BLOOD-BASED IMMUNE-RELATED DNA METHYLATION SIGNATURE IN MULTIPLE INFLAMMAGING DISEASES ASSOCIATED WITH CHANGES IN BLOOD IMMUNE CELL COUNTS AND PREDICTIVE FOR IMMUNE CELL INFILTRATION IN DISEASED TISSUES. IN ADDITION TO EPIGENETIC CLOCK MEASUREMENTS, THIS IMMUNE-METHYLATION SIGNATURE MAY BECOME A VALUABLE BLOOD-BASED BIOMARKER TO PREVENT CHRONIC INFLAMMATORY DISEASE DEVELOPMENT OR MONITOR LIFESTYLE INTERVENTION STRATEGIES WHICH PROMOTE HEALTHY AGING. 2019 12 812 49 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 13 6149 39 THE EXPRESSION PROFILE OF MIR-23B IS NOT ALTERED IN PERIPHERAL BLOOD MONONUCLEAR CELLS OF PATIENTS WITH IDIOPATHIC INFLAMMATORY MYOPATHIES. IDIOPATHIC INFLAMMATORY MYOPATHIES (IIM) BELONG TO A GROUP OF AUTOIMMUNE DISORDERS, PRIMARILY CHARACTERIZED BY CHRONIC INFLAMMATION OF HUMAN SKELETAL MUSCLE TISSUE. THE ETIOLOGY OF THESE DISEASES IS UNKNOWN, HOWEVER, GENETIC PREDISPOSITION PLAYS A SIGNIFICANT ROLE IN DISEASE ONSET. BESIDE THE KNOWN GENETIC RISK LOCATED IN THE MHC COMPLEX, THE EPIGENETIC MODIFICATIONS INCLUDING CHANGES IN MIRNAS EXPRESSION PROFILES HAVE BEEN RECENTLY IMPLICATED RECENTLY IN MANY AUTOIMMUNE DISEASES. MICRO RNA MOLECULES ARE INVOLVED IN MANY PHYSIOLOGICAL PROCESSES, INCLUDING THE REGULATION OF THE IMMUNE RESPONSE. IN OUR STUDY WE HAVE FOCUSED ON THE MIR-23B, AS IT REPRESENTS A NOVEL PROMISING AUTOIMMUNITY REGULATOR MOLECULE. DOWNREGULATION OF MIR-23B WAS RECENTLY DESCRIBED IN PATIENTS WITH RHEUMATOID ARTHRITIS AND SYSTEMIC LUPUS ERYTHEMATOSUS. WE HAVE MEASURED THE EXPRESSION MIR-23B PERIPHERAL BLOOD MONONUCLEAR CELLS OF PATIENTS WITH DERMATOMYOSITIS AND POLYMYOSITIS. NO MEANINGFUL DIFFERENCE WAS FOUND IN COMPARISON WITH HEALTHY CONTROLS. 2013 14 5305 44 PROTEOMICS ANALYSIS OF HUMAN OBESITY REVEALS THE EPIGENETIC FACTOR HDAC4 AS A POTENTIAL TARGET FOR OBESITY. SEDENTARY LIFESTYLE AND EXCESSIVE ENERGY INTAKE ARE PROMINENT CONTRIBUTORS TO OBESITY; A MAJOR RISK FACTORS FOR THE DEVELOPMENT OF INSULIN RESISTANCE, TYPE 2 DIABETES AND CARDIOVASCULAR DISEASES. ELUCIDATING THE MOLECULAR MECHANISMS UNDERLYING THESE CHRONIC CONDITIONS IS OF RELEVANT IMPORTANCE AS IT MIGHT LEAD TO THE IDENTIFICATION OF NOVEL ANTI-OBESITY TARGETS. THE PURPOSE OF THE CURRENT STUDY IS TO INVESTIGATE DIFFERENTIALLY EXPRESSED PROTEINS BETWEEN LEAN AND OBESE SUBJECTS THROUGH A SHOT-GUN QUANTITATIVE PROTEOMICS APPROACH USING PERIPHERAL BLOOD MONONUCLEAR CELLS (PBMCS) EXTRACTS AS WELL AS POTENTIAL MODULATION OF THOSE PROTEINS BY PHYSICAL EXERCISE. USING THIS APPROACH, A TOTAL OF 47 PROTEINS SHOWED AT LEAST 1.5 FOLD CHANGE BETWEEN LEAN AND OBESE SUBJECTS. IN OBESE, THE PROTEOMIC PROFILING BEFORE AND AFTER 3 MONTHS OF PHYSICAL EXERCISE SHOWED DIFFERENTIAL EXPRESSION OF 38 PROTEINS. THROMBOSPONDIN 1 (TSP1) WAS AMONG THE PROTEINS THAT WERE UPREGULATED IN OBESE SUBJECTS AND THEN DECREASED BY PHYSICAL EXERCISE. CONVERSELY, THE HISTONE DEACETYLASE 4 (HDAC4) WAS DOWNREGULATED IN OBESE SUBJECTS AND THEN INDUCED BY PHYSICAL EXERCISE. THE PROTEOMIC DATA WAS FURTHER VALIDATED BY QRT-PCR, WESTERN BLOT AND IMMUNOHISTOCHEMISTRY IN BOTH PBMCS AND ADIPOSE TISSUE. WE ALSO SHOWED THAT HDAC4 LEVELS CORRELATED POSITIVELY WITH MAXIMUM OXYGEN CONSUMPTION (VO2 MAX) BUT NEGATIVELY WITH BODY MASS INDEX, PERCENT BODY FAT, AND THE INFLAMMATORY CHEMOKINE RANTES. IN FUNCTIONAL ASSAYS, OUR DATA INDICATED THAT ECTOPIC EXPRESSION OF HDAC4 SIGNIFICANTLY IMPAIRED TNF-ALPHA-DEPENDENT ACTIVATION OF NF-KAPPAB, ESTABLISHING THUS A LINK BETWEEN HDAC4 AND REGULATION OF THE IMMUNE SYSTEM. TOGETHER, THE EXPRESSION PATTERN OF HDAC4 IN OBESE SUBJECTS BEFORE AND AFTER PHYSICAL EXERCISE, ITS CORRELATION WITH VARIOUS PHYSICAL, CLINICAL AND METABOLIC PARAMETERS ALONG WITH ITS INHIBITORY EFFECT ON NF-KAPPAB ARE SUGGESTIVE OF A PROTECTIVE ROLE OF HDAC4 AGAINST OBESITY. HDAC4 COULD THEREFORE REPRESENT A POTENTIAL THERAPEUTIC TARGET FOR THE CONTROL AND MANAGEMENT OF OBESITY AND PRESUMABLY INSULIN RESISTANCE. 2013 15 2909 36 GENE EXPRESSION PROFILING IN FIBROMYALGIA INDICATES AN AUTOIMMUNE ORIGIN OF THE DISEASE AND OPENS NEW AVENUES FOR TARGETED THERAPY. FIBROMYALGIA IS A CHRONIC DISORDER CHARACTERIZED BY WIDESPREAD PAIN AND BY SEVERAL NON-PAIN SYMPTOMS. AUTOIMMUNITY, SMALL FIBER NEUROPATHY AND NEUROINFLAMMATION HAVE BEEN SUGGESTED TO BE INVOLVED IN THE PATHOGENESIS OF THE DISEASE. WE HAVE INVESTIGATED THE GENE EXPRESSION PROFILE IN PERIPHERAL BLOOD MONONUCLEAR CELLS OBTAINED FROM TEN PATIENTS AND TEN HEALTHY SUBJECTS. OF THE 545,500 TRANSCRIPTS ANALYZED, 1673 RESULTED MODULATED IN FIBROMYALGIC PATIENTS. THE MAJORITY OF THESE GENES ARE INVOLVED IN BIOLOGICAL PROCESSES AND PATHWAYS LINKED TO THE CLINICAL MANIFESTATIONS OF THE DISEASE. MOREOVER, GENES INVOLVED IN IMMUNOLOGICAL PATHWAYS CONNECTED TO INTERLEUKIN-17 AND TO TYPE I INTERFERON SIGNATURES WERE ALSO MODULATED, SUGGESTING THAT AUTOIMMUNITY PLAYS A ROLE IN THE DISEASE. WE THEN AIMED AT IDENTIFYING DIFFERENTIALLY EXPRESSED LONG NON-CODING RNAS (LNCRNAS) FUNCTIONALLY CONNECTED TO MODULATED GENES BOTH DIRECTLY AND VIA MICRORNA TARGETING. ONLY TWO LNCRNAS OF THE 298 FOUND MODULATED IN PATIENTS, WERE ABLE TO TARGET THE MOST HIGHLY CONNECTED GENES IN THE FIBROMYALGIA INTERACTOME, SUGGESTING THEIR INVOLVEMENT IN CRUCIAL GENE REGULATION. OUR GENE EXPRESSION DATA WERE CONFIRMED BY REAL TIME PCR, BY AUTOANTIBODY TESTING, DETECTION OF SOLUBLE MEDIATORS AND TH-17 POLARIZATION IN A VALIDATION COHORT OF 50 PATIENTS. OUR RESULTS INDICATE THAT GENETIC AND EPIGENETIC MECHANISMS AS WELL AS AUTOIMMUNITY PLAY A PIVOTAL ROLE IN THE PATHOGENESIS OF FIBROMYALGIA. 2020 16 1717 29 DYSREGULATED IMMUNE SYSTEM NETWORKS IN WAR VETERANS WITH PTSD IS AN OUTCOME OF ALTERED MIRNA EXPRESSION AND DNA METHYLATION. POST-TRAUMATIC STRESS DISORDER PATIENTS EXPERIENCE CHRONIC SYSTEMIC INFLAMMATION. HOWEVER, THE MOLECULAR PATHWAYS INVOLVED AND MECHANISMS REGULATING THE EXPRESSION OF GENES INVOLVED IN INFLAMMATORY PATHWAYS IN PTSD ARE REPORTED INADEQUATELY. THROUGH RNA SEQUENCING AND MIRNA MICROARRAY, WE IDENTIFIED 326 GENES AND 190 MIRNAS THAT WERE SIGNIFICANTLY DIFFERENT IN THEIR EXPRESSION LEVELS IN THE PBMCS OF PTSD PATIENTS. EXPRESSION PAIRING OF THE DIFFERENTIALLY EXPRESSED GENES AND MIRNAS INDICATED AN INVERSE RELATIONSHIP IN THEIR EXPRESSION. FUNCTIONAL ANALYSIS OF THE DIFFERENTIALLY EXPRESSED GENES INDICATED THEIR INVOLVEMENT IN THE CANONICAL PATHWAYS SPECIFIC TO IMMUNE SYSTEM BIOLOGY. DNA METHYLATION ANALYSIS OF DIFFERENTIALLY EXPRESSED GENES ALSO SHOWED A GRADUAL TREND TOWARDS DIFFERENCES BETWEEN CONTROL AND PTSD PATIENTS, AGAIN INDICATING A POSSIBLE ROLE OF THIS EPIGENETIC MECHANISM IN PTSD INFLAMMATION. OVERALL, COMBINING DATA FROM THE THREE TECHNIQUES PROVIDED A HOLISTIC VIEW OF SEVERAL PATHWAYS IN WHICH THE DIFFERENTIALLY EXPRESSED GENES WERE IMPACTED THROUGH EPIGENETIC MECHANISMS, IN PTSD. THUS, ANALYSIS COMBINING DATA FROM RNA-SEQ, MIRNA ARRAY AND DNA METHYLATION, CAN PROVIDE KEY EVIDENCE ABOUT DYSREGULATED PATHWAYS AND THE CONTROLLING MECHANISM IN PTSD. MOST IMPORTANTLY, THE PRESENT STUDY PROVIDES FURTHER EVIDENCE THAT INFLAMMATION IN PTSD COULD BE EPIGENETICALLY REGULATED. 2016 17 5856 35 SUBSTRATE UTILISATION OF CULTURED SKELETAL MUSCLE CELLS IN PATIENTS WITH CFS. CHRONIC FATIGUE SYNDROME (CFS) PATIENTS OFTEN SUFFER FROM SEVERE MUSCLE PAIN AND AN INABILITY TO EXERCISE DUE TO MUSCLE FATIGUE. IT HAS PREVIOUSLY BEEN SHOWN THAT CFS SKELETAL MUSCLE CELLS HAVE LOWER LEVELS OF ATP AND HAVE AMP-ACTIVATED PROTEIN KINASE DYSFUNCTION. THIS STUDY OUTLINES EXPERIMENTS LOOKING AT THE UTILISATION OF DIFFERENT SUBSTRATES BY SKELETAL MUSCLE CELLS FROM CFS PATIENTS (N = 9) AND HEALTHY CONTROLS (N = 11) USING EXTRACELLULAR FLUX ANALYSIS. RESULTS SHOW THAT CFS SKELETAL MUSCLE CELLS ARE UNABLE TO UTILISE GLUCOSE TO THE SAME EXTENT AS HEALTHY CONTROL CELLS. CFS SKELETAL MUSCLE CELLS WERE SHOWN TO OXIDISE GALACTOSE AND FATTY ACIDS NORMALLY, INDICATING THAT THE BIOENERGETIC DYSFUNCTION LIES UPSTREAM OF THE TCA CYCLE. THE DYSFUNCTION IN GLUCOSE OXIDATION IS SIMILAR TO WHAT HAS PREVIOUSLY BEEN SHOWN IN BLOOD CELLS FROM CFS PATIENTS. THE CONSISTENCY OF CELLULAR BIOENERGETIC DYSFUNCTION IN DIFFERENT CELL TYPES SUPPORTS THE HYPOTHESIS THAT CFS IS A SYSTEMIC DISEASE. THE RETENTION OF BIOENERGETIC DEFECTS IN CULTURED CELLS INDICATES THAT THERE IS A GENETIC OR EPIGENETIC COMPONENT TO THE DISEASE. THIS IS THE FIRST STUDY TO USE CELLS DERIVED FROM SKELETAL MUSCLE BIOPSIES IN CFS PATIENTS AND HEALTHY CONTROLS TO LOOK AT CELLULAR BIOENERGETIC FUNCTION IN WHOLE CELLS. 2020 18 3 42 "EPIGENOME-WIDE METHYLATION PROFILE OF CHRONIC KIDNEY DISEASE-DERIVED ARTERIAL DNA UNCOVERS NOVEL PATHWAYS IN DISEASE-ASSOCIATED CARDIOVASCULAR PATHOLOGY.". CHRONIC KIDNEY DISEASE (CKD) RELATED CARDIOVASCULAR DISEASE (CVD) IS CHARACTERIZED BY VASCULAR REMODELLING WITH WELL-ESTABLISHED STRUCTURAL AND FUNCTIONAL CHANGES IN THE VASCULAR WALL SUCH AS ARTERIAL STIFFNESS, MATRIX DEPOSITION, AND CALCIFICATION. THESE PHENOTYPIC CHANGES RESEMBLE PATHOLOGY SEEN IN AGEING, AND ARE LIKELY TO BE MEDIATED BY SUSTAINED ALTERATIONS IN GENE EXPRESSION, WHICH MAY BE CAUSED BY EPIGENETIC CHANGES SUCH AS TISSUE-SPECIFIC DNA METHYLATION. WE AIMED TO INVESTIGATE TISSUE SPECIFIC CHANGES IN DNA METHYLATION THAT OCCUR IN CKD-RELATED CVD. GENOME-WIDE DNA METHYLATION CHANGES WERE EXAMINED IN BISULPHITE CONVERTED GENOMIC DNA ISOLATED FROM THE VASCULAR MEDIA OF CKD AND HEALTHY ARTERIES. METHYLATION-SPECIFIC PCR WAS USED TO VALIDATE THE ARRAY DATA, AND THE ASSOCIATION BETWEEN DNA METHYLATION AND GENE AND PROTEIN EXPRESSION WAS EXAMINED. THE DNA METHYLATION AGE WAS COMPARED TO THE CHRONOLOGICAL AGE IN BOTH CASES AND CONTROLS. THREE HUNDRED AND NINETEEN DIFFERENTIALLY METHYLATED REGIONS (DMR) WERE IDENTIFIED SPREAD ACROSS THE GENOME. PATHWAY ANALYSIS REVEALED THAT DMRS ASSOCIATED WITH GENES WERE INVOLVED IN EMBRYONIC AND VASCULAR DEVELOPMENT, AND SIGNALLING PATHWAYS SUCH AS TGFBETA AND FGF. EXPRESSION OF TOP DIFFERENTIALLY METHYLATED GENE HOXA5 SHOWED A SIGNIFICANT NEGATIVE CORRELATION WITH DNA METHYLATION. INTERESTINGLY, DNA METHYLATION AGE AND CHRONOLOGICAL AGE WERE HIGHLY CORRELATED, BUT THERE WAS NO EVIDENCE OF ACCELERATED AGE-RELATED DNA METHYLATION IN THE ARTERIES OF CKD PATIENTS. IN CONCLUSION, WE DEMONSTRATED THAT DIFFERENTIAL DNA METHYLATION IN THE ARTERIAL TISSUE OF CKD PATIENTS REPRESENTS A POTENTIAL MEDIATOR OF ARTERIAL PATHOLOGY AND MAY BE USED TO UNCOVER NOVEL PATHWAYS IN THE GENESIS OF CKD-ASSOCIATED COMPLICATIONS. 2021 19 1269 35 CYTOSINE METHYLATION CHANGES IN ENHANCER REGIONS OF CORE PRO-FIBROTIC GENES CHARACTERIZE KIDNEY FIBROSIS DEVELOPMENT. BACKGROUND: ONE IN ELEVEN PEOPLE IS AFFECTED BY CHRONIC KIDNEY DISEASE, A CONDITION CHARACTERIZED BY KIDNEY FIBROSIS AND PROGRESSIVE LOSS OF KIDNEY FUNCTION. EPIDEMIOLOGICAL STUDIES INDICATE THAT ADVERSE INTRAUTERINE AND POSTNATAL ENVIRONMENTS HAVE A LONG-LASTING ROLE IN CHRONIC KIDNEY DISEASE DEVELOPMENT. EPIGENETIC INFORMATION REPRESENTS A PLAUSIBLE CARRIER FOR MEDIATING THIS PROGRAMMING EFFECT. HERE WE DEMONSTRATE THAT GENOME-WIDE CYTOSINE METHYLATION PATTERNS OF HEALTHY AND CHRONIC KIDNEY DISEASE TUBULE SAMPLES OBTAINED FROM PATIENTS SHOW SIGNIFICANT DIFFERENCES. RESULTS: WE IDENTIFY DIFFERENTIALLY METHYLATED REGIONS AND VALIDATE THESE IN A LARGE REPLICATION DATASET. THE DIFFERENTIALLY METHYLATED REGIONS ARE RARELY OBSERVED ON PROMOTERS, BUT MOSTLY OVERLAP WITH PUTATIVE ENHANCER REGIONS, AND THEY ARE ENRICHED IN CONSENSUS BINDING SEQUENCES FOR IMPORTANT RENAL TRANSCRIPTION FACTORS. THIS INDICATES THEIR IMPORTANCE IN GENE EXPRESSION REGULATION. A CORE SET OF GENES THAT ARE KNOWN TO BE RELATED TO KIDNEY FIBROSIS, INCLUDING GENES ENCODING COLLAGENS, SHOW CYTOSINE METHYLATION CHANGES CORRELATING WITH DOWNSTREAM TRANSCRIPT LEVELS. CONCLUSIONS: OUR REPORT RAISES THE POSSIBILITY THAT EPIGENETIC DYSREGULATION PLAYS A ROLE IN CHRONIC KIDNEY DISEASE DEVELOPMENT VIA INFLUENCING CORE PRO-FIBROTIC PATHWAYS AND CAN AID THE DEVELOPMENT OF NOVEL BIOMARKERS AND FUTURE THERAPEUTICS. 2013 20 2920 43 GENE-SET ANALYSIS IS SEVERELY BIASED WHEN APPLIED TO GENOME-WIDE METHYLATION DATA. MOTIVATION: DNA METHYLATION IS AN EPIGENETIC MARK THAT CAN STABLY REPRESS GENE EXPRESSION. BECAUSE OF ITS BIOLOGICAL AND CLINICAL SIGNIFICANCE, SEVERAL METHODS HAVE BEEN DEVELOPED TO COMPARE GENOME-WIDE PATTERNS OF METHYLATION BETWEEN GROUPS OF SAMPLES. THE APPLICATION OF GENE SET ANALYSIS TO IDENTIFY RELEVANT GROUPS OF GENES THAT ARE ENRICHED FOR DIFFERENTIALLY METHYLATED GENES IS OFTEN A MAJOR COMPONENT OF THE ANALYSIS OF THESE DATA. THIS CAN BE USED, FOR EXAMPLE, TO IDENTIFY PROCESSES OR PATHWAYS THAT ARE PERTURBED IN DISEASE DEVELOPMENT. WE SHOW THAT GENE-SET ANALYSIS, AS IT IS TYPICALLY APPLIED TO GENOME-WIDE METHYLATION ASSAYS, IS SEVERELY BIASED AS A RESULT OF DIFFERENCES IN THE NUMBERS OF CPG SITES ASSOCIATED WITH DIFFERENT CLASSES OF GENES AND GENE PROMOTERS. RESULTS: WE DEMONSTRATE THIS BIAS USING PUBLISHED DATA FROM A STUDY OF DIFFERENTIAL CPG ISLAND METHYLATION IN LUNG CANCER AND A DATASET WE GENERATED TO STUDY METHYLATION CHANGES IN PATIENTS WITH LONG-STANDING ULCERATIVE COLITIS. WE SHOW THAT SEVERAL OF THE GENE SETS THAT SEEM ENRICHED WOULD ALSO BE IDENTIFIED WITH RANDOMIZED DATA. WE SUGGEST TWO EXISTING APPROACHES THAT CAN BE ADAPTED TO CORRECT THE BIAS. ACCOUNTING FOR THE BIAS IN THE LUNG CANCER AND ULCERATIVE COLITIS DATASETS PROVIDES NOVEL BIOLOGICAL INSIGHTS INTO THE ROLE OF METHYLATION IN CANCER DEVELOPMENT AND CHRONIC INFLAMMATION, RESPECTIVELY. OUR RESULTS HAVE SIGNIFICANT IMPLICATIONS FOR MANY PREVIOUS GENOME-WIDE METHYLATION STUDIES THAT HAVE DRAWN CONCLUSIONS ON THE BASIS OF SUCH STRONGLY BIASED ANALYSIS. CONTACT: CATHAL.SEOIGHE@NUIGALWAY.IE SUPPLEMENTARY INFORMATION: SUPPLEMENTARY DATA ARE AVAILABLE AT BIOINFORMATICS ONLINE. 2013