1 5094 138 PLASMA EXTRACELLULAR VESICLE SUBTYPES MAY BE USEFUL AS POTENTIAL BIOMARKERS OF IMMUNE ACTIVATION IN PEOPLE WITH HIV. BACKGROUND: EXTRACELLULAR VESICLES (EVS) ARE INTERCELLULAR MESSENGERS WITH EPIGENETIC POTENTIAL SINCE THEY CAN SHUTTLE MICRORNA (MIRNA). EVS AND MIRNA PLAY A ROLE IN HUMAN IMMUNODEFICIENCY VIRUS (HIV) INFECTION IMMUNOPATHOGENESIS. CHRONIC IMMUNE ACTIVATION AND SYSTEMIC INFLAMMATION DURING HIV INFECTION DESPITE EFFECTIVE ANTIRETROVIRAL THERAPY (ART) ARE ASSOCIATED WITH NON-ACQUIRED IMMUNODEFICIENCY SYNDROME (AIDS) COMORBIDITIES IN PEOPLE LIVING WITH HIV (PLWH). ANALYSIS OF PLASMA EVS AND THEIR MIRNA CONTENT MAY BE USEFUL AS IMMUNE ACTIVATION OR INFLAMMATORY BIOMARKERS IN PLWH RECEIVING ART. IN THIS STUDY, WE HYPOTHESIZED THAT THE NUMBER, SIZE, AND MIRNA OF LARGE AND SMALL EVS COULD REFLECT IMMUNE ACTIVATION ASSOCIATED WITH AN ELEVATED CD8 T-CELL COUNT OR A LOW CD4/CD8 RATIO IN PLWH. METHODS: PLASMA EVS SUBTYPE PURIFIED FROM PLWH AND UNINFECTED CONTROLS WERE SIZED USING DYNAMIC LIGHT SCATTERING AND QUANTIFIED USING FLOW CYTOMETRY AND ACETYLCHOLINE ESTERASE (ACHE) ACTIVITY. EXPRESSION OF MATURE MIRNAS MIR-92, MIR-155, MIR-223 WAS MEASURED BY QUANTITATIVE REVERSE-TRANSCRIPTASE POLYMERASE CHAIN REACTION IN EVS AND LEUCOCYTES. RESULTS: HIV INFECTION INDUCES INCREASED PRODUCTION OF SMALL EVS IN PLASMA. EV SUBTYPES WERE DIFFERENTIALLY ENRICHED IN MIR-92, MIR-155, AND MIR-223. POSITIVE CORRELATIONS BETWEEN CD8 T-CELL COUNT AND LARGE EVS ABUNDANCE AND SMALL EVS ACHE ACTIVITY WERE OBSERVED. CD4/CD8 RATIO WAS NEGATIVELY CORRELATED WITH SMALL EV ACHE ACTIVITY, AND MIRNA-155 LEVEL PER SMALL EV WAS NEGATIVELY CORRELATED WITH CD8 T-CELL COUNT. CONCLUSIONS: THESE FINDINGS SUGGEST THAT QUANTIFYING LARGE OR SMALL EVS AND PROFILING MIRNA CONTENT PER EV MIGHT PROVIDE NEW FUNCTIONAL BIOMARKERS OF IMMUNE ACTIVATION AND INFLAMMATION. 2021 2 3555 34 IMPACT OF AGE, ANTIRETROVIRAL THERAPY, AND CANCER ON EPIGENETIC AGING IN PEOPLE LIVING WITH HIV. BACKGROUND: PREMATURE AGING HAS BEEN IDENTIFIED AS A GLOBAL RISK FACTOR FOR CANCER. CAUSES OF PREMATURE AGING ARE MULTIFACTORIAL, INCLUDING INFLAMMATION, INFECTION, CHRONIC STRESS, AND LIFESTYLE FACTORS. METHOD: WE EVALUATED WHETHER PREMATURE AGING IN PEOPLE LIVING WITH HIV (PLWH) WAS ASSOCIATED WITH ANTIRETROVIRAL THERAPY (ART) OR THE DIAGNOSIS OF CANCER. WE USED WELL-ESTABLISHED DNA METHYLATION PATTERNS TO ASSESS PREMATURE AGING, USING HORVATH ET AL., IN INDIVIDUALS WITH HIV LOCATED IN CLEVELAND, OHIO AND COMPARED THESE TO STANDARDIZED DATASETS OF US HISTORICAL BLOOD SAMPLES. SOME OF THE PLWH DEVELOPED CANCER OVER TIME. RESULTS: WE FOUND THAT DNA METHYLATION ANALYSIS IDENTIFIED ACCELERATED AGING IN PLWH WHEREAS ART THERAPY MITIGATED THE ADVANCEMENT OF DNA METHYLATION AGE. A VARIETY OF CANCERS WERE OBSERVED IN THIS POPULATION, BUT A CANCER DIAGNOSIS WAS NOT SIGNIFICANTLY ASSOCIATED WITH MORE ADVANCED DNA METHYLATION AGE. CONCLUSION: WE FIND THAT THE AGE ACCELERATION DETECTED IN PLWH IS MITIGATED BY ART THERAPY AND IS NOT FURTHER ACCELERATED BY A DIAGNOSIS OF CANCER. 2023 3 353 36 ALTERED LEVELS OF IMMUNE-REGULATORY MICRORNAS IN PLASMA SAMPLES OF PATIENTS WITH LUPUS NEPHRITIS. INTRODUCTION: LUPUS NEPHRITIS (LN) IS A MAJOR CAUSE OF MORTALITY AND MORBIDITY IN THE PATIENTS WITH LUPUS, A CHRONIC AUTOIMMUNE DISEASE. THE ROLE OF GENETIC AND EPIGENETIC FACTORS IS EMPHASIZED IN THE PATHOGENESIS OF LN. THE AIM OF THE PRESENT STUDY WAS TO EVALUATE THE LEVELS OF IMMUNE-REGULATORY MICRORNAS (E.G., MIR-31, MIR-125A, MIR-142-3P, MIR-146A, AND MIR-155) IN PLASMA SAMPLES OF PATIENTS WITH LN. METHODS: IN THIS STUDY, 26 PATIENTS WITH LN AND 26 HEALTHY INDIVIDUALS WERE INCLUDED. THE PLASMA LEVELS OF THE MICRORNAS WERE EVALUATED BY A QUANTITATIVE REAL-TIME PCR. MOREOVER, THE CORRELATION OF CIRCULATING PLASMA MICRORNAS WITH DISEASE ACTIVITY AND PATHOLOGICAL FINDINGS ALONG WITH THEIR ABILITY TO DISTINGUISH PATIENTS WITH LN WERE ASSESSED. RESULTS: PLASMA LEVELS OF MIR-125A (P = 0.048), MIR-146A (P = 0.005), AND MIR-155 (P< 0.001) WERE SIGNIFICANTLY HIGHER IN COMPARISON BETWEEN THE CASES AND CONTROLS. THE PLASMA LEVEL OF MIR-146A SIGNIFICANTLY CORRELATED WITH THE LEVEL OF ANTI-DOUBLE STRAND-DNA ANTIBODY AND PROTEINURIA. MOREOVER, THERE WAS A SIGNIFICANT CORRELATION BETWEEN MIR-142-3P LEVELS AND DISEASE CHRONICITY AND ACTIVITY INDEX (P <0.05). THE MULTIVARIATE ROC CURVE ANALYSIS INDICATED THE PLASMA CIRCULATING MIR-125A, MIR-142-3P, MIR-146, AND MIR-155 TOGETHER COULD DISCRIMINATE MOST OF THE PATIENTS WITH LN FROM CONTROLS WITH AREA AN UNDER CURVE (AUC) OF 0.89 [95% CI, 0.80-0.98, P<0.001], 88% SENSITIVITY, AND 78% SPECIFICITY. CONCLUSION: BASED ON THE FINDINGS OF THE PRESENT STUDY, THE STUDIED MICRORNAS MAY BE INVOLVED IN THE PATHOGENESIS AND DEVELOPMENT OF LN AND HAVE THE POTENTIAL TO BE USED AS DIAGNOSTIC AND THERAPEUTIC MARKERS IN LN. 2018 4 4255 27 METHYLOME-WIDE ANALYSIS OF CHRONIC HIV INFECTION REVEALS FIVE-YEAR INCREASE IN BIOLOGICAL AGE AND EPIGENETIC TARGETING OF HLA. HIV-INFECTED INDIVIDUALS ARE LIVING LONGER ON ANTIRETROVIRAL THERAPY, BUT MANY PATIENTS DISPLAY SIGNS THAT IN SOME WAYS RESEMBLE PREMATURE AGING. TO INVESTIGATE AND QUANTIFY THE IMPACT OF CHRONIC HIV INFECTION ON AGING, WE REPORT A GLOBAL ANALYSIS OF THE WHOLE-BLOOD DNA METHYLOMES OF 137 HIV+ INDIVIDUALS UNDER SUSTAINED THERAPY ALONG WITH 44 MATCHED HIV- INDIVIDUALS. FIRST, WE DEVELOP AND VALIDATE EPIGENETIC MODELS OF AGING THAT ARE INDEPENDENT OF BLOOD CELL COMPOSITION. USING THESE MODELS, WE FIND THAT BOTH CHRONIC AND RECENT HIV INFECTION LEAD TO AN AVERAGE AGING ADVANCEMENT OF 4.9 YEARS, INCREASING EXPECTED MORTALITY RISK BY 19%. IN ADDITION, SUSTAINED INFECTION RESULTS IN GLOBAL DEREGULATION OF THE METHYLOME ACROSS >80,000 CPGS AND SPECIFIC HYPOMETHYLATION OF THE REGION ENCODING THE HUMAN LEUKOCYTE ANTIGEN LOCUS (HLA). WE FIND THAT DECREASED HLA METHYLATION IS PREDICTIVE OF LOWER CD4 / CD8 T CELL RATIO, LINKING MOLECULAR AGING, EPIGENETIC REGULATION, AND DISEASE PROGRESSION. 2016 5 4348 44 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 6 6311 32 THE RELATION BETWEEN DNA METHYLATION PATTERNS AND SERUM CYTOKINE LEVELS IN COMMUNITY-DWELLING ADULTS: A PRELIMINARY STUDY. BACKGROUND: THE LEVELS OF CIRCULATING CYTOKINES FLUCTUATE WITH AGE, ACUTE ILLNESS, AND CHRONIC DISEASE, AND ARE PREDICTIVE OF MORTALITY; THIS IS ALSO TRUE FOR PATTERNS OF DNA (CPG) METHYLATION. GIVEN THAT IMMUNE CELLS ARE PARTICULARLY SENSITIVE TO CHANGES IN THE CONCENTRATION OF CYTOKINES IN THEIR MICROENVIRONMENT, WE HYPOTHESIZED THAT SERUM LEVELS OF TNF, IL-6, IL-8 AND IL-10 WOULD CORRELATE WITH GENOME-WIDE ALTERATIONS IN THE DNA METHYLATION LEVELS OF BLOOD LEUKOCYTES. TO TEST THIS, WE EVALUATED COMMUNITY-DWELLING ADULTS (N = 14; 48-78 YEARS OLD) RECRUITED TO A PILOT STUDY FOR THE CANADIAN LONGITUDINAL STUDY ON AGING (CLSA), EXAMINING DNA METHYLATION PATTERNS IN PERIPHERAL BLOOD MONONUCLEAR CELLS USING THE ILLUMINA HUMANMETHYLATION 450 K BEADCHIP. RESULTS: WE SHOW THAT, APART FROM AGE, SERUM IL-10 LEVELS EXHIBITED THE MOST SUBSTANTIAL ASSOCIATION TO DNA METHYLATION PATTERNS, FOLLOWED BY TNF, IL-6 AND IL-8. FURTHERMORE, WHILE THE LEVELS OF THESE CYTOKINES WERE HIGHER IN ELDERLY ADULTS, NO ASSOCIATIONS WITH EPIGENETIC ACCELERATED AGING, DERIVED USING THE EPIGENETIC CLOCK, WERE OBSERVED. CONCLUSIONS: AS A PRELIMINARY STUDY WITH A SMALL SAMPLE SIZE, THE CONCLUSIONS DRAWN FROM THIS WORK MUST BE VIEWED WITH CAUTION; HOWEVER, OUR OBSERVATIONS ARE ENCOURAGING AND CERTAINLY WARRANT MORE SUITABLY POWERED STUDIES OF THIS RELATIONSHIP. 2017 7 3936 30 LIVING IN ENDEMIC AREA FOR INFECTIOUS DISEASES ACCELERATES EPIGENETIC AGE. INFLAMMAGING IS A LOW-GRADE INFLAMMATORY STATE GENERATED BY THE AGING PROCESS THAT CAN CONTRIBUTE TO FRAILTY AND AGE-RELATED DISEASES IN THE ELDERLY. HOWEVER, IT CAN HAVE DISTINCT EFFECTS IN THE ELDERLY LIVING IN ENDEMIC AREAS FOR INFECTIOUS DISEASES. AN INCREASED INFLAMMATORY RESPONSE MAY CONFER PROTECTION AGAINST INFECTIOUS AGENTS IN THESE AREAS, ALTHOUGH THIS ADVANTAGE CAN CAUSE ACCELERATING EPIGENETIC AGING. IN THIS STUDY, WE EVALUATED THE INFLAMMATORY PROFILE AND THE EPIGENETIC AGE OF INFECTED AND NONINFECTED INDIVIDUALS FROM AN ENDEMIC AREA IN BRAZIL. THE PROFILE OF CYTOKINES, CHEMOKINES AND GROWTH FACTORS ANALYZED IN THE SERA OF THE TWO GROUPS OF INDIVIDUALS SHOWED SIMILARITIES, ALTHOUGH INFECTED INDIVIDUALS HAD A HIGHER CONCENTRATION OF THESE MEDIATORS. A SIGNIFICANT INCREASE IN IL-1RA, CXCL8, CCL2, CCL3 AND CCL4 PRODUCTION WAS ASSOCIATED WITH LEPROSY INFECTION. NOTABLY, ELDERLY INDIVIDUALS DISPLAYED DISTINCT IMMUNE RESPONSES ASSOCIATED WITH THEIR INFECTION STATUS WHEN COMPARED TO ADULTS SUGGESTING AN ADAPTIVE REMODELLING OF THEIR IMMUNE RESPONSES. EPIGENETIC ANALYSIS ALSO SHOWED THAT THERE WAS NO DIFFERENCE IN EPIGENETIC AGE BETWEEN THE TWO GROUPS OF INDIVIDUALS. HOWEVER, INDIVIDUALS FROM THE ENDEMIC AREA HAD A SIGNIFICANT ACCELERATED AGING WHEN COMPARED TO INDIVIDUALS FROM SAO PAULO, A NON-ENDEMIC AREA IN BRAZIL. MOREOVER, THE LATTER COHORT WAS ALSO EPIGENETICALLY AGED IN RELATION TO AN ITALIAN COHORT. OUR DATA SHOWS THAT LIVING IN ENDEMIC AREAS FOR CHRONIC INFECTIOUS DISEASES RESULTS IN REMODELLING OF INFLAMMAGING AND ACCELERATION OF EPIGENETIC AGING IN INDIVIDUALS REGARDLESS OF THEIR INFECTIOUS STATUS. IT ALSO HIGHLIGHTS THAT GEOGRAPHICAL, GENETIC AND ENVIRONMENTAL FACTORS INFLUENCE AGING AND IMMUNOSENESCENCE IN THEIR PACE AND PROFILE. 2022 8 1307 29 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 9 2400 34 EPIGENETIC REPROGRAMMING OF IMMUNE CELLS IN WOMEN WITH PCOS IMPACT GENES CONTROLLING REPRODUCTIVE FUNCTION. CONTEXT: POLYCYSTIC OVARY SYNDROME (PCOS) IS A CHRONIC DISEASE AFFECTING REPRODUCTIVE FUNCTION AND WHOLE-BODY METABOLISM. ALTHOUGH THE ETIOLOGY IS UNCLEAR, EMERGING EVIDENCE INDICATES THAT THE EPIGENETICS MAY BE A CONTRIBUTING FACTOR. OBJECTIVE: TO DETERMINE THE ROLE OF GLOBAL AND GENOME-WIDE EPIGENETIC MODIFICATIONS IN SPECIFIC IMMUNE CELLS IN PCOS COMPARED WITH CONTROLS AND WHETHER THESE COULD BE RELATED TO CLINICAL FEATURES OF PCOS. DESIGN: CROSS-SECTIONAL STUDY. PARTICIPANTS: WOMEN WITH (N = 17) OR WITHOUT PCOS (N = 17). SETTING: RECRUITED FROM THE GENERAL COMMUNITY. MAIN OUTCOME MEASURES: ISOLATED PERIPHERAL BLOOD MONONUCLEAR CELLS WERE ANALYZED USING MULTICOLOR FLOW CYTOMETRY METHODS TO DETERMINE GLOBAL DNA METHYLATION LEVELS IN A CELL-SPECIFIC FASHION. TRANSCRIPTOMIC AND GENOME-WIDE DNA METHYLATION ANALYSES WERE PERFORMED ON T HELPER CELLS USING RNA SEQUENCING AND REDUCED REPRESENTATION BISULFITE SEQUENCING. RESULTS: WOMEN WITH PCOS HAD LOWER GLOBAL DNA METHYLATION IN MONOCYTES (P = 0.006) AND IN T HELPER (P = 0.004), T CYTOTOXIC (P = 0.004), AND B CELLS (P = 0.03). SPECIFIC GENOME-WIDE DNA METHYLATION ANALYSIS OF T HELPER CELLS FROM WOMEN WITH PCOS IDENTIFIED 5581 DIFFERENTIALLY METHYLATED CPG SITES. FUNCTIONAL GENE ONTOLOGY ENRICHMENT ANALYSIS SHOWED THAT GENES LOCATED AT THE PROXIMITY OF DIFFERENTIALLY METHYLATED CPG SITES BELONG TO PATHWAYS RELATED TO REPRODUCTIVE FUNCTION AND IMMUNE CELL FUNCTION. HOWEVER, THESE GENES WERE NOT ALTERED AT THE TRANSCRIPTOMIC LEVEL. CONCLUSIONS: IT WAS SHOWN THAT PCOS IS ASSOCIATED WITH GLOBAL AND GENE-SPECIFIC DNA METHYLATION REMODELING IN A CELL TYPE-SPECIFIC MANNER. FURTHER INVESTIGATION IS WARRANTED TO DETERMINE WHETHER EPIGENETIC REPROGRAMMING OF IMMUNE CELLS IS IMPORTANT IN DETERMINING THE DIFFERENT PHENOTYPES OF PCOS. 2019 10 492 28 ASSESSMENT OF HIV-1 INTEGRATION IN TISSUES AND SUBSETS ACROSS INFECTION STAGES. THE INTEGRATION OF HIV DNA INTO THE HOST GENOME CONTRIBUTES TO LIFELONG INFECTION IN MOST INDIVIDUALS. FEW STUDIES HAVE EXAMINED INTEGRATION IN LYMPHOID TISSUE, WHERE HIV PREDOMINANTLY PERSISTS BEFORE AND AFTER ANTIRETROVIRAL TREATMENT (ART). OF PARTICULAR INTEREST IS WHETHER INTEGRATION SITE DISTRIBUTIONS DIFFER BETWEEN INFECTION STAGES WITH PAIRED BLOOD AND TISSUE COMPARISONS. HERE, WE PROFILED HIV INTEGRATION SITE DISTRIBUTIONS IN SORTED MEMORY, TISSUE-RESIDENT, AND/OR FOLLICULAR HELPER CD4+ T CELL SUBSETS FROM PAIRED BLOOD AND LYMPHOID TISSUE SAMPLES FROM ACUTE, CHRONIC, AND ART-TREATED INDIVIDUALS. WE OBSERVED MINOR DIFFERENCES IN THE FREQUENCY OF NONINTRONIC AND NONDISTAL INTERGENIC SITES, VARYING WITH TISSUE AND RESIDENCY PHENOTYPES DURING ART. GENOMIC AND EPIGENETIC ANNOTATIONS WERE GENERALLY SIMILAR. CLONAL EXPANSION OF CELLS MARKED BY IDENTICAL INTEGRATION SITES WAS DETECTED, WITH INCREASED DETECTION IN CHRONIC AND ART-TREATED INDIVIDUALS. HOWEVER, OVERLAP BETWEEN OR WITHIN CD4+ T CELL SUBSETS OR TISSUE COMPARTMENTS WAS ONLY OBSERVED IN 8 UNIQUE SITES OF THE 3540 SITES STUDIED. TOGETHER, THESE FINDINGS SUGGEST THAT SHARED INTEGRATION SITES BETWEEN BLOOD AND TISSUE MAY, DEPENDING ON THE TISSUE SITE, BE THE EXCEPTION RATHER THAN THE RULE AND INDICATE THAT ADDITIONAL STUDIES ARE NECESSARY TO FULLY UNDERSTAND THE HETEROGENEITY OF TISSUE-SEQUESTERED HIV RESERVOIRS. 2020 11 1500 36 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 12 4287 37 MICRORNA EXPRESSION PROFILING IN BEHCET'S DISEASE. BACKGROUND: BEHCET'S DISEASE (BD) IS A CHRONIC INFLAMMATORY MULTISYSTEM DISEASE CHARACTERIZED BY ORAL AND GENITAL ULCERS, UVEITIS, AND SKIN LESIONS. MICRORNAS (MIRNAS) ARE KEY REGULATORS OF IMMUNE RESPONSES. DIFFERENTIAL EXPRESSION OF MIRNAS HAS BEEN REPORTED IN SEVERAL INFLAMMATORY AUTOIMMUNE DISEASES; HOWEVER, THEIR ROLE IN BD IS NOT FULLY ELUCIDATED. WE AIMED TO IDENTIFY MIRNA EXPRESSION SIGNATURES ASSOCIATED WITH BD AND TO INVESTIGATE THEIR POTENTIAL IMPLICATION IN THE DISEASE PATHOGENESIS. METHODS: MIRNA MICROARRAY ANALYSIS WAS PERFORMED IN BLOOD CELLS OF BD PATIENTS AND HEALTHY CONTROLS. MIRNA EXPRESSION PROFILES WERE ANALYZED USING AFFYMETRIX ARRAYS WITH A COMPREHENSIVE COVERAGE OF MIRNA SEQUENCES. PATHWAY ANALYSES WERE PERFORMED, AND THE GLOBAL MIRNA PROFILING WAS COMBINED WITH TRANSCRIPTOMA DATA IN BD. DEREGULATION OF SELECTED MIRNAS WAS VALIDATED BY REAL-TIME PCR. RESULTS: WE IDENTIFIED SPECIFIC MIRNA SIGNATURES ASSOCIATED WITH BD PATIENTS WITH ACTIVE DISEASE. THESE MIRNAS TARGET PATHWAYS RELEVANT IN BD, SUCH AS TNF, IFN GAMMA, AND VEGF-VEGFR SIGNALING CASCADES. NETWORK ANALYSIS REVEALED SEVERAL MIRNAS REGULATING HIGHLY CONNECTED GENES WITHIN THE BD TRANSCRIPTOMA. CONCLUSIONS: THE COMBINED ANALYSIS OF DEREGULATED MIRNAS AND BD TRANSCRIPTOME SHEDS LIGHT ON SOME EPIGENETIC ASPECTS OF BD IDENTIFYING SPECIFIC MIRNAS, WHICH MAY REPRESENT PROMISING CANDIDATES AS BIOMARKERS AND/OR FOR THE DESIGN OF NOVEL THERAPEUTIC STRATEGIES IN BD. 2018 13 287 27 AGING AND CHRONIC SUN EXPOSURE CAUSE DISTINCT EPIGENETIC CHANGES IN HUMAN SKIN. EPIGENETIC CHANGES ARE WIDELY CONSIDERED TO PLAY AN IMPORTANT ROLE IN AGING, BUT EXPERIMENTAL EVIDENCE TO SUPPORT THIS HYPOTHESIS HAS BEEN SCARCE. WE HAVE USED ARRAY-BASED ANALYSIS TO DETERMINE GENOME-SCALE DNA METHYLATION PATTERNS FROM HUMAN SKIN SAMPLES AND TO INVESTIGATE THE EFFECTS OF AGING, CHRONIC SUN EXPOSURE, AND TISSUE VARIATION. OUR RESULTS REVEAL A HIGH DEGREE OF TISSUE SPECIFICITY IN THE METHYLATION PATTERNS AND ALSO SHOWED VERY LITTLE INTERINDIVIDUAL VARIATION WITHIN TISSUES. DATA STRATIFICATION BY AGE REVEALED THAT DNA FROM OLDER INDIVIDUALS WAS CHARACTERIZED BY A SPECIFIC HYPERMETHYLATION PATTERN AFFECTING LESS THAN 1% OF THE MARKERS ANALYZED. INTERESTINGLY, STRATIFICATION BY SUN EXPOSURE PRODUCED A FUNDAMENTALLY DIFFERENT PATTERN WITH A SIGNIFICANT TREND TOWARDS HYPOMETHYLATION. OUR RESULTS THUS IDENTIFY DEFINED AGE-RELATED DNA METHYLATION CHANGES AND SUGGEST THAT THESE ALTERATIONS MIGHT CONTRIBUTE TO THE PHENOTYPIC CHANGES ASSOCIATED WITH SKIN AGING. 2010 14 2920 33 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 15 3765 40 INTEGRATIVE ANALYSIS OF TRANSCRIPTOMIC AND PROTEOMIC PROFILING IN INFLAMMATORY BOWEL DISEASE COLON BIOPSIES. BACKGROUND: CROHN'S DISEASE (CD) AND ULCERATIVE COLITIS (UC) ARE INTESTINAL CHRONIC INFLAMMATORY CONDITIONS CHARACTERIZED BY ALTERED EPITHELIAL BARRIER FUNCTION AND TISSUE DAMAGE. DESPITE SIGNIFICANT EFFORTS TO UNDERSTANDING THE BIOLOGICAL MECHANISMS RESPONSIBLE FOR GUT INFLAMMATION, THE PATHOPHYSIOLOGY OF CD AND UC REMAINS POORLY UNDERSTOOD. METHODS: TO HELP ELUCIDATE THE POTENTIAL MECHANISMS RESPONSIBLE FOR GUT INFLAMMATION IN CD AND UC, TRANSCRIPTOMIC AND PROTEOMIC PROFILING OF HUMAN COLON BIOPSY SPECIMENS WAS PERFORMED. DYSREGULATED GENES AND PROTEINS IN DISEASE TISSUES COMPARED WITH NORMAL TISSUES WERE CHARACTERIZED FROM THE EXPRESSION PROFILES AND FURTHER SUBJECTED TO PATHWAY ANALYSIS TO IDENTIFY ALTERED BIOLOGICAL PROCESSES AND SIGNALING PATHWAYS. RESULTS: SAMPLE ANALYSIS SHOWED 4250 GENES WITH MATCHED PROTEIN EXPRESSION AND A WIDE RANGE OF CORRELATION OF RNA-PROTEIN ABUNDANCE ACROSS SAMPLES. PATHWAY ANALYSIS OF DYSREGULATED GENES AND PROTEINS IN CD AND UC SHOWED ALTERATIONS IN IMMUNE AND INFLAMMATORY RESPONSES, COMPLEMENT CASCADE, AND THE SUPPRESSION OF METABOLIC PROCESSES AND PPAR SIGNALING. IN CD, INCREASED T-HELPER CELL DIFFERENTIATION AND ELEVATED TOLL-LIKE RECEPTOR AND JAK/STAT SIGNALING WERE OBSERVED. INTERESTINGLY, INCREASED MAPK SIGNALING WAS ONLY OBSERVED IN UC. WEIGHTED GENE CO-EXPRESSION NETWORK ANALYSIS SUGGESTED A POSSIBLE ROLE OF EPIGENETIC REGULATION IN UC. OF NOTE, A LARGE DISCREPANCY BETWEEN REGULATION OF RNA AND PROTEIN LEVELS IN INFLAMED COLON SAMPLES WAS DETECTED FOR PREVIOUSLY IDENTIFIED BIOMARKERS INCLUDING MMP14 AND LAMP1. CONCLUSIONS: WITH THE ANALYSIS OF DYSREGULATED GENES AND PATHWAYS, THE PRESENT STUDY UNRAVELS KEY MECHANISMS CONTRIBUTING TO CD AND UC PATHOGENESIS AND EMPHASIZES THAT INTEGRATIVE ANALYSIS OF MULTI-OMICS DATA SETS CAN PROVIDE MORE INSIGHT INTO UNDERSTANDING COMPLEX DISEASE MECHANISMS. 2019 16 822 26 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 17 304 39 AIRWAY AGING AND METHYLATION DISRUPTIONS IN HIV-ASSOCIATED CHRONIC OBSTRUCTIVE PULMONARY DISEASE. RATIONALE: AGE-RELATED DISEASES LIKE CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) OCCUR AT HIGHER RATES IN PEOPLE LIVING WITH HUMAN IMMUNODEFICIENCY VIRUS (PLWH) THAN IN UNINFECTED POPULATIONS. OBJECTIVES: TO IDENTIFY WHETHER ACCELERATED AGING CAN BE OBSERVED IN THE AIRWAYS OF PLWH WITH COPD, MANIFEST BY A UNIQUE DNA METHYLATION SIGNATURE. METHODS: BRONCHIAL EPITHELIAL BRUSHINGS FROM PLWH WITH AND WITHOUT COPD AND HIV-UNINFECTED ADULTS WITH AND WITHOUT COPD (N = 76) WERE PROFILED FOR DNA METHYLATION AND GENE EXPRESSION. WE EVALUATED GLOBAL ALU AND LINE-1 METHYLATION AND CALCULATED THE EPIGENETIC AGE USING THE HORVATH CLOCK AND THE METHYLATION TELOMERE LENGTH ESTIMATOR. TO IDENTIFY GENOME-WIDE DIFFERENTIAL DNA METHYLATION AND GENE EXPRESSION ASSOCIATED WITH HIV AND COPD, ROBUST LINEAR MODELS WERE USED FOLLOWED BY AN EXPRESSION QUANTITATIVE TRAIT METHYLATION (EQTM) ANALYSIS. MEASUREMENTS AND MAIN RESULTS: EPIGENETIC AGE ACCELERATION AND SHORTER METHYLATION ESTIMATES OF TELOMERE LENGTH WERE FOUND IN PLWH WITH COPD COMPARED WITH PLWH WITHOUT COPD AND UNINFECTED PATIENTS WITH AND WITHOUT COPD. GLOBAL HYPOMETHYLATION WAS IDENTIFIED IN PLWH. WE IDENTIFIED 7,970 CYTOSINE BASES LOCATED NEXT TO A GUANINE BASE (CPG SITES), 293 GENES, AND 9 EXPRESSION QUANTITATIVE TRAIT METHYLATION-GENE PAIRS ASSOCIATED WITH THE INTERACTION BETWEEN HIV AND COPD. ACTIN BINDING LIM PROTEIN FAMILY MEMBER 3 (ABLIM3) WAS ONE OF THE NOVEL CANDIDATE GENES FOR HIV-ASSOCIATED COPD HIGHLIGHTED BY OUR ANALYSIS. CONCLUSIONS: METHYLATION AGE ACCELERATION IS OBSERVED IN THE AIRWAY EPITHELIUM OF PLWH WITH COPD, A PROCESS THAT MAY BE RESPONSIBLE FOR THE HEIGHTENED RISK OF COPD IN THIS POPULATION. THEIR DISTINCT METHYLATION PROFILE, DIFFERING FROM THAT OBSERVED IN PATIENTS WITH COPD ALONE, SUGGESTS A UNIQUE PATHOGENESIS TO HIV-ASSOCIATED COPD. THE ASSOCIATIONS WARRANT FURTHER INVESTIGATION TO ESTABLISH CAUSALITY. 2022 18 1556 29 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 19 3503 28 IDENTIFICATION OF POTENTIAL DIFFERENTIALLY METHYLATED GENE-RELATED BIOMARKERS IN ENDOMETRIOSIS. AIM: TO IDENTIFY EPIGENETIC ALTERATIONS OF DIFFERENTIALLY EXPRESSED GENES AND SCREEN OUT TARGETED THERAPEUTIC DRUGS IN ENDOMETRIOSIS. METHODS: BASED ON THE GENE EXPRESSION OMNIBUS DATABASE AND A SERIES OF BIOLOGICAL INFORMATION ANALYSIS TOOLS, SUPPLEMENTED BY VALIDATION OF CLINICAL SAMPLES, ABERRANT DNA METHYLATION-DRIVEN GENES AND THEIR FUNCTIONS WERE EXPLORED, AS WELL AS POSSIBLE TARGETED DRUGS. RESULTS: THIS STUDY SCREENED OUT A RANGE OF DNA METHYLATION-DRIVEN GENES THAT WERE ASSOCIATED WITH POWERFUL PROPERTIES AND CORRESPONDING PATHWAYS. AMONG THEM, BDNF AND CCL2 WERE KEY GENES IN THE DEVELOPMENT OF ENDOMETRIOSIS. FOUR CHEMICAL AGENTS HAVE BEEN FLAGGED AS POTENTIAL TREATMENTS FOR ENDOMETRIOSIS. CONCLUSION: THESE CANDIDATE GENES AND SMALL-MOLECULE AGENTS MAY BE FURTHER EXPLORED AS POTENTIAL TARGETS AND DRUGS FOR ENDOMETRIOSIS DIAGNOSIS AND THERAPY, RESPECTIVELY. 2022 20 1699 24 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