1 5587 145 ROLE OF S-ADENOSYLHOMOCYSTEINE IN CARDIOVASCULAR DISEASE AND ITS POTENTIAL EPIGENETIC MECHANISM. TRANSMETHYLATION REACTIONS UTILIZE S-ADENOSYLMETHIONINE (SAM) AS A METHYL DONOR AND ARE CENTRAL TO THE REGULATION OF MANY BIOLOGICAL PROCESSES: MORE THAN FIFTY SAM-DEPENDENT METHYLTRANSFERASES METHYLATE A BROAD SPECTRUM OF CELLULAR COMPOUNDS INCLUDING DNA, HISTONES, PHOSPHOLIPIDS AND OTHER SMALL MOLECULES. COMMON TO ALL SAM-DEPENDENT TRANSMETHYLATION REACTIONS IS THE RELEASE OF THE POTENT INHIBITOR S-ADENOSYLHOMOCYSTEINE (SAH) AS A BY-PRODUCT. SAH IS REVERSIBLY HYDROLYZED TO ADENOSINE AND HOMOCYSTEINE BY SAH HYDROLASE. HYPERHOMOCYSTEINEMIA IS AN INDEPENDENT RISK FACTOR FOR CARDIOVASCULAR DISEASE. HOWEVER, A MAJOR UNANSWERED QUESTION IS IF HOMOCYSTEINE IS CAUSALLY INVOLVED IN DISEASE PATHOGENESIS OR SIMPLY A PASSIVE AND INDIRECT INDICATOR OF A MORE COMPLEX MECHANISM. A CHRONIC ELEVATION IN HOMOCYSTEINE LEVELS RESULTS IN A PARALLEL INCREASE IN INTRACELLULAR OR PLASMA SAH, WHICH IS A MORE SENSITIVE BIOMARKER OF CARDIOVASCULAR DISEASE THAN HOMOCYSTEINE AND SUGGESTS THAT SAH IS A CRITICAL PATHOLOGICAL FACTOR IN HOMOCYSTEINE-ASSOCIATED DISORDERS. PREVIOUS REPORTS INDICATE THAT SUPPLEMENTATION WITH FOLATE AND B VITAMINS EFFICIENTLY LOWERS HOMOCYSTEINE LEVELS BUT NOT PLASMA SAH LEVELS, WHICH POSSIBLY EXPLAINS THE FAILURE OF HOMOCYSTEINE-LOWERING VITAMINS TO REDUCE VASCULAR EVENTS IN SEVERAL RECENT CLINICAL INTERVENTION STUDIES. FURTHERMORE, MORE STUDIES ARE FOCUSING ON THE ROLE AND MECHANISMS OF SAH IN DIFFERENT CHRONIC DISEASES RELATED TO HYPERHOMOCYSTEINEMIA, SUCH AS CARDIOVASCULAR DISEASE, KIDNEY DISEASE, DIABETES, AND OBESITY. THIS REVIEW SUMMARIZES THE CURRENT ROLE OF SAH IN CARDIOVASCULAR DISEASE AND ITS EFFECT ON SEVERAL RELATED RISK FACTORS. IT ALSO EXPLORES POSSIBLE THE MECHANISMS, SUCH AS EPIGENETICS AND OXIDATIVE STRESS, OF SAH. THIS ARTICLE IS PART OF A DIRECTED ISSUE ENTITLED: EPIGENETIC DYNAMICS IN DEVELOPMENT AND DISEASE. 2015 2 1855 50 ELEVATION IN S-ADENOSYLHOMOCYSTEINE AND DNA HYPOMETHYLATION: POTENTIAL EPIGENETIC MECHANISM FOR HOMOCYSTEINE-RELATED PATHOLOGY. CHRONIC NUTRITIONAL DEFICIENCIES IN FOLATE, CHOLINE, METHIONINE, VITAMIN B-6 AND/OR VITAMIN B-12 CAN PERTURB THE COMPLEX REGULATORY NETWORK THAT MAINTAINS NORMAL ONE-CARBON METABOLISM AND HOMOCYSTEINE HOMEOSTASIS. GENETIC POLYMORPHISMS IN THESE PATHWAYS CAN ACT SYNERGISTICALLY WITH NUTRITIONAL DEFICIENCIES TO ACCELERATE METABOLIC PATHOLOGY ASSOCIATED WITH OCCLUSIVE HEART DISEASE, BIRTH DEFECTS AND DEMENTIA. A MAJOR UNANSWERED QUESTION IS WHETHER HOMOCYSTEINE IS CAUSALLY INVOLVED IN DISEASE PATHOGENESIS OR WHETHER HOMOCYSTEINEMIA IS SIMPLY A PASSIVE AND INDIRECT INDICATOR OF A MORE COMPLEX MECHANISM. S-ADENOSYLMETHIONINE AND S-ADENOSYLHOMOCYSTEINE (SAH), AS THE SUBSTRATE AND PRODUCT OF METHYLTRANSFERASE REACTIONS, ARE IMPORTANT METABOLIC INDICATORS OF CELLULAR METHYLATION STATUS. CHRONIC ELEVATION IN HOMOCYSTEINE LEVELS RESULTS IN PARALLEL INCREASES IN INTRACELLULAR SAH AND POTENT PRODUCT INHIBITION OF DNA METHYLTRANSFERASES. SAH-MEDIATED DNA HYPOMETHYLATION AND ASSOCIATED ALTERATIONS IN GENE EXPRESSION AND CHROMATIN STRUCTURE MAY PROVIDE NEW HYPOTHESES FOR PATHOGENESIS OF DISEASES RELATED TO HOMOCYSTEINEMIA. 2002 3 4016 27 LOW-DOSE HYDRALAZINE PREVENTS FIBROSIS IN A MURINE MODEL OF ACUTE KIDNEY INJURY-TO-CHRONIC KIDNEY DISEASE PROGRESSION. ACUTE KIDNEY INJURY (AKI) AND PROGRESSIVE CHRONIC KIDNEY DISEASE (CKD) ARE INTRINSICALLY TIED SYNDROMES. IN THIS REGARD, THE ACUTELY INJURED KIDNEY OFTEN DOES NOT ACHIEVE ITS FULL REGENERATIVE CAPACITY AND AKI DIRECTLY TRANSITIONS INTO PROGRESSIVE CKD ASSOCIATED WITH TUBULOINTERSTITIAL FIBROSIS. UNDERLYING MECHANISMS OF SUCH AKI-TO-CKD PROGRESSION ARE STILL INCOMPLETELY UNDERSTOOD AND SPECIFIC THERAPEUTIC INTERVENTIONS ARE STILL ELUSIVE. BECAUSE EPIGENETIC MODIFICATIONS PLAY A ROLE IN MAINTAINING TISSUE FIBROSIS, WE USED A MURINE MODEL OF ISCHEMIA-REPERFUSION INJURY TO DETERMINE WHETHER ABERRANT PROMOTER METHYLATION OF RASAL1 CONTRIBUTES CAUSALLY TO THE SWITCH BETWEEN PHYSIOLOGICAL REGENERATION AND TUBULOINTERSTITIAL FIBROGENESIS, A HALLMARK OF AKI-TO-CKD PROGRESSION. IT IS KNOWN THAT THE ANTIHYPERTENSIVE DRUG HYDRALAZINE HAS DEMETHYLATING ACTIVITY, AND THAT ITS OPTIMUM DEMETHYLATING ACTIVITY OCCURS AT CONCENTRATIONS BELOW BLOOD PRESSURE-LOWERING DOSES. ADMINISTRATION OF LOW-DOSE HYDRALAZINE EFFECTIVELY INDUCED EXPRESSION OF HYDROXYLASE TET3, WHICH CATALYZED RASAL1 HYDROXYMETHYLATION AND SUBSEQUENT RASAL1 PROMOTER DEMETHYLATION. HYDRALAZINE-INDUCED CPG PROMOTER DEMETHYLATION SUBSEQUENTLY ATTENUATED RENAL FIBROSIS AND PRESERVED EXCRETORY RENAL FUNCTION INDEPENDENT OF ITS BLOOD PRESSURE-LOWERING EFFECTS. IN COMPARISON, RASAL1 DEMETHYLATION AND INHIBITION OF TUBULOINTERSTITIAL FIBROSIS WAS NOT DETECTED UPON ADMINISTRATION OF THE ANGIOTENSIN-CONVERTING ENZYME INHIBITOR RAMIPRIL IN THIS MODEL. THUS, RASAL1 PROMOTER METHYLATION AND SUBSEQUENT TRANSCRIPTIONAL RASAL1 SUPPRESSION PLAYS A CAUSAL ROLE IN AKI-TO-CKD PROGRESSION. 2017 4 3663 22 INDUCTION OF TET3-DEPENDENT EPIGENETIC REMODELING BY LOW-DOSE HYDRALAZINE ATTENUATES PROGRESSION OF CHRONIC KIDNEY DISEASE. PROGRESSION OF CHRONIC KIDNEY DISEASE REMAINS A PRINCIPAL PROBLEM IN CLINICAL NEPHROLOGY AND THERE IS A PRESSING NEED FOR NOVEL THERAPEUTICS AND BIOMARKERS. ABERRANT PROMOTER CPG ISLAND METHYLATION AND SUBSEQUENT TRANSCRIPTIONAL SILENCING OF SPECIFIC GENES HAVE EMERGED AS CONTRIBUTORS TO PROGRESSION OF CHRONIC KIDNEY DISEASE. HERE, WE REPORT THAT TRANSCRIPTIONAL SILENCING OF THE RAS-GTP SUPPRESSOR RASAL1 CONTRIBUTES CAUSALLY TO PROGRESSION OF KIDNEY FIBROSIS AND WE IDENTIFIED THAT CIRCULATING METHYLATED RASAL1 PROMOTER DNA FRAGMENTS IN PERIPHERAL BLOOD CORRESPOND WITH LEVELS OF INTRARENAL LEVELS OF RASAL1 PROMOTER METHYLATION AND DEGREE OF FIBROSIS IN KIDNEY BIOPSIES, ENABLING NON-INVASIVE LONGITUDINAL ANALYSIS OF INTRARENAL CPG ISLAND METHYLATION. 2015 5 6220 37 THE KIDNEY IS THE MAJOR SITE OF S-ADENOSYLHOMOCYSTEINE DISPOSAL IN HUMANS. S-ADENOSYLHOMOCYSTEINE (SAH), THE METABOLIC PRECURSOR OF HOMOCYSTEINE IN THE BODY, IS A POTENT INHIBITOR OF METHYLATION REACTIONS. SEVERAL METHYLATION REACTIONS PLAY A MAJOR ROLE IN EPIGENETIC REGULATION OF PROTEIN EXPRESSION, ATHEROSCLEROSIS, AND CANCER DEVELOPMENT. HERE WE STUDIED THE MECHANISMS RESPONSIBLE FOR THE MAINTENANCE OF CIRCULATING SAH LEVELS BY MEASUREMENT OF THE ARTERIO-VENOUS DIFFERENCES ACROSS THE KIDNEY, SPLANCHNIC ORGANS, AND THE LUNG IN HUMANS. THE LUNGS DID NOT REMOVE OR ADD ANY CIRCULATING SAH, WHEREAS THE LIVER RELEASED IT INTO THE HEPATIC VEINS. THE KIDNEY EXTRACTED 40% OF SAH AND THE SAH ARTERIO-VENOUS DIFFERENCE ACROSS THE KIDNEY WAS DIRECTLY AND SIGNIFICANTLY RELATED TO ITS ARTERIAL LEVELS. THUS, THE KIDNEY PLAYS A MAJOR ROLE IN MAINTAINING SAH LEVELS AND MAY, INDIRECTLY, CONTROL TISSUE TRANSMETHYLATION REACTIONS. OUR FINDINGS OF A PIVOTAL ROLE FOR THE HUMAN KIDNEY IN SULFUR AMINO ACID METABOLISM MAY ALSO ACCOUNT FOR THE INCREASED PLASMA LEVELS OF SAH IN PATIENTS WITH CHRONIC KIDNEY DISEASES. 2009 6 1557 24 DNA METHYLATION MODIFICATIONS INDUCED BY HEXAVALENT CHROMIUM. HEXAVALENT CHROMIUM [CR (VI)] CONTRIBUTES A SIGNIFICANT HEALTH RISK AND CAUSES A NUMBER OF CHRONIC DISEASES AND CANCERS. WHILE THE GENOTOXIC AND CARCINOGENIC EFFECTS OF HEXAVALENT CHROMIUM EXPOSURE ARE EXPLICIT AND BETTER-CHARACTERIZED, THE EXACT MECHANISM UNDERLYING THE CARCINOGENIC PROCESS OF CR (VI) IS STILL A MATTER OF DEBATE. IN RECENT YEARS, STUDIES HAVE SHOWN THAT EPIGENETIC MODIFICATIONS, ESPECIALLY DNA METHYLATION, MAY PLAY A SIGNIFICANT ROLE IN CR (VI)-INDUCED CARCINOGENESIS. THE AIM OF THIS REVIEW IS TO SUMMARIZE OUR UNDERSTANDING REGARDING THE EFFECTS OF CR (VI) ON GLOBAL AND GENE-SPECIFIC DNA METHYLATION. 2019 7 2230 40 EPIGENETIC MODIFICATIONS OF KLOTHO EXPRESSION IN KIDNEY DISEASES. DEVELOPMENTS OF MANY RENAL DISEASES ARE SUBSTANTIALLY INFLUENCED BY EPIGENETIC MODIFICATIONS OF NUMEROUS GENES, MAINLY MEDIATED BY DNA METHYLATIONS, HISTONE MODIFICATIONS, AND MICRORNA INTERFERENCE; HOWEVER, NOT ALL GENE MODIFICATIONS CAUSALLY AFFECT THE DISEASE ONSET OR PROGRESSION. KLOTHO IS A CRITICAL GENE WHOSE REPRESSIONS IN VARIOUS PATHOLOGICAL CONDITIONS REPORTEDLY INVOLVE EPIGENETIC REGULATORY MECHANISMS. KLOTHO IS ALMOST UNEXCEPTIONALLY REPRESSED EARLY AFTER ACUTE OR CHRONIC RENAL INJURIES AND ITS LEVELS INVERSELY CORRELATED WITH THE DISEASE PROGRESSION AND SEVERITY. MOREOVER, THE STRATEGIES OF KLOTHO DEREPRESSION VIA EPIGENETIC MODULATIONS BENEFICIALLY CHANGE THE PATHOLOGICAL COURSES BOTH IN VITRO AND IN VIVO. HENCE, KLOTHO IS NOT ONLY CONSIDERED A BIOMARKER OF THE RENAL DISEASE BUT ALSO A POTENTIAL OR EVEN AN IDEAL TARGET OF THERAPEUTIC EPIGENETIC INTERVENTION. HERE, WE SUMMARIZE AND DISCUSS STUDIES THAT INVESTIGATE THE KLOTHO REPRESSION AND INTERVENTION IN RENAL DISEASES FROM AN EPIGENETIC POINT OF VIEW. THESE INFORMATION MIGHT SHED NEW SIGHTS INTO THE EFFECTIVE THERAPEUTIC STRATEGIES TO PREVENT AND TREAT VARIOUS RENAL DISORDERS. 2021 8 3451 25 HYPERMETHYLATIONS OF RASAL1 AND KLOTHO IS ASSOCIATED WITH RENAL DYSFUNCTION IN A CHINESE POPULATION ENVIRONMENTALLY EXPOSED TO CADMIUM. EXPOSURE TO CADMIUM (CD) CAN AFFECT BOTH DNA METHYLATION AND RENAL FUNCTION, BUT THERE ARE FEW EXAMPLES OF THE ASSOCIATION BETWEEN EPIGENETIC MARKERS AND CD-INDUCED KIDNEY DAMAGE. IT HAS BEEN SUGGESTED THAT HYPERMETHYLATION OF THE GENES RASAL1 AND KLOTHO IS ASSOCIATED WITH RENAL FIBROGENESIS. TO INVESTIGATE WHETHER HYPERMETHYLATION OF RASAL1 AND KLOTHO IN PERIPHERAL BLOOD DNA CAN BE ASSOCIATED WITH CD EXPOSURE AND/OR CD-INDUCED RENAL DYSFUNCTION, THE DEGREES OF METHYLATION OF RASAL1 AND KLOTHO IN PERIPHERAL BLOOD DNA FROM 81 RESIDENTS IN CD-POLLUTED AND NON-POLLUTED AREAS WERE MEASURED USING BISULFATE-PCR-PYROSEQUENCING. CHANGES IN BLOOD CADMIUM (BCD), URINARY CADMIUM (UCD), AND KIDNEY PARAMETERS WERE MEASURED, AND THE GLOMERULAR FILTRATION RATE (EGFR) WAS ESTIMATED. THE LEVELS OF BCD AND UCD CORRELATED POSITIVELY WITH THE LEVELS OF DNA METHYLATION IN RASAL1 AND IN KLOTHO. THE MORE HEAVILY EXPOSED RESIDENTS (BCD, 4.23-13.22MUG/L; UCD, 8.65-32.90MUG/G CREATININE) EXHIBITED OBVIOUS RENAL DYSFUNCTION. NOTABLY, WHEN CD CONCENTRATION IN BLOOD AND URINE WAS ADJUSTED, THE INCREASED METHYLATION LEVEL IN RASAL1 WAS INVERSELY CORRELATED WITH EGFR (P<0.01) BUT THE RELATIONSHIP BETWEEN HYPERMETHYLATION OF KLOTHO AND EGFR WAS NOT STATISTICALLY SIGNIFICANT. THE METHYLATION OF RASAL1 INCREASED ALONG WITH THE INCREASED ABNORMAL PREVALENCE OF EGFR. OUR FINDINGS SUGGEST THAT CD EXPOSURE CAN INDUCE THE HYPERMETHYLATION OF RASAL1 AND KLOTHO. HYPERMETHYLATION OF RASAL1 MAY BE AN INDICATOR OF THE PROGRESS FOR CHRONIC KIDNEY DISEASE. 2013 9 3326 50 HISTONE DEACETYLASE 3 (HDAC3) AS AN IMPORTANT EPIGENETIC REGULATOR OF KIDNEY DISEASES. DEVELOPMENT AND PROGRESSION OF MANY KIDNEY DISEASES ARE SUBSTANTIALLY INFLUENCED BY ABERRANT PROTEIN ACETYLATION MODIFICATIONS OF GENE EXPRESSION CRUCIAL FOR KIDNEY FUNCTIONS. HISTONE DEACETYLASE (HDAC) EXPRESSION ALTERATIONS ARE DETECTED FROM RENAL SAMPLES OF PATIENTS AND ANIMAL MODELS OF VARIOUS KIDNEY DISEASES, AND THE ADMINISTRATIONS OF HDAC INHIBITORS DISPLAY IMPRESSIVE RENAL PROTECTIVE EFFECTS IN VITRO AND IN VIVO. HOWEVER, WHEN THE EXPRESSION ALTERATIONS OF MULTIPLE HDACS OCCUR, NOT ALL THE HDACS CAUSALLY AFFECT THE DISEASE ONSET OR PROGRESSION. IDENTIFICATION OF A SINGLE HDAC AS A DISEASE-CAUSING FACTOR WILL ALLOW SUBTYPE-TARGETED INTERVENTION WITH LESS SIDE EFFECT. HDAC3 IS A UNIQUE HDAC WITH DISTINCT STRUCTURAL AND SUBCELLULAR DISTRIBUTION FEATURES AND CO-REPRESSOR DEPENDENCY. HDAC3 IS REQUIRED FOR KIDNEY DEVELOPMENT AND ITS ABERRATIONS ACTIVELY PARTICIPATE IN MANY PATHOLOGICAL PROCESSES, SUCH AS CANCER, CARDIOVASCULAR DISEASES, DIABETES, AND NEURODEGENERATIVE DISORDERS, AND CONTRIBUTE SIGNIFICANTLY TO THE PATHOGENESIS OF KIDNEY DISEASES. THIS REVIEW WILL DISCUSS THE RECENT STUDIES THAT INVESTIGATE THE CRITICAL ROLES OF HDAC3 ABERRATIONS IN KIDNEY DEVELOPMENT, RENAL AGING, RENAL CELL CARCINOMA, RENAL FIBROSIS, CHRONIC KIDNEY DISEASE, POLYCYSTIC KIDNEY DISEASE, GLOMERULAR PODOCYTE INJURY, AND DIABETIC NEPHROPATHY. THESE STUDIES REVEAL THE DISTINCT CHARACTERS OF HDAC3 ABERRATIONS THAT ACT ON DIFFERENT MOLECULES/SIGNALING PATHWAYS UNDER VARIOUS RENAL PATHOLOGICAL CONDITIONS, WHICH MIGHT SHED LIGHTS INTO THE EPIGENETIC MECHANISMS OF RENAL DISEASES AND THE POTENTIALLY THERAPEUTIC STRATEGIES. 2022 10 1781 36 EFFECT OF 1 YEAR B AND D VITAMIN SUPPLEMENTATION ON LINE-1 REPETITIVE ELEMENT METHYLATION IN OLDER SUBJECTS. BACKGROUND: DISTURBED DNA METHYLATION IS CAUSALLY RELATED TO CHRONIC DISEASES LIKE CANCER AND ATHEROSCLEROSIS. B VITAMINS ARE COFACTORS REQUIRED FOR METHYL GROUP SYNTHESIS AND MAY THEREFORE AFFECT DNA METHYLATION. VITAMIN D HAS EPIGENETIC EFFECTS. WE TESTED IF B AND D VITAMIN SUPPLEMENTATION HAS AN EFFECT ON GENOMIC LONG INTERSPERSED NUCLEAR ELEMENT-1 (LINE-1) METHYLATION AND THE METABOLITES S-ADENOSYLMETHIONINE (SAM) AND S-ADENOSYLHOMOCYSTEINE (SAH). METHODS: FIFTY SUBJECTS (MEDIAN AGE 68.0 YEARS) WERE SUPPLEMENTED WITH A DAILY ORAL DOSE OF B VITAMINS (500 MICROG FOLIC ACID, 500 MICROG VITAMIN B12 AND 50 MG VITAMIN B6), 1200 IU VITAMIN D AND 456 MG CALCIUM. FASTING BLOOD SAMPLES WERE COLLECTED BEFORE AND AFTER 1 YEAR OF SUPPLEMENTATION. LINE-1 METHYLATION WAS DETERMINED IN GENOMIC DNA FROM BLOOD CELLS AS A SURROGATE FOR WHOLE GENOME METHYLATION. IN ADDITION, SAM, SAH AND TOTAL HOMOCYSTEINE (THCY) WERE MEASURED IN PLASMA SAMPLES. RESULTS: PLASMA HOMOCYSTEINE DECREASED SIGNIFICANTLY AFTER SUPPLEMENTATION (12.8 VS. 9.1 MICROMOL/L; P<0.05), WHEREAS SAM, SAH, THE SAM/SAH RATIO AND LINE-1 METHYLATION DID NOT CHANGE SIGNIFICANTLY. LINE-1 METHYLATION WAS NOT SIGNIFICANTLY CORRELATED WITH SAH, HOMOCYSTEINE OR B VITAMINS. CONCLUSIONS: LONG-TERM VITAMIN B SUPPLEMENTATION HAD NO EFFECT ON LINE-1 METHYLATION IN BLOOD CELLS NOR ON PLASMA LEVELS OF SAM AND SAH. VITAMIN B AND D SUPPLEMENTATION SEEMS TO HAVE NO EFFECT ON DNA METHYLATION, ESPECIALLY IN CASES WHERE NO SEVERE DEFICIENCY EXISTS. 2013 11 2631 38 EPIGENOME-WIDE ASSOCIATION STUDY OF WHOLE BLOOD GENE EXPRESSION IN FRAMINGHAM HEART STUDY PARTICIPANTS PROVIDES MOLECULAR INSIGHT INTO THE POTENTIAL ROLE OF CHRNA5 IN CIGARETTE SMOKING-RELATED LUNG DISEASES. BACKGROUND: DNA METHYLATION IS A KEY EPIGENETIC MODIFICATION THAT CAN DIRECTLY AFFECT GENE REGULATION. DNA METHYLATION IS HIGHLY INFLUENCED BY ENVIRONMENTAL FACTORS SUCH AS CIGARETTE SMOKING, WHICH IS CAUSALLY RELATED TO CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) AND LUNG CANCER. TO DATE, THERE HAVE BEEN FEW LARGE-SCALE, COMBINED ANALYSES OF DNA METHYLATION AND GENE EXPRESSION AND THEIR INTERRELATIONS WITH LUNG DISEASES. RESULTS: WE PERFORMED AN EPIGENOME-WIDE ASSOCIATION STUDY OF WHOLE BLOOD GENE EXPRESSION IN ~ 6000 INDIVIDUALS FROM FOUR COHORTS. WE DISCOVERED AND REPLICATED NUMEROUS CPGS ASSOCIATED WITH THE EXPRESSION OF CIS GENES WITHIN 500 KB OF EACH CPG, WITH 148 TO 1,741 CIS CPG-TRANSCRIPT PAIRS IDENTIFIED ACROSS COHORTS. WE FOUND THAT THE CLOSER A CPG RESIDED TO A TRANSCRIPTION START SITE, THE LARGER ITS EFFECT SIZE, AND THAT 36% OF CIS CPG-TRANSCRIPT PAIRS SHARE THE SAME CAUSAL GENETIC VARIANT. MENDELIAN RANDOMIZATION ANALYSES REVEALED THAT HYPOMETHYLATION AND LOWER EXPRESSION OF CHRNA5, WHICH ENCODES A SMOKING-RELATED NICOTINIC RECEPTOR, ARE CAUSALLY LINKED TO INCREASED RISK OF COPD AND LUNG CANCER. THIS PUTATIVELY CAUSAL RELATIONSHIP WAS FURTHER VALIDATED IN LUNG TISSUE DATA. CONCLUSIONS: OUR RESULTS PROVIDE A LARGE AND COMPREHENSIVE ASSOCIATION STUDY OF WHOLE BLOOD DNA METHYLATION WITH GENE EXPRESSION. EXPRESSION PLATFORM DIFFERENCES RATHER THAN POPULATION DIFFERENCES ARE CRITICAL TO THE REPLICATION OF CIS CPG-TRANSCRIPT PAIRS. THE LOW REPRODUCIBILITY OF TRANS CPG-TRANSCRIPT PAIRS SUGGESTS THAT DNA METHYLATION REGULATES NEARBY RATHER THAN REMOTE GENE EXPRESSION. THE PUTATIVELY CAUSAL ROLES OF METHYLATION AND EXPRESSION OF CHRNA5 IN RELATION TO COPD AND LUNG CANCER PROVIDE EVIDENCE FOR A MECHANISTIC LINK BETWEEN PATTERNS OF SMOKING-RELATED EPIGENETIC VARIATION AND LUNG DISEASES, AND HIGHLIGHT POTENTIAL THERAPEUTIC TARGETS FOR LUNG DISEASES AND SMOKING CESSATION. 2021 12 6717 44 VITAMIN B SUPPLEMENTATION AND NUTRITIONAL INTAKE OF METHYL DONORS IN PATIENTS WITH CHRONIC KIDNEY DISEASE: A CRITICAL REVIEW OF THE IMPACT ON EPIGENETIC MACHINERY. CARDIOVASCULAR MORBIDITY AND MORTALITY ARE SEVERAL-FOLD HIGHER IN PATIENTS WITH ADVANCED CHRONIC KIDNEY DISEASE (CKD) AND END-STAGE RENAL DISEASE (ESRD) THAN IN THE GENERAL POPULATION. HYPERHOMOCYSTEINEMIA HAS UNDOUBTEDLY A CENTRAL ROLE IN SUCH A PROMINENT CARDIOVASCULAR BURDEN. THE LEVELS OF HOMOCYSTEINE ARE REGULATED BY METHYL DONORS (FOLATE, METHIONINE, CHOLINE, BETAINE), AND COFACTORS (VITAMIN B6, VITAMIN B12,). UREMIA-INDUCED HYPERHOMOCYSTEINEMIA HAS AS ITS MAIN TARGETS DNA METHYLTRANSFERASES, AND THIS LEADS TO AN ALTERED EPIGENETIC CONTROL OF GENES REGULATED THROUGH METHYLATION. IN RENAL PATIENTS, THE EPIGENETIC LANDSCAPE IS STRICTLY CORRELATED WITH THE UREMIC PHENOTYPE AND DEPENDENT ON DIETARY INTAKE OF MICRONUTRIENTS, INFLAMMATION, GUT MICROBIOME, INFLAMMATORY STATUS, OXIDATIVE STRESS, AND LIFESTYLE HABITS. ALL THESE FACTORS ARE KEY CONTRIBUTORS IN METHYLOME MAINTENANCE AND IN THE MODULATION OF GENE TRANSCRIPTION THROUGH DNA HYPO- OR HYPERMETHYLATION IN CKD. THIS IS AN OVERVIEW OF THE EPIGENETIC CHANGES RELATED TO DNA METHYLATION IN PATIENTS WITH ADVANCED CKD AND ESRD. WE EXPLORED THE CURRENTLY AVAILABLE DATA ON THE MOLECULAR DYSREGULATIONS RESULTING FROM ALTERED GENE EXPRESSION IN UREMIA. SPECIAL ATTENTION WAS PAID TO THE EFFICACY OF B-VITAMINS SUPPLEMENTATION AND DIETARY INTAKE OF METHYL DONORS ON HOMOCYSTEINE LOWERING AND CARDIOVASCULAR PROTECTION. 2020 13 4655 31 NEUROTROPHIN MEDIATED HPA AXIS DYSREGULATION IN STRESS INDUCED GENESIS OF PSYCHIATRIC DISORDERS: ORCHESTRATION BY EPIGENETIC MODIFICATIONS. APART FROM THEIR ESTABLISHED ROLE IN EMBRYONIC DEVELOPMENT, NEUROTROPHINS (NTS) HAVE DIVERSE FUNCTIONS IN THE NERVOUS SYSTEM. THEIR ROLE IN THE INTEGRATION OF PHYSIOLOGICAL AND BIOCHEMICAL ASPECTS OF THE NERVOUS SYSTEM IS CURRENTLY ATTRACTING MUCH ATTENTION. BASED ON A SYSTEMATIC ANALYSIS OF THE LITERATURE, WE HERE PROPOSE A NEW PARADIGM THAT, BY EXPLOITING A NOVEL ROLE OF NTS, MAY HELP EXPLAIN THE GENESIS OF STRESS-RELATED PSYCHIATRIC DISORDERS, OPENING NEW AVENUES FOR BETTER MANAGEMENT OF THE SAME. WE HYPOTHESIZE THAT NTS AS AN INTEGRATED NETWORK PLAY A CRUCIAL ROLE IN MAINTAINING AN INDIVDUAL'S PSYCHOLOGICAL WELLBEING. GIVEN THE EVIDENCE THAT STRESS CAN INDUCE CHRONIC DISRUPTION OF THE HYPOTHALAMIC-PITUITARY-ADRENAL (HPA) AXIS WHICH, IN TURN, IS CAUSALLY LINKED TO SEVERAL PSYCHIATRIC DISORDERS, THIS FUNCTION MAY BE MEDIATED THROUGH THE HOMEOSTATIC MECHANISMS GOVERNING REGULATION OF THIS AXIS. IN FACT, NTS, SUCH AS NERVE GROWTH FACTOR (NGF) AND BRAIN DERIVED NEUROTROPHIC FACTOR (BDNF) ARE KNOWN TO PARTICIPATE IN NEUROENDOCRINE REGULATION. RECENT STUDIES SUGGEST EPIGENETIC MODIFICATION OF NT-HPA AXIS INTERPLAY IN THE PRECIPITATION OF PSYCHIATRIC DISORDERS. OUR ARTICLE HIGHLIGHTS WHY THIS NEW KNOWLEDGE REGARDING NTS SHOULD BE CONSIDERED IN THE ETIOGENESIS AND TREATMENT OF STRESS-INDUCED PSYCHOPATHOLOGY. 2019 14 4217 31 METHYL DONOR NUTRIENTS IN CHRONIC KIDNEY DISEASE: IMPACT ON THE EPIGENETIC LANDSCAPE. EPIGENETIC ALTERATIONS, SUCH AS THOSE LINKED TO DNA METHYLATION, MAY POTENTIALLY PROVIDE MOLECULAR EXPLANATIONS FOR COMPLICATIONS ASSOCIATED WITH ALTERED GENE EXPRESSION IN ILLNESSES, SUCH AS CHRONIC KIDNEY DISEASE (CKD). ALTHOUGH BOTH DNA HYPO- AND HYPERMETHYLATION HAVE BEEN OBSERVED IN THE UREMIC MILIEU, THIS REMAINS ONLY A SINGLE ASPECT OF THE EPIGENETIC LANDSCAPE AND, THUS, OF ANY BIOCHEMICAL DYSREGULATION ASSOCIATED WITH CKD. NEVERTHELESS, THE ROLE OF UREMIA-PROMOTING ALTERATIONS ON THE EPIGENETIC LANDSCAPE REGULATING GENE EXPRESSION IS STILL A NOVEL AND SCARCELY STUDIED FIELD. ALTHOUGH FEW STUDIES HAVE ACTUALLY REPORTED ALTERATIONS OF DNA METHYLATION VIA METHYL DONOR NUTRIENT INTAKE, EMERGING EVIDENCE INDICATES THAT NUTRITIONAL MODIFICATION OF THE MICROBIOME CAN AFFECT ONE-CARBON METABOLISM AND THE CAPACITY TO METHYLATE THE GENOME IN CKD. IN THIS REVIEW, WE DISCUSS THE NUTRITIONAL MODIFICATIONS THAT MAY AFFECT ONE-CARBON METABOLISM AND THE POSSIBLE IMPACT OF METHYL DONOR NUTRIENTS ON THE MICROBIOME, CKD, AND ITS PHENOTYPE. 2019 15 976 38 CHRONIC OPIOID USE IS ASSOCIATED WITH INCREASED DNA METHYLATION CORRELATING WITH INCREASED CLINICAL PAIN. ENVIRONMENTALLY CAUSED CHANGES IN CHROMOSOMES THAT DO NOT ALTER THE DNA SEQUENCE BUT CAUSE PHENOTYPIC CHANGES BY ALTERING GENE TRANSCRIPTION ARE SUMMARIZED AS EPIGENETICS. A MAJOR EPIGENETIC MECHANISM IS METHYLATION OR DEMETHYLATION AT CPG-RICH DNA ISLANDS. DNA METHYLATION TRIGGERED BY DRUGS HAS LARGELY UNEXPLORED THERAPEUTIC CONSEQUENCES. HERE WE REPORT INCREASED METHYLATION AT A CPG RICH ISLAND IN THE OPRM1 GENE CODING FOR MU-OPIOID RECEPTORS AND AT A GLOBAL METHYLATION SITE (LINE-1) IN LEUKOCYTES OF METHADONE-SUBSTITUTED FORMER OPIATE ADDICTS COMPARED WITH MATCHED HEALTHY CONTROLS. HIGHER DNA METHYLATION ASSOCIATED WITH CHRONIC OPIOID EXPOSURE WAS REPRODUCED IN AN INDEPENDENT COHORT OF OPIOID-TREATED AS COMPARED TO NON-OPIOID-TREATED PAIN PATIENTS. THIS SUGGESTS THAT OPIOIDS MAY STIMULATE DNA METHYLATION. THE OPRM1 METHYLATION HAD NO IMMEDIATE EFFECT ON MU-OPIOID RECEPTOR TRANSCRIPTION AND WAS NOT ASSOCIATED WITH OPIOID DOSING REQUIREMENTS. HOWEVER, THE GLOBAL DNA METHYLATION AT LINE-1 WAS SIGNIFICANTLY CORRELATED WITH INCREASED CHRONIC PAIN. THIS SUGGESTS INHIBITORY EFFECTS ON THE TRANSCRIPTION OF STILL UNSPECIFIED NOCIFENSIVE GENE PRODUCTS. IT FURTHER IMPLIES THAT OPIOIDS MAY BE CAUSALLY ASSOCIATED WITH INCREASED GENOME-WIDE DNA METHYLATION, ALTHOUGH CURRENTLY THERE IS NO DIRECT EVIDENCE OF THIS. THIS HAS PHENOTYPIC CONSEQUENCES FOR PAIN AND MAY PROVIDE A NEW, EPIGENETICS-ASSOCIATED MECHANISM OF OPIOID-INDUCED HYPERALGESIA. THE RESULTS INDICATE A POTENTIAL INFLUENCE OF OPIOID ANALGESICS ON THE PATIENTS' EPIGENOME. THEY EMPHASIZE THE NEED FOR RELIABLE AND COST-EFFECTIVE SCREENING TOOLS AND MAY IMPLY THAT HIGH-THROUGHPUT SCREENING FOR LEAD COMPOUNDS IN ARTIFICIAL EXPRESSION SYSTEMS MAY NOT PROVIDE THE BEST TOOLS FOR IDENTIFYING NEW PAIN MEDICATIONS. 2013 16 6726 32 VITAMIN-DEPENDENT METHIONINE METABOLISM AND ALCOHOLIC LIVER DISEASE. EMERGING EVIDENCE INDICATES THAT ETHANOL-INDUCED ALTERATIONS IN HEPATIC METHIONINE METABOLISM PLAY A CENTRAL ROLE IN THE PATHOGENESIS OF ALCOHOLIC LIVER DISEASE (ALD). BECAUSE MALNUTRITION IS A UNIVERSAL CLINICAL FINDING IN THIS DISEASE AND HEPATIC METHIONINE METABOLISM IS DEPENDENT UPON DIETARY FOLATE AND VITAMINS B-6 AND B-12, ALD CAN BE CONSIDERED AN INDUCED NUTRITIONAL DISORDER THAT IS CONDITIONED BY ALCOHOL ABUSE. THE PRESENT REVIEW DESCRIBES THE ETIOLOGIES OF THESE 3 VITAMIN DEFICIENCIES IN ALD AND HOW THEY INTERACT WITH CHRONIC ETHANOL EXPOSURE TO ALTER HEPATIC METHIONINE METABOLISM. SUBSEQUENT SECTIONS FOCUS ON MOLECULAR MECHANISMS FOR THE INTERACTIONS OF ABERRANT METHIONINE METABOLISM WITH ETHANOL IN THE PATHOGENESIS OF ALD, IN PARTICULAR THE ROLE OF S-ADENOSYLMETHIONINE (SAM) IN REGULATING THE EPIGENETIC EXPRESSIONS OF GENES RELEVANT TO PATHWAYS OF LIVER INJURY. THE REVIEW WILL CONCLUDE WITH DESCRIPTIONS OF STUDIES ON THE EFFICACY OF SAM IN THE TREATMENT OF ALD AND WITH DISCUSSION OF POTENTIALLY FRUITFUL FUTURE AVENUES OF RESEARCH. 2011 17 339 44 ALTERATIONS IN HOMOCYSTEINE METABOLISM AMONG ALCOHOL DEPENDENT PATIENTS--CLINICAL, PATHOBIOCHEMICAL AND GENETIC ASPECTS. ADDICTION RESEARCH FOCUSING ON HOMOCYSTEINE METABOLISM AND ITS ASSOCIATION WITH ASPECTS OF ALCOHOL DEPENDENCE HAS REVEALED IMPORTANT FINDINGS. RECENT LITERATURE ON THIS TOPIC HAS BEEN TAKEN INTO ACCOUNT FOR THE REVIEW PROVIDED. METHYLENETETRAHYDROFOLATE REDUCTASE (MTHFR) IS A KEY ENZYME IN THE HOMOCYSTEINE METABOLISM. PLASMA HOMOCYSTEINE LEVELS ARE INFLUENCED BY THE SINGLE-NUCLEOTIDE POLYMORPHISM (SNP) MTHFR C677T. BESIDES GENETIC FACTORS, ENVIRONMENTAL FACTORS HAVE AN IMPACT ON HOMOCYSTEINE PLASMA LEVELS TOO. THUS, CHRONIC ALCOHOL INTAKE IS ASSOCIATED WITH ELEVATED HOMOCYSTEINE PLASMA CONCENTRATIONS. ELEVATION OF PLASMA HOMOCYSTEINE CONCENTRATION IS CONSIDERED AS A PREDICTOR FOR THE OCCURRENCE OF ALCOHOL WITHDRAWAL SEIZURES AND--AS HOMOCYSTEINE IS A CARDIOVASCULAR RISK FACTOR--MIGHT CONTRIBUTE TO THE HIGHER RISK FOR MYOCARDIAL INFARCTION AMONG ALCOHOL DEPENDENT PATIENTS. HOMOCYSTEINE ACTS AS AN N-METHYL-D-ASPARTATE (NMDA) RECEPTOR AGONIST AND HAS EXCITOTOXIC EFFECTS. FURTHERMORE, IT HAS BEEN DEMONSTRATED THAT HOMOCYSTEINE HAS NEUROTOXIC EFFECTS ESPECIALLY ON DOPAMINERGIC NEURONS. AS THE REWARDING EFFECTS OF ALCOHOL ARE MEDIATED BY THE DOPAMINERGIC SYSTEM, A HOMOCYSTEINE-DEPENDENT IMPAIRMENT OF THE REWARD SYSTEM POSSIBLY LEADS TO AN ALTERED DRINKING BEHAVIOUR ACCORDING TO THE DEFICIT HYPOTHESIS OF ADDICTION. HOMOCYSTEINE IS INVOLVED IN THE METABOLISM OF METHYL GROUPS AND DNA-METHYLATION PLAYS A ROLE IN REGULATION OF GENE EXPRESSION. THEREFORE IT HAS BEEN SUGGESTED THAT HOMOCYSTEINE IS AN IMPORTANT EPIGENETIC FACTOR. IT REMAINS TO BE DETERMINED WHETHER ALCOHOL DEPENDENT PATIENTS BENEFIT FROM HOMOCYSTEINE LOWERING STRATEGIES, E.G., VIA SUPPLEMENTATION OF FOLATE, VITAMIN B6 AND B12. IN THIS RESPECT IT IS NOT CLEAR YET, IF A SUPPLEMENTATION THERAPY CAN REDUCE THE RISK FOR THE OCCURRENCE OF ALCOHOL WITHDRAWAL SEIZURES. 2008 18 3887 22 KLOTHO METHYLATION IS LINKED TO UREMIC TOXINS AND CHRONIC KIDNEY DISEASE. EPIGENETIC REGULATION PLAYS A MAJOR ROLE IN UREMIC TOXIN-INDUCED CHRONIC KIDNEY DISEASE (CKD) PROGRESSION. THE KLOTHO PROTEIN IS A KEY MODULATOR OF HOMEOSTASIS IN RENAL FUNCTION. UREMIC TOXIN ACCUMULATION CAN INDUCE DNA METHYLTRANSFERASE (DNMT) PROTEIN EXPRESSION, WHICH IS INVOLVED IN THE SILENCING OF KLOTHO THROUGH HYPERMETHYLATION. TREATMENT WITH DNMT INHIBITORS CAN INDUCE A HYPERMETHYLATED STATUS OF KLOTHO AND SUPPRESS MRNA AND PROTEIN EXPRESSION. EPIGENETIC TARGETING OF SPECIFIC GENES MAY BECOME AN EFFECTIVE STRATEGY TO PREVENT PROGRESSION OF UREMIA-RELATED CKD. 2012 19 2560 46 EPIGENETICS IN THE DEVELOPMENT, MODIFICATION, AND PREVENTION OF CARDIOVASCULAR DISEASE. EPIGENETICS HAS MAJOR RELEVANCE TO ALL DISEASE PROCESSES; CARDIOVASCULAR (CV) DISEASE AND ITS RELATED CONDITIONS ARE NO EXCEPTION. EPIGENETICS IS DEFINED AS THE STUDY OF HERITABLE ALTERATIONS IN GENE EXPRESSION, OR CELLULAR PHENOTYPE, AND GOES FAR BEYOND A PURE GENETIC APPROACH. A MORE PRECISE DEFINITION IS THAT EPIGENETICS REPRESENTS ALL THE MEIOTICALLY AND MITOTICALLY INHERITED CHANGES IN GENE EXPRESSION THAT ARE NOT ENCODED ON THE DEOXYRIBONUCLEIC ACID (DNA) SEQUENCE ITSELF. MAJOR EPIGENETIC MECHANISMS ARE MODIFICATIONS OF HISTONE PROTEINS IN CHROMATIN AND DNA METHYLATION (WHICH DOES NOT ALTER THE DNA SEQUENCE). THERE IS INCREASING EVIDENCE FOR THE INVOLVEMENT OF EPIGENETICS IN HUMAN DISEASE SUCH AS CANCER, INFLAMMATORY DISEASE AND CV DISEASE. OTHER CHRONIC DISEASES ARE ALSO SUSCEPTIBLE TO EPIGENETIC MODIFICATION SUCH AS METABOLIC DISEASES INCLUDING OBESITY, METABOLIC SYNDROME, AND DIABETES MELLITUS. THERE IS MUCH EVIDENCE FOR THE MODIFICATION OF EPIGENETICS BY NUTRITION AND EXERCISE. THROUGH THESE MODIFICATIONS, THERE IS INFINITE POTENTIAL FOR BENEFIT FOR THE FETUS, THE NEWBORN, AND THE INDIVIDUAL AS WELL AS POPULATION EFFECTS. ASSOCIATION WITH CV DISEASE, INCLUDING CORONARY HEART DISEASE AND PERIPHERAL VASCULAR DISEASE, IS EVIDENT THROUGH EPIGENETIC RELATIONSHIPS AND MODIFICATION BY MAJOR CV RISK FACTORS SUCH AS TOBACCO ABUSE. AGING ITSELF MAY BE ALTERED BY EPIGENETIC MODIFICATION. KNOWLEDGE OF EPIGENETICS AND ITS RELEVANCE TO THE DEVELOPMENT, MODIFICATION, AND PREVENTION OF CV DISEASE IS IN A VERY PRELIMINARY STAGE BUT HAS AN INFINITE FUTURE. 2015 20 4861 27 ORGANIC ANION TRANSPORTER 1 IS AN HDAC4-REGULATED MEDIATOR OF NOCICEPTIVE HYPERSENSITIVITY IN MICE. PERSISTENT PAIN IS SUSTAINED BY MALADAPTIVE CHANGES IN GENE TRANSCRIPTION RESULTING IN ALTERED FUNCTION OF THE RELEVANT CIRCUITS; THERAPIES ARE STILL UNSATISFACTORY. THE EPIGENETIC MECHANISMS AND AFFECTED GENES LINKING NOCICEPTIVE ACTIVITY TO TRANSCRIPTIONAL CHANGES AND PATHOLOGICAL SENSITIVITY ARE UNCLEAR. HERE, WE FOUND THAT, AMONG SEVERAL HISTONE DEACETYLASES (HDACS), SYNAPTIC ACTIVITY SPECIFICALLY AFFECTS HDAC4 IN MURINE SPINAL CORD DORSAL HORN NEURONS. NOXIOUS STIMULI THAT INDUCE LONG-LASTING INFLAMMATORY HYPERSENSITIVITY CAUSE NUCLEAR EXPORT AND INACTIVATION OF HDAC4. THE DEVELOPMENT OF INFLAMMATION-ASSOCIATED MECHANICAL HYPERSENSITIVITY, BUT NEITHER ACUTE NOR BASAL SENSITIVITY, IS IMPAIRED BY THE EXPRESSION OF A CONSTITUTIVELY NUCLEAR LOCALIZED HDAC4 MUTANT. NEXT GENERATION RNA-SEQUENCING REVEALED AN HDAC4-REGULATED GENE PROGRAM COMPRISING MEDIATORS OF SENSITIZATION INCLUDING THE ORGANIC ANION TRANSPORTER OAT1, KNOWN FOR ITS RENAL TRANSPORT FUNCTION. USING PHARMACOLOGICAL AND MOLECULAR TOOLS TO MODULATE OAT1 ACTIVITY OR EXPRESSION, WE CAUSALLY LINK OAT1 TO PERSISTENT INFLAMMATORY HYPERSENSITIVITY IN MICE. THUS, HDAC4 IS A KEY EPIGENETIC REGULATOR THAT TRANSLATES NOCICEPTIVE ACTIVITY INTO SENSITIZATION BY REGULATING OAT1, WHICH IS A POTENTIAL TARGET FOR PAIN-RELIEVING THERAPIES. 2022