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Schaffner SL, Kobor MS. DNA methylation as a mediator of genetic and environmental influences on Parkinson's disease susceptibility: Impacts of alpha-Synuclein, physical activity, and pesticide exposure on the epigenome. Front Genet 2022; 13:971298. [PMID: 36061205 PMCID: PMC9437223 DOI: 10.3389/fgene.2022.971298] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder with a complex etiology and increasing prevalence worldwide. As PD is influenced by a combination of genetic and environment/lifestyle factors in approximately 90% of cases, there is increasing interest in identification of the interindividual mechanisms underlying the development of PD as well as actionable lifestyle factors that can influence risk. This narrative review presents an outline of the genetic and environmental factors contributing to PD risk and explores the possible roles of cytosine methylation and hydroxymethylation in the etiology and/or as early-stage biomarkers of PD, with an emphasis on epigenome-wide association studies (EWAS) of PD conducted over the past decade. Specifically, we focused on variants in the SNCA gene, exposure to pesticides, and physical activity as key contributors to PD risk. Current research indicates that these factors individually impact the epigenome, particularly at the level of CpG methylation. There is also emerging evidence for interaction effects between genetic and environmental contributions to PD risk, possibly acting across multiple omics layers. We speculated that this may be one reason for the poor replicability of the results of EWAS for PD reported to date. Our goal is to provide direction for future epigenetics studies of PD to build upon existing foundations and leverage large datasets, new technologies, and relevant statistical approaches to further elucidate the etiology of this disease.
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Affiliation(s)
- Samantha L. Schaffner
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
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Zhao X, Du C. Effect of smoking status on spirometric lung age in adult Chinese Men. HEALTH & SOCIAL CARE IN THE COMMUNITY 2022; 30:1384-1390. [PMID: 34080728 DOI: 10.1111/hsc.13468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/18/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
Smoking is one of the most unhealthy behaviours and responsible for a variety of respiratory diseases. Although spirometric lung age (SLA) is regarded as an effective way to augment the smoking quit rate in other countries, it has not been calculated in Chinese smokers. Thus, the aim of this study was to determine the association of SLA with smoking status, and further explore whether smoking duration, dependence and other factors such as obesity and physical exercise affect SLA in Chinese current smokers. A total of 431 healthy men aged 20 years and older took part in the study from September 2018 to August 2019. Spirometric test was measured through a portable spirometry, and smoking status including smoking duration and dependence was investigated by using a questionnaire. SLA was calculated from an established equation which is based on the inverse calculation of the forced expiratory volume in one second in the Chinese population. Lung age difference (∆LA) could be obtained by counting the difference between SLA and chronological age. Results indicated that ∆LA is remarkably higher in current smokers than that in ex-smokers and non-smokers (p < 0.01). The study also revealed that smoking duration and dependence are related to ∆LA. Smokers with long smoking duration (smoked ≥10 years) and high dependence (consumed ≥20 cigarettes per day) had a significantly higher ∆LA than their counterparties (p < 0.01). Multiple regression analysis showed that body mass index, smoking duration and cigarettes per day were independently correlated with ∆LA in the current smokers (p < 0.01). The findings suggest that not only smoking or not, but smoking duration, dependence and obesity are strongly associated with SLA.
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Affiliation(s)
- Xiaoguang Zhao
- Department of Research Academy of Grand Health, Ningbo University, Zhejiang, China
- Faculty of Sport Science, Ningbo University, Zhejiang, China
| | - Chenya Du
- Faculty of Sport Science, Ningbo University, Zhejiang, China
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Varela RB, Cararo JH, Tye SJ, Carvalho AF, Valvassori SS, Fries GR, Quevedo J. Contributions of epigenetic inheritance to the predisposition of major psychiatric disorders: theoretical framework, evidence, and implications. Neurosci Biobehav Rev 2022; 135:104579. [DOI: 10.1016/j.neubiorev.2022.104579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/10/2022] [Accepted: 02/11/2022] [Indexed: 02/08/2023]
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Environmental Impact on the Epigenetic Mechanisms Underlying Parkinson’s Disease Pathogenesis: A Narrative Review. Brain Sci 2022; 12:brainsci12020175. [PMID: 35203939 PMCID: PMC8870303 DOI: 10.3390/brainsci12020175] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 02/04/2023] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disorder with an unclear etiology and no disease-modifying treatment to date. PD is considered a multifactorial disease, since both genetic and environmental factors contribute to its pathogenesis, although the molecular mechanisms linking these two key disease modifiers remain obscure. In this context, epigenetic mechanisms that alter gene expression without affecting the DNA sequence through DNA methylation, histone post-transcriptional modifications, and non-coding RNAs may represent the key mediators of the genetic–environmental interactions underlying PD pathogenesis. Environmental exposures may cause chemical alterations in several cellular functions, including gene expression. Emerging evidence has highlighted that smoking, coffee consumption, pesticide exposure, and heavy metals (manganese, arsenic, lead, etc.) may potentially affect the risk of PD development at least partially via epigenetic modifications. Herein, we discuss recent accumulating pre-clinical and clinical evidence of the impact of lifestyle and environmental factors on the epigenetic mechanisms underlying PD development, aiming to shed more light on the pathogenesis and stimulate future research.
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Wigner P, Synowiec E, Jóźwiak P, Czarny P, Bijak M, Białek K, Szemraj J, Gruca P, Papp M, Śliwiński T. The Effect of Chronic Mild Stress and Venlafaxine on the Expression and Methylation Levels of Genes Involved in the Tryptophan Catabolites Pathway in the Blood and Brain Structures of Rats. J Mol Neurosci 2020; 70:1425-1436. [PMID: 32406039 PMCID: PMC7399689 DOI: 10.1007/s12031-020-01563-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/22/2020] [Indexed: 12/21/2022]
Abstract
A growing body of evidence suggests that depression may be associated with impairment of the tryptophan catabolites (TRYCATs) pathway. The present study investigated the effects of the chronic administration of venlafaxine on the expression and methylation status of Katl, Tph1/2, Ido1, Kmo and Kynu in the brain and blood of rats exposed to the CMS model of depression. The rats were subjected to the CMS procedure for 2 or 7 weeks and administered venlafaxine (10 mg/kg/day, IP) for 5 weeks. mRNA and protein expression and the methylation status of gene promoters in PBMCs and six brain structures were evaluated and analysed using the TaqMan Gene Expression Assay and Western blotting, and methylation-sensitive high-resolution melting (MS-HRM), respectively. We found that the CMS procedure increased KatI expression in the midbrain and KatII expression in the midbrain and the amygdala, while venlafaxine administration decreased KatII expression in the hypothalamus and the cerebral cortex. The methylation status of the Tph1 and Kmo promoters in peripheral blood mononuclear cells (PBMCs) was significantly increased in the stressed group after antidepressant therapy. The protein levels of Tph1 and Ido1 were decreased following venlafaxine administration. Our results confirmed that CMS and venlafaxine modulate the expression levels and methylation status of genes involved in the TRYCATs pathway.
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Affiliation(s)
- Paulina Wigner
- Faculty of Biology and Environmental Protection, Laboratory of Medical Genetics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Ewelina Synowiec
- Faculty of Biology and Environmental Protection, Laboratory of Medical Genetics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Paweł Jóźwiak
- Faculty of Biology and Environmental Protection, Department of Cytobiochemistry, University of Lodz, Lodz, Poland
| | - Piotr Czarny
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Michał Bijak
- Faculty of Biology and Environmental Protection, Department of General Biochemistry, University of Lodz, Lodz, Poland
| | - Katarzyna Białek
- Faculty of Biology and Environmental Protection, Laboratory of Medical Genetics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland
| | - Janusz Szemraj
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Piotr Gruca
- Polish Academy of Sciences, Institute of Pharmacology, Krakow, Poland
| | - Mariusz Papp
- Polish Academy of Sciences, Institute of Pharmacology, Krakow, Poland
| | - Tomasz Śliwiński
- Faculty of Biology and Environmental Protection, Laboratory of Medical Genetics, University of Lodz, Pomorska 141/143, 90-236, Lodz, Poland.
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The effect of SLC6A3 variable number of tandem repeats and methylation levels on individual susceptibility to start tobacco smoking and on the ability of smokers to quit smoking. Pharmacogenet Genomics 2020; 30:117-123. [PMID: 32371614 DOI: 10.1097/fpc.0000000000000403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
OBJECTIVE Nicotine acts through the dopamine pathway in the brain affecting reward processing through cigarette consumption. Thus, both genetic and epigenetic factors related to dopamine metabolism may influence individual's smoking behavior. MATERIALS AND METHODS We studied variations of two variable numbers of tandem repeats (VNTRs), 40 and 30 bp in length, in SLC6A3 gene together with six DNA methylation sites located in a first intron of the gene in relation to several smoking-related phenotypes in a study population consisting of 1230 Whites of Russian origin. RESULTS Both the 5R allele of 30 bp VNTR and the 9R allele of 40 bp VNTR in SLC6A3 were associated with a reduced risk to tobacco smoking [odds ratio (OR) 0.53, 95% confidence interval (CI) 0.37-0.75; OR 0.62, 95% CI 0.43-0.88]. Although the carriers of 9R allele also had high Fagerström test for nicotine dependence scores (OR 1.65, 95% CI 1.04-2.60), they were still more likely to succeed in smoking cessation (OR 0.59, 95% CI 0.40-0.88). Also, current smokers had more than 2.5-fold likelihood to have increased SLC6A3 methylation levels than former smokers (OR 2.72, 95% CI 1.63-4.53). CONCLUSION The SLC6A3 5R of 30 bp and 9R of 40 bp VNTR variants may lead to a reduced risk to start smoking through decreased dopamine availability, and can also affect the success in subsequent smoking cessation attempts. Moreover, the elevated mean methylation values in the first intron of SLC6A3 may be related to nicotine dependence via a more active dopamine transporter.
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The Relationship between DNA Methylation and Antidepressant Medications: A Systematic Review. Int J Mol Sci 2020; 21:ijms21030826. [PMID: 32012861 PMCID: PMC7037192 DOI: 10.3390/ijms21030826] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/25/2020] [Accepted: 01/26/2020] [Indexed: 01/31/2023] Open
Abstract
Major depressive disorder (MDD) is the leading cause of disability worldwide and is associated with high rates of suicide and medical comorbidities. Current antidepressant medications are suboptimal, as most MDD patients fail to achieve complete remission from symptoms. At present, clinicians are unable to predict which antidepressant is most effective for a particular patient, exposing patients to multiple medication trials and side effects. Since MDD’s etiology includes interactions between genes and environment, the epigenome is of interest for predictive utility and treatment monitoring. Epigenetic mechanisms of antidepressant medications are incompletely understood. Differences in epigenetic profiles may impact treatment response. A systematic literature search yielded 24 studies reporting the interaction between antidepressants and eight genes (BDNF, MAOA, SLC6A2, SLC6A4, HTR1A, HTR1B, IL6, IL11) and whole genome methylation. Methylation of certain sites within BDNF, SLC6A4, HTR1A, HTR1B, IL11, and the whole genome was predictive of antidepressant response. Comparing DNA methylation in patients during depressive episodes, during treatment, in remission, and after antidepressant cessation would help clarify the influence of antidepressant medications on DNA methylation. Individuals’ unique methylation profiles may be used clinically for personalization of antidepressant choice in the future.
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Abstract
The cytochromes P450 comprise a family of enzymes that are responsible for around three-quarters of all drug metabolism reactions that occur in human populations. Many isoforms of cytochrome P450 exist but most reactions are undertaken by CYP2C9, CYP2C19, CYP2D6 and CYP3A4. This brief review focusses on the first three isozymes which exhibit polymorphism of phenotype.If there is a wide variation in drug metabolising capacity within the population, this may precipitate clinical consequences and influence the drug treatment of patients. Such problems range from a lack of efficacy to unanticipated toxicity. In order to minimise untoward events and "personalise" a patient's treatment, efforts have been made to discover an individual's drug metabolism status. This requires knowledge of the subject's phenotype at the time of clinical treatment. Since such testing is difficult, time-consuming and costly, the simpler approach of genotyping has been advocated.However, the correlation between genotype and phenotype is not good, with values of up to 50% misprediction being reported. Genotype-assisted forecasts cannot therefore be used with confidence to replace actual phenotype measurements. Obfuscating factors discussed include gene splicing, single nucleotide polymorphisms, epigenetics and microRNA, transcription regulation and multiple gene copies.
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Mirzaev KB, Fedorinov DS, Ivashchenko DV, Sychev DA. Multi-Ethnic Analysis of Cardiac Pharmacogenetic Markers of Cytochrome P450 and Membrane Transporters Genes in the Russian Population. RATIONAL PHARMACOTHERAPY IN CARDIOLOGY 2019. [DOI: 10.20996/1819-6446-2019-15-3-393-406] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim. To summarize Russian studies using pharmacogenetic testing as applied to cardiology.Material and methods. The authors conducted an online search for articles in December 2018 using the following databases: PubMed, Google Scholar, eLIBRARY. The search was carried out by keywords: "Russia", "Russian", "cardiology" together with the terms associated with the polymorphic marker, including: «P450», «CYP2C19», «CYP2D6», «CYP2B1», «CYP2B6», «CYP2Е1», «CYP2C8», «CYP2C9», «CYP3A4», «CYP3A5», «CYP1A1», «CYP1A2», «CYP4F2», «CYP4F1», «ABCB1», «SLCO1B1», «VKORC1», «GGCX», «SULT1A1», «CULT1», «CES1», «gene», «genes», «pharmacogenetics», «pharmacogenomics», «ethnic group».Results. Generalization of information allowed to identify obscure genes that need to be investigated in pharmacogenetic studies. This information can be used for the development of dosing algorithms and the priority choice of drugs, considering the results of pharmacogenetic testing and planning future research.Conclusion. The results of the literature review indicate the importance of studying the most clinically valid and clinically useful pharmacogenetic markers (CYP2C19, CYP2C9, VKORC1, SLCO1B1) among various ethnic groups in the Russian Federation. With the accumulation of evidence of clinical validity and clinical utility of other pharmacogenetic markers (CES1, CYP2D6*4, etc.), the problem of interethnic differences in the carriage of clinically significant polymorphisms of these genes identified in previous studies in the Russian Federation increasingly requires attention. The most promising for the introduction into the clinical practice in the Russian Federation in the near future are polymorphic markers of the CYP2C19, CYP2C9, VKORC1 and SLCO1B1 genes.
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Affiliation(s)
- K. B. Mirzaev
- Russian Medical Academy of Continuing Professional Education
| | - D. S. Fedorinov
- I.M. Sechenov First Moscow State Medical University (Sechenov University)
| | | | - D. A. Sychev
- Russian Medical Academy of Continuing Professional Education
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Mirzaev KB, Fedorinov DS, Ivashchenko DV, Sychev DA. ADME pharmacogenetics: future outlook for Russia. Pharmacogenomics 2019; 20:847-865. [DOI: 10.2217/pgs-2019-0013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
This systematic review reflects the results of pharmacogenetic studies in the Russian Federation aimed at studying the genes involved in the drug biotransformation system. The works of Russian researchers found by us are mostly devoted to microsomal liver oxidation enzymes (metabolism) and membrane transporter systems (absorption and excretion). This review presents population-ethnic and associative clinical studies on the genes of the CYP450 system, noncytochrome oxidation enzymes ( SULT1A1, CES1), membrane transporter system genes ( ABCB1, SLCO1B1) and warfarin biotransformation enzymes ( VKORC1, GGCX). The information is structured in the form of 11 tables, divided by regions of the Russian Federation.
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Affiliation(s)
- Karin B Mirzaev
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare, Moscow, Russian Federation
| | - Denis S Fedorinov
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare, Moscow, Russian Federation
| | - Dmitry V Ivashchenko
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare, Moscow, Russian Federation
| | - Dmitry A Sychev
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare, Moscow, Russian Federation
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Fragou D, Pakkidi E, Aschner M, Samanidou V, Kovatsi L. Smoking and DNA methylation: Correlation of methylation with smoking behavior and association with diseases and fetus development following prenatal exposure. Food Chem Toxicol 2019; 129:312-327. [PMID: 31063835 DOI: 10.1016/j.fct.2019.04.059] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/13/2022]
Abstract
Among epigenetic mechanisms, DNA methylation has been widely studied with respect to many environmental factors. Smoking is a common factor which affects both global and gene-specific DNA methylation. It is supported that smoking directly affects DNA methylation, and these effects contribute to the development and progression of various diseases, such as cancer, lung and cardiovascular diseases and male infertility. In addition, prenatal smoking influences the normal development of the fetus via DNA methylation changes. The DNA methylation profile and its smoking-induced alterations helps to distinguish current from former smokers and non-smokers and can be used to predict the risk for the development of a disease. This review summarizes the DNA methylation changes induced by smoking, their correlation with smoking behavior and their association with various diseases and fetus development.
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Affiliation(s)
- Domniki Fragou
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Greece
| | - Eleni Pakkidi
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Greece
| | - Michael Aschner
- Departments of Molecular Pharmacology, Neuroscience, and Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Victoria Samanidou
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Greece
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Greece.
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Abstract
OBJECTIVE Smoking dependence is the main cause for tobacco-related illnesses. The addiction-causing substance in tobacco, nicotine, acts through the dopamine pathway in the brain, causing several pleasurable experiences through cigarette smoking. Thus, both genetic and epigenetic factors related to dopamine metabolism may play an important role in influencing an individual's smoking behavior. MATERIALS AND METHODS We studied the 1460 C/T variation and the variable number tandem repeat polymorphism in the MAOA gene and A/G variation in intron 13 in the MAOB gene together with four DNA methylation sites in both of these genes in relation to several smoking-related phenotypes in a study population of 1230 Whites of Russian origin. RESULTS The genotypes studied were found to be associated with smoking status in women; the MAOB G variant allele was more prevalent in female smokers than nonsmokers [odds ratio (OR): 2.16, 95% confidence interval (CI): 1.08-4.33], whereas a reverse relation was observed for the MAOA 1460 T-variant allele (OR: 0.44, 95% CI: 0.21-0.91) and variable number tandem repeat low-activity alleles (OR: 0.49, 95% CI: 0.24-0.98). Moreover, the mean methylation values of the CpG sites studied in the MAOA gene were related to smoking behavior in women. Similarly, several methylation patterns in the MAOB gene were associated with a smoking history, with each CpG site showing a remarkable sex dependence. CONCLUSION Smoking behavior seems to be related to the genetic and epigenetic profile of MAO genes, with considerable individual and sex-related differences.
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DNA methylation and clinical response to antidepressant medication in major depressive disorder: A review and recommendations. Neurosci Lett 2018; 669:14-23. [DOI: 10.1016/j.neulet.2016.12.071] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 12/29/2016] [Accepted: 12/30/2016] [Indexed: 12/28/2022]
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Pitfalls and Opportunities for Epigenomic Analyses Focused on Disease Diagnosis, Prognosis, and Therapy. Trends Pharmacol Sci 2017. [PMID: 28625497 DOI: 10.1016/j.tips.2017.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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