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Arfmann W, Achenbach J, Meyer-Bockenkamp F, Proskynitopoulos PJ, Groh A, Muschler MAN, Glahn A, Hagemeier L, Preuss V, Klintschar M, Frieling H, Rhein M. Comparing DRD2 Promoter Methylation Between Blood and Brain in Alcohol Dependence. Alcohol Alcohol 2023; 58:216-223. [PMID: 36747480 DOI: 10.1093/alcalc/agad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 02/08/2023] Open
Abstract
AIMS The dopamine receptor D2 (DRD2) is substantially involved in several forms of addiction. In addition to genetic polymorphisms, epigenetic mechanisms have emerged as an important means of regulation. Previously, DRD2 hypo- and hyper-methylation have been observed in alcohol use disorder (AUD). Blood samples are commonly used as a surrogate marker of epigenetic alterations in epigenetic research, but few specific comparisons between blood and brain tissue samples in AUD exist. METHODS We used post-mortem brain tissue samples of 17 deceased patients with AUD and 31 deceased controls to investigate the relationship between blood and brain methylation of the DRD2 promoter. RESULTS When investigating individual cytosine methylation sites (CpG), several significant differences were found in the nucleus accumbens and hippocampus in the study population. Investigating binding sites with significant differences in methylation levels revealed hypomethylated CpGs targeting mainly activating transcription factors. CONCLUSION These findings support an altered transcription of the DRD2 gene in AUD specimens with a consecutively changed reward response in the brain. While methylation between specific brain regions and blood is comparable, our study further suggests that blood methylation cannot provide meaningful perspectives on DRD2 promoter methylation in the brain.
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Affiliation(s)
- Wiebke Arfmann
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Johannes Achenbach
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Department of Anesthesiology and Intensive Care Medicine, Pain Clinic, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Fiona Meyer-Bockenkamp
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Phileas J Proskynitopoulos
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Adrian Groh
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Marc A N Muschler
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Alexander Glahn
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Lars Hagemeier
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Vanessa Preuss
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Michael Klintschar
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Helge Frieling
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Mathias Rhein
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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Maretina MA, Valetdinova KR, Tsyganova NA, Egorova AA, Ovechkina VS, Schiöth HB, Zakian SM, Baranov VS, Kiselev AV. Identification of specific gene methylation patterns during motor neuron differentiation from spinal muscular atrophy patient-derived iPSC. Gene 2022; 811:146109. [PMID: 34871761 DOI: 10.1016/j.gene.2021.146109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 05/08/2021] [Accepted: 11/16/2021] [Indexed: 11/04/2022]
Abstract
Spinal muscular atrophy is a progressive motor neuron disorder caused by deletions or point mutations in the SMN1 gene. It is not known why motor neurons are particularly sensitive to a decrease in SMN protein levels and what factors besides SMN2 underlie the high clinical heterogeneity of the disease. Here we studied the methylation patterns of genes on sequential stages of motor neuron differentiation from induced pluripotent stem cells derived from the patients with SMA type I and II. The genes involved in the regulation of pluripotency, neural differentiation as well as those associated with spinal muscular atrophy development were included. The results show that the PAX6, HB9, CHAT, ARHGAP22, and SMN2 genes are differently methylated in cells derived from SMA patients compared to the cells of healthy individuals. This study clarifies the specificities of the disease pathogenesis and extends the knowledge of pathways involved in the SMA progression.
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Affiliation(s)
- M A Maretina
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia
| | - K R Valetdinova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novsibirsk, Russia
| | - N A Tsyganova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia
| | - A A Egorova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia
| | - V S Ovechkina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novsibirsk, Russia; Novosibirsk State University, 630090 Novosibirsk, Russia
| | - H B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, S-75124 Uppsala, Sweden; Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - S M Zakian
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novsibirsk, Russia; Meshalkin National Medical Research Center, Ministry of Healthcare of the Russian Federation, 630055 Novosibirsk, Russia
| | - V S Baranov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia
| | - A V Kiselev
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia.
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Taka N, Baba Y, Iwasaki Y, Yoshida W. Bioluminescence Resonance Energy Transfer for Global DNA Methylation Quantification. Methods Mol Biol 2022; 2525:267-279. [PMID: 35836075 DOI: 10.1007/978-1-0716-2473-9_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Global hypomethylation of genomic DNA is associated with genomic instability and carcinogenic processes. The loss of DNA methylation has been reported in several cancers; therefore, global methylation levels have been considered as biomarkers for cancer diagnosis. Bisulfite conversion analysis has been widely used as the gold standard method for quantification of DNA methylation levels. However, this method requires cumbersome and time-consuming steps. To quantify global DNA methylation levels in homogeneous solutions, we exemplify a sensing system based on bioluminescence resonance energy transfer (BRET) using methyl-CpG binding domain (MBD)-fused firefly luciferase (MBD-FLuc) and unmethyl-CpG binding domain (CXXC)-fused firefly luciferase (CXXC-FLuc). MBD-FLuc and CXXC-FLuc bind to methylated and unmethylated CpGs, respectively, in the genomic DNA to excite BOBO-3, an intercalating dye on genomic DNA. These BOBO-3 emission intensities depend on the methylated and unmethylated CpG content. The global DNA methylation levels can be quantified from the BOBO-3 emission intensities. Moreover, we introduce a multicolor BRET assay using MBD-FLuc and CXXC-fused Oplophorus luciferase (CXXC-OLuc) for the simultaneous quantification of methylated and unmethylated CpG content in genomic DNA. CXXC-OLuc excites the BOBO-1 DNA-intercalating dye depending on the unmethylated CpG content. Thus, the emission intensities of BOBO-1 and BOBO-3 excited by CXXC-OLuc and MBD-FLuc, respectively, can be simultaneously measured, thereby enabling the determination of global DNA methylation level in a single step. Here, we describe the detailed protocols for the expression of MBD-FLuc, CXXC-FLuc, and CXXC-OLuc in Escherichia coli and determine the global DNA methylation levels using these BRET assays.
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Affiliation(s)
- Natsumi Taka
- Graduate School of Bionics, Tokyo University of Technology, Tokyo, Japan
| | - Yuji Baba
- Graduate School of Bionics, Tokyo University of Technology, Tokyo, Japan
| | - Yuka Iwasaki
- Graduate School of Bionics, Tokyo University of Technology, Tokyo, Japan
| | - Wataru Yoshida
- Graduate School of Bionics, Tokyo University of Technology, Tokyo, Japan.
- School of Bioscience and Biotechnology, Tokyo University of Technology, Tokyo, Japan.
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4
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Shirvani-Farsani Z, Maloum Z, Bagheri-Hosseinabadi Z, Vilor-Tejedor N, Sadeghi I. DNA methylation signature as a biomarker of major neuropsychiatric disorders. J Psychiatr Res 2021; 141:34-49. [PMID: 34171761 DOI: 10.1016/j.jpsychires.2021.06.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/27/2021] [Accepted: 06/09/2021] [Indexed: 02/07/2023]
Abstract
DNA methylation is a broadly-investigated epigenetic modification that has been considered as a heritable and reversible change. Previous findings have indicated that DNA methylation regulates gene expression in the central nervous system (CNS). Also, disturbance of DNA methylation patterns has been associated with destructive consequences that lead to human brain diseases such as neuropsychiatric disorders (NPDs). In this review, we comprehensively discuss the mechanism and function of DNA methylation and its most recent associations with the pathology of NPDs-including major depressive disorder (MDD), schizophrenia (SZ), autism spectrum disorder (ASD), bipolar disorder (BD), and attention/deficit hyperactivity disorder (ADHD). We also discuss how heterogeneous findings demand further investigations. Finally, based on the recent studies we conclude that DNA methylation status may have implications in clinical diagnostics and therapeutics as a potential epigenetic biomarker of NPDs.
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Affiliation(s)
- Zeinab Shirvani-Farsani
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C., Tehran, IR, Iran.
| | - Zahra Maloum
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University G.C., Tehran, IR, Iran.
| | - Zahra Bagheri-Hosseinabadi
- Department of Clinical Biochemistry, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran.
| | - Natalia Vilor-Tejedor
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Carrer Wellington 30, 08005, Barcelona, Spain; Center for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain; Erasmus University Medical Center, Department of Clinical Genetics, Rotterdam, the Netherlands; Pompeu Fabra University, Barcelona, Spain.
| | - Iman Sadeghi
- BarcelonaBeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Carrer Wellington 30, 08005, Barcelona, Spain; Center for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.
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5
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Omics Application in Animal Science-A Special Emphasis on Stress Response and Damaging Behaviour in Pigs. Genes (Basel) 2020; 11:genes11080920. [PMID: 32796712 PMCID: PMC7464449 DOI: 10.3390/genes11080920] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/13/2022] Open
Abstract
Increasing stress resilience of livestock is important for ethical and profitable meat and dairy production. Susceptibility to stress can entail damaging behaviours, a common problem in pig production. Breeding animals with increased stress resilience is difficult for various reasons. First, studies on neuroendocrine and behavioural stress responses in farm animals are scarce, as it is difficult to record adequate phenotypes under field conditions. Second, damaging behaviours and stress susceptibility are complex traits, and their biology is not yet well understood. Dissecting complex traits into biologically better defined, heritable and easily measurable proxy traits and developing biomarkers will facilitate recording these traits in large numbers. High-throughput molecular technologies (“omics”) study the entirety of molecules and their interactions in a single analysis step. They can help to decipher the contributions of different physiological systems and identify candidate molecules that are representative of different physiological pathways. Here, we provide a general overview of different omics approaches and we give examples of how these techniques could be applied to discover biomarkers. We discuss the genetic dissection of the stress response by different omics techniques and we provide examples and outline potential applications of omics tools to understand and prevent outbreaks of damaging behaviours.
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Liu YR, Ba F, Cheng LJ, Li X, Zhang SW, Zhang SC. Efficacy of Sox10 Promoter Methylation in the Diagnosis of Intestinal Neuronal Dysplasia From the Peripheral Blood. Clin Transl Gastroenterol 2019; 10:e00093. [PMID: 31789936 PMCID: PMC6970557 DOI: 10.14309/ctg.0000000000000093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 09/19/2019] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Intestinal neuronal dysplasia (IND) is a common malformation of the enteric nervous system. Diagnosis requires a full-thickness colonic specimen and an experienced pathologist, emphasizing the need for noninvasive analytical methods. Recently, the methylation level of the Sox10 promoter has been found to be critical for enteric nervous system development. However, whether it can be used for diagnostic purposes in IND is unclear. METHODS Blood and colon specimens were collected from 32 patients with IND, 60 patients with Hirschsprung disease (HD), and 60 controls. Sox10 promoter methylation in the blood and the Sox10 expression level in the colon were determined, and their correlation was analyzed. The diagnostic efficacy of blood Sox10 promoter methylation was analyzed by receiver operating characteristic curve. RESULTS The blood level of Sox10 promoter methylation at the 32nd locus was 100% (90%-100%; 95% confidence interval [CI], 92.29%-96.37%) in control, 90% (80%-90%; 95% CI, 82.84%-87.83%) in HD, and 60% (50%-80%; 95% CI, 57.12%-69.76%) in IND specimens. Sox10 promoter methylation in the peripheral blood was negatively correlated with Sox10 expression in the colon, which was low in control, moderate in HD, and high in IND specimens (r = -0.89). The area under the curve of Sox10 promoter methylation in the diagnosis of IND was 0.94 (95% CI, 0.874-1.000, P = 0.000), with a cutoff value of 85% (sensitivity, 90.6%; specificity, 95.0%). By applying a cutoff value of 65%, promoter methylation was more indicative of IND than HD. DISCUSSION The analysis of Sox10 promoter methylation in the peripheral blood can be used as a noninvasive method for IND diagnosis.
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Affiliation(s)
- Yu-Rong Liu
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Fang Ba
- Department of Rehabilitation, Shengjing Hospital of China Medical University, Shenyang, China
| | - Lan-Jie Cheng
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xu Li
- Department of Pediatric Surgery, Capital Institute of Pediatrics of Capital Medical University, Beijing, China
| | - Shi-Wei Zhang
- Department of Pediatric Surgery, Harbin Children's Hospital, Harbin, China
| | - Shu-Cheng Zhang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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7
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He R, Hu Y, Yao L, Tian Y, Zhou Y, Yi F, Zhou L, Xu H, Sun Q. Clinical features and genetic characteristics of two Chinese pedigrees with fatal family insomnia. Prion 2019; 13:116-123. [PMID: 31122137 PMCID: PMC6629183 DOI: 10.1080/19336896.2019.1617027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background: Fatal familial insomnia (FFI) is a rare autosomal-dominant inherited prion disease characterized clinically by severe sleep disorder, motor signs, dysautonomia and abnormal behaviour. FFI is caused by a missense mutation at codon 178 of the prion protein gene (PRNP). Our study is aimed to explore typical clinical and genetic features of two Chinese pedigrees with FFI and review the related literatures. Methods: Two FFI cases with family histories were recruited in our study. The main clinical features, genetic features and possible pathophysiologic mechanisms of these two FFI cases were analysed. Results: The foremost symptoms seemed to be sleep disturbances and psychosis. Progressive sympathetic symptoms, movement disturbances and memory loss were frequently observed as well. Electroencephalography (EEG) showed a minor slowing without periodic triphasic waves. Polysomnography (PSG) showed reduction in total sleep time and disturbance of sleep-related respiratory. Brain magnetic resonance imaging (MRI) did not reveal obvious abnormality. Genetic analysis disclosed the prion protein gene mutation at codon 178 (D178N), with methionine (Met) homozygosity at the polymorphic position 129 (Met129Met). Conclusions: The major clinical features of Chinese FFI are sleep dysfunction, psychiatric symptoms and sympathetic symptoms. Our patients have similar clinical characteristics as that of the typical FFI cases.
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Affiliation(s)
- Runcheng He
- a Department of Neurology , Xiangya Hospital, Central South University , Changsha , Hunan , China.,b National Clinical Research Center for Geriatric Disorders , Changsha , Hunan , China
| | - Yacen Hu
- b National Clinical Research Center for Geriatric Disorders , Changsha , Hunan , China.,c Department of Geriatrics , Xiangya Hospital, Central South University , Changsha , China
| | - Lingyan Yao
- b National Clinical Research Center for Geriatric Disorders , Changsha , Hunan , China.,c Department of Geriatrics , Xiangya Hospital, Central South University , Changsha , China
| | - Yun Tian
- b National Clinical Research Center for Geriatric Disorders , Changsha , Hunan , China.,c Department of Geriatrics , Xiangya Hospital, Central South University , Changsha , China
| | - Yafang Zhou
- b National Clinical Research Center for Geriatric Disorders , Changsha , Hunan , China.,c Department of Geriatrics , Xiangya Hospital, Central South University , Changsha , China
| | - Fang Yi
- b National Clinical Research Center for Geriatric Disorders , Changsha , Hunan , China.,c Department of Geriatrics , Xiangya Hospital, Central South University , Changsha , China
| | - Lin Zhou
- b National Clinical Research Center for Geriatric Disorders , Changsha , Hunan , China.,c Department of Geriatrics , Xiangya Hospital, Central South University , Changsha , China
| | - Hongwei Xu
- b National Clinical Research Center for Geriatric Disorders , Changsha , Hunan , China.,c Department of Geriatrics , Xiangya Hospital, Central South University , Changsha , China
| | - Qiying Sun
- b National Clinical Research Center for Geriatric Disorders , Changsha , Hunan , China.,c Department of Geriatrics , Xiangya Hospital, Central South University , Changsha , China
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8
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Bidwell LC, Karoly HC, Thayer RE, Claus ED, Bryan AD, Weiland BJ, YorkWilliams S, Hutchison KE. DRD2 promoter methylation and measures of alcohol reward: functional activation of reward circuits and clinical severity. Addict Biol 2019; 24:539-548. [PMID: 29464814 DOI: 10.1111/adb.12614] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 01/02/2018] [Accepted: 01/24/2018] [Indexed: 12/13/2022]
Abstract
Studies have identified strong associations between D2 receptor binding potential and neural responses to rewarding stimuli and substance use. Thus, D2 receptor perturbations are central to theoretical models of the pathophysiology of substance dependence, and epigenetic changes may represent one of the fundamental molecular mechanisms impacting the effects of alcohol exposure on the brain. We hypothesized that epigenetic alterations in the promoter region of the dopamine D2 receptor (DRD2) gene would be associated with cue-elicited activation of neural reward regions, as well as severity of alcohol use behavior. The current study leveraged functional neuroimaging (fMRI) during an alcohol reward paradigm (n = 383) to test associations among DRD2 promoter methylation in peripheral tissue, signal change in the striatum during the presentation of alcohol cues, and severity of alcohol use disorder (AUD). Controlling for age, DRD2 promoter methylation was positively associated with responses to alcohol cues in the right accumbens (partial r = 0.144, P = 0.005), left putamen (partial r = 0.133, P = 0.009), right putamen (partial r = 0.106, P = 0.039), left caudate (partial r = 0.117, P = 0.022), and right caudate (partial r = 0.133, P = 0.009), suggesting that DRD2 methylation was positively associated with robust activation in the striatum in response to reward cues. DRD2 methylation was also positively associated with clinical metrics of AUD severity. Specifically, controlling for age, DRD2 methylation was associated with Alcohol Use Disorders Identification Test total (partial r = 0.140, P = 0.002); Impaired Control Scale total (partial r = 0.097, P = 0.044) and Alcohol Dependence Scale total (partial r = 0.152, P = 0.001). Thus, DRD2 methylation may be a critical mechanism linking D2 receptors with functional striatal brain changes and clinical severity among alcohol users.
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Affiliation(s)
| | - Hollis C. Karoly
- Department of Psychology & NeuroscienceUniversity of Colorado Boulder Boulder CO USA
| | - Rachel E. Thayer
- Department of Psychology & NeuroscienceUniversity of Colorado Boulder Boulder CO USA
| | | | - Angela D. Bryan
- Institute of Cognitive ScienceUniversity of Colorado Boulder Boulder CO USA
- Department of Psychology & NeuroscienceUniversity of Colorado Boulder Boulder CO USA
| | - Barbara J. Weiland
- Institute of Cognitive ScienceUniversity of Colorado Boulder Boulder CO USA
| | - Sophie YorkWilliams
- Department of Psychology & NeuroscienceUniversity of Colorado Boulder Boulder CO USA
| | - Kent E. Hutchison
- Institute of Cognitive ScienceUniversity of Colorado Boulder Boulder CO USA
- Department of Psychology & NeuroscienceUniversity of Colorado Boulder Boulder CO USA
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Zhang K, Li C, Liu J, Tang X, Li Z. DNA methylation alterations as therapeutic prospects in thyroid cancer. J Endocrinol Invest 2019; 42:363-370. [PMID: 29992502 DOI: 10.1007/s40618-018-0922-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/29/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND Thyroid cancer is one of the most common endocrine malignancies. Although the 10-year survival rate of differentiated thyroid cancer (DTC) is about 90% after conventional treatments, a small proportion of patients still suffer from tumor recurrence or drug resistance. OBJECTIVE This review article summarizes recent researches and clinical trials related to target drugs that reduce mortality in thyroid cancer. METHODS This is a review of the recent literature and clinical trials on the three main aspects including methylation genes in thyroid cancers, the relationship between BRAF mutation and gene methylation, target and dehypermethylation drugs in clinical trials. RESULTS We propose new approaches to treating malignant thyroid cancer, based on advances in understanding the relationship between genetic and epigenetic changes in thyroid cancer. Although the effect of traditional treatment for thyroid cancer is relatively good, a small proportion of patients still suffer from tumor recurrence or drug resistance. Molecular targeted drugs and dehypermethylation drugs have more promising outcomes in aggressive thyroid cancer compared with conventional treatments. CONCLUSION Based on what was discussed in this review, we suggest that integration of epigenetic and targeted therapies into conventional treatments will reduce the occurrence of refractory radioiodine differentiated thyroid cancer and improve the outcomes in aggressive thyroid cancer patients.
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Affiliation(s)
- K Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Central South University and Hunan Key Laboratory of Pharmacogenetics, Xiangya Road #110, Changsha, 410078, Hunan, People's Republic of China
| | - C Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Central South University and Hunan Key Laboratory of Pharmacogenetics, Xiangya Road #110, Changsha, 410078, Hunan, People's Republic of China
- Department of Pharmacy, ZhuZhou Central Hospital, ZhuZhou, 410078, People's Republic of China
| | - J Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Central South University and Hunan Key Laboratory of Pharmacogenetics, Xiangya Road #110, Changsha, 410078, Hunan, People's Republic of China
| | - X Tang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
- Institute of Clinical Pharmacology, Central South University and Hunan Key Laboratory of Pharmacogenetics, Xiangya Road #110, Changsha, 410078, Hunan, People's Republic of China
- Department of Center for ADR monitoring of Hubei, Wuhan, 430071, People's Republic of China
| | - Z Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.
- Institute of Clinical Pharmacology, Central South University and Hunan Key Laboratory of Pharmacogenetics, Xiangya Road #110, Changsha, 410078, Hunan, People's Republic of China.
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10
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Maretina M, Egorova A, Baranov V, Kiselev A. DYNC1H1 gene methylation correlates with severity of spinal muscular atrophy. Ann Hum Genet 2018; 83:73-81. [PMID: 30246859 DOI: 10.1111/ahg.12288] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 12/20/2022]
Abstract
Methylation profiles of CpG islands within the SLC23A2, CDK2AP1, and DYNC1H1 genes and their association with spinal muscular atrophy (SMA) severity were studied. High clinical heterogeneity of SMA suggests the existence of different factors modifying SMA phenotype with gene methylation as a plausible one. The genes picked up in our earlier genome-wide methylation studies of SMA patients demonstrated obvious differences in their methylation patterns, thus suggesting the likely involvement of their protein products in SMA development. Significantly decreased methylation of CpG islands within exon 37 of the DYNC1H1 gene was observed in patients with a severe SMA manifestation (type I) compared to mildly affected SMA patients (types III-IV). This finding provides new information on peculiarities of methylation in clinically different types of SMA patients and gives a clue for identification of new SMA modifiers.
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Affiliation(s)
- Marianna Maretina
- Laboratory of Prenatal Diagnostics of Inherited Diseases, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint-Petersburg, Russia.,Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Anna Egorova
- Laboratory of Prenatal Diagnostics of Inherited Diseases, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint-Petersburg, Russia
| | - Vladislav Baranov
- Laboratory of Prenatal Diagnostics of Inherited Diseases, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint-Petersburg, Russia.,Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint-Petersburg, Russia
| | - Anton Kiselev
- Laboratory of Prenatal Diagnostics of Inherited Diseases, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Saint-Petersburg, Russia
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11
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Maretina MA, Zheleznyakova GY, Lanko KM, Egorova AA, Baranov VS, Kiselev AV. Molecular Factors Involved in Spinal Muscular Atrophy Pathways as Possible Disease-modifying Candidates. Curr Genomics 2018; 19:339-355. [PMID: 30065610 PMCID: PMC6030859 DOI: 10.2174/1389202919666180101154916] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 12/15/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023] Open
Abstract
Spinal Muscular Atrophy (SMA) is a neuromuscular disorder caused by mutations in the SMN1 gene. Being a monogenic disease, it is characterized by high clinical heterogeneity. Variations in penetrance and severity of symptoms, as well as clinical discrepancies between affected family members can result from modifier genes influence on disease manifestation. SMN2 gene copy number is known to be the main phenotype modifier and there is growing evidence of additional factors contributing to SMA severity. Potential modifiers of spinal muscular atrophy can be found among the wide variety of different factors, such as multiple proteins interacting with SMN or promoting motor neuron survival, epigenetic modifications, transcriptional or splicing factors influencing SMN2 expression. Study of these factors enables to reveal mechanisms underlying SMA pathology and can have pronounced clinical application.
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Affiliation(s)
- Marianna A. Maretina
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya line, 3, Saint Petersburg199034, Russia
- Saint Petersburg State University, Universitetskaya emb. 7/9, 199034Saint Petersburg, Russia
| | - Galina Y. Zheleznyakova
- Department of Clinical Neuroscience, Karolinska Institutet, Karolinska Universitetssjukhuset, 171 76 Stockholm, Sweden
| | - Kristina M. Lanko
- Saint Petersburg State Institute of Technology, Moskovsky prospect, 26, Saint Petersburg190013, Russia
| | - Anna A. Egorova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya line, 3, Saint Petersburg199034, Russia
| | - Vladislav S. Baranov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya line, 3, Saint Petersburg199034, Russia
- Saint Petersburg State University, Universitetskaya emb. 7/9, 199034Saint Petersburg, Russia
| | - Anton V. Kiselev
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya line, 3, Saint Petersburg199034, Russia
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12
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Xie B, Xu Y, Liu Z, Liu W, Jiang L, Zhang R, Cui D, Zhang Q, Xu S. Elevation of Peripheral BDNF Promoter Methylation Predicts Conversion from Amnestic Mild Cognitive Impairment to Alzheimer's Disease: A 5-Year Longitudinal Study. J Alzheimers Dis 2018; 56:391-401. [PMID: 27935556 DOI: 10.3233/jad-160954] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Epigenetic aberrations have been identified as biomarkers to predict the risk of Alzheimer's disease (AD). This study aimed to evaluate whether altered DNA methylation status of BDNF promoter could be used as potential epigenetic biomarkers for predicting the progression from amnestic mild cognitive impairment (aMCI) to AD. A total of 506 aMCI patients and 728 cognitively normal controls were recruited in the cross-sectional analyses. Patients (n = 458) from aMCI cohort were classified into two groups after 5-year follow-up: aMCI-stable group (n = 330) and AD-conversion group (n = 128). DNA methylation of BDNF promoter was detected by bisulfite-PCR amplification and pyrosequencing. The DNA methylation levels of CpG1 and CpG2 in promoter I and CpG5 and CpG6 in promoter IV of BDNF gene were significantly higher in the aMCI group than in the control group at baseline and also were increased in the conversion group compared with the non-conversion group at 5-year follow up time point. CpG5 in BDNF promoter IV had the highest AUC of 0.910 (95% CI: 0.817-0.983, p < 0.05). Kaplan-Meier analysis showed a significant AD conversion propensity for aMCI patients with high methylation levels of CpG5 (HR = 1.96, 95% CI: 1.07-2.98, p < 0.001). Multivariate Cox regression analysis revealed elevated methylation status of CpG5 was a significant independent predictor for AD conversion (HR = 3.51, p = 0.013). These results suggest that elevation of peripheral BDNF promoter methylation might be used as potential epigenetic biomarkers for predicting the conversion from aMCI to AD.
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Affiliation(s)
- Bing Xie
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, P.R. China
| | - Yao Xu
- Division of Nephrology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, P.R. China
| | - Zanchao Liu
- Department of Endocrinology, The Second Hospital of Shijiazhuang City, Shijiazhuang, P.R. China
| | - Wenxuan Liu
- Department of Epidemiology and Statistics, School of Public Health, Hebei Medical University, Shijiazhuang, P.R. China
| | - Lei Jiang
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, P.R. China
| | - Rui Zhang
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, P.R. China
| | - Dongsheng Cui
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, P.R. China
| | - Qingfu Zhang
- Burn Engineering Center of Hebei Province, Shijiazhuang, P.R. China
| | - Shunjiang Xu
- Central Laboratory, The First Hospital of Hebei Medical University, Shijiazhuang, P.R. China
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Andersen GB, Tost J. A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation. Methods Mol Biol 2018; 1708:3-30. [PMID: 29224136 DOI: 10.1007/978-1-4939-7481-8_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life. Changes of DNA methylation levels and patterns have been widely studied in several diseases, especially cancer, where interest has focused on biomarkers for early detection of cancer development, accurate diagnosis, and response to treatment, but have also been shown to occur in many other complex diseases. Recent advances in epigenome engineering technologies allow now for the large-scale assessment of the functional relevance of DNA methylation. As a stable nucleic acid-based modification that is technically easy to handle and which can be analyzed with great reproducibility and accuracy by different laboratories, DNA methylation is a promising biomarker for many applications.
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Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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14
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Gutierrez Najera NA, Resendis-Antonio O, Nicolini H. "Gestaltomics": Systems Biology Schemes for the Study of Neuropsychiatric Diseases. Front Physiol 2017; 8:286. [PMID: 28536537 PMCID: PMC5422874 DOI: 10.3389/fphys.2017.00286] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 04/19/2017] [Indexed: 01/28/2023] Open
Abstract
The integration of different sources of biological information about what defines a behavioral phenotype is difficult to unify in an entity that reflects the arithmetic sum of its individual parts. In this sense, the challenge of Systems Biology for understanding the “psychiatric phenotype” is to provide an improved vision of the shape of the phenotype as it is visualized by “Gestalt” psychology, whose fundamental axiom is that the observed phenotype (behavior or mental disorder) will be the result of the integrative composition of every part. Therefore, we propose the term “Gestaltomics” as a term from Systems Biology to integrate data coming from different sources of information (such as the genome, transcriptome, proteome, epigenome, metabolome, phenome, and microbiome). In addition to this biological complexity, the mind is integrated through multiple brain functions that receive and process complex information through channels and perception networks (i.e., sight, ear, smell, memory, and attention) that in turn are programmed by genes and influenced by environmental processes (epigenetic). Today, the approach of medical research in human diseases is to isolate one disease for study; however, the presence of an additional disease (co-morbidity) or more than one disease (multimorbidity) adds complexity to the study of these conditions. This review will present the challenge of integrating psychiatric disorders at different levels of information (Gestaltomics). The implications of increasing the level of complexity, for example, studying the co-morbidity with another disease such as cancer, will also be discussed.
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Affiliation(s)
| | - Osbaldo Resendis-Antonio
- Instituto Nacional de Medicina GenómicaMexico City, Mexico.,Human Systems Biology Laboratory, Coordinación de la Investigación Científica - Red de Apoyo a la Investigación, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, National Autonomous University of Mexico (UNAM)Mexico City, Mexico
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15
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Marsh AG, Cottrell MT, Goldman MF. Epigenetic DNA Methylation Profiling with MSRE: A Quantitative NGS Approach Using a Parkinson's Disease Test Case. Front Genet 2016; 7:191. [PMID: 27853465 PMCID: PMC5090125 DOI: 10.3389/fgene.2016.00191] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 10/14/2016] [Indexed: 11/22/2022] Open
Abstract
Epigenetics is a rapidly developing field focused on deciphering chemical fingerprints that accumulate on human genomes over time. As the nascent idea of precision medicine expands to encompass epigenetic signatures of diagnostic and prognostic relevance, there is a need for methodologies that provide high-throughput DNA methylation profiling measurements. Here we report a novel quantification methodology for computationally reconstructing site-specific CpG methylation status from next generation sequencing (NGS) data using methyl-sensitive restriction endonucleases (MSRE). An integrated pipeline efficiently incorporates raw NGS metrics into a statistical discrimination platform to identify functional linkages between shifts in epigenetic DNA methylation and disease phenotypes in samples being analyzed. In this pilot proof-of-concept study we quantify and compare DNA methylation in blood serum of individuals with Parkinson's Disease relative to matched healthy blood profiles. Even with a small study of only six samples, a high degree of statistical discrimination was achieved based on CpG methylation profiles between groups, with 1008 statistically different CpG sites (p < 0.0025, after false discovery rate correction). A methylation load calculation was used to assess higher order impacts of methylation shifts on genes and pathways and most notably identified FGF3, FGF8, HTT, KMTA5, MIR8073, and YWHAG as differentially methylated genes with high relevance to Parkinson's Disease and neurodegeneration (based on PubMed literature citations). Of these, KMTA5 is a histone methyl-transferase gene and HTT is Huntington Disease Protein or Huntingtin, for which there are well established neurodegenerative impacts. The future need for precision diagnostics now requires more tools for exploring epigenetic processes that may be linked to cellular dysfunction and subsequent disease progression.
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Affiliation(s)
- Adam G Marsh
- Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, University of DelawareNewark, DE, USA; Genome Profiling LLC, Helen F. Graham Cancer Center and Research Institute, Center for Translational Cancer ResearchNewark, DE USA; Marine Biosciences, School of Marine Science and Policy, University of DelawareLewes, DE, USA
| | - Matthew T Cottrell
- Genome Profiling LLC, Helen F. Graham Cancer Center and Research Institute, Center for Translational Cancer ResearchNewark, DE USA; Marine Biosciences, School of Marine Science and Policy, University of DelawareLewes, DE, USA
| | - Morton F Goldman
- Genome Profiling LLC, Helen F. Graham Cancer Center and Research Institute, Center for Translational Cancer Research Newark, DE USA
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16
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Giuliani C, Sazzini M, Bacalini MG, Pirazzini C, Marasco E, Fontanesi E, Franceschi C, Luiselli D, Garagnani P. Epigenetic Variability across Human Populations: A Focus on DNA Methylation Profiles of the KRTCAP3, MAD1L1 and BRSK2 Genes. Genome Biol Evol 2016; 8:2760-73. [PMID: 27503294 PMCID: PMC5630933 DOI: 10.1093/gbe/evw186] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Natural epigenetic diversity has been suggested as a key mechanism in microevolutionary processes due to its capability to create phenotypic variability within individuals and populations. It constitutes an important reservoir of variation potentially useful for rapid adaptation in response to environmental stimuli. The analysis of population epigenetic structure represents a possible tool to study human adaptation and to identify external factors that are able to naturally shape human DNA methylation variability. The aim of this study is to investigate the dynamics that create epigenetic diversity between and within different human groups. To this end, we first used publicly available epigenome-wide data to explore population-specific DNA methylation changes that occur at macro-geographic scales. Results from this analysis suggest that nutrients, UVA exposure and pathogens load might represent the main environmental factors able to shape DNA methylation profiles. Then, we evaluated DNA methylation of candidate genes (KRTCAP3, MAD1L1, and BRSK2), emerged from the previous analysis, in individuals belonging to different populations from Morocco, Nigeria, Philippines, China, and Italy, but living in the same Italian city. DNA methylation of the BRSK2 gene is significantly different between Moroccans and Nigerians (pairwise t-test: CpG 6 P-value = 5.2*10 (-) (3); CpG 9 P-value = 2.6*10 (-) (3); CpG 10 P-value = 3.1*10 (-) (3); CpG 11 P-value = 2.8*10 (-) (3)). Comprehensively, these results suggest that DNA methylation diversity is a source of variability in human groups at macro and microgeographical scales and that population demographic and adaptive histories, as well as the individual ancestry, actually influence DNA methylation profiles.
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Affiliation(s)
- Cristina Giuliani
- Department of Biological Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Italy
| | - Marco Sazzini
- Department of Biological Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Italy
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Italy
| | - Elisa Fontanesi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Italy IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Donata Luiselli
- Department of Biological Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy Interdepartmental Center "L. Galvani" (C.I.G.), University of Bologna, Italy Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy
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17
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Zheleznyakova GY, Nilsson EK, Kiselev AV, Maretina MA, Tishchenko LI, Fredriksson R, Baranov VS, Schiöth HB. Methylation levels of SLC23A2 and NCOR2 genes correlate with spinal muscular atrophy severity. PLoS One 2015; 10:e0121964. [PMID: 25821969 PMCID: PMC4378931 DOI: 10.1371/journal.pone.0121964] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/09/2015] [Indexed: 11/19/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a monogenic neurodegenerative disorder subdivided into four different types. Whole genome methylation analysis revealed 40 CpG sites associated with genes that are significantly differentially methylated between SMA patients and healthy individuals of the same age. To investigate the contribution of methylation changes to SMA severity, we compared the methylation level of found CpG sites, designed as "targets", as well as the nearest CpG sites in regulatory regions of ARHGAP22, CDK2AP1, CHML, NCOR2, SLC23A2 and RPL9 in three groups of SMA patients. Of notable interest, compared to type I SMA male patients, the methylation level of a target CpG site and one nearby CpG site belonging to the 5'UTR of SLC23A2 were significantly hypomethylated 19-22% in type III-IV patients. In contrast to type I SMA male patients, type III-IV patients demonstrated a 16% decrease in the methylation levels of a target CpG site, belonging to the 5'UTR of NCOR2. To conclude, this study validates the data of our previous study and confirms significant methylation changes in the SLC23A2 and NCOR2 regulatory regions correlates with SMA severity.
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Affiliation(s)
- Galina Yu. Zheleznyakova
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
- Faculty of Biology, Saint-Petersburg State University, Saint-Petersburg, Russia
- Laboratory for Prenatal Diagnostics of Inherited Diseases, D.O. Ott Research Institute of Obstetrics and Gynecology RAMS, Saint-Petersburg, Russia
- * E-mail:
| | - Emil K. Nilsson
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Anton V. Kiselev
- Laboratory for Prenatal Diagnostics of Inherited Diseases, D.O. Ott Research Institute of Obstetrics and Gynecology RAMS, Saint-Petersburg, Russia
| | - Marianna A. Maretina
- Faculty of Biology, Saint-Petersburg State University, Saint-Petersburg, Russia
- Laboratory for Prenatal Diagnostics of Inherited Diseases, D.O. Ott Research Institute of Obstetrics and Gynecology RAMS, Saint-Petersburg, Russia
| | | | | | - Vladislav S. Baranov
- Faculty of Biology, Saint-Petersburg State University, Saint-Petersburg, Russia
- Laboratory for Prenatal Diagnostics of Inherited Diseases, D.O. Ott Research Institute of Obstetrics and Gynecology RAMS, Saint-Petersburg, Russia
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18
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Chemobrain: a critical review and causal hypothesis of link between cytokines and epigenetic reprogramming associated with chemotherapy. Cytokine 2015; 72:86-96. [PMID: 25573802 DOI: 10.1016/j.cyto.2014.12.006] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 10/29/2014] [Accepted: 12/08/2014] [Indexed: 01/21/2023]
Abstract
One consequence of modern cancer therapy is chemotherapy related cognitive dysfunction or "chemobrain", the subjective experience of cognitive deficits at any point during or following chemotherapy. Chemobrain, a well-established clinical syndrome, has become an increasing concern because the number of long-term cancer survivors is growing dramatically. There is strong evidence that correlates changes in peripheral cytokines with the development of chemobrain in commonly used chemotherapeutic drugs for different types of cancer. However, the mechanisms by which these cytokines elicit change in the central nervous system are still unclear. In this review, we hypothesize that the administration of chemotherapy agents initiates a cascade of biological changes, with short-lived alterations in the cytokine milieu inducing persistent epigenetic alterations. These epigenetic changes lead to changes in gene expression, alterations in metabolic activity and neuronal transmission that are responsible for generating the subjective experience of cognition. This speculative but testable hypothesis should help to gain a comprehensive understanding of the mechanism underlying cognitive dysfunction in cancer patients. Such knowledge is critical to identify pharmaceutical targets with the potential to prevent and treat cancer-treatment related cognitive dysfunction and similar disorders.
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Carless MA. Investigation of genomic methylation status using methylation-specific and bisulfite sequencing polymerase chain reaction. Methods Mol Biol 2015; 1288:193-212. [PMID: 25827881 DOI: 10.1007/978-1-4939-2474-5_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Epigenetic modification plays a central role in the regulation of gene expression and therefore in the development of disease states. In particular, genomic methylation of cytosines within CpG dinucleotides is crucial to development, gene silencing, and chromosome inactivation. Importantly, aberrant methylation profiles of various genes are associated with cancer as well as autoimmune disease, psychiatric and neurodegenerative disorders, diabetes, and heart disease. Various methods are available for the detection and quantification of methylation in a given sample. Most of these methods rely upon bisulfite conversion of DNA, which converts unmethylated cytosines to uracil, while methylated cytosines remain as cytosines. Methylation-specific amplification of DNA can be used to detect methylation at one or more (typically up to about 4) CpG sites by using primers specific to either methylated or unmethylated DNA. Alternatively, amplification of both methylated and unmethylated DNA followed by sequencing can be used to detect methylation status at multiple CpG sites. The following chapter provides protocols for bisulfite conversion of DNA, methylation-specific PCR and bisulfite sequencing PCR.
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Affiliation(s)
- Melanie A Carless
- Texas Biomedical Research Institute, P.O. Box 760549, 7620 N. W. Loop 410 (at Military Drive), San Antonio, TX, 78245-0549, USA,
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20
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Pesticides, depression and suicide: A systematic review of the epidemiological evidence. Int J Hyg Environ Health 2013; 216:445-60. [DOI: 10.1016/j.ijheh.2012.12.003] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 12/13/2012] [Accepted: 12/18/2012] [Indexed: 11/22/2022]
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Doehring A, Oertel BG, Sittl R, Lötsch J. Chronic opioid use is associated with increased DNA methylation correlating with increased clinical pain. Pain 2013; 154:15-23. [PMID: 23273101 DOI: 10.1016/j.pain.2012.06.011] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 06/13/2012] [Accepted: 06/13/2012] [Indexed: 01/17/2023]
Abstract
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 μ-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 μ-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.
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Affiliation(s)
- Alexandra Doehring
- Institute of Clinical Pharmacology, Goethe-University, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany Fraunhofer Project Group Translational Medicine and Pharmacology (IME-TMP), Theodor Stern Kai 7, D-60590 Frankfurt am Main, Germany Department of Anesthesiology, Universitätsklinikum Erlangen, Krankenhausstraße 12, D-91054 Erlangen, Germany
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22
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Grafodatskaya D, Chung BHY, Butcher DT, Turinsky AL, Goodman SJ, Choufani S, Chen YA, Lou Y, Zhao C, Rajendram R, Abidi FE, Skinner C, Stavropoulos J, Bondy CA, Hamilton J, Wodak S, Scherer SW, Schwartz CE, Weksberg R. Multilocus loss of DNA methylation in individuals with mutations in the histone H3 lysine 4 demethylase KDM5C. BMC Med Genomics 2013; 6:1. [PMID: 23356856 PMCID: PMC3573947 DOI: 10.1186/1755-8794-6-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/14/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A number of neurodevelopmental syndromes are caused by mutations in genes encoding proteins that normally function in epigenetic regulation. Identification of epigenetic alterations occurring in these disorders could shed light on molecular pathways relevant to neurodevelopment. RESULTS Using a genome-wide approach, we identified genes with significant loss of DNA methylation in blood of males with intellectual disability and mutations in the X-linked KDM5C gene, encoding a histone H3 lysine 4 demethylase, in comparison to age/sex matched controls. Loss of DNA methylation in such individuals is consistent with known interactions between DNA methylation and H3 lysine 4 methylation. Further, loss of DNA methylation at the promoters of the three top candidate genes FBXL5, SCMH1, CACYBP was not observed in more than 900 population controls. We also found that DNA methylation at these three genes in blood correlated with dosage of KDM5C and its Y-linked homologue KDM5D. In addition, parallel sex-specific DNA methylation profiles in brain samples from control males and females were observed at FBXL5 and CACYBP. CONCLUSIONS We have, for the first time, identified epigenetic alterations in patient samples carrying a mutation in a gene involved in the regulation of histone modifications. These data support the concept that DNA methylation and H3 lysine 4 methylation are functionally interdependent. The data provide new insights into the molecular pathogenesis of intellectual disability. Further, our data suggest that some DNA methylation marks identified in blood can serve as biomarkers of epigenetic status in the brain.
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Affiliation(s)
- Daria Grafodatskaya
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Barian HY Chung
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada
- Centre of Reproduction, Growth & Development, Department of Pediatrics & Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Darci T Butcher
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Andrei L Turinsky
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah J Goodman
- Centre of Reproduction, Growth & Development, Department of Pediatrics & Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sana Choufani
- Centre of Reproduction, Growth & Development, Department of Pediatrics & Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yi-An Chen
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Youliang Lou
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Chunhua Zhao
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Rageen Rajendram
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Fatima E Abidi
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
| | - Cindy Skinner
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
| | - James Stavropoulos
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Carolyn A Bondy
- Developmental Endocrinology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jill Hamilton
- Division of Endocrinology, Department of Pediatrics, Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Shoshana Wodak
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, Canada
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada
| | - Charles E Schwartz
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
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