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Panduga S, Vasishta S, Subramani R, Vincent S, Mutalik S, Joshi MB. Epidrugs in the clinical management of atherosclerosis: Mechanisms, challenges and promises. Eur J Pharmacol 2024; 980:176827. [PMID: 39038635 DOI: 10.1016/j.ejphar.2024.176827] [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] [Received: 05/14/2024] [Revised: 07/03/2024] [Accepted: 07/18/2024] [Indexed: 07/24/2024]
Abstract
Atherosclerosis is a complex and multigenic pathology associated with significant epigenetic reprogramming. Traditional factors (age, sex, obesity, hyperglycaemia, dyslipidaemia, hypertension) and non-traditional factors (foetal indices, microbiome alteration, clonal hematopoiesis, air pollution, sleep disorders) induce endothelial dysfunction, resulting in reduced vascular tone and increased vascular permeability, inflammation and shear stress. These factors induce paracrine and autocrine interactions between several cell types, including vascular smooth muscle cells, endothelial cells, monocytes/macrophages, dendritic cells and T cells. Such cellular interactions lead to tissue-specific epigenetic reprogramming regulated by DNA methylation, histone modifications and microRNAs, which manifests in atherosclerosis. Our review outlines epigenetic signatures during atherosclerosis, which are viewed as potential clinical biomarkers that may be adopted as new therapeutic targets. Additionally, we emphasize epigenetic modifiers referred to as 'epidrugs' as potential therapeutic molecules to correct gene expression patterns and restore vascular homeostasis during atherosclerosis. Further, we suggest nanomedicine-based strategies involving the use of epidrugs, which may selectively target cells in the atherosclerotic microenvironment and reduce off-target effects.
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Affiliation(s)
- Sushma Panduga
- Department of Biochemistry, Palamur Biosciences Private Limited, Hyderabad, 500026, Telangana, India; PhD Program, Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Sampara Vasishta
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Ramamoorthy Subramani
- Department of Biochemistry, Palamur Biosciences Private Limited, Hyderabad, 500026, Telangana, India
| | - Sthevaan Vincent
- Department of Pathology, Palamur Biosciences Private Limited, Hyderabad, 500026, Telangana, India
| | - Srinivas Mutalik
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Manjunath B Joshi
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
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2
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Yang T, Wei Q, Pang D, Cheng Y, Huang J, Lin J, Xiao Y, Jiang Q, Wang S, Li C, Shang H. Clinical and genetic characteristics of ALS patients with variants in genes regulating DNA methylation. J Neurol 2024; 271:5556-5566. [PMID: 38907861 DOI: 10.1007/s00415-024-12508-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/04/2024] [Accepted: 06/09/2024] [Indexed: 06/24/2024]
Abstract
BACKGROUND Aberrant DNA methylation alterations are implicated in amyotrophic lateral sclerosis (ALS). Nevertheless, the influence of genetic variants in genes regulating DNA methylation on ALS patients is not well understood. Therefore, we aim to provide a comprehensive variant profile of genes related to DNA methylation (DNMT1, DNMT3A, DNMT3B, DNMT3L) and demethylation (TET1, TET2, TET3, TDG) and to investigate the association of these variants with ALS. METHODS Variants were screened in a cohort of 2240 ALS patients from Southwest China, using controls from the Genome Aggregation Database (n = 9976) and the China Metabolic Analytics Project (n = 10,588). The over-representation of rare variants and their association with ALS risk were evaluated using Fisher's exact test with Bonferroni correction at both allele and gene levels. Kaplan-Meier analysis and Cox regression analysis were employed to explore the relationship between variants and survival. RESULTS A total of 210 variants meeting the criteria were identified. Gene-based burden analysis identified a significant increase in ALS risk associated with rare variants in the TET2 gene (OR = 1.95, 95% CI = 1.29-2.88, P = 0.001). Survival analysis demonstrated that patients carrying variants in demethylation-related genes had a higher risk of death compared to those with methylation-related gene variants (HR = 1.29, 95% CI = 1.03-1.86, P = 0.039). CONCLUSIONS This study provides a genetic variant profile of genes involved in DNA methylation and demethylation regulation, along with the clinical characteristics of ALS patients carrying these variants. The findings offer genetic evidence implicating disrupted DNA methylation dynamics in ALS.
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Affiliation(s)
- Tianmi Yang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Qianqian Wei
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Dejiang Pang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Yangfan Cheng
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Jingxuan Huang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Junyu Lin
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Yi Xiao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Qirui Jiang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Shichan Wang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China
| | - Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China.
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Diseases Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Chengdu, 610041, Sichuan, China.
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Younesian S, Mohammadi MH, Younesian O, Momeny M, Ghaffari SH, Bashash D. DNA methylation in human diseases. Heliyon 2024; 10:e32366. [PMID: 38933971 PMCID: PMC11200359 DOI: 10.1016/j.heliyon.2024.e32366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Aberrant epigenetic modifications, particularly DNA methylation, play a critical role in the pathogenesis and progression of human diseases. The current review aims to reveal the role of aberrant DNA methylation in the pathogenesis and progression of diseases and to discuss the original data obtained from international research laboratories on this topic. In the review, we mainly summarize the studies exploring the role of aberrant DNA methylation as diagnostic and prognostic biomarkers in a broad range of human diseases, including monogenic epigenetics, autoimmunity, metabolic disorders, hematologic neoplasms, and solid tumors. The last section provides a general overview of the possibility of the DNA methylation machinery from the perspective of pharmaceutic approaches. In conclusion, the study of DNA methylation machinery is a phenomenal intersection that each of its ways can reveal the mysteries of various diseases, introduce new diagnostic and prognostic biomarkers, and propose a new patient-tailored therapeutic approach for diseases.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Ommolbanin Younesian
- School of Medicine, Tonekabon Branch, Islamic Azad University, Tonekabon, 46841-61167 Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, 1411713135 Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
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Stephens GS, Park J, Eagle A, You J, Silva-Pérez M, Fu CH, Choi S, Romain CPS, Sugimoto C, Buffington SA, Zheng Y, Costa-Mattioli M, Liu Y, Robison AJ, Chin J. Persistent ∆FosB expression limits recurrent seizure activity and provides neuroprotection in the dentate gyrus of APP mice. Prog Neurobiol 2024; 237:102612. [PMID: 38642602 DOI: 10.1016/j.pneurobio.2024.102612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 03/14/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
Recurrent seizures lead to accumulation of the activity-dependent transcription factor ∆FosB in hippocampal dentate granule cells in both mouse models of epilepsy and mouse models of Alzheimer's disease (AD), which is also associated with increased incidence of seizures. In patients with AD and related mouse models, the degree of ∆FosB accumulation corresponds with increasing severity of cognitive deficits. We previously found that ∆FosB impairs spatial memory in mice by epigenetically regulating expression of target genes such as calbindin that are involved in synaptic plasticity. However, the suppression of calbindin in conditions of neuronal hyperexcitability has been demonstrated to provide neuroprotection to dentate granule cells, indicating that ∆FosB may act over long timescales to coordinate neuroprotective pathways. To test this hypothesis, we used viral-mediated expression of ∆JunD to interfere with ∆FosB signaling over the course of several months in transgenic mice expressing mutant human amyloid precursor protein (APP), which exhibit spontaneous seizures and develop AD-related neuropathology and cognitive deficits. Our results demonstrate that persistent ∆FosB activity acts through discrete modes of hippocampal target gene regulation to modulate neuronal excitability, limit recurrent seizure activity, and provide neuroprotection to hippocampal dentate granule cells in APP mice.
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Affiliation(s)
| | - Jin Park
- Department of Neuroscience, Baylor College of Medicine, USA
| | - Andrew Eagle
- Department of Physiology, Michigan State University, USA
| | - Jason You
- Department of Neuroscience, Baylor College of Medicine, USA
| | | | - Chia-Hsuan Fu
- Department of Neuroscience, Baylor College of Medicine, USA
| | - Sumin Choi
- Department of Neuroscience, Baylor College of Medicine, USA
| | | | - Chiho Sugimoto
- Department of Physiology, Michigan State University, USA
| | - Shelly A Buffington
- Center for Precision Environmental Health, Department of Neuroscience, Baylor College of Medicine, USA
| | - Yi Zheng
- Department of Neuroscience, Baylor College of Medicine, USA
| | | | - Yin Liu
- Department of Neurobiology and Anatomy, McGovern Medical School at UT Health, USA
| | - A J Robison
- Department of Physiology, Michigan State University, USA
| | - Jeannie Chin
- Department of Neuroscience, Baylor College of Medicine, USA.
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Hayashida H, Arita Y, Koh K, Takiyama Y, Ikezoe K. [Hereditary sensory and autonomic neuropathy 1E showing hyperreflexia: a case report]. Rinsho Shinkeigaku 2024; 64:286-291. [PMID: 38508732 DOI: 10.5692/clinicalneurol.cn-001938] [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: 03/22/2024]
Abstract
A 52-year-old man had developed hearing loss since childhood, as well as recurrent foot ulcers and osteomyelitis since his forties. He presented with gait disturbance and dysarthria that had worsened over four years and a month, respectively. Neurological exams revealed cognitive impairment, proximal weakness of the lower extremities, generalized hyperrflexia, ataxia, sensory disturbances predominant in deep sensation, urinary retention, and gait instability. On nerve conduction study, no sensory nerve action potentials were evoked in the upper and lower limbs. Since his grandmother suffered from similar symptoms, we investigated genetic analysis, which revealed a missense mutation (c.1483T>C, p.Y495H) in DNA methyltransferase 1 gene. He was subsequently diagnosed with hereditary sensory and autonomic neuropathy 1E (HSAN1E). It is important to recognize that increased deep tendon reflex can be observed in HSAN1E.
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Affiliation(s)
| | | | - Kishin Koh
- Department of Neurology, Graduate School of Medical Sciences, University of Yamanashi
- Department of Neurology, Yumura Onsen Hospital
| | - Yoshihisa Takiyama
- Department of Neurology, Graduate School of Medical Sciences, University of Yamanashi
- Department of Neurology, Fuefuki Central Hospital
| | - Koji Ikezoe
- Department of Neurology, Matsuyama Red Cross Hospital
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Ping J, Wan J, Luo J, Du B, Liu X, Jiang T, Zhang J. The interaction of RELN-DNMT genes involving in neurotrophin signaling pathway contributes to schizophrenia susceptibility. Int J Dev Neurosci 2024; 84:154-159. [PMID: 38296839 DOI: 10.1002/jdn.10316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/26/2023] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Abstract
OBJECTIVE Schizophrenia belongs to a severe mental illness with complicated clinical presentations, an ill-defined pathogenesis, and no known cause. Many genetic studies imply that polygenic interaction is important in the development of schizophrenia. The main mechanism of the RELN-BDNF-CREB-DNMT signaling pathway in neurodevelopment involves RELN, brain-derived neurotrophic factor (BDNF), transcription factor cyclic adenosine monophosphate response element binding protein (CREB), DNA methyltransferase 1 (DNMT1), as well as DNA methyltransferase 3B (DNMT3B). An early case-control research on 15 polymorphisms in the RELN, CREB, BDNF, DNMT1, and DNMT3B genes was done. A single gene variation has little effect on the pathogenesis of schizophrenia, but the combination of intergenic variation loci has a bigger impact because schizophrenia is a complex polygenic disorder. The objective of the current study sought to explore the impact of genetic interactions between RELN, BDNF, CREB, DNMT1, and DNMT3B on schizophrenia in order to further highlight the genetic factors influencing the risk of schizophrenia. METHODS Taking the case-control study design, with the Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition (DSM-5) to be the evaluation norm, 134 individuals suffering from schizophrenia hospitalized in the Third People's Hospital of Zhongshan City within January 2018 to April 2020 (case group) were selected, and 64 healthy individuals (control group) from the same geographical area had been chosen as well. MassArray identified DNMT1 gene single nucleotide polymorphisms (rs2114724 and rs2228611) and DNMT3B gene SNPs (rs2424932, rs1569686, rs6119954, and rs2424908). Using the generalized multifactor dimensionality reduction (GMDR), the RELN-BDNF-CREB-DNMT pathway's gene interactions were examined for their impact on schizophrenia. RESULTS GMDR analysis showed that the three-order interaction model RELN (rs2073559, rs2229864)-DNMT3B (rs2424908) was the optimal model (p = 0.001), with the consistency of cross-validation of 10/10 and the test accuracy of 0.8711. CONCLUSION The interaction between the RELN (rs2073559, rs2229864)-DNMT3B (rs2424908) may be related to schizophrenia, and large sample sizes should be verified in different population.
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Affiliation(s)
- Junjiao Ping
- Department of Psychiatry, Third People's Hospital of Zhongshan City, Zhongshan, China
- Joint Laboratory of Psychiatric Genetic Research, The Third People's Hospital of Zhongshan, Zhongshan, China
| | - Jing Wan
- Department of Early Intervention, Third People's Hospital of Zhongshan City, Zhongshan, China
| | - Jiali Luo
- Joint Laboratory of Psychiatric Genetic Research, The Third People's Hospital of Zhongshan, Zhongshan, China
| | - Baoguo Du
- Department of Clinical Psychology, The Third People's Hospital of Zhongshan City, Zhongshan, China
| | - Xinxia Liu
- Department of Psychiatry, Third People's Hospital of Zhongshan City, Zhongshan, China
- Joint Laboratory of Psychiatric Genetic Research, The Third People's Hospital of Zhongshan, Zhongshan, China
| | - Tingyun Jiang
- Department of Psychiatry, Third People's Hospital of Zhongshan City, Zhongshan, China
| | - Jie Zhang
- Department of Psychiatry, Third People's Hospital of Zhongshan City, Zhongshan, China
- Joint Laboratory of Psychiatric Genetic Research, The Third People's Hospital of Zhongshan, Zhongshan, China
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7
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Choudhury S, Anne A, Singh M, Chaillet JR, Mohan KN. DNMT1 Y495C mutation interferes with maintenance methylation of imprinting control regions. Int J Biochem Cell Biol 2024; 169:106535. [PMID: 38281697 DOI: 10.1016/j.biocel.2024.106535] [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] [Received: 09/19/2023] [Revised: 01/05/2024] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
Hereditary Sensory and Autonomic Neuropathy Type 1E (HSAN1E) is a rare autosomal dominant neurological disorder due to missense mutations in DNA methyltransferase 1 (DNMT1). To investigate the nature of the dominant effect, we compared methylomes of transgenic R1wtDnmt1 and R1Dnmt1Y495C mouse embryonic stem cells (mESCs) overexpressing WT and the mutant mouse proteins respectively, with the R1 (wild-type) cells. In case of R1Dnmt1Y495C, 15 out of the 20 imprinting control regions were hypomethylated with transcript level dysregulation of multiple imprinted genes in ESCs and neurons. Non-imprinted regions, minor satellites, major satellites, LINE1 and IAP repeats were unaffected. These data mirror the specific imprinting defects associated with transient removal of DNMT1 in mESCs, deletion of the maternal-effect DNMT1o variant in preimplantation mouse embryos, and in part, reprogramming to naïve human iPSCs. This is the first DNMT1 mutation demonstrated to specifically affect Imprinting Control Regions (ICRs), and reinforces the differences in maintenance methylation of ICRs over non-imprinted regions. Consistent with nervous system abnormalities in the HSAN1E disorder and involvement of imprinted genes in normal development and neurogenesis, R1Dnmt1Y495C cells showed dysregulated pluripotency and neuron marker genes, and yielded more slender, shorter, and extensively branched neurons. We speculate that R1Dnmt1Y495C cells produce predominantly dimers containing mutant proteins, leading to a gradual and specific loss of ICR methylation during early human development.
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Affiliation(s)
- Sumana Choudhury
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India; Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad 500078, India
| | - Anuhya Anne
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India; Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad 500078, India
| | - Minali Singh
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India
| | - John Richard Chaillet
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kommu Naga Mohan
- Molecular Biology and Genetics Laboratory, Department of Biological Sciences, BITS Pilani Hyderabad Campus, Hyderabad 500078, India; Centre for Human Disease Research, BITS Pilani Hyderabad Campus, Hyderabad 500078, India.
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Hu Q, Botuyan MV, Mer G. Identification of a conserved α-helical domain at the N terminus of human DNA methyltransferase 1. J Biol Chem 2024; 300:105775. [PMID: 38382673 PMCID: PMC10950863 DOI: 10.1016/j.jbc.2024.105775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/03/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024] Open
Abstract
In vertebrates, DNA methyltransferase 1 (DNMT1) contributes to preserving DNA methylation patterns, ensuring the stability and heritability of epigenetic marks important for gene expression regulation and the maintenance of cellular identity. Previous structural studies have elucidated the catalytic mechanism of DNMT1 and its specific recognition of hemimethylated DNA. Here, using solution nuclear magnetic resonance spectroscopy and small-angle X-ray scattering, we demonstrate that the N-terminal region of human DNMT1, while flexible, encompasses a conserved globular domain with a novel α-helical bundle-like fold. This work expands our understanding of the structure and dynamics of DNMT1 and provides a structural framework for future functional studies in relation with this new domain.
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Affiliation(s)
- Qi Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Maria Victoria Botuyan
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA; Department of Cancer Biology, Mayo Clinic, Rochester, Minnesota, USA.
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de Miguel-Sanchez CJ, Gomez-Roldós A, Leal-Hidalgo R, Lafuente-Gómez G, Estrada-Huesa D, Bravo-Quelle N, González-Sánchez M. First case of autosomal dominant cerebellar ataxia with deafness and narcolepsy (ADCA-DN) with confirmed DMNT1 gene mutation in Spain. Review of the DMNT1 mutation syndromes. Neurol Sci 2024; 45:791-793. [PMID: 37828385 DOI: 10.1007/s10072-023-07094-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023]
Affiliation(s)
| | - Ana Gomez-Roldós
- Neurology Department, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Rafael Leal-Hidalgo
- Neurology Department, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Gemma Lafuente-Gómez
- Neurology Department, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Dalila Estrada-Huesa
- Neurophysiology Department, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Natalia Bravo-Quelle
- Neurophysiology Department, Gregorio Marañón General University Hospital, Madrid, Spain
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10
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Zhao J, Han Z, Ding L, Wang P, He X, Lin L. The molecular mechanism of aging and the role in neurodegenerative diseases. Heliyon 2024; 10:e24751. [PMID: 38312598 PMCID: PMC10835255 DOI: 10.1016/j.heliyon.2024.e24751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/09/2023] [Accepted: 01/12/2024] [Indexed: 02/06/2024] Open
Abstract
Aging is a complex and inevitable biological process affected by a combination of external environmental and genetic factors. Humans are currently living longer than ever before, accompanied with aging-related alterations such as diminished autophagy, decreased immunological function, mitochondrial malfunction, stem cell failure, accumulation of somatic and mitochondrial DNA mutations, loss of telomere, and altered nutrient metabolism. Aging leads to a decline in body functions and age-related diseases, for example, Alzheimer's disease, which adversely affects human health and longevity. The quality of life of the elderly is greatly diminished by the increase in their life expectancy rather than healthy life expectancy. With the rise in the age of the global population, aging and related diseases have become the focus of attention worldwide. In this review, we discuss several major mechanisms of aging, including DNA damage and repair, free radical oxidation, telomeres and telomerase, mitochondrial damage, inflammation, and their role in neurodegenerative diseases to provide a reference for the prevention of aging and its related diseases.
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Affiliation(s)
- Juanli Zhao
- Laboratory of Medical Molecular and Cellular Biology, College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, 430065, China
- Department of Pharmacology, College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Zhenjie Han
- Laboratory of Medical Molecular and Cellular Biology, College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Li Ding
- Department of Pharmacology, College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Ping Wang
- Hubei Research Institute of Geriatrics, Collaborative Innovation Center of Hubei Province, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Xiutang He
- Center for Monitoring and Evaluation of Teaching Quality, Jingchu University of Technology, Jingmen, 448000, China
| | - Li Lin
- Laboratory of Medical Molecular and Cellular Biology, College of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, 430065, China
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11
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Lawir DF, Soza-Ried C, Iwanami N, Siamishi I, Bylund GO, O Meara C, Sikora K, Kanzler B, Johansson E, Schorpp M, Cauchy P, Boehm T. Antagonistic interactions safeguard mitotic propagation of genetic and epigenetic information in zebrafish. Commun Biol 2024; 7:31. [PMID: 38182651 PMCID: PMC10770094 DOI: 10.1038/s42003-023-05692-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024] Open
Abstract
The stability of cellular phenotypes in developing organisms depends on error-free transmission of epigenetic and genetic information during mitosis. Methylation of cytosine residues in genomic DNA is a key epigenetic mark that modulates gene expression and prevents genome instability. Here, we report on a genetic test of the relationship between DNA replication and methylation in the context of the developing vertebrate organism instead of cell lines. Our analysis is based on the identification of hypomorphic alleles of dnmt1, encoding the DNA maintenance methylase Dnmt1, and pole1, encoding the catalytic subunit of leading-strand DNA polymerase epsilon holoenzyme (Pole). Homozygous dnmt1 mutants exhibit genome-wide DNA hypomethylation, whereas the pole1 mutation is associated with increased DNA methylation levels. In dnmt1/pole1 double-mutant zebrafish larvae, DNA methylation levels are restored to near normal values, associated with partial rescue of mutant-associated transcriptional changes and phenotypes. Hence, a balancing antagonism between DNA replication and maintenance methylation buffers against replicative errors contributing to the robustness of vertebrate development.
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Affiliation(s)
- Divine-Fondzenyuy Lawir
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Cristian Soza-Ried
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Iliana Siamishi
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Göran O Bylund
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Connor O Meara
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Katarzyna Sikora
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bioinformatic Unit, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Benoît Kanzler
- Transgenic Mouse Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Erik Johansson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Pierre Cauchy
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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12
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Valizadeh P, Momtazmanesh S, Plazzi G, Rezaei N. Connecting the dots: An updated review of the role of autoimmunity in narcolepsy and emerging immunotherapeutic approaches. Sleep Med 2024; 113:378-396. [PMID: 38128432 DOI: 10.1016/j.sleep.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Narcolepsy type 1 (NT1) is a chronic disorder characterized by pathological daytime sleepiness and cataplexy due to the disappearance of orexin immunoreactive neurons in the hypothalamus. Genetic and environmental factors point towards a potential role for inflammation and autoimmunity in the pathogenesis of the disease. This study aims to comprehensively review the latest evidence on the autoinflammatory mechanisms and immunomodulatory treatments aimed at suspected autoimmune pathways in NT1. METHODS Recent relevant literature in the field of narcolepsy, its autoimmune hypothesis, and purposed immunomodulatory treatments were reviewed. RESULTS Narcolepsy is strongly linked to specific HLA alleles and T-cell receptor polymorphisms. Furthermore, animal studies and autopsies have found infiltration of T cells in the hypothalamus, supporting T cell-mediated immunity. However, the role of autoantibodies has yet to be definitively established. Increased risk of NT1 after H1N1 infection and vaccination supports the autoimmune hypothesis, and the potential role of coronavirus disease 2019 and vaccination in triggering autoimmune neurodegeneration is a recent finding. Alterations in cytokine levels, gut microbiota, and microglial activation indicate a potential role for inflammation in the disease's development. Reports of using immunotherapies in NT1 patients are limited and inconsistent. Early treatment with IVIg, corticosteroids, plasmapheresis, and monoclonal antibodies has seldomly shown some potential benefits in some studies. CONCLUSION The current body of literature supports that narcolepsy is an autoimmune disorder most likely caused by T-cell involvement. However, the potential for immunomodulatory treatments to reverse the autoinflammatory process remains understudied. Further clinical controlled trials may provide valuable insights into this area.
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Affiliation(s)
- Parya Valizadeh
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Sara Momtazmanesh
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Giuseppe Plazzi
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Biomedical, Metabolic, and Neural Sciences, Università Degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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13
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Lischka A, Eggermann K, Record CJ, Dohrn MF, Laššuthová P, Kraft F, Begemann M, Dey D, Eggermann T, Beijer D, Šoukalová J, Laura M, Rossor AM, Mazanec R, Van Lent J, Tomaselli PJ, Ungelenk M, Debus KY, Feely SME, Gläser D, Jagadeesh S, Martin M, Govindaraj GM, Singhi P, Baineni R, Biswal N, Ibarra-Ramírez M, Bonduelle M, Gess B, Romero Sánchez J, Suthar R, Udani V, Nalini A, Unnikrishnan G, Marques W, Mercier S, Procaccio V, Bris C, Suresh B, Reddy V, Skorupinska M, Bonello-Palot N, Mochel F, Dahl G, Sasidharan K, Devassikutty FM, Nampoothiri S, Rodovalho Doriqui MJ, Müller-Felber W, Vill K, Haack TB, Dufke A, Abele M, Stucka R, Siddiqi S, Ullah N, Spranger S, Chiabrando D, Bolgül BS, Parman Y, Seeman P, Lampert A, Schulz JB, Wood JN, Cox JJ, Auer-Grumbach M, Timmerman V, de Winter J, Themistocleous AC, Shy M, Bennett DL, Baets J, Hübner CA, Leipold E, Züchner S, Elbracht M, Çakar A, Senderek J, Hornemann T, Woods CG, Reilly MM, Kurth I. Genetic landscape of congenital insensitivity to pain and hereditary sensory and autonomic neuropathies. Brain 2023; 146:4880-4890. [PMID: 37769650 PMCID: PMC10689924 DOI: 10.1093/brain/awad328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/16/2023] [Accepted: 09/03/2023] [Indexed: 10/02/2023] Open
Abstract
Congenital insensitivity to pain (CIP) and hereditary sensory and autonomic neuropathies (HSAN) are clinically and genetically heterogeneous disorders exclusively or predominantly affecting the sensory and autonomic neurons. Due to the rarity of the diseases and findings based mainly on single case reports or small case series, knowledge about these disorders is limited. Here, we describe the molecular workup of a large international cohort of CIP/HSAN patients including patients from normally under-represented countries. We identify 80 previously unreported pathogenic or likely pathogenic variants in a total of 73 families in the >20 known CIP/HSAN-associated genes. The data expand the spectrum of disease-relevant alterations in CIP/HSAN, including novel variants in previously rarely recognized entities such as ATL3-, FLVCR1- and NGF-associated neuropathies and previously under-recognized mutation types such as larger deletions. In silico predictions, heterologous expression studies, segregation analyses and metabolic tests helped to overcome limitations of current variant classification schemes that often fail to categorize a variant as disease-related or benign. The study sheds light on the genetic causes and disease-relevant changes within individual genes in CIP/HSAN. This is becoming increasingly important with emerging clinical trials investigating subtype or gene-specific treatment strategies.
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Affiliation(s)
- Annette Lischka
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Katja Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Christopher J Record
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Maike F Dohrn
- Department of Neurology, Medical Faculty of the RWTH Aachen University, 52074 Aachen, Germany
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Petra Laššuthová
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, 150 06 Praha, Czechia
| | - Florian Kraft
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Matthias Begemann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Daniela Dey
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Thomas Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Danique Beijer
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Jana Šoukalová
- Department of Medical Genetics, University Hospital Brno, 625 00 Brno, Czechia
| | - Matilde Laura
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Alexander M Rossor
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Radim Mazanec
- Department of Neurology, Faculty of Medicine, Charles University in Prague and Motol University Hospital, 150 06 Prague, Czechia
| | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, 2160 Antwerp, Belgium
| | - Pedro J Tomaselli
- Department of Neurosciences and Behaviour Sciences, Clinical Hospital of Ribeirão Preto, University of São Paulo, Ribeirão Preto, 14015-130, Brazil
| | - Martin Ungelenk
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Karlien Y Debus
- Center for Molecular Biomedicine Institute for Biophysics, Friedrich-Schiller Universität Jena, 07745 Jena, Germany
| | - Shawna M E Feely
- Department of Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Division of Pediatric Neurology, Seattle Children’s Hospital, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Dieter Gläser
- Center for Human Genetics, Genetikum®, 89231 Neu-Ulm, Germany
| | - Sujatha Jagadeesh
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai 600032, Tamilnadu, India
| | - Madelena Martin
- Davis and Davis Children's Hospital, University of California, Sacramento, CA 95817, USA
| | - Geeta M Govindaraj
- Department of Pediatrics, Government Medical College, Kozhikode, Kerala 673 008, India
| | - Pratibha Singhi
- Pediatric Neurology and Neurodevelopment, Medanta, The Medicity, Gurgaon, Haryana 122 001, India
| | - Revanth Baineni
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry 605 006, India
| | - Niranjan Biswal
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry 605 006, India
| | - Marisol Ibarra-Ramírez
- Genetics Department, Hospital Universitario Dr. José Eleuterio González Universidad Autónoma de Nuevo León, 64460 Monterrey, Nuevo León, México
| | - Maryse Bonduelle
- Centre for Medical Genetics, Universitair Ziekenhuis Brussel, 1090 Jette, Brussels, Belgium
| | - Burkhard Gess
- Department of Neurology, Medical Faculty of the RWTH Aachen University, 52074 Aachen, Germany
- Department of Neurology, University Hospital, Evangelisches Klinikum Bethel, University of Bielefeld, 33617 Bielefeld, Germany
| | | | - Renu Suthar
- Pediatric Neurology and Neurodevelopment Unit, Department of Pediatrics, Advanced Pediatric Centre, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh 160 012, India
| | - Vrajesh Udani
- Department of Child Neurology, PD Hinduja Hospital and Medical Research Centre, Mumbai, Maharashtra 400 016, India
| | - Atchayaram Nalini
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru 560 029, India
| | - Gopikrishnan Unnikrishnan
- Department of Neurology, National Institute of Mental Health and Neurosciences, Bengaluru 560 029, India
| | - Wilson Marques
- Department of Neurosciences and Behaviour Sciences, Clinical Hospital of Ribeirão Preto, University of São Paulo, Ribeirão Preto, 14015-130, Brazil
| | - Sandra Mercier
- CHU Nantes, Service de Génétique Médicale, Centre de Référence des Maladies Neuromusculaires AOC, 44000 Nantes, France
| | - Vincent Procaccio
- Department of Biochemistry and Genetics, MitoVasc Institute, UMR CNRS 6015- INSERM U1083, CHU Angers, 49055 Angers, France
| | - Céline Bris
- Department of Biochemistry and Genetics, MitoVasc Institute, UMR CNRS 6015- INSERM U1083, CHU Angers, 49055 Angers, France
| | - Beena Suresh
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai 600032, Tamilnadu, India
| | - Vaishnavi Reddy
- Department of Clinical Genetics and Genetic Counselling, Mediscan Systems, Chennai 600032, Tamilnadu, India
| | - Mariola Skorupinska
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | | | - Fanny Mochel
- Genetics Department, Sorbonne Université, Paris Brain Institute, APHP, INSERM, CNRS, 75013 Paris, France
| | - Georg Dahl
- Pediatric Neurology, Children’s Hospital of the King’s Daughters in Norfolk, Norfolk, VA 23507, USA
| | - Karthika Sasidharan
- Department of Pediatrics, Government Medical College, Kozhikode, Kerala 673 008, India
| | - Fiji M Devassikutty
- Department of Pediatrics, Government Medical College, Kozhikode, Kerala 673 008, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Center, Cochin, Kerala 682 041, India
| | - Maria J Rodovalho Doriqui
- Department of Genetics, Hospital Infantil Doutor Juvêncio Mattos, São Luis, Maranhão 65015-460, Brazil
| | - Wolfgang Müller-Felber
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, LMU Campus Innenstadt, University of Munich, 80337 Munich, Germany
| | - Katharina Vill
- Department of Pediatric Neurology and Developmental Medicine, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, 80337 Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
| | - Michael Abele
- Neurologie, Praxis für Neurologie und Schlafmedizin, 53359 Rheinbach, Germany
| | - Rolf Stucka
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Saima Siddiqi
- Genomics Group, Institute of Biomedical and Genetic Engineering (IBGE), Islamabad 44000, Pakistan
| | - Noor Ullah
- Institute for Paramedical Sciences, Khyber Medical University, Peshawar, KPK 25100, Pakistan
| | | | - Deborah Chiabrando
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center ‘Guido Tarone’, University of Torino, 10124 Turin, Italy
| | - Behiye S Bolgül
- Department of Pedodontics, Faculty of Dentistry, Dicle University, 21200 Diyarbakir, Turkey
| | - Yesim Parman
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Turkey
| | - Pavel Seeman
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, 150 06 Praha, Czechia
| | - Angelika Lampert
- Institute of Neurophysiology, Medical Faculty, Uniklinik RWTH Aachen University, 52074 Aachen, Germany
| | - Jörg B Schulz
- Department of Neurology, Medical Faculty of the RWTH Aachen University, 52074 Aachen, Germany
- JARA-BRAIN Institute Molecular Neuroscience and Neuroimaging, Research Centre Jülich GmbH, and RWTH Aachen University, 52056 Aachen, Germany
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London WC1E 6BT, UK
| | - Michaela Auer-Grumbach
- Department of Orthopedics and Trauma Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, 2160 Antwerp, Belgium
| | - Jonathan de Winter
- Translational Neurosciences and Institute Born Bunge, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
- Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, 2610 Antwerp, Belgium
| | | | - Michael Shy
- Department of Neurology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - David L Bennett
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX3 9DU, UK
| | - Jonathan Baets
- Translational Neurosciences and Institute Born Bunge, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
- Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, 2610 Antwerp, Belgium
| | - Christian A Hübner
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Enrico Leipold
- Department of Anesthesiology and Intensive Care and CBBM—Center of Brain, Behavior and Metabolism, University of Luebeck, 23562 Luebeck, Germany
| | - Stephan Züchner
- Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Miriam Elbracht
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Arman Çakar
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Turkey
| | - Jan Senderek
- Friedrich Baur Institute at the Department of Neurology, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Thorsten Hornemann
- Department of Clinical Chemistry, University Hospital Zurich, University of Zurich, 8006 Zurich, Switzerland
| | - C Geoffrey Woods
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Mary M Reilly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, 52074 Aachen, Germany
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14
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Wang Z, Yang H, Han Y, Teng J, Kong X, Qi X. Screening and identification of key biomarkers associated with amyotrophic lateral sclerosis and depression using bioinformatics. Medicine (Baltimore) 2023; 102:e36265. [PMID: 38013317 PMCID: PMC10681454 DOI: 10.1097/md.0000000000036265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023] Open
Abstract
This study aims to identify common molecular biomarkers between amyotrophic lateral sclerosis (ALS) and depression using bioinformatics methods, in order to provide potential targets and new ideas and methods for the diagnosis and treatment of these diseases. Microarray datasets GSE139384, GSE35978 and GSE87610 were obtained from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) between ALS and depression were identified. After screening for overlapping DEGs, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. Furthermore, a protein-protein interaction (PPI) network was constructed using the STRING database and Cytoscape software, and hub genes were identified. Finally, a network between miRNAs and hub genes was constructed using the NetworkAnalyst tool, and possible key miRNAs were predicted. A total of 357 genes have been identified as common DEGs between ALS and depression. GO and KEGG enrichment analyses of the 357 DEGs showed that they were mainly involved in cytoplasmic translation. Further analysis of the PPI network using Cytoscape and MCODE plugins identified 6 hub genes, including mitochondrial ribosomal protein S12 (MRPS12), poly(rC) binding protein 1 (PARP1), SNRNP200, PCBP1, small G protein signaling modulator 1 (SGSM1), and DNA methyltransferase 1 (DNMT1). Five possible target miRNAs, including miR-221-5p, miR-21-5p, miR-100-5p, miR-30b-5p, and miR-615-3p, were predicted by constructing a miRNA-gene network. This study used bioinformatics techniques to explore the potential association between ALS and depression, and identified potential biomarkers. These biomarkers may provide new ideas and methods for the early diagnosis, treatment, and monitoring of ALS and depression.
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Affiliation(s)
- Ziyue Wang
- Shandong University of Traditional Chinese Medicine, Jinan City, Shandong Province, China
| | - Hao Yang
- Shandong University of Traditional Chinese Medicine, Jinan City, Shandong Province, China
| | - Yu Han
- Shandong University of Traditional Chinese Medicine, Jinan City, Shandong Province, China
| | - Jing Teng
- Shandong University of Traditional Chinese Medicine, Jinan City, Shandong Province, China
| | - Xinru Kong
- Shandong University of Traditional Chinese Medicine, Jinan City, Shandong Province, China
| | - Xianghua Qi
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan City, Shandong Province, China
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15
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Wang Z, Xiang S, Zhou C, Xu Q. DeepMethylation: a deep learning based framework with GloVe and Transformer encoder for DNA methylation prediction. PeerJ 2023; 11:e16125. [PMID: 37780374 PMCID: PMC10538282 DOI: 10.7717/peerj.16125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/27/2023] [Indexed: 10/03/2023] Open
Abstract
DNA methylation is a crucial topic in bioinformatics research. Traditional wet experiments are usually time-consuming and expensive. In contrast, machine learning offers an efficient and novel approach. In this study, we propose DeepMethylation, a novel methylation predictor with deep learning. Specifically, the DNA sequence is encoded with word embedding and GloVe in the first step. After that, dilated convolution and Transformer encoder are utilized to extract the features. Finally, full connection and softmax operators are applied to predict the methylation sites. The proposed model achieves an accuracy of 97.8% on the 5mC dataset, which outperforms state-of-the-art methods. Furthermore, our predictor exhibits good generalization ability as it achieves an accuracy of 95.8% on the m1A dataset. To ease access for other researchers, our code is publicly available at https://github.com/sb111169/tf-5mc.
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Affiliation(s)
- Zhe Wang
- Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Sen Xiang
- Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Chao Zhou
- China Three Gorges University, Yichang, Hubei, China
| | - Qing Xu
- China Three Gorges University, Yichang, Hubei, China
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16
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Menon PJ, Bogdanova-Mihaylova P, McDermott G, Crowley P, Killeen RP, Alexander MD, O'Dowd S, Murphy SM. DNMT1-associated sensory neuropathy and cerebellar ataxia: A novel variant and review of genotype-phenotype correlation. J Peripher Nerv Syst 2023; 28:508-512. [PMID: 37199681 DOI: 10.1111/jns.12560] [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] [Received: 03/12/2023] [Revised: 05/01/2023] [Accepted: 05/06/2023] [Indexed: 05/19/2023]
Abstract
AIM Hereditary sensory neuropathy (HSN) 1E is a neurodegenerative disorder caused by pathogenic variants in DNA methyltransferase 1 (DNMT1). It is characterised by sensorineural deafness, sensory neuropathy and cognitive decline. Variants in DNMT1 are also associated with autosomal dominant cerebellar ataxia, deafness and narcolepsy. METHODS A 42-year-old man presented with imbalance, lancinating pain, numerous paucisymptomatic injuries, progressive deafness since his mid-20s, mild cognitive decline and apathy. Examination revealed abnormalities of eye movements, distal sensory loss to all modalities, areflexia without weakness and lower limb ataxia. MRI brain and FDG-PET scan demonstrated biparietal and cerebellar atrophy/hypometabolism. Whole exome sequencing detected a heterozygous likely pathogenic missense variant in DNMT1, c.1289G > A, p.Cys430Tyr. Cochlear implant was performed at 44 years for the bilateral high frequency sensorineural hearing loss with improvement in hearing and day-to-day function. RESULTS AND CONCLUSION We describe a novel variant in DNMT1 and confirm that an overlapping HSN1E-cerebellar phenotype can occur. Only one prior case of cochlear implant in HSN1E has been reported to date but this case adds to that literature, suggesting that cochlear implant can be successful in such patients. We further explore the clinical and radiological signature of the cognitive syndrome associated with this disorder.
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Affiliation(s)
| | | | - Garret McDermott
- Department of Neuropsychology, Tallaght University Hospital, Dublin, Ireland
| | - Paul Crowley
- Department of Neurology, Aut Even Hospital, Kilkenny, Ireland
| | - Ronan P Killeen
- Department of Radiology, St. Vincent's University Hospital, Dublin, Ireland
| | - Michael D Alexander
- Department of Neurophysiology, Tallaght University Hospital, Dublin, Ireland
| | - Sean O'Dowd
- Department of Neurology, Tallaght University Hospital, Dublin, Ireland
- Academic Unit of Neurology, Trinity College Dublin, Dublin, Ireland
| | - Sinéad M Murphy
- Department of Neurology, Tallaght University Hospital, Dublin, Ireland
- Academic Unit of Neurology, Trinity College Dublin, Dublin, Ireland
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17
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Switzer RL, Hartman ZJ, Hewett GR, Carroll CF. Disease-Associated Mutation A554V Disrupts Normal Autoinhibition of DNMT1. DNA 2023; 3:119-133. [PMID: 37663147 PMCID: PMC10470860 DOI: 10.3390/dna3030010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
DNA methyltransferase 1 (DNMT1) is the enzyme primarily responsible for propagation of the methylation pattern in cells. Mutations in DNMT1 have been linked to the development of adult-onset neurodegenerative disorders; these disease-associated mutations occur in the regulatory replication foci-targeting sequence (RFTS) domain of the protein. The RFTS domain is an endogenous inhibitor of DNMT1 activity that binds to the active site and prevents DNA binding. Here, we examine the impact of the disease-associated mutation A554V on normal RFTS-mediated inhibition of DNMT1. Wild-type and mutant proteins were expressed and purified to homogeneity for biochemical characterization. The mutation increased DNA binding affinity ~8-fold. In addition, the mutant enzyme exhibited increased DNA methylation activity. Circular dichroism (CD) spectroscopy revealed that the mutation does not significantly impact the secondary structure or relative thermal stability of the isolated RFTS domain. However, the mutation resulted in changes in the CD spectrum in the context of the larger protein; a decrease in relative thermal stability was also observed. Collectively, this evidence suggests that A554V disrupts normal RFTS-mediated autoinhibition of DNMT1, resulting in a hyperactive mutant enzyme. While the disease-associated mutation does not significantly impact the isolated RFTS domain, the mutation results in a weakening of the interdomain stabilizing interactions generating a more open, active conformation of DNMT1. Hyperactive mutant DNMT1 could be responsible for the increased DNA methylation observed in affected individuals.
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Affiliation(s)
| | - Zach J. Hartman
- Department of Biology, Bucknell University, Lewisburg, PA 17837, USA
| | - Geoffrey R. Hewett
- Program in Cell Biology/Biochemistry, Bucknell University, Lewisburg, PA 17837, USA
| | - Clara F. Carroll
- Department of Chemistry, Bucknell University, Lewisburg, PA 17837, USA
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18
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Mukherjee A, Pandey S. Cerebellar Ataxia without Deafness or Narcolepsy and the Hot Cross Bun Sign-an Unusual Ensemble in DNMT1 Mutation. Mov Disord Clin Pract 2023; 10:1219-1221. [PMID: 37635777 PMCID: PMC10450233 DOI: 10.1002/mdc3.13791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/17/2023] [Accepted: 05/09/2023] [Indexed: 08/29/2023] Open
Affiliation(s)
- Adreesh Mukherjee
- Department of Neurology and Stroke MedicineAmrita HospitalFaridabad, Delhi NCRIndia
| | - Sanjay Pandey
- Department of Neurology and Stroke MedicineAmrita HospitalFaridabad, Delhi NCRIndia
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19
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PerezGrovas-Saltijeral A, Rajkumar AP, Knight HM. Differential expression of m 5C RNA methyltransferase genes NSUN6 and NSUN7 in Alzheimer's disease and traumatic brain injury. Mol Neurobiol 2023; 60:2223-2235. [PMID: 36646969 PMCID: PMC9984329 DOI: 10.1007/s12035-022-03195-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/23/2022] [Indexed: 01/18/2023]
Abstract
Epigenetic processes have become increasingly relevant in understanding disease-modifying mechanisms. 5-Methylcytosine methylations of DNA (5mC) and RNA (m5C) have functional transcriptional and RNA translational consequences and are tightly regulated by writer, reader and eraser effector proteins. To investigate the involvement of 5mC/5hmC and m5C effector proteins contributing to the development of dementia neuropathology, RNA sequencing data of 31 effector proteins across four brain regions was examined in 56 aged non-affected and 51 Alzheimer's disease (AD) individuals obtained from the Aging, Dementia and Traumatic Brain Injury Study. Gene expression profiles were compared between AD and controls, between neuropathological Braak and CERAD scores and in individuals with a history of traumatic brain injury (TBI). We found an increase in the DNA methylation writers DNMT1, DNMT3A and DNMT3B messenger RNA (mRNA) and a decrease in the reader UHRF1 mRNA in AD samples across three brain regions whilst the DNA erasers GADD45B and AICDA showed changes in mRNA abundance within neuropathological load groupings. RNA methylation writers NSUN6 and NSUN7 showed significant expression differences with AD and, along with the reader ALYREF, differences in expression for neuropathologic ranking. A history of TBI was associated with a significant increase in the DNA readers ZBTB4 and MeCP2 (p < 0.05) and a decrease in NSUN6 (p < 0.001) mRNA. These findings implicate regulation of protein pathways disrupted in AD and TBI via multiple pre- and post-transcriptional mechanisms including potentially acting upon transfer RNAs, enhancer RNAs as well as nuclear-cytoplasmic shuttling and cytoplasmic translational control. The targeting of such processes provides new therapeutic avenues for neurodegenerative brain conditions.
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Affiliation(s)
| | - Anto P Rajkumar
- Institute of Mental Health, Mental Health and Clinical Neurosciences Academic Unit, School of Medicine, University of Nottingham, Nottingham, UK.,Mental Health Services for Older People, Nottinghamshire Healthcare NHS Foundation Trust, Nottingham, UK
| | - Helen Miranda Knight
- Division of Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK.
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20
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Novel de novo DNMT1 gene mutation associated with hereditary sensory and autonomic neuropathy 1E (HSAN1E). Neurol Sci 2023; 44:2199-2201. [PMID: 36746843 DOI: 10.1007/s10072-023-06652-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/29/2023] [Indexed: 02/08/2023]
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21
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Wang K, Liu H, Hu Q, Wang L, Liu J, Zheng Z, Zhang W, Ren J, Zhu F, Liu GH. Epigenetic regulation of aging: implications for interventions of aging and diseases. Signal Transduct Target Ther 2022; 7:374. [PMID: 36336680 PMCID: PMC9637765 DOI: 10.1038/s41392-022-01211-8] [Citation(s) in RCA: 134] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022] Open
Abstract
Aging is accompanied by the decline of organismal functions and a series of prominent hallmarks, including genetic and epigenetic alterations. These aging-associated epigenetic changes include DNA methylation, histone modification, chromatin remodeling, non-coding RNA (ncRNA) regulation, and RNA modification, all of which participate in the regulation of the aging process, and hence contribute to aging-related diseases. Therefore, understanding the epigenetic mechanisms in aging will provide new avenues to develop strategies to delay aging. Indeed, aging interventions based on manipulating epigenetic mechanisms have led to the alleviation of aging or the extension of the lifespan in animal models. Small molecule-based therapies and reprogramming strategies that enable epigenetic rejuvenation have been developed for ameliorating or reversing aging-related conditions. In addition, adopting health-promoting activities, such as caloric restriction, exercise, and calibrating circadian rhythm, has been demonstrated to delay aging. Furthermore, various clinical trials for aging intervention are ongoing, providing more evidence of the safety and efficacy of these therapies. Here, we review recent work on the epigenetic regulation of aging and outline the advances in intervention strategies for aging and age-associated diseases. A better understanding of the critical roles of epigenetics in the aging process will lead to more clinical advances in the prevention of human aging and therapy of aging-related diseases.
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Affiliation(s)
- Kang Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Huicong Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Qinchao Hu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China
- Hospital of Stomatology, Sun Yat-sen University, 510060, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University, 510060, Guangzhou, China
| | - Lingna Wang
- School of Biomedical Engineering, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Jiaqing Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 200030, Shanghai, China
| | - Zikai Zheng
- University of Chinese Academy of Sciences, 100049, Beijing, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China
| | - Weiqi Zhang
- University of Chinese Academy of Sciences, 100049, Beijing, China
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jie Ren
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Fangfang Zhu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 200030, Shanghai, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, 100101, Beijing, China.
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, 100053, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China.
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22
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Lischka A, Lassuthova P, Çakar A, Record CJ, Van Lent J, Baets J, Dohrn MF, Senderek J, Lampert A, Bennett DL, Wood JN, Timmerman V, Hornemann T, Auer-Grumbach M, Parman Y, Hübner CA, Elbracht M, Eggermann K, Geoffrey Woods C, Cox JJ, Reilly MM, Kurth I. Genetic pain loss disorders. Nat Rev Dis Primers 2022; 8:41. [PMID: 35710757 DOI: 10.1038/s41572-022-00365-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 01/05/2023]
Abstract
Genetic pain loss includes congenital insensitivity to pain (CIP), hereditary sensory neuropathies and, if autonomic nerves are involved, hereditary sensory and autonomic neuropathy (HSAN). This heterogeneous group of disorders highlights the essential role of nociception in protecting against tissue damage. Patients with genetic pain loss have recurrent injuries, burns and poorly healing wounds as disease hallmarks. CIP and HSAN are caused by pathogenic genetic variants in >20 genes that lead to developmental defects, neurodegeneration or altered neuronal excitability of peripheral damage-sensing neurons. These genetic variants lead to hyperactivity of sodium channels, disturbed haem metabolism, altered clathrin-mediated transport and impaired gene regulatory mechanisms affecting epigenetic marks, long non-coding RNAs and repetitive elements. Therapies for pain loss disorders are mainly symptomatic but the first targeted therapies are being tested. Conversely, chronic pain remains one of the greatest unresolved medical challenges, and the genes and mechanisms associated with pain loss offer new targets for analgesics. Given the progress that has been made, the coming years are promising both in terms of targeted treatments for pain loss disorders and the development of innovative pain medicines based on knowledge of these genetic diseases.
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Affiliation(s)
- Annette Lischka
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Petra Lassuthova
- Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic
| | - Arman Çakar
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Christopher J Record
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium
| | - Jonathan Baets
- Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium.,Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerp, Belgium
| | - Maike F Dohrn
- Department of Neurology, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany.,Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Jan Senderek
- Friedrich-Baur-Institute, Department of Neurology, Ludwig-Maximilians-University, Munich, Germany
| | - Angelika Lampert
- Institute of Physiology, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - David L Bennett
- Nuffield Department of Clinical Neuroscience, Oxford University, Oxford, UK
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born Bunge, Antwerp, Belgium
| | - Thorsten Hornemann
- Department of Clinical Chemistry, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Michaela Auer-Grumbach
- Department of Orthopedics and Trauma Surgery, Medical University of Vienna, Vienna, Austria
| | - Yesim Parman
- Neuromuscular Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | | | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - Katja Eggermann
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany
| | - C Geoffrey Woods
- Cambridge Institute for Medical Research, Keith Peters Building, Cambridge Biomedical Campus, Cambridge, UK
| | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Mary M Reilly
- Centre for Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, Uniklinik RWTH Aachen University, Aachen, Germany.
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23
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Seale K, Horvath S, Teschendorff A, Eynon N, Voisin S. Making sense of the ageing methylome. Nat Rev Genet 2022; 23:585-605. [PMID: 35501397 DOI: 10.1038/s41576-022-00477-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2022] [Indexed: 12/22/2022]
Abstract
Over time, the human DNA methylation landscape accrues substantial damage, which has been associated with a broad range of age-related diseases, including cardiovascular disease and cancer. Various age-related DNA methylation changes have been described, including at the level of individual CpGs, such as differential and variable methylation, and at the level of the whole methylome, including entropy and correlation networks. Here, we review these changes in the ageing methylome as well as the statistical tools that can be used to quantify them. We detail the evidence linking DNA methylation to ageing phenotypes and the longevity strategies aimed at altering both DNA methylation patterns and machinery to extend healthspan and lifespan. Lastly, we discuss theories on the mechanistic causes of epigenetic ageing.
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Affiliation(s)
- Kirsten Seale
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Altos Labs, San Diego, CA, USA
| | - Andrew Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.,UCL Cancer Institute, University College London, London, UK
| | - Nir Eynon
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia.
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, Melbourne, Victoria, Australia.
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24
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Indelicato E, Zech M, Amprosi M, Boesch S. Untangling neurodevelopmental disorders in the adulthood: a movement disorder is the clue. Orphanet J Rare Dis 2022; 17:55. [PMID: 35172867 PMCID: PMC8848801 DOI: 10.1186/s13023-022-02218-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/06/2022] [Indexed: 11/23/2022] Open
Abstract
Background The genetic landscape of neurodevelopmental disorders is constantly expanding and children with early-onset neurological phenotypes increasingly receive a genetic diagnosis. Nonetheless, the awareness of the chronic course of these conditions, and consequently their recognition and management in the adult population, is still limited. Results Herein, we describe four patients with rare neurodevelopmental disorders (SON, ZMYND11, DNMT1 and YY1-related diseases), who received a genetic assignment only in the adulthood. All these patients had an early developmental delay and displayed a movement disorder (dystonia/ataxia/tremor) which manifested for the first time, or worsened, in the adulthood, prompting the referral to a neurologist. This phenotypic combination led eventually to the genetic testing. We report previously unrecognized features and highlight the peculiarities of the adult presentation of four neurodevelopmental disorders. Conclusions This report expands the current knowledge on four rare neurodevelopmental disorders (SON, ZMYND11, DNMT1 and YY1), which was mainly based on reports from paediatric cases. This case series emphasize the importance of a tight neurological surveillance extending beyond the childhood.
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Affiliation(s)
- Elisabetta Indelicato
- Center for Rare Movement Disorders Innsbruck, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria.
| | - Michael Zech
- Institut for Neurogenetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Oberschleißheim, Munich-Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Matthias Amprosi
- Center for Rare Movement Disorders Innsbruck, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
| | - Sylvia Boesch
- Center for Rare Movement Disorders Innsbruck, Medical University of Innsbruck, Anichstrasse 35, 6020, Innsbruck, Austria
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25
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Wang W, Zhao X, Shao Y, Duan X, Wang Y, Li J, Li J, Li D, Li X, Wong J. Mutation-induced DNMT1 cleavage drives neurodegenerative disease. SCIENCE ADVANCES 2021; 7:eabe8511. [PMID: 34516921 PMCID: PMC8442919 DOI: 10.1126/sciadv.abe8511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Specific mutations within the replication foci targeting sequence (RFTS) domain of human DNMT1 are causative of two types of adult-onset neurodegenerative diseases, HSAN1E and ADCA-DN, but the underlying mechanisms are largely unknown. We generated Dnmt1-M1 and Dnmt1-M2 knock-in mouse models that are equivalent to Y495C and D490E-P491Y mutation in patients with HSAN1E, respectively. We found that both mutant heterozygous mice are viable, have reduced DNMT1 proteins, and exhibit neurodegenerative phenotypes including impaired learning and memory. The homozygous mutants die around embryonic day 10.5 and are apparently devoid of DNMT1 proteins. We present the evidence that the mutant DNMT1 proteins are unstable, most likely because of cleavage within RFTS domain by an unidentified proteinase. Moreover, we provide evidence that the RFTS mutation–induced cleavage of DNMT1, but not mutation itself, is responsible for functional defect of mutant DNMT1. Our study shed light on the mechanism of DNMT1 RFTS mutation causing neurodegenerative diseases.
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Affiliation(s)
- Wencai Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai 201499, China
| | - Xingsen Zhao
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
- Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
- National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Yanjiao Shao
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xiaoya Duan
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yaling Wang
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jialun Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xuekun Li
- The Children’s Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
- Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
- National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Fengxian District Central Hospital–ECNU Joint Center of Translational Medicine, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai 201499, China
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26
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Maresca A, Del Dotto V, Capristo M, Scimonelli E, Tagliavini F, Morandi L, Tropeano CV, Caporali L, Mohamed S, Roberti M, Scandiffio L, Zaffagnini M, Rossi J, Cappelletti M, Musiani F, Contin M, Riva R, Liguori R, Pizza F, La Morgia C, Antelmi E, Loguercio Polosa P, Mignot E, Zanna C, Plazzi G, Carelli V. DNMT1 mutations leading to neurodegeneration paradoxically reflect on mitochondrial metabolism. Hum Mol Genet 2021; 29:1864-1881. [PMID: 31984424 PMCID: PMC7372549 DOI: 10.1093/hmg/ddaa014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
ADCA-DN and HSN-IE are rare neurodegenerative syndromes caused by dominant mutations in the replication foci targeting sequence (RFTS) of the DNA methyltransferase 1 (DNMT1) gene. Both phenotypes resemble mitochondrial disorders, and mitochondrial dysfunction was first observed in ADCA-DN. To explore mitochondrial involvement, we studied the effects of DNMT1 mutations in fibroblasts from four ADCA-DN and two HSN-IE patients. We documented impaired activity of purified DNMT1 mutant proteins, which in fibroblasts results in increased DNMT1 amount. We demonstrated that DNMT1 is not localized within mitochondria, but it is associated with the mitochondrial outer membrane. Concordantly, mitochondrial DNA failed to show meaningful CpG methylation. Strikingly, we found activated mitobiogenesis and OXPHOS with significant increase of H2O2, sharply contrasting with a reduced ATP content. Metabolomics profiling of mutant cells highlighted purine, arginine/urea cycle and glutamate metabolisms as the most consistently altered pathways, similar to primary mitochondrial diseases. The most severe mutations showed activation of energy shortage AMPK-dependent sensing, leading to mTORC1 inhibition. We propose that DNMT1 RFTS mutations deregulate metabolism lowering ATP levels, as a result of increased purine catabolism and urea cycle pathways. This is associated with a paradoxical mitochondrial hyper-function and increased oxidative stress, possibly resulting in neurodegeneration in non-dividing cells.
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Affiliation(s)
- Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy
| | - Valentina Del Dotto
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Mariantonietta Capristo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy
| | - Emanuela Scimonelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Francesca Tagliavini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy
| | - Luca Morandi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | | | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy
| | - Susan Mohamed
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy
| | - Marina Roberti
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari 70126, Italy
| | - Letizia Scandiffio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari 70126, Italy
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Jacopo Rossi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Manuela Contin
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Roberto Riva
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Rocco Liguori
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Fabio Pizza
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Chiara La Morgia
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Elena Antelmi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Paola Loguercio Polosa
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari 70126, Italy
| | - Emmanuel Mignot
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94304, USA
| | - Claudia Zanna
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Giuseppe Plazzi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna 40139, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40139, Italy
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27
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Functional Interplay between Methyltransferases and Inflammasomes in Inflammatory Responses and Diseases. Int J Mol Sci 2021; 22:ijms22147580. [PMID: 34299198 PMCID: PMC8306412 DOI: 10.3390/ijms22147580] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 02/08/2023] Open
Abstract
An inflammasome is an intracellular protein complex that is activated in response to a pathogenic infection and cellular damage. It triggers inflammatory responses by promoting inflammatory cell death (called pyroptosis) and the secretion of pro-inflammatory cytokines, interleukin (IL)-1β and IL-18. Many types of inflammasomes have been identified and demonstrated to play a central role in inducing inflammatory responses, leading to the onset and progression of numerous inflammatory diseases. Methylation is a biological process by which methyl groups are transferred from methyl donors to proteins, nucleic acids, and other cellular molecules. Methylation plays critical roles in various biological functions by modulating gene expression, protein activity, protein localization, and molecular stability, and aberrant regulation of methylation causes deleterious outcomes in various human diseases. Methylation is a key determinant of inflammatory responses and diseases. This review highlights the current understanding of the functional relationship between inflammasome regulation and methylation of cellular molecules in inflammatory responses and diseases.
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28
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Ghosh S, Tourtellotte WG. The Complex Clinical and Genetic Landscape of Hereditary Peripheral Neuropathy. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2021; 16:487-509. [PMID: 33497257 DOI: 10.1146/annurev-pathol-030320-100822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hereditary peripheral neuropathy (HPN) is a complex group of neurological disorders caused by mutations in genes expressed by neurons and Schwann cells. The inheritance of a single mutation or multiple mutations in several genes leads to disease phenotype. Patients exhibit symptoms during development, at an early age or later in adulthood. Most of the mechanistic understanding about these neuropathies comes from animal models and histopathological analyses of postmortem human tissues. Diagnosis is often very complex due to the heterogeneity and overlap in symptoms and the frequent overlap between various genes and different mutations they possess. Some symptoms in HPN are common through different subtypes such as axonal degeneration, demyelination, and loss of motor and sensory neurons, leading to similar physiologic abnormalities. Recent advances in gene-targeted therapies, genetic engineering, and next-generation sequencing have augmented our understanding of the underlying pathogenetic mechanisms of HPN.
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Affiliation(s)
- Soumitra Ghosh
- Department of Pathology and Laboratory Medicine, Neurology, and Neurological Surgery, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA;
| | - Warren G Tourtellotte
- Department of Pathology and Laboratory Medicine, Neurology, and Neurological Surgery, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA;
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29
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Jones R, Wijesinghe S, Wilson C, Halsall J, Liloglou T, Kanhere A. A long intergenic non-coding RNA regulates nuclear localization of DNA methyl transferase-1. iScience 2021; 24:102273. [PMID: 33851096 PMCID: PMC8022221 DOI: 10.1016/j.isci.2021.102273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 12/21/2020] [Accepted: 03/02/2021] [Indexed: 01/10/2023] Open
Abstract
DNA methyl transferase-1 or DNMT1 maintains DNA methylation in the genome and is important for regulating gene expression in cells. Aberrant changes in DNMT1 activity and DNA methylation are commonly observed in cancers and many other diseases. Recently, a number of long intergenic non-protein-coding RNAs or lincRNAs have been shown to play a role in regulating DNMT1 activity. CCDC26 is a nuclear lincRNA that is frequently mutated in cancers and is a hotbed for disease-associated single nucleotide changes. However, the functional mechanism of CCDC26 is not understood. Here, we show that this lincRNA is concentrated on the nuclear periphery. Strikingly, in the absence of CCDC26 lincRNA, DNMT1 is mis-located in the cytoplasm, and the genomic DNA is significantly hypomethylated. This is accompanied by double-stranded DNA breaks and increased cell death. These results point to a previously unrecognized mechanism of lincRNA-mediated subcellular localization of DNMT1 and regulation of DNA methylation.
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Affiliation(s)
- Rhian Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Susanne Wijesinghe
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham, UK
| | - Claire Wilson
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John Halsall
- Institute of Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Triantafillos Liloglou
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Aditi Kanhere
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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30
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Chen J, Liu J, Jiang J, Qian S, Song J, Kabara R, Delo I, Serino G, Liu F, Hua Z, Zhong X. F-box protein CFK1 interacts with and degrades de novo DNA methyltransferase in Arabidopsis. THE NEW PHYTOLOGIST 2021; 229:3303-3317. [PMID: 33216996 PMCID: PMC7902366 DOI: 10.1111/nph.17103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 11/16/2020] [Indexed: 05/07/2023]
Abstract
DNA methylation plays crucial roles in cellular development and stress responses through gene regulation and genome stability control. Precise regulation of DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), the de novo Arabidopsis DNA methyltransferase, is crucial to maintain DNA methylation homeostasis to ensure genome integrity. Compared with the extensive studies on DRM2 targeting mechanisms, little information is known regarding the quality control of DRM2 itself. Here, we conducted yeast two-hybrid screen assay and identified an E3 ligase, COP9 INTERACTING F-BOX KELCH 1 (CFK1), as a novel DRM2-interacting partner and targets DRM2 for degradation via the ubiquitin-26S proteasome pathway in Arabidopsis thaliana. We also performed whole genome bisulfite sequencing (BS-seq) to determine the biological significance of CFK1-mediated DRM2 degradation. Loss-of-function CFK1 leads to increased DRM2 protein abundance and overexpression of CFK1 showed reduced DRM2 protein levels. Consistently, CFK1 overexpression induces genome-wide CHH hypomethylation and transcriptional de-repression at specific DRM2 target loci. This study uncovered a distinct mechanism regulating de novo DNA methyltransferase by CFK1 to control DNA methylation level.
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Affiliation(s)
- Jiani Chen
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
| | - Jie Liu
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
| | - Jianjun Jiang
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu 210014, China
| | - Shuiming Qian
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
| | - Jingwen Song
- Department of Environmental and Plant Biology & Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
| | - Rachel Kabara
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Isabel Delo
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Giovanna Serino
- Department of Biology and Biotechnology, Sapienza Università di Roma, 00185 Rome, Italy
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu 210014, China
| | - Zhihua Hua
- Department of Environmental and Plant Biology & Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
| | - Xuehua Zhong
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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31
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Camacho-Ordonez N, Ballestar E, Timmers HTM, Grimbacher B. What can clinical immunology learn from inborn errors of epigenetic regulators? J Allergy Clin Immunol 2021; 147:1602-1618. [PMID: 33609625 DOI: 10.1016/j.jaci.2021.01.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/20/2022]
Abstract
The epigenome is at the interface between environmental factors and the genome, regulating gene transcription, DNA repair, and replication. Epigenetic modifications play a crucial role in establishing and maintaining cell identity and are especially crucial for neurology, musculoskeletal integrity, and the function of the immune system. Mutations in genes encoding for the components of the epigenetic machinery lead to the development of distinct disorders, especially involving the central nervous system and host defense. In this review, we focus on the role of epigenetic modifications for the function of the immune system. By studying the immune phenotype of patients with monogenic mutations in components of the epigenetic machinery (inborn errors of epigenetic regulators), we demonstrate the importance of DNA methylation, histone modifications, chromatin remodeling, noncoding RNAs, and mRNA processing for immunity. Moreover, we give a short overview on therapeutic strategies targeting the epigenome.
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Affiliation(s)
- Nadezhda Camacho-Ordonez
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain
| | - H Th Marc Timmers
- German Cancer Consortium (DKTK), partner site Freiburg, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Urology, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST- Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Freiburg, Germany.
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32
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Kikuchi JK, Nagashima Y, Mano T, Ishiura H, Hayashi T, Shimizu J, Matsukawa T, Ichikawa Y, Takahashi Y, Karino S, Kanbayashi T, Kira J, Goto J, Tsuji S. Cerebellar Ataxia as a Common Clinical Presentation Associated with DNMT1 p.Y511H and a Review of the Literature. J Mol Neurosci 2021; 71:1796-1801. [PMID: 33433851 DOI: 10.1007/s12031-020-01784-5] [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: 07/24/2020] [Accepted: 12/23/2020] [Indexed: 10/22/2022]
Abstract
The phenotypes of patients with disease-associated variants in DNMT1 have been classified into two syndromes: hereditary sensory and autonomic neuropathy type 1E (HSAN1E, MIM614116, https://www.omim.org/ ) and autosomal dominant cerebellar ataxia, deafness, and narcolepsy (ADCA-DN, MIM604121). The amino acid codon 511 is a hotspot, and p.Y511C is the most frequently observed disease-associated variant among those in HSAN1E patients, whereas there have been only a few reports on patients with p.Y511H. In this study, we report on the cases of a kindred carrying the DNMT1 variant NM_001130823.2:c.1531 T > C (p.Y511H) presenting with the ADCA-DN phenotype. The review of the literature further revealed that later ages at onset and the presence of cerebellar ataxia are the main characteristics of patients carrying the DNMT1 p.Y511H as compared with those carrying DNMT1 p.Y511C. Although HSAN1E and ADCA-DN are proposed to be called DNMT1-complex disorders owing to their overlapping symptoms, this finding suggests a distinct genotype-phenotype correlation regarding the DNMT1 p.Y511H and p.Y511C variants.
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Affiliation(s)
- Junko Kanda Kikuchi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yu Nagashima
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Tatsuo Mano
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Toshihiro Hayashi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Jun Shimizu
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Takashi Matsukawa
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yaeko Ichikawa
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yuji Takahashi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | | | - Takashi Kanbayashi
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Japan
| | - Junichi Kira
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University, 3-1-1, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Jun Goto
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan.,International University of Health and Welfare, Chiba, 286-8686, Japan
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33
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Kumar R, Deshmukh PS, Sharma S, Banerjee BD. Effect of mobile phone signal radiation on epigenetic modulation in the hippocampus of Wistar rat. ENVIRONMENTAL RESEARCH 2021; 192:110297. [PMID: 33035560 DOI: 10.1016/j.envres.2020.110297] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 06/11/2023]
Abstract
Exponential increase in mobile phone uses, given rise to public concern regarding the alleged deleterious health hazards as a consequence of prolonged exposure. In 2018, the U.S. National toxicology program reported, two year toxicological studies for potential health hazards from exposure to cell phone radiations. Epigenetic modulations play a critical regulatory role in many cellular functions and pathological conditions. In this study, we assessed the dose-dependent and frequency-dependent epigenetic modulation (DNA and Histone methylation) in the hippocampus of Wistar rats. A Total of 96 male Wistar rats were segregated into 12 groups exposed to 900 MHz, 1800 MHz and 2450 MHz RF-MW at a specific absorption rate (SAR) of 5.84 × 10-4 W/kg, 5.94 × 10-4 W/kg and 6.4 × 10-4 W/kg respectively for 2 h per day for 1-month, 3-month and 6-month periods. At the end of the exposure duration, animals were sacrificed to collect the hippocampus. Global hippocampal DNA methylation and histone methylation were estimated by ELISA. However, DNA methylating enzymes, DNA methyltransferase1 (DNMT1) and histone methylating enzymes euchromatic histone methylthransferase1 (EHMT1) expression was evaluated by real-time PCR, as well as further validated with Western blot. Alteration in epigenetic modulation was observed in the hippocampus. Global DNA methylation was decreased and histone methylation was increased in the hippocampus. We observed that microwave exposure led to significant epigenetic modulations in the hippocampus with increasing frequency and duration of exposure. Microwave exposure with increasing frequency and exposure duration brings significant (p < 0.05) epigenetic modulations which alters gene expression in the hippocampus.
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Affiliation(s)
- Ranjeet Kumar
- Environmental Biochemistry and Molecular Biology Laboratory, Department of Biochemistry, University College of Medical Sciences & GTB Hospital (University of Delhi), Dilshad Garden, Delhi, 110095, India.
| | - Pravin S Deshmukh
- Environmental Biochemistry and Molecular Biology Laboratory, Department of Biochemistry, University College of Medical Sciences & GTB Hospital (University of Delhi), Dilshad Garden, Delhi, 110095, India.
| | - Sonal Sharma
- Department of Pathology, University College of Medical Sciences & GTB Hospital (University of Delhi), Dilshad Garden, Delhi, 110095, India.
| | - Basu Dev Banerjee
- Environmental Biochemistry and Molecular Biology Laboratory, Department of Biochemistry, University College of Medical Sciences & GTB Hospital (University of Delhi), Dilshad Garden, Delhi, 110095, India.
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34
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Koriath C, Kenny J, Adamson G, Druyeh R, Taylor W, Beck J, Quinn L, Mok TH, Dimitriadis A, Norsworthy P, Bass N, Carter J, Walker Z, Kipps C, Coulthard E, Polke JM, Bernal-Quiros M, Denning N, Thomas R, Raybould R, Williams J, Mummery CJ, Wild EJ, Houlden H, Tabrizi SJ, Rossor MN, Hummerich H, Warren JD, Rowe JB, Rohrer JD, Schott JM, Fox NC, Collinge J, Mead S. Predictors for a dementia gene mutation based on gene-panel next-generation sequencing of a large dementia referral series. Mol Psychiatry 2020; 25:3399-3412. [PMID: 30279455 PMCID: PMC6330090 DOI: 10.1038/s41380-018-0224-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/28/2018] [Accepted: 07/18/2018] [Indexed: 11/09/2022]
Abstract
Next-generation genetic sequencing (NGS) technologies facilitate the screening of multiple genes linked to neurodegenerative dementia, but there are few reports about their use in clinical practice. Which patients would most profit from testing, and information on the likelihood of discovery of a causal variant in a clinical syndrome, are conspicuously absent from the literature, mostly for a lack of large-scale studies. We applied a validated NGS dementia panel to 3241 patients with dementia and healthy aged controls; 13,152 variants were classified by likelihood of pathogenicity. We identified 354 deleterious variants (DV, 12.6% of patients); 39 were novel DVs. Age at clinical onset, clinical syndrome and family history each strongly predict the likelihood of finding a DV, but healthcare setting and gender did not. DVs were frequently found in genes not usually associated with the clinical syndrome. Patients recruited from primary referral centres were compared with those seen at higher-level research centres and a national clinical neurogenetic laboratory; rates of discovery were comparable, making selection bias unlikely and the results generalisable to clinical practice. We estimated penetrance of DVs using large-scale online genomic population databases and found 71 with evidence of reduced penetrance. Two DVs in the same patient were found more frequently than expected. These data should provide a basis for more informed counselling and clinical decision making.
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Affiliation(s)
- C Koriath
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK
| | - J Kenny
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK
| | - G Adamson
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK
| | - R Druyeh
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK
| | - W Taylor
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK
| | - J Beck
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK
| | - L Quinn
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK
| | - T H Mok
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK
| | - A Dimitriadis
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK
| | - P Norsworthy
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK
| | - N Bass
- UCL Division of Psychiatry, Maple House, University College London, London, UK
| | - J Carter
- UCL Division of Psychiatry, Maple House, University College London, London, UK
| | - Z Walker
- UCL Division of Psychiatry, Maple House, University College London, London, UK
- Essex Partnership University NHS Foundation Trust, Essex, SS11 7XX, UK
| | - C Kipps
- Wessex Neurological Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - E Coulthard
- Institute of Clinical Neuroscience, University of Bristol, Level 1 Learning and Research Building, Bristol, BS10 5NB, UK
| | - J M Polke
- Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - M Bernal-Quiros
- Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - N Denning
- Division of Psychological Medicine & Clinical Neurosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - R Thomas
- Division of Psychological Medicine & Clinical Neurosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - R Raybould
- Division of Psychological Medicine & Clinical Neurosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - J Williams
- Division of Psychological Medicine & Clinical Neurosciences, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff, CF24 4HQ, UK
| | - C J Mummery
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - E J Wild
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - H Houlden
- Neurogenetics Laboratory, National Hospital for Neurology and Neurosurgery, Queen Square, London, WC1N 3BG, UK
| | - S J Tabrizi
- Huntington's Disease Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - M N Rossor
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - H Hummerich
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK
| | - J D Warren
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - J B Rowe
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0SZ, UK
- Medical Research Council Cognition and Brain Sciences Unit, Cambridge, CB2 7EF, UK
| | - J D Rohrer
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - J M Schott
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - N C Fox
- Dementia Research Centre, Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - J Collinge
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK
| | - S Mead
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, Courtauld Building, London, W1W 7FF, UK.
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Hornemann T. Mini review: Lipids in Peripheral Nerve Disorders. Neurosci Lett 2020; 740:135455. [PMID: 33166639 DOI: 10.1016/j.neulet.2020.135455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 02/06/2023]
Abstract
Neurons are polarized cells whose fundamental functions are to receive, conduct and transmit signals. In bilateral animals, the nervous system is divided into the central (CNS) and peripheral (PNS) nervous system. The main function of the PNS is to connect the CNS to the limbs and organs, essentially serving as a relay between the brain and spinal cord and the rest of the body. Sensory axons can be up to 3 feet in length. Because of its long-reaching and complex structure, the peripheral nervous system (PNS) is exposed and vulnerable to many genetic, metabolic and environmental predispositions. Lipids and lipid intermediates are essential components of nerves. About 50 % of the brain dry weight consist of lipids, which makes it the second highest lipid rich tissue after adipose tissue. However, the role of lipids in neurological disorders in particular of the peripheral nerves is not well understood. This review aims to provide an overview about the role of lipids in the disorders of the PNS.
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Affiliation(s)
- Th Hornemann
- Institute for Clinical Chemistry, University Hospital and University Zurich, 8091, Zürich, Switzerland.
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36
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Chang KC, Kuo YC, Hsueh HW, Lee NC, Yang CC, Hsieh ST, Chao CC. Autosomal dominant cerebellar ataxia, deafness, and narcolepsy with amenorrhea, subclinical optic atrophy, and electroencephalographic abnormality: A case report. eNeurologicalSci 2020; 21:100271. [PMID: 32984563 PMCID: PMC7493042 DOI: 10.1016/j.ensci.2020.100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/01/2020] [Accepted: 09/04/2020] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kai-Chieh Chang
- Department of Neurology, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Yih-Chih Kuo
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsueh-Wen Hsueh
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
- Corresponding author at: Department of Neurology, National Taiwan University Hospital, No. 7 Chung-Shan South Road, Taipei 10002, Taiwan.
| | - Ni-Chung Lee
- Department of Pediatric and Medical Genetics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chih-Chao Yang
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Sung-Tsang Hsieh
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chi-Chao Chao
- Department of Neurology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
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37
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Guirguis AA, Liddicoat BJ, Dawson MA. The old and the new: DNA and RNA methylation in normal and malignant hematopoiesis. Exp Hematol 2020; 90:1-11. [PMID: 32961299 DOI: 10.1016/j.exphem.2020.09.193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022]
Abstract
Whilst DNA cytosine methylation is the oldest and most well-studied epigenetic modification, basking in its glory days, it may be soon overshadowed by the new kid on the block: RNA adenosine methylation. This juxtaposition is indeed superficial, and a deep exploration toward the fundamental requirements for these essential epigenetic marks provides a clear perspective on their converging and synergistic roles. The recent discovery that both of these modifications are essential for preventing inappropriate activation of the intracellular innate immune responses to endogenous transcripts has provided a lot of interest in targeting them therapeutically as a means to improve cancer immunogenicity. Here we discuss the potential physiological function for DNA and RNA methylation in normal hematopoiesis and how these pervasive epigenetic marks are exploited in cancer, and provide suggestions for future research with a focus on leveraging this knowledge to uncover novel therapeutic targets.
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Affiliation(s)
- Andrew A Guirguis
- Peter MacCallum Cancer Centre, Melbourne Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia.
| | - Brian J Liddicoat
- Peter MacCallum Cancer Centre, Melbourne Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia.
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia; Centre for Cancer Research, University of Melbourne, Melbourne, Australia.
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Bi H, Hojo K, Watanabe M, Yee C, Maski K, Saba S, Graff-Radford J, Machulda MM, St Louis EK, Humes IS, Flanagan EP, Nicolau S, Jones DT, Patterson MC, Kotagal S, Raz Y, Niu Z, Li J, Klein CJ. Expanded genetic insight and clinical experience of DNMT1-complex disorder. NEUROLOGY-GENETICS 2020; 6:e456. [PMID: 32754641 PMCID: PMC7357420 DOI: 10.1212/nxg.0000000000000456] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/30/2020] [Indexed: 11/16/2022]
Abstract
Objective To report novel causal mutations, expanded clinical phenotypes, and clinical management of DNA methyltransferase 1 (DNMT1)-complex disorder. Methods Neurophysiologic testing, imaging, and genetic findings were summarized in clinical context for 5 cases with DNMT1-complex disorder. Results We identified 2 novel DNMT1 mutations (p.E510K and p.P1546A) by whole-exome sequencing (WES). Case 1 (p.E510K) presented with childhood ataxia, treatment-refractory seizures, and rapid cognitive decline in his 50s. Case 2 also had childhood onset and presented with seizures, language regression, hearing loss, narcolepsy with cataplexy symptoms, optic atrophy, sensory neuropathy, and hypogammaglobulinemia requiring IV immunoglobulin. Case 2 (p.P1546A) was identified with a de novo and the first mutation residing outside the targeting sequence domain. Case 3 (p.A570V) had paralytic asymmetric onset attacks triggered by emotionality and lasting sometimes for weeks. Neuropsychological testing showed executive dysfunction localizing to frontosubcortical and frontoparietal structures. He gradually developed left predominant brain atrophy. MRI showed T2 hyperintense lesions that enhanced on T1 postgadolinium images, and brain PET showed hypometabolism in atrophied regions. Case 4 (p.T497P) underwent left cochlear implant, resulting in significant hearing improvements at all tested frequencies (250–6,000 Hz). Case 5 (p.Y511H) had profound gait ataxia with posterior column atrophy of the spinal cord and abnormal evoked potentials primarily affecting the fasciculus gracilis. Conclusions Broader application of WES further expands genotype-phenotype correlations of DNMT1-complex disorder. Two mutations are identified with early childhood onsets. The expanded new phenotypes include asymmetric brain hemiatrophy with parenchymal gadolinium enhancement, spinal cord atrophy, prolonged cataplectic spells, and hypogammaglobulinemia. Hearing loss treatment by cochlear implantation is helpful and should be considered.
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Affiliation(s)
- Hongyan Bi
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Kaori Hojo
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Masashi Watanabe
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Christina Yee
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Kiran Maski
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Sadaf Saba
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Jonathan Graff-Radford
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Mary M Machulda
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Erik K St Louis
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Ilona Spitsyna Humes
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Eoin P Flanagan
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Stefan Nicolau
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - David T Jones
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Marc C Patterson
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Suresh Kotagal
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Yael Raz
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Zhiyv Niu
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Jun Li
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
| | - Christopher J Klein
- Department of Neurology (H.B., J.G.-R., E.K.S.L., E.P.F., S.N., D.T.J., M.C.P., S.K., C.J.K.), Mayo Clinic, Rochester, MN; Department of Neurology (H.B.), Beijing Friendship Hospital, China; Division of Neuropsychiatry (K.H.), Harima Sanatorium, Hyogo, Japan; Department of Neurology (M.W.), Ehime Prefectural Central Hospital, Matsuyama, Japan; Harvard Medical School (C.Y., K.M.), Boston Children's Hospital, MA; Center for Molecular Medicine and Genetics (S.S.), School of Medicine, Wayne State University, Detroit, MI; Department of Psychology (M.M.M.), Mayo Clinic, Rochester, MN; Atrium Health (I.S.H.), Neurosciences Institute, Concord, NC; Deapartment of Head and Neck Surgery (Y.R.), Oregon Health and Science University, Portland; Department of Laboratory Medicine and Pathology (Z.N., C.J.K.), Mayo Clinic, Rochester, MN; and Department of Neurology and Translational Neuroscience Initiative (J.L.), School of Medicine. Wayne State University, Detroit, MI
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Coelho P, Oliveira Santos M. First Portuguese patient presenting with hereditary sensory and autonomic neuropathy type 1E associated with a novel mutation in DNMT1 gene. Neurol Sci 2020; 41:1289-1290. [DOI: 10.1007/s10072-019-04179-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 11/25/2019] [Indexed: 11/30/2022]
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Postiglione E, Antelmi E, Pizza F, Vandi S, La Morgia C, Carelli V, Nassetti S, Seri M, Plazzi G. Cataplexy and ataxia: red flags for the diagnosis of DNA methyltransferase 1 mutation. J Clin Sleep Med 2020; 16:143-147. [DOI: 10.5664/jcsm.8140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Emanuela Postiglione
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna,Bologna, Italy
| | - Elena Antelmi
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna,Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy
| | - Fabio Pizza
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna,Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy
| | - Stefano Vandi
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna,Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy
| | - Chiara La Morgia
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna,Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy
| | - Valerio Carelli
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna,Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy
| | | | - Marco Seri
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Giuseppe Plazzi
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna,Bologna, Italy
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Dolen EK, McGinnis JH, Tavory RN, Weiss JA, Switzer RL. Disease-Associated Mutations G589A and V590F Relieve Replication Focus Targeting Sequence-Mediated Autoinhibition of DNA Methyltransferase 1. Biochemistry 2019; 58:5151-5159. [PMID: 31804802 DOI: 10.1021/acs.biochem.9b00749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In eukaryotes, the most common epigenetic DNA modification is methylation of carbon 5 of cytosines, predominantly in CpG dinucleotides. Methylation patterns are established and maintained by a family of proteins known as DNA methyltransferases (DNMTs). DNA methylation is an important epigenetic mark associated with gene repression, and disruption of the normal DNA methylation pattern is known to play a role in several disease states. Methylation patterns are primarily maintained by DNMT1, which possesses specificity for methylation of hemimethylated DNA. DNMT1 is a multidomain protein with a C-terminal catalytic methyltransferase domain and a large N-terminal regulatory region. The replication focus targeting sequence (RFTS) domain, found in the regulatory region, is an endogenous inhibitor of DNMT1 activity. Recently, several mutations in the RFTS domain were shown to be causal for two adult onset neurodegenerative diseases; however, little is known about the impact of these mutations on the structure and function of DNMT1. Two of these mutations, G589A and V590F, are associated with development of autosomal dominant cerebellar ataxia, deafness, and narcolepsy (ADCA-DN). We have successfully expressed and purified G589A and V590F DNMT1 for in vitro studies. The mutations significantly decrease the thermal stability of DNMT1, yet the mutant proteins exhibit 2.5-3.5-fold increases in DNA binding affinity. In addition, the mutations weaken RFTS-mediated inhibition of DNA methylation activity. Taken together, these data suggest these disease-associated mutations decrease protein stability and, at least partially, relieve normal RFTS-mediated autoinhibition of DNMT1.
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Affiliation(s)
- Emma K Dolen
- Department of Chemistry , Bucknell University , Lewisburg , Pennsylvania 17837 , United States
| | - James H McGinnis
- Program in Cell Biology/Biochemistry , Bucknell University , Lewisburg , Pennsylvania 17837 , United States
| | - Rachel N Tavory
- Program in Cell Biology/Biochemistry , Bucknell University , Lewisburg , Pennsylvania 17837 , United States
| | - Jill A Weiss
- Program in Cell Biology/Biochemistry , Bucknell University , Lewisburg , Pennsylvania 17837 , United States
| | - Rebecca L Switzer
- Department of Chemistry , Bucknell University , Lewisburg , Pennsylvania 17837 , United States
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Malloy MA, Kochmanski JJ, Jones TR, Colacino JA, Goodrich JM, Dolinoy DC, Svoboda LK. Perinatal Bisphenol A Exposure and Reprogramming of Imprinted Gene Expression in the Adult Mouse Brain. Front Genet 2019; 10:951. [PMID: 31649729 PMCID: PMC6796247 DOI: 10.3389/fgene.2019.00951] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/05/2019] [Indexed: 12/11/2022] Open
Abstract
Genomic imprinting, a phenomenon by which genes are expressed in a monoallelic, parent-of-origin-dependent fashion, is critical for normal brain development. Expression of imprinted genes is regulated via epigenetic mechanisms, including DNA methylation (5-methylcytosine, 5mC), and disruptions in imprinting can lead to disease. Early-life exposure to the endocrine disrupting chemical bisphenol A (BPA) is associated with abnormalities in brain development and behavior, as well as with disruptions in epigenetic patterning, including 5mC and DNA hydroxymethylation (5-hydroxymethylcytosine, 5hmC). Using an established mouse model of perinatal environmental exposure, the objective of this study was to examine the effects of perinatal BPA exposure on epigenetic regulation of imprinted gene expression in adult mice. Two weeks prior to mating, dams were assigned to control chow or chow containing an environmentally relevant dose (50 µg/kg) of BPA. Exposure continued until offspring were weaned at post-natal day 21, and animals were followed until 10 months of age. Expression of three imprinted genes—Pde10a, Ppp1r9a, and Kcnq1, as well as three genes encoding proteins critical for regulation of 5mC and 5hmC—Dnmt1, Tet1, and Tet2, were evaluated in the right cortex and midbrain using qRT-PCR. Perinatal BPA exposure was associated with a significant increase in adult Kcnq1 (p = 0.04) and Dnmt1 (p = 0.02) expression in the right cortex, as well as increased expression of Tet2 in the midbrain (p = 0.03). Expression of Tet2 and Kcnq1 were positively correlated in the midbrain. Analysis of 5mC and 5hmC at the Kcnq1 locus was conducted in parallel samples using standard and oxidative bisulfite conversion followed by pyrosequencing. This analysis revealed enrichment of both 5mC and 5hmC at this locus in both brain regions. No significant changes in 5mC and 5hmC at Kcnq1 were observed with perinatal BPA exposure. Together, these data suggest that perinatal BPA exposure results in altered expression of Kcnq1, Dnmt1, and Tet2 in the adult mouse brain. Further studies with larger sample sizes are necessary to understand the mechanistic basis for these changes, as well as to determine the implications they have for brain development and function.
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Affiliation(s)
- Maureen A Malloy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Joseph J Kochmanski
- Department of Translational Science & Molecular Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Tamara R Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States.,Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Laurie K Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
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43
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The diverse roles of DNA methylation in mammalian development and disease. Nat Rev Mol Cell Biol 2019; 20:590-607. [PMID: 31399642 DOI: 10.1038/s41580-019-0159-6] [Citation(s) in RCA: 1129] [Impact Index Per Article: 225.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 12/22/2022]
Abstract
DNA methylation is of paramount importance for mammalian embryonic development. DNA methylation has numerous functions: it is implicated in the repression of transposons and genes, but is also associated with actively transcribed gene bodies and, in some cases, with gene activation per se. In recent years, sensitive technologies have been developed that allow the interrogation of DNA methylation patterns from a small number of cells. The use of these technologies has greatly improved our knowledge of DNA methylation dynamics and heterogeneity in embryos and in specific tissues. Combined with genetic analyses, it is increasingly apparent that regulation of DNA methylation erasure and (re-)establishment varies considerably between different developmental stages. In this Review, we discuss the mechanisms and functions of DNA methylation and demethylation in both mice and humans at CpG-rich promoters, gene bodies and transposable elements. We highlight the dynamic erasure and re-establishment of DNA methylation in embryonic, germline and somatic cell development. Finally, we provide insights into DNA methylation gained from studying genetic diseases.
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44
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Jönsson ME, Ludvik Brattås P, Gustafsson C, Petri R, Yudovich D, Pircs K, Verschuere S, Madsen S, Hansson J, Larsson J, Månsson R, Meissner A, Jakobsson J. Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors. Nat Commun 2019; 10:3182. [PMID: 31320637 PMCID: PMC6639357 DOI: 10.1038/s41467-019-11150-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 06/20/2019] [Indexed: 01/14/2023] Open
Abstract
DNA methylation contributes to the maintenance of genomic integrity in somatic cells, in part through the silencing of transposable elements. In this study, we use CRISPR-Cas9 technology to delete DNMT1, the DNA methyltransferase key for DNA methylation maintenance, in human neural progenitor cells (hNPCs). We observe that inactivation of DNMT1 in hNPCs results in viable, proliferating cells despite a global loss of DNA CpG-methylation. DNA demethylation leads to specific transcriptional activation and chromatin remodeling of evolutionarily young, hominoid-specific LINE-1 elements (L1s), while older L1s and other classes of transposable elements remain silent. The activated L1s act as alternative promoters for many protein-coding genes involved in neuronal functions, revealing a hominoid-specific L1-based transcriptional network controlled by DNA methylation that influences neuronal protein-coding genes. Our results provide mechanistic insight into the role of DNA methylation in silencing transposable elements in somatic human cells, as well as further implicating L1s in human brain development and disease. DNA methylation plays an important role in silencing transposable elements. Here the authors find that loss of DNMT1 and DNA methylation leads to transcriptional activation and chromatin remodelling of evolutionarily young—hominoid-specific —LINE-1 elements which then act as alternative promoters for neuronal genes.
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Affiliation(s)
- Marie E Jönsson
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden
| | - Per Ludvik Brattås
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden
| | - Charlotte Gustafsson
- Center for Hematology and Regenerative Medicine Huddinge, Karolinska Institute, 141 52, Stockholm, Sweden
| | - Rebecca Petri
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden
| | - David Yudovich
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, BMC A12, Lund University, 221 84, Lund, Sweden
| | - Karolina Pircs
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden
| | - Shana Verschuere
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden
| | - Sofia Madsen
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden
| | - Jenny Hansson
- Laboratory of Proteomic Hematology, Department of Laboratory Medicine and Lund Stem Cell Center, BMC B12, Lund University, 221 84, Lund, Sweden
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, BMC A12, Lund University, 221 84, Lund, Sweden
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine Huddinge, Karolinska Institute, 141 52, Stockholm, Sweden
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Johan Jakobsson
- Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden.
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Santos‐Bezerra DP, Admoni SN, Mori RC, Pelaes TS, Perez RV, Machado CG, Monteiro MB, Parisi MC, Pavin EJ, Queiroz MS, Passarelli M, Machado UF, Correa‐Giannella ML. Genetic variants in DNMT1 and the risk of cardiac autonomic neuropathy in women with type 1 diabetes. J Diabetes Investig 2019; 10:985-989. [PMID: 30548403 PMCID: PMC6626951 DOI: 10.1111/jdi.12988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/29/2018] [Accepted: 12/09/2018] [Indexed: 11/28/2022] Open
Abstract
AIMS/INTRODUCTION Epigenetics participate in the pathogenesis of metabolic memory, a situation in which hyperglycemia exerts prolonged deleterious effects even after its normalization. We tested the hypothesis that genetic variants in an epigenetic gene could predispose to diabetes complications. MATERIAL AND METHODS We assessed the frequency of five single-nucleotide polymorphisms in the gene encoding deoxyribonucleic acid methytransferase 1 (DNMT1; rs8112895, rs7254567, rs11085721, rs17291414 and rs10854076), and their associations with diabetic kidney disease, retinopathy, distal polyneuropathy and autonomic cardiovascular neuropathy in 359 individuals with long-term type 1 diabetes. RESULTS None of the single-nucleotide polymorphisms studied was significantly associated with the presence of chronic complications in the overall population. However, after sex stratification, the minor allele C of rs11085721 conferred risk for cardiovascular neuropathy in women after adjustment for confounding variables (odds ratio 2.32; 95% confidence interval 1.26-4.33; P = 0.006). CONCLUSIONS The fact that heterozygous mutations in DNMT1 are associated with hereditary sensory autonomic neuropathy provides plausibility to the present finding. If confirmed in independent samples, it suggests that genetic variants in epigenetic genes might predispose to more or fewer epigenetic changes in the face of similar metabolic derangements triggered by hyperglycemia, constituting the "genetics of epigenetics" for microvascular diabetes complications.
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Affiliation(s)
- Daniele Pereira Santos‐Bezerra
- Laboratory of Carbohydrates and Radioimuneassays (LIM‐18)Clinical HospitalMedical SchoolUniversity of Sao PauloUniversidade de Sao PauloSao PauloBrazil
| | - Sharon Nina Admoni
- Laboratory of Carbohydrates and Radioimuneassays (LIM‐18)Clinical HospitalMedical SchoolUniversity of Sao PauloUniversidade de Sao PauloSao PauloBrazil
- Division of EndocrinologyClinical HospitalMedical SchoolUniversity of Sao PauloUniversidade de Sao PauloSao PauloBrazil
| | - Rosana Cristina Mori
- Department of Physiology and BiophysicsInstitute of Biomedical SciencesUniversity of Sao PauloUniversity of São PauloSão PauloBrazil
| | - Tatiana Souza Pelaes
- Laboratory of Carbohydrates and Radioimuneassays (LIM‐18)Clinical HospitalMedical SchoolUniversity of Sao PauloUniversidade de Sao PauloSao PauloBrazil
| | - Ricardo Vesoni Perez
- Laboratory of Carbohydrates and Radioimuneassays (LIM‐18)Clinical HospitalMedical SchoolUniversity of Sao PauloUniversidade de Sao PauloSao PauloBrazil
| | | | - Maria Beatriz Monteiro
- Laboratory of Carbohydrates and Radioimuneassays (LIM‐18)Clinical HospitalMedical SchoolUniversity of Sao PauloUniversidade de Sao PauloSao PauloBrazil
| | - Maria Candida Parisi
- Department of Internal MedicineFaculty of Medical SciencesState University of Campinas (UNICAMP)CampinasSao PauloBrazil
| | - Elizabeth Joao Pavin
- Department of Internal MedicineFaculty of Medical SciencesState University of Campinas (UNICAMP)CampinasSao PauloBrazil
| | - Marcia Silva Queiroz
- Division of EndocrinologyClinical HospitalMedical SchoolUniversity of Sao PauloUniversidade de Sao PauloSao PauloBrazil
| | - Marisa Passarelli
- Laboratory of Carbohydrates and Radioimuneassays (LIM‐18)Clinical HospitalMedical SchoolUniversity of Sao PauloSao PauloBrazil
| | - Ubiratan Fabres Machado
- Department of Physiology and BiophysicsInstitute of Biomedical SciencesUniversity of Sao PauloUniversity of São PauloSão PauloBrazil
| | - Maria Lucia Correa‐Giannella
- Laboratory of Carbohydrates and Radioimuneassays (LIM‐18)Clinical HospitalMedical SchoolUniversity of Sao PauloUniversidade de Sao PauloSao PauloBrazil
- Department of Post‐graduation in MedicineNove de Julho University (UNINOVE)Sao PauloBrazil
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46
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Effect of Disease-Associated Germline Mutations on Structure Function Relationship of DNA Methyltransferases. Genes (Basel) 2019; 10:genes10050369. [PMID: 31091831 PMCID: PMC6562416 DOI: 10.3390/genes10050369] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 12/21/2022] Open
Abstract
Despite a large body of evidence supporting the role of aberrant DNA methylation in etiology of several human diseases, the fundamental mechanisms that regulate the activity of mammalian DNA methyltransferases (DNMTs) are not fully understood. Recent advances in whole genome association studies have helped identify mutations and genetic alterations of DNMTs in various diseases that have a potential to affect the biological function and activity of these enzymes. Several of these mutations are germline-transmitted and associated with a number of hereditary disorders, which are potentially caused by aberrant DNA methylation patterns in the regulatory compartments of the genome. These hereditary disorders usually cause neurological dysfunction, growth defects, and inherited cancers. Biochemical and biological characterization of DNMT variants can reveal the molecular mechanism of these enzymes and give insights on their specific functions. In this review, we introduce roles and regulation of DNA methylation and DNMTs. We discuss DNMT mutations that are associated with rare diseases, the characterized effects of these mutations on enzyme activity and provide insights on their potential effects based on the known crystal structure of these proteins.
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47
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Nguyen KV. Potential epigenomic co-management in rare diseases and epigenetic therapy. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:752-780. [PMID: 31079569 DOI: 10.1080/15257770.2019.1594893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The purpose of this review is to highlight the impact of the alternative splicing process on human disease. Epigenetic regulation determines not only what parts of the genome are expressed but also how they are spliced. The recent progress in the field of epigenetics has important implications for the study of rare diseases. The role of epigenetics in rare diseases is a key issue in molecular physiology and medicine because not only rare diseases can benefit from epigenetic research, but can also provide useful principles for other common and complex disorders such as cancer, cardiovascular, type 2 diabetes, obesity, and neurological diseases. Predominantly, epigenetic modifications include DNA methylation, histone modification, and RNA-associated silencing. These modifications in the genome regulate numerous cellular activities. Disruption of epigenetic regulation process can contribute to the etiology of numerous diseases during both prenatal and postnatal life. Here, I discuss current knowledge about this matter including some current epigenetic therapies and future directions in the field by emphasizing on the RNA-based therapy via antisense oligonucleotides to correct splicing defects.
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Affiliation(s)
- Khue Vu Nguyen
- a Department of Medicine, Biochemical Genetics and Metabolism, The Mitochondrial and Metabolic Disease Center, School of Medicine, University of California, San Diego , San Diego , CA , USA.,b Department of Pediatrics, UC San Diego School of Medicine , La Jolla , CA , USA
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48
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Wang B, Wang Z, Wang D, Zhang B, Ong SG, Li M, Yu W, Wang Y. krCRISPR: an easy and efficient strategy for generating conditional knockout of essential genes in cells. J Biol Eng 2019; 13:35. [PMID: 31049076 PMCID: PMC6480908 DOI: 10.1186/s13036-019-0150-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 02/15/2019] [Indexed: 02/06/2023] Open
Abstract
Background CRISPR/Cas9 system is a powerful tool for knocking out genes in cells. However, genes essential for cell survival cannot be directly knocked out. Traditionally, generation of conditional knockout cells requires multiple steps. Results In this study, we developed an easy and efficient strategy to generate conditional knockout cells by using double episomal vectors – one which expresses gRNA and Cas9 nuclease, and the other expresses an inducible rescue gene. Using this system which we named “krCRISPR” (knockout-rescue CRISPR), we showed that essential genes, HDAC3 and DNMT1, can be efficiently knocked out. When cells reach a desired confluency, the exogenous rescue genes can be silenced by the addition of doxycycline. Furthermore, the krCRISPR system enabled us to study the effects of the essential gene mutations on cells. We showed that the P507L mutation in DNMT1 led to downregulation of global DNA methylation in cells, indicating that it is a disease-causing mutation. Conclusions The krCRISPR system offers an easy and efficient platform that facilitates the study of essential genes’ function. Electronic supplementary material The online version of this article (10.1186/s13036-019-0150-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bei Wang
- 1MOE Key Laboratory of Contemporary Anthropology at School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 China
| | - Zishi Wang
- 1MOE Key Laboratory of Contemporary Anthropology at School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 China
| | - Daqi Wang
- 1MOE Key Laboratory of Contemporary Anthropology at School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 China
| | - Baolong Zhang
- 2Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508 China
| | - Sang-Ging Ong
- 3Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612 USA.,4Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, IL 60612 USA
| | - Mingqing Li
- 5The Key Lab of Reproduction Regulation of NPFPC in SIPPR, Institute of Reproduction & Development in Obstetrics & Gynecology Hospital, Fudan University, Shanghai, 200011 China
| | - Wenqiang Yu
- 2Shanghai Public Health Clinical Center & Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 201508 China
| | - Yongming Wang
- 1MOE Key Laboratory of Contemporary Anthropology at School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438 China
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DNA Methylation Clocks in Aging: Categories, Causes, and Consequences. Mol Cell 2019; 71:882-895. [PMID: 30241605 DOI: 10.1016/j.molcel.2018.08.008] [Citation(s) in RCA: 312] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/03/2018] [Accepted: 08/06/2018] [Indexed: 02/07/2023]
Abstract
Age-associated changes to the mammalian DNA methylome are well documented and thought to promote diseases of aging, such as cancer. Recent studies have identified collections of individual methylation sites whose aggregate methylation status measures chronological age, referred to as the DNA methylation clock. DNA methylation may also have value as a biomarker of healthy versus unhealthy aging and disease risk; in other words, a biological clock. Here we consider the relationship between the chronological and biological clocks, their underlying mechanisms, potential consequences, and their utility as biomarkers and as targets for intervention to promote healthy aging and longevity.
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50
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Catania A, Peverelli L, Tabano S, Ghezzi D, Lamperti C. DNMT1-complex disorder caused by a novel mutation associated with an overlapping phenotype of autosomal-dominant cerebellar ataxia, deafness, and narcolepsy (ADCA-DN) and hereditary sensory neuropathy with dementia and hearing loss (HSN1E). Neurol Sci 2019; 40:1963-1966. [PMID: 30911858 DOI: 10.1007/s10072-019-03859-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/19/2019] [Indexed: 10/27/2022]
Affiliation(s)
- Alessia Catania
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.
| | - Lorenzo Peverelli
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Neuromuscular and Rare Disease Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, University of Milan, Milan, Italy
| | - Silvia Tabano
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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