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Coppens G, Vanhorebeek I, Verlinden I, Derese I, Wouters PJ, Joosten KF, Verbruggen SC, Güiza F, Van den Berghe G. Assessment of aberrant DNA methylation two years after paediatric critical illness: a pre-planned secondary analysis of the international PEPaNIC trial. Epigenetics 2023; 18:2146966. [PMID: 36384393 PMCID: PMC9980627 DOI: 10.1080/15592294.2022.2146966] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Critically ill children requiring intensive care suffer from impaired physical/neurocognitive development 2 y later, partially preventable by omitting early use of parenteral nutrition (early-PN) in the paediatric intensive-care-unit (PICU). Altered methylation of DNA from peripheral blood during PICU-stay provided a molecular basis hereof. Whether DNA-methylation of former PICU patients, assessed 2 y after critical illness, is different from that of healthy children remained unknown. In a pre-planned secondary analysis of the PEPaNIC-RCT (clinicaltrials.gov-NCT01536275) 2-year follow-up, we assessed buccal-mucosal DNA-methylation (Infinium-HumanMethylation-EPIC-BeadChip) of former PICU-patients (N = 406 early-PN; N = 414 late-PN) and matched healthy children (N = 392). CpG-sites differentially methylated between groups were identified with multivariable linear regression and differentially methylated DNA-regions via clustering of differentially methylated CpG-sites using kernel-estimates. Analyses were adjusted for technical variation and baseline risk factors, and corrected for multiple testing (false-discovery-rate <0.05). Differentially methylated genes were functionally annotated (KEGG-pathway database), and allocated to three classes depending on involvement in physical/neurocognitive development, critical illness and intensive medical care, or pre-PICU-admission disorders. As compared with matched healthy children, former PICU-patients showed significantly different DNA-methylation at 4047 CpG-sites (2186 genes) and 494 DNA-regions (468 genes), with most CpG-sites being hypomethylated (90.3%) and with an average absolute 2% effect-size, irrespective of timing of PN initiation. Of the differentially methylated KEGG-pathways, 41.2% were related to physical/neurocognitive development, 32.8% to critical illness and intensive medical care and 26.0% to pre-PICU-admission disorders. Two years after critical illness in children, buccal-mucosal DNA showed abnormal methylation of CpG-sites and DNA-regions located in pathways known to be important for physical/neurocognitive development.
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Affiliation(s)
- Grégoire Coppens
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
| | - Ilse Vanhorebeek
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
| | - Ines Verlinden
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
| | - Inge Derese
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
| | - Pieter J Wouters
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
| | - Koen F Joosten
- Intensive Care Unit, Department of Paediatrics and Paediatric Surgery, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Sascha C Verbruggen
- Intensive Care Unit, Department of Paediatrics and Paediatric Surgery, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Fabian Güiza
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
| | - Greet Van den Berghe
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven,Leuven, Belgium
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2
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O'Connor LM, O'Connor BA, Lim SB, Zeng J, Lo CH. Integrative multi-omics and systems bioinformatics in translational neuroscience: A data mining perspective. J Pharm Anal 2023; 13:836-850. [PMID: 37719197 PMCID: PMC10499660 DOI: 10.1016/j.jpha.2023.06.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 09/19/2023] Open
Abstract
Bioinformatic analysis of large and complex omics datasets has become increasingly useful in modern day biology by providing a great depth of information, with its application to neuroscience termed neuroinformatics. Data mining of omics datasets has enabled the generation of new hypotheses based on differentially regulated biological molecules associated with disease mechanisms, which can be tested experimentally for improved diagnostic and therapeutic targeting of neurodegenerative diseases. Importantly, integrating multi-omics data using a systems bioinformatics approach will advance the understanding of the layered and interactive network of biological regulation that exchanges systemic knowledge to facilitate the development of a comprehensive human brain profile. In this review, we first summarize data mining studies utilizing datasets from the individual type of omics analysis, including epigenetics/epigenomics, transcriptomics, proteomics, metabolomics, lipidomics, and spatial omics, pertaining to Alzheimer's disease, Parkinson's disease, and multiple sclerosis. We then discuss multi-omics integration approaches, including independent biological integration and unsupervised integration methods, for more intuitive and informative interpretation of the biological data obtained across different omics layers. We further assess studies that integrate multi-omics in data mining which provide convoluted biological insights and offer proof-of-concept proposition towards systems bioinformatics in the reconstruction of brain networks. Finally, we recommend a combination of high dimensional bioinformatics analysis with experimental validation to achieve translational neuroscience applications including biomarker discovery, therapeutic development, and elucidation of disease mechanisms. We conclude by providing future perspectives and opportunities in applying integrative multi-omics and systems bioinformatics to achieve precision phenotyping of neurodegenerative diseases and towards personalized medicine.
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Affiliation(s)
- Lance M. O'Connor
- College of Biological Sciences, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Blake A. O'Connor
- School of Pharmacy, University of Wisconsin, Madison, WI, 53705, USA
| | - Su Bin Lim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, 16499, South Korea
| | - Jialiu Zeng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Chih Hung Lo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
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3
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Bryzgalov LO, Korbolina EE, Merkulova TI. Exploring the Genetic Predisposition to Epigenetic Changes in Alzheimer's Disease. Int J Mol Sci 2023; 24:ijms24097955. [PMID: 37175659 PMCID: PMC10177989 DOI: 10.3390/ijms24097955] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/05/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Alzheimer's disease (AD) is a prevalent type of dementia in elderly populations with a significant genetic component. The accumulating evidence suggests that AD involves a reconfiguration of the epigenetic landscape, including DNA methylation, post-translational modification of histone proteins, and chromatin remodeling. Along with environmental factors, individual specific genetic features play a considerable role in the formation of epigenetic architecture. In this study, we attempt to identify the non-coding regulatory SNPs (rSNPs) able to affect the epigenetic mechanisms in AD. To this end, the multi-omics approach is used. The GEO (Gene Expression Omnibus) available data (GSE153875) for AD patients and controls are integrated to reveal the rSNPs that display allele-specific features in both ChIP-seq profiles of four histone modifications and RNA-seq. Furthermore, we analyze the presence of rSNPs in the promoters of genes reported to be differentially expressed between AD and the normal brain (AD-related genes) and involved in epigenetic regulation according to the EpiFactors database. We also searched for the rSNPs in the promoters of the genes coding for transcription regulators of the identified AD-related genes. These regulators were selected based on the corresponding ChIP-seq peaks (ENCODE) in the promoter regions of these genes. Finally, we formed a panel of rSNPs localized to the promoters of genes that contribute to the epigenetic landscape in AD and, thus, to the genetic predisposition for this disease.
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Affiliation(s)
- Leonid O Bryzgalov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, 630090 Novosibirsk, Russia
- Vector-Best, 630117 Novosibirsk, Russia
| | - Elena E Korbolina
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, 630090 Novosibirsk, Russia
| | - Tatiana I Merkulova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, 630090 Novosibirsk, Russia
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4
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Kamal SR, Potukutchi S, Gelovani DJ, Bonomi RE, Kallakuri S, Cavanaugh JM, Mangner T, Conti A, Liu RS, Pasqualini R, Arap W, Sidman RL, Perrine SA, Gelovani JG. Spatial and temporal dynamics of HDACs class IIa following mild traumatic brain injury in adult rats. Mol Psychiatry 2022; 27:1683-1693. [PMID: 35027678 DOI: 10.1038/s41380-021-01369-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 09/28/2021] [Accepted: 10/15/2021] [Indexed: 11/09/2022]
Abstract
The fundamental role of epigenetic regulatory mechanisms involved in neuroplasticity and adaptive responses to traumatic brain injury (TBI) is gaining increased recognition. TBI-induced neurodegeneration is associated with several changes in the expression-activity of various epigenetic regulatory enzymes, including histone deacetylases (HDACs). In this study, PET/CT with 6-([18F]trifluoroacetamido)-1- hexanoicanilide ([18F]TFAHA) to image spatial and temporal dynamics of HDACs class IIa expression-activity in brains of adult rats subjected to a weight drop model of diffuse, non-penetrating, mild traumatic brain injury (mTBI). The mTBI model was validated by histopathological and immunohistochemical analyses of brain tissue sections for localization and magnitude of expression of heat-shock protein-70 kDa (HSP70), amyloid precursor protein (APP), cannabinoid receptor-2 (CB2), ionized calcium-binding adapter protein-1 (IBA1), histone deacetylase-4 and -5 (HDAC4 and HDAC5). In comparison to baseline, the expression-activities of HDAC4 and HDAC5 were downregulated in the hippocampus, nucleus accumbens, peri-3rd ventricular part of the thalamus, and substantia nigra at 1-3 days post mTBI, and remained low at 7-8 days post mTBI. Reduced levels of HDAC4 and HDAC5 expression observed in neurons of these brain regions post mTBI were associated with the reduced nuclear and neuropil levels of HDAC4 and HDAC5 with the shift to perinuclear localization of these enzymes. These results support the rationale for the development of therapeutic strategies to upregulate expression-activity of HDACs class IIa post-TBI. PET/CT (MRI) with [18F]TFAHA can facilitate the development and clinical translation of unique therapeutic approaches to upregulate the expression and activity of HDACs class IIa enzymes in the brain after TBI.
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Affiliation(s)
- Swatabdi R Kamal
- Department of Biomedical Engineering, College of Engineering and School of Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - Shreya Potukutchi
- Department of Biomedical Engineering, College of Engineering and School of Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - David J Gelovani
- School of Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - Robin E Bonomi
- School of Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - Srinivasu Kallakuri
- Department of Psychiatry and Behavioral Neurosciences, School of Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - John M Cavanaugh
- Department of Biomedical Engineering, College of Engineering and School of Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - Thomas Mangner
- Cyclotron-Radiochemistry Facility, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA.,Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Alana Conti
- Research and Development Service, John D. Dingell VA Medical Center, Detroit, MI, 48201, USA.,Departments of Neurosurgery and Psychiatry and Behavioral Neurosciences, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Ren-Shyan Liu
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan.,Department of Nuclear Medicine, Cheng-Hsin General Hospital, Taipei, 112, Taiwan.,Department of Nuclear Medicine, Taipei Veterans General Hospital, Taipei, 112, Taiwan
| | - Renata Pasqualini
- Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.,Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA.,Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Richard L Sidman
- Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA
| | - Shane A Perrine
- Department of Psychiatry and Behavioral Neurosciences, School of Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - Juri G Gelovani
- Department of Biomedical Engineering, College of Engineering and School of Medicine, Wayne State University, Detroit, MI, 48201, USA. .,Molecular Imaging Program, Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA. .,College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE.
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5
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Novel pyrano 1,3 oxazine based ligand inhibits the epigenetic reader hBRD2 in glioblastoma. Biochem J 2020; 477:2263-2279. [PMID: 32484211 DOI: 10.1042/bcj20200339] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/27/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022]
Abstract
Glioblastoma (GBM) is the most common primary brain malignancy, rarely amenable to treatment with a high recurrence rate. GBM are prone to develop resistance to the current repertoire of drugs, including the first-line chemotherapeutic agents with frequent recurrence, limiting therapeutic success. Recent clinical data has evidenced the BRD2 and BRD4 of the BET family proteins as the new druggable targets against GBM. In this relevance, we have discovered a compound (pyrano 1,3 oxazine derivative; NSC 328111; NS5) as an inhibitor of hBRD2 by the rational structure-based approach. The crystal structure of the complex, refined to 1.5 Å resolution, revealed that the NS5 ligand significantly binds to the N-terminal bromodomain (BD1) of BRD2 at the acetylated (Kac) histone binding site. The quantitative binding studies, by SPR and MST assay, indicate that NS5 binds to BD1 of BRD2 with a KD value of ∼1.3 µM. The cell-based assay, in the U87MG glioma cells, confirmed that the discovered compound NS5 significantly attenuated proliferation and migration. Furthermore, evaluation at the translational level established significant inhibition of BRD2 upon treatment with NS5. Hence, we propose that the novel lead compound NS5 has an inhibitory effect on BRD2 in glioblastoma.
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6
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Xiao X, Liu X, Jiao B. Epigenetics: Recent Advances and Its Role in the Treatment of Alzheimer's Disease. Front Neurol 2020; 11:538301. [PMID: 33178099 PMCID: PMC7594522 DOI: 10.3389/fneur.2020.538301] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/03/2020] [Indexed: 12/14/2022] Open
Abstract
Objective: This review summarizes recent findings on the epigenetics of Alzheimer's disease (AD) and provides therapeutic strategies for AD. Methods: We searched the following keywords: “genetics,” “epigenetics,” “Alzheimer's disease,” “DNA methylation,” “DNA hydroxymethylation,” “histone modifications,” “non-coding RNAs,” and “therapeutic strategies” in PubMed. Results: In this review, we summarizes recent studies of epigenetics in AD, including DNA methylation/hydroxymethylation, histone modifications, and non-coding RNAs. There are no consistent results of global DNA methylation/hydroxymethylation in AD. Epigenetic genome-wide association studies show that many differentially methylated sites exist in AD. Several studies investigate the role of histone modifications in AD; for example, histone acetylation decreases, whereas H3 phosphorylation increases significantly in AD. In addition, non-coding RNAs, such as microRNA-16 and BACE1-antisense transcript (BACE1-AS), are associated with the pathology of AD. These epigenetic changes provide us with novel insights into the pathogenesis of AD and may be potential therapeutic strategies for AD. Conclusion: Epigenetics is associated with the pathogenesis of AD, including DNA methylation/hydroxymethylation, histone modifications, and non-coding RNAs, which provide potential therapeutic strategies for AD.
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Affiliation(s)
- Xuewen Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xixi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
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7
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Altered ANRIL Methylation in Epileptic Patients. J Mol Neurosci 2020; 71:193-199. [PMID: 32662045 DOI: 10.1007/s12031-020-01666-w] [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: 06/26/2020] [Accepted: 07/08/2020] [Indexed: 10/23/2022]
Abstract
Long non-coding RNAs (lncRNAs) have regulatory roles in several aspects of cellular physiology. Recent studies have also revealed their role in neuronal differentiation and the pathophysiology of neurologic disorders such as epilepsy. We have recently reported altered expression of a number of lncRNAs in the peripheral blood of epileptic patients in association with their response to antiepileptic drugs. One the most significantly altered lncRNAs in epileptic patients is the antisense non-coding RNA in the INK4 locus (ANRIL), whose expression has been found to be higher in both refractory and non-refractory groups compared with controls. In the current study, we aimed to identify the methylation status of this lncRNA to suggest a potential mechanism for deregulated ANRIL expression. Thus, we assessed the methylation status of the ANRIL promoter in 40 patients with refractory epilepsy, 40 patients with non-refractory epilepsy and 40 normal controls using the high-resolution melting (HRM) method. The HRM results showed hypomethylation of the ANRIL promoter region in both refractory epilepsy and non-refractory epilepsy patients compared with normal controls. This methylation pattern was consistent with the recently reported upregulation of this lncRNA in patients with epilepsy. Thus, we suggest altered methylation of the ANRIL promoter as a potential cause of its aberrant expression in peripheral blood of epileptic patients.
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8
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Xiao W, Liu C, Zhong K, Ning S, Hou R, Deng N, Xu Y, Luo Z, Fu Y, Zeng Y, Xiao B, Long H, Long L. CpG methylation signature defines human temporal lobe epilepsy and predicts drug-resistant. CNS Neurosci Ther 2020; 26:1021-1030. [PMID: 32519815 PMCID: PMC7539843 DOI: 10.1111/cns.13394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
Aims Temporal lobe epilepsy (TLE) is the most common focal epilepsy syndrome in adults and frequently develops drug resistance. Studies have investigated the value of peripheral DNA methylation signature as molecular biomarker for diagnosis or prognosis. We aimed to explore methylation biomarkers for TLE diagnosis and pharmacoresistance prediction. Methods We initially conducted genome‐wide DNA methylation profiling in TLE patients, and then selected candidate CpGs in training cohort and validated in another independent cohort by employing machine learning algorithms. Furthermore, nomogram comprising DNA methylation and clinicopathological data was generated to predict the drug response in the entire patient cohort. Lastly, bioinformatics analysis for CpG‐associated genes was performed using Ingenuity Pathway Analysis. Results After screening and validation, eight CpGs were identified for diagnostic biomarker with an area under the curve (AUC) of 0.81 and six CpGs for drug‐resistant prediction biomarker with an AUC of 0.79. The nomogram for drug‐resistant prediction comprised methylation risk score, disease course, seizure frequency, and hippocampal sclerosis, with AUC as high as 0.96. Bioinformatics analysis indicated drug response–related CpGs corresponding genes closely related to DNA methylation. Conclusions This study demonstrates the ability to use peripheral DNA methylation signature as molecular biomarker for epilepsy diagnosis and drug‐resistant prediction.
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Affiliation(s)
- Wenbiao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Chaorong Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Kuo Zhong
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Rui Hou
- Shanghai Biotechnology Corporation, Shanghai, China
| | - Na Deng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuchen Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaohui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yujiao Fu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Zeng
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lili Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
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9
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Rexach J, Lee H, Martinez-Agosto JA, Németh AH, Fogel BL. Clinical application of next-generation sequencing to the practice of neurology. Lancet Neurol 2020; 18:492-503. [PMID: 30981321 DOI: 10.1016/s1474-4422(19)30033-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 12/21/2018] [Accepted: 01/02/2019] [Indexed: 01/05/2023]
Abstract
Next-generation sequencing technologies allow for rapid and inexpensive large-scale genomic analysis, creating unprecedented opportunities to integrate genomic data into the clinical diagnosis and management of neurological disorders. However, the scale and complexity of these data make them difficult to interpret and require the use of sophisticated bioinformatics applied to extensive datasets, including whole exome and genome sequences. Detailed analysis of genetic data has shown that accurate phenotype information is essential for correct interpretation of genetic variants and might necessitate re-evaluation of the patient in some cases. A multidisciplinary approach that incorporates bioinformatics, clinical evaluation, and human genetics can help to address these challenges. However, despite numerous studies that show the efficacy of next-generation sequencing in establishing molecular diagnoses, pathogenic mutations are generally identified in fewer than half of all patients with genetic neurological disorders, exposing considerable gaps in the understanding of the human genome and providing opportunities to focus research on improving the usefulness of genomics in clinical practice. Looking forward, the emergence of precision health in neurological care will increasingly apply genomic data analysis to pharmacogenetics, preventive medicine, and patient-targeted therapies.
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Affiliation(s)
- Jessica Rexach
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Andrea H Németh
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Service Foundation Trust, Oxford, UK
| | - Brent L Fogel
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; Clinical Neurogenomics Research Center, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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10
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Güiza F, Vanhorebeek I, Verstraete S, Verlinden I, Derese I, Ingels C, Dulfer K, Verbruggen SC, Garcia Guerra G, Joosten KF, Wouters PJ, Van den Berghe G. Effect of early parenteral nutrition during paediatric critical illness on DNA methylation as a potential mediator of impaired neurocognitive development: a pre-planned secondary analysis of the PEPaNIC international randomised controlled trial. THE LANCET RESPIRATORY MEDICINE 2020; 8:288-303. [DOI: 10.1016/s2213-2600(20)30046-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/07/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022]
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11
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Paul JL, Dashtipour K, Chen Z, Wang C. DNA methylome study of human cerebellar tissues identified genes and pathways possibly involved in essential tremor. PRECISION CLINICAL MEDICINE 2019; 2:221-234. [PMID: 31886034 PMCID: PMC6927097 DOI: 10.1093/pcmedi/pbz028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/30/2019] [Accepted: 12/01/2019] [Indexed: 01/13/2023] Open
Abstract
Background Essential tremor (ET) is a neurological syndrome of unknown origin with poorly understood etiology and pathogenesis. It is suggested that the cerebellum and its tracts may be involved in the pathophysiology of ET. DNA methylome interrogation of cerebellar tissue may help shine some light on the understanding of the mechanism of the development of ET. Our study used postmortem human cerebellum tissue samples collected from 12 ET patients and 11 matched non-ET controls for DNA methylome study to identify differentially methylated genes in ET. Results Using Nugen’s Ovation reduced representation bisulfite sequencing (RRBS), we identified 753 genes encompassing 938 CpG sites with significant differences in DNA methylation between the ET and the control group. Identified genes were further analyzed with Ingenuity Pathway Analysis (IPA) by which we identified certain significant pathways, upstream regulators, diseases and functions, and networks associated with ET. Conclusions Our study provides evidence that there are significant differences in DNA methylation patterns between the ET and control samples, suggesting that the methylation alteration of certain genes in the cerebellum may be associated with ET pathogenesis. The identified genes allude to the GABAergic hypothesis which supports the notation that ET is a neurodegenerative disease, particularly involving the cerebellum.
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Affiliation(s)
- Jennifer L Paul
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Khashayar Dashtipour
- Division of Movement Disorders, Department of Neurology, Loma Linda University Medical Center, Loma Linda, CA 92350, USA
| | - Zhong Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA.,Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
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12
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La Rovere M, Franzago M, Stuppia L. Epigenetics and Neurological Disorders in ART. Int J Mol Sci 2019; 20:ijms20174169. [PMID: 31454921 PMCID: PMC6747212 DOI: 10.3390/ijms20174169] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022] Open
Abstract
About 1–4% of children are currently generated by Assisted Reproductive Technologies (ART) in developed countries. These babies show only a slightly increased risk of neonatal malformations. However, follow-up studies have suggested a higher susceptibility to multifactorial, adult onset disorders like obesity, diabetes and cardiovascular diseases in ART offspring. It has been suggested that these conditions could be the consequence of epigenetic, alterations, due to artificial manipulations of gametes and embryos potentially able to alter epigenetic stability during zygote reprogramming. In the last years, epigenetic alterations have been invoked as a possible cause of increased risk of neurological disorders, but at present the link between epigenetic modifications and long-term effects in terms of neurological diseases in ART children remains unclear, due to the short follow up limiting retrospective studies. In this review, we summarize the current knowledge about neurological disorders promoted by epigenetics alterations in ART. Based on data currently available, it is possible to conclude that little, if any, evidence of an increased risk of neurological disorders in ART conceived children is provided. Most important, the large majority of reports appears to be limited to epidemiological studies, not providing any experimental evidence about epigenetic modifications responsible for an increased risk.
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Affiliation(s)
- Marina La Rovere
- Department of Psychological, Health and Territorial Sciences, School of Medicine and Health Sciences, "G. d'Annunzio" University, 66100 Chieti-Pescara, Italy
| | - Marica Franzago
- Department of Medicine and Aging, School of Medicine and Health Sciences, "G. d'Annunzio" University, 66100 Chieti-Pescara, Italy
- Aging Center Studies-Translational Medicine (CeSI-Met), "G. d'Annunzio" University, 66100 Chieti-Pescara, Italy
| | - Liborio Stuppia
- Department of Psychological, Health and Territorial Sciences, School of Medicine and Health Sciences, "G. d'Annunzio" University, 66100 Chieti-Pescara, Italy.
- Aging Center Studies-Translational Medicine (CeSI-Met), "G. d'Annunzio" University, 66100 Chieti-Pescara, Italy.
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Jacobs A, Verlinden I, Vanhorebeek I, Van den Berghe G. Early Supplemental Parenteral Nutrition in Critically Ill Children: An Update. J Clin Med 2019; 8:jcm8060830. [PMID: 31212639 PMCID: PMC6616588 DOI: 10.3390/jcm8060830] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 05/29/2019] [Accepted: 06/05/2019] [Indexed: 11/06/2022] Open
Abstract
In critically ill children admitted to pediatric intensive care units (PICUs), enteral nutrition (EN) is often delayed due to gastrointestinal dysfunction or interrupted. Since a macronutrient deficit in these patients has been associated with adverse outcomes in observational studies, supplemental parenteral nutrition (PN) in PICUs has long been widely advised to meeting nutritional requirements. However, uncertainty of timing of initiation, optimal dose and composition of PN has led to a wide variation in previous guidelines and current clinical practices. The PEPaNIC (Early versus Late Parenteral Nutrition in the Pediatric ICU) randomized controlled trial recently showed that withholding PN in the first week in PICUs reduced incidence of new infections and accelerated recovery as compared with providing supplemental PN early (within 24 hours after PICU admission), irrespective of diagnosis, severity of illness, risk of malnutrition or age. The early withholding of amino acids in particular, which are powerful suppressors of intracellular quality control by autophagy, statistically explained this outcome benefit. Importantly, two years after PICU admission, not providing supplemental PN early in PICUs did not negatively affect mortality, growth or health status, and significantly improved neurocognitive development. These findings have an important impact on the recently issued guidelines for PN administration to critically ill children. In this review, we summarize the most recent literature that provides evidence on the implications for clinical practice with regard to the use of early supplemental PN in critically ill children.
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Affiliation(s)
- An Jacobs
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven University Hospital, 3000 Leuven, Belgium.
| | - Ines Verlinden
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven University Hospital, 3000 Leuven, Belgium.
| | - Ilse Vanhorebeek
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven University Hospital, 3000 Leuven, Belgium.
| | - Greet Van den Berghe
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven University Hospital, 3000 Leuven, Belgium.
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14
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Landires I, Núñez-Samudio V. Epigenética, memoria y herencia. Neurologia 2019; 34:138-139. [DOI: 10.1016/j.nrl.2017.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/14/2017] [Indexed: 11/26/2022] Open
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15
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Epigenetics, memory, and inheritance. NEUROLOGÍA (ENGLISH EDITION) 2019. [DOI: 10.1016/j.nrleng.2017.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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16
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Verstraete S, Verbruggen SC, Hordijk JA, Vanhorebeek I, Dulfer K, Güiza F, van Puffelen E, Jacobs A, Leys S, Durt A, Van Cleemput H, Eveleens RD, Garcia Guerra G, Wouters PJ, Joosten KF, Van den Berghe G. Long-term developmental effects of withholding parenteral nutrition for 1 week in the paediatric intensive care unit: a 2-year follow-up of the PEPaNIC international, randomised, controlled trial. THE LANCET RESPIRATORY MEDICINE 2018; 7:141-153. [PMID: 30224325 DOI: 10.1016/s2213-2600(18)30334-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/25/2018] [Accepted: 07/26/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND The paediatric early versus late parenteral nutrition in critical illness (PEPaNIC) multicentre, randomised, controlled trial showed that, compared with early parenteral nutrition, withholding supplemental parenteral nutrition for 1 week in the paediatric intensive care unit (PICU; late parenteral nutrition) reduced infections and accelerated recovery from critical illness in children. We aimed to investigate the long-term impact on physical and neurocognitive development of early versus late parenteral nutrition. METHODS In this preplanned 2-year follow-up study, all patients included in the PEPaNIC trial (which was done in University Hospitals Leuven, Belgium; Erasmus Medical Centre-Sophia Children's Hospital, Rotterdam, Netherlands; and Stollery Children's Hospital, Edmonton, AB, Canada) were approached for possible assessment of physical and neurocognitive development compared with healthy children who were matched for age and sex, and who had never been admitted to a neonatal ICU or a PICU. Assessed outcomes comprised anthropometric data; health status; parent-reported or caregiver-reported executive functions and emotional and behavioural problems; and tests for intelligence, visual-motor integration, alertness, motor coordination, inhibitory control, cognitive flexibility, and memory. To address partial responses among the children tested, we did multiple data imputation by chained equations before univariable and multivariable linear and logistic regression analyses adjusted for risk factors. This trial is registered with ClinicalTrials.gov, number NCT01536275. FINDINGS At the 2-year follow-up, 60 (8%) of 717 children who received late parenteral nutrition and 63 (9%) of 723 children who received early parenteral nutrition had died (p=0·81). 68 (9%) of 717 children who received late and 91 (13%) of 723 children who received early parenteral nutrition were too disabled for neurocognitive assessment (p=0·059), and 786 patients (395 assigned to late and 391 assigned to early parenteral nutrition) consented for testing. 786 patients and 405 healthy control children underwent long-term outcome testing between Aug 4, 2014, and Jan 19, 2018, and were included in the imputation model for subsequent multivariable analyses. Late parenteral nutrition did not adversely affect anthropometric data, health status, or neurological functioning, and improved parent-reported or caregiver-reported executive functioning (late vs early parenteral nutrition β estimate -2·258, 95% CI -4·012 to -0·504; p=0·011), more specifically inhibition (-3·422, -5·171 to -1·673; p=0·0001), working memory (-2·016, -3·761 to -0·270; p=0·023), and meta-cognition (-1·957, -3·694 to -0·220; p=0·027). Externalising behavioural problems (β estimate -1·715, 95% CI -3·325 to -0·106; p=0·036) and visual-motor integration (0·468, 0·087 to 0·850; p=0·016) were also improved in the late parenteral nutrition group compared with the early parenteral nutrition group. After Bonferroni correction for multiple comparisons, the effect on inhibitory control remained significant (p=0·0001). INTERPRETATION Withholding early parenteral nutrition for 1 week in the PICU did not negatively affect survival, anthropometrics, health status, and neurocognitive development, and improved inhibitory control 2 years after PICU admission. FUNDING European Research Council Advanced Grant, Methusalem programme provided by the Flemish Government, Flemish Agency for Innovation by Science and Technology (IWT), Research Foundation Flanders (FWO), Sophia Children's Hospital Foundation (SSWO), Stichting Agis Zorginnovatie, Erasmus Trustfonds, and European Society for Parenteral and Enteral Nutrition (ESPEN) research grant.
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Affiliation(s)
- Sören Verstraete
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Sascha C Verbruggen
- Intensive Care Unit, Department of Paediatrics and Paediatric Surgery, Erasmus Medical Centre-Sophia Children's Hospital, Rotterdam, Netherlands
| | - José A Hordijk
- Intensive Care Unit, Department of Paediatrics and Paediatric Surgery, Erasmus Medical Centre-Sophia Children's Hospital, Rotterdam, Netherlands; Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Centre-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Ilse Vanhorebeek
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Karolijn Dulfer
- Intensive Care Unit, Department of Paediatrics and Paediatric Surgery, Erasmus Medical Centre-Sophia Children's Hospital, Rotterdam, Netherlands; Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Centre-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Fabian Güiza
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Esther van Puffelen
- Intensive Care Unit, Department of Paediatrics and Paediatric Surgery, Erasmus Medical Centre-Sophia Children's Hospital, Rotterdam, Netherlands
| | - An Jacobs
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Sandra Leys
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Astrid Durt
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Hanna Van Cleemput
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Renate D Eveleens
- Intensive Care Unit, Department of Paediatrics and Paediatric Surgery, Erasmus Medical Centre-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Gonzalo Garcia Guerra
- Department of Paediatrics, Intensive Care Unit, University of Alberta, Stollery Children's Hospital, Edmonton, AB, Canada
| | - Pieter J Wouters
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Koen F Joosten
- Intensive Care Unit, Department of Paediatrics and Paediatric Surgery, Erasmus Medical Centre-Sophia Children's Hospital, Rotterdam, Netherlands
| | - Greet Van den Berghe
- Clinical Division and Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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Salter M, Corfield E, Ramadass A, Grand F, Green J, Westra J, Lim CR, Farrimond L, Feneberg E, Scaber J, Thompson A, Ossher L, Turner M, Talbot K, Cudkowicz M, Berry J, Hunter E, Akoulitchev A. Initial Identification of a Blood-Based Chromosome Conformation Signature for Aiding in the Diagnosis of Amyotrophic Lateral Sclerosis. EBioMedicine 2018; 33:169-184. [PMID: 29941342 PMCID: PMC6085506 DOI: 10.1016/j.ebiom.2018.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/11/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The identification of blood-based biomarkers specific to the diagnosis of amyotrophic lateral sclerosis (ALS) is an active field of academic and clinical research. While inheritance studies have advanced the field, a majority of patients do not have a known genetic link to the disease, making direct sequence-based genetic testing for ALS difficult. The ability to detect biofluid-based epigenetic changes in ALS would expand the relevance of using genomic information for disease diagnosis. METHODS Assessing differences in chromosomal conformations (i.e. how they are positioned in 3-dimensions) represents one approach for assessing epigenetic changes. In this study, we used an industrial platform, EpiSwitch™, to compare the genomic architecture of healthy and diseased patient samples (blood and tissue) to discover a chromosomal conformation signature (CCS) with diagnostic potential in ALS. A three-step biomarker selection process yielded a distinct CCS for ALS, comprised of conformation changes in eight genomic loci and detectable in blood. FINDINGS We applied the ALS CCS to determine a diagnosis for 74 unblinded patient samples and subsequently conducted a blinded diagnostic study of 16 samples. Sensitivity and specificity for ALS detection in the 74 unblinded patient samples were 83∙33% (CI 51∙59 to 97∙91%) and 76∙92% (46∙19 to 94∙96%), respectively. In the blinded cohort, sensitivity reached 87∙50% (CI 47∙35 to 99∙68%) and specificity was 75∙0% (34∙91 to 96∙81%). INTERPRETATIONS The sensitivity and specificity values achieved using the ALS CCS identified and validated in this study provide an indication that the detection of chromosome conformation signatures is a promising approach to disease diagnosis and can potentially augment current strategies for diagnosing ALS. FUND: This research was funded by Oxford BioDynamics and Innovate UK. Work in the Oxford MND Care and Research Centre is supported by grants from the Motor Neurone Disease Association and the Medical Research Council. Additional support was provided by the Northeast ALS Consortium (NEALS).
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Affiliation(s)
| | | | | | | | | | | | | | - Lucy Farrimond
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Emily Feneberg
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Jakub Scaber
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Alexander Thompson
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Lynn Ossher
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Martin Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Merit Cudkowicz
- Neurology Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - James Berry
- Neurology Clinical Research Institute, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
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Modulation of miRNA expression in aged rat hippocampus by buttermilk and krill oil. Sci Rep 2018; 8:3993. [PMID: 29507352 PMCID: PMC5838111 DOI: 10.1038/s41598-018-22148-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/16/2018] [Indexed: 12/17/2022] Open
Abstract
The increasing incidence of age-induced cognitive decline justifies the search for complementary ways of prevention or delay. We studied the effects of concentrates of phospholipids, sphingolipids, and/or 3-n fatty acids on the expression of genes or miRNAs related to synaptic activity and/or neurodegeneration, in the hippocampus of aged Wistar rats following a 3-month supplementation. The combination of two phospholipidic concentrates of krill oil (KOC) and buttermilk (BMFC) origin modulated the hippocampal expression of 119 miRNAs (11 were common to both BMFC and BMFC + KOC groups). miR-191a-5p and miR-29a-3p changed significantly only in the BMFC group, whereas miR-195-3p and miR-148a-5p did so only in the combined-supplemented group. Thirty-eight, 58, and 72 differentially expressed genes (DEG) were found in the groups supplemented with KOC, BMFC and BMFC + KOC, respectively. Interaction analysis unveiled networks of selected miRNAs with their potential target genes. DEG found in the KOC and BMFC groups were mainly involved in neuroactive processes, whereas they were associated with lysosomes and mRNA surveillance pathways in the BMFC + KOC group. We also report a significant reduction in hippocampal ceramide levels with BMFC + KOC. Our results encourage additional in-depth investigations regarding the potential beneficial effects of these compounds.
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Kawamura Y, Takouda J, Yoshimoto K, Nakashima K. New aspects of glioblastoma multiforme revealed by similarities between neural and glioblastoma stem cells. Cell Biol Toxicol 2018; 34:425-440. [PMID: 29383547 DOI: 10.1007/s10565-017-9420-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/29/2017] [Indexed: 12/31/2022]
Abstract
Neural stem cells (NSCs) undergo self-renewal and generate neurons and glial cells under the influence of specific signals from surrounding environments. Glioblastoma multiforme (GBM) is a highly lethal brain tumor arising from NSCs or glial precursor cells owing to dysregulation of transcriptional and epigenetic networks that control self-renewal and differentiation of NSCs. Highly tumorigenic glioblastoma stem cells (GSCs) constitute a small subpopulation of GBM cells, which share several characteristic similarities with NSCs. GSCs exist atop a stem cell hierarchy and generate heterogeneous populations that participate in tumor propagation, drug resistance, and relapse. During multimodal treatment, GSCs de-differentiate and convert into cells with malignant characteristics, and thus play critical roles in tumor propagation. In contrast, differentiation therapy that induces GBM cells or GSCs to differentiate into a neuronal or glial lineage is expected to inhibit their proliferation. Since stem cell differentiation is specified by the cells' epigenetic status, understanding their stemness and the epigenomic situation in the ancestor, NSCs, is important and expected to be helpful for developing treatment modalities for GBM. Here, we review the current findings regarding the epigenetic regulatory mechanisms of NSC fate in the developing brain, as well as those of GBM and GSCs. Furthermore, considering the similarities between NSCs and GSCs, we also discuss potential new strategies for GBM treatment.
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Affiliation(s)
- Yoichiro Kawamura
- Division of Basic Stem Cell Biology, Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan.,Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jun Takouda
- Division of Basic Stem Cell Biology, Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kinichi Nakashima
- Division of Basic Stem Cell Biology, Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan.
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20
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Mishra SK, Jain N, Shankar U, Tawani A, Mishra A, Kumar A. SMMDB: a web-accessible database for small molecule modulators and their targets involved in neurological diseases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:1-12. [PMID: 30219840 PMCID: PMC6146116 DOI: 10.1093/database/bay082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/13/2018] [Indexed: 12/27/2022]
Abstract
High-throughput screening and better understanding of small molecule's structure-activity relationship (SAR) using computational biology techniques have greatly expanded the face of drug discovery process in better discovery of therapeutics for various disease. Small Molecule Modulators Database (SMMDB) includes >1100 small molecules that have been either approved by US Food and Drug Administration, are under investigation or were rejected in clinical trial for any kind of neurological diseases. The comprehensive information about small molecules includes the details about their molecular targets (such as protein or enzyme, DNA, RNA, antisense RNA etc.), pharmacokinetic and pharmacodynamic properties such as binding affinity to their targets (Kd, Ki, IC50 and EC50 if available), mode of action, log P-value, number of hydrogen bond donor and acceptors, their clinical trial status, their 2D and three-dimensional structures etc. To enrich the basic annotation of every small molecule entry present in SMMDB, it is hyperlinked to their description present in PubChem, DrugBank, PubMed and KEGG database. The annotation about their molecular targets was enriched by linking it with UniProt and GenBank and STRING database that can be utilized to study the interaction and relation between various targets involved in single neurological disease. All molecules present in the SMMDB are made available to download in single file and can be further used in establishing the SAR, structure-based drug designing as well as shape-based virtual screening for developing the novel therapeutics against neurological diseases. The scope of this database majorly covers the interest of scientific community and researchers who are engaged in putting their endeavor toward therapeutic development and investigating the pathogenic mechanism of various neurological diseases. The graphical user interface of the SMMDB is accessible on http://bsbe.iiti.ac.in/bsbe/smmdb.
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Affiliation(s)
- Subodh Kumar Mishra
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, India
| | - Neha Jain
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, India
| | - Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, India
| | - Arpita Tawani
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Simrol, India
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Qureshi IA, Mehler MF. Epigenetic mechanisms underlying nervous system diseases. HANDBOOK OF CLINICAL NEUROLOGY 2018; 147:43-58. [PMID: 29325627 DOI: 10.1016/b978-0-444-63233-3.00005-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing. These mechanisms are intimately involved in executing fundamental genomic programs, including gene transcription, posttranscriptional RNA processing and transport, translation, X-chromosome inactivation, genomic imprinting, retrotransposon regulation, DNA replication, and DNA repair and the maintenance of genomic stability. For the nervous system, epigenetics offers a novel and robust framework for explaining how brain development and aging occur, neural cellular diversity is generated, synaptic and neural network connectivity and plasticity are mediated, and complex cognitive and behavioral phenotypes are inherited transgenerationally. Epigenetic factors and processes are, not surprisingly, implicated in nervous system disease pathophysiology through several emerging paradigms - mutations and genetic variation in genes encoding epigenetic factors; impairments in epigenetic factor expression, localization, and function; epigenetic mechanisms modulating disease-associated factors and pathways; and the presence of deregulated epigenetic profiles in central and peripheral tissues.
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Affiliation(s)
- Irfan A Qureshi
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine; Institute for Brain Disorders and Neural Regeneration; Departments of Neurology, Neuroscience, Psychiatry and Behavioral Sciences and Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Mark F Mehler
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine; Institute for Brain Disorders and Neural Regeneration; Departments of Neurology, Neuroscience, Psychiatry and Behavioral Sciences; Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities; Einstein Cancer Center; Ruth L. and David S. Gottesman Stem Cell Institute; and Center for Epigenomics and Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY, United States.
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22
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Mir SE, Smits M, Biesmans D, Julsing M, Bugiani M, Aronica E, Kaspers GJL, Cloos J, Würdinger T, Hulleman E. Trimethylation of H3K27 during human cerebellar development in relation to medulloblastoma. Oncotarget 2017; 8:78978-78988. [PMID: 29108280 PMCID: PMC5668013 DOI: 10.18632/oncotarget.20741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 08/17/2017] [Indexed: 12/30/2022] Open
Abstract
Medulloblastoma (MB), the most common malignant childhood brain tumor, encompasses a collection of four clinically and molecularly distinct tumor subgroups, i.e. WNT, SHH, Group 3 and Group 4. These tumors are believed to originate from precursor cells during cerebellar development. Although the exact etiology of these brain tumors is not yet known, histone modifications are increasingly recognized as key events during cerebellum development and MB tumorigenesis. Recent studies show that key components involved in post-translational modifications of histone H3 lysine 27 (H3K27) are commonly deregulated in MB. In this descriptive study, we have investigated the trimethylation status of H3K27, as well as the expression of the H3K27 methylase EZH2 and demethylases KDM6A and KDM6B, during human cerebellum development in relation to MB. H3K27 Trimethylation status differed between the MB subgroups. Moreover, trimethylation of H3K27 and expression of its modifiers EZH2, KDM6A and KDM6B were detected in a spatio-temporal manner during development of the human cerebellum, with consistent high occurrence in the four proliferative zones, which are believed to harbor the precursor cells of the different MB subgroups. Our results suggest that H3K27 trimethylation in MB is deregulated by EZH2, KDM6A and KDM6B. Moreover, we provide evidence that during development of the human cerebellum H3K27me3 and its regulators are expressed in a spatio-temporal manner.
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Affiliation(s)
- Shahryar E Mir
- Department of Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands.,Neuro-oncology Research Group, Departments of Neurosurgery and Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Michiel Smits
- Neuro-oncology Research Group, Departments of Neurosurgery and Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Dennis Biesmans
- Department of Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands.,Neuro-oncology Research Group, Departments of Neurosurgery and Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Machteld Julsing
- Neuro-oncology Research Group, Departments of Neurosurgery and Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Marianna Bugiani
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Academic Medical Center and Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
| | - Gertjan J L Kaspers
- Department of Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands.,Neuro-oncology Research Group, Departments of Neurosurgery and Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Jacqueline Cloos
- Department of Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands.,Neuro-oncology Research Group, Departments of Neurosurgery and Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Thomas Würdinger
- Neuro-oncology Research Group, Departments of Neurosurgery and Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Esther Hulleman
- Department of Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands.,Neuro-oncology Research Group, Departments of Neurosurgery and Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands
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23
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Zhang L, Tao W, Feng H, Chen Y. Transcriptional and Genomic Targets of Neural Stem Cells for Functional Recovery after Hemorrhagic Stroke. Stem Cells Int 2017; 2017:2412890. [PMID: 28133486 PMCID: PMC5241497 DOI: 10.1155/2017/2412890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/21/2016] [Indexed: 01/27/2023] Open
Abstract
Hemorrhagic stroke is a life-threatening disease characterized by a sudden rupture of cerebral blood vessels, and it is widely believed that neural cell death occurs after exposure to blood metabolites or subsequently damaged cells. Neural stem cells (NSCs), which maintain neurogenesis and are found in subgranular zone and subventricular zone, are thought to be an endogenous neuroprotective mechanism for these brain injuries. However, due to the complexity of NSCs and their microenvironment, current strategies cannot satisfactorily enhance functional recovery after hemorrhagic stroke. It is well known that transcriptional and genomic pathways play important roles in ensuring the normal functions of NSCs, including proliferation, migration, differentiation, and neural reconnection. Recently, emerging evidence from the use of new technologies such as next-generation sequencing and transcriptome profiling has provided insight into our understanding of genomic function and regulation of NSCs. In the present article, we summarize and present the current data on the control of NSCs at both the transcriptional and genomic levels. Using bioinformatics methods, we sought to predict novel therapeutic targets of endogenous neurogenesis and exogenous NSC transplantation for functional recovery after hemorrhagic stroke, which could also advance our understanding of its pathophysiology.
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Affiliation(s)
- Le Zhang
- College of Computer and Information Science, Southwest University, Chongqing, China
| | - Wenjing Tao
- College of Computer and Information Science, Southwest University, Chongqing, China
| | - Hua Feng
- Department of Neurosurgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Yujie Chen
- Department of Neurosurgery, Southwest Hospital, Third Military Medical University, Chongqing, China
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24
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Grzybek M, Golonko A, Walczak M, Lisowski P. Epigenetics of cell fate reprogramming and its implications for neurological disorders modelling. Neurobiol Dis 2016; 99:84-120. [PMID: 27890672 DOI: 10.1016/j.nbd.2016.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 11/03/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
The reprogramming of human induced pluripotent stem cells (hiPSCs) proceeds in a stepwise manner with reprogramming factors binding and epigenetic composition changes during transition to maintain the epigenetic landscape, important for pluripotency. There arises a question as to whether the aberrant epigenetic state after reprogramming leads to epigenetic defects in induced stem cells causing unpredictable long term effects in differentiated cells. In this review, we present a comprehensive view of epigenetic alterations accompanying reprogramming, cell maintenance and differentiation as factors that influence applications of hiPSCs in stem cell based technologies. We conclude that sample heterogeneity masks DNA methylation signatures in subpopulations of cells and thus believe that beside a genetic evaluation, extensive epigenomic screening should become a standard procedure to ensure hiPSCs state before they are used for genome editing and differentiation into neurons of interest. In particular, we suggest that exploitation of the single-cell composition of the epigenome will provide important insights into heterogeneity within hiPSCs subpopulations to fast forward development of reliable hiPSC-based analytical platforms in neurological disorders modelling and before completed hiPSC technology will be implemented in clinical approaches.
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Affiliation(s)
- Maciej Grzybek
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-950 Lublin, Poland; Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland.
| | - Aleksandra Golonko
- Department of Biotechnology, Faculty of Civil and Environmental Engineering, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland.
| | - Marta Walczak
- Department of Animal Behavior, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland.
| | - Pawel Lisowski
- Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland; iPS Cell-Based Disease Modelling Group, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany.
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25
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Xie XQ, Zhang P, Tian B, Chen XQ. Downregulation of NAD-Dependent Deacetylase SIRT2 Protects Mouse Brain Against Ischemic Stroke. Mol Neurobiol 2016; 54:7251-7261. [DOI: 10.1007/s12035-016-0173-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/28/2016] [Indexed: 12/20/2022]
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26
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Willbanks A, Leary M, Greenshields M, Tyminski C, Heerboth S, Lapinska K, Haskins K, Sarkar S. The Evolution of Epigenetics: From Prokaryotes to Humans and Its Biological Consequences. GENETICS & EPIGENETICS 2016; 8:25-36. [PMID: 27512339 PMCID: PMC4973776 DOI: 10.4137/geg.s31863] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/03/2016] [Accepted: 07/06/2016] [Indexed: 12/11/2022]
Abstract
The evolution process includes genetic alterations that started with prokaryotes and now continues in humans. A distinct difference between prokaryotic chromosomes and eukaryotic chromosomes involves histones. As evolution progressed, genetic alterations accumulated and a mechanism for gene selection developed. It was as if nature was experimenting to optimally utilize the gene pool without changing individual gene sequences. This mechanism is called epigenetics, as it is above the genome. Curiously, the mechanism of epigenetic regulation in prokaryotes is strikingly different from that in eukaryotes, mainly higher eukaryotes, like mammals. In fact, epigenetics plays a significant role in the conserved process of embryogenesis and human development. Malfunction of epigenetic regulation results in many types of undesirable effects, including cardiovascular disease, metabolic disorders, autoimmune diseases, and cancer. This review provides a comparative analysis and new insights into these aspects.
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Affiliation(s)
- Amber Willbanks
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Meghan Leary
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Molly Greenshields
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Camila Tyminski
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Sarah Heerboth
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Karolina Lapinska
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Kathryn Haskins
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Sibaji Sarkar
- Cancer Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.; Genome Science Institute, Boston University School of Medicine, Boston, MA, USA
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27
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Wüllner U, Kaut O, deBoni L, Piston D, Schmitt I. DNA methylation in Parkinson's disease. J Neurochem 2016; 139 Suppl 1:108-120. [DOI: 10.1111/jnc.13646] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/21/2016] [Accepted: 04/15/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Ullrich Wüllner
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Oliver Kaut
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Laura deBoni
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Dominik Piston
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
| | - Ina Schmitt
- German Center for Neurodegenerative Diseases (DZNE) and Department of Neurology; University of Bonn; Bonn Germany
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28
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Ausió J. MeCP2 and the enigmatic organization of brain chromatin. Implications for depression and cocaine addiction. Clin Epigenetics 2016; 8:58. [PMID: 27213019 PMCID: PMC4875624 DOI: 10.1186/s13148-016-0214-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/20/2016] [Indexed: 12/21/2022] Open
Abstract
Methyl CpG binding protein 2 (MeCP2) is a highly abundant chromosomal protein within the brain. It is hence not surprising that perturbations in its genome-wide distribution, and at particular loci within this tissue, can result in widespread neurological disorders that transcend the early implications of this protein in Rett syndrome (RTT). Yet, the details of its role and involvement in chromatin organization are still poorly understood. This paper focuses on what is known to date about all of this with special emphasis on the relation to different epigenetic modifications (DNA methylation, histone acetylation/ubiquitination, MeCP2 phosphorylation and miRNA). We showcase all of the above in two particular important neurological functional alterations in the brain: depression (major depressive disorder [MDD]) and cocaine addiction, both of which affect the MeCP2 homeostasis and result in significant changes in the overall levels of these epigenetic marks.
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Affiliation(s)
- Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6 Canada
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29
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Emamalizadeh B, Jamshidi J, Movafagh A, Ohadi M, khaniani MS, Kazeminasab S, Biglarian A, Taghavi S, Motallebi M, Fazeli A, Ahmadifard A, Shahidi GA, Petramfar P, Shahmohammadibeni N, Dadkhah T, Khademi E, Tafakhori A, Khaligh A, Safaralizadeh T, Kowsari A, Mirabzadeh A, Zarneh AES, Khorrami M, Shokraeian P, Banavandi MJS, Lima BS, Andarva M, Alehabib E, Atakhorrami M, Darvish H. RIT2 Polymorphisms: Is There a Differential Association? Mol Neurobiol 2016; 54:2234-2240. [DOI: 10.1007/s12035-016-9815-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 02/23/2016] [Indexed: 10/22/2022]
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30
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Archer T, Kostrzewa RM. Exercise and Nutritional Benefits in PD: Rodent Models and Clinical Settings. Curr Top Behav Neurosci 2016; 29:333-351. [PMID: 26728168 DOI: 10.1007/7854_2015_409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Physical exercise offers a highly effective health-endowering activity as has been evidence using rodent models of Parkinson's disease (PD). It is a particularly useful intervention in individuals employed in sedentary occupations or afflicted by a neurodegenerative disorder, such as PD. The several links between exercise and quality-of-life, disorder progression and staging, risk factors and symptoms-biomarkers in PD all endower a promise for improved prognosis. Nutrition provides a strong determinant for disorder vulnerability and prognosis with fish oils and vegetables with a mediterranean diet offering both protection and resistance. Three factors determining the effects of exercise on disorder severity of patients may be presented: (i) Exercise effects upon motor impairment, gait, posture and balance, (ii) Exercise reduction of oxidative stress, stimulation of mitochondrial biogenesis and up-regulation of autophagy, and (iii) Exercise stimulation of dopamine (DA) neurochemistry and trophic factors. Running-wheel performance, as measured by distance run by individual mice from different treatment groups, was related to DA-integrity, indexed by striatal DA levels. Finally, both nutrition and exercise may facilitate positive epigenetic outcomes, such as lowering the dosage of L-Dopa required for a therapeutic effect.
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Affiliation(s)
- Trevor Archer
- Department of Psychology, University of Gothenburg, Gothenburg, Sweden.
| | - Richard M Kostrzewa
- Department of Biomedical Sciences, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, 37604, USA
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31
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Abstract
Epigenetic processes in the brain involve the transfer of information arising from short-lived cellular signals and changes in neuronal activity into lasting effects on gene expression. Key molecular mediators of epigenetics include methylation of DNA, histone modifications, and noncoding RNAs. Emerging findings in animal models and human brain tissue reveal that epilepsy and epileptogenesis are associated with changes to each of these contributors to the epigenome. Understanding and influencing the molecular mechanisms controlling epigenetic change could open new avenues for treatment. DNA methylation, particularly hypermethylation, has been found to increase within gene body regions and interference with DNA methylation in epilepsy can change gene expression profiles and influence epileptogenesis. Posttranscriptional modification of histones, including transient as well as sustained changes to phosphorylation and acetylation, have been reported, which appear to influence gene expression. Finally, roles have emerged for noncoding RNAs in brain excitability and seizure thresholds, including microRNA and long noncoding RNA. Together, research supports strong effects of epigenetics influencing gene expression in epilepsy, suggesting future therapeutic approaches to manipulate epigenetic processes to treat or prevent epilepsy.
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Affiliation(s)
- David C Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Katja Kobow
- Department of Neuropathology, University Hospital Erlangen, 91054 Erlangen, Germany
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32
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Mendioroz Iriarte M, Pulido Fontes L, Méndez-López I. [Neuroepigenetics: Desoxyribonucleic acid methylation in Alzheimer's disease and other dementias]. Med Clin (Barc) 2015; 144:457-64. [PMID: 24907105 DOI: 10.1016/j.medcli.2014.03.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 03/04/2014] [Indexed: 11/19/2022]
Abstract
DNA methylation is an epigenetic mechanism that controls gene expression. In Alzheimer's disease (AD), global DNA hypomethylation of neurons has been described in the human cerebral cortex. Moreover, several variants in the methylation pattern of candidate genes have been identified in brain tissue when comparing AD patients and controls. Specifically, DNA methylation changes have been observed in PSEN1 and APOE, both genes previously being involved in the pathophysiology of AD. In other degenerative dementias, methylation variants have also been described in key genes, such as hypomethylation of the SNCA gene in Parkinson's disease and dementia with Lewy bodies or hypermethylation of the GRN gene promoter in frontotemporal dementia. The finding of aberrant DNA methylation patterns shared by brain tissue and peripheral blood opens the door to use those variants as epigenetic biomarkers in the diagnosis of neurodegenerative diseases.
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Affiliation(s)
- Maite Mendioroz Iriarte
- Complejo Hospitalario de Navarra, Pamplona, Navarra, España; Navarrabiomed, Pamplona, Navarra, España.
| | - Laura Pulido Fontes
- Complejo Hospitalario de Navarra, Pamplona, Navarra, España; Navarrabiomed, Pamplona, Navarra, España
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33
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Groh KJ, Carvalho RN, Chipman JK, Denslow ND, Halder M, Murphy CA, Roelofs D, Rolaki A, Schirmer K, Watanabe KH. Development and application of the adverse outcome pathway framework for understanding and predicting chronic toxicity: I. Challenges and research needs in ecotoxicology. CHEMOSPHERE 2015; 120:764-77. [PMID: 25439131 DOI: 10.1016/j.chemosphere.2014.09.068] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/11/2014] [Accepted: 09/19/2014] [Indexed: 05/02/2023]
Abstract
To elucidate the effects of chemicals on populations of different species in the environment, efficient testing and modeling approaches are needed that consider multiple stressors and allow reliable extrapolation of responses across species. An adverse outcome pathway (AOP) is a concept that provides a framework for organizing knowledge about the progression of toxicity events across scales of biological organization that lead to adverse outcomes relevant for risk assessment. In this paper, we focus on exploring how the AOP concept can be used to guide research aimed at improving both our understanding of chronic toxicity, including delayed toxicity as well as epigenetic and transgenerational effects of chemicals, and our ability to predict adverse outcomes. A better understanding of the influence of subtle toxicity on individual and population fitness would support a broader integration of sublethal endpoints into risk assessment frameworks. Detailed mechanistic knowledge would facilitate the development of alternative testing methods as well as help prioritize higher tier toxicity testing. We argue that targeted development of AOPs supports both of these aspects by promoting the elucidation of molecular mechanisms and their contribution to relevant toxicity outcomes across biological scales. We further discuss information requirements and challenges in application of AOPs for chemical- and site-specific risk assessment and for extrapolation across species. We provide recommendations for potential extension of the AOP framework to incorporate information on exposure, toxicokinetics and situation-specific ecological contexts, and discuss common interfaces that can be employed to couple AOPs with computational modeling approaches and with evolutionary life history theory. The extended AOP framework can serve as a venue for integration of knowledge derived from various sources, including empirical data as well as molecular, quantitative and evolutionary-based models describing species responses to toxicants. This will allow a more efficient application of AOP knowledge for quantitative chemical- and site-specific risk assessment as well as for extrapolation across species in the future.
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Affiliation(s)
- Ksenia J Groh
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Department of Chemistry and Applied Biosciences, 8093 Zürich, Switzerland.
| | - Raquel N Carvalho
- European Commission, Joint Research Centre, Institute for Environment and Sustainability, Water Resources Unit, 21027 Ispra, Italy
| | | | - Nancy D Denslow
- University of Florida, Department of Physiological Sciences, Center for Environmental and Human Toxicology and Genetics Institute, 32611 Gainesville, FL, USA
| | - Marlies Halder
- European Commission, Joint Research Centre, Institute for Health and Consumer Protection, Systems Toxicology Unit, 21027 Ispra, Italy
| | - Cheryl A Murphy
- Michigan State University, Fisheries and Wildlife, Lyman Briggs College, 48824 East Lansing, MI, USA
| | - Dick Roelofs
- VU University, Institute of Ecological Science, 1081 HV Amsterdam, The Netherlands
| | - Alexandra Rolaki
- European Commission, Joint Research Centre, Institute for Health and Consumer Protection, Systems Toxicology Unit, 21027 Ispra, Italy
| | - Kristin Schirmer
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Department of Environmental Systems Science, 8092 Zürich, Switzerland; EPF Lausanne, School of Architecture, Civil and Environmental Engineering, 1015 Lausanne, Switzerland
| | - Karen H Watanabe
- Oregon Health & Science University, Institute of Environmental Health, Division of Environmental and Biomolecular Systems, 97239-3098 Portland, OR, USA
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Abstract
There have been considerable advances in uncovering the complex genetic mechanisms that underlie nervous system disease pathogenesis, particularly with the advent of exome and whole genome sequencing techniques. The emerging field of epigenetics is also providing further insights into these mechanisms. Here, we discuss our understanding of the interplay that exists between genetic and epigenetic mechanisms in these disorders, highlighting the nascent field of epigenetic epidemiology-which focuses on analyzing relationships between the epigenome and environmental exposures, development and aging, other health-related phenotypes, and disease states-and next-generation research tools (i.e., those leveraging synthetic and chemical biology and optogenetics) for examining precisely how epigenetic modifications at specific genomic sites affect disease processes.
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Affiliation(s)
- Irfan A. Qureshi
- />Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461 USA
| | - Mark F. Mehler
- />Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461 USA
- />Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Ruth L. and David S. Gottesman Stem Cell Institute, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- />Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461 USA
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35
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Ma Q, Xiong F, Zhang L. Gestational hypoxia and epigenetic programming of brain development disorders. Drug Discov Today 2014; 19:1883-96. [PMID: 25256780 DOI: 10.1016/j.drudis.2014.09.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/23/2014] [Accepted: 09/16/2014] [Indexed: 01/04/2023]
Abstract
Adverse environmental conditions faced by an individual early during its life, such as gestational hypoxia, can have a profound influence on the risk of diseases, such as neurological disorders, in later life. Clinical and preclinical studies suggest that epigenetic programming of gene expression patterns in response to maternal stress have a crucial role in the fetal origins of neurological diseases. Herein, we summarize recent studies regarding the role of epigenetic mechanisms in the developmental programming of neurological diseases in offspring, primarily focusing on DNA methylation/demethylation and miRNAs. Such information could increase our understanding of the fetal origins of adult diseases and help develop effective prevention and intervention against neurological diseases.
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Affiliation(s)
- Qingyi Ma
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Fuxia Xiong
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Lubo Zhang
- Center for Perinatal Biology, Division of Pharmacology, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA.
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36
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Dauncey MJ. Nutrition, the brain and cognitive decline: insights from epigenetics. Eur J Clin Nutr 2014; 68:1179-85. [PMID: 25182020 DOI: 10.1038/ejcn.2014.173] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 07/11/2014] [Indexed: 02/07/2023]
Abstract
Nutrition affects the brain throughout life, with profound implications for cognitive decline and dementia. These effects are mediated by changes in expression of multiple genes, and responses to nutrition are in turn affected by individual genetic variability. An important layer of regulation is provided by the epigenome: nutrition is one of the many epigenetic regulators that modify gene expression without changes in DNA sequence. Epigenetic mechanisms are central to brain development, structure and function, and include DNA methylation, histone modifications and non-protein-coding RNAs. They enable cell-specific and age-related gene expression. Although epigenetic events can be highly stable, they can also be reversible, highlighting a critical role for nutrition in prevention and treatment of disease. Moreover, they suggest key mechanisms by which nutrition is involved in the pathogenesis of age-related cognitive decline: many nutrients, foods and diets have both immediate and long-term effects on the epigenome, including energy status, that is, energy intake, physical activity, energy metabolism and related changes in body composition, and micronutrients involved in DNA methylation, for example, folate, vitamins B6 and B12, choline, methionine. Optimal brain function results from highly complex interactions between numerous genetic and environmental factors, including food intake, physical activity, age and stress. Future studies linking nutrition with advances in neuroscience, genomics and epigenomics should provide novel approaches to the prevention of cognitive decline, and treatment of dementia and Alzheimer's disease.
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Affiliation(s)
- M J Dauncey
- Wolfson College, University of Cambridge, Cambridge, UK
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37
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Sex, epilepsy, and epigenetics. Neurobiol Dis 2014; 72 Pt B:210-6. [PMID: 24998474 DOI: 10.1016/j.nbd.2014.06.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 06/19/2014] [Accepted: 06/24/2014] [Indexed: 02/05/2023] Open
Abstract
Epilepsy refers to a heterogeneous group of disorders that are associated with a wide range of pathogenic mechanisms, seizure manifestations, comorbidity profiles, and therapeutic responses. These characteristics are all influenced quite significantly by sex. As with other conditions exhibiting such patterns, sex differences in epilepsy are thought to arise-at the most fundamental level-from the "organizational" and "activational" effects of sex hormones as well as from the direct actions of the sex chromosomes. However, our understanding of the specific molecular, cellular, and network level processes responsible for mediating sex differences in epilepsy remains limited. Because increasing evidence suggests that epigenetic mechanisms are involved both in epilepsy and in brain sexual dimorphism, we make the case here that analyzing epigenetic regulation will provide novel insights into the basis for sex differences in epilepsy.
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38
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Abstract
The circadian clock choreographs fundamental biological rhythms. This system is comprised of the master circadian pacemaker in the suprachiasmatic nucleus and associated pacemakers in other tissues that coordinate complex physiological processes and behaviors, such as sleep, feeding, and metabolism. The molecular circuitry that underlies these clocks and orchestrates circadian gene expression has been the focus of intensive investigation, and it is becoming clear that epigenetic factors are highly integrated into these networks. In this review, we draw attention to the fundamental roles played by epigenetic mechanisms in transcriptional and post-transcriptional regulation within the circadian clock system. We also highlight how alterations in epigenetic factors and mechanisms are being linked with sleep-wake disorders. These observations provide important insights into the pathogenesis and potential treatment of these disorders and implicate epigenetic deregulation in the significant but poorly understood interconnections now emerging between circadian processes and neurodegeneration, metabolic diseases, cancer, and aging.
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Affiliation(s)
- Irfan A. Qureshi
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Mark F. Mehler
- Roslyn and Leslie Goldstein Laboratory for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Brain Disorders and Neural Regeneration, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Rose F. Kennedy Center for Research on Intellectual and Developmental Disabilities, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Ruth S. and David L. Gottesman Stem Cell Institute, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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