1
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Saffari A, Brechmann B, Böger C, Saber WA, Jumo H, Whye D, Wood D, Wahlster L, Alecu JE, Ziegler M, Scheffold M, Winden K, Hubbs J, Buttermore ED, Barrett L, Borner GHH, Davies AK, Ebrahimi-Fakhari D, Sahin M. High-content screening identifies a small molecule that restores AP-4-dependent protein trafficking in neuronal models of AP-4-associated hereditary spastic paraplegia. Nat Commun 2024; 15:584. [PMID: 38233389 PMCID: PMC10794252 DOI: 10.1038/s41467-023-44264-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/06/2023] [Indexed: 01/19/2024] Open
Abstract
Unbiased phenotypic screens in patient-relevant disease models offer the potential to detect therapeutic targets for rare diseases. In this study, we developed a high-throughput screening assay to identify molecules that correct aberrant protein trafficking in adapter protein complex 4 (AP-4) deficiency, a rare but prototypical form of childhood-onset hereditary spastic paraplegia characterized by mislocalization of the autophagy protein ATG9A. Using high-content microscopy and an automated image analysis pipeline, we screened a diversity library of 28,864 small molecules and identified a lead compound, BCH-HSP-C01, that restored ATG9A pathology in multiple disease models, including patient-derived fibroblasts and induced pluripotent stem cell-derived neurons. We used multiparametric orthogonal strategies and integrated transcriptomic and proteomic approaches to delineate potential mechanisms of action of BCH-HSP-C01. Our results define molecular regulators of intracellular ATG9A trafficking and characterize a lead compound for the treatment of AP-4 deficiency, providing important proof-of-concept data for future studies.
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Affiliation(s)
- Afshin Saffari
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Division of Child Neurology and Inherited Metabolic Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Barbara Brechmann
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Cedric Böger
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Wardiya Afshar Saber
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Hellen Jumo
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Dosh Whye
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Delaney Wood
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lara Wahlster
- Department of Hematology & Oncology, Boston Children's Hospital & Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Julian E Alecu
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marvin Ziegler
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marlene Scheffold
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Kellen Winden
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jed Hubbs
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Elizabeth D Buttermore
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lee Barrett
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, 82152, Germany
| | - Alexandra K Davies
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Martinsried, 82152, Germany
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PT, UK
| | - Darius Ebrahimi-Fakhari
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
- Movement Disorders Program, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Mustafa Sahin
- Department of Neurology & F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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2
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Saffari A, Brechmann B, Boeger C, Saber WA, Jumo H, Whye D, Wood D, Wahlster L, Alecu J, Ziegler M, Scheffold M, Winden K, Hubbs J, Buttermore E, Barrett L, Borner G, Davies A, Sahin M, Ebrahimi-Fakhari D. High-Content Small Molecule Screen Identifies a Novel Compound That Restores AP-4-Dependent Protein Trafficking in Neuronal Models of AP-4-Associated Hereditary Spastic Paraplegia. RESEARCH SQUARE 2023:rs.3.rs-3036166. [PMID: 37398196 PMCID: PMC10312991 DOI: 10.21203/rs.3.rs-3036166/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Unbiased phenotypic screens in patient-relevant disease models offer the potential to detect novel therapeutic targets for rare diseases. In this study, we developed a high-throughput screening assay to identify molecules that correct aberrant protein trafficking in adaptor protein complex 4 (AP-4) deficiency, a rare but prototypical form of childhood-onset hereditary spastic paraplegia, characterized by mislocalization of the autophagy protein ATG9A. Using high-content microscopy and an automated image analysis pipeline, we screened a diversity library of 28,864 small molecules and identified a lead compound, C-01, that restored ATG9A pathology in multiple disease models, including patient-derived fibroblasts and induced pluripotent stem cell-derived neurons. We used multiparametric orthogonal strategies and integrated transcriptomic and proteomic approaches to delineate putative molecular targets of C-01 and potential mechanisms of action. Our results define molecular regulators of intracellular ATG9A trafficking and characterize a lead compound for the treatment of AP-4 deficiency, providing important proof-of-concept data for future Investigational New Drug (IND)-enabling studies.
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Affiliation(s)
| | | | | | | | | | - Dosh Whye
- Boston Children's Hospital, Harvard Medical School
| | - Delaney Wood
- Boston Children's Hospital, Harvard Medical School
| | | | - Julian Alecu
- Boston Children's Hospital, Harvard Medical School
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3
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Chong D, Jones NC, Schittenhelm RB, Anderson A, Casillas-Espinosa PM. Multi-omics Integration and Epilepsy: Towards a Better Understanding of Biological Mechanisms. Prog Neurobiol 2023:102480. [PMID: 37286031 DOI: 10.1016/j.pneurobio.2023.102480] [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: 02/15/2023] [Revised: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 06/09/2023]
Abstract
The epilepsies are a group of complex neurological disorders characterised by recurrent seizures. Approximately 30% of patients fail to respond to anti-seizure medications, despite the recent introduction of many new drugs. The molecular processes underlying epilepsy development are not well understood and this knowledge gap impedes efforts to identify effective targets and develop novel therapies against epilepsy. Omics studies allow a comprehensive characterisation of a class of molecules. Omics-based biomarkers have led to clinically validated diagnostic and prognostic tests for personalised oncology, and more recently for non-cancer diseases. We believe that, in epilepsy, the full potential of multi-omics research is yet to be realised and we envisage that this review will serve as a guide to researchers planning to undertake omics-based mechanistic studies.
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Affiliation(s)
- Debbie Chong
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, 3004, Victoria, Australia
| | - Nigel C Jones
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, 3004, Victoria, Australia; Department of Medicine (The Royal Melbourne Hospital), The University of Melbourne, 3000, Victoria, Australia; Department of Neurology, Alfred Health, Melbourne, 3004, Victoria, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility and Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Alison Anderson
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, 3004, Victoria, Australia; Department of Medicine (The Royal Melbourne Hospital), The University of Melbourne, 3000, Victoria, Australia; Department of Neurology, Alfred Health, Melbourne, 3004, Victoria, Australia
| | - Pablo M Casillas-Espinosa
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, 3004, Victoria, Australia; Department of Medicine (The Royal Melbourne Hospital), The University of Melbourne, 3000, Victoria, Australia; Department of Neurology, Alfred Health, Melbourne, 3004, Victoria, Australia
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4
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Sandouka S, Saadi A, Olowe R, Singh PK, Shekh-Ahmad T. Nrf2 is expressed more extensively in neurons than in astrocytes following an acute epileptic seizure in rats. J Neurochem 2023; 165:550-562. [PMID: 36807051 DOI: 10.1111/jnc.15786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/20/2023]
Abstract
The modulation of the nuclear factor erythroid 2-like 2 (Nrf2) activity has been reported to be implicated in the pathology of various neurological disorders, including epilepsy. Previous studies have demonstrated that Nrf2 is activated in the post-status epilepticus rat model; however, the spatiotemporal as well as cell type-specific expression of Nrf2 following brief epileptic seizures remains unclear. Here, we evaluated how an acute epileptic seizure affected the expression of Nrf2 and its downstream genes in the rats' cortex and the hippocampus up to 1 week following the induced seizure. We found that after a pentylenetetrazol-induced seizure, Nrf2 significantly increased at 24 h at the mRNA level and 3 h at the protein level in the cortex. In the hippocampus, the Nrf2 mRNA level peaked at 3 h after the seizure, and no significant changes were observed in the protein level. Interestingly, the mRNA level of Nrf2 downstream genes peaked at 3-6 h after seizure in both the cortex and the hippocampus. A significant increase in the expression of Nrf2 was observed in the neuronal population of CA1 and CA3 regions of the hippocampus, as well as in the cortex. Moreover, we observed no change in the co-localization of Nrf2 with astrocytes neither in the cortex nor in CA1 and CA3. Our results revealed that following a brief acute epileptic seizure, the expression of Nrf2 and its downstream genes is transiently increased and peaked at early timepoints after the seizure predominantly in the hippocampus, and this expression is restricted to the neuronal population.
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Affiliation(s)
- Sereen Sandouka
- The Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Aseel Saadi
- The Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rhoda Olowe
- The Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Prince Kumar Singh
- The Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tawfeeq Shekh-Ahmad
- The Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Chen WX, Liu B, Zhou L, Xiong X, Fu J, Huang ZF, Tan T, Tang M, Wang J, Tang YP. De novo mutations within metabolism networks of amino acid/protein/energy in Chinese autistic children with intellectual disability. Hum Genomics 2022; 16:52. [PMID: 36320054 PMCID: PMC9623983 DOI: 10.1186/s40246-022-00427-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is often accompanied by intellectual disability (ID). Despite extensive studies, however, the genetic basis for this comorbidity is still not clear. In this study, we tried to develop an analyzing pipeline for de novo mutations and possible pathways related to ID phenotype in ASD. Whole-exome sequencing (WES) was performed to screen de novo mutations and candidate genes in 79 ASD children together with their parents (trios). The de novo altering genes and relative pathways which were associated with ID phenotype were analyzed. The connection nodes (genes) of above pathways were selected, and the diagnostic value of these selected genes for ID phenotype in the study population was also evaluated. RESULTS We identified 89 de novo mutant genes, of which 34 genes were previously reported to be associated with ASD, including double hits in the EGF repeats of NOTCH1 gene (p.V999M and p.S1027L). Interestingly, of these 34 genes, 22 may directly affect intelligence quotient (IQ). Further analyses revealed that these IQ-related genes were enriched in protein synthesis, energy metabolism, and amino acid metabolism, and at least 9 genes (CACNA1A, ALG9, PALM2, MGAT4A, PCK2, PLEKHA1, PSME3, ADI1, and TLE3) were involved in all these three pathways. Seven patients who harbored these gene mutations showed a high prevalence of a low IQ score (< 70), a non-verbal language, and an early diagnostic age (< 4 years). Furthermore, our panel of these 9 genes reached a 10.2% diagnostic rate (5/49) in early diagnostic patients with a low IQ score and also reached a 10% diagnostic yield in those with both a low IQ score and non-verbal language (4/40). CONCLUSION We found some new genetic disposition for ASD accompanied with intellectual disability in this study. Our results may be helpful for etiologic research and early diagnoses of intellectual disability in ASD. Larger population studies and further mechanism studies are warranted.
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Affiliation(s)
- Wen-Xiong Chen
- grid.410737.60000 0000 8653 1072The Assessment and Intervention Center for Autistic Children, Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 Guangdong China
| | - Bin Liu
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China ,grid.258164.c0000 0004 1790 3548Department of Biobank, Shenzhen Baoan Women’s and Children’s Hospital, Jinan University, Shenzhen, 518102 Guangdong China
| | - Lijie Zhou
- grid.412719.8Department of Pediatric Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Xiaoli Xiong
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
| | - Jie Fu
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
| | - Zhi-Fang Huang
- grid.410737.60000 0000 8653 1072The Assessment and Intervention Center for Autistic Children, Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 Guangdong China
| | - Ting Tan
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
| | - Mingxi Tang
- grid.488387.8Department of Pathology, Affiliated Hospital of Southwest Medical University, Luzhou, 646000 Sichuan China
| | - Jun Wang
- grid.412719.8Department of Pediatric Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Ya-Ping Tang
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China ,grid.412719.8Department of Pediatric Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
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Zhang Y, Heylen L, Partoens M, Mills JD, Kaminski RM, Godard P, Gillard M, de Witte PAM, Siekierska A. Connectivity Mapping Using a Novel sv2a Loss-of-Function Zebrafish Epilepsy Model as a Powerful Strategy for Anti-epileptic Drug Discovery. Front Mol Neurosci 2022; 15:881933. [PMID: 35686059 PMCID: PMC9172968 DOI: 10.3389/fnmol.2022.881933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/08/2022] [Indexed: 12/03/2022] Open
Abstract
Synaptic vesicle glycoprotein 2A (SV2A) regulates action potential-dependent neurotransmitter release and is commonly known as the primary binding site of an approved anti-epileptic drug, levetiracetam. Although several rodent knockout models have demonstrated the importance of SV2A for functional neurotransmission, its precise physiological function and role in epilepsy pathophysiology remains to be elucidated. Here, we present a novel sv2a knockout model in zebrafish, a vertebrate with complementary advantages to rodents. We demonstrated that 6 days post fertilization homozygous sv2a–/– mutant zebrafish larvae, but not sv2a+/– and sv2a+/+ larvae, displayed locomotor hyperactivity and spontaneous epileptiform discharges, however, no major brain malformations could be observed. A partial rescue of this epileptiform brain activity could be observed after treatment with two commonly used anti-epileptic drugs, valproic acid and, surprisingly, levetiracetam. This observation indicated that additional targets, besides Sv2a, maybe are involved in the protective effects of levetiracetam against epileptic seizures. Furthermore, a transcriptome analysis provided insights into the neuropathological processes underlying the observed epileptic phenotype. While gene expression profiling revealed only one differentially expressed gene (DEG) between wildtype and sv2a+/– larvae, there were 4386 and 3535 DEGs between wildtype and sv2a–/–, and sv2a+/– and sv2a–/– larvae, respectively. Pathway and gene ontology (GO) enrichment analysis between wildtype and sv2a–/– larvae revealed several pathways and GO terms enriched amongst up- and down-regulated genes, including MAPK signaling, synaptic vesicle cycle, and extracellular matrix organization, all known to be involved in epileptogenesis and epilepsy. Importantly, we used the Connectivity map database to identify compounds with opposing gene signatures compared to the one observed in sv2a–/– larvae, to finally rescue the epileptic phenotype. Two out of three selected compounds rescued electrographic discharges in sv2a–/– larvae, while negative controls did not. Taken together, our results demonstrate that sv2a deficiency leads to increased seizure vulnerability and provide valuable insight into the functional importance of sv2a in the brain in general. Furthermore, we provided evidence that the concept of connectivity mapping represents an attractive and powerful approach in the discovery of novel compounds against epilepsy.
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Affiliation(s)
- Yifan Zhang
- Laboratory for Molecular Biodiscovery, KU Leuven, Leuven, Belgium
| | - Lise Heylen
- Laboratory for Molecular Biodiscovery, KU Leuven, Leuven, Belgium
| | - Michèle Partoens
- Laboratory for Molecular Biodiscovery, KU Leuven, Leuven, Belgium
| | - James D. Mills
- Department of Neuropathology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, United Kingdom
- Chalfont Centre for Epilepsy, Chalfont St Peter, United Kingdom
| | - Rafal M. Kaminski
- Department of Medicinal Chemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Kraków, Poland
- UCB Pharma, Braine-l’Alleud, Belgium
| | | | | | - Peter A. M. de Witte
- Laboratory for Molecular Biodiscovery, KU Leuven, Leuven, Belgium
- *Correspondence: Peter A. M. de Witte,
| | - Aleksandra Siekierska
- Laboratory for Molecular Biodiscovery, KU Leuven, Leuven, Belgium
- Aleksandra Siekierska,
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Alan T. Antiseizure medication discovery: Recent and future paradigm shifts. Epilepsia Open 2022; 7 Suppl 1:S133-S141. [PMID: 35090197 PMCID: PMC9340309 DOI: 10.1002/epi4.12581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 11/06/2022] Open
Abstract
Despite the ever-increasing number of available options for the treatment of epilepsies and the remarkable advances on the understanding of their pathophysiology, the proportion of refractory patients has remained approximately unmodified during the last 100 years. How efficient are we translating positive outcomes from basic research to clinical trials and/or the clinical scenario? It is possible that fresh thinking and exploration of new paradigms is required to arrive at truly novel therapeutic solutions, as seemingly proven by recently approved first-in-class antiseizure medications and drug candidates undergoing late clinical trials. Here, the author discusses some approximations in line with the network pharmacology philosophy, which may result in highly innovative (and, hopefully, safer and/or more efficacious) medications for the control of seizures, as embodied with some recent examples in the field, namely tailored multi-target agents and low-affinity ligands.
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Affiliation(s)
- Talevi Alan
- Laboratory of Bioactive Research and Development (LIDeB), Faculty of exact Sciences, University of La Plata (UNLP), 47 & 15, La Plata (B1900AJK), Buenos Aires, Argentina
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8
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Bando SY, Bertonha FB, Pimentel-Silva LR, de Oliveira JGM, Carneiro MAD, Oku MHM, Wen HT, Castro LHM, Moreira-Filho CA. Hippocampal CA3 transcriptional modules associated with granule cell alterations and cognitive impairment in refractory mesial temporal lobe epilepsy patients. Sci Rep 2021; 11:10257. [PMID: 33986407 PMCID: PMC8119682 DOI: 10.1038/s41598-021-89802-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/30/2021] [Indexed: 01/03/2023] Open
Abstract
In about a third of the patients with epilepsy the seizures are not drug-controlled. The current limitation of the antiepileptic drug therapy derives from an insufficient understanding of epilepsy pathophysiology. In order to overcome this situation, it is necessary to consider epilepsy as a disturbed network of interactions, instead of just looking for changes in single molecular components. Here, we studied CA3 transcriptional signatures and dentate gyrus histopathologic alterations in hippocampal explants surgically obtained from 57 RMTLE patients submitted to corticoamygdalohippocampectomy. By adopting a systems biology approach, integrating clinical, histopathological, and transcriptomic data (weighted gene co-expression network analysis), we were able to identify transcriptional modules highly correlated with age of disease onset, cognitive dysfunctions, and granule cell alterations. The enrichment analysis of transcriptional modules and the functional characterization of the highly connected genes in each trait-correlated module allowed us to unveil the modules’ main biological functions, paving the way for further investigations on their roles in RMTLE pathophysiology. Moreover, we found 15 genes with high gene significance values which have the potential to become novel biomarkers and/or therapeutic targets in RMTLE.
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Affiliation(s)
- Silvia Yumi Bando
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, 05403-900, Brazil
| | - Fernanda Bernardi Bertonha
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, 05403-900, Brazil
| | - Luciana Ramalho Pimentel-Silva
- Department of Neurology, Faculdade de Ciências Médicas da Universidade Estadual de Campinas, UNICAMP, Campinas, SP, 13083-887, Brazil
| | | | | | - Mariana Hiromi Manoel Oku
- Department of Neurology, Faculdade de Medicina da Universidade de São Paulo, São Paulo, SP, 05403-900, Brazil
| | - Hung-Tzu Wen
- Epilepsy Surgery Group, Hospital das Clínicas da FMUSP, São Paulo, SP, 05403-900, Brazil
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Bountress KE, Vladimirov V, McMichael G, Taylor ZN, Hardiman G, Chung D, Adams ZW, Danielson CK, Amstadter AB. Gene Expression Differences Between Young Adults Based on Trauma History and Post-traumatic Stress Disorder. Front Psychiatry 2021; 12:581093. [PMID: 33897478 PMCID: PMC8060466 DOI: 10.3389/fpsyt.2021.581093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 03/15/2021] [Indexed: 11/29/2022] Open
Abstract
Background: The purpose of this study was to identify gene expression differences associated with post-traumatic stress disorder (PTSD) and trauma exposure (TE) in a three-group study design comprised of those with and without trauma exposure and PTSD. Methods: We conducted gene expression and gene network analyses in a sample (n = 45) composed of female subjects of European Ancestry (EA) with PTSD, TE without PTSD, and controls. Results: We identified 283 genes differentially expressed between PTSD-TE groups. In an independent sample of Veterans (n = 78) a small minority of these genes were also differentially expressed. We identified 7 gene network modules significantly associated with PTSD and TE (Bonferroni corrected p ≤ 0.05), which at a false discovery rate (FDR) of q ≤ 0.2, were significantly enriched for biological pathways involved in focal adhesion, neuroactive ligand receptor interaction, and immune related processes among others. Conclusions: This study uses gene network analyses to identify significant gene modules associated with PTSD, TE, and controls. On an individual gene level, we identified a large number of differentially expressed genes between PTSD-TE groups, a minority of which were also differentially expressed in the independent sample. We also demonstrate a lack of network module preservation between PTSD and TE, suggesting that the molecular signature of PTSD and trauma are likely independent of each other. Our results provide a basis for the identification of likely disease pathways and biomarkers involved in the etiology of PTSD.
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Affiliation(s)
- Kaitlin E. Bountress
- Virginia Institute for Psychiatry and Behavioral Genetics, Virginia Commonwealth University (VCU), Richmond, VA, United States
| | - Vladimir Vladimirov
- Department of Psychiatry and Behavioral Sciences, College of Medicine Texas A&M University, Richmond, VA, United States
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD, United States
| | - Gowon McMichael
- Virginia Institute for Psychiatry and Behavioral Genetics, Virginia Commonwealth University (VCU), Richmond, VA, United States
| | - Z. Nathan Taylor
- Virginia Institute for Psychiatry and Behavioral Genetics, Virginia Commonwealth University (VCU), Richmond, VA, United States
| | - Gary Hardiman
- Institute for Global Food Security, Queens University Belfast, Belfast, United Kingdom
| | - Dongjun Chung
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Zachary W. Adams
- Department of Psychiatry, Indiana University of Medicine, Indianapolis, IN, United States
| | - Carla Kmett Danielson
- National Crime Victim Research and Treatment Center, Medical University of South Carolina, Charleston, SC, United States
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Ananda B. Amstadter
- Virginia Institute for Psychiatry and Behavioral Genetics, Virginia Commonwealth University (VCU), Richmond, VA, United States
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10
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Wang Y, Yang Z, Zhang K, Wan Y, Zhou Y, Yang Z. miR-135a-5p inhibitor protects glial cells against apoptosis via targeting SIRT1 in epilepsy. Exp Ther Med 2021; 21:431. [PMID: 33747170 PMCID: PMC7967866 DOI: 10.3892/etm.2021.9848] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022] Open
Abstract
Epilepsy is a common neurological disease that can induce severe physiological brain damage, including nerve cell apoptosis. MicroRNAs (miRs) have been widely investigated in epilepsy therapy. miR-135a-5p expression levels in children with temporal lobe epilepsy were found to be significantly increased. However, whether miR-135a-5p participates in epilepsy-induced cell apoptosis is not completely understood. In the present study, an in vitro model of epilepsy in BV2 microglia cells was induced using 6-µm kainic acid (KA). Reverse-transcription quantitative PCR was performed to analyze miR-135a-5p and sirtuin 1 (SIRT1) mRNA expression levels. Western blotting was performed to measure SIRT1 protein expression levels. BV2 cell proliferation and apoptosis were assessed by performing MTT assays and flow cytometry, respectively. A BCA protein assay kit was used to detect caspase-3 and caspase-9 activities. TargetScan and dual luciferase reporter assays were performed to investigate the interaction between miR-135a-5p and the 3'-untranslated region (UTR) of SIRT1. miR-135a-5p expression was significantly increased in the KA-induced in vitro model of epilepsy in BV2 microglia. miR-135a-5p inhibitor effectively promoted BV2 microglia proliferation and inhibited microglia apoptosis, whereas small interfering RNA targeting SIRT1 significantly repressed BV2 microglia proliferation and induced microglia apoptosis. In addition, the results demonstrated that the 3'-UTR of SIRT1 mRNA was targeted by miR-135a-5p, and SIRT1 knockdown attenuated miR-135a-5p inhibitor-mediated effects on epilepsy. In summary, the results of the present study identified the role of miR-135a-5p inhibitor pretreatment in protecting nerve cells against epilepsy-induced apoptosis and provided a novel strategy for the treatment of neural damage in seizures.
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Affiliation(s)
- Ying Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China.,Department of Pathology, School of Basic Medical Science, Central South University, P.R. China
| | - Zhiquan Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Kai Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yi Wan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yu Zhou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Zhuanyi Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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11
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Berger TC, Vigeland MD, Hjorthaug HS, Nome CG, Taubøll E, Selmer KK, Heuser K. Differential Glial Activation in Early Epileptogenesis-Insights From Cell-Specific Analysis of DNA Methylation and Gene Expression in the Contralateral Hippocampus. Front Neurol 2020; 11:573575. [PMID: 33312155 PMCID: PMC7702971 DOI: 10.3389/fneur.2020.573575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/06/2020] [Indexed: 12/23/2022] Open
Abstract
Background and Aims: Morphological changes in mesial temporal lobe epilepsy with hippocampal sclerosis (mTLE-HS) are well-characterized. Yet, it remains elusive whether these are a consequence of seizures or originate from a hitherto unknown underlying pathology. We recently published data on changes in gene expression and DNA methylation in the ipsilateral hippocampus (ILH) using the intracortical kainate mouse model of mTLE-HS. In order to explore the effects of epileptic activity alone and also to further disentangle what triggers morphological alterations, we investigated glial and neuronal changes in gene expression and DNA methylation in the contralateral hippocampus (CLH). Methods: The intracortical kainic acid mouse model of mTLE-HS was used to elicit status epilepticus. Hippocampi contralateral to the injection site from eight kainate-injected and eight sham mice were extracted and shock frozen at 24 h post-injection. Glial and neuronal nuclei were sorted by flow cytometry. Alterations in gene expression and DNA methylation were assessed using reduced representation bisulfite sequencing and RNA sequencing. The R package edgeR was used for statistical analysis. Results: The CLH featured substantial, mostly cell-specific changes in both gene expression and DNA methylation in glia and neurons. While changes in gene expression overlapped to a great degree between CLH and ILH, alterations in DNA methylation did not. In the CLH, we found a significantly lower number of glial genes up- and downregulated compared to previous results from the ILH. Furthermore, several genes and pathways potentially involved in anti-epileptogenic effects were upregulated in the CLH. By comparing gene expression data from the CLH to previous results from the ILH (featuring hippocampal sclerosis), we derive potential upstream targets for epileptogenesis, including glial Cox2 and Cxcl10. Conclusion: Despite the absence of morphological changes, the CLH displays substantial changes in gene expression and DNA methylation. We find that gene expression changes related to potential anti-epileptogenic effects seem to dominate compared to the pro-epileptogenic effects in the CLH and speculate whether this imbalance contributes to prevent morphological alterations like neuronal death and reactive gliosis.
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Affiliation(s)
- Toni C Berger
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Magnus D Vigeland
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Hanne S Hjorthaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | | | - Erik Taubøll
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Kaja K Selmer
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.,Division of Clinical Neuroscience, Department of Research and Innovation, Oslo University Hospital, Oslo, Norway.,National Centre for Epilepsy, Oslo University Hospital, Sandvika, Norway
| | - Kjell Heuser
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,University of Oslo, Oslo, Norway
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12
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Colasante G, Qiu Y, Massimino L, Di Berardino C, Cornford JH, Snowball A, Weston M, Jones SP, Giannelli S, Lieb A, Schorge S, Kullmann DM, Broccoli V, Lignani G. In vivo CRISPRa decreases seizures and rescues cognitive deficits in a rodent model of epilepsy. Brain 2020; 143:891-905. [PMID: 32129831 PMCID: PMC7089667 DOI: 10.1093/brain/awaa045] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/31/2019] [Accepted: 01/14/2020] [Indexed: 01/20/2023] Open
Abstract
Epilepsy is a major health burden, calling for new mechanistic insights and therapies. CRISPR-mediated gene editing shows promise to cure genetic pathologies, although hitherto it has mostly been applied ex vivo. Its translational potential for treating non-genetic pathologies is still unexplored. Furthermore, neurological diseases represent an important challenge for the application of CRISPR, because of the need in many cases to manipulate gene function of neurons in situ. A variant of CRISPR, CRISPRa, offers the possibility to modulate the expression of endogenous genes by directly targeting their promoters. We asked if this strategy can effectively treat acquired focal epilepsy, focusing on ion channels because their manipulation is known be effective in changing network hyperactivity and hypersynchronziation. We applied a doxycycline-inducible CRISPRa technology to increase the expression of the potassium channel gene Kcna1 (encoding Kv1.1) in mouse hippocampal excitatory neurons. CRISPRa-mediated Kv1.1 upregulation led to a substantial decrease in neuronal excitability. Continuous video-EEG telemetry showed that AAV9-mediated delivery of CRISPRa, upon doxycycline administration, decreased spontaneous generalized tonic-clonic seizures in a model of temporal lobe epilepsy, and rescued cognitive impairment and transcriptomic alterations associated with chronic epilepsy. The focal treatment minimizes concerns about off-target effects in other organs and brain areas. This study provides the proof-of-principle for a translational CRISPR-based approach to treat neurological diseases characterized by abnormal circuit excitability.
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Affiliation(s)
- Gaia Colasante
- San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milan, Italy
| | - Yichen Qiu
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, London, UK
| | - Luca Massimino
- San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milan, Italy
| | | | - Jonathan H Cornford
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, London, UK
| | - Albert Snowball
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, London, UK
| | - Mikail Weston
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, London, UK
| | - Steffan P Jones
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, London, UK
| | - Serena Giannelli
- San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milan, Italy
| | - Andreas Lieb
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, London, UK
| | - Stephanie Schorge
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, London, UK.,Department of Pharmacology, UCL School of Pharmacy, University College London, London, UK
| | - Dimitri M Kullmann
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, London, UK
| | - Vania Broccoli
- San Raffaele Scientific Institute, Via Olgettina 58, 20132, Milan, Italy.,CNR Institute of Neuroscience, Via Vanvitelli 32, 20129, Milan, Italy
| | - Gabriele Lignani
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, University College London, London, UK
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13
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Díaz-Rodríguez SM, López-López D, Herrero-Turrión MJ, Gómez-Nieto R, Canal-Alonso A, Lopéz DE. Inferior Colliculus Transcriptome After Status Epilepticus in the Genetically Audiogenic Seizure-Prone Hamster GASH/Sal. Front Neurosci 2020; 14:508. [PMID: 32528245 PMCID: PMC7264424 DOI: 10.3389/fnins.2020.00508] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/22/2020] [Indexed: 01/31/2023] Open
Abstract
The Genetic Audiogenic Seizure Hamster from Salamanca (GASH/Sal), an animal model of reflex epilepsy, exhibits generalized tonic–clonic seizures in response to loud sound with the epileptogenic focus localized in the inferior colliculus (IC). Ictal events in seizure-prone strains cause gene deregulation in the epileptogenic focus, which can provide insights into the epileptogenic mechanisms. Thus, the present study aimed to determine the expression profile of key genes in the IC of the GASH/Sal after the status epilepticus. For such purpose, we used RNA-Seq to perform a comparative study between the IC transcriptome of GASH/Sal and that of control hamsters both subjected to loud sound stimulation. After filtering for normalization and gene selection, a total of 36 genes were declared differentially expressed from the RNA-seq analysis in the IC. A set of differentially expressed genes were validated by RT-qPCR showing significant differentially expression between GASH/Sal hamsters and Syrian control hamsters. The confirmed differentially expressed genes were classified on ontological categories associated with epileptogenic events similar to those produced by generalized tonic seizures in humans. Subsequently, based on the result of metabolomics, we found the interleukin-4 and 13-signaling, and nucleoside transport as presumably altered routes in the GASH/Sal model. This research suggests that seizures in GASH/Sal hamsters are generated by multiple molecular substrates, which activate biological processes, molecular processes, cellular components and metabolic pathways associated with epileptogenic events similar to those produced by tonic seizures in humans. Therefore, our study supports the use of the GASH/Sal as a valuable animal model for epilepsy research, toward establishing correlations with human epilepsy and searching new biomarkers of epileptogenesis.
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Affiliation(s)
- Sandra M Díaz-Rodríguez
- Institute of Neurosciences of Castilla y León, University of Salamanca, Salamanca, Spain.,Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain.,Department of Cellular Biology and Pathology, University of Salamanca, Salamanca, Spain
| | - Daniel López-López
- Institute of Neurosciences of Castilla y León, University of Salamanca, Salamanca, Spain
| | - Manuel J Herrero-Turrión
- Institute of Neurosciences of Castilla y León, University of Salamanca, Salamanca, Spain.,Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain.,Neurological Tissue Bank INCYL (BTN-INCYL), Salamanca, Spain
| | - Ricardo Gómez-Nieto
- Institute of Neurosciences of Castilla y León, University of Salamanca, Salamanca, Spain.,Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain.,Department of Cellular Biology and Pathology, University of Salamanca, Salamanca, Spain
| | - Angel Canal-Alonso
- Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain.,BISITE Research Group, University of Salamanca, Salamanca, Spain
| | - Dolores E Lopéz
- Institute of Neurosciences of Castilla y León, University of Salamanca, Salamanca, Spain.,Institute of Biomedical Research of Salamanca, University of Salamanca, Salamanca, Spain.,Department of Cellular Biology and Pathology, University of Salamanca, Salamanca, Spain
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14
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Fu Y, Wu Z, Guo Z, Chen L, Ma Y, Wang Z, Xiao W, Wang Y. Systems-level analysis identifies key regulators driving epileptogenesis in temporal lobe epilepsy. Genomics 2020; 112:1768-1780. [DOI: 10.1016/j.ygeno.2019.09.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/31/2019] [Accepted: 09/25/2019] [Indexed: 01/05/2023]
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15
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Rambousek L, Gschwind T, Lafourcade C, Paterna JC, Dib L, Fritschy JM, Fontana A. Aberrant expression of PAR bZIP transcription factors is associated with epileptogenesis, focus on hepatic leukemia factor. Sci Rep 2020; 10:3760. [PMID: 32111960 PMCID: PMC7048777 DOI: 10.1038/s41598-020-60638-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/12/2020] [Indexed: 11/08/2022] Open
Abstract
Epilepsy is a widespread neurological disease characterized by abnormal neuronal activity resulting in recurrent seizures. There is mounting evidence that a circadian system disruption, involving clock genes and their downstream transcriptional regulators, is associated with epilepsy. In this study, we characterized the hippocampal expression of clock genes and PAR bZIP transcription factors (TFs) in a mouse model of temporal lobe epilepsy induced by intrahippocampal injection of kainic acid (KA). The expression of PAR bZIP TFs was significantly altered following KA injection as well as in other rodent models of acquired epilepsy. Although the PAR bZIP TFs are regulated by proinflammatory cytokines in peripheral tissues, we discovered that the regulation of their expression is inflammation-independent in hippocampal tissue and rather mediated by clock genes and hyperexcitability. Furthermore, we report that hepatic leukemia factor (Hlf), a member of PAR bZIP TFs family, is invariably downregulated in animal models of acquired epilepsy, regulates neuronal activity in vitro and its overexpression in dentate gyrus neurons in vivo leads to altered expression of genes associated with seizures and epilepsy. Overall, our study provides further evidence of PAR bZIP TFs involvement in epileptogenesis and points to Hlf as the key player.
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Affiliation(s)
- Lukas Rambousek
- Institute of Experimental Immunology, Winterthurerstrasse 190, University of Zurich, 8057, Zurich, Switzerland.
| | - Tilo Gschwind
- Institute of Pharmacology and Toxicology, Winterthurerstrasse 190, University of Zurich, 8057, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, 8057, Zurich, Switzerland
| | - Carlos Lafourcade
- Laboratorio de Neurociencias, Universidad de los Andes, 7620157, Santiago, Chile
| | - Jean-Charles Paterna
- Viral Vector Facility, Neuroscience Center Zurich, University of Zurich and ETH Zurich, 8057, Zurich, Switzerland
| | - Linda Dib
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Jean-Marc Fritschy
- Institute of Pharmacology and Toxicology, Winterthurerstrasse 190, University of Zurich, 8057, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, 8057, Zurich, Switzerland
| | - Adriano Fontana
- Institute of Experimental Immunology, Winterthurerstrasse 190, University of Zurich, 8057, Zurich, Switzerland
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16
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Styr B, Gonen N, Zarhin D, Ruggiero A, Atsmon R, Gazit N, Braun G, Frere S, Vertkin I, Shapira I, Harel M, Heim LR, Katsenelson M, Rechnitz O, Fadila S, Derdikman D, Rubinstein M, Geiger T, Ruppin E, Slutsky I. Mitochondrial Regulation of the Hippocampal Firing Rate Set Point and Seizure Susceptibility. Neuron 2019; 102:1009-1024.e8. [PMID: 31047779 PMCID: PMC6559804 DOI: 10.1016/j.neuron.2019.03.045] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 02/07/2019] [Accepted: 03/28/2019] [Indexed: 01/08/2023]
Abstract
Maintaining average activity within a set-point range constitutes a fundamental property of central neural circuits. However, whether and how activity set points are regulated remains unknown. Integrating genome-scale metabolic modeling and experimental study of neuronal homeostasis, we identified mitochondrial dihydroorotate dehydrogenase (DHODH) as a regulator of activity set points in hippocampal networks. The DHODH inhibitor teriflunomide stably suppressed mean firing rates via synaptic and intrinsic excitability mechanisms by modulating mitochondrial Ca2+ buffering and spare respiratory capacity. Bi-directional activity perturbations under DHODH blockade triggered firing rate compensation, while stabilizing firing to the lower level, indicating a change in the firing rate set point. In vivo, teriflunomide decreased CA3-CA1 synaptic transmission and CA1 mean firing rate and attenuated susceptibility to seizures, even in the intractable Dravet syndrome epilepsy model. Our results uncover mitochondria as a key regulator of activity set points, demonstrate the differential regulation of set points and compensatory mechanisms, and propose a new strategy to treat epilepsy.
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Affiliation(s)
- Boaz Styr
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Nir Gonen
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Daniel Zarhin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Antonella Ruggiero
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Refaela Atsmon
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Neta Gazit
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Gabriella Braun
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Samuel Frere
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Irena Vertkin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ilana Shapira
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Michal Harel
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Leore R Heim
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Maxim Katsenelson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ohad Rechnitz
- Department of Neuroscience, Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, 31096 Haifa, Israel
| | - Saja Fadila
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel; The Goldschleger Eye Research Institute, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Dori Derdikman
- Department of Neuroscience, Rappaport Faculty of Medicine and Research Institute, Technion - Israel Institute of Technology, 31096 Haifa, Israel
| | - Moran Rubinstein
- Sagol School of Neuroscience, Tel Aviv University, 69978 Tel Aviv, Israel; Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel; The Goldschleger Eye Research Institute, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Tamar Geiger
- Department of Human Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Eytan Ruppin
- Cancer Data Science Lab (CDSL), National Cancer Institute, NIH, Bethesda, MD, USA
| | - Inna Slutsky
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, 69978 Tel Aviv, Israel.
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17
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Duncan D, Vespa P, Pitkänen A, Braimah A, Lapinlampi N, Toga AW. Big data sharing and analysis to advance research in post-traumatic epilepsy. Neurobiol Dis 2019; 123:127-136. [PMID: 29864492 PMCID: PMC6274619 DOI: 10.1016/j.nbd.2018.05.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/24/2018] [Accepted: 05/31/2018] [Indexed: 11/26/2022] Open
Abstract
We describe the infrastructure and functionality for a centralized preclinical and clinical data repository and analytic platform to support importing heterogeneous multi-modal data, automatically and manually linking data across modalities and sites, and searching content. We have developed and applied innovative image and electrophysiology processing methods to identify candidate biomarkers from MRI, EEG, and multi-modal data. Based on heterogeneous biomarkers, we present novel analytic tools designed to study epileptogenesis in animal model and human with the goal of tracking the probability of developing epilepsy over time.
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Affiliation(s)
- Dominique Duncan
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
| | - Paul Vespa
- Division of Neurosurgery and Department of Neurology, University of California at Los Angeles School of Medicine, Los Angeles, CA, USA
| | - Asla Pitkänen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Adebayo Braimah
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Niina Lapinlampi
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Arthur W Toga
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
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18
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Wang A, Shu X, Niu X, Zhao W, Ai P, Li P, Zheng A. Comparison of gene co-networks analysis provide a systems view of rice (Oryza sativa L.) response to Tilletia horrida infection. PLoS One 2018; 13:e0202309. [PMID: 30372430 PMCID: PMC6205584 DOI: 10.1371/journal.pone.0202309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/09/2018] [Indexed: 01/29/2023] Open
Abstract
The biotrophic soil-borne fungus Tilletia horrida causes rice kernel smut, an important disease affecting the production of rice male sterile lines in most hybrid rice growing regions of the world. There are no successful ways of controlling this disease and there has been little study of mechanisms of resistance to T. horrida. Based on transcriptional data of different infection time points, we found 23, 782 and 23, 718 differentially expressed genes (fragments per kilobase of transcript sequence per million, FPKM >1) in Jiangcheng 3A (resistant to T. horrida) and 9311A (susceptible to T. horrida), respectively. In order to illuminate the differential responses of the two rice male sterile lines to T. horrida, we identified gene co-expression modules using the method of weighted gene co-expression network analysis (WGCNA) and compared the different biological functions of gene co-expression networks in key modules at different infection time points. The results indicated that gene co-expression networks in the two rice genotypes were different and that genes contained in some modules of the two groups may play important roles in resistance to T. horrida, such as DTH8 and OsHop/Sti1a. Furthermore, these results provide a global view of the responses of two different phenotypes to T. horrida, and assist our understanding of the regulation of expression changes after T. horrida infection.
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Affiliation(s)
- Aijun Wang
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Xinyue Shu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Xianyu Niu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Wenjuan Zhao
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Peng Ai
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ping Li
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
| | - Aiping Zheng
- Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China
- Key laboratory of Sichuan Crop Major Disease, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Southwest Crop Gene Resource and Genetic Improvement of Ministry of Education, Sichuan Agricultural University, Ya’ an, Sichuan, China
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19
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Dircio-Bautista M, Colín-González AL, Aguilera G, Maya-López M, Villeda-Hernández J, Galván-Arzate S, García E, Túnez I, Santamaría A. The Antiepileptic Drug Levetiracetam Protects Against Quinolinic Acid-Induced Toxicity in the Rat Striatum. Neurotox Res 2017; 33:837-845. [PMID: 29124680 DOI: 10.1007/s12640-017-9836-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 10/07/2017] [Accepted: 10/19/2017] [Indexed: 12/28/2022]
Abstract
Levetiracetam (LVT) is a relatively novel antiepileptic drug (AED) known to act through binding with the synaptic vesicular 2A (SV2A) protein, thus modulating the presynaptic neurotransmitter release. The tryptophan metabolite quinolinic acid (QUIN) acts as an excitotoxin when its brain concentrations reach toxic levels under pathological conditions. Since increased neuronal excitability induced by QUIN recruits degenerative events in the brain, and novel AED is also expected to exert neuroprotective effects in their pharmacological profiles, in this work the effect of LVT (54 mg/kg, i.p., administered for seven consecutive days) was tested as a pretreatment against the toxicity evoked by the bilateral intrastriatal injection of QUIN (60 nmol/μl) to adult rats. QUIN increased the striatal levels of peroxidized lipids and carbonylated proteins as indexes of oxidative damage 24 h after its infusion. In addition, in synaptosomal fractions isolated from QUIN-lesioned rats 24 h after the toxin infusion, γ-aminobutyric acid (GABA) release was decreased, whereas glutamate (Glu) release was increased. QUIN also decreased motor activity and augmented the rate of cell damage at 7 days post-lesion. All these alterations were significantly prevented by pretreatment of rats with LVT. The results of this study show a neuroprotective role and antioxidant action of LVT against the brain damage induced by excitotoxic events.
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Affiliation(s)
- Maricela Dircio-Bautista
- Laboratorio de Aminoácidos Excitadores, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., Insurgentes Sur 3877, 14269, Mexico City, Mexico.,Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Ana Laura Colín-González
- Laboratorio de Aminoácidos Excitadores, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., Insurgentes Sur 3877, 14269, Mexico City, Mexico
| | - Gabriela Aguilera
- Laboratorio de Aminoácidos Excitadores, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., Insurgentes Sur 3877, 14269, Mexico City, Mexico
| | - Marisol Maya-López
- Laboratorio de Aminoácidos Excitadores, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., Insurgentes Sur 3877, 14269, Mexico City, Mexico
| | - Juana Villeda-Hernández
- Laboratorio de Patología Experimental, Instituto Nacional de Neurología y Neurocirugía, S.S.A., 14269, Mexico City, Mexico
| | - Sonia Galván-Arzate
- Departamento de Neuroquímica, Instituto Nacional de Neurología y Neurocirugía, S.S.A., 14269, Mexico City, Mexico
| | - Esperanza García
- Laboratorio de Neuroinmunología, Instituto Nacional de Neurología y Neurocirugía, S.S.A., 14269, Mexico City, Mexico
| | - Isaac Túnez
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina y Enfermería, Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba, 14004, Cordoba, Spain
| | - Abel Santamaría
- Laboratorio de Aminoácidos Excitadores, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, S.S.A., Insurgentes Sur 3877, 14269, Mexico City, Mexico.
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20
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Dingledine R, Coulter DA, Fritsch B, Gorter JA, Lelutiu N, McNamara J, Nadler JV, Pitkänen A, Rogawski MA, Skene P, Sloviter RS, Wang Y, Wadman WJ, Wasterlain C, Roopra A. Transcriptional profile of hippocampal dentate granule cells in four rat epilepsy models. Sci Data 2017; 4:170061. [PMID: 28485718 PMCID: PMC5423390 DOI: 10.1038/sdata.2017.61] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/04/2017] [Indexed: 12/11/2022] Open
Abstract
Global expression profiling of neurologic or psychiatric disorders has been confounded by variability among laboratories, animal models, tissues sampled, and experimental platforms, with the result being that few genes demonstrate consistent expression changes. We attempted to minimize these confounds by pooling dentate granule cell transcriptional profiles from 164 rats in seven laboratories, using three status epilepticus (SE) epilepsy models (pilocarpine, kainate, self-sustained SE), plus amygdala kindling. In each epilepsy model, RNA was harvested from laser-captured dentate granule cells from six rats at four time points early in the process of developing epilepsy, and data were collected from two independent laboratories in each rodent model except SSSE. Hierarchical clustering of differentially-expressed transcripts in the three SE models revealed complete separation between controls and SE rats isolated 1 day after SE. However, concordance of gene expression changes in the SE models was only 26–38% between laboratories, and 4.5% among models, validating the consortium approach. Transcripts with unusually highly variable control expression across laboratories provide a ‘red herring’ list for low-powered studies.
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Affiliation(s)
- Raymond Dingledine
- Department of Pharmacology, Emory University, Atlanta, Georgia 30322, USA
| | - Douglas A Coulter
- Department of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Brita Fritsch
- Department of Neurology, University Hospital Freiburg, 79106 Freiburg, Germany
| | - Jan A Gorter
- Swammerdam Institute for Life Science, Center for Neuroscience, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, Netherlands
| | - Nadia Lelutiu
- Department of Pharmacology, Emory University, Atlanta, Georgia 30322, USA
| | - James McNamara
- Department of Neurobiology, Duke University, Durham, North Carolina 27710, USA
| | - J Victor Nadler
- Department of Neurobiology, Duke University, Durham, North Carolina 27710, USA
| | - Asla Pitkänen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, Kuopio FIN-70211, Finland
| | - Michael A Rogawski
- Departments of Neurology and Pharmacology, School of Medicine, University of California, Davis, Sacramento, California 95817, USA
| | - Pate Skene
- Department of Neurobiology, Duke University, Durham, North Carolina 27710, USA
| | - Robert S Sloviter
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
| | - Yu Wang
- Department of Neurobiology, Duke University, Durham, North Carolina 27710, USA
| | - Wytse J Wadman
- Swammerdam Institute for Life Science, Center for Neuroscience, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, Netherlands
| | - Claude Wasterlain
- Department of Neurology and Brain Research Institute, and VA Greater Los Angeles Health Care System, Univ. California Los Angeles, Los Angeles, California 90073, USA
| | - Avtar Roopra
- Department of Neuroscience, Univ. Wisconsin, Madison, Wisconsin 53705, USA
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21
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Long HY, Feng L, Kang J, Luo ZH, Xiao WB, Long LL, Yan XX, Zhou L, Xiao B. Blood DNA methylation pattern is altered in mesial temporal lobe epilepsy. Sci Rep 2017; 7:43810. [PMID: 28276448 PMCID: PMC5343463 DOI: 10.1038/srep43810] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/31/2017] [Indexed: 12/28/2022] Open
Abstract
Mesial temporal lobe epilepsy (MTLE) is a common epileptic disorder; little is known whether it is associated with peripheral epigenetic changes. Here we compared blood whole genomic DNA methylation pattern in MTLE patients (n = 30) relative to controls (n = 30) with the Human Methylation 450 K BeadChip assay, and explored genes and pathways that were differentially methylated using bioinformatics profiling. The MTLE and control groups showed significantly different (P < 1.03e-07) DNA methylation at 216 sites, with 164 sites involved hyper- and 52 sites hypo- methylation. Two hyper- and 32 hypo-methylated sites were associated with promoters, while 87 hyper- and 43 hypo-methylated sites corresponded to coding regions. The differentially methylated genes were largely related to pathways predicted to participate in anion binding, oxidoreductant activity, growth regulation, skeletal development and drug metabolism, with the most distinct ones included SLC34A2, CLCN6, CLCA4, CYP3A43, CYP3A4 and CYP2C9. Among the MTLE patients, panels of genes also appeared to be differentially methylated relative to disease duration, resistance to anti-epileptics and MRI alterations of hippocampal sclerosis. The peripheral epigenetic changes observed in MTLE could be involved in certain disease-related modulations and warrant further translational investigations.
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Affiliation(s)
- Hong-Yu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Li Feng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jin Kang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhao-Hui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Wen-Biao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Li-Li Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xiao-Xin Yan
- Department of Anatomy and Neurobiology, Central South University School of Basic Medicine, Changsha, Hunan 410013, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Changsha, Hunan 410008, China
| | - Luo Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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22
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mTOR and MAPK: from localized translation control to epilepsy. BMC Neurosci 2016; 17:73. [PMID: 27855659 PMCID: PMC5114760 DOI: 10.1186/s12868-016-0308-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/09/2016] [Indexed: 01/03/2023] Open
Abstract
Background Epilepsy is one of the most common neurological diseases characterized by excessive hyperexcitability of neurons. Molecular mechanisms of epilepsy are diverse and not really understood. All in common is the misregulation of proteins that determine excitability such as potassium and sodium channels as well as GABA receptors; which are all known as biomarkers for epilepsy. Two recently identified key pathways involve the kinases mechanistic target of rapamycin (mTOR) and mitogen-activated protein kinases (MAPK). Interestingly, mRNAs coding for those biomarkers are found to be localized at or near synapses indicating a local misregulation of synthesis and activity. Results Research in the last decade indicates that RNA-binding proteins (RBPs) responsible for mRNA localization, stability and translation mediate local expression control. Among others, they are affected by mTOR and MAPK to guide expression of epileptic factors. These results suggest that mTOR/MAPK act on RBPs to regulate the fate of mRNAs, indicating a misregulation of protein expression at synapses in epilepsy. Conclusion We propose that mTOR and MAPK regulate RBPs, thereby guiding the local expression of their target-mRNAs encoding for markers of epilepsy. Thus, misregulated mTOR/MAPK-RBP interplay may result in excessive local synthesis of ion channels and receptors thereby leading to hyperexcitability. Continuous stimulation of synapses further activates mTOR/MAPK pathway reinforcing their effect on RBP-mediated expression control establishing the basis for epilepsy. Here, we highlight findings showing the tight interplay between mTOR as well as MAPK with RBPs to control expression for epileptic biomarkers.
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23
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Haenisch S, von Rüden EL, Wahmkow H, Rettenbeck ML, Michler C, Russmann V, Bruckmueller H, Waetzig V, Cascorbi I, Potschka H. miRNA-187-3p-Mediated Regulation of the KCNK10/TREK-2 Potassium Channel in a Rat Epilepsy Model. ACS Chem Neurosci 2016; 7:1585-1594. [PMID: 27609046 DOI: 10.1021/acschemneuro.6b00222] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Regulatory RNAs play a key role in the regulation of protein expression patterns in neurological diseases. Here we studied the regulation of miRNAs in a chronic rat model of temporal lobe epilepsy. The analysis was focused on a putative link with pharmacoresponsiveness as well as the functional implications of the regulation of a selected miRNA. The findings did not reveal a difference in hippocampal miRNA expression between phenobarbital responders and nonresponders. However, when comparing rats following status epilepticus with control rats we identified 13 differentially expressed miRNAs with miRNA-187-3p being most strongly regulated. mRNAs encoding KCNK10/TREK-2 as well as DYRK2 were confirmed as targets of miRNA-187-3p. Expression of the potassium channel protein KCNK10/TREK-2 negatively correlated with hippocampal miRNA-187-3p expression and proved to be upregulated in the chronic phase of the epilepsy model. In conclusion, our data do not suggest a relevant impact of miRNA expression patterns on pharmacoresponsiveness. However, we confirmed regulation of miRNA-187-3p and demonstrated that it impacts the expression of the two-pore domain potassium channel protein KCNK10/TREK-2. Considering evidence from brain ischemia models, KCNK10/TREK-2 upregulation might serve a protective function with a beneficial impact on astrocytic potassium and glutamate homeostasis.
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Affiliation(s)
- Sierk Haenisch
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein , 24105 Campus Kiel, Germany
| | - Eva-Lotta von Rüden
- Institute of Pharmacology, Toxicology, and Pharmacy, Ludwig-Maximilians-University (LMU) , 80539 Munich, Germany
| | - Hannes Wahmkow
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein , 24105 Campus Kiel, Germany
| | - Maruja L Rettenbeck
- Institute of Pharmacology, Toxicology, and Pharmacy, Ludwig-Maximilians-University (LMU) , 80539 Munich, Germany
| | - Christina Michler
- Institute of Pharmacology, Toxicology, and Pharmacy, Ludwig-Maximilians-University (LMU) , 80539 Munich, Germany
| | - Vera Russmann
- Institute of Pharmacology, Toxicology, and Pharmacy, Ludwig-Maximilians-University (LMU) , 80539 Munich, Germany
| | - Henrike Bruckmueller
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein , 24105 Campus Kiel, Germany
| | - Vicki Waetzig
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein , 24105 Campus Kiel, Germany
| | - Ingolf Cascorbi
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein , 24105 Campus Kiel, Germany
| | - Heidrun Potschka
- Institute of Pharmacology, Toxicology, and Pharmacy, Ludwig-Maximilians-University (LMU) , 80539 Munich, Germany
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24
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Löscher W, Gillard M, Sands ZA, Kaminski RM, Klitgaard H. Synaptic Vesicle Glycoprotein 2A Ligands in the Treatment of Epilepsy and Beyond. CNS Drugs 2016; 30:1055-1077. [PMID: 27752944 PMCID: PMC5078162 DOI: 10.1007/s40263-016-0384-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The synaptic vesicle glycoprotein SV2A belongs to the major facilitator superfamily (MFS) of transporters and is an integral constituent of synaptic vesicle membranes. SV2A has been demonstrated to be involved in vesicle trafficking and exocytosis, processes crucial for neurotransmission. The anti-seizure drug levetiracetam was the first ligand to target SV2A and displays a broad spectrum of anti-seizure activity in various preclinical models. Several lines of preclinical and clinical evidence, including genetics and protein expression changes, support an important role of SV2A in epilepsy pathophysiology. While the functional consequences of SV2A ligand binding are not fully elucidated, studies suggest that subsequent SV2A conformational changes may contribute to seizure protection. Conversely, the recently discovered negative SV2A modulators, such as UCB0255, counteract the anti-seizure effect of levetiracetam and display procognitive properties in preclinical models. More broadly, dysfunction of SV2A may also be involved in Alzheimer's disease and other types of cognitive impairment, suggesting potential novel therapies for levetiracetam and its congeners. Furthermore, emerging data indicate that there may be important roles for two other SV2 isoforms (SV2B and SV2C) in the pathogenesis of epilepsy, as well as other neurodegenerative diseases. Utilization of recently developed SV2A positron emission tomography ligands will strengthen and reinforce the pharmacological evidence that SV2A is a druggable target, and will provide a better understanding of its role in epilepsy and other neurological diseases, aiding in further defining the full therapeutic potential of SV2A modulation.
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Affiliation(s)
- Wolfgang Löscher
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Bünteweg 17, 30559, Hannover, Germany.
- Center for Systems Neuroscience, Hannover, Germany.
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25
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Chen H, Xu G, Du H, Yi M, Li C. Integrative analysis of gene expression associated with epilepsy in human epilepsy and animal models. Mol Med Rep 2016; 13:4920-6. [PMID: 27081788 DOI: 10.3892/mmr.2016.5122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 03/21/2016] [Indexed: 11/05/2022] Open
Abstract
Epilepsy is a severe neuropsychiatric disorder, the cause of which remains to be elucidated. Genome‑wide association studies, DNA microarrays and proteomes have been widely applied to identify the candidate genes involved in epileptogenesis, and integrative analyses are often capable of extracting more detailed biological information from the data. In the present study, a total number of 1,065 genes in different animal models were collected to construct an epilepsy candidate gene database. Further analyses suggested that the response to organic substances, the intracellular signaling cascade and neurological system processes were significantly enriched biological processes, and the mitogen-activated protein kinase pathway was identified as a putative epileptogenic signaling pathway. In addition, the five key genes, growth factor receptor bound 2, amyloid β (A4) precursor protein, transforming growth factor‑β, vascular endothelial growth factor and cyclin‑dependent kinase inhibitor 1, were identified as being critical as central nodes in the protein networks. Reverse transcription‑quantitative polymerase chain reaction analysis revealed that these genes were all upregulated at the mRNA level in the epileptic loci compared with the resection margin of tissue samples from the same patients diagnosed with epilepsy. The data mining performed in the present study thus was shown to be a useful tool, which may contribute to obtaining further information on epileptic disorders and delineating the molecular mechanism of the associated genes.
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Affiliation(s)
- Hengling Chen
- The Laboratory of Membrane Ion Channels and Medicine, Key Laboratory of Cognitive Science of State Ethnic Affairs Commission, Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis and Treatment, College of Biomedical Engineering, South‑Central University for Nationalities, Wuhan, Hubei 430074, P.R. China
| | - Guozheng Xu
- Department of Neurosurgery, Wuhan General Hospital of Guangzhou Military Command, Wuhan, Hubei 430070, P.R. China
| | - Hao Du
- Department of Neurosurgery, Wuhan General Hospital of Guangzhou Military Command, Wuhan, Hubei 430070, P.R. China
| | - Minhan Yi
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, P.R. China
| | - Chenhong Li
- The Laboratory of Membrane Ion Channels and Medicine, Key Laboratory of Cognitive Science of State Ethnic Affairs Commission, Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis and Treatment, College of Biomedical Engineering, South‑Central University for Nationalities, Wuhan, Hubei 430074, P.R. China
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26
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Abstract
The difficulty to understand, diagnose, and treat neurological disorders stems from the great complexity of the central nervous system on different levels of physiological granularity. The individual components, their interactions, and dynamics involved in brain development and function can be represented as molecular, cellular, or functional networks, where diseases are perturbations of networks. These networks can become a useful research tool in investigating neurological disorders if they are properly tailored to reflect corresponding mechanisms. Here, we review approaches to construct networks specific for neurological disorders describing disease-related pathology on different scales: the molecular, cellular, and brain level. We also briefly discuss cross-scale network analysis as a necessary integrator of these scales.
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27
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Mamdani M, Williamson V, McMichael GO, Blevins T, Aliev F, Adkins A, Hack L, Bigdeli T, D. van der Vaart A, Web BT, Bacanu SA, Kalsi G, Kendler KS, Miles MF, Dick D, Riley BP, Dumur C, Vladimirov VI. Integrating mRNA and miRNA Weighted Gene Co-Expression Networks with eQTLs in the Nucleus Accumbens of Subjects with Alcohol Dependence. PLoS One 2015; 10:e0137671. [PMID: 26381263 PMCID: PMC4575063 DOI: 10.1371/journal.pone.0137671] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/05/2015] [Indexed: 11/18/2022] Open
Abstract
Alcohol consumption is known to lead to gene expression changes in the brain. After performing weighted gene co-expression network analyses (WGCNA) on genome-wide mRNA and microRNA (miRNA) expression in Nucleus Accumbens (NAc) of subjects with alcohol dependence (AD; N = 18) and of matched controls (N = 18), six mRNA and three miRNA modules significantly correlated with AD were identified (Bonferoni-adj. p≤ 0.05). Cell-type-specific transcriptome analyses revealed two of the mRNA modules to be enriched for neuronal specific marker genes and downregulated in AD, whereas the remaining four mRNA modules were enriched for astrocyte and microglial specific marker genes and upregulated in AD. Gene set enrichment analysis demonstrated that neuronal specific modules were enriched for genes involved in oxidative phosphorylation, mitochondrial dysfunction and MAPK signaling. Glial-specific modules were predominantly enriched for genes involved in processes related to immune functions, i.e. cytokine signaling (all adj. p≤ 0.05). In mRNA and miRNA modules, 461 and 25 candidate hub genes were identified, respectively. In contrast to the expected biological functions of miRNAs, correlation analyses between mRNA and miRNA hub genes revealed a higher number of positive than negative correlations (χ2 test p≤ 0.0001). Integration of hub gene expression with genome-wide genotypic data resulted in 591 mRNA cis-eQTLs and 62 miRNA cis-eQTLs. mRNA cis-eQTLs were significantly enriched for AD diagnosis and AD symptom counts (adj. p = 0.014 and p = 0.024, respectively) in AD GWAS signals in a large, independent genetic sample from the Collaborative Study on Genetics of Alcohol (COGA). In conclusion, our study identified putative gene network hubs coordinating mRNA and miRNA co-expression changes in the NAc of AD subjects, and our genetic (cis-eQTL) analysis provides novel insights into the etiological mechanisms of AD.
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Affiliation(s)
- Mohammed Mamdani
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Vernell Williamson
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Gowon O. McMichael
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Tana Blevins
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Fazil Aliev
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Amy Adkins
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Laura Hack
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Tim Bigdeli
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Andrew D. van der Vaart
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Bradley Todd Web
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Gursharan Kalsi
- Department of Social, Genetic and Developmental Psychiatry, Institute of Psychiatry, London SE5 8AF, United Kingdom
| | | | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Michael F. Miles
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Danielle Dick
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Brien P. Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Catherine Dumur
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Vladimir I. Vladimirov
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond, VA, United States of America
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD, United States of America
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28
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Abstract
Epileptogenesis is a chronic process that can be triggered by genetic or acquired factors, and that can continue long after epilepsy diagnosis. In 2015, epileptogenesis is not a treatment indication, and there are no therapies available in clinic to treat individuals at risk of epileptogenesis. However, thanks to active research, a large number of animal models have become available for search of molecular mechanisms of epileptogenesis. The first glimpses of treatment targets and biomarkers that could be developed to become useful in clinic are in sight. However, the heterogeneity of the epilepsy condition, and the dynamics of molecular changes over the course of epileptogenesis remain as challenges to overcome.
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Affiliation(s)
- Asla Pitkänen
- Department of Neurobiology, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, FI-70211 Kuopio, Finland Department of Neurology, Kuopio University Hospital, FI-70211 Kuopio, Finland
| | - Katarzyna Lukasiuk
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - F Edward Dudek
- Department of Neurosurgery, University of Utah School of Medicine, Salt Lake City, Utah 84108
| | - Kevin J Staley
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts 02114
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29
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Becherel OJ, Sun J, Yeo AJ, Nayler S, Fogel BL, Gao F, Coppola G, Criscuolo C, De Michele G, Wolvetang E, Lavin MF. A new model to study neurodegeneration in ataxia oculomotor apraxia type 2. Hum Mol Genet 2015; 24:5759-74. [PMID: 26231220 DOI: 10.1093/hmg/ddv296] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 07/20/2015] [Indexed: 12/18/2022] Open
Abstract
Ataxia oculomotor apraxia type 2 (AOA2) is a rare autosomal recessive cerebellar ataxia. Recent evidence suggests that the protein defective in this syndrome, senataxin (SETX), functions in RNA processing to protect the integrity of the genome. To date, only patient-derived lymphoblastoid cells, fibroblasts and SETX knockdown cells were available to investigate AOA2. Recent disruption of the Setx gene in mice did not lead to neurobehavioral defects or neurodegeneration, making it difficult to study the etiology of AOA2. To develop a more relevant neuronal model to study neurodegeneration in AOA2, we derived neural progenitors from a patient with AOA2 and a control by induced pluripotent stem cell (iPSC) reprogramming of fibroblasts. AOA2 iPSC and neural progenitors exhibit increased levels of oxidative damage, DNA double-strand breaks, increased DNA damage-induced cell death and R-loop accumulation. Genome-wide expression and weighted gene co-expression network analysis in these neural progenitors identified both previously reported and novel affected genes and cellular pathways associated with senataxin dysfunction and the pathophysiology of AOA2, providing further insight into the role of senataxin in regulating gene expression on a genome-wide scale. These data show that iPSCs can be generated from patients with the autosomal recessive ataxia, AOA2, differentiated into neurons, and that both cell types recapitulate the AOA2 cellular phenotype. This represents a novel and appropriate model system to investigate neurodegeneration in this syndrome.
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Affiliation(s)
- Olivier J Becherel
- UQ Centre for Clinical Research (UQCCR), School of Chemistry and Molecular Biosciences and
| | - Jane Sun
- Australian Institute for Bioengineering and Nanotechnology
| | - Abrey J Yeo
- UQ Centre for Clinical Research (UQCCR), School of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia
| | - Sam Nayler
- Australian Institute for Bioengineering and Nanotechnology
| | | | - Fuying Gao
- Department of Psychiatry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA and
| | - Giovanni Coppola
- Department of Neurology and Department of Psychiatry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA and
| | - Chiara Criscuolo
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, Federico II University, Napoli, Italy
| | - Giuseppe De Michele
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, Federico II University, Napoli, Italy
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Lee RS, Pirooznia M, Guintivano J, Ly M, Ewald ER, Tamashiro KL, Gould TD, Moran TH, Potash JB. Search for common targets of lithium and valproic acid identifies novel epigenetic effects of lithium on the rat leptin receptor gene. Transl Psychiatry 2015; 5:e600. [PMID: 26171981 PMCID: PMC5068731 DOI: 10.1038/tp.2015.90] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 05/21/2015] [Accepted: 06/01/2015] [Indexed: 12/24/2022] Open
Abstract
Epigenetics may have an important role in mood stabilizer action. Valproic acid (VPA) is a histone deacetylase inhibitor, and lithium (Li) may have downstream epigenetic actions. To identify genes commonly affected by both mood stabilizers and to assess potential epigenetic mechanisms that may be involved in their mechanism of action, we administered Li (N = 12), VPA (N = 12), and normal chow (N = 12) to Brown Norway rats for 30 days. Genomic DNA and mRNA were extracted from the hippocampus. We used the mRNA to perform gene expression analysis on Affymetrix microarray chips, and for genes commonly regulated by both Li and VPA, we validated expression levels using quantitative real-time PCR. To identify potential mechanisms underlying expression changes, genomic DNA was bisulfite treated for pyrosequencing of key CpG island 'shores' and promoter regions, and chromatin was prepared from both hippocampal tissue and a hippocampal-derived cell line to assess modifications of histones. For most genes, we found little evidence of DNA methylation changes in response to the medications. However, we detected histone H3 methylation and acetylation in the leptin receptor gene, Lepr, following treatment with both drugs. VPA-mediated effects on histones are well established, whereas the Li effects constitute a novel mechanism of transcriptional derepression for this drug. These data support several shared transcriptional targets of Li and VPA, and provide evidence suggesting leptin signaling as an epigenetic target of two mood stabilizers. Additional work could help clarify whether leptin signaling in the brain has a role in the therapeutic action of Li and VPA in bipolar disorder.
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Affiliation(s)
- R S Lee
- Johns Hopkins Mood Disorders Center of the Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA,Johns Hopkins Mood Disorders Center of the Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Ross 1068, Baltimore, MD 21205, USA. E-mail:
| | - M Pirooznia
- Johns Hopkins Mood Disorders Center of the Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - J Guintivano
- Johns Hopkins Mood Disorders Center of the Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA,Graduate Program in Human Genetics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - M Ly
- Johns Hopkins Mood Disorders Center of the Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - E R Ewald
- Johns Hopkins Mood Disorders Center of the Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - K L Tamashiro
- Johns Hopkins Mood Disorders Center of the Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - T D Gould
- Departments of Psychiatry, Pharmacology, and Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - T H Moran
- Johns Hopkins Mood Disorders Center of the Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - J B Potash
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
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Gorter JA, van Vliet EA, Lopes da Silva FH. Which insights have we gained from the kindling and post-status epilepticus models? J Neurosci Methods 2015; 260:96-108. [PMID: 25842270 DOI: 10.1016/j.jneumeth.2015.03.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 11/24/2022]
Abstract
Experimental animal epilepsy research got a big boost since the discovery that daily mild and short (seconds) tetanic stimulations in selected brain regions led to seizures with increasing duration and severity. This model that was developed by Goddard (1967) became known as the kindling model for epileptogenesis and has become a widely used model for temporal lobe epilepsy with complex partial seizures. During the late ninety-eighties the number of publications related to electrical kindling reached its maximum. However, since the kindling procedure is rather labor intensive and animals only develop spontaneous seizures (epilepsy) after hundreds of stimulations, research has shifted toward models in which the animals exhibit spontaneous seizures after a relatively short latent period. This led to post-status epilepticus (SE) models in which animals experience SE after injection of pharmacological compounds (e.g. kainate or pilocarpine) or via electrical stimulation of (limbic) brain regions. These post-SE models are the most widely used models in epilepsy research today. However, not all aspects of mesial temporal lobe epilepsy (MTLE) are reproduced and the widespread brain damage is often a caricature of the situation in the patient. Therefore, there is a need for models that can better replicate the disease. Kindling, although already a classic model, can still offer valid clues in this context. In this paper, we review different aspects of the kindling model with emphasis on experiments in the rat. Next, we review characteristic properties of the post-SE models and compare the neuropathological, electrophysiological and molecular differences between kindling and post-SE epilepsy models. Finally, we shortly discuss the advantages and disadvantages of these models.
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Affiliation(s)
- Jan A Gorter
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
| | - Erwin A van Vliet
- Department of (Neuro)Pathology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Fernando H Lopes da Silva
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands; Instituto Superior Técnico, University of Lisbon, 1049-001 Lisbon, Portugal
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Winden KD, Bragin A, Engel J, Geschwind DH. Molecular alterations in areas generating fast ripples in an animal model of temporal lobe epilepsy. Neurobiol Dis 2015; 78:35-44. [PMID: 25818007 DOI: 10.1016/j.nbd.2015.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 01/26/2015] [Accepted: 02/13/2015] [Indexed: 01/05/2023] Open
Abstract
The molecular basis of epileptogenesis is poorly characterized. Studies in humans and animal models have identified an electrophysiological signature that precedes the onset of epilepsy, which has been termed fast ripples (FRs) based on its frequency. Multiple lines of evidence implicate regions generating FRs in epileptogenesis, and FRs appear to demarcate the seizure onset zone, suggesting a role in ictogenesis as well. We performed gene expression analysis comparing areas of the dentate gyrus that generate FRs to those that do not generate FRs in a well-characterized rat model of epilepsy. We identified a small cohort of genes that are differentially expressed in FR versus non-FR brain tissue and used quantitative PCR to validate some of those that modulate neuronal excitability. Gene expression network analysis demonstrated conservation of gene co-expression between non-FR and FR samples, but examination of gene connectivity revealed changes that were most pronounced in the cm-40 module, which contains several genes associated with synaptic function and the differentially expressed genes Kcna4, Kcnv1, and Npy1r that are down-regulated in FRs. We then demonstrate that the genes within the cm-40 module are regulated by seizure activity and enriched for the targets of the RNA binding protein Elavl4. Our data suggest that seizure activity induces co-expression of genes associated with synaptic transmission and that this pattern is attenuated in areas displaying FRs, implicating the failure of this mechanism in the generation of FRs.
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Affiliation(s)
- Kellen D Winden
- Interdepartmental Program for Neuroscience, University of California, Los Angeles, Los Angeles, CA, USA; Program in Neurogenetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anatol Bragin
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA; The Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jerome Engel
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA; Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, USA; The Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA; Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Dan H Geschwind
- Interdepartmental Program for Neuroscience, University of California, Los Angeles, Los Angeles, CA, USA; Program in Neurogenetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA; Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
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33
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Margineanu DG. Systems biology, complexity, and the impact on antiepileptic drug discovery. Epilepsy Behav 2014; 38:131-42. [PMID: 24090772 DOI: 10.1016/j.yebeh.2013.08.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 08/26/2013] [Indexed: 12/16/2022]
Abstract
The number of available anticonvulsant drugs increased in the period spanning over more than a century, amounting to the current panoply of nearly two dozen so-called antiepileptic drugs (AEDs). However, none of them actually prevents/reduces the post-brain insult development of epilepsy in man, and in no less than a third of patients with epilepsy, the seizures are not drug-controlled. Plausibly, the enduring limitation of AEDs' efficacy derives from the insufficient understanding of epileptic pathology. This review pinpoints the unbalanced reductionism of the analytic approaches that overlook the intrinsic complexity of epilepsy and of the drug resistance in epilepsy as the core conceptual flaw hampering the discovery of truly antiepileptogenic drugs. A rising awareness of the complexity of epileptic pathology is, however, brought about by the emergence of nonreductionist systems biology (SB) that considers the networks of interactions underlying the normal organismic functions and of SB-based systems (network) pharmacology that aims to restore pathological networks. By now, the systems pharmacology approaches of AED discovery are fairly meager, but their forthcoming development is both a necessity and a realistic prospect, explored in this review.
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Affiliation(s)
- Doru Georg Margineanu
- Department of Neurosciences, Faculty of Medicine and Pharmacy, University of Mons, Ave. Champ de Mars 6, B-7000 Mons, Belgium.
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Ferguson LB, Most D, Blednov YA, Harris RA. PPAR agonists regulate brain gene expression: relationship to their effects on ethanol consumption. Neuropharmacology 2014; 86:397-407. [PMID: 25036611 DOI: 10.1016/j.neuropharm.2014.06.024] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/06/2014] [Accepted: 06/24/2014] [Indexed: 02/08/2023]
Abstract
Peroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that act as ligand-activated transcription factors. Although prescribed for dyslipidemia and type-II diabetes, PPAR agonists also possess anti-addictive characteristics. PPAR agonists decrease ethanol consumption and reduce withdrawal severity and susceptibility to stress-induced relapse in rodents. However, the cellular and molecular mechanisms facilitating these properties have yet to be investigated. We tested three PPAR agonists in a continuous access two-bottle choice (2BC) drinking paradigm and found that tesaglitazar (PPARα/γ; 1.5 mg/kg) and fenofibrate (PPARα; 150 mg/kg) decreased ethanol consumption in male C57BL/6J mice while bezafibrate (PPARα/γ/β; 75 mg/kg) did not. We hypothesized that changes in brain gene expression following fenofibrate and tesaglitazar treatment lead to reduced ethanol drinking. We studied unbiased genomic profiles in areas of the brain known to be important for ethanol dependence, the prefrontal cortex (PFC) and amygdala, and also profiled gene expression in liver. Genomic profiles from the non-effective bezafibrate treatment were used to filter out genes not associated with ethanol consumption. Because PPAR agonists are anti-inflammatory, they would be expected to target microglia and astrocytes. Surprisingly, PPAR agonists produced a strong neuronal signature in mouse brain, and fenofibrate and tesaglitazar (but not bezafibrate) targeted a subset of GABAergic interneurons in the amygdala. Weighted gene co-expression network analysis (WGCNA) revealed co-expression of treatment-significant genes. Functional annotation of these gene networks suggested that PPAR agonists might act via neuropeptide and dopaminergic signaling pathways in the amygdala. Our results reveal gene targets through which PPAR agonists can affect alcohol consumption behavior.
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Affiliation(s)
- Laura B Ferguson
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, United States; The Institute for Neuroscience (INS), The University of Texas at Austin, Austin, TX 78712, United States.
| | - Dana Most
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, United States; The Institute for Neuroscience (INS), The University of Texas at Austin, Austin, TX 78712, United States
| | - Yuri A Blednov
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, United States
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, United States
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Kaminski RM, Rogawski MA, Klitgaard H. The potential of antiseizure drugs and agents that act on novel molecular targets as antiepileptogenic treatments. Neurotherapeutics 2014; 11:385-400. [PMID: 24671870 PMCID: PMC3996125 DOI: 10.1007/s13311-014-0266-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A major goal of contemporary epilepsy research is the identification of therapies to prevent the development of recurrent seizures in individuals at risk, including those with brain injuries, infections, or neoplasms; status epilepticus; cortical dysplasias; or genetic epilepsy susceptibility. In this review we consider the evidence largely from preclinical models for the antiepileptogenic activity of a diverse range of potential therapies, including some marketed antiseizure drugs, as well as agents that act by immune and inflammatory mechanisms; reduction of oxidative stress; activation of the mammalian target of rapamycin or peroxisome proliferator-activated receptors γ pathways; effects on factors related to thrombolysis, hematopoesis, and angiogenesis; inhibition of 3-hydroxy-3-methylglutaryl-coenzyme A reducatase; brain-derived neurotrophic factor signaling; and blockade of α2 adrenergic and cannabinoid receptors. Antiepileptogenesis refers to a therapy of which the beneficial action is to reduce seizure frequency or severity outlasting the treatment period. To date, clinical trials have failed to demonstrate that antiseizure drugs have such disease-modifying activity. However, studies in animal models with levetiracetam and ethosuximide are encouraging, and clinical trials with these agents are warranted. Other promising strategies are inhibition of interleukin 1β signaling by drugs such as VX-765; modulation of sphingosine 1-phosphate signaling by drugs such as fingolimod; activation of the mammalian target of rapamycin by drugs such as rapamycin; the hormone erythropoietin; and, paradoxically, drugs such as the α2 adrenergic receptor antagonist atipamezole and the CB1 cannabinoid antagonist SR141716A (rimonabant) with proexcitatory activity. These approaches could lead to a new paradigm in epilepsy drug therapy where treatment for a limited period prevents the occurrence of spontaneous seizures, thus avoiding lifelong commitment to symptomatic treatment.
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Affiliation(s)
| | - Michael A. Rogawski
- />Department of Neurology, University of California, Davis School of Medicine, Sacramento, CA USA
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Chen H, Luo R, Gong S, Matta SG, Sharp BM. Protection genes in nucleus accumbens shell affect vulnerability to nicotine self-administration across isogenic strains of adolescent rat. PLoS One 2014; 9:e86214. [PMID: 24465966 PMCID: PMC3899218 DOI: 10.1371/journal.pone.0086214] [Citation(s) in RCA: 10] [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: 08/22/2013] [Accepted: 12/06/2013] [Indexed: 01/20/2023] Open
Abstract
Classical genetic studies show the heritability of cigarette smoking is 0.4–0.6, and that multiple genes confer susceptibility and resistance to smoking. Despite recent advances in identifying genes associated with smoking behaviors, the major source of this heritability and its impact on susceptibility and resistance are largely unknown. Operant self-administration (SA) of intravenous nicotine is an established model for smoking behavior. We recently confirmed that genetic factors exert strong control over nicotine intake in isogenic rat strains. Because the processing of afferent dopaminergic signals by nucleus accumbens shell (AcbS) is critical for acquisition and maintenance of motivated behaviors reinforced by nicotine, we hypothesized that differential basal gene expression in AcbS accounts for much of the strain-to-strain variation in nicotine SA. We therefore sequenced the transcriptome of AcbS samples obtained by laser capture microdissection from 10 isogenic adolescent rat strains and compared all RNA transcript levels with behavior. Weighted gene co-expression network analysis, a systems biology method, found 12 modules (i.e., unique sets of genes that covary across all samples) that correlated (p<0.05) with amount of self-administered nicotine; 9 of 12 correlated negatively, implying a protective role. PCR confirmed selected genes from these modules. Chilibot, a literature mining tool, identified 15 genes within 1 module that were nominally associated with cigarette smoking, thereby providing strong support for the analytical approach. This is the first report demonstrating that nicotine intake by adolescent rodents is associated with the expression of specific genes in AcbS of the mesolimbic system, which controls motivated behaviors. These findings provide new insights into genetic mechanisms that predispose or protect against tobacco addiction.
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Affiliation(s)
- Hao Chen
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- * E-mail: (HC); (BS)
| | - Rui Luo
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Suzhen Gong
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Shannon G. Matta
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Burt M. Sharp
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- * E-mail: (HC); (BS)
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Evaluation of seizure foci and genes in the Lgi1(L385R/+) mutant rat. Neurosci Res 2014; 80:69-75. [PMID: 24406746 DOI: 10.1016/j.neures.2013.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 11/26/2013] [Accepted: 12/25/2013] [Indexed: 01/13/2023]
Abstract
Mutations in the leucine-rich, glioma inactivated 1 (LGI1) gene have been identified in patients with autosomal dominant lateral temporal lobe epilepsy (ADLTE). We previously reported that Lgi1 mutant rats, carrying a missense mutation (L385R) generated by gene-driven N-ethyl-N-nitrosourea (ENU) mutagenesis, showed generalized tonic-clonic seizures (GTCS) in response to acoustic stimuli. In the present study, we assessed clinically relevant features of Lgi1 heterozygous mutant rats (Lgi1(L385R/+)) as an animal model of ADLTE. First, to explore the focus of the audiogenic seizures, we performed electroencephalography (EEG) and brain Fos immunohistochemistry in Lgi1(L385R/+) and wild type rats. EEG showed unique seizure patterns (e.g., bilateral rhythmic spikes) in Lgi1(L385R/+) rats with GTCS. An elevated level of Fos expression indicated greater neural excitability to acoustic stimuli in Lgi1(L385R/+) rats, especially in the temporal lobe, thalamus and subthalamic nucleus. Finally, microarray analysis revealed a number of differentially expressed genes that may be involved in epilepsy. These results suggest that Lgi1(L385R/+) rats are useful as an animal model of human ADLTE.
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Are alterations in transmitter receptor and ion channel expression responsible for epilepsies? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 813:211-29. [PMID: 25012379 DOI: 10.1007/978-94-017-8914-1_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neuronal voltage-gated ion channels and ligand-gated synaptic receptors play a critical role in maintaining the delicate balance between neuronal excitation and inhibition within neuronal networks in the brain. Changes in expression of voltage-gated ion channels, in particular sodium, hyperpolarization-activated cyclic nucleotide-gated (HCN) and calcium channels, and ligand-gated synaptic receptors, in particular GABA and glutamate receptors, have been reported in many types of both genetic and acquired epilepsies, in animal models and in humans. In this chapter we review these and discuss the potential pathogenic role they may play in the epilepsies.
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Guo C, Liu XJ, Cheng ZX, Liu YJ, Li H, Peng X. Characterization of protein species and weighted protein co-expression network regulation of Escherichia coli in response to serum killing using a 2-DE based proteomics approach. MOLECULAR BIOSYSTEMS 2013; 10:475-84. [PMID: 24366695 DOI: 10.1039/c3mb70404a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Posttranslational modifications, providing covalent alterations to extend their functions, show protein species on 2-DE gels, but our knowledge on protein species is still limited. In the present study, characteristics of protein species are determined in Escherichia coli using 2-DE based proteomics. In the E. coli proteome, 691 unique proteins (representing 1096 protein spots) accounting for 15.37% of gene-coding proteins of the bacterium are identified. Out of them, 191 have 596 protein species. Proteins with higher abundance, a higher proportion of Glu, Gly, Lys, and higher pI are more likely to have protein species. Further investigation on bacterial serum resistance indicates that more proteins with protein species are found in the bacterium in response to serum stress. A weighted protein co-expression network shows that protein species are related to topological connection as a result of protein regulation. The node protein IleS is demonstrated to contribute to serum resistance using a gene-deleted mutant. These results have revealed general characteristic features of bacterial species, and also provided novel insights into the biological significance of bacterial protein species, particularly the role in serum resistance.
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Affiliation(s)
- Chang Guo
- Center for Proteomics, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.
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Levetiracetam resistance: Synaptic signatures & corresponding promoter SNPs in epileptic hippocampi. Neurobiol Dis 2013; 60:115-25. [DOI: 10.1016/j.nbd.2013.08.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/22/2013] [Accepted: 08/27/2013] [Indexed: 01/16/2023] Open
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Bankstahl M, Bankstahl JP, Löscher W. Pilocarpine-induced epilepsy in mice alters seizure thresholds and the efficacy of antiepileptic drugs in the 6-Hertz psychomotor seizure model. Epilepsy Res 2013; 107:205-16. [DOI: 10.1016/j.eplepsyres.2013.09.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 09/02/2013] [Accepted: 09/27/2013] [Indexed: 12/25/2022]
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Bando SY, Silva FN, Costa LDF, Silva AV, Pimentel-Silva LR, Castro LHM, Wen HT, Amaro E, Moreira-Filho CA. Complex network analysis of CA3 transcriptome reveals pathogenic and compensatory pathways in refractory temporal lobe epilepsy. PLoS One 2013; 8:e79913. [PMID: 24278214 PMCID: PMC3836787 DOI: 10.1371/journal.pone.0079913] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 09/25/2013] [Indexed: 12/21/2022] Open
Abstract
We previously described - studying transcriptional signatures of hippocampal CA3 explants - that febrile (FS) and afebrile (NFS) forms of refractory mesial temporal lobe epilepsy constitute two distinct genomic phenotypes. That network analysis was based on a limited number (hundreds) of differentially expressed genes (DE networks) among a large set of valid transcripts (close to two tens of thousands). Here we developed a methodology for complex network visualization (3D) and analysis that allows the categorization of network nodes according to distinct hierarchical levels of gene-gene connections (node degree) and of interconnection between node neighbors (concentric node degree). Hubs are highly connected nodes, VIPs have low node degree but connect only with hubs, and high-hubs have VIP status and high overall number of connections. Studying the whole set of CA3 valid transcripts we: i) obtained complete transcriptional networks (CO) for FS and NFS phenotypic groups; ii) examined how CO and DE networks are related; iii) characterized genomic and molecular mechanisms underlying FS and NFS phenotypes, identifying potential novel targets for therapeutic interventions. We found that: i) DE hubs and VIPs are evenly distributed inside the CO networks; ii) most DE hubs and VIPs are related to synaptic transmission and neuronal excitability whereas most CO hubs, VIPs and high hubs are related to neuronal differentiation, homeostasis and neuroprotection, indicating compensatory mechanisms. Complex network visualization and analysis is a useful tool for systems biology approaches to multifactorial diseases. Network centrality observed for hubs, VIPs and high hubs of CO networks, is consistent with the network disease model, where a group of nodes whose perturbation leads to a disease phenotype occupies a central position in the network. Conceivably, the chance for exerting therapeutic effects through the modulation of particular genes will be higher if these genes are highly interconnected in transcriptional networks.
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Affiliation(s)
- Silvia Yumi Bando
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, São Paulo, Brazil
| | | | | | - Alexandre V. Silva
- Department of Biosciences, Universidade Federal de São Paulo, Santos, São Paulo, Brazil
| | | | - Luiz HM. Castro
- Clinical Neurology Division, Hospital das Clínicas da FMUSP, São Paulo, São Paulo, Brazil
| | - Hung-Tzu Wen
- Epilepsy Surgery Group, Hospital das Clínicas da FMUSP, São Paulo, São Paulo, Brazil
| | - Edson Amaro
- Department of Radiology, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, São Paulo, Brazil
| | - Carlos Alberto Moreira-Filho
- Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, São Paulo, Brazil
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Abstract
Background Cell survival and development are orchestrated by complex interlocking programs of gene activation and repression. Understanding how this gene regulatory network (GRN) functions in normal states, and is altered in cancers subtypes, offers fundamental insight into oncogenesis and disease progression, and holds great promise for guiding clinical decisions. Inferring a GRN from empirical microarray gene expression data is a challenging task in cancer systems biology. In recent years, module-based approaches for GRN inference have been proposed to address this challenge. Despite the demonstrated success of module-based approaches in uncovering biologically meaningful regulatory interactions, their application remains limited a single condition, without supporting the comparison of multiple disease subtypes/conditions. Also, their use remains unnecessarily restricted to computational biologists, as accurate inference of modules and their regulators requires integration of diverse tools and heterogeneous data sources, which in turn requires scripting skills, data infrastructure and powerful computational facilities. New analytical frameworks are required to make module-based GRN inference approach more generally useful to the research community. Results We present the RMaNI (Regulatory Module Network Inference) framework, which supports cancer subtype-specific or condition specific GRN inference and differential network analysis. It combines both transcriptomic as well as genomic data sources, and integrates heterogeneous knowledge resources and a set of complementary bioinformatic methods for automated inference of modules, their condition specific regulators and facilitates downstream network analyses and data visualization. To demonstrate its utility, we applied RMaNI to a hepatocellular microarray data containing normal and three disease conditions. We demonstrate that how RMaNI can be employed to understand the genetic architecture underlying three disease conditions. RMaNI is freely available at http://inspect.braembl.org.au/bi/inspect/rmani Conclusion RMaNI makes available a workflow with comprehensive set of tools that would otherwise be challenging for non-expert users to install and apply. The framework presented in this paper is flexible and can be easily extended to analyse any dataset with multiple disease conditions.
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Gene expression profiling of a hypoxic seizure model of epilepsy suggests a role for mTOR and Wnt signaling in epileptogenesis. PLoS One 2013; 8:e74428. [PMID: 24086344 PMCID: PMC3785482 DOI: 10.1371/journal.pone.0074428] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 08/01/2013] [Indexed: 01/09/2023] Open
Abstract
Microarray profiling was used to investigate gene expression in the hypoxic seizure model of acquired epilepsy in the rat, with the aim of characterizing functional pathways which are persistently activated or repressed during epileptogenesis. Hippocampal and cortical tissues were transcriptionally profiled over a one week period following an initial series of seizures induced by mild hypoxia at post-natal day 10 (P10), and the gene expression data was then analyzed with a focus on gene set enrichment analysis, an approach which emphasizes regulation of entire pathways rather than of individual genes. Animals were subjected to one of three conditions: a control with no hypoxia, hypoxic seizures, and hypoxic seizures followed by treatment with the AMPAR antagonist NBQX, a compound currently proposed to be a modulator of epileptogenesis. While temporal gene expression in the control samples was found to be consistent with known processes of neuronal maturation in the rat for the given time window, the hypoxic seizure response was found to be enriched for components of the PI3K/mTOR and Wnt signaling pathways, alongside gene sets representative of glutamatergic, synaptic and axonal processes, perhaps regulated as a downstream consequence of activation of these pathways. Wnt signaling components were also found enriched in the more specifically epileptogenic NBQX-responsive gene set. While activation of the mTOR pathway is consistent with its known role in epileptogenesis and strengthens the case for mTOR or PI3K pathway inhibitors as potential anti-epileptogenic drugs, investigation of the role of Wnt signaling and the effect of appropriate inhibitors might offer a parallel avenue of research toward anti-epileptogenic treatment of epilepsy.
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Löscher W, Klitgaard H, Twyman RE, Schmidt D. New avenues for anti-epileptic drug discovery and development. Nat Rev Drug Discov 2013; 12:757-76. [DOI: 10.1038/nrd4126] [Citation(s) in RCA: 424] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Wang ZI, Alexopoulos AV, Jones SE, Jaisani Z, Najm IM, Prayson RA. The pathology of magnetic-resonance-imaging-negative epilepsy. Mod Pathol 2013; 26:1051-8. [PMID: 23558575 DOI: 10.1038/modpathol.2013.52] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 11/09/2022]
Abstract
Patients with magnetic-resonance-imaging (MRI)-negative (or 'nonlesional') pharmacoresistant focal epilepsy are the most challenging group undergoing presurgical evaluation. Few large-scale studies have systematically reviewed the pathological substrates underlying MRI-negative epilepsies. In the current study, histopathological specimens were retrospectively reviewed from MRI-negative epilepsy patients (n=95, mean age=30 years, 50% female subjects). Focal cortical dysplasia cases were classified according to the International League Against Epilepsy (ILAE) and Palmini et al classifications. The most common pathologies found in this MRI-negative cohort included: focal cortical dysplasia (n=43, 45%), gliosis (n=21, 22%), hamartia+gliosis (n=12, 13%), and hippocampal sclerosis (n=9, 9%). The majority of focal cortical dysplasia were ILAE type I (n=37) or Palmini type I (n=39). Seven patients had no identifiable pathological abnormalities. The existence of positive pathology was not significantly associated with age or temporal/extratemporal resection. Follow-up data post surgery was available in 90 patients; 63 (70%) and 57 (63%) attained seizure freedom at 6 and 12 months, respectively. The finding of positive pathology was significantly associated with seizure-free outcome at 6 months (P=0.035), but not at 12 months. In subgroup analysis, the focal cortical dysplasia group was not significantly correlated with seizure-free outcome, as compared with the negative-pathology groups at either 6 or 12 months. Of note, the finding of hippocampal sclerosis had a significant positive correlation with seizure-free outcome when compared with the negative-pathology group (P=0.009 and 0.004 for 6- and 12-month outcome, respectively). Absence of a significant histopathology in the resected surgical specimen did not preclude seizure freedom. In conclusion, our study highlights the heterogeneity of epileptic pathologies in MRI-negative epilepsies, with focal cortical dysplasia being the most common finding. The existence of positive pathology in surgical specimen may be a good indication for short-term good seizure outcome. There is a small subset of cases in which no pathological abnormalities are identified.
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Affiliation(s)
- Z Irene Wang
- Cleveland Clinic Epilepsy Center, Cleveland, OH, USA
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Bronicki LM, Jasmin BJ. Emerging complexity of the HuD/ELAVl4 gene; implications for neuronal development, function, and dysfunction. RNA (NEW YORK, N.Y.) 2013; 19:1019-1037. [PMID: 23861535 PMCID: PMC3708524 DOI: 10.1261/rna.039164.113] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Precise control of messenger RNA (mRNA) processing and abundance are increasingly being recognized as critical for proper spatiotemporal gene expression, particularly in neurons. These regulatory events are governed by a large number of trans-acting factors found in neurons, most notably RNA-binding proteins (RBPs) and micro-RNAs (miRs), which bind to specific cis-acting elements or structures within mRNAs. Through this binding mechanism, trans-acting factors, particularly RBPs, control all aspects of mRNA metabolism, ranging from altering the transcription rate to mediating mRNA degradation. In this context the best-characterized neuronal RBP, the Hu/ELAVl family member HuD, is emerging as a key component in multiple regulatory processes--including pre-mRNA processing, mRNA stability, and translation--governing the fate of a substantial amount of neuronal mRNAs. Through its ability to regulate mRNA metabolism of diverse groups of functionally similar genes, HuD plays important roles in neuronal development and function. Furthermore, compelling evidence indicates supplementary roles for HuD in neuronal plasticity, in particular, recovery from axonal injury, learning and memory, and multiple neurological diseases. The purpose of this review is to provide a detailed overview of the current knowledge surrounding the expression and roles of HuD in the nervous system. Additionally, we outline the present understanding of the molecular mechanisms presiding over the localization, abundance, and function of HuD in neurons.
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Mazzuferi M, Kumar G, van Eyll J, Danis B, Foerch P, Kaminski RM. Nrf2 defense pathway: Experimental evidence for its protective role in epilepsy. Ann Neurol 2013; 74:560-8. [DOI: 10.1002/ana.23940] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/27/2013] [Accepted: 05/10/2013] [Indexed: 12/12/2022]
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Filteau M, Pavey SA, St-Cyr J, Bernatchez L. Gene coexpression networks reveal key drivers of phenotypic divergence in lake whitefish. Mol Biol Evol 2013; 30:1384-96. [PMID: 23519315 DOI: 10.1093/molbev/mst053] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A functional understanding of processes involved in adaptive divergence is one of the awaiting opportunities afforded by high-throughput transcriptomic technologies. Functional analysis of coexpressed genes has succeeded in the biomedical field in identifying key drivers of disease pathways. However, in ecology and evolutionary biology, functional interpretation of transcriptomic data is still limited. Here, we used Weighted Gene Co-Expression Network Analysis (WGCNA) to identify modules of coexpressed genes in muscle and brain tissue of a lake whitefish backcross progeny. Modules were connected to gradients of known adaptive traits involved in the ecological speciation process between benthic and limnetic ecotypes. Key drivers, that is, hub genes of functional modules related to reproduction, growth, and behavior were identified, and module preservation was assessed in natural populations. Using this approach, we identified modules of coexpressed genes involved in phenotypic divergence and their key drivers, and further identified a module part specifically rewired in the backcross progeny. Functional analysis of transcriptomic data can significantly contribute to the understanding of the mechanisms underlying ecological speciation. Our findings point to bone morphogenetic protein and calcium signaling as common pathways involved in coordinated evolution of trophic behavior, trophic morphology (gill rakers), and reproduction. Results also point to pathways implicating hemoglobins and constitutive stress response (HSP70) governing growth in lake whitefish.
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Affiliation(s)
- Marie Filteau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
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Broderick G, Craddock TJA. Systems biology of complex symptom profiles: capturing interactivity across behavior, brain and immune regulation. Brain Behav Immun 2013; 29:1-8. [PMID: 23022717 PMCID: PMC3554865 DOI: 10.1016/j.bbi.2012.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 09/13/2012] [Accepted: 09/14/2012] [Indexed: 12/15/2022] Open
Abstract
As our thinking about the basic principles of biology and medicine continue to evolve, the importance of context and regulatory interaction is becoming increasingly obvious. Biochemical and physiological components do not exist in isolation but instead are part of a tightly integrated network of interacting elements that ensure robustness and support the emergence of complex behavior. This integration permeates all levels of biology from gene regulation, to immune cell signaling, to coordinated patterns of neuronal activity and the resulting psychosocial interaction. Systems biology is an emerging branch of science that sits as a translational catalyst at the interface of the life and computational sciences. While there is no universally accepted definition of systems biology, we attempt to provide an overview of some the basic unifying concepts and current efforts in the field as they apply to illnesses where brain and subsequent behavior are a chief component, for example autism, schizophrenia, depression, and others. Methods in this field currently constitute a broad mosaic that stretches across multiple scales of biology and physiological compartments. While this work by no means constitutes an exhaustive list of all these methods, this work highlights the principal sub-disciplines presently driving the field as well as future directions of progress.
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Affiliation(s)
- Gordon Broderick
- Department of Medicine, University of Alberta, Edmonton, Canada.
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