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Epigenetics and noncoding RNA: Recent developments and future therapeutic opportunities. Eur J Paediatr Neurol 2020; 24:30-34. [PMID: 31235424 DOI: 10.1016/j.ejpn.2019.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/22/2019] [Accepted: 06/06/2019] [Indexed: 01/10/2023]
Abstract
Acquired and genetic forms of epilepsy are associated with dysregulation of gene expression within the brain. Identifying mechanisms controlling gene expression may provide novel opportunities for the development of disease-modifying therapies. Epigenetic processes influence the medium-to long-term readability and accessibility of the genome to transcription. The mediators include biochemical modifications to DNA and the histones around which DNA is wrapped, as well as non-coding RNAs. Here, the main epigenetic processes are briefly reviewed. Examples are provided of altered epigenetic processes and mutations in genes with epigenetic functions in experimental models and human epilepsy. The outcome of recent studies manipulating epigenetics to protect the brain or reduce seizures in preclinical models is considered, with specific focus on RNA therapies. Last, future applications of epigenetics research are appraised, including opportunities to map and change epigenetic marks and the prospects for therapies based on manipulation of epigenetics and noncoding RNAs. In summary, epigenetics and noncoding RNAs are important mechanisms and targets to modulate brain excitability which together provides novel insight into patho-mechanisms, biomarkers and novel therapies for epilepsy.
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Berger TC, Vigeland MD, Hjorthaug HS, Etholm L, Nome CG, Taubøll E, Heuser K, Selmer KK. Neuronal and glial DNA methylation and gene expression changes in early epileptogenesis. PLoS One 2019; 14:e0226575. [PMID: 31887157 PMCID: PMC6936816 DOI: 10.1371/journal.pone.0226575] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/28/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND AND AIMS Mesial Temporal Lobe Epilepsy is characterized by progressive changes of both neurons and glia, also referred to as epileptogenesis. No curative treatment options, apart from surgery, are available. DNA methylation (DNAm) is a potential upstream mechanism in epileptogenesis and may serve as a novel therapeutic target. To our knowledge, this is the first study to investigate epilepsy-related DNAm, gene expression (GE) and their relationship, in neurons and glia. METHODS We used the intracortical kainic acid injection model to elicit status epilepticus. At 24 hours post injection, hippocampi from eight kainic acid- (KA) and eight saline-injected (SH) mice were extracted and shock frozen. Separation into neurons and glial nuclei was performed by flow cytometry. Changes in DNAm and gene expression were measured with reduced representation bisulfite sequencing (RRBS) and mRNA-sequencing (mRNAseq). Statistical analyses were performed in R with the edgeR package. RESULTS We observed fulminant DNAm- and GE changes in both neurons and glia at 24 hours after initiation of status epilepticus. The vast majority of these changes were specific for either neurons or glia. At several epilepsy-related genes, like HDAC11, SPP1, GAL, DRD1 and SV2C, significant differential methylation and differential gene expression coincided. CONCLUSION We found neuron- and glia-specific changes in DNAm and gene expression in early epileptogenesis. We detected single genetic loci in several epilepsy-related genes, where DNAm and GE changes coincide, worth further investigation. Further, our results may serve as an information source for neuronal and glial alterations in both DNAm and GE in early epileptogenesis.
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Affiliation(s)
- Toni C. Berger
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
- * E-mail:
| | - 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
| | - Lars Etholm
- National Center for Epilepsy, Oslo University Hospital, Sandvika, Norway
- Department of Neurology, Section for Neurophysiology, Oslo University Hospital, Oslo, Norway
| | | | - Erik Taubøll
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- University of Oslo, Oslo, Norway
| | - Kjell Heuser
- 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
- National Center for Epilepsy, Oslo University Hospital, Sandvika, Norway
- Division of Clinical Neuroscience, Department of Research and Development, Oslo University Hospital, Oslo, Norway
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53
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Zhao J, Xu C, Cao H, Zhang L, Wang X, Chen S. Identification of target genes in neuroinflammation and neurodegeneration after traumatic brain injury in rats. PeerJ 2019; 7:e8324. [PMID: 31875163 PMCID: PMC6925952 DOI: 10.7717/peerj.8324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/01/2019] [Indexed: 01/01/2023] Open
Abstract
Background Traumatic brain injury (TBI) is a common neurological emergency observed in hospitals. A considerable number of patients suffer from long-term disabilities after TBI. This study aimed to identify altered gene expression signatures and mechanisms related to TBI-induced chronic neuroinflammation and neurodegeneration. Methods An integrated analysis was performed using published RNA-sequencing studies to determine TBI-induced differentially expressed genes (DEGs). Based on the DEG data, functional annotation, signal-net, and transcription factor analyses were conducted to understand the mechanism of chronic neuroinflammation and neurodegeneration induced after TBI. Results Two datasets were obtained using the Gene Expression Omnibus database, of which, 6,513 DEGs were identified (6,464 upregulated and 49 downregulated). Positive regulation of biological process, positive regulation of cellular process, nucleus, and heterocyclic compound binding were Gene Ontology terms significantly enriched in post-TBI rat models. Leukocyte transendothelial migration, chemokine signaling pathway, neurotrophin signaling pathway, and longevity-regulating pathway were significantly enriched after TBI. With regard to the signal-net analysis, FOXO3, DGKZ and ILK were considered the most critical genes derived using high–betweenness centrality calculation. A total of 44 TFs, including FOXO1, SRY and KLF4, were predicted to play an important role in the upregulation of gene expression. Using integrated bioinformatics analysis, TBI was found to be associated with a significant inflammatory response and neurodegeneration. FOXO3, apolipoprotein (APOE), microtubule-associated protein tau (MAPT), and TREM2 were probably associated with the TBI pathological process. The mitochondrial electron transport chain may be associated with neurodegeneration in patients with TBI, serving as a potential therapeutic target.
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Affiliation(s)
- Jianwei Zhao
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Chen Xu
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Heli Cao
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Lin Zhang
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xuyang Wang
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Shiwen Chen
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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54
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de Nijs L, Choe K, Steinbusch H, Schijns OEMG, Dings J, van den Hove DLA, Rutten BPF, Hoogland G. DNA methyltransferase isoforms expression in the temporal lobe of epilepsy patients with a history of febrile seizures. Clin Epigenetics 2019; 11:118. [PMID: 31426844 PMCID: PMC6701147 DOI: 10.1186/s13148-019-0721-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/02/2019] [Indexed: 11/10/2022] Open
Abstract
Background Temporal lobe epilepsy (TLE) with hippocampal sclerosis (HS) is a common pharmaco-resistant epilepsy referred for adult epilepsy surgery. Though associated with prolonged febrile seizures (FS) in childhood, the neurobiological basis for this relationship is not fully understood and currently no preventive or curative therapies are available. DNA methylation, an epigenetic mechanism catalyzed by DNA methyltransferases (DNMTs), potentially plays a pivotal role in epileptogenesis associated with FS. In an attempt to start exploring this notion, the present cross-sectional pilot study investigated whether global DNA methylation levels (5-mC and 5-hmC markers) and DNMT isoforms (DNMT1, DNMT3a1, and DNMT3a2) expression would be different in hippocampal and neocortical tissues between controls and TLE patients with or without a history of FS. Results We found that global DNA methylation levels and DNMT3a2 isoform expression were lower in the hippocampus for all TLE groups when compared to control patients, with a more significant decrease amongst the TLE groups with a history of FS. Interestingly, we showed that DNMT3a1 expression was severely diminished in the hippocampus of TLE patients with a history of FS in comparison with control and other TLE groups. In the neocortex, we found a higher expression of DNMT1 and DNMT3a1 as well as increased levels of global DNA methylation for all TLE patients compared to controls. Conclusion Together, the findings of this descriptive cross-sectional pilot study demonstrated brain region-specific changes in DNMT1 and DNMT3a isoform expression as well as global DNA methylation levels in human TLE with or without a history of FS. They highlighted a specific implication of DNMT3a isoforms in TLE after FS. Therefore, longitudinal studies that aim at targeting DNMT3a isoforms to evaluate the potential causal relationship between FS and TLE or treatment of FS-induced epileptogenesis seem warranted. Electronic supplementary material The online version of this article (10.1186/s13148-019-0721-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laurence de Nijs
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands. .,GIGA-Neurosciences, University of Liège, Liège, Belgium.
| | - Kyonghwan Choe
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands
| | - Hellen Steinbusch
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands
| | - Olaf E M G Schijns
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands.,Department of Neurosurgery, Maastricht University Medical Center, Maastricht, The Netherlands.,Academic Center for Epileptology (ACE), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jim Dings
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands.,Department of Neurosurgery, Maastricht University Medical Center, Maastricht, The Netherlands.,Academic Center for Epileptology (ACE), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Daniel L A van den Hove
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands.,Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Bart P F Rutten
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands
| | - Govert Hoogland
- School for Mental Health and Neuroscience (MHeNS), Department of Psychiatry and Neuropsychology, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6229, ER, Maastricht, The Netherlands.,Department of Neurosurgery, Maastricht University Medical Center, Maastricht, The Netherlands.,Academic Center for Epileptology (ACE), Maastricht University Medical Center, Maastricht, The Netherlands
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Carvill GL, Dulla CG, Lowenstein DH, Brooks-Kayal AR. The path from scientific discovery to cures for epilepsy. Neuropharmacology 2019; 167:107702. [PMID: 31301334 DOI: 10.1016/j.neuropharm.2019.107702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/05/2019] [Accepted: 07/06/2019] [Indexed: 02/06/2023]
Abstract
The epilepsies are a complex group of disorders that can be caused by a myriad of genetic and acquired factors. As such, identifying interventions that will prevent development of epilepsy, as well as cure the disorder once established, will require a multifaceted approach. Here we discuss the progress in scientific discovery propelling us towards this goal, including identification of genetic risk factors and big data approaches that integrate clinical and molecular 'omics' datasets to identify common pathophysiological signatures and biomarkers. We discuss the many animal and cellular models of epilepsy, what they have taught us about pathophysiology, and the cutting edge cellular, optogenetic, chemogenetic and anti-seizure drug screening approaches that are being used to find new cures in these models. Finally, we reflect on the work that still needs to be done towards identify at-risk individuals early, targeting and stopping epileptogenesis, and optimizing promising treatment approaches. Ultimately, developing and implementing cures for epilepsy will require a coordinated and immense effort from clinicians and basic scientists, as well as industry, and should always be guided by the needs of individuals affected by epilepsy and their families. This article is part of the special issue entitled 'New Epilepsy Therapies for the 21st Century - From Antiseizure Drugs to Prevention, Modification and Cure of Epilepsy'.
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Affiliation(s)
- Gemma L Carvill
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
| | - Chris G Dulla
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA.
| | - Dan H Lowenstein
- Department of Neurology, University of California, San Francisco, CA, 94941, USA
| | - Amy R Brooks-Kayal
- Department of Pediatrics and Neurology, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, 80045, USA
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Mahoney JM, Mills JD, Muhlebner A, Noebels J, Potschka H, Simonato M, Kobow K. 2017 WONOEP appraisal: Studying epilepsy as a network disease using systems biology approaches. Epilepsia 2019; 60:1045-1053. [DOI: 10.1111/epi.15216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/17/2019] [Accepted: 04/17/2019] [Indexed: 12/15/2022]
Affiliation(s)
- John M. Mahoney
- Department of Neurological Sciences Department of Computer Science University of Vermont Larner College of Medicine Burlington Vermont
| | - James D. Mills
- Department of (Neuro)Pathology Amsterdam University Medical CenterUniversity of Amsterdam Amsterdam The Netherlands
| | - Angelika Muhlebner
- Department of (Neuro)Pathology Amsterdam University Medical CenterUniversity of Amsterdam Amsterdam The Netherlands
| | - Jeffrey Noebels
- Department of Neurology Baylor College of Medicine Houston Texas
| | - Heidrun Potschka
- Institute of Pharmacology, Toxicology, and Pharmacy Ludwig Maximilian University of Munich Munich Germany
| | - Michele Simonato
- Department of Medical Sciences University of Ferrara and School of Medicine University Vita‐Salute San Raffaele Milan Italy
| | - Katja Kobow
- Department of Neuropathology Universitätsklinikum ErlangenFriedrich‐Alexander University Erlangen‐Nürnberg Erlangen Germany
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57
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Kobow K, Ziemann M, Kaipananickal H, Khurana I, Mühlebner A, Feucht M, Hainfellner JA, Czech T, Aronica E, Pieper T, Holthausen H, Kudernatsch M, Hamer H, Kasper BS, Rössler K, Conti V, Guerrini R, Coras R, Blümcke I, El-Osta A, Kaspi A. Genomic DNA methylation distinguishes subtypes of human focal cortical dysplasia. Epilepsia 2019; 60:1091-1103. [PMID: 31074842 PMCID: PMC6635741 DOI: 10.1111/epi.14934] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 12/26/2022]
Abstract
Objectives Focal cortical dysplasia (FCD) is a major cause of drug‐resistant focal epilepsy in children, and the clinicopathological classification remains a challenging issue in daily practice. With the recent progress in DNA methylation–based classification of human brain tumors we examined whether genomic DNA methylation and gene expression analysis can be used to also distinguish human FCD subtypes. Methods DNA methylomes and transcriptomes were generated from massive parallel sequencing in 15 surgical FCD specimens, matched with 5 epilepsy and 6 nonepilepsy controls. Results Differential hierarchical cluster analysis of DNA methylation distinguished major FCD subtypes (ie, Ia, IIa, and IIb) from patients with temporal lobe epilepsy patients and nonepileptic controls. Targeted panel sequencing identified a novel likely pathogenic variant in DEPDC5 in a patient with FCD type IIa. However, no enrichment of differential DNA methylation or gene expression was observed in mechanistic target of rapamycin (mTOR) pathway–related genes. Significance Our studies extend the evidence for disease‐specific methylation signatures toward focal epilepsies in favor of an integrated clinicopathologic and molecular classification system of FCD subtypes incorporating genomic methylation.
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Affiliation(s)
- Katja Kobow
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Mark Ziemann
- Epigenetics in Human Health and Disease, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Harikrishnan Kaipananickal
- Epigenetics in Human Health and Disease, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ishant Khurana
- Epigenetics in Human Health and Disease, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Angelika Mühlebner
- Department of Pediatrics and Adolescent Medicine, Medical University Vienna, Vienna, Austria.,Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Martha Feucht
- Department of Pediatrics and Adolescent Medicine, Medical University Vienna, Vienna, Austria
| | | | - Thomas Czech
- Department of Neurosurgery, Medical University Vienna, Vienna, Austria
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.,Stichting Epilepsie Instellingen Nederland (SEIN), Zwolle, The Netherlands
| | - Tom Pieper
- Department of Neuropaediatrics and Neurological Rehabilitation, Epilepsy Centre for Children and Adolescents, Schoen Clinic Vogtareuth, Vogtareuth, Germany
| | - Hans Holthausen
- Department of Neuropaediatrics and Neurological Rehabilitation, Epilepsy Centre for Children and Adolescents, Schoen Clinic Vogtareuth, Vogtareuth, Germany
| | - Manfred Kudernatsch
- Department of Neurosurgery and Epilepsy Surgery, Schoen Clinic Vogtareuth, Vogtareuth, Germany
| | - Hajo Hamer
- Department of Neurology, Erlangen Epilepsy Center, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Burkhard S Kasper
- Department of Neurology, Erlangen Epilepsy Center, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Karl Rössler
- Department of Neurosurgery, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Valerio Conti
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Neuroscience Department, A Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Roland Coras
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ingmar Blümcke
- Department of Neuropathology, Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Assam El-Osta
- Epigenetics in Human Health and Disease, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong City, Hong Kong SAR
| | - Antony Kaspi
- Epigenetics in Human Health and Disease, Central Clinical School, Monash University, Melbourne, Victoria, Australia
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Karttunen J, Heiskanen M, Lipponen A, Poulsen D, Pitkänen A. Extracellular Vesicles as Diagnostics and Therapeutics for Structural Epilepsies. Int J Mol Sci 2019; 20:E1259. [PMID: 30871144 PMCID: PMC6470789 DOI: 10.3390/ijms20061259] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 12/16/2022] Open
Abstract
Extracellular vesicles (EVs) are small vesicles involved in intercellular communication. Data is emerging that EVs and their cargo have potential as diagnostic biomarkers and treatments for brain diseases, including traumatic brain injury and epilepsy. Here, we summarize the current knowledge regarding changes in EV numbers and cargo in status epilepticus (SE) and traumatic brain injury (TBI), which are clinically significant etiologies for acquired epileptogenesis in animals and humans. We also review encouraging data, which suggests that EVs secreted by stem cells may serve as recovery-enhancing treatments for SE and TBI. Using Gene Set Enrichment Analysis, we show that brain EV-related transcripts are positively enriched in rodent models of epileptogenesis and epilepsy, and altered in response to anti-seizure drugs. These data suggest that EVs show promise as biomarkers, treatments and drug targets for epilepsy. In parallel to gathering conceptual knowledge, analytics platforms for the isolation and analysis of EV contents need to be further developed.
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Affiliation(s)
- Jenni Karttunen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
| | - Mette Heiskanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
| | - Anssi Lipponen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
| | - David Poulsen
- University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Clinical and Translational Research Center (CTRC), Department of Neurosurgery, Buffalo, NY 14203, USA.
| | - Asla Pitkänen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland.
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Navarrete-Modesto V, Orozco-Suárez S, Feria-Romero IA, Rocha L. The molecular hallmarks of epigenetic effects mediated by antiepileptic drugs. Epilepsy Res 2019; 149:53-65. [DOI: 10.1016/j.eplepsyres.2018.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 10/16/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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60
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Bhattarai UR, Li F, Katuwal Bhattarai M, Masoudi A, Wang D. Phototransduction and circadian entrainment are the key pathways in the signaling mechanism for the baculovirus induced tree-top disease in the lepidopteran larvae. Sci Rep 2018; 8:17528. [PMID: 30510155 PMCID: PMC6277413 DOI: 10.1038/s41598-018-35885-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 11/07/2018] [Indexed: 01/13/2023] Open
Abstract
The tree-top disease is an altered behavioral state, displayed by baculovirus-infected lepidopteran larvae, and characterized by climbing to an elevated position before death. The detailed molecular mechanism underlying this phenomenal behavior change has not been reported yet. Our study focused on the transcriptomic changes in the host larvae due to baculovirus infection from pre-symptomatic to tree-top disease stage. Enrichment map visualization of the gene sets grouped based on the functional annotation similarity revealed 34 enriched pathways in signaling mechanism cluster during LdMNPV induced tree-top disease in third instar Lymantria dispar asiatica larvae. Directed light bioassay demonstrated the positively phototactic larvae during tree-top disease and the gene expression analysis showed altered rhythmicity of the host’s core circadian genes (per and tim) during the course of infection emphasizing the role of Circadian entrainment and Phototransduction pathways in the process, which also showed maximum interactions (>50% shared genes with 24 and 23 pathways respectively) among other signaling pathways in the enrichment map. Our study provided valuable insights into different pathways and genes, their coordinated response and molecular regulation during baculovirus infection and also improved our understanding regarding signaling mechanisms in LdMNPV induced tree-top disease.
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Affiliation(s)
- Upendra Raj Bhattarai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Fengjiao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Mandira Katuwal Bhattarai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Abolfazl Masoudi
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China
| | - Dun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, 712100, P. R. China.
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61
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Bhattarai UR, Katuwal Bhattarai M, Li F, Wang D. Insights into the Temporal Gene Expression Pattern in Lymantria dispar Larvae During the Baculovirus Induced Hyperactive Stage. Virol Sin 2018; 33:345-358. [PMID: 30046995 DOI: 10.1007/s12250-018-0046-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/10/2018] [Indexed: 01/10/2023] Open
Abstract
Baculoviruses are effective biological control agents for many insect pests. They not only efficiently challenge the host immune system but also make them hyperactive for better virus dispersal. Some investigations have focused on the viral mechanisms for induction of such altered response from the host. However, there are no current studies monitoring changes in gene expression during this altered phenotype in infected larvae. The L. dispar multiple nucleopolyhedrovirus (LdMNPV) induces hyperactivity in third instar L. dispar larvae at 3-days post infection (dpi), to continued till 6 dpi. The transcriptome profiles of the infected and uninfected larvae at these time points were analyzed to provide new clues on the response of the larvae towards infection during hyperactivity. Gene ontology enrichment analysis revealed, most of the differentially expressed genes (DEGs) were involved in proteolysis, extracellular region, and serine-type endopeptidase activity. Similarly, Kyoto Encyclopedia of Genes and Genome enrichment analysis showed maximum enrichment of 487 genes of the signal transduction category and neuroactive ligand-receptor interaction sub-category with 85 annotated genes. In addition, enrichment map visualization of gene set enrichment analysis showed the coordinated response of neuroactive ligand-receptor interaction genes with other functional gene sets, as an important signal transduction mechanism during the hyperactive stage. Interestingly all the DEGs in neuroactive ligand-receptor interactions were serine proteases, their differential expression during the hyperactive stage correlated with their conceivable involvement in disease progression and the resulting altered phenotype during this period. The outcome provides a basic understanding of L. dispar larval responses to LdMNPV infection during the hyperactive stage and helps to determine the important host factors involved in this process.
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Affiliation(s)
- Upendra Raj Bhattarai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Mandira Katuwal Bhattarai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Fengjiao Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
| | - Dun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China.
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62
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Villaluz MM, Lomax LB, Jadhav T, Cross JH, Scheffer IE. The ketogenic diet is effective for refractory epilepsy associated with acquired structural epileptic encephalopathy. Dev Med Child Neurol 2018; 60:718-723. [PMID: 29451698 DOI: 10.1111/dmcn.13687] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/19/2017] [Indexed: 01/01/2023]
Abstract
AIM Ketogenic diet therapies have proven efficacy for refractory epilepsy. There are many reports of their use in the genetic developmental and epileptic encephalopathies; however, little attention has been paid as to whether the diet is also effective in individuals with an acquired structural aetiology. We observed remarkable efficacy of the diet in two patients with hypoxic-ischaemic encephalopathy. We then analysed our cases with refractory structural epilepsies of acquired origin to characterize their response to the ketogenic diet. METHOD The classical ketogenic diet was implemented with dietary ratios of 3:1 to 4.4:1. Seizure frequency at 1 month, 3 months, 6 months, 1 year, and 2 years was ascertained. A responder was defined as greater than 50% seizure reduction compared to baseline. RESULTS Seven of the nine patients were responders at 3 months. INTERPRETATION Somewhat surprisingly we found that the ketogenic diet was effective in patients with a developmental and epileptic encephalopathy due to an acquired structural aetiology. This cohort may not be routinely considered for the ketogenic diet because of their structural and acquired, rather than genetic, basis. The ketogenic diet should be considered early in the management of patients with acquired structural encephalopathies as it can improve seizure control with the potential to improve developmental outcome. WHAT THIS PAPER ADDS The ketogenic diet was effective in children with epilepsy associated with an acquired structural aetiology.
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Affiliation(s)
- Mel Michel Villaluz
- Epilepsy Research Centre, Austin Health, The University of Melbourne, Heidelberg, Vic., Australia
| | - Lysa Boissé Lomax
- Epilepsy Research Centre, Austin Health, The University of Melbourne, Heidelberg, Vic., Australia
| | - Trupti Jadhav
- Neurosciences Unit, Great Ormond Street Hospital, UCL Institute of Child Health, London, UK
| | - J Helen Cross
- Neurosciences Unit, Great Ormond Street Hospital, UCL Institute of Child Health, London, UK.,Young Epilepsy, London, UK
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Austin Health, The University of Melbourne, Heidelberg, Vic., Australia.,Department of Paediatrics, Royal Children's Hospital, The University of Melbourne, Melbourne, Vic., Australia.,Florey Institute of Neuroscience and Mental Health, Melbourne, Vic., Australia
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63
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Balestrini S, Sisodiya SM. Personalized treatment in the epilepsies: challenges and opportunities. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2018. [DOI: 10.1080/23808993.2018.1486189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Simona Balestrini
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, and Epilepsy Society, Chalfont-St-Peter, Bucks, United Kingdom
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, and Epilepsy Society, Chalfont-St-Peter, Bucks, United Kingdom
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64
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Lipponen A, El-Osta A, Kaspi A, Ziemann M, Khurana I, KN H, Navarro-Ferrandis V, Puhakka N, Paananen J, Pitkänen A. Transcription factors Tp73, Cebpd, Pax6, and Spi1 rather than DNA methylation regulate chronic transcriptomics changes after experimental traumatic brain injury. Acta Neuropathol Commun 2018; 6:17. [PMID: 29482641 PMCID: PMC5828078 DOI: 10.1186/s40478-018-0519-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/15/2018] [Indexed: 11/10/2022] Open
Abstract
Traumatic brain injury (TBI) induces a wide variety of cellular and molecular changes that can continue for days to weeks to months, leading to functional impairments. Currently, there are no pharmacotherapies in clinical use that favorably modify the post-TBI outcome, due in part to limited understanding of the mechanisms of TBI-induced pathologies. Our system biology analysis tested the hypothesis that chronic transcriptomics changes induced by TBI are controlled by altered DNA-methylation in gene promoter areas or by transcription factors. We performed genome-wide methyl binding domain (MBD)-sequencing (seq) and RNA-seq in perilesional, thalamic, and hippocampal tissue sampled at 3 months after TBI induced by lateral fluid percussion in adult male Sprague-Dawley rats. We investigated the regulated molecular networks and mechanisms underlying the chronic regulation, particularly DNA methylation and transcription factors. Finally, we identified compounds that modulate the transcriptomics changes and could be repurposed to improve recovery. Unexpectedly, DNA methylation was not a major regulator of chronic post-TBI transcriptomics changes. On the other hand, the transcription factors Cebpd, Pax6, Spi1, and Tp73 were upregulated at 3 months after TBI (False discovery rate < 0.05), which was validated using digital droplet polymerase chain reaction. Transcription regulatory network analysis revealed that these transcription factors regulate apoptosis, inflammation, and microglia, which are well-known contributors to secondary damage after TBI. Library of Integrated Network-based Cellular Signatures (LINCS) analysis identified 118 pharmacotherapies that regulate the expression of Cebpd, Pax6, Spi1, and Tp73. Of these, the antidepressant and/or antipsychotic compounds trimipramine, rolipramine, fluspirilene, and chlorpromazine, as well as the anti-cancer therapies pimasertib, tamoxifen, and vorinostat were strong regulators of the identified transcription factors, suggesting their potential to modulate the regulated transcriptomics networks to improve post-TBI recovery.
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Affiliation(s)
- Anssi Lipponen
- Epilepsy Research Laboratory, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC Australia
- Prince of Wales Hospital, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC Australia
| | - Mark Ziemann
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC Australia
| | - Ishant Khurana
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC Australia
| | - Harikrishnan KN
- Epigenetics in Human Health and Disease Laboratory, Central Clinical School, Faculty of Medicine, Monash University, Melbourne, VIC Australia
| | - Vicente Navarro-Ferrandis
- Epilepsy Research Laboratory, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Noora Puhakka
- Epilepsy Research Laboratory, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
| | - Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- University of Eastern Finland Bioinformatics Center, University of Eastern Finland, Kuopio, Finland
| | - Asla Pitkänen
- Epilepsy Research Laboratory, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland
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65
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Becker AJ. Review: Animal models of acquired epilepsy: insights into mechanisms of human epileptogenesis. Neuropathol Appl Neurobiol 2018; 44:112-129. [DOI: 10.1111/nan.12451] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/27/2017] [Indexed: 02/06/2023]
Affiliation(s)
- A. J. Becker
- Section for Translational Epilepsy Research; Department of Neuropathology; University of Bonn Medical Center; Bonn Germany
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66
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Bales KL, Ianov L, Kennedy AJ, Sweatt JD, Gross AK. Autosomal dominant retinitis pigmentosa rhodopsin mutant Q344X drives specific alterations in chromatin complex gene transcription. Mol Vis 2018; 24:153-164. [PMID: 29463953 PMCID: PMC5815338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 02/13/2018] [Indexed: 10/25/2022] Open
Abstract
Purpose Epigenetic and transcriptional mechanisms have been shown to contribute to long-lasting functional changes in adult neurons. The purpose of this study was to identify any such modifications in diseased retinal tissues from a mouse model of rhodopsin mutation-associated autosomal dominant retinitis pigmentosa (ADRP), Q344X, relative to age-matched wild-type (WT) controls. Methods We performed RNA sequencing (RNA-seq) at poly(A) selected RNA to profile the transcriptional patterns in 3-week-old ADRP mouse model rhodopsin Q344X compared to WT controls. Differentially expressed genes were determined by DESeq2 using the Benjamini & Hochberg p value adjustment and an absolute log2 fold change cutoff. Quantitative western blots were conducted to evaluate protein expression levels of histone H3 phosphorylated at serine 10 and histone H4. qRT-PCR was performed to validate the expression patterns of differentially expressed genes. Results We observed significant differential expression in 2151 genes in the retina of Q344X mice compared to WT controls, including downregulation in the potassium channel gene, Kcnv2, and differential expression of histone genes, including the H1 family histone member, H1foo; the H3 histone family 3B, H3f3b; and the histone deacetylase 9, Hdac9. Quantitative western blots revealed statistically significant decreased protein expression of both histone H3 phosphorylated at serine 10 and histone H4 in 3-week-old Q344X retinas. Furthermore, qRT-PCR performed on select differentially expressed genes based on our RNA-seq results revealed matched expression patterns of up or downregulation. Conclusions These findings provide evidence that transcriptomic alterations occur in the ADRP mouse model rhodopsin Q344X retina and that these processes may contribute to the dysfunction and neurodegeneration seen in this animal model.
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Affiliation(s)
- Katie L. Bales
- School of Optometry, Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL
| | - Lara Ianov
- School of Medicine, Civitan International Research Center, University of Alabama at Birmingham, AL
| | - Andrew J. Kennedy
- Department of Chemistry and Biochemistry, Bates College, Lewiston, ME
| | - J. David Sweatt
- School of Medicine, Department of Pharmacology, Vanderbilt University, TN
| | - Alecia K. Gross
- School of Optometry, Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, AL
- School of Medicine, Civitan International Research Center, University of Alabama at Birmingham, AL
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67
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Klein P, Dingledine R, Aronica E, Bernard C, Blümcke I, Boison D, Brodie MJ, Brooks-Kayal AR, Engel J, Forcelli PA, Hirsch LJ, Kaminski RM, Klitgaard H, Kobow K, Lowenstein DH, Pearl PL, Pitkänen A, Puhakka N, Rogawski MA, Schmidt D, Sillanpää M, Sloviter RS, Steinhäuser C, Vezzani A, Walker MC, Löscher W. Commonalities in epileptogenic processes from different acute brain insults: Do they translate? Epilepsia 2018; 59:37-66. [PMID: 29247482 PMCID: PMC5993212 DOI: 10.1111/epi.13965] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2017] [Indexed: 12/12/2022]
Abstract
The most common forms of acquired epilepsies arise following acute brain insults such as traumatic brain injury, stroke, or central nervous system infections. Treatment is effective for only 60%-70% of patients and remains symptomatic despite decades of effort to develop epilepsy prevention therapies. Recent preclinical efforts are focused on likely primary drivers of epileptogenesis, namely inflammation, neuron loss, plasticity, and circuit reorganization. This review suggests a path to identify neuronal and molecular targets for clinical testing of specific hypotheses about epileptogenesis and its prevention or modification. Acquired human epilepsies with different etiologies share some features with animal models. We identify these commonalities and discuss their relevance to the development of successful epilepsy prevention or disease modification strategies. Risk factors for developing epilepsy that appear common to multiple acute injury etiologies include intracranial bleeding, disruption of the blood-brain barrier, more severe injury, and early seizures within 1 week of injury. In diverse human epilepsies and animal models, seizures appear to propagate within a limbic or thalamocortical/corticocortical network. Common histopathologic features of epilepsy of diverse and mostly focal origin are microglial activation and astrogliosis, heterotopic neurons in the white matter, loss of neurons, and the presence of inflammatory cellular infiltrates. Astrocytes exhibit smaller K+ conductances and lose gap junction coupling in many animal models as well as in sclerotic hippocampi from temporal lobe epilepsy patients. There is increasing evidence that epilepsy can be prevented or aborted in preclinical animal models of acquired epilepsy by interfering with processes that appear common to multiple acute injury etiologies, for example, in post-status epilepticus models of focal epilepsy by transient treatment with a trkB/PLCγ1 inhibitor, isoflurane, or HMGB1 antibodies and by topical administration of adenosine, in the cortical fluid percussion injury model by focal cooling, and in the albumin posttraumatic epilepsy model by losartan. Preclinical studies further highlight the roles of mTOR1 pathways, JAK-STAT3, IL-1R/TLR4 signaling, and other inflammatory pathways in the genesis or modulation of epilepsy after brain injury. The wealth of commonalities, diversity of molecular targets identified preclinically, and likely multidimensional nature of epileptogenesis argue for a combinatorial strategy in prevention therapy. Going forward, the identification of impending epilepsy biomarkers to allow better patient selection, together with better alignment with multisite preclinical trials in animal models, should guide the clinical testing of new hypotheses for epileptogenesis and its prevention.
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Affiliation(s)
- Pavel Klein
- Mid-Atlantic Epilepsy and Sleep Center, Bethesda, MD, USA
| | | | - Eleonora Aronica
- Department of (Neuro) Pathology, Academic Medical Center and Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
- Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, The Netherlands
| | - Christophe Bernard
- Aix Marseille Univ, Inserm, INS, Instit Neurosci Syst, Marseille, 13005, France
| | - Ingmar Blümcke
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Detlev Boison
- Robert Stone Dow Neurobiology Laboratories, Legacy Research Institute, Portland, OR, USA
| | - Martin J Brodie
- Epilepsy Unit, West Glasgow Ambulatory Care Hospital-Yorkhill, Glasgow, UK
| | - Amy R Brooks-Kayal
- Division of Neurology, Departments of Pediatrics and Neurology, University of Colorado School of Medicine, Aurora, CO, USA
- Children's Hospital Colorado, Aurora, CO, USA
- Neuroscience Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jerome Engel
- Departments of Neurology, Neurobiology, and Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, Brain Research Institute, University of California, Los Angeles, CA, USA
| | | | | | | | | | - Katja Kobow
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | | | - Phillip L Pearl
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Asla Pitkänen
- Department of Neurobiology, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Noora Puhakka
- Department of Neurobiology, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Michael A Rogawski
- Department of Neurology, University of California, Davis, Sacramento, CA, USA
| | | | - Matti Sillanpää
- Departments of Child Neurology and General Practice, University of Turku and Turku University Hospital, Turku, Finland
| | - Robert S Sloviter
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Christian Steinhäuser
- Institute of Cellular Neurosciences, Medical Faculty, University of Bonn, Bonn, Germany
| | - Annamaria Vezzani
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Institute for Pharmacological Research, Milan,, Italy
| | - Matthew C Walker
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK
| | - Wolfgang Löscher
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine, Hannover, Germany
- Center for Systems Neuroscience, Hannover, Germany
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68
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Nagalakshmi B., Sagarkar S, Sakharkar AJ. Epigenetic Mechanisms of Traumatic Brain Injuries. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:263-298. [DOI: 10.1016/bs.pmbts.2017.12.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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69
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Sokhranyaeva LS, Aniol VA, Gulyaeva NV. [Epigenetic modifications of chromatin in epilepsy: a potential mechanism of pharmacoresistance?]. Zh Nevrol Psikhiatr Im S S Korsakova 2017; 117:17-21. [PMID: 29213033 DOI: 10.17116/jnevro20171179217-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pharmacoresistance in epilepsy is an important problem from both clinical and fundamental perspectives. The existent hypotheses of pharmacoresistance are based on long term plastic rebuilding of the epileptic brain. One of potential mechanisms mediating such protracted changes are alterations of gene expression induced by epigenetic modifications of chromatin in brain cells of epileptic patients. Recently, changes in DNA methylation and histone post-translational modifications were reported in brain tissues of patients with pharmacoresistant epilepsy. Unfortunately, these data remain fragmentary and contradictory, therefore the results of animal models can partially fill this gap. The authors present a short review of the data concerning a potential role of epigenetic modifications in epilepsy.
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Affiliation(s)
- L S Sokhranyaeva
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, Russia
| | - V A Aniol
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, Russia
| | - N V Gulyaeva
- Institute of Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences, Moscow, Russia
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70
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Magagna-Poveda A, Moretto JN, Scharfman HE. Increased gyrification and aberrant adult neurogenesis of the dentate gyrus in adult rats. Brain Struct Funct 2017; 222:4219-4237. [PMID: 28656372 PMCID: PMC5909844 DOI: 10.1007/s00429-017-1457-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 06/06/2017] [Indexed: 02/08/2023]
Abstract
A remarkable example of maladaptive plasticity is the development of epilepsy after a brain insult or injury to a normal animal or human. A structure that is considered central to the development of this type of epilepsy is the dentate gyrus (DG), because it is normally a relatively inhibited structure and its quiescence is thought to reduce hippocampal seizure activity. This characteristic of the DG is also considered to be important for normal hippocampal-dependent cognitive functions. It has been suggested that the brain insults which cause epilepsy do so because they cause the DG to be more easily activated. One type of brain insult that is commonly used is induction of severe seizures (status epilepticus; SE) by systemic injection of a convulsant drug. Here we describe an alteration in the DG after this type of experimental SE that may contribute to chronic seizures that has not been described before: large folds or gyri that develop in the DG by 1 month after SE. Large gyri appeared to increase network excitability because epileptiform discharges recorded in hippocampal slices after SE were longer in duration when recorded inside gyri relative to locations outside gyri. Large gyri may also increase excitability because immature adult-born neurons accumulated at the base of gyri with time after SE, and previous studies have suggested that abnormalities in adult-born DG neurons promote seizures after SE. In summary, large gyri after SE are a common finding in adult rats, show increased excitability, and are associated with the development of an abnormal spatial distribution of adult-born neurons. Together these alterations may contribute to chronic seizures and associated cognitive comorbidities after SE.
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Affiliation(s)
- Alejandra Magagna-Poveda
- The Nathan Kline Institute of Psychiatric Research, Center for Dementia Research, 140 Old Orangeburg Rd. Bldg. 35, Orangeburg, NY, 10962, USA
| | - Jillian N Moretto
- The Nathan Kline Institute of Psychiatric Research, Center for Dementia Research, 140 Old Orangeburg Rd. Bldg. 35, Orangeburg, NY, 10962, USA
| | - Helen E Scharfman
- The Nathan Kline Institute of Psychiatric Research, Center for Dementia Research, 140 Old Orangeburg Rd. Bldg. 35, Orangeburg, NY, 10962, USA.
- Department of Child and Adolescent Psychiatry, New York University Langone Medical Center, One Park Ave., New York, NY, 10016, USA.
- Department of Physiology and Neuroscience, New York University Langone Medical Center, One Park Ave., New York, NY, 10016, USA.
- Department of Psychiatry, New York University Langone Medical Center, One Park Ave., New York, NY, 10016, USA.
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71
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Kiese K, Jablonski J, Hackenbracht J, Wrosch JK, Groemer TW, Kornhuber J, Blümcke I, Kobow K. Epigenetic control of epilepsy target genes contributes to a cellular memory of epileptogenesis in cultured rat hippocampal neurons. Acta Neuropathol Commun 2017; 5:79. [PMID: 29089052 PMCID: PMC5664434 DOI: 10.1186/s40478-017-0485-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/25/2017] [Indexed: 02/01/2023] Open
Abstract
Hypersynchronous neuronal excitation manifests clinically as seizure (ictogenesis), and may recur spontaneously and repetitively after a variable latency period (epileptogenesis). Despite tremendous research efforts to describe molecular pathways and signatures of epileptogenesis, molecular pathomechanisms leading to chronic epilepsy remain to be clarified. We hypothesized that epigenetic modifications may form the basis for a cellular memory of epileptogenesis, and used a primary neuronal cell culture model of the rat hippocampus to study the translation of massive neuronal excitation into persisting changes of epigenetic signatures and pro-epileptogenic target gene expression. Increased spontaneous activation of cultured neurons was detected 3 and 7 days after stimulation with 10 μM glutamate when compared to sham-treated time-matched controls using calcium-imaging in vitro. Chromatin-immunoprecipitation experiments revealed short-term (3 h, 7 h, and 24 h) and long-term (3 d and 2 weeks) changes in histone modifications, which were directly linked to decreased expression of two selected epilepsy target genes, e.g. excitatory glutamate receptor genes Gria2 and Grin2a. Increased promoter methylation observed 4 weeks after glutamate stimulation at respective genes suggested long-term repression of Gria2 and Grin2a genes. Inhibition of glutamatergic activation or blocking the propagation of action potentials in cultured neurons rescued altered gene expression and regulatory epigenetic modifications. Our data support the concept of a cellular memory of epileptogenesis and persisting epigenetic modifications of epilepsy target genes, which are able to turn normal into pro-epileptic neurons and circuits.
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Abstract
This article highlights the emerging therapeutic potential of specific epigenetic modulators as promising antiepileptogenic or disease-modifying agents for curing epilepsy. Currently, there is an unmet need for antiepileptogenic agents that truly prevent the development of epilepsy in people at risk. There is strong evidence that epigenetic signaling, which exerts high fidelity regulation of gene expression, plays a crucial role in the pathophysiology of epileptogenesis and chronic epilepsy. These modifications are not hard-wired into the genome and are constantly reprogrammed by environmental influences. The potential epigenetic mechanisms, including histone modifications, DNA methylation, microRNA-based transcriptional control, and bromodomain reading activity, can drastically alter the neuronal gene expression profile by exerting their summative effects in a coordinated fashion. Such an epigenetic intervention appears more rational strategy for preventing epilepsy because it targets the primary pathway that initially triggers the numerous downstream cellular and molecular events mediating epileptogenesis. Among currently approved epigenetic drugs, the majority are anticancer drugs with well-established profiles in clinical trials and practice. Evidence from preclinical studies supports the premise that these drugs may be applied to a wide range of brain disorders. Targeting histone deacetylation by inhibiting histone deacetylase enzymes appears to be one promising epigenetic therapy since certain inhibitors have been shown to prevent epileptogenesis in animal models. However, developing neuronal specific epigenetic modulators requires rational, pathophysiology-based optimization to efficiently intercept the upstream pathways in epileptogenesis. Overall, epigenetic agents have been well positioned as new frontier tools towards the national goal of curing epilepsy.
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Affiliation(s)
- Iyan Younus
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M Health Science Center, Bryan, TX 77807, USA
| | - Doodipala Samba Reddy
- Department of Neuroscience and Experimental Therapeutics, College of Medicine, Texas A&M Health Science Center, Bryan, TX 77807, USA.
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73
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Mateen BA, Hill CS, Biddie SC, Menon DK. DNA Methylation: Basic Biology and Application to Traumatic Brain Injury. J Neurotrauma 2017; 34:2379-2388. [DOI: 10.1089/neu.2017.5007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Bilal A. Mateen
- Division of Medicine, University College London, London, United Kingdom
| | - Ciaran S. Hill
- John van Geest Centre for Brain Repair, School of Clinical Medicine, Addenbrookes Hospital, Cambridge, United Kingdom
| | - Simon C. Biddie
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - David K. Menon
- John van Geest Centre for Brain Repair, School of Clinical Medicine, Addenbrookes Hospital, Cambridge, United Kingdom
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
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74
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Ianov L, Riva A, Kumar A, Foster TC. DNA Methylation of Synaptic Genes in the Prefrontal Cortex Is Associated with Aging and Age-Related Cognitive Impairment. Front Aging Neurosci 2017; 9:249. [PMID: 28824413 PMCID: PMC5539085 DOI: 10.3389/fnagi.2017.00249] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/14/2017] [Indexed: 01/17/2023] Open
Abstract
The current study investigates DNA methylation as a possible epigenetic regulator of transcription associated with aging and cognitive function. Young and aged male Fischer 344 rats were behaviorally characterized on a set shifting task, and whole genome bisulfite sequencing was employed to profile the DNA methylome of the medial prefrontal cortex (mPFC). DNA methylation was also compared to RNA expression in the mPFC from the same animals. Variability in methylation was mainly observed for CpG sites as opposed to CHG and CHH sites. Gene bodies, specifically introns, contain the highest levels of methylation. During aging, hypermethylation was observed for genes linked to synaptic function and GTPase activity. Furthermore, impaired cognitive flexibility during aging was associated with hypermethylation of genes linked to postsynaptic density, dendrites, the axon terminus, and Ca2+ channels. Finally, comparison with RNA expression confirmed that hypermethylation was correlated with decreased expression of synaptic genes. The results indicate that DNA methylation over the lifespan contributes to synaptic modification observed in brain aging and age-related cognitive impairment.
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Affiliation(s)
- Lara Ianov
- Department of Neuroscience, McKnight Brain Institute, University of Florida, GainesvilleFL, United States.,Genetics and Genomics Program, Genetics Institute, University of Florida, GainesvilleFL, United States
| | - Alberto Riva
- Bioinformatics Core, Interdisciplinary Center for Biotechnology Research, University of Florida, GainesvilleFL, United States
| | - Ashok Kumar
- Department of Neuroscience, McKnight Brain Institute, University of Florida, GainesvilleFL, United States
| | - Thomas C Foster
- Department of Neuroscience, McKnight Brain Institute, University of Florida, GainesvilleFL, United States.,Genetics and Genomics Program, Genetics Institute, University of Florida, GainesvilleFL, United States
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75
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Jozwiak S, Becker A, Cepeda C, Engel J, Gnatkovsky V, Huberfeld G, Kaya M, Kobow K, Simonato M, Loeb JA. WONOEP appraisal: Development of epilepsy biomarkers-What we can learn from our patients? Epilepsia 2017; 58:951-961. [PMID: 28387933 PMCID: PMC5806696 DOI: 10.1111/epi.13728] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Current medications for patients with epilepsy work in only two of three patients. For those medications that do work, they only suppress seizures. They treat the symptoms, but do not modify the underlying disease, forcing patients to take these drugs with significant side effects, often for the rest of their lives. A major limitation in our ability to advance new therapeutics that permanently prevent, reduce the frequency of, or cure epilepsy comes from a lack of understanding of the disease coupled with a lack of reliable biomarkers that can predict who has or who will get epilepsy. METHODS The main goal of this report is to present a number of approaches for identifying reliable biomarkers from observing patients with brain disorders that have a high probability of producing epilepsy. RESULTS A given biomarker, or more likely a profile of biomarkers, will have both a quantity and a time course during epileptogenesis that can be used to predict who will get the disease, to confirm epilepsy as a diagnosis, to identify coexisting pathologies, and to monitor the course of treatments. SIGNIFICANCE Additional studies in patients and animal models could identify common and clinically valuable biomarkers to successfully translate animal studies into new and effective clinical trials.
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Affiliation(s)
- Sergiusz Jozwiak
- Department of Child Neurology, Medical University of Warsaw, Poland
- Department of Child Neurology, The Children’s Memorial Health Institute, Warsaw, Poland
| | - Albert Becker
- Section for Translational Epilepsy Research, Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Carlos Cepeda
- IDDRC, Semel Institute for Neuroscience & Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Jerome Engel
- Departments of Neurology, Neurobiology, and Psychiatry & Biobehavioral Sciences and the Brain Research Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Vadym Gnatkovsky
- Unit of Epilepsy and Experimental Neurophysiology, Fondazione Istituto Neurologico Carlo Besta, Milan, Italy
| | - Gilles Huberfeld
- Sorbonne and UPMC University, AP-HP, Department of Neurophysiology, UPMC and La Pitié-Salpêtrière Hospital, Paris, France
- INSERM U1129, Paris Descartes University, PRES Sorbonne Paris, Cité, Paris, CEA, France
| | - Mehmet Kaya
- Department of Physiology, Koc University School of Medicine, Rumelifeneri Yolu, Sariver, Istanbul, Turkey
| | - Katja Kobow
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Michele Simonato
- Department of Medical Sciences, University of Ferrara and Division of Neuroscience, University Vita-Salute San Raffaele, Milan, Italy
| | - Jeffrey A. Loeb
- Department of Neurology and Rehabilitation, The University of Illinois at Chicago, Chicago, IL
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Abstract
Epilepsy is a common and devastating neurological disorder characterized by recurrent and unprovoked spontaneous seizures. One leading hypothesis for the development and progression of epilepsy is that large-scale changes in gene transcription and protein expression contribute to aberrant network restructuring and hyperexcitability, resulting in the genesis of repeated seizures. Current research shows that epigenetic mechanisms, including posttranslational alterations to the proteins around which DNA is coiled, chemical modifications to DNA, and the activity of various noncoding RNA molecules exert important influences on these gene networks in experimental epilepsy. Key findings from animal models have been replicated in humans using brain tissue obtained from living patients at the time of neurosurgical resection for pharmacoresistant epilepsy. These findings have spurred efforts to target epigenetic processes to disrupt or modify epilepsy in experimental models with varying degrees of success. In this review, we will (1) summarize the epigenetic mechanisms implicated in epileptogenesis and epilepsy, (2) explore the influence of metabolic factors on epigenetic mechanisms, and (3) assess the potential of using epigenetic markers to support diagnosis and prognosis. Translation of these findings may guide the development of molecular biomarkers and novel therapeutics for prevention or modification of epileptic disorders.
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Affiliation(s)
- Rebecca M. Hauser
- Evelyn F. McKnight Brain Institute, Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - David C. Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Farah D. Lubin
- Evelyn F. McKnight Brain Institute, Department of Neurobiology, The University of Alabama at Birmingham, Birmingham, AL, USA
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77
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Puhakka N, Bot AM, Vuokila N, Debski KJ, Lukasiuk K, Pitkänen A. Chronically dysregulated NOTCH1 interactome in the dentate gyrus after traumatic brain injury. PLoS One 2017; 12:e0172521. [PMID: 28273100 PMCID: PMC5342204 DOI: 10.1371/journal.pone.0172521] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/06/2017] [Indexed: 12/13/2022] Open
Abstract
Traumatic brain injury (TBI) can result in several dentate gyrus-regulated disabilities. Almost nothing is known about the chronic molecular changes after TBI, and their potential as treatment targets. We hypothesized that chronic transcriptional alterations after TBI are under microRNA (miRNA) control. Expression of miRNAs and their targets in the dentate gyrus was analyzed using microarrays at 3 months after experimental TBI. Of 305 miRNAs present on the miRNA-array, 12 were downregulated (p<0.05). In parallel, 75 of their target genes were upregulated (p<0.05). A bioinformatics analysis of miRNA targets highlighted the dysregulation of the transcription factor NOTCH1 and 39 of its target genes (NOTCH1 interactome). Validation assays confirmed downregulation of miR-139-5p, upregulation of Notch1 and its activated protein, and positive enrichment of NOTCH1 target gene expression. These findings demonstrate that miRNA-based transcriptional regulation can be present at chronic time points after TBI, and highlight the NOTCH1 interactome as one of the mechanisms behind the dentate gyrus pathology-related morbidities.
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Affiliation(s)
- Noora Puhakka
- Department of Neurobiology, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Anna Maria Bot
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Niina Vuokila
- Department of Neurobiology, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Konrad Jozef Debski
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Lukasiuk
- The Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Asla Pitkänen
- Department of Neurobiology, A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- * E-mail:
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78
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Kobow K, Blümcke I. Epigenetics in epilepsy. Neurosci Lett 2017; 667:40-46. [PMID: 28111355 DOI: 10.1016/j.neulet.2017.01.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/02/2017] [Accepted: 01/06/2017] [Indexed: 11/19/2022]
Abstract
Approximately 50 million people have epilepsy, making it the most common chronic and severe neurological disease worldwide, with increased risk of mortality and psychological and socioeconomic consequences impairing quality of life. More than 30% of patients with epilepsy have inadequate control of their seizures with drug therapy. Any structural brain lesion can provoke epilepsy. However, progression of seizure activity as well as the development of drug-resistance remains difficult to predict, irrespective of the underlying epileptogenic condition, i.e., traumatic brain injury, developmental brain lesions, brain tumors or genetic inheritance. Mutated DNA sequences in genes encoding for ion channels or neurotransmitter receptors have been identified in hereditary focal or generalized epilepsies, but genotype-phenotype correlations are poor, arguing for additional factors determining the effect of a genetic predisposition. The dynamics of epigenetic mechanisms (e.g. DNA methylation, histone modifications, chromatin remodelling, and non-coding RNAs) provide likely explanations for common features in epilepsy and other complex diseases, including late onset, parent-of-origin effects, discordance of monozygotic twins, and fluctuation of symptoms. In addition, many focal epilepsies, including focal cortical dysplasias (FCDs), glio-neuronal tumors (e.g. ganglioglioma), or temporal lobe epilepsy with hippocampal sclerosis (TLE-HS), do not seem to primarily associate with hereditary traits, suggesting other pathogenic mechanisms. Herein we will discuss the many faces of the epigenetic machinery, which provides powerful tools and mechanisms to propagate epileptogenicity and likely also contribute to the epileptogenic memory in chronic and difficult-to-treat epilepsies.
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Affiliation(s)
- K Kobow
- Department of Neuropathology, University Hospital Erlangen, Germany.
| | - I Blümcke
- Department of Neuropathology, University Hospital Erlangen, Germany
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79
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Brennan GP, Henshall DC. microRNAs in the pathophysiology of epilepsy. Neurosci Lett 2017; 667:47-52. [PMID: 28104433 DOI: 10.1016/j.neulet.2017.01.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/06/2017] [Accepted: 01/08/2017] [Indexed: 12/12/2022]
Abstract
Temporal lobe epilepsy is a common and often drug-resistant seizure disorder. The underlying pathological processes which give rise to the development of spontaneous seizures include neuroinflammation, cell loss, neurogenesis and dendritic abnormalities and many of these are driven by insult-induced changes in gene expression and gene expression regulation. MicroRNAs are powerful modulators of post-transcriptional gene expression which are dysregulated during epileptogenesis. The advent of locked nucleic acid (LNA) based inhibitory methods and mimic technology has facilitated in vivo functional assessment of these molecules in epilepsy. Here we review recent advances in our understanding of the role of these short non-coding RNAs in the pathophysiology of epilepsy.
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Affiliation(s)
- Gary P Brennan
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland,123 St. Stephens Green, Dublin D02 YN77, Ireland
| | - David C Henshall
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland,123 St. Stephens Green, Dublin D02 YN77, Ireland.
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