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Zhang Y, Qu W, Yan R, Liu H, Zhang C, Li Z, Dong G. A reliable and quick method for screening alternative splicing variants for low-abundance genes. PLoS One 2024; 19:e0305201. [PMID: 38935635 PMCID: PMC11210779 DOI: 10.1371/journal.pone.0305201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 05/24/2024] [Indexed: 06/29/2024] Open
Abstract
Alternative splicing (AS) is a universal phenomenon in eukaryotes, and it is still challenging to identify AS events. Several methods have been developed to identify AS events, such as expressed sequence tags (EST), microarrays and RNA-seq. However, EST has limitations in identifying low-abundance genes, while microarray and RNA-seq are high-throughput technologies, and PCR-based technology is needed for validation. To overcome the limitations of EST and shortcomings of high-throughput technologies, we established a method to identify AS events, especially for low-abundance genes, by reverse transcription (RT) PCR with gene-specific primers (GSPs) followed by nested PCR. This process includes two major steps: 1) the use of GSPs to amplify as long as the specific gene segment and 2) multiple rounds of nested PCR to screen the AS and confirm the unknown splicing variants. With this method, we successfully identified three new splicing variants, namely, GenBank Accession No. HM623886 for the bdnf gene (GenBank GeneID: 12064), GenBank Accession No. JF417977 for the trkc gene (GenBank GeneID: 18213) and GenBank Accession No. HM623888 for the glb-18 gene (GenBank GeneID: 172485). In addition to its reliability and simplicity, the method is also cost-effective and labor-intensive. In conclusion, we developed an RT-nested PCR method using gene-specific primers to efficiently identify known and novel AS variants. This approach overcomes the limitations of existing methods for detecting rare transcripts. By enabling the discovery of new isoforms, especially for low-abundance genes, this technique can aid research into aberrant splicing in disease. Future studies can apply this method to uncover AS variants involved in cancer, neurodegeneration, and other splicing-related disorders.
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Affiliation(s)
- Yanchun Zhang
- Department of Blood Transfusion Medicine, The Seventh Medical Center of PLA General Hospital, Beijing, China
- Laboratory of Electromagnetic Biological Effects, Beijing Institute of Radiation and Medicine, Beijing, China
| | - Wubin Qu
- Laboratory of Electromagnetic Biological Effects, Beijing Institute of Radiation and Medicine, Beijing, China
| | - Ruifen Yan
- Laboratory of Electromagnetic Biological Effects, Beijing Institute of Radiation and Medicine, Beijing, China
- College of Life Science, Northwest Agriculture and Forest University, Yangling, China
| | - Huqi Liu
- College of Life Science, Northwest Agriculture and Forest University, Yangling, China
| | - Chenggang Zhang
- Laboratory of Electromagnetic Biological Effects, Beijing Institute of Radiation and Medicine, Beijing, China
| | - Zhihui Li
- Laboratory of Electromagnetic Biological Effects, Beijing Institute of Radiation and Medicine, Beijing, China
| | - Guofu Dong
- Laboratory of Electromagnetic Biological Effects, Beijing Institute of Radiation and Medicine, Beijing, China
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Zhang Y, Shaabani S, Vowinkel K, Trombetta-Lima M, Sabogal-Guáqueta AM, Chen T, Hoekstra J, Lembeck J, Schmidt M, Decher N, Dömling A, Dolga AM. Novel SK channel positive modulators prevent ferroptosis and excitotoxicity in neuronal cells. Biomed Pharmacother 2024; 171:116163. [PMID: 38242037 DOI: 10.1016/j.biopha.2024.116163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/07/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024] Open
Abstract
Small conductance calcium-activated potassium (SK) channel activity has been proposed to play a role in the pathology of several neurological diseases. Besides regulating plasma membrane excitability, SK channel activation provides neuroprotection against ferroptotic cell death by reducing mitochondrial Ca2+ uptake and reactive oxygen species (ROS). In this study, we employed a multifaceted approach, integrating structure-based and computational techniques, to strategically design and synthesize an innovative class of potent small-molecule SK2 channel modifiers through highly efficient multicomponent reactions (MCRs). The compounds' neuroprotective activity was compared with the well-studied SK positive modulator, CyPPA. Pharmacological SK channel activation by selected compounds confers neuroprotection against ferroptosis at low nanomolar ranges compared to CyPPA, that mediates protection at micromolar concentrations, as shown by an MTT assay, real-time cell impedance measurements and propidium iodide staining (PI). These novel compounds suppress increased mitochondrial ROS and Ca2+ level induced by ferroptosis inducer RSL3. Moreover, axonal degeneration was rescued by these novel SK channel activators in primary mouse neurons and they attenuated glutamate-induced neuronal excitability, as shown via microelectrode array. Meanwhile, functional afterhyperpolarization of the novel SK2 channel modulators was validated by electrophysiological measurements showing more current change induced by the novel modulators than the reference compound, CyPPA. These data support the notion that SK2 channel activation can represent a therapeutic target for brain diseases in which ferroptosis and excitotoxicity contribute to the pathology.
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Affiliation(s)
- Yuequ Zhang
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Shabnam Shaabani
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Kirsty Vowinkel
- Institute of Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, 35037 Marburg, Germany
| | - Marina Trombetta-Lima
- Department of Pharmaceutical Technologies and Biopharmacy, Research Institute of Pharmacy, University of Groningen, the Netherlands
| | | | - Tingting Chen
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Jan Hoekstra
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Jan Lembeck
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Martina Schmidt
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands
| | - Niels Decher
- Institute of Physiology and Pathophysiology, Vegetative Physiology, University of Marburg, 35037 Marburg, Germany
| | - Alexander Dömling
- Department of Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands.
| | - Amalia M Dolga
- Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy, University of Groningen, the Netherlands.
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Tang T, Li X, Yu E, Li M, Pan X. Identification of common core ion channel genes in epilepsy and Alzheimer's disease. Ir J Med Sci 2024; 193:417-424. [PMID: 37477849 DOI: 10.1007/s11845-023-03447-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Although available literature indicates that the incidence of dementia in the epilepsy population and the risk of seizures in the Alzheimer's disease (AD) population are high, the specific genetic risk factors and the interaction mechanism are unclear, rendering rational genetic interpretation rather challenging. AIMS Our work aims to identify the common core ion channel genes in epilepsy and AD. METHODS In this study, we first integrated gene expression omnibus datasets (GSE48350 and GSE6834) on AD and epilepsy to identify differentially expressed genes (DEGs), performing Gene Ontology function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs. The related protein-protein interaction (PPI) network was constructed for DEGs, and the hub gene was evaluated. RESULTS A total of 2800 and 35 genes were identified in GSE48350 and GSE6834, and 12 DEGs were significantly differentially expressed between the datasets. KEGG pathway analysis showed that DEGs were primarily enriched in glutamatergic synapse and dopaminergic synapse pathways. SCN2A, GRIA1, and KCNJ9 were the hub genes with high connectivity. CONCLUSIONS The findings suggest that the three genes, SCN2A, GRIA1, and KCNJ9, may serve as potential targets for treating AD comorbid with epilepsy.
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Affiliation(s)
- Ting Tang
- Department of Neurology, The Second Affiliated Hospital of Fujian Medical University, 34 Zhongshan North Road, Quanzhou, Fujian, 362000, People's Republic of China
| | - Xiang Li
- Department of Neurology, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, Fujian, 350001, People's Republic of China
| | - Erhan Yu
- Department of Neurology, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, Fujian, 350001, People's Republic of China
| | - Man Li
- Department of Neurology, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, Fujian, 350001, People's Republic of China
| | - Xiaodong Pan
- Department of Neurology, Center for Cognitive Neurology, Fujian Institute of Geriatrics, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, Fujian, 350001, People's Republic of China.
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Monteil A, Guérineau NC, Gil-Nagel A, Parra-Diaz P, Lory P, Senatore A. New insights into the physiology and pathophysiology of the atypical sodium leak channel NALCN. Physiol Rev 2024; 104:399-472. [PMID: 37615954 DOI: 10.1152/physrev.00014.2022] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/13/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Abstract
Cell excitability and its modulation by hormones and neurotransmitters involve the concerted action of a large repertoire of membrane proteins, especially ion channels. Unique complements of coexpressed ion channels are exquisitely balanced against each other in different excitable cell types, establishing distinct electrical properties that are tailored for diverse physiological contributions, and dysfunction of any component may induce a disease state. A crucial parameter controlling cell excitability is the resting membrane potential (RMP) set by extra- and intracellular concentrations of ions, mainly Na+, K+, and Cl-, and their passive permeation across the cell membrane through leak ion channels. Indeed, dysregulation of RMP causes significant effects on cellular excitability. This review describes the molecular and physiological properties of the Na+ leak channel NALCN, which associates with its accessory subunits UNC-79, UNC-80, and NLF-1/FAM155 to conduct depolarizing background Na+ currents in various excitable cell types, especially neurons. Studies of animal models clearly demonstrate that NALCN contributes to fundamental physiological processes in the nervous system including the control of respiratory rhythm, circadian rhythm, sleep, and locomotor behavior. Furthermore, dysfunction of NALCN and its subunits is associated with severe pathological states in humans. The critical involvement of NALCN in physiology is now well established, but its study has been hampered by the lack of specific drugs that can block or agonize NALCN currents in vitro and in vivo. Molecular tools and animal models are now available to accelerate our understanding of how NALCN contributes to key physiological functions and the development of novel therapies for NALCN channelopathies.
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Affiliation(s)
- Arnaud Monteil
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
- LabEx "Ion Channel Science and Therapeutics," Montpellier, France
- Department of Physiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nathalie C Guérineau
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
- LabEx "Ion Channel Science and Therapeutics," Montpellier, France
| | - Antonio Gil-Nagel
- Department of Neurology, Epilepsy Program, Hospital Ruber Internacional, Madrid, Spain
| | - Paloma Parra-Diaz
- Department of Neurology, Epilepsy Program, Hospital Ruber Internacional, Madrid, Spain
| | - Philippe Lory
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
- LabEx "Ion Channel Science and Therapeutics," Montpellier, France
| | - Adriano Senatore
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
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Gomes Moreira D, Jan A. A beginner's guide into curated analyses of open access datasets for biomarker discovery in neurodegeneration. Sci Data 2023; 10:432. [PMID: 37414779 PMCID: PMC10325954 DOI: 10.1038/s41597-023-02338-1] [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: 02/21/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
The discovery of surrogate biomarkers reflecting neuronal dysfunction in neurodegenerative diseases (NDDs) remains an active area of research. To boost these efforts, we demonstrate the utility of publicly available datasets for probing the pathogenic relevance of candidate markers in NDDs. As a starting point, we introduce the readers to several open access resources, which contain gene expression profiles and proteomics datasets from patient studies in common NDDs, including proteomics analyses of cerebrospinal fluid (CSF). Then, we illustrate the method for curated gene expression analyses across select brain regions from four cohorts of Parkinson disease patients (and from one study in common NDDs), probing glutathione biogenesis, calcium signaling and autophagy. These data are complemented by findings of select markers in CSF-based studies in NDDs. Additionally, we enclose several annotated microarray studies, and summarize reports on CSF proteomics across the NDDs, which the readers can utilize for translational purposes. We anticipate that this "beginner's guide" will benefit the research community in NDDs, and would serve as a useful educational tool.
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Affiliation(s)
- Diana Gomes Moreira
- Department of Clinical Medicine, Palle Juul-Jensens Boulevard 165, DK-8200, Aarhus N, Denmark
| | - Asad Jan
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, DK-8000, Aarhus C, Denmark.
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Identification of a Novel Idiopathic Epilepsy Risk Locus and a Variant in the CCDC85A Gene in the Dutch Partridge Dog. Animals (Basel) 2023; 13:ani13050810. [PMID: 36899667 PMCID: PMC10000155 DOI: 10.3390/ani13050810] [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: 01/18/2023] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
(1) Idiopathic epilepsy (IE) is thought to have a genetic cause in several dog breeds. However, only two causal variants have been identified to date, and few risk loci are known. No genetic studies have been conducted on IE in the Dutch partridge dog (DPD), and little has been reported on the epileptic phenotype in this breed. (2) Owner-filled questionnaires and diagnostic investigations were used to characterize IE in the DPD. A genome-wide association study (GWAS) involving 16 cases and 43 controls was performed, followed by sequencing of the coding sequence and splice site regions of a candidate gene within the associated region. Subsequent whole-exome sequencing (WES) of one family (including one IE-affected dog, both parents, and an IE-free sibling) was performed. (3) IE in the DPD has a broad range in terms of age at onset, frequency, and duration of epileptic seizures. Most dogs showed focal epileptic seizures evolving into generalized seizures. A new risk locus on chromosome 12 (BICF2G630119560; praw = 4.4 × 10-7; padj = 0.043) was identified through GWAS. Sequencing of the GRIK2 candidate gene revealed no variants of interest. No WES variants were located within the associated GWAS region. However, a variant in CCDC85A (chromosome 10; XM_038680630.1: c.689C > T) was discovered, and dogs homozygous for the variant (T/T) had an increased risk of developing IE (OR: 6.0; 95% CI: 1.6-22.6). This variant was identified as likely pathogenic according to ACMG guidelines. (4) Further research is necessary before the risk locus or CCDC85A variant can be used for breeding decisions.
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Oatman SR, Reddy JS, Quicksall Z, Carrasquillo MM, Wang X, Liu CC, Yamazaki Y, Nguyen TT, Malphrus K, Heckman M, Biswas K, Nho K, Baker M, Martens YA, Zhao N, Kim JP, Risacher SL, Rademakers R, Saykin AJ, DeTure M, Murray ME, Kanekiyo T, Dickson DW, Bu G, Allen M, Ertekin-Taner N. Genome-wide association study of brain biochemical phenotypes reveals distinct genetic architecture of Alzheimer's disease related proteins. Mol Neurodegener 2023; 18:2. [PMID: 36609403 PMCID: PMC9825010 DOI: 10.1186/s13024-022-00592-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/19/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is neuropathologically characterized by amyloid-beta (Aβ) plaques and neurofibrillary tangles. The main protein components of these hallmarks include Aβ40, Aβ42, tau, phosphor-tau, and APOE. We hypothesize that genetic variants influence the levels and solubility of these AD-related proteins in the brain; identifying these may provide key insights into disease pathogenesis. METHODS Genome-wide genotypes were collected from 441 AD cases, imputed to the haplotype reference consortium (HRC) panel, and filtered for quality and frequency. Temporal cortex levels of five AD-related proteins from three fractions, buffer-soluble (TBS), detergent-soluble (Triton-X = TX), and insoluble (Formic acid = FA), were available for these same individuals. Variants were tested for association with each quantitative biochemical measure using linear regression, and GSA-SNP2 was used to identify enriched Gene Ontology (GO) terms. Implicated variants and genes were further assessed for association with other relevant variables. RESULTS We identified genome-wide significant associations at seven novel loci and the APOE locus. Genes and variants at these loci also associate with multiple AD-related measures, regulate gene expression, have cell-type specific enrichment, and roles in brain health and other neuropsychiatric diseases. Pathway analysis identified significant enrichment of shared and distinct biological pathways. CONCLUSIONS Although all biochemical measures tested reflect proteins core to AD pathology, our results strongly suggest that each have unique genetic architecture and biological pathways that influence their specific biochemical states in the brain. Our novel approach of deep brain biochemical endophenotype GWAS has implications for pathophysiology of proteostasis in AD that can guide therapeutic discovery efforts focused on these proteins.
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Affiliation(s)
- Stephanie R. Oatman
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Joseph S. Reddy
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
| | - Zachary Quicksall
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
| | | | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
| | - Chia-Chen Liu
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Yu Yamazaki
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Thuy T. Nguyen
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Kimberly Malphrus
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Michael Heckman
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
| | - Kristi Biswas
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Kwangsik Nho
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
- School of Informatics and Computing, Indiana University School of Medicine, Indianapolis, IN USA
| | - Matthew Baker
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Yuka A. Martens
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Na Zhao
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Jun Pyo Kim
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
| | - Shannon L. Risacher
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
- VIB-UA Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, Belgium
| | - Andrew J. Saykin
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN USA
| | - Michael DeTure
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Melissa E. Murray
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Takahisa Kanekiyo
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - for the Alzheimer’s Disease Neuroimaging Initiative
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL USA
- Indiana Alzheimer Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
- School of Informatics and Computing, Indiana University School of Medicine, Indianapolis, IN USA
- VIB-UA Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, Belgium
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Birdsall 3, Jacksonville, FL 32224 USA
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224 USA
- Department of Neurology, Mayo Clinic, 4500 San Pablo Road, Birdsall 3, Jacksonville, FL 32224 USA
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Wang S, Li Z, Ding X, Zhao Z, Zhang M, Xu H, Lu J, Dai L. Integrative Analyses Identify KCNJ15 as a Candidate Gene in Patients with Epilepsy. Neurol Ther 2022; 11:1767-1776. [PMID: 36168094 DOI: 10.1007/s40120-022-00407-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION Although there is accumulating evidence that genetic factors play a vital role in the pathogenesis of epilepsy, few epilepsy-associated genes have been identified. Additionally, the role of KCNJ15 in epilepsy has not been evaluated so far. METHODS Here, we performed differentially expressed gene analysis, expression quantitative trait loci analysis, gene co-expression analysis, and protein-protein interaction analysis to evaluate the role of KCNJ15 in epilepsy. RESULTS Analysis of gene expression and expression quantitative trait loci data revealed that KCNJ15 was significantly downregulated in patients with epilepsy (adjusted P = 0.0146 and log2 Fold change = - 1.0025), and an epilepsy-associated polymorphism (rs2833098) was linked to altered KCNJ15 expression level in human temporal lobe brain tissue (P = 0.0036). Gene co-expression analysis revealed that KCNJ15 was co-expressed with genes that have been reported to be associated with epilepsy in human brain tissue. Furthermore, protein-protein interaction analysis revealed strong supportive evidence for the role of KCNJ15 in epilepsy. CONCLUSION Our results show that KCNJ15 may be a candidate target for epilepsy. Functional analysis of KCNJ15 may provide novel insights for epilepsy treatment.
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Affiliation(s)
- Shitao Wang
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, Anhui, China.
| | - Zongyou Li
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, Anhui, China
| | - Xiangqian Ding
- Department of Neurosurgery, Qilu Hospital of Shandong University, Shandong, China
| | - Zongyou Zhao
- Department of Neurology, Funan County People's Hospital, Funan, Anhui, China
| | - Mengen Zhang
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, Anhui, China
| | - Hui Xu
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, Anhui, China
| | - Jinghong Lu
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, Anhui, China
| | - Lili Dai
- Department of Geriatrics, Funan County People's Hospital, Funan, Anhui, China.
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Olah VJ, Goettemoeller AM, Rayaprolu S, Dammer EB, Seyfried NT, Rangaraju S, Dimidschstein J, Rowan MJM. Biophysical Kv3 channel alterations dampen excitability of cortical PV interneurons and contribute to network hyperexcitability in early Alzheimer's. eLife 2022; 11:75316. [PMID: 35727131 PMCID: PMC9278953 DOI: 10.7554/elife.75316] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
In Alzheimer’s disease (AD), a multitude of genetic risk factors and early biomarkers are known. Nevertheless, the causal factors responsible for initiating cognitive decline in AD remain controversial. Toxic plaques and tangles correlate with progressive neuropathology, yet disruptions in circuit activity emerge before their deposition in AD models and patients. Parvalbumin (PV) interneurons are potential candidates for dysregulating cortical excitability as they display altered action potential (AP) firing before neighboring excitatory neurons in prodromal AD. Here, we report a novel mechanism responsible for PV hypoexcitability in young adult familial AD mice. We found that biophysical modulation of Kv3 channels, but not changes in their mRNA or protein expression, were responsible for dampened excitability in young 5xFAD mice. These K+ conductances could efficiently regulate near-threshold AP firing, resulting in gamma-frequency-specific network hyperexcitability. Thus, biophysical ion channel alterations alone may reshape cortical network activity prior to changes in their expression levels. Our findings demonstrate an opportunity to design a novel class of targeted therapies to ameliorate cortical circuit hyperexcitability in early AD.
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Affiliation(s)
- Viktor J Olah
- Department of Cell Biology, Emory University, Atlanta, United States
| | | | - Sruti Rayaprolu
- Department of Neurology, Emory University, Atlanta, United States
| | - Eric B Dammer
- Department of Biochemistry, Emory University, Atlanta, United States
| | | | | | | | - Matthew J M Rowan
- Department of Cell Biology, Emory University, Atlanta, United States
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Mechanisms Involved in Epileptogenesis in Alzheimer's Disease and Their Therapeutic Implications. Int J Mol Sci 2022; 23:ijms23084307. [PMID: 35457126 PMCID: PMC9030029 DOI: 10.3390/ijms23084307] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 12/22/2022] Open
Abstract
Epilepsy and Alzheimer's disease (AD) incidence increases with age. There are reciprocal relationships between epilepsy and AD. Epilepsy is a risk factor for AD and, in turn, AD is an independent risk factor for developing epilepsy in old age, and abnormal AD biomarkers in PET and/or CSF are frequently found in late-onset epilepsies of unknown etiology. Accordingly, epilepsy and AD share pathophysiological processes, including neuronal hyperexcitability and an early excitatory-inhibitory dysregulation, leading to dysfunction in the inhibitory GABAergic and excitatory glutamatergic systems. Moreover, both β-amyloid and tau protein aggregates, the anatomopathological hallmarks of AD, have proepileptic effects. Finally, these aggregates have been found in the resection material of refractory temporal lobe epilepsies, suggesting that epilepsy leads to amyloid and tau aggregates. Some epileptic syndromes, such as medial temporal lobe epilepsy, share structural and functional neuroimaging findings with AD, leading to overlapping symptomatology, such as episodic memory deficits and toxic synergistic effects. In this respect, the existence of epileptiform activity and electroclinical seizures in AD appears to accelerate the progression of cognitive decline, and the presence of cognitive decline is much more prevalent in epileptic patients than in elderly patients without epilepsy. Notwithstanding their clinical significance, the diagnosis of clinical seizures in AD is a challenge. Most are focal and manifest with an altered level of consciousness without motor symptoms, and are often interpreted as cognitive fluctuations. Finally, despite the frequent association of epilepsy and AD dementia, there is a lack of clinical trials to guide the use of antiseizure medications (ASMs). There is also a potential role for ASMs to be used as disease-modifying drugs in AD.
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Gomes-Duarte A, Venø MT, de Wit M, Senthilkumar K, Broekhoven MH, van den Herik J, Heeres FR, van Rossum D, Rybiczka-Tesulov M, Legnini I, van Rijen PC, van Eijsden P, Gosselaar PH, Rajewsky N, Kjems J, Vangoor VR, Pasterkamp RJ. Expression of Circ_Satb1 Is Decreased in Mesial Temporal Lobe Epilepsy and Regulates Dendritic Spine Morphology. Front Mol Neurosci 2022; 15:832133. [PMID: 35310884 PMCID: PMC8927295 DOI: 10.3389/fnmol.2022.832133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/10/2022] [Indexed: 11/24/2022] Open
Abstract
Mesial temporal lobe epilepsy (mTLE) is a chronic disease characterized by recurrent seizures that originate in the temporal lobes of the brain. Anti-epileptic drugs (AEDs) are the standard treatment for managing seizures in mTLE patients, but are frequently ineffective. Resective surgery is an option for some patients, but does not guarantee a postoperative seizure-free period. Therefore, further insight is needed into the pathogenesis of mTLE to enable the design of new therapeutic strategies. Circular RNAs (circRNAs) have been identified as important regulators of neuronal function and have been implicated in epilepsy. However, the mechanisms through which circRNAs contribute to epileptogenesis remain unknown. Here, we determine the circRNA transcriptome of the hippocampus and cortex of mTLE patients by using RNA-seq. We report 333 differentially expressed (DE) circRNAs between healthy individuals and mTLE patients, of which 23 circRNAs displayed significant adjusted p-values following multiple testing correction. Interestingly, hippocampal expression of circ_Satb1, a circRNA derived from special AT-rich sequence binding protein 1 (SATB1), is decreased in both mTLE patients and in experimental epilepsy. Our work shows that circ_Satb1 displays dynamic patterns of neuronal expression in vitro and in vivo. Further, circ_Satb1-specific knockdown using CRISPR/CasRx approaches in hippocampal cultures leads to defects in dendritic spine morphology, a cellular hallmark of mTLE. Overall, our results identify a novel epilepsy-associated circRNA with disease-specific expression and previously unidentified cellular effects that are relevant for epileptogenesis.
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Affiliation(s)
- Andreia Gomes-Duarte
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Morten T. Venø
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Omiics ApS, Aarhus, Denmark
| | - Marina de Wit
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Ketharini Senthilkumar
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mark H. Broekhoven
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Joëlle van den Herik
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Fleur R. Heeres
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Daniëlle van Rossum
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Mateja Rybiczka-Tesulov
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Ivano Legnini
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Peter C. van Rijen
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Pieter van Eijsden
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Peter H. Gosselaar
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Vamshidhar R. Vangoor
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - R. Jeroen Pasterkamp
- Affiliated Partner of the European Reference Network EpiCARE, Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
- *Correspondence: R. Jeroen Pasterkamp,
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Revelation of Pivotal Genes Pertinent to Alzheimer's Pathogenesis: A Methodical Evaluation of 32 GEO Datasets. J Mol Neurosci 2021; 72:303-322. [PMID: 34668150 PMCID: PMC8526053 DOI: 10.1007/s12031-021-01919-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/18/2021] [Indexed: 11/26/2022]
Abstract
Alzheimer’s disease (AD), a dreadful neurodegenerative disorder that affects cognitive and behavioral function in geriatric populations, is characterized by the presence of amyloid deposits and neurofibrillary tangles in brain regions. The International D World Alzheimer Report2018 noted a global prevalence of 50 million AD cases and forecasted a threefold rise to 139 million by 2050. Although there exist numerous genetic association studies pertinent to AD in different ethnicities, critical genetic factors and signaling pathways underlying its pathogenesis remain ambiguous. This study was aimed to analyze the genetic data retrieved from 32 Gene Expression Omnibus datasets belonging to diverse ethnic cohorts in order to identify overlapping differentially expressed genes (DEGs). Stringent selection criteria were framed to shortlist appropriate datasets based on false discovery rate (FDR) p-value and log FC, and relevant details of upregulated and downregulated DEGs were retrieved. Among the 32 datasets, only six satisfied the selection criteria. The GEO2R tool was employed to retrieve significant DEGs. Nine common DEGs, i.e., SLC5A3, BDNF, SST, SERPINA3, RTN3, RGS4, NPTX, ENC1 and CRYM were found in more than 60% of the selected datasets. These DEGs were later subjected to protein–protein interaction analysis with 18 AD-specific literature-derived genes. Among the nine common DEGs, BDNF, SST, SERPINA3, RTN3 and RGS4 exhibited significant interactions with crucial proteins including BACE1, GRIN2B, APP, APOE, COMT, PSEN1, INS, NEP and MAPT. Functional enrichment analysis revealed involvement of these genes in trans-synaptic signaling, chemical transmission, PI3K pathway signaling, receptor–ligand activity and G protein signaling. These processes are interlinked with AD pathways.
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Shah S, Richter JD. Do Fragile X Syndrome and Other Intellectual Disorders Converge at Aberrant Pre-mRNA Splicing? Front Psychiatry 2021; 12:715346. [PMID: 34566717 PMCID: PMC8460907 DOI: 10.3389/fpsyt.2021.715346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/20/2021] [Indexed: 11/13/2022] Open
Abstract
Fragile X Syndrome is a neuro-developmental disorder caused by the silencing of the FMR1 gene, resulting in the loss of its protein product, FMRP. FMRP binds mRNA and represses general translation in the brain. Transcriptome analysis of the Fmr1-deficient mouse hippocampus reveals widespread dysregulation of alternative splicing of pre-mRNAs. Many of these aberrant splicing changes coincide with those found in post-mortem brain tissue from individuals with autism spectrum disorders (ASDs) as well as in mouse models of intellectual disability such as PTEN hamartoma syndrome (PHTS) and Rett Syndrome (RTT). These splicing changes could result from chromatin modifications (e.g., in FXS, RTT) and/or splicing factor alterations (e.g., PTEN, autism). Based on the identities of the RNAs that are mis-spliced in these disorders, it may be that they are at least partly responsible for some shared pathophysiological conditions. The convergence of splicing aberrations among these autism spectrum disorders might be crucial to understanding their underlying cognitive impairments.
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Affiliation(s)
- Sneha Shah
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States
| | - Joel D Richter
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States
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14
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Trombetta-Lima M, Krabbendam IE, Dolga AM. Calcium-activated potassium channels: implications for aging and age-related neurodegeneration. Int J Biochem Cell Biol 2020; 123:105748. [PMID: 32353429 DOI: 10.1016/j.biocel.2020.105748] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/11/2020] [Accepted: 04/14/2020] [Indexed: 12/16/2022]
Abstract
Population aging, as well as the handling of age-associated diseases, is a worldwide increasing concern. Among them, Alzheimer's disease stands out as the major cause of dementia culminating in full dependence on other people for basic functions. However, despite numerous efforts, in the last decades, there was no new approved therapeutic drug for the treatment of the disease. Calcium-activated potassium channels have emerged as a potential tool for neuronal protection by modulating intracellular calcium signaling. Their subcellular localization is determinant of their functional effects. When located on the plasma membrane of neuronal cells, they can modulate synaptic function, while their activation at the inner mitochondrial membrane has a neuroprotective potential via the attenuation of mitochondrial reactive oxygen species in conditions of oxidative stress. Here we review the dual role of these channels in the aging phenotype and Alzheimer's disease pathology and discuss their potential use as a therapeutic tool.
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Affiliation(s)
- Marina Trombetta-Lima
- Faculty of Science and Engineering, Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, 9713 AV Groningen, the Netherlands; Medical School, Neurology Department, University of São Paulo (USP), 01246903 São Paulo, Brazil
| | - Inge E Krabbendam
- Faculty of Science and Engineering, Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, 9713 AV Groningen, the Netherlands
| | - Amalia M Dolga
- Faculty of Science and Engineering, Department of Molecular Pharmacology, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, 9713 AV Groningen, the Netherlands.
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Arnold EC, McMurray C, Gray R, Johnston D. Epilepsy-Induced Reduction in HCN Channel Expression Contributes to an Increased Excitability in Dorsal, But Not Ventral, Hippocampal CA1 Neurons. eNeuro 2019; 6:ENEURO.0036-19.2019. [PMID: 30957013 PMCID: PMC6449163 DOI: 10.1523/eneuro.0036-19.2019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022] Open
Abstract
CA1 neurons in epileptic animals are vulnerable to selective changes in ion channel expression, called acquired channelopathies, which can increase the excitability of a neuron. Under normal conditions there is a gradient of ion channel expression and intrinsic excitability along the longitudinal, dorsoventral axis of hippocampal area CA1 of the rodent. Many of these channels, including M-channels, GIRK channels and HCN channels, all have dorsoventral expression gradients that might be altered in rodent models of epilepsy. Here, we show that the excitability of dorsal, but not ventral CA1 neurons, had an increased firing rate, reduced interspike interval (ISI) and increased input resistance in a status epilepticus (SE) model of temporal lobe epilepsy (TLE). As a result, the excitability of CA1 neurons became uniform across the dorsoventral axis of the rat hippocampus post-SE. Using current clamp recordings with pharmacology and immunohistochemistry, we demonstrate that the expression of HCN channels was downregulated in the dorsal CA1 region post-SE, while the expression of M and GIRK channels were unchanged. We did not find this acquired channelopathy in ventral CA1 neurons post-SE. Our results suggest that the excitability of dorsal CA1 neurons post-SE increase to resemble the intrinsic properties of ventral CA1 neurons, which likely makes the hippocampal circuit more permissible to seizures, and contributes to the cognitive impairments associated with chronic epilepsy.
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Affiliation(s)
- Elizabeth C. Arnold
- Institute for Neuroscience, University of Texas at Austin, Austin, TX 78712
- Center for Learning and Memory, University of Texas at Austin, Austin, TX 78712
| | - Calli McMurray
- Center for Learning and Memory, University of Texas at Austin, Austin, TX 78712
| | - Richard Gray
- Center for Learning and Memory, University of Texas at Austin, Austin, TX 78712
| | - Daniel Johnston
- Institute for Neuroscience, University of Texas at Austin, Austin, TX 78712
- Center for Learning and Memory, University of Texas at Austin, Austin, TX 78712
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16
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Regulation of voltage-gated sodium channel expression, control of excitability and implications for seizure generation. CURRENT OPINION IN PHYSIOLOGY 2018. [DOI: 10.1016/j.cophys.2017.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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18
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Izadi F, Soheilifar MH. Exploring Potential Biomarkers Underlying Pathogenesis of Alzheimer's Disease by Differential Co-expression Analysis. Avicenna J Med Biotechnol 2018; 10:233-241. [PMID: 30555656 PMCID: PMC6252023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Alzheimer's Disease (AD) is the most common form of dementia in the elderly. Due to the facts that biological causes of AD are complex in addition to increasing rates of AD worldwide, a deeper understanding of AD etiology is required for AD treatment and diagnosis. METHODS To identify molecular pathological alterations in AD brains, GSE36980 series containing microarray data samples from temporal cortex, frontal cortex and hippocampus were downloaded from Gene Expression Omnibus (GEO) database and valid gene symbols were subjected to building a gene co-expression network by a bioinformatics tool known as differential regulation from differential co-expression (DCGL) software package. Then, a network-driven integrative analysis was performed to find significant genes and underlying biological terms. RESULTS A total of 17088 unique genes were parsed into three independent differential co-expression networks. As a result, a small number of differentially co-regulated genes mostly in frontal and hippocampus lobs were detected as potential biomarkers related to AD brains. Ultimately differentially co-regulated genes were enriched in biological terms including response to lipid and fatty acid and pathways mainly signaling pathway such as G-protein signaling pathway and glutamate receptor groups II and III. By conducting co-expression analysis, our study identified multiple genes that may play an important role in the pathogenesis of AD. CONCLUSION The study aimed to provide a systematic understanding of the potential relationships among these genes and it is hoped that it could aid in AD biomarker discovery.
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Affiliation(s)
- Fereshteh Izadi
- Department of Genetics, Evolution and Environment, Darwin Building, University College London (UCL), London, UK,Corresponding author: Fereshteh Izadi, PhD, Department of Genetics, Evolution and Environment, Darwin Building, University College London (UCL), Gower Street, London WC1E 6BT, UK, Tel: +44 7846280861, E-mail:
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19
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Cázares-Ordoñez V, Pardo L. Kv10.1 potassium channel: from the brain to the tumors. Biochem Cell Biol 2017; 95:531-536. [DOI: 10.1139/bcb-2017-0062] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The KCNH1 gene encodes the Kv10.1 (Eag1) ion channel, a member of the EAG (ether-à-go-go) family of voltage-gated potassium channels. Recent studies have demonstrated that KCHN1 mutations are implicated in Temple–Baraitser and Zimmermann–Laband syndromes and other forms of developmental deficits that all present with mental retardation and epilepsy, suggesting that Kv10.1 might be important for cognitive development in humans. Although the Kv10.1 channel is mainly expressed in the mammalian brain, its ectopic expression occurs in 70% of human cancers. Cancer cells and tumors expressing Kv10.1 acquire selective advantages that favor cancer progression through molecular mechanisms that involve several cellular pathways, indicating that protein–protein interactions may be important for Kv10.1 influence in cell proliferation and tumorigenesis. Several studies on transcriptional and post-transcriptional regulation of Kv10.1 expression have shown interesting mechanistic insights about Kv10.1 role in oncogenesis, increasing the importance of identifying the cellular factors that regulate Kv10.1 expression in tumors.
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Affiliation(s)
- V. Cázares-Ordoñez
- Oncophysiology Group, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
- Oncophysiology Group, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
| | - L.A. Pardo
- Oncophysiology Group, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
- Oncophysiology Group, Max Planck Institute of Experimental Medicine, Hermann-Rein-Strasse 3, 37075 Göttingen, Germany
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20
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Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensão-Ferreira M, Barbosa-Morais NL. Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems. Hum Genet 2017; 136:1015-1042. [PMID: 28374191 PMCID: PMC5602094 DOI: 10.1007/s00439-017-1790-y] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/25/2017] [Indexed: 02/06/2023]
Abstract
Alternative pre-mRNA splicing is a tightly controlled process conducted by the spliceosome, with the assistance of several regulators, resulting in the expression of different transcript isoforms from the same gene and increasing both transcriptome and proteome complexity. The differences between alternative isoforms may be subtle but enough to change the function or localization of the translated proteins. A fine control of the isoform balance is, therefore, needed throughout developmental stages and adult tissues or physiological conditions and it does not come as a surprise that several diseases are caused by its deregulation. In this review, we aim to bring the splicing machinery on stage and raise the curtain on its mechanisms and regulation throughout several systems and tissues of the human body, from neurodevelopment to the interactions with the human microbiome. We discuss, on one hand, the essential role of alternative splicing in assuring tissue function, diversity, and swiftness of response in these systems or tissues, and on the other hand, what goes wrong when its regulatory mechanisms fail. We also focus on the possibilities that splicing modulation therapies open for the future of personalized medicine, along with the leading techniques in this field. The final act of the spliceosome, however, is yet to be fully revealed, as more knowledge is needed regarding the complex regulatory network that coordinates alternative splicing and how its dysfunction leads to disease.
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Affiliation(s)
- L M Gallego-Paez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M C Bordone
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - A C Leote
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N Saraiva-Agostinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M Ascensão-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N L Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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Elevated Expression of the Delta-Subunit of Epithelial Sodium Channel in Temporal Lobe Epilepsy Patients and Rat Model. J Mol Neurosci 2015; 57:510-8. [DOI: 10.1007/s12031-015-0630-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 07/23/2015] [Indexed: 01/13/2023]
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22
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Hassan MA, Saeij JP. Incorporating alternative splicing and mRNA editing into the genetic analysis of complex traits. Bioessays 2014; 36:1032-40. [PMID: 25171292 PMCID: PMC4280019 DOI: 10.1002/bies.201400079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nomination of candidate genes underlying complex traits is often focused on genetic variations that alter mRNA abundance or result in non-conservative changes in amino acids. Although inconspicuous in complex trait analysis, genetic variants that affect splicing or RNA editing can also generate proteomic diversity and impact genetic traits. Indeed, it is known that splicing and RNA editing modulate several traits in humans and model organisms. Using high-throughput RNA sequencing (RNA-seq) analysis, it is now possible to integrate the genetics of transcript abundance, alternative splicing (AS) and editing with the analysis of complex traits. We recently demonstrated that both AS and mRNA editing are modulated by genetic and environmental factors, and potentially engender phenotypic diversity in a genetically segregating mouse population. Therefore, the analysis of splicing and RNA editing can expand not only the regulatory landscape of transcriptome and proteome complexity, but also the repertoire of candidate genes for complex traits.
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Affiliation(s)
- Musa A. Hassan
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA
| | - Jeroen P.J. Saeij
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA, USA
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Abstract
Alzheimer's disease (AD) and epilepsy are common disorders in the elderly. Evidence demonstrates that patients with AD have an increased risk of developing epilepsy and seizures. Objective To review epidemiological, clinical and treatment aspects of epilepsy and AD. Methods We reviewed databases (PubMED, LiLACS, Scielo) conducting a search for manuscripts using the terms Alzheimer's disease and epilepsy. Results Manuscripts related to the areas of interest were reviewed. Studies revealed that epilepsy is more frequent among AD patients. The combined presence of the two disorders may be related to mechanisms of neuronal hyperexcitability as a consequence of amyloid-beta protein (Aβ) or phosphorylated tau accumulation, as well as to structural changes in cortical and hippocampal regions. Available data suggest that the new generation of antiepileptic drugs (AEDs) are better tolerated in the elderly population, and may also be the best option in patients with AD and epilepsy. Conclusion Further prospective studies involving evaluation of concomitant dementia and epilepsy, neurophysiological findings and biomarkers need to be performed.
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Affiliation(s)
| | - Sonia Maria Dozzi Brucki
- PhD, Neurologist, Hospital Santa Marcelina; Cognitive and Behavioral Neurology Unit, University of São Paulo, São Paulo, Brazil
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Ji HL, Zhao RZ, Chen ZX, Shetty S, Idell S, Matalon S. δ ENaC: a novel divergent amiloride-inhibitable sodium channel. Am J Physiol Lung Cell Mol Physiol 2012; 303:L1013-26. [PMID: 22983350 DOI: 10.1152/ajplung.00206.2012] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The fourth subunit of the epithelial sodium channel, termed delta subunit (δ ENaC), was cloned in human and monkey. Increasing evidence shows that this unique subunit and its splice variants exhibit biophysical and pharmacological properties that are divergent from those of α ENaC channels. The widespread distribution of epithelial sodium channels in both epithelial and nonepithelial tissues implies a range of physiological functions. The altered expression of SCNN1D is associated with numerous pathological conditions. Genetic studies link SCNN1D deficiency with rare genetic diseases with developmental and functional disorders in the brain, heart, and respiratory systems. Here, we review the progress of research on δ ENaC in genomics, biophysics, proteomics, physiology, pharmacology, and clinical medicine.
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Affiliation(s)
- Hong-Long Ji
- Department of Cellular and Molecular Biology, University of Texas Health Science Center at Tyler, Tyler, Texas, USA.
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25
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Activity-dependent alternative splicing increases persistent sodium current and promotes seizure. J Neurosci 2012; 32:7267-77. [PMID: 22623672 DOI: 10.1523/jneurosci.6042-11.2012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Activity of voltage-gated Na channels (Na(v)) is modified by alternative splicing. However, whether altered splicing of human Na(v)s contributes to epilepsy remains to be conclusively shown. We show here that altered splicing of the Drosophila Na(v) (paralytic, DmNa(v)) contributes to seizure-like behavior in identified seizure mutants. We focus attention on a pair of mutually exclusive alternate exons (termed K and L), which form part of the voltage sensor (S4) in domain III of the expressed channel. The presence of exon L results in a large, non-inactivating, persistent I(Nap). Many forms of human epilepsy are associated with an increase in this current. In wild-type (WT) Drosophila larvae, ∼70-80% of DmNa(v) transcripts contain exon L, and the remainder contain exon K. Splicing of DmNa(v) to include exon L is increased to ∼100% in both the slamdance and easily-shocked seizure mutants. This change to splicing is prevented by reducing synaptic activity levels through exposure to the antiepileptic phenytoin or the inhibitory transmitter GABA. Conversely, enhancing synaptic activity in WT, by feeding of picrotoxin is sufficient to increase I(Nap) and promote seizure through increased inclusion of exon L to 100%. We also show that the underlying activity-dependent mechanism requires the presence of Pasilla, an RNA-binding protein. Finally, we use computational modeling to show that increasing I(Nap) is sufficient to potentiate membrane excitability consistent with a seizure phenotype. Thus, increased synaptic excitation favors inclusion of exon L, which, in turn, further increases neuronal excitability. Thus, at least in Drosophila, this self-reinforcing cycle may promote the incidence of seizure.
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Ishunina TA, Swaab DF. Decreased alternative splicing of estrogen receptor-α mRNA in the Alzheimer's disease brain. Neurobiol Aging 2012; 33:286-296.e3. [DOI: 10.1016/j.neurobiolaging.2010.03.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 02/19/2010] [Accepted: 03/16/2010] [Indexed: 01/15/2023]
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27
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Tollervey JR, Wang Z, Hortobágyi T, Witten JT, Zarnack K, Kayikci M, Clark TA, Schweitzer AC, Rot G, Curk T, Zupan B, Rogelj B, Shaw CE, Ule J. Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. Genome Res 2011; 21:1572-82. [PMID: 21846794 PMCID: PMC3202275 DOI: 10.1101/gr.122226.111] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 07/05/2011] [Indexed: 01/15/2023]
Abstract
Age is the most important risk factor for neurodegeneration; however, the effects of aging and neurodegeneration on gene expression in the human brain have most often been studied separately. Here, we analyzed changes in transcript levels and alternative splicing in the temporal cortex of individuals of different ages who were cognitively normal, affected by frontotemporal lobar degeneration (FTLD), or affected by Alzheimer's disease (AD). We identified age-related splicing changes in cognitively normal individuals and found that these were present also in 95% of individuals with FTLD or AD, independent of their age. These changes were consistent with increased polypyrimidine tract binding protein (PTB)-dependent splicing activity. We also identified disease-specific splicing changes that were present in individuals with FTLD or AD, but not in cognitively normal individuals. These changes were consistent with the decreased neuro-oncological ventral antigen (NOVA)-dependent splicing regulation, and the decreased nuclear abundance of NOVA proteins. As expected, a dramatic down-regulation of neuronal genes was associated with disease, whereas a modest down-regulation of glial and neuronal genes was associated with aging. Whereas our data indicated that the age-related splicing changes are regulated independently of transcript-level changes, these two regulatory mechanisms affected expression of genes with similar functions, including metabolism and DNA repair. In conclusion, the alternative splicing changes identified in this study provide a new link between aging and neurodegeneration.
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Affiliation(s)
- James R. Tollervey
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| | - Zhen Wang
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| | - Tibor Hortobágyi
- MRC Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, United Kingdom
| | - Joshua T. Witten
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| | - Kathi Zarnack
- EMBL–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Melis Kayikci
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
| | - Tyson A. Clark
- Expression Research, Affymetrix, Inc., Santa Clara, California 95051, USA
| | | | - Gregor Rot
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000 Ljubljana, Slovenia
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000 Ljubljana, Slovenia
| | - Blaž Zupan
- Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, SI-1000 Ljubljana, Slovenia
| | - Boris Rogelj
- MRC Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, United Kingdom
| | - Christopher E. Shaw
- MRC Centre for Neurodegeneration Research, King's College London, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, United Kingdom
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom
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Calciano MA, Zhou W, Snyder PJ, Einstein R. Drug treatment of Alzheimer's disease patients leads to expression changes in peripheral blood cells. Alzheimers Dement 2010; 6:386-93. [PMID: 20185375 DOI: 10.1016/j.jalz.2009.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 12/10/2009] [Accepted: 12/14/2009] [Indexed: 10/19/2022]
Abstract
BACKGROUND Increasing cholinergic activity has been the primary mechanism for treating dementia due to Alzheimer's disease. However, the effectiveness of cholinesterase inhibitors (ChEIs) is still widely debated. The identification of specific biomarkers capable of identifying patients more likely to respond to these treatments could potentially provide specific evidence to clearly address this controversy through patient stratification. The goal of this study was to determine the feasibility of discovering biomarkers specific for the treatment of Alzheimer's disease. METHODS Peripheral blood was collected from a cohort of patients treated with different ChEIs. Total RNA was isolated and profiled on the human Genome-Wide SpliceArray (GWSA) to test the feasibility of discriminating the different treatment subgroups of subjects based on the expression patterns generated from the Genome-Wide SpliceArray. RESULTS Specific expression differences were identified for the various treatment groups that lead to a clear separation between patients treated with ChEIs versus naïve patients when Principal Component Analysis was performed on probe sets selected for differential expression. In addition, specific probe sets were identified to be dependent on the inhibitor used among the treated patients. CONCLUSIONS Distinct separation between non-treated, galantamine, donepezil, and rivastigmine-treated patients was clearly identified based on small sets of expression probes. The ability to identify drug-specific treatment expression differences strengthens the potential for using peripheral gene signatures for the identification of individuals responding to drug treatment.
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Toward an Alzheimer's disease diagnosis via high‐resolution blood gene expression. Alzheimers Dement 2010; 6:25-38. [DOI: 10.1016/j.jalz.2009.07.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 07/02/2009] [Accepted: 07/02/2009] [Indexed: 11/21/2022]
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30
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Zhou W, Calciano MA, Jordan H, Brenner M, Johnson S, Wu D, Lei L, Pallares D, Beurdeley P, Rouet F, Gill PS, Bracco L, Soucaille C, Einstein R. High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity. BMC Genet 2009; 10:63. [PMID: 19804644 PMCID: PMC2768739 DOI: 10.1186/1471-2156-10-63] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Accepted: 10/05/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Commercially available microarrays have been used in many settings to generate expression profiles for a variety of applications, including target selection for disease detection, classification, profiling for pharmacogenomic response to therapeutics, and potential disease staging. However, many commercially available microarray platforms fail to capture transcript diversity produced by alternative splicing, a major mechanism for driving proteomic diversity through transcript heterogeneity. RESULTS The human Genome-Wide SpliceArray(TM) (GWSA), a novel microarray platform, utilizes an existing probe design concept to monitor such transcript diversity on a genome scale. The human GWSA allows the detection of alternatively spliced events within the human genome through the use of exon body and exon junction probes to provide a direct measure of each transcript, through simple calculations derived from expression data. This report focuses on the performance and validation of the array when measured against standards recently published by the Microarray Quality Control (MAQC) Project. The array was shown to be highly quantitative, and displayed greater than 85% correlation with the HG-U133 Plus 2.0 array at the gene level while providing more extensive coverage of each gene. Almost 60% of splice events among genes demonstrating differential expression of greater than 3 fold also contained extensive splicing alterations. Importantly, almost 10% of splice events within the gene set displaying constant overall expression values had evidence of transcript diversity. Two examples illustrate the types of events identified: LIM domain 7 showed no differential expression at the gene level, but demonstrated deregulation of an exon skip event, while erythrocyte membrane protein band 4.1 -like 3 was differentially expressed and also displayed deregulation of a skipped exon isoform. CONCLUSION Significant changes were detected independent of transcriptional activity, indicating that the controls for transcript generation and transcription are distinct, and require novel tools in order to detect changes in specific transcript quantity. Our results demonstrate that the SpliceArray(TM) design will provide researchers with a robust platform to detect and quantify specific changes not only in overall gene expression, but also at the individual transcript level.
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Affiliation(s)
- Weiyin Zhou
- ExonHit Therapeutics Inc, 217 Perry Parkway, Bldg 5, Gaithersburg, MD, 20877 USA.
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Shubina DM, Suchkova IO, Slominskaya NA, Alenina N, Bader M, Patkin EL. CENTB5 gene expression in humans and mice. Mol Biol 2009. [DOI: 10.1134/s0026893309030042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Buckingham SD, Jones AK, Brown LA, Sattelle DB. Nicotinic acetylcholine receptor signalling: roles in Alzheimer's disease and amyloid neuroprotection. Pharmacol Rev 2009; 61:39-61. [PMID: 19293145 DOI: 10.1124/pr.108.000562] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Alzheimer's disease (AD), the major contributor to dementia in the elderly, involves accumulation in the brain of extracellular plaques containing the beta-amyloid protein (Abeta) and intracellular neurofibrillary tangles of hyperphosphorylated tau protein. AD is also characterized by a loss of neurons, particularly those expressing nicotinic acetylcholine receptors (nAChRs), thereby leading to a reduction in nAChR numbers. The Abeta(1-42) protein, which is toxic to neurons, is critical to the onset and progression of AD. The discovery of new drug therapies for AD is likely to be accelerated by an improved understanding of the mechanisms whereby Abeta causes neuronal death. We examine the evidence for a role in Abeta(1-42) toxicity of nAChRs; paradoxically, nAChRs can also protect neurons when activated by nicotinic ligands. Abeta peptides and nicotine differentially activate several intracellular signaling pathways, including the phosphatidylinositol 3-kinase/v-akt murine thymoma viral oncogene homolog pathway, the extracellular signal-regulated kinase/mitogen-activated protein kinase, and JAK-2/STAT-3 pathways. These pathways control cell death or survival and the secretion of Abeta peptides. We propose that understanding the differential activation of these pathways by nicotine and/or Abeta(1-42) may offer the prospect of new routes to therapy for AD.
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Affiliation(s)
- Steven D Buckingham
- Medical Research Council Functional Genomics Unit, Department of Physiology Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, UK, OX1 3QX
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Kechris K, Yang YH, Yeh RF. Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays. BMC Genomics 2008; 9:551. [PMID: 19021909 PMCID: PMC2631580 DOI: 10.1186/1471-2164-9-551] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2008] [Accepted: 11/20/2008] [Indexed: 12/22/2022] Open
Abstract
Background Alternative splicing of exons in a pre-mRNA transcript is an important mechanism which contributes to protein diversity in human. Arrays for detecting alternative splicing are available using several different probe designs, including those based on exon-junctions. In this work, we introduce a new method for predicting alternatively skipped exons from exon-junction arrays. Predictions based on our method are compared against controls and their sequences are analyzed to identify motifs important for regulating alternative splicing. Results Our comparison of several alternative methods shows that an exon-skipping score based on neighboring junctions best discriminates between positive and negative controls. Sequence analysis of our predicted exons confirms the presence of known splicing regulatory sequences. In addition, we also derive a set of development-related alternatively spliced genes based on fetal versus adult tissue comparisons and find that our predictions are consistent with their functional annotations. Ab initio motif finding algorithms are applied to identify several motifs that may be relevant for splicing during development. Conclusion This work describes a new method for analyzing exon-junction arrays, identifies sequence motifs that are specific for alternative and constitutive splicing and suggests a role for several known splicing factors and their motifs in developmental regulation.
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Affiliation(s)
- Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, 4200 East 9th Avenue, B-119, Denver, CO 80262, USA.
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Ravits J, Traynor BJ. Current and future directions in genomics of amyotrophic lateral sclerosis. Phys Med Rehabil Clin N Am 2008; 19:461-77, viii. [PMID: 18625410 PMCID: PMC3524513 DOI: 10.1016/j.pmr.2008.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
New knowledge of the structure and function of the human genome and novel genomic technologies are being applied to the study of sporadic amyotrophic lateral sclerosis (ALS). These studies can examine tens to hundreds of thousands of items at once, and depend on sophisticated computer processing. Current studies are focused on genetic susceptibility and gene expression and future studies will likely focus on structural variation, gene regulation and non-protein coding regions. The hope is that they will lead to deeper understanding of molecular aspects of the disease and to rational therapeutic targets.
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Affiliation(s)
- John Ravits
- Virginia Mason Medical Center, 1100 Ninth Avenue, Seattle, WA 98101, USA.
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Splicing and splice factor SRp55 participate in the response to DNA damage by changing isoform ratios of target genes. Gene 2008; 420:34-41. [PMID: 18571879 DOI: 10.1016/j.gene.2008.05.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 04/18/2008] [Accepted: 05/17/2008] [Indexed: 11/20/2022]
Abstract
Alternative splicing is an important source of protein diversity, and is an established but not yet fully understood mechanism for gene regulation in higher eukaryotes. Its regulation is governed by a variety of mechanisms, including variation in the expression levels of splicing factors engaged in spliceosome formation. SRp55 is one of the most ubiquitous splicing factors and one that can be up-regulated by DNA damage in the absence of p53, and we had previously found that depletion of its activity increased resistance to DNA damage in p53-dependant manner. To assess its influence on the splicing patterns of genes involved in apoptosis, we performed splice-specific microarray analysis of cells treated with siRNA specific for this gene. This analysis, backed by RT-PCR verification, identified three genes, KSR1, ZAK and mda7/IL24, which are sensitive to SRp55 depletion. We also analyzed the splice patterns of apoptosis-related genes in p53-deficient U2OS cells following treatment with the genotoxic drug mitomycin C. This analysis revealed that DNA damage resulted in changes in splicing activity that modified the splicing pattern of Fas, a key pro-apoptotic, p53-inducible death receptor. Interestingly, this modification led to an enrichment of the anti-apoptotic soluble Fas isoform, and this secreted isoform was detected in the media surrounding cells subjected to DNA damage. These findings show that modulation of splicing activity in p53-deficient cells during the early response to sub-lethal DNA damage results in a change in the splicing of target genes, thus modifying the cellular response to genotoxic agents.
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Abstract
Multidrug resistance is one of the most serious problems in the treatment of epilepsy and is likely to have a complex genetic and environmental basis. Various experimental data support the hypothesis that overexpression of antiepileptic drug transporters may be important. However, key questions concerning their functionality remain unanswered. The first study reporting a positive association--between genetic variation in a putative antiepileptic drug transporter (P-glycoprotein, encoded by ABCB1) and multidrug resistant epilepsy was published in 2003. Since then, several other association genetics studies have sought to confirm this result, but, taken overall, do not support a major role for this polymorphism. Lessons learnt from the ABCB1 studies can help guide future association genetics studies, both for multidrug resistance in epilepsy, and for other epilepsy phenotypes.
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Affiliation(s)
- Sarah K Tate
- University College London, Department of Clinical and Experimental Epilepsy, Institute of Neurology, Queen Square, London, UK
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