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Northrup V, Perez LJ, Edgett BA, Karakach T, Simpson JA, Brunt KR. Intron retention is a mechanism of erythropoietin regulation in brain cell models. Gene 2024; 898:148099. [PMID: 38128788 DOI: 10.1016/j.gene.2023.148099] [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: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
Intron retention is a mechanism of post-transcriptional gene regulation, including genes involved in erythropoiesis. Erythropoietin (EPO) is a hormone without evidence of intracellular vesicle storage that regulates erythropoiesis. We hypothesize that EPO uses intron retention as a mechanism of post-transcriptional regulation in response to hypoxia and ischemia. Cell models of hypoxia and ischemia for kidney, liver, and brain cells were examined for intron retention by real time quantitative PCR. EPO expression increased in most cells except for blood brain barrier and liver cells. The intron retained transcript ratio decreased in brain cells, except for Astrocytes, but showed no change in kidney or liver after 24 h of ischemia. The shift in intron ratio was maintained when using poly (A) enriched cDNA, suggesting that intron retention is not due to immature transcripts. The expression of EPO was elevated at variable time points amongst cell models with the intron ratio also changing over a time course of 2 to 16 h after ischemia. We conclude that intron retention is a mechanism regulating EPO expression in response to ischemia in a tissue specific manner.
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Affiliation(s)
- Victoria Northrup
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; Dalhousie Medicine New Brunswick, Saint John, New Brunswick, Canada; IMPART investigator team Canada
| | - Lester J Perez
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; Dalhousie Medicine New Brunswick, Saint John, New Brunswick, Canada; IMPART investigator team Canada
| | - Brittany A Edgett
- Department of Kinesiology, University of Calgary, Calgary, Alberta, Canada; IMPART investigator team Canada
| | - Tobias Karakach
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; IMPART investigator team Canada
| | - Jeremy A Simpson
- Department of Human and Nutritional Science, University of Guelph, Guelph, Ontario, Canada; IMPART investigator team Canada
| | - Keith R Brunt
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada; Dalhousie Medicine New Brunswick, Saint John, New Brunswick, Canada; IMPART investigator team Canada.
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2
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He L, Guo H, Wang H, Zhu K, Li D, Zhang C, Ai Y, Yang JJ. Rbfox1 regulates alternative splicing of Nrcam in primary sensory neurons to mediate peripheral nerve injury-induced neuropathic pain. Neurotherapeutics 2024; 21:e00309. [PMID: 38241164 PMCID: PMC10903086 DOI: 10.1016/j.neurot.2023.e00309] [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: 10/13/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/21/2024] Open
Abstract
The primary sensory neurons of the dorsal root ganglia (DRG) are subject to transcriptional alterations following peripheral nerve injury. These alterations are believed to play a pivotal role in the genesis of neuropathic pain. Alternative RNA splicing is a process that generates multiple transcript variants from a single gene, significantly contributing to the complexity of the transcriptome. However, little is known about the functional significance and control of alternative RNA splicing in injured DRG after spinal nerve ligation (SNL). In our study, we conducted a comprehensive transcriptome profiling and bioinformatic analysis to approach and identified a neuron-specific isoform of an RNA splicing regulator, RNA-binding Fox1 (Rbfox1, also known as A2BP1), as a crucial regulator of alternative RNA splicing in injured DRG after SNL. Notably, Rbfox1 expression is markedly reduced in injured DRG following peripheral nerve injury. Restoring this reduction effectively mitigates nociceptive hypersensitivity. Conversely, mimicking the downregulation of Rbfox1 expression generates neuropathic pain symptoms. Mechanistically, we uncovered that Rbfox1 may be a key factor influencing alternative RNA splicing of neuron-glial related cell adhesion molecule (NrCAM), a key neuronal cell adhesion molecule. In injured DRG after SNL, the downregulation of Rbfox1amplifies the insertion of exon 10 in Nrcam transcripts, leading to an increase in long Nrcam variants (L-Nrcam) and a corresponding decrease in short Nrcam variants (S-Nrcam) within injured DRG. In summary, our study supports the essential role of Rbfox1 in neuropathic pain within DRG, probably via the regulation of Nrcam splicing. These findings suggest that Rbfox1 could be a potential target for neuropathic pain therapy.
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Affiliation(s)
- Long He
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Haoyu Guo
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China; Department of Laboratory Animal Resources, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Hongwei Wang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Kuicheng Zhu
- Department of Laboratory Animal Resources, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Da Li
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Chaofan Zhang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Yanqiu Ai
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China.
| | - Jian-Jun Yang
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China.
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3
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Verdile V, Palombo R, Ferrante G, Ferri A, Amadio S, Volonté C, Paronetto MP. Dysregulation of alternative splicing underlies synaptic defects in familial amyotrophic lateral sclerosis. Prog Neurobiol 2023; 231:102529. [PMID: 37739207 DOI: 10.1016/j.pneurobio.2023.102529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/11/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease characterized by the degeneration of upper and lower motor neurons, progressive wasting and paralysis of voluntary muscles. A hallmark of ALS is the frequent nuclear loss and cytoplasmic accumulation of RNA binding proteins (RBPs) in motor neurons (MN), which leads to aberrant alternative splicing regulation. However, whether altered splicing patterns are also present in familial models of ALS without mutations in RBP-encoding genes has not been investigated yet. Herein, we found that altered splicing of synaptic genes is a common trait of familial ALS MNs. Similar deregulation was also observed in hSOD1G93A MN-like cells. In silico analysis identified the potential regulators of these pre-mRNAs, including the RBP Sam68. Immunofluorescence analysis and biochemical fractionation experiments revealed that Sam68 accumulates in the cytoplasmic insoluble ribonucleoprotein fraction of MN. Remarkably, the synaptic splicing events deregulated in ALS MNs were also affected in Sam68-/- spinal cords. Recombinant expression of Sam68 protein was sufficient to rescue these splicing changes in ALS hSOD1G93A MN-like cells. Hence, our study highlights an aberrant function of Sam68, which leads to splicing changes in synaptic genes and may contribute to the MN phenotype that characterizes ALS.
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Affiliation(s)
- Veronica Verdile
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135 Rome, Italy; Division of Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, Rome 00143, Italy
| | - Ramona Palombo
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135 Rome, Italy
| | - Gabriele Ferrante
- Division of Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, Rome 00143, Italy
| | - Alberto Ferri
- Division of Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, Rome 00143, Italy; National Research Council (CNR), Institute of Translational Pharmacology (IFT), Rome, Italy
| | - Susanna Amadio
- Division of Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, Rome 00143, Italy
| | - Cinzia Volonté
- Division of Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, Rome 00143, Italy; National Research Council (CNR), Institute for Systems Analysis and Computer Science (IASI), Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Piazza Lauro de Bosis 6, 00135 Rome, Italy; Division of Experimental Neuroscience, IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano 64, Rome 00143, Italy.
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4
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Pino MG, Rich KA, Hall NJ, Jones ML, Fox A, Musier-Forsyth K, Kolb SJ. Heterogeneous splicing patterns resulting from KIF5A variants associated with amyotrophic lateral sclerosis. Hum Mol Genet 2023; 32:3166-3180. [PMID: 37593923 DOI: 10.1093/hmg/ddad134] [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: 04/24/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023] Open
Abstract
Single-nucleotide variants (SNVs) in the gene encoding Kinesin Family Member 5A (KIF5A), a neuronal motor protein involved in anterograde transport along microtubules, have been associated with amyotrophic lateral sclerosis (ALS). ALS is a rapidly progressive and fatal neurodegenerative disease that primarily affects the motor neurons. Numerous ALS-associated KIF5A SNVs are clustered near the splice-site junctions of the penultimate exon 27 and are predicted to alter the carboxy-terminal (C-term) cargo-binding domain of KIF5A. Mis-splicing of exon 27, resulting in exon exclusion, is proposed to be the mechanism by which these SNVs cause ALS. Whether all SNVs proximal to exon 27 result in exon exclusion is unclear. To address this question, we designed an in vitro minigene splicing assay in human embryonic kidney 293 cells, which revealed heterogeneous site-specific effects on splicing: only 5' splice-site (5'ss) SNVs resulted in exon skipping. We also quantified splicing in select clustered, regularly interspaced, short palindromic repeats-edited human stem cells, differentiated to motor neurons, and in neuronal tissues from a 5'ss SNV knock-in mouse, which showed the same result. Moreover, the survival of representative 3' splice site, 5'ss, and truncated C-term variant KIF5A (v-KIF5A) motor neurons was severely reduced compared with wild-type motor neurons, and overt morphological changes were apparent. While the total KIF5A mRNA levels were comparable across the cell lines, the total KIF5A protein levels were decreased for v-KIF5A lines, suggesting an impairment of protein synthesis or stability. Thus, despite the heterogeneous effect on ribonucleic acid splicing, KIF5A SNVs similarly reduce the availability of the KIF5A protein, leading to axonal transport defects and motor neuron pathology.
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Affiliation(s)
- Megan G Pino
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
- Department of Biological Chemistry & Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Kelly A Rich
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Nicholas J Hall
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
| | - Meredith L Jones
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Ashley Fox
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Karin Musier-Forsyth
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
- Department of Chemistry & Biochemistry, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Stephen J Kolb
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
- Department of Biological Chemistry & Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
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5
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Fu RH, Chen HJ, Hong SY. Interaction of the C9orf72-Amyotrophic Lateral Sclerosis-Related Proline-Arginine Dipeptide Repeat Protein with the RNA-Binding Protein NOVA1 Causes Decreased Expression of UNC13A Due to Enhanced Inclusion of Cryptic Exons, Which Is Reversed by Betulin Treatment. Cells 2023; 12:2476. [PMID: 37887320 PMCID: PMC10605128 DOI: 10.3390/cells12202476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
C9orf72 mutations are the most common form of familial amyotrophic lateral sclerosis (C9-ALS). It causes the production of proline-arginine dipeptide repeat proteins (PR-DPRs) in motor neurons (MNs), leading to the molecular pathology characteristic of ALS. UNC13A is critical for maintaining the synaptic function of MNs. Most ALS patients have nuclear deletion of the splicing repressor TDP-43 in MNs, which causes inclusion of the cryptic exon (CE) of UNC13A mRNA, resulting in nonsense-mediated mRNA decay and reduced protein expression. Therefore, in this study, we explored the role of PR-DPR in CE inclusion of UNC13A mRNA. Our results showed that PR-DPR (PR50) induced CE inclusion and decreased the protein expression of UNC13A in human neuronal cell lines. We also identified an interaction between the RNA-binding protein NOVA1 and PR50 by yeast two-hybrid screening. NOVA1 expression is known to be reduced in patients with ALS. We found that knockdown of NOVA1 enhanced CE inclusion of UNC13A mRNA. Furthermore, the naturally occurring triterpene betulin can inhibit the interaction between NOVA1 and PR50, thus preventing CE inclusion of UNC13A mRNA and protein reduction in human neuronal cell lines. This study linked PR-DPR with CE inclusion of UNC13A mRNA and developed candidate therapeutic strategies for C9-ALS using betulin.
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Affiliation(s)
- Ru-Huei Fu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
- Translational Medicine Research Center, China Medical University Hospital, Taichung 40447, Taiwan
- Ph.D. Program for Aging, China Medical University, Taichung 40402, Taiwan
| | - Hui-Jye Chen
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
| | - Syuan-Yu Hong
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
- Department of Medicine, School of Medicine, China Medical University, Taichung 40447, Taiwan
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
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6
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Liu HL, Lu XM, Wang HY, Hu KB, Wu QY, Liao P, Li S, Long ZY, Wang YT. The role of RNA splicing factor PTBP1 in neuronal development. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119506. [PMID: 37263298 DOI: 10.1016/j.bbamcr.2023.119506] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023]
Abstract
Alternative pre-mRNA splicing, which produces various mRNA isoforms with distinct structures and functions from a single gene, is regulated by specific RNA-binding proteins and is an essential method for regulating gene expression in mammals. Recent studies have shown that abnormal change during neuronal development triggered by splicing mis-regulation is an important feature of various neurological diseases. Polypyrimidine tract binding protein 1 (PTBP1) is a kind of RNA-binding proteins with extensive biological functions. As a well-known splicing regulator, it affects the neuronal development process through its involvement in axon formation, synaptogenesis, and neuronal apoptosis, according to the most recent studies. Here, we summarized the mechanism of alternative splicing, structure and function of PTBP1, and the latest research progress on the role of alternative splicing events regulated by PTBP1 in axon formation, synaptogenesis and neuronal apoptosis, to reveal the mechanism of PTBP1-regulated changes in neuronal development process.
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Affiliation(s)
- Hui-Lin Liu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China; State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Xiu-Min Lu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Hai-Yan Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Kai-Bin Hu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Qing-Yun Wu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Ping Liao
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Sen Li
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Zai-Yun Long
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Yong-Tang Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China.
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7
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Nikom D, Zheng S. Alternative splicing in neurodegenerative disease and the promise of RNA therapies. Nat Rev Neurosci 2023; 24:457-473. [PMID: 37336982 DOI: 10.1038/s41583-023-00717-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2023] [Indexed: 06/21/2023]
Abstract
Alternative splicing generates a myriad of RNA products and protein isoforms of different functions from a single gene. Dysregulated alternative splicing has emerged as a new mechanism broadly implicated in the pathogenesis of neurodegenerative diseases such as Alzheimer disease, amyotrophic lateral sclerosis, frontotemporal dementia, Parkinson disease and repeat expansion diseases. Understanding the mechanisms and functional outcomes of abnormal splicing in neurological disorders is vital in developing effective therapies to treat mis-splicing pathology. In this Review, we discuss emerging research and evidence of the roles of alternative splicing defects in major neurodegenerative diseases and summarize the latest advances in RNA-based therapeutic strategies to target these disorders.
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Affiliation(s)
- David Nikom
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA, USA
- Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA, USA
| | - Sika Zheng
- Neuroscience Graduate Program, University of California, Riverside, Riverside, CA, USA.
- Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA, USA.
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, USA.
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8
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Willemse SW, Harley P, van Eijk RPA, Demaegd KC, Zelina P, Pasterkamp RJ, van Damme P, Ingre C, van Rheenen W, Veldink JH, Kiernan MC, Al-Chalabi A, van den Berg LH, Fratta P, van Es MA. UNC13A in amyotrophic lateral sclerosis: from genetic association to therapeutic target. J Neurol Neurosurg Psychiatry 2023; 94:649-656. [PMID: 36737245 PMCID: PMC10359588 DOI: 10.1136/jnnp-2022-330504] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with limited treatment options and an incompletely understood pathophysiology. Although genomewide association studies (GWAS) have advanced our understanding of the disease, the precise manner in which risk polymorphisms contribute to disease pathogenesis remains unclear. Of relevance, GWAS have shown that a polymorphism (rs12608932) in the UNC13A gene is associated with risk for both ALS and frontotemporal dementia (FTD). Homozygosity for the C-allele at rs12608932 modifies the ALS phenotype, as these patients are more likely to have bulbar-onset disease, cognitive impairment and FTD at baseline as well as shorter survival. UNC13A is expressed in neuronal tissue and is involved in maintaining synaptic active zones, by enabling the priming and docking of synaptic vesicles. In the absence of functional TDP-43, risk variants in UNC13A lead to the inclusion of a cryptic exon in UNC13A messenger RNA, subsequently leading to nonsense mediated decay, with loss of functional protein. Depletion of UNC13A leads to impaired neurotransmission. Recent discoveries have identified UNC13A as a potential target for therapy development in ALS, with a confirmatory trial with lithium carbonate in UNC13A cases now underway and future approaches with antisense oligonucleotides currently under consideration. Considering UNC13A is a potent phenotypic modifier, it may also impact clinical trial outcomes. This present review describes the path from the initial discovery of UNC13A as a risk gene in ALS to the current therapeutic options being explored and how knowledge of its distinct phenotype needs to be taken into account in future trials.
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Affiliation(s)
- Sean W Willemse
- Department of Neurology, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, The Netherlands
| | - Peter Harley
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Ruben P A van Eijk
- Department of Neurology, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, The Netherlands
- Biostatistics & Research Support, Julius Center for Health Sciences and Primary Care, UMC Utrecht, Utrecht, The Netherlands
| | - Koen C Demaegd
- Department of Neurology, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, The Netherlands
| | - Pavol Zelina
- Department of Translational Neuroscience, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, The Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, The Netherlands
| | - Philip van Damme
- Department of Neurology, KU Leuven Hospital, Leuven, Belgium
- Laboratory of Neurobiology, VIB KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Caroline Ingre
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, The Netherlands
| | - Jan H Veldink
- Department of Neurology, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, The Netherlands
| | - Matthew C Kiernan
- Bushell Chair of Neurology, Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
- Neurology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | | | - Leonard H van den Berg
- Department of Neurology, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, The Netherlands
| | - Pietro Fratta
- UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Michael A van Es
- Department of Neurology, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, The Netherlands
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9
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La Cognata V, D’Amico AG, Maugeri G, Morello G, Guarnaccia M, Magrì B, Aronica E, D’Agata V, Cavallaro S. CXCR2 Is Deregulated in ALS Spinal Cord and Its Activation Triggers Apoptosis in Motor Neuron-Like Cells Overexpressing hSOD1-G93A. Cells 2023; 12:1813. [PMID: 37508478 PMCID: PMC10377984 DOI: 10.3390/cells12141813] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/08/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a multifactorial neurodegenerative disease characterized by progressive depletion of motor neurons (MNs). Recent evidence suggests a role in ALS pathology for the C-X-C motif chemokine receptor 2 (CXCR2), whose expression was found increased at both mRNA and protein level in cortical neurons of sporadic ALS patients. Previous findings also showed that the receptor inhibition is able to prevent iPSC-derived MNs degeneration in vitro and improve neuromuscular function in SOD1-G93A mice. Here, by performing transcriptional analysis and immunofluorescence studies, we detailed the increased expression and localization of CXCR2 and its main ligand CXCL8 in the human lumbar spinal cord of sporadic ALS patients. We further investigated the functional role of CXCR2/ligands axis in NSC-34 motor neuron-like cells expressing human wild-type (WT) or mutant (G93A) SOD1. A significant expression of CXCR2 was found in doxycycline-induced G93A-SOD1-expressing cells, but not in WT cells. In vitro assays showed CXCR2 activation by GROα and MIP2α, two murine endogenous ligands and functional homologs of CXCL8, reduces cellular viability and triggers apoptosis in a dose dependent manner, while treatment with reparixin, a non-competitive allosteric CXCR2 inhibitor, effectively counteracts GROα and MIP2α toxicity, significantly inhibiting the chemokine-induced cell death. Altogether, data further support a role of CXCR2 axis in ALS etiopathogenesis and confirm its pharmacological modulation as a candidate therapeutic strategy.
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Affiliation(s)
- Valentina La Cognata
- Institute for Biomedical Research and Innovation, National Research Council, 95126 Catania, Italy
| | - Agata Grazia D’Amico
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Grazia Maugeri
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Giovanna Morello
- Institute for Biomedical Research and Innovation, National Research Council, 95126 Catania, Italy
| | - Maria Guarnaccia
- Institute for Biomedical Research and Innovation, National Research Council, 95126 Catania, Italy
| | - Benedetta Magrì
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Eleonora Aronica
- Department of (Neuro) Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105 Amsterdam, The Netherlands
| | - Velia D’Agata
- Section of Human Anatomy and Histology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Sebastiano Cavallaro
- Institute for Biomedical Research and Innovation, National Research Council, 95126 Catania, Italy
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10
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Rezvykh A, Ustyugov A, Chaprov K, Teterina E, Nebogatikov V, Spasskaya D, Evgen’ev M, Morozov A, Funikov S. Cytoplasmic aggregation of mutant FUS causes multistep RNA splicing perturbations in the course of motor neuron pathology. Nucleic Acids Res 2023; 51:5810-5830. [PMID: 37115004 PMCID: PMC10287951 DOI: 10.1093/nar/gkad319] [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: 08/29/2022] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Dysfunction of the RNA-binding protein (RBP) FUS implicated in RNA metabolism can cause amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases. Mutations affecting FUS nuclear localization can drive RNA splicing defects and stimulate the formation of non-amyloid inclusions in affected neurons. However, the mechanism by which FUS mutations contribute to the development of ALS remains uncertain. Here we describe a pattern of RNA splicing changes in the dynamics of the continuous proteinopathy induced by mislocalized FUS. We show that the decrease in intron retention of FUS-associated transcripts represents the hallmark of the pathogenesis of ALS and is the earliest molecular event in the course of progression of the disease. As FUS aggregation increases, the pattern of RNA splicing changes, becoming more complex, including a decrease in the inclusion of neuron-specific microexons and induction of cryptic exon splicing due to the sequestration of additional RBPs into FUS aggregates. Crucially, the identified features of the pathological splicing pattern are also observed in ALS patients in both sporadic and familial cases. Our data provide evidence that both a loss of nuclear FUS function due to mislocalization and the subsequent cytoplasmic aggregation of mutant protein lead to the disruption of RNA splicing in a multistep fashion during FUS aggregation.
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Affiliation(s)
- Alexander P Rezvykh
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Aleksey A Ustyugov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Kirill D Chaprov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Ekaterina V Teterina
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Vladimir O Nebogatikov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Daria S Spasskaya
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Michael B Evgen’ev
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Alexey V Morozov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Sergei Yu Funikov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
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11
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Tassinari V, La Rosa P, Guida E, Colopi A, Caratelli S, De Paolis F, Gallo A, Cenciarelli C, Sconocchia G, Dolci S, Cesarini V. Contribution of A-to-I RNA editing, M6A RNA Methylation, and Alternative Splicing to physiological brain aging and neurodegenerative diseases. Mech Ageing Dev 2023; 212:111807. [PMID: 37023929 DOI: 10.1016/j.mad.2023.111807] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Aging is a physiological and progressive phenomenon in all organisms' life cycle, characterized by the accumulation of degenerative processes triggered by several alterations within molecular pathways. These changes compromise cell fate, resulting in the loss of functions in tissues throughout the body, including the brain. Physiological brain aging has been linked to structural and functional alterations, as well as to an increased risk of neurodegenerative diseases. Post-transcriptional RNA modifications modulate mRNA coding properties, stability, translatability, expanding the coding capacity of the genome, and are involved in all cellular processes. Among mRNA post-transcriptional modifications, the A-to-I RNA editing, m6A RNA Methylation and Alternative Splicing play a critical role in all the phases of a neuronal cell life cycle and alterations in their mechanisms of action significantly contribute to aging and neurodegeneration. Here we review our current understanding of the contribution of A-to-I RNA editing, m6A RNA Methylation, and Alternative Splicing to physiological brain aging process and neurodegenerative diseases.
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Affiliation(s)
- Valentina Tassinari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy; Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy.
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, Rome, Italy; European Center for Brain Research, IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Eugenia Guida
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Ambra Colopi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Sara Caratelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Francesca De Paolis
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Angela Gallo
- RNA Editing Lab., Oncohaematology Department, Cellular and Gene Therapy Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carlo Cenciarelli
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Giuseppe Sconocchia
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy
| | - Susanna Dolci
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Valeriana Cesarini
- Department of Biomedicine, Institute of Translational Pharmacology (IFT), National Research Council (CNR), Rome, Italy.
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12
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Hell AK, Grages A, Braunschweig L, Lueders KA, Austein F, Lorenz HM, Lippross S, Tsaknakis K. Children with Spinal Muscular Atrophy Have Reduced Vertebral Body Height and Depth and Pedicle Size in Comparison to Age-Matched Healthy Controls. World Neurosurg 2022; 165:e352-e356. [PMID: 35717014 DOI: 10.1016/j.wneu.2022.06.054] [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: 05/04/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Most children with spinal muscular atrophy (SMA) develop spinal deformity, which may require surgical intervention. In addition to poor bone stock, vertebral body shape may hinder the placement of spinal implants resulting in complications and poor outcome. The aim of this study was to analyze whether vertebral body morphology of children and adolescents with SMA is altered in comparison to healthy age-matched controls. METHODS In this prospective cohort study, 17 children with SMA (mean age 8.7 ±1.0 years) and 13 adolescents with SMA (mean age 13.6 ±1.4 years), all with some degree of neuromuscular scoliosis, were analyzed by standardized radiographic measurements to evaluate vertebral body height and depth. Results were compared with age-matched healthy controls (n = 10 children; mean age 9.1 ± 1.6 years; n = 20 adolescents, mean age 13.1 ± 0.5 years). Computed tomography scans of 27 adolescents with SMA (13.5 ±1.2 years) and 25 healthy age-matched controls (13.8 ±2.0 years) were analyzed to define pedicle diameters. RESULTS All children and adolescents with SMA had decreased vertebral height and depth in comparison to age-matched healthy controls. In adolescents, reduced depth was more pronounced than height in the thoracic spine. Pedicle size was significantly reduced in the lower thoracic and lumbar area. CONCLUSIONS Reduced vertebral body height and depth and pedicle size in children and adolescents with SMA may influence surgical treatment of spinal deformity. Surgeons should be aware of anatomical differences and choose implant devices accordingly.
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Affiliation(s)
- Anna K Hell
- Department of Trauma, Orthopaedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany.
| | - Antonia Grages
- Department of Trauma, Orthopaedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Lena Braunschweig
- Department of Trauma, Orthopaedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Katja A Lueders
- Department of Trauma, Orthopaedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Friederike Austein
- Department of Diagnostic and Interventional Neuroradiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Heiko M Lorenz
- Department of Trauma, Orthopaedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany
| | - Sebastian Lippross
- Department of Orthopaedic and Trauma Surgery, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Konstantinos Tsaknakis
- Department of Trauma, Orthopaedic and Plastic Surgery, University Medical Center Goettingen, Goettingen, Germany
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13
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Shenouda M, Xiao S, MacNair L, Lau A, Robertson J. A C-Terminally Truncated TDP-43 Splice Isoform Exhibits Neuronal Specific Cytoplasmic Aggregation and Contributes to TDP-43 Pathology in ALS. Front Neurosci 2022; 16:868556. [PMID: 35801182 PMCID: PMC9253772 DOI: 10.3389/fnins.2022.868556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/24/2022] [Indexed: 01/01/2023] Open
Abstract
Neuronal cytoplasmic aggregation and ubiquitination of TDP-43 is the most common disease pathology linking Amyotrophic Lateral Sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). TDP-43 pathology is characterized by the presence of low molecular weight TDP-43 species generated through proteolytic cleavage and/or abnormal RNA processing events. In addition to N-terminally truncated TDP-43 species, it has become evident that C-terminally truncated variants generated through alternative splicing in exon 6 also contribute to the pathophysiology of ALS/FTLD. Three such variants are listed in UCSD genome browser each sharing the same C-terminal unique sequence of 18 amino acids which has been shown to contain a putative nuclear export sequence. Here we have identified an additional C-terminally truncated variant of TDP-43 in human spinal cord tissue. This variant, called TDP43C-spl, is generated through use of non-canonical splice sites in exon 6, skipping 1,020 bp and encoding a 272 aa protein lacking the C-terminus with the first 256 aa identical to full-length TDP-43 and the same 18 amino acid C-terminal unique sequence. Ectopic expression studies in cells revealed that TDP43C-spl was localized to the nucleus in astrocytic and microglial cell lines but formed cytoplasmic ubiquitinated aggregates in neuronal cell lines. An antibody raised to the unique 18 amino acid sequence showed elevated levels of C-terminally truncated variants in ALS spinal cord tissues, and co-labeled TDP-43 pathology in disease affected spinal motor neurons. The retention of this 18 amino acid sequence among several C-terminally truncated TDP-43 variants suggests important functional relevance. Our studies of TDP43C-spl suggest this may be related to the selective vulnerability of neurons to TDP-43 pathology and cell-subtype differences in nuclear export.
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Affiliation(s)
- Marc Shenouda
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Shangxi Xiao
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, Canada
| | - Laura MacNair
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Agnes Lau
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, Canada
| | - Janice Robertson
- Tanz Centre for Research in Neurodegenerative Diseases, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- *Correspondence: Janice Robertson
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14
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Thonda S, Vinnakota RL, Kona SV, Kalivendi SV. Identification of RBMX as a splicing regulator in Parkinsonian mimetic induced alternative splicing of α-synuclein. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194825. [PMID: 35577270 DOI: 10.1016/j.bbagrm.2022.194825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
α-Synuclein (α-syn) plays a precipitating role in Parkinson's disease (PD) due to its tendency to form oligomers and fibrils. The presence of smaller isoforms of α-syn was widely noticed in the affected brain regions of PD patients. 112-synuclein (112-syn) which lacks exon-5, possess enhanced aggregation propensity and forms intracellular inclusions. However, the factors responsible for the skipping of exon-5 are not completely understood. In this context, we aimed to identity the cis & trans-acting elements governing alternative splicing (AS) events by the Parkinsonian agent (MPP+) using minigene constructs. Minigene-I and -II were constructed by pruning the intron-4 and -5 regions respectively without altering the branch point adenosine to preserve splicing machinery. Also, chimeric minigenes were engineered by replacing either 5' (Mini-III) or 3' (Mini-IV) flanking intronic regions of exon-5 with other intronic regions (intron-3 and -2) that are not responsive to MPP+ induced splicing. While all the above minigenes exhibited MPP+-induced skipping of exon-5, Minigene-III did not generate the spliced product indicating that the 5' flanking intronic region (316 bp) of exon-5 possess cis-acting elements responsible for oxidant-induced alternative splicing. RNA-Binding Protein Database (RBDP) analysis revealed the presence of four putative RNA binding proteins (RBPs), namely, RBMX, MBNL1, KHDRBS3 and SFRS1 that may bind to the 316 bp region of intron-4and their expression was substantially reduced following MPP+ treatment. Further, overexpression of RBMX mitigated MPP+-induced generation of 112-syn and also reduced intracellular α-syn aggregates. Overall, our study identified the pivotal role of the splicing regulator, RBMX, in the pathophysiology of PD.
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Affiliation(s)
- Swaroop Thonda
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ravali L Vinnakota
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Swathi V Kona
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shasi V Kalivendi
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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15
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RNA Modifications and RNA Metabolism in Neurological Disease Pathogenesis. Int J Mol Sci 2021; 22:ijms222111870. [PMID: 34769301 PMCID: PMC8584444 DOI: 10.3390/ijms222111870] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/16/2021] [Accepted: 10/26/2021] [Indexed: 02/06/2023] Open
Abstract
The intrinsic cellular heterogeneity and molecular complexity of the mammalian nervous system relies substantially on the dynamic nature and spatiotemporal patterning of gene expression. These features of gene expression are achieved in part through mechanisms involving various epigenetic processes such as DNA methylation, post-translational histone modifications, and non-coding RNA activity, amongst others. In concert, another regulatory layer by which RNA bases and sugar residues are chemically modified enhances neuronal transcriptome complexity. Similar RNA modifications in other systems collectively constitute the cellular epitranscriptome that integrates and impacts various physiological processes. The epitranscriptome is dynamic and is reshaped constantly to regulate vital processes such as development, differentiation and stress responses. Perturbations of the epitranscriptome can lead to various pathogenic conditions, including cancer, cardiovascular abnormalities and neurological diseases. Recent advances in next-generation sequencing technologies have enabled us to identify and locate modified bases/sugars on different RNA species. These RNA modifications modulate the stability, transport and, most importantly, translation of RNA. In this review, we discuss the formation and functions of some frequently observed RNA modifications—including methylations of adenine and cytosine bases, and isomerization of uridine to pseudouridine—at various layers of RNA metabolism, together with their contributions to abnormal physiological conditions that can lead to various neurodevelopmental and neurological disorders.
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16
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Alternative Splicing Role in New Therapies of Spinal Muscular Atrophy. Genes (Basel) 2021; 12:genes12091346. [PMID: 34573328 PMCID: PMC8468182 DOI: 10.3390/genes12091346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
It has been estimated that 80% of the pre-mRNA undergoes alternative splicing, which exponentially increases the flow of biological information in cellular processes and can be an attractive therapeutic target. It is a crucial mechanism to increase genetic diversity. Disturbed alternative splicing is observed in many disorders, including neuromuscular diseases and carcinomas. Spinal Muscular Atrophy (SMA) is an autosomal recessive neurodegenerative disease. Homozygous deletion in 5q13 (the region coding for the motor neuron survival gene (SMN1)) is responsible for 95% of SMA cases. The nearly identical SMN2 gene does not compensate for SMN loss caused by SMN1 gene mutation due to different splicing of exon 7. A pathologically low level of survival motor neuron protein (SMN) causes degeneration of the anterior horn cells in the spinal cord with associated destruction of α-motor cells and manifested by muscle weakness and loss. Understanding the regulation of the SMN2 pre-mRNA splicing process has allowed for innovative treatment and the introduction of new medicines for SMA. After describing the concept of splicing modulation, this review will cover the progress achieved in this field, by highlighting the breakthrough accomplished recently for the treatment of SMA using the mechanism of alternative splicing.
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17
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Jakubauskienė E, Kanopka A. Alternative Splicing and Hypoxia Puzzle in Alzheimer's and Parkinson's Diseases. Genes (Basel) 2021; 12:genes12081272. [PMID: 34440445 PMCID: PMC8394294 DOI: 10.3390/genes12081272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 01/08/2023] Open
Abstract
Alternative pre-mRNA splicing plays a very important role in expanding protein diversity as it generates numerous transcripts from a single protein-coding gene. Therefore, alterations lead this process to neurological human disorders, including Alzheimer’s and Parkinson’s diseases. Moreover, accumulating evidence indicates that the splicing machinery highly contributes to the cells’ ability to adapt to different altered cellular microenvironments, such as hypoxia. Hypoxia is known to have an effect on the expression of proteins involved in a multiple of biological processes, such as erythropoiesis, angiogenesis, and neurogenesis, and is one of the important risk factors in neuropathogenesis. In this review, we discuss the current knowledge of alternatively spliced genes, which, as it is reported, are associated with Alzheimer’s and Parkinson’s diseases. Additionally, we highlight the possible influence of cellular hypoxic microenvironment for the formation of mRNA isoforms contributing to the development of these neurodegenerative diseases.
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18
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Mir H, Elieh Ali Komi D, Pouramir M, Parsian H, Moghadamnia AA, Seyfizadeh N, Lakzaei M. The hepatoprotective effects of Pyrus biossieriana buhse leaf extract on tert-butyl hydroperoxide toxicity in HepG2 cell line. BMC Res Notes 2021; 14:298. [PMID: 34344447 PMCID: PMC8336407 DOI: 10.1186/s13104-021-05713-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/26/2021] [Indexed: 01/22/2023] Open
Abstract
OBJECTIVE In present study, the effects of the leaf extract of Pyrus biossieriana Buhse on tert-Butyl hydroperoxide (t-BHP) induced toxicity in the HepG2 cell line were investigated. RESULTS HepG2 cells were exposed to different concentrations of both extract (1.5, 2.0, and 2.5 mg/mL) and t-BHP (100, 150, and 200 μM). The total flavonoid and phenolic contents, the cell viability, lipid peroxidation, NO generation, and the total antioxidant capacity in cell media were assessed. The amount of arbutin was estimated 12.6% of the dry weight of leaves (equivalent to 126 mg/g). Additionally, the amounts of flavonoids and phenols in extract were estimated 119 mg/g and 418 mg/g, respectively. The cells incubated with t-BHP showed a significant decrease in survival (p < 0.001). Preincubation with extract (1.5 mg/mL and 2.0 mg/mL) attenuated the t-BHP toxicity and increased the cell viability in cells exposed even to the highest concentration of t-BHP (200 μM) (p value < 0.001, and p value = 0.035) respectively. Additionally, treatment with extract reduced the cell growth suppression caused by t-BHP. The P. biossieriana Buhse leaf extract at concentrations of 1.5 and 2.0 mg/mL is capable of attenuating t-BHP-induced cytotoxicity in HepG2 cells.
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Affiliation(s)
- Hamed Mir
- Department of Nutrition, School of Allied Medical Sciences, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran. .,Department of Biochemistry, School of Medicine, Jahrom University of Medical Sciences, Jahrom, Iran.
| | - Daniel Elieh Ali Komi
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Mahdi Pouramir
- Department of Clinical Biochemistry, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.,Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Hadi Parsian
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Ali Akbar Moghadamnia
- Department of Pharmacology & Toxicology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Nayer Seyfizadeh
- Neuroscience Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mostafa Lakzaei
- Department of Clinical Biochemistry, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
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19
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Amyotrophic Lateral Sclerosis: Molecular Mechanisms, Biomarkers, and Therapeutic Strategies. Antioxidants (Basel) 2021; 10:antiox10071012. [PMID: 34202494 PMCID: PMC8300638 DOI: 10.3390/antiox10071012] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/16/2021] [Accepted: 06/23/2021] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with the progressive loss of motor neurons, leading to a fatal paralysis. According to whether there is a family history of ALS, ALS can be roughly divided into two types: familial and sporadic. Despite decades of research, the pathogenesis of ALS is still unelucidated. To this end, we review the recent progress of ALS pathogenesis, biomarkers, and treatment strategies, mainly discuss the roles of immune disorders, redox imbalance, autophagy dysfunction, and disordered iron homeostasis in the pathogenesis of ALS, and introduce the effects of RNA binding proteins, ALS-related genes, and non-coding RNA as biomarkers on ALS. In addition, we also mention other ALS biomarkers such as serum uric acid (UA), cardiolipin (CL), chitotriosidase (CHIT1), and neurofilament light chain (NFL). Finally, we discuss the drug therapy, gene therapy, immunotherapy, and stem cell-exosomal therapy for ALS, attempting to find new therapeutic targets and strategies. A challenge is to study the various mechanisms of ALS as a syndrome. Biomarkers that have been widely explored are indispensable for the diagnosis, treatment, and prevention of ALS. Moreover, the development of new genes and targets is an urgent task in this field.
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20
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Li D, McIntosh CS, Mastaglia FL, Wilton SD, Aung-Htut MT. Neurodegenerative diseases: a hotbed for splicing defects and the potential therapies. Transl Neurodegener 2021; 10:16. [PMID: 34016162 PMCID: PMC8136212 DOI: 10.1186/s40035-021-00240-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/23/2021] [Indexed: 12/14/2022] Open
Abstract
Precursor messenger RNA (pre-mRNA) splicing is a fundamental step in eukaryotic gene expression that systematically removes non-coding regions (introns) and ligates coding regions (exons) into a continuous message (mature mRNA). This process is highly regulated and can be highly flexible through a process known as alternative splicing, which allows for several transcripts to arise from a single gene, thereby greatly increasing genetic plasticity and the diversity of proteome. Alternative splicing is particularly prevalent in neuronal cells, where the splicing patterns are continuously changing to maintain cellular homeostasis and promote neurogenesis, migration and synaptic function. The continuous changes in splicing patterns and a high demand on many cis- and trans-splicing factors contribute to the susceptibility of neuronal tissues to splicing defects. The resultant neurodegenerative diseases are a large group of disorders defined by a gradual loss of neurons and a progressive impairment in neuronal function. Several of the most common neurodegenerative diseases involve some form of splicing defect(s), such as Alzheimer's disease, Parkinson's disease and spinal muscular atrophy. Our growing understanding of RNA splicing has led to the explosion of research in the field of splice-switching antisense oligonucleotide therapeutics. Here we review our current understanding of the effects alternative splicing has on neuronal differentiation, neuronal migration, synaptic maturation and regulation, as well as the impact on neurodegenerative diseases. We will also review the current landscape of splice-switching antisense oligonucleotides as a therapeutic strategy for a number of common neurodegenerative disorders.
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Affiliation(s)
- Dunhui Li
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Craig Stewart McIntosh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Frank Louis Mastaglia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - Steve Donald Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia.,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia. .,Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Perth, Western Australia, Australia.
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21
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Wu D, Zang YY, Shi YY, Ye C, Cai WM, Tang XH, Zhao L, Liu Y, Gan Z, Chen GQ, Xu Y, Yang JJ, Shi YS. Distant coupling between RNA editing and alternative splicing of the osmosensitive cation channel Tmem63b. J Biol Chem 2020; 295:18199-18212. [PMID: 33100268 PMCID: PMC7939439 DOI: 10.1074/jbc.ra120.016049] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/17/2020] [Indexed: 11/06/2022] Open
Abstract
Post-transcriptional modifications of pre-mRNAs expand the diversity of proteomes in higher eukaryotes. In the brain, these modifications diversify the functional output of many critical neuronal signal molecules. In this study, we identified a brain-specific A-to-I RNA editing that changed glutamine to arginine (Q/R) at exon 20 and an alternative splicing of exon 4 in Tmem63b, which encodes a ubiquitously expressed osmosensitive cation channel. The channel isoforms lacking exon 4 occurred in ∼80% of Tmem63b mRNAs in the brain but were not detected in other tissues, suggesting a brain-specific splicing. We found that the Q/R editing was catalyzed by Adar2 (Adarb1) and required an editing site complementary sequence located in the proximal 5' end of intron 20. Moreover, the Q/R editing was almost exclusively identified in the splicing isoform lacking exon 4, indicating a coupling between the editing and the splicing. Elimination of the Q/R editing in brain-specific Adar2 knockout mice did not affect the splicing efficiency of exon 4. Furthermore, transfection with the splicing isoform containing exon 4 suppressed the Q/R editing in primary cultured cerebellar granule neurons. Thus, our study revealed a coupling between an RNA editing and a distant alternative splicing in the Tmem63b pre-mRNA, in which the splicing plays a dominant role. Finally, physiological analysis showed that the splicing and the editing coordinately regulate Ca2+ permeability and osmosensitivity of channel proteins, which may contribute to their functions in the brain.
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Affiliation(s)
- Dan Wu
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Yan-Yu Zang
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Yong-Yun Shi
- Department of Orthopaedics, Luhe People's Hospital Affiliated to Yangzhou University, Nanjing, China
| | - Chang Ye
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Wen-Min Cai
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Xiao-Hui Tang
- Department of Anesthesiology and Perioperative Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; School of Medicine, Southeast University, Nanjing, China
| | - Liyun Zhao
- Translational Science and Clinical Biomarker, BeiGene (Shanghai) Co., Ltd., Shanghai, China
| | - Yong Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Zhenji Gan
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Gui-Quan Chen
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China; Institute for Brain Sciences, Nanjing University, Nanjing, China
| | - Yun Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China; Institute for Brain Sciences, Nanjing University, Nanjing, China
| | - Jian-Jun Yang
- Department of Anesthesiology and Perioperative Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Yun Stone Shi
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China; Institute for Brain Sciences, Nanjing University, Nanjing, China; Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China.
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Zakharova M. Modern approaches in gene therapy of motor neuron diseases. Med Res Rev 2020; 41:2634-2655. [PMID: 32638429 DOI: 10.1002/med.21705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 12/12/2022]
Abstract
Motor neuron disorders are a group of neurodegenerative diseases characterized by muscle weakness, loss of ambulation, respiratory insufficiency, leading to an early death. Spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis are the most common and fatal motor neuron diseases. The last 3 years became very successful for novel gene therapy approaches in SMA in infants. Two innovative drugs-nusinersen (Spinraza) and onasemnogene abeparvovec (Zolgensma) have been approved by health authorities. The numerous molecular and genetic overlaps between different neurodegenerative diseases are of great importance in the development of innovative therapeutic strategies, including viral vector therapy and RNA modulating approaches.
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Affiliation(s)
- Maria Zakharova
- Sixth Neurology Department (Department of Neuroinfectious Diseases), Research Center of Neurology, Moscow, Russia
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Karagiannis P, Inoue H. ALS, a cellular whodunit on motor neuron degeneration. Mol Cell Neurosci 2020; 107:103524. [PMID: 32629110 DOI: 10.1016/j.mcn.2020.103524] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/09/2020] [Accepted: 06/25/2020] [Indexed: 12/24/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease that primarily targets motor neurons. Motor neurons from ALS patients show cytoplasmic inclusions that are reflective of an altered RNA metabolism and protein degradation. Causal gene mutations are found in all cell types even though patient motor neurons are by far the most susceptible to the degeneration. Using induced pluripotent stem cell (iPSC) technology, researchers have generated motor neurons with the same genotype as the patient including sporadic ones. They have also generated other cell types associated with the disease such as astrocytes, microglia and oligodendrocytes. These cells provide not only new insights on the mechanisms of the disease from the early stage, but also a platform for drug screening that has led to several clinical trials. This review examines the knowledge gained from iPSC studies using patient cells on the gene mutations and cellular networks in ALS and relevant experimental therapies.
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Affiliation(s)
- Peter Karagiannis
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.
| | - Haruhisa Inoue
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; iPSC-based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto, Japan; Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, Japan.
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Disease-modifying therapies in amyotrophic lateral sclerosis. Neuropharmacology 2020; 167:107986. [DOI: 10.1016/j.neuropharm.2020.107986] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/21/2020] [Accepted: 01/31/2020] [Indexed: 02/08/2023]
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Splicing Players Are Differently Expressed in Sporadic Amyotrophic Lateral Sclerosis Molecular Clusters and Brain Regions. Cells 2020; 9:cells9010159. [PMID: 31936368 PMCID: PMC7017305 DOI: 10.3390/cells9010159] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/23/2019] [Accepted: 01/04/2020] [Indexed: 12/12/2022] Open
Abstract
Splicing is a tightly orchestrated process by which the brain produces protein diversity over time and space. While this process specializes and diversifies neurons, its deregulation may be responsible for their selective degeneration. In amyotrophic lateral sclerosis (ALS), splicing defects have been investigated at the singular gene level without considering the higher-order level, involving the entire splicing machinery. In this study, we analyzed the complete spectrum (396) of genes encoding splicing factors in the motor cortex (41) and spinal cord (40) samples from control and sporadic ALS (SALS) patients. A substantial number of genes (184) displayed significant expression changes in tissue types or disease states, were implicated in distinct splicing complexes and showed different topological hierarchical roles based on protein–protein interactions. The deregulation of one of these splicing factors has a central topological role, i.e., the transcription factor YBX1, which might also have an impact on stress granule formation, a pathological marker associated with ALS.
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Isoform-specific NF1 mRNA levels correlate with disease severity in Neurofibromatosis type 1. Orphanet J Rare Dis 2019; 14:261. [PMID: 31730495 PMCID: PMC6858644 DOI: 10.1186/s13023-019-1223-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 10/09/2019] [Indexed: 12/29/2022] Open
Abstract
Background Neurofibromatosis type 1 (NF1) is characterized by an extreme clinical variability both within and between families that cannot be explained solely by the nature of the pathogenic NF1 gene mutations. A proposed model hypothesizes that variation in the levels of protein isoforms generated via alternative transcript processing acts as modifier and contributes to phenotypic variability. Results Here we used real-time quantitative PCR to investigate the levels of two major NF1 mRNA isoforms encoding proteins differing in their ability to control RAS signaling (isoforms I and II) in the peripheral blood leukocytes of 138 clinically well-characterized NF1 patients and 138 aged-matched healthy controls. As expected, expression analysis showed that NF1 isoforms I and II levels were significantly lower in patients than controls. Notably, these differences were more evident when patients were stratified according to the severity of phenotype. Moreover, a correlation was identified when comparing the levels of isoform I mRNA and the severity of NF1 features, with statistically significant lower levels associated with a severe phenotype (i.e., occurrence of learning disability/intellectual disability, optic gliomas and/or other neoplasias, and/or cerebrovascular disease) as well as in patients with cognitive impairment. Conclusions The present findings provide preliminary evidence for a role of circuits controlling NF1 transcript processing in modulating NF1 expressivity, and document an association between the levels of neurofibromin isoform I mRNA and the severity of phenotype and cognitive impairment in NF1.
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