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Wen X, Xu H, Woolley PR, Conway OM, Yao J, Matouschek A, Lambowitz AM, Paull TT. Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregation. J Cell Biol 2024; 223:e202309036. [PMID: 38717338 PMCID: PMC11080644 DOI: 10.1083/jcb.202309036] [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: 09/06/2023] [Revised: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 05/12/2024] Open
Abstract
Senataxin is an evolutionarily conserved RNA-DNA helicase involved in DNA repair and transcription termination that is associated with human neurodegenerative disorders. Here, we investigated whether Senataxin loss affects protein homeostasis based on previous work showing R-loop-driven accumulation of DNA damage and protein aggregates in human cells. We find that Senataxin loss results in the accumulation of insoluble proteins, including many factors known to be prone to aggregation in neurodegenerative disorders. These aggregates are located primarily in the nucleolus and are promoted by upregulation of non-coding RNAs expressed from the intergenic spacer region of ribosomal DNA. We also map sites of R-loop accumulation in human cells lacking Senataxin and find higher RNA-DNA hybrids within the ribosomal DNA, peri-centromeric regions, and other intergenic sites but not at annotated protein-coding genes. These findings indicate that Senataxin loss affects the solubility of the proteome through the regulation of transcription-dependent lesions in the nucleus and the nucleolus.
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Affiliation(s)
- Xuemei Wen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hengyi Xu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Phillip R. Woolley
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Olivia M. Conway
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jun Yao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Alan M. Lambowitz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Tanya T. Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
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2
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Giannini M, Porrua O. Senataxin: A key actor in RNA metabolism, genome integrity and neurodegeneration. Biochimie 2024; 217:10-19. [PMID: 37558082 DOI: 10.1016/j.biochi.2023.08.001] [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: 05/08/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023]
Abstract
The RNA/DNA helicase senataxin (SETX) has been involved in multiple crucial processes related to genome expression and integrity such us transcription termination, the regulation of transcription-replication conflicts and the resolution of R-loops. SETX has been the focus of numerous studies since the discovery that mutations in its coding gene are the root cause of two different neurodegenerative diseases: Ataxia with Oculomotor Apraxia type 2 (AOA2) and a juvenile form of Amyotrophic Lateral Sclerosis (ALS4). A plethora of cellular phenotypes have been described as the result of SETX deficiency, yet the precise molecular function of SETX as well as the molecular pathways leading from SETX mutations to AOA2 and ALS4 pathologies have remained unclear. However, recent data have shed light onto the biochemical activities and biological roles of SETX, thus providing new clues to understand the molecular consequences of SETX mutation. In this review we summarize near two decades of scientific effort to elucidate SETX function, we discuss strengths and limitations of the approaches and models used thus far to investigate SETX-associated diseases and suggest new possible research avenues for the study of AOA2 and ALS4 pathogenesis.
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Affiliation(s)
- Marta Giannini
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Odil Porrua
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.
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3
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Tommasini D, Fox R, Ngo KJ, Hinman JD, Fogel BL. Alterations in oligodendrocyte transcriptional networks reveal region-specific vulnerabilities to neurological disease. iScience 2023; 26:106358. [PMID: 36994077 PMCID: PMC10040735 DOI: 10.1016/j.isci.2023.106358] [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: 07/20/2022] [Revised: 12/22/2022] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Neurological disease is characterized the by dysfunction of specific neuroanatomical regions. To determine whether region-specific vulnerabilities have a transcriptional basis at cell-type-specific resolution, we analyzed gene expression in mouse oligodendrocytes across various brain regions. Oligodendrocyte transcriptomes cluster in an anatomical arrangement along the rostrocaudal axis. Moreover, regional oligodendrocyte populations preferentially regulate genes implicated in diseases that target their region of origin. Systems-level analyses identify five region-specific co-expression networks representing distinct molecular pathways in oligodendrocytes. The cortical network exhibits alterations in mouse models of intellectual disability and epilepsy, the cerebellar network in ataxia, and the spinal network in multiple sclerosis. Bioinformatic analyses reveal potential molecular regulators of these networks, which were confirmed to modulate network expression in vitro in human oligodendroglioma cells, including reversal of the disease-associated transcriptional effects of a pathogenic Spinocerebellar ataxia type 1 allele. These findings identify targetable region-specific vulnerabilities to neurological disease mediated by oligodendrocytes.
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Affiliation(s)
- Dario Tommasini
- Department of Neurology, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Rachel Fox
- Department of Human Genetics, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kathie J. Ngo
- Department of Neurology, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jason D. Hinman
- Department of Neurology, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brent L. Fogel
- Department of Neurology, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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4
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Butchbach MER, Scott RC. Biological networks and complexity in early-onset motor neuron diseases. Front Neurol 2022; 13:1035406. [PMID: 36341099 PMCID: PMC9634177 DOI: 10.3389/fneur.2022.1035406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Motor neuron diseases (MNDs) are neuromuscular disorders where the spinal motor neurons-either the cell bodies themselves or their axons-are the primary cells affected. To date, there are 120 different genes that are lost or mutated in pediatric-onset MNDs. Most of these childhood-onset disorders, aside from spinal muscular atrophy (SMA), lack viable therapeutic options. Previous research on MNDs has focused on understanding the pathobiology of a single, specific gene mutation and targeting therapies to that pathobiology. This reductionist approach has yielded therapeutic options for a specific disorder, in this case SMA. Unfortunately, therapies specific for SMA have not been effective against other pediatric-onset MNDs. Pursuing the same approach for the other defined MNDs would require development of at least 120 independent treatments raising feasibility issues. We propose an alternative to this this type of reductionist approach by conceptualizing MNDs in a complex adaptive systems framework that will allow identification of common molecular and cellular pathways which form biological networks that are adversely affected in early-onset MNDs and thus MNDs with similar phenotypes despite diverse genotypes. This systems biology approach highlights the complexity and self-organization of the motor system as well as the ways in which it can be affected by these genetic disorders. Using this integrated approach to understand early-onset MNDs, we would be better poised to expand the therapeutic repertoire for multiple MNDs.
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Affiliation(s)
- Matthew E. R. Butchbach
- Division of Neurology, Nemours Children's Hospital Delaware, Wilmington, DE, United States,Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, United States,Department of Biological Sciences, University of Delaware, Newark, DE, United States,*Correspondence: Matthew E. R. Butchbach
| | - Rod C. Scott
- Division of Neurology, Nemours Children's Hospital Delaware, Wilmington, DE, United States,Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, United States,Department of Psychological and Brain Sciences, University of Delaware, Newark, DE, United States,Neurosciences Unit, Institute of Child Health, University College London, London, United Kingdom,Rod C. Scott
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5
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Cuartas J, Gangwani L. R-loop Mediated DNA Damage and Impaired DNA Repair in Spinal Muscular Atrophy. Front Cell Neurosci 2022; 16:826608. [PMID: 35783101 PMCID: PMC9243258 DOI: 10.3389/fncel.2022.826608] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/23/2022] [Indexed: 12/02/2022] Open
Abstract
Defects in DNA repair pathways are a major cause of DNA damage accumulation leading to genomic instability and neurodegeneration. Efficient DNA damage repair is critical to maintain genomicstability and support cell function and viability. DNA damage results in the activation of cell death pathways, causing neuronal death in an expanding spectrum of neurological disorders, such as amyotrophic lateral sclerosis (ALS), Parkinson’s disease (PD), Alzheimer’s disease (AD), and spinal muscular atrophy (SMA). SMA is a neurodegenerative disorder caused by mutations in the Survival Motor Neuron 1 (SMN1) gene. SMA is characterized by the degeneration of spinal cord motor neurons due to low levels of the SMN protein. The molecular mechanism of selective motor neuron degeneration in SMA was unclear for about 20 years. However, several studies have identified biochemical and molecular mechanisms that may contribute to the predominant degeneration of motor neurons in SMA, including the RhoA/ROCK, the c-Jun NH2-terminal kinase (JNK), and p53-mediated pathways, which are involved in mediating DNA damage-dependent cell death. Recent studies provided insight into selective degeneration of motor neurons, which might be caused by accumulation of R-loop-mediated DNA damage and impaired non-homologous end joining (NHEJ) DNA repair pathway leading to genomic instability. Here, we review the latest findings involving R-loop-mediated DNA damage and defects in neuron-specific DNA repair mechanisms in SMA and discuss these findings in the context of other neurodegenerative disorders linked to DNA damage.
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Affiliation(s)
- Juliana Cuartas
- Center of Emphasis in Neurosciences, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Laxman Gangwani
- Center of Emphasis in Neurosciences, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
- Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
- *Correspondence: Laxman Gangwani
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Ponger P, Kurolap A, Lerer I, Dagan J, Chai Gadot C, Mory A, Wilnai Y, Oniashvili N, Giladi N, Gurevich T, Meiner V, Lossos A, Baris Feldman H. Unique Ataxia-Oculomotor Apraxia 2 (AOA2) in Israel with Novel Variants, Atypical Late Presentation, and Possible Identification of a Poison Exon. J Mol Neurosci 2022; 72:1715-1723. [PMID: 35676594 DOI: 10.1007/s12031-022-02035-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 10/18/2022]
Abstract
AOA2 is a rare progressive adolescent-onset disease characterised by cerebellar vermis atrophy, peripheral neuropathy and elevated serum alpha-fetoprotein (AFP) caused by pathogenic bi-allelic variants in SETX, encoding senataxin, involved in DNA repair and RNA maturation. Sanger sequencing of genomic DNA, co-segregation and oxidative stress functional studies were performed in Family 1. Trio whole-exome sequencing (WES), followed by SETX RNA and qRT-PCR analysis, were performed in Family 2. Sanger sequencing in Family 1 revealed two novel in-frame SETX deletion and duplication variants in trans (c.7009_7011del; p.Val2337del and c.7369_7371dup; p.His2457dup). Patients had increased induced chromosomal aberrations at baseline and following exposure to higher mitomycin-C concentration and increased sensitivity to oxidative stress at the lower mitomycin-C concentration in cell viability test. Trio WES in Family 2 revealed two novel SETX variants in trans, a nonsense variant (c.568C > T; p.Gln190*), and a deep intronic variant (c.5549-107A > G). Intronic variant analysis and SETX mRNA expression revealed activation of a cryptic exon introducing a premature stop codon (p.Met1850Lysfs*18) and resulting in aberrant splicing, as shown by qRT-PCR analysis, thus leading to higher levels of cryptic exon activation. Along with a second deleterious allele, this variant leads to low levels of SETX mRNA and disease manifestations. Our report expands the phenotypic spectrum of AOA2. Results provide initial support for the hypomorphic nature of the novel in-frame deletion and duplication variants in Family 1. Deep-intronic variant analysis of Family 2 variants potentially reveals a previously undescribed poison exon in the SETX gene, which may contribute to tailored therapy development.
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Affiliation(s)
- Penina Ponger
- Movement Disorders Unit, Department of Neurology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel. .,The Genetics Institute and Genomics Center, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel.
| | - Alina Kurolap
- The Genetics Institute and Genomics Center, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Israela Lerer
- Department of Genetics, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Judith Dagan
- Department of Genetics, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Chofit Chai Gadot
- The Genetics Institute and Genomics Center, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Adi Mory
- The Genetics Institute and Genomics Center, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Yael Wilnai
- The Genetics Institute and Genomics Center, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Nino Oniashvili
- Cytogenetic Laboratory, Oncology Department, Schneider Children's Medical Center in Israel, Petah Tikva, Israel
| | - Nir Giladi
- Movement Disorders Unit, Department of Neurology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Tanya Gurevich
- Movement Disorders Unit, Department of Neurology, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Vardiella Meiner
- Department of Genetics, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Alexander Lossos
- Department of Neurology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Hagit Baris Feldman
- The Genetics Institute and Genomics Center, Tel-Aviv Sourasky Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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7
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Molecular Characterization of Portuguese Patients with Hereditary Cerebellar Ataxia. Cells 2022; 11:cells11060981. [PMID: 35326432 PMCID: PMC8946949 DOI: 10.3390/cells11060981] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 01/02/2023] Open
Abstract
Hereditary cerebellar ataxia (HCA) comprises a clinical and genetic heterogeneous group of neurodegenerative disorders characterized by incoordination of movement, speech, and unsteady gait. In this study, we performed whole-exome sequencing (WES) in 19 families with HCA and presumed autosomal recessive (AR) inheritance, to identify the causal genes. A phenotypic classification was performed, considering the main clinical syndromes: spastic ataxia, ataxia and neuropathy, ataxia and oculomotor apraxia (AOA), ataxia and dystonia, and ataxia with cognitive impairment. The most frequent causal genes were associated with spastic ataxia (SACS and KIF1C) and with ataxia and neuropathy or AOA (PNKP). We also identified three families with autosomal dominant (AD) forms arising from de novo variants in KIF1A, CACNA1A, or ATP1A3, reinforcing the importance of differential diagnosis (AR vs. AD forms) in families with only one affected member. Moreover, 10 novel causal-variants were identified, and the detrimental effect of two splice-site variants confirmed through functional assays. Finally, by reviewing the molecular mechanisms, we speculated that regulation of cytoskeleton function might be impaired in spastic ataxia, whereas DNA repair is clearly associated with AOA. In conclusion, our study provided a genetic diagnosis for HCA families and proposed common molecular pathways underlying cerebellar neurodegeneration.
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Kannan A, Cuartas J, Gangwani P, Branzei D, Gangwani L. Mutation in senataxin alters the mechanism of R-loop resolution in amyotrophic lateral sclerosis 4. Brain 2022; 145:3072-3094. [PMID: 35045161 PMCID: PMC9536298 DOI: 10.1093/brain/awab464] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/08/2021] [Accepted: 12/03/2021] [Indexed: 11/22/2022] Open
Abstract
Mutation in the senataxin (SETX) gene causes an autosomal dominant neuromuscular disorder, amyotrophic lateral sclerosis 4 (ALS4), characterized by degeneration of motor neurons, muscle weakness and atrophy. SETX is an RNA-DNA helicase that mediates resolution of co-transcriptional RNA:DNA hybrids (R-loops). The process of R-loop resolution is essential for the normal functioning of cells, including neurons. The molecular basis of ALS4 pathogenesis and the mechanism of R-loop resolution are unclear. We report that the zinc finger protein ZPR1 binds to RNA:DNA hybrids, recruits SETX onto R-loops and is critical for R-loop resolution. ZPR1 deficiency disrupts the integrity of R-loop resolution complexes containing SETX and causes increased R-loop accumulation throughout gene transcription. We uncover that SETX is a downstream target of ZPR1 and that overexpression of ZPR1 can rescue R-loop resolution complexe assembly in SETX-deficient cells but not vice versa. To uncover the mechanism of R-loop resolution, we examined the function of SETX-ZPR1 complexes using two genetic motor neuron disease models with altered R-loop resolution. Notably, chronic low levels of SETX-ZPR1 complexes onto R-loops result in a decrease of R-loop resolution activity causing an increase in R-loop levels in spinal muscular atrophy. ZPR1 overexpression increases recruitment of SETX onto R-loops, decreases R-loops and rescues the spinal muscular atrophy phenotype in motor neurons and patient cells. Strikingly, interaction of SETX with ZPR1 is disrupted in ALS4 patients that have heterozygous SETX (L389S) mutation. ZPR1 fails to recruit the mutant SETX homodimer but recruits the heterodimer with partially disrupted interaction between SETX and ZPR1. Interestingly, disruption of SETX-ZPR1 complexes causes increase in R-loop resolution activity leading to fewer R-loops in ALS4. Modulation of ZPR1 levels regulates R-loop accumulation and rescues the pathogenic R-loop phenotype in ALS4 patient cells. These findings originate a new concept, ‘opposite alterations in a cell biological activity (R-loop resolution) result in similar pathogenesis (neurodegeneration) in different genetic motor neuron disorders’. We propose that ZPR1 collaborates with SETX and may function as a molecular brake to regulate SETX-dependent R-loop resolution activity critical for the normal functioning of motor neurons.
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Affiliation(s)
- Annapoorna Kannan
- Center of Emphasis in Neurosciences, Texas Tech University Health Sciences Center El Paso, El Paso, Texas 79905, USA
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas 79905, USA
| | - Juliana Cuartas
- Center of Emphasis in Neurosciences, Texas Tech University Health Sciences Center El Paso, El Paso, Texas 79905, USA
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas 79905, USA
| | - Pratik Gangwani
- Automated Driving Compute System Architecture, GM Global Technical Center - Sloan Engineering Center, Warren, Michigan 48092, USA
| | - Dana Branzei
- The FIRC Institute of Molecular Oncology Foundation, IFOM Foundation, Via Adamello 16, Milan 20139, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Laxman Gangwani
- Center of Emphasis in Neurosciences, Texas Tech University Health Sciences Center El Paso, El Paso, Texas 79905, USA
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, Texas 79905, USA
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9
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Hadjinicolaou A, Ngo KJ, Conway DY, Provias JP, Baker SK, Brady LI, Bennett CL, La Spada AR, Fogel BL, Yoon G. De novo pathogenic variant in SETX causes a rapidly progressive neurodegenerative disorder of early childhood-onset with severe axonal polyneuropathy. Acta Neuropathol Commun 2021; 9:194. [PMID: 34922620 PMCID: PMC8684165 DOI: 10.1186/s40478-021-01277-5] [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: 09/02/2021] [Accepted: 10/13/2021] [Indexed: 01/01/2023] Open
Abstract
Pathogenic variants in SETX cause two distinct neurological diseases, a loss-of-function recessive disorder, ataxia with oculomotor apraxia type 2 (AOA2), and a dominant gain-of-function motor neuron disorder, amyotrophic lateral sclerosis type 4 (ALS4). We identified two unrelated patients with the same de novo c.23C > T (p.Thr8Met) variant in SETX presenting with an early-onset, severe polyneuropathy. As rare private gene variation is often difficult to link to genetic neurological disease by DNA sequence alone, we used transcriptional network analysis to functionally validate these patients with severe de novo SETX-related neurodegenerative disorder. Weighted gene co-expression network analysis (WGCNA) was used to identify disease-associated modules from two different ALS4 mouse models and compared to confirmed ALS4 patient data to derive an ALS4-specific transcriptional signature. WGCNA of whole blood RNA-sequencing data from a patient with the p.Thr8Met SETX variant was compared to ALS4 and control patients to determine if this signature could be used to identify affected patients. WGCNA identified overlapping disease-associated modules in ALS4 mouse model data and ALS4 patient data. Mouse ALS4 disease-associated modules were not associated with AOA2 disease modules, confirming distinct disease-specific signatures. The expression profile of a patient carrying the c.23C > T (p.Thr8Met) variant was significantly associated with the human and mouse ALS4 signature, confirming the relationship between this SETX variant and disease. The similar clinical presentations of the two unrelated patients with the same de novo p.Thr8Met variant and the functional data provide strong evidence that the p.Thr8Met variant is pathogenic. The distinct phenotype expands the clinical spectrum of SETX-related disorders.
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10
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Uruci S, Lo CSY, Wheeler D, Taneja N. R-Loops and Its Chro-Mates: The Strange Case of Dr. Jekyll and Mr. Hyde. Int J Mol Sci 2021; 22:ijms22168850. [PMID: 34445553 PMCID: PMC8396322 DOI: 10.3390/ijms22168850] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/22/2022] Open
Abstract
Since their discovery, R-loops have been associated with both physiological and pathological functions that are conserved across species. R-loops are a source of replication stress and genome instability, as seen in neurodegenerative disorders and cancer. In response, cells have evolved pathways to prevent R-loop accumulation as well as to resolve them. A growing body of evidence correlates R-loop accumulation with changes in the epigenetic landscape. However, the role of chromatin modification and remodeling in R-loops homeostasis remains unclear. This review covers various mechanisms precluding R-loop accumulation and highlights the role of chromatin modifiers and remodelers in facilitating timely R-loop resolution. We also discuss the enigmatic role of RNA:DNA hybrids in facilitating DNA repair, epigenetic landscape and the potential role of replication fork preservation pathways, active fork stability and stalled fork protection pathways, in avoiding replication-transcription conflicts. Finally, we discuss the potential role of several Chro-Mates (chromatin modifiers and remodelers) in the likely differentiation between persistent/detrimental R-loops and transient/benign R-loops that assist in various physiological processes relevant for therapeutic interventions.
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Affiliation(s)
- Sidrit Uruci
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - Calvin Shun Yu Lo
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA;
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
- Correspondence:
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11
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Ramachandran S, Ma TS, Griffin J, Ng N, Foskolou IP, Hwang MS, Victori P, Cheng WC, Buffa FM, Leszczynska KB, El-Khamisy SF, Gromak N, Hammond EM. Hypoxia-induced SETX links replication stress with the unfolded protein response. Nat Commun 2021; 12:3686. [PMID: 34140498 PMCID: PMC8211819 DOI: 10.1038/s41467-021-24066-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/31/2021] [Indexed: 02/07/2023] Open
Abstract
Tumour hypoxia is associated with poor patient prognosis and therapy resistance. A unique transcriptional response is initiated by hypoxia which includes the rapid activation of numerous transcription factors in a background of reduced global transcription. Here, we show that the biological response to hypoxia includes the accumulation of R-loops and the induction of the RNA/DNA helicase SETX. In the absence of hypoxia-induced SETX, R-loop levels increase, DNA damage accumulates, and DNA replication rates decrease. Therefore, suggesting that, SETX plays a role in protecting cells from DNA damage induced during transcription in hypoxia. Importantly, we propose that the mechanism of SETX induction in hypoxia is reliant on the PERK/ATF4 arm of the unfolded protein response. These data not only highlight the unique cellular response to hypoxia, which includes both a replication stress-dependent DNA damage response and an unfolded protein response but uncover a novel link between these two distinct pathways.
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Affiliation(s)
- Shaliny Ramachandran
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Tiffany S Ma
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Jon Griffin
- Department of Molecular Biology and Biotechnology, Healthy Lifespan and Neuroscience Institute, Firth Court, University of Sheffield, Sheffield, UK
- Department of Histopathology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Natalie Ng
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Iosifina P Foskolou
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Ming-Shih Hwang
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Pedro Victori
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Wei-Chen Cheng
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Francesca M Buffa
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Katarzyna B Leszczynska
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
- Laboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Sherif F El-Khamisy
- Department of Molecular Biology and Biotechnology, Healthy Lifespan and Neuroscience Institute, Firth Court, University of Sheffield, Sheffield, UK
- Institute of Cancer Therapeutics, University of Bradford, Bradford, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ester M Hammond
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK.
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12
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Kajitani GS, Nascimento LLDS, Neves MRDC, Leandro GDS, Garcia CCM, Menck CFM. Transcription blockage by DNA damage in nucleotide excision repair-related neurological dysfunctions. Semin Cell Dev Biol 2021; 114:20-35. [DOI: 10.1016/j.semcdb.2020.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 08/18/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
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13
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Richard P, Feng S, Tsai YL, Li W, Rinchetti P, Muhith U, Irizarry-Cole J, Stolz K, Sanz LA, Hartono S, Hoque M, Tadesse S, Seitz H, Lotti F, Hirano M, Chédin F, Tian B, Manley JL. SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation. Autophagy 2020; 17:1889-1906. [PMID: 32686621 DOI: 10.1080/15548627.2020.1796292] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
SETX (senataxin) is an RNA/DNA helicase that has been implicated in transcriptional regulation and the DNA damage response through resolution of R-loop structures. Mutations in SETX result in either of two distinct neurodegenerative disorders. SETX dominant mutations result in a juvenile form of amyotrophic lateral sclerosis (ALS) called ALS4, whereas recessive mutations are responsible for ataxia called ataxia with oculomotor apraxia type 2 (AOA2). How mutations in the same protein can lead to different phenotypes is still unclear. To elucidate AOA2 disease mechanisms, we first examined gene expression changes following SETX depletion. We observed the effects on both transcription and RNA processing, but surprisingly observed decreased R-loop accumulation in SETX-depleted cells. Importantly, we discovered a strong connection between SETX and the macroautophagy/autophagy pathway, reflecting a direct effect on transcription of autophagy genes. We show that SETX depletion inhibits the progression of autophagy, leading to an accumulation of ubiquitinated proteins, decreased ability to clear protein aggregates, as well as mitochondrial defects. Analysis of AOA2 patient fibroblasts also revealed a perturbation of the autophagy pathway. Our work has thus identified a novel function for SETX in the regulation of autophagy, whose modulation may have a therapeutic impact for AOA2.Abbreviations: 3'READS: 3' region extraction and deep sequencing; ACTB: actin beta; ALS4: amyotrophic lateral sclerosis type 4; AOA2: ataxia with oculomotor apraxia type 2; APA: alternative polyadenylation; AS: alternative splicing; ATG7: autophagy-related 7; ATP6V0D2: ATPase H+ transporting V0 subunit D2; BAF: bafilomycin A1; BECN1: beclin 1; ChIP: chromatin IP; Chloro: chloroquine; CPT: camptothecin; DDR: DNA damage response; DNMT1: DNA methyltransferase 1; DRIP: DNA/RNA IP; DSBs: double strand breaks; EBs: embryoid bodies; FTD: frontotemporal dementia; GABARAP: GABA type A receptor-associated protein; GO: gene ontology; HR: homologous recombination; HTT: huntingtin; IF: immunofluorescence; IP: immunoprecipitation; iPSCs: induced pluripotent stem cells; KD: knockdown; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MN: motor neuron; MTORC1: mechanistic target of rapamycin kinase complex 1; PASS: PolyA Site Supporting; PFA: paraformaldehyde; RNAPII: RNA polymerase II; SCA: spinocerebellar ataxia; SETX: senataxin; SMA: spinal muscular atrophy; SMN1: survival of motor neuron 1, telomeric; SQSTM1/p62: sequestosome 1; TFEB: transcription factor EB; TSS: transcription start site; TTS: transcription termination site; ULK1: unc-51 like autophagy activating kinase 1; WB: western blot; WIPI2: WD repeat domain, phosphoinositide interacting 2; XRN2: 5'-3' exoribonuclease 2.
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Affiliation(s)
- Patricia Richard
- Department of Biological Sciences, Columbia University, New York, NY, USA.,Stellate Therapeutics, JLABS @ NYC, New York, NY, USA
| | | | - Yueh-Lin Tsai
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Wencheng Li
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Paola Rinchetti
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.,Dino Ferrari Centre, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
| | - Ubayed Muhith
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Juan Irizarry-Cole
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Katharine Stolz
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Lionel A Sanz
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Stella Hartono
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Mainul Hoque
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Saba Tadesse
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Hervé Seitz
- Institut de Génétique Humaine, UMR 9002 CNRS and Université de Montpellier, Montpellier, France
| | - Francesco Lotti
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Michio Hirano
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, University of California, Davis, CA, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA.,Gene Expression and Regulation Program, and Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY, USA
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14
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Protective Mechanisms Against DNA Replication Stress in the Nervous System. Genes (Basel) 2020; 11:genes11070730. [PMID: 32630049 PMCID: PMC7397197 DOI: 10.3390/genes11070730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
The precise replication of DNA and the successful segregation of chromosomes are essential for the faithful transmission of genetic information during the cell cycle. Alterations in the dynamics of genome replication, also referred to as DNA replication stress, may lead to DNA damage and, consequently, mutations and chromosomal rearrangements. Extensive research has revealed that DNA replication stress drives genome instability during tumorigenesis. Over decades, genetic studies of inherited syndromes have established a connection between the mutations in genes required for proper DNA repair/DNA damage responses and neurological diseases. It is becoming clear that both the prevention and the responses to replication stress are particularly important for nervous system development and function. The accurate regulation of cell proliferation is key for the expansion of progenitor pools during central nervous system (CNS) development, adult neurogenesis, and regeneration. Moreover, DNA replication stress in glial cells regulates CNS tumorigenesis and plays a role in neurodegenerative diseases such as ataxia telangiectasia (A-T). Here, we review how replication stress generation and replication stress response (RSR) contribute to the CNS development, homeostasis, and disease. Both cell-autonomous mechanisms, as well as the evidence of RSR-mediated alterations of the cellular microenvironment in the nervous system, were discussed.
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15
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Brambati A, Zardoni L, Nardini E, Pellicioli A, Liberi G. The dark side of RNA:DNA hybrids. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 784:108300. [PMID: 32430097 DOI: 10.1016/j.mrrev.2020.108300] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/07/2020] [Accepted: 02/23/2020] [Indexed: 12/15/2022]
Abstract
RNA:DNA hybrids form when nascent transcripts anneal to the DNA template strand or any homologous DNA region. Co-transcriptional RNA:DNA hybrids, organized in R-loop structures together with the displaced non-transcribed strand, assist gene expression, DNA repair and other physiological cellular functions. A dark side of the matter is that RNA:DNA hybrids are also a cause of DNA damage and human diseases. In this review, we summarize recent advances in the understanding of the mechanisms by which the impairment of hybrid turnover promotes DNA damage and genome instability via the interference with DNA replication and DNA double-strand break repair. We also discuss how hybrids could contribute to cancer, neurodegeneration and susceptibility to viral infections, focusing on dysfunctions associated with the anti-R-loop helicase Senataxin.
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Affiliation(s)
- Alessandra Brambati
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy.
| | - Luca Zardoni
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy; Scuola Universitaria Superiore, IUSS, 27100, Pavia, Italy
| | - Eleonora Nardini
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Achille Pellicioli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Giordano Liberi
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy; IFOM Foundation, Via Adamello 16, 20139, Milan, Italy.
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16
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Disruption of Spermatogenesis and Infertility in Ataxia with Oculomotor Apraxia Type 2 (AOA2). THE CEREBELLUM 2019; 18:448-456. [PMID: 30778901 DOI: 10.1007/s12311-019-01012-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ataxia with oculomotor apraxia type 2 (AOA2) is a rare autosomal recessive cerebellar ataxia characterized by onset between 10 and 20 years of age and a range of neurological features that include progressive cerebellar atrophy, axonal sensorimotor neuropathy, oculomotor apraxia in a majority of patients, and elevated serum alpha-fetoprotein (AFP). AOA2 is caused by mutation of the SETX gene which encodes senataxin, a DNA/RNA helicase involved in transcription regulation, RNA processing, and DNA maintenance. Disruption of senataxin in rodents led to defective spermatogenesis and sterility in males uncovering a key role for senataxin in male germ cell survival. Here, we report the first clinical and cellular evidence of impaired spermatogenesis in AOA2 patients. We assessed sperm production in three AOA2 patients and testicular pathology in one patient and compared the findings to those of Setx-knockout mice. Sperm production was impaired in all patients assessed (3/3, 100%). Analyses of testicular biopsies from an AOA2 patient recapitulate features of the histology seen in Setx-knockout mice, strongly suggesting an underlying mechanism centering on DNA-damage-mediated germ cell apoptosis. These findings support a role for senataxin in human reproductive function and highlight a novel clinical feature of AOA2 that extends the extra-neurological roles of senataxin. This raises an important reproductive counseling issue for clinicians, and fertility specialists should be aware of SETX mutations as a possible diagnosis in young male patients presenting with oligospermia or azoospermia since infertility may presage the later onset of neurological manifestations in some individuals.
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17
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Beaudin M, Matilla-Dueñas A, Soong BW, Pedroso JL, Barsottini OG, Mitoma H, Tsuji S, Schmahmann JD, Manto M, Rouleau GA, Klein C, Dupre N. The Classification of Autosomal Recessive Cerebellar Ataxias: a Consensus Statement from the Society for Research on the Cerebellum and Ataxias Task Force. CEREBELLUM (LONDON, ENGLAND) 2019; 18:1098-1125. [PMID: 31267374 PMCID: PMC6867988 DOI: 10.1007/s12311-019-01052-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There is currently no accepted classification of autosomal recessive cerebellar ataxias, a group of disorders characterized by important genetic heterogeneity and complex phenotypes. The objective of this task force was to build a consensus on the classification of autosomal recessive ataxias in order to develop a general approach to a patient presenting with ataxia, organize disorders according to clinical presentation, and define this field of research by identifying common pathogenic molecular mechanisms in these disorders. The work of this task force was based on a previously published systematic scoping review of the literature that identified autosomal recessive disorders characterized primarily by cerebellar motor dysfunction and cerebellar degeneration. The task force regrouped 12 international ataxia experts who decided on general orientation and specific issues. We identified 59 disorders that are classified as primary autosomal recessive cerebellar ataxias. For each of these disorders, we present geographical and ethnical specificities along with distinctive clinical and imagery features. These primary recessive ataxias were organized in a clinical and a pathophysiological classification, and we present a general clinical approach to the patient presenting with ataxia. We also identified a list of 48 complex multisystem disorders that are associated with ataxia and should be included in the differential diagnosis of autosomal recessive ataxias. This classification is the result of a consensus among a panel of international experts, and it promotes a unified understanding of autosomal recessive cerebellar disorders for clinicians and researchers.
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Affiliation(s)
- Marie Beaudin
- Axe Neurosciences, CHU de Québec-Université Laval, Québec, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, QC, Canada
| | - Antoni Matilla-Dueñas
- Department of Neuroscience, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona, Badalona, Barcelona, Spain
| | - Bing-Weng Soong
- Department of Neurology, Shuang Ho Hospital and Taipei Neuroscience Institute, Taipei Medical University, Taipei, Taiwan, Republic of China
- National Yang-Ming University School of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, Republic of China
| | - Jose Luiz Pedroso
- Ataxia Unit, Department of Neurology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Orlando G Barsottini
- Ataxia Unit, Department of Neurology, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Hiroshi Mitoma
- Medical Education Promotion Center, Tokyo Medical University, Tokyo, Japan
| | - Shoji Tsuji
- The University of Tokyo, Tokyo, Japan
- International University of Health and Welfare, Chiba, Japan
| | - Jeremy D Schmahmann
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mario Manto
- Service de Neurologie, Médiathèque Jean Jacquy, CHU-Charleroi, 6000, Charleroi, Belgium
- Service des Neurosciences, UMons, Mons, Belgium
| | | | | | - Nicolas Dupre
- Axe Neurosciences, CHU de Québec-Université Laval, Québec, QC, Canada.
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, QC, Canada.
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18
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Paucar M, Taylor AMR, Hadjivassiliou M, Fogel BL, Svenningsson P. Progressive Ataxia with Elevated Alpha-Fetoprotein: Diagnostic Issues and Review of the Literature. TREMOR AND OTHER HYPERKINETIC MOVEMENTS (NEW YORK, N.Y.) 2019; 9:tre-09-708. [PMID: 31656689 PMCID: PMC6790008 DOI: 10.7916/tohm.v0.708] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/13/2019] [Indexed: 12/23/2022]
Abstract
Background Ataxias represent a challenging group of disorders due to significant clinical overlap. Here, we present a patient with early-onset progressive ataxia, polyneuropathy and discuss how elevation of alpha fetoprotein (AFP) narrows the differential diagnosis. Case report Ataxia, polyneuropathy, and mild elevation of AFP are features compatible with ataxia with oculomotor apraxia type 2 (AOA2) but also with ataxia with oculomotor apraxia type 4 (AOA4). A genetic analysis demonstrated biallelic mutations in senataxin (SETX), confirming the diagnosis of AOA2. Discussion Mild elevation of AFP is found in patients with AOA2 and AOA4, and higher levels are commonly seen in ataxia-telangiectasia. AFP is a useful diagnostic tool but not a biomarker for disease progression in AOA2.
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Affiliation(s)
- Martin Paucar
- Department of Neurology, Karolinska University Hospital, Stockholm, SE.,Department of Clinical Neuroscience, Karolinska Institute, Stockholm, SE
| | - Alexander M R Taylor
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Brent L Fogel
- Department of Neurology, UCLA Program in Neurogenetics, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, CA, USA
| | - Per Svenningsson
- Department of Neurology, Karolinska University Hospital, Stockholm, SE.,Department of Clinical Neuroscience, Karolinska Institute, Stockholm, SE
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19
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Kannan A, Bhatia K, Branzei D, Gangwani L. Combined deficiency of Senataxin and DNA-PKcs causes DNA damage accumulation and neurodegeneration in spinal muscular atrophy. Nucleic Acids Res 2019; 46:8326-8346. [PMID: 30010942 PMCID: PMC6144794 DOI: 10.1093/nar/gky641] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/05/2018] [Indexed: 12/12/2022] Open
Abstract
Chronic low levels of survival motor neuron (SMN) protein cause spinal muscular atrophy (SMA). SMN is ubiquitously expressed, but the mechanisms underlying predominant neuron degeneration in SMA are poorly understood. We report that chronic low levels of SMN cause Senataxin (SETX)-deficiency, which results in increased RNA–DNA hybrids (R-loops) and DNA double-strand breaks (DSBs), and deficiency of DNA-activated protein kinase-catalytic subunit (DNA-PKcs), which impairs DSB repair. Consequently, DNA damage accumulates in patient cells, SMA mice neurons and patient spinal cord tissues. In dividing cells, DSBs are repaired by homologous recombination (HR) and non-homologous end joining (NHEJ) pathways, but neurons predominantly use NHEJ, which relies on DNA-PKcs activity. In SMA dividing cells, HR repairs DSBs and supports cellular proliferation. In SMA neurons, DNA-PKcs-deficiency causes defects in NHEJ-mediated repair leading to DNA damage accumulation and neurodegeneration. Restoration of SMN levels rescues SETX and DNA-PKcs deficiencies and DSB accumulation in SMA neurons and patient cells. Moreover, SETX overexpression in SMA neurons reduces R-loops and DNA damage, and rescues neurodegeneration. Our findings identify combined deficiency of SETX and DNA-PKcs stemming downstream of SMN as an underlying cause of DSBs accumulation, genomic instability and neurodegeneration in SMA and suggest SETX as a potential therapeutic target for SMA.
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Affiliation(s)
- Annapoorna Kannan
- Center of Emphasis in Neurosciences, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905.,Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905
| | - Kanchan Bhatia
- Center of Emphasis in Neurosciences, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905.,Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905
| | - Dana Branzei
- The FIRC Institute of Molecular Oncology Foundation, IFOM Foundation, Via Adamello 16, Milan 20139, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Via Abbiategrasso 207, Pavia 27100, Italy
| | - Laxman Gangwani
- Center of Emphasis in Neurosciences, Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905.,Department of Biomedical Sciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905.,Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA
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20
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Gentile F, Scarlino S, Falzone YM, Lunetta C, Tremolizzo L, Quattrini A, Riva N. The Peripheral Nervous System in Amyotrophic Lateral Sclerosis: Opportunities for Translational Research. Front Neurosci 2019; 13:601. [PMID: 31293369 PMCID: PMC6603245 DOI: 10.3389/fnins.2019.00601] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/27/2019] [Indexed: 12/11/2022] Open
Abstract
Although amyotrophic lateral sclerosis (ALS) has been considered as a disorder of the motor neuron (MN) cell body, recent evidences show the non-cell-autonomous pathogenic nature of the disease. Axonal degeneration, loss of peripheral axons and destruction of nerve terminals are early events in the disease pathogenic cascade, anticipating MN degeneration, and the onset of clinical symptoms. Therefore, although ALS and peripheral axonal neuropathies should be differentiated in clinical practice, they also share damage to common molecular pathways, including axonal transport, RNA metabolism and proteostasis. Thus, an extensive evaluation of the molecular events occurring in the peripheral nervous system (PNS) could be fundamental to understand the pathogenic mechanisms of ALS, favoring the discovery of potential disease biomarkers, and new therapeutic targets.
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Affiliation(s)
- Francesco Gentile
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology - San Raffaele Scientific Institute, Milan, Italy
| | - Stefania Scarlino
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology - San Raffaele Scientific Institute, Milan, Italy
| | - Yuri Matteo Falzone
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology - San Raffaele Scientific Institute, Milan, Italy.,Department of Neurology, San Raffaele Scientific Institute, Milan, Italy
| | | | - Lucio Tremolizzo
- Neurology Unit, ALS Clinic, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Angelo Quattrini
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology - San Raffaele Scientific Institute, Milan, Italy
| | - Nilo Riva
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology - San Raffaele Scientific Institute, Milan, Italy.,Department of Neurology, San Raffaele Scientific Institute, Milan, Italy
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21
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Algahtani H, Shirah B, Algahtani R, Naseer MI, Al-Qahtani MH, Abdulkareem AA. Ataxia with ocular apraxia type 2 not responding to 4-aminopyridine: A rare mutation in the SETX gene in a Saudi patient. Intractable Rare Dis Res 2018; 7:275-279. [PMID: 30560021 PMCID: PMC6290838 DOI: 10.5582/irdr.2018.01107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Ataxia with ocular apraxia type 2 is an autosomal recessive disorder caused by a mutation in the senataxin (SETX) gene. The disease is characterized by early onset cerebellar ataxia, cerebellar atrophy, axonal sensorimotor neuropathy, oculomotor apraxia, and increased levels of α-fetoprotein. Reported here is a rare homozygous frameshift deletion c.5308_5311del, p.(Glu1770Ilefs*15) in the SETX gene in a Saudi family. Ataxia with ocular apraxia type 2 was diagnosed based on the patient's history, an examination, and genetic testing. Genetic testing remains the only definitive method with which to identify the gene responsible. This is the third case report of this rare mutation in the literature. Ataxia with ocular apraxia type 2 continues to be a challenging disease to manage with no therapeutic options available to date. In the current case, the medication 4-aminopyridine was inefficacious in improving walking or balance. Further research is needed to identify potential treatments for this challenging condition.
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Affiliation(s)
- Hussein Algahtani
- King Abdulaziz Medical City, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- Address correspondence to:Dr. Hussein Algahtani, King Abdulaziz Medical City, King Saud bin Abdulaziz University for Health Sciences, Contact No.: 00966556633130. P.O. Box: 12723, Jeddah, Saudi Arabia 21483. E-mail:
| | - Bader Shirah
- King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Raghad Algahtani
- King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad H. Al-Qahtani
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
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22
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Tariq H, Imran R, Naz S. A Novel Homozygous Variant of SETX Causes Ataxia with Oculomotor Apraxia Type 2. J Clin Neurol 2018; 14:498-504. [PMID: 30198223 PMCID: PMC6172491 DOI: 10.3988/jcn.2018.14.4.498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 01/21/2023] Open
Abstract
Background and Purpose Autosomal recessive cerebellar ataxias constitute a highly heterogeneous group of neurodegenerative disorders. This study was carried out to determine the clinical and genetic causes of ataxia in two families from Pakistan. Methods Detailed clinical investigations were carried out on probands in two consanguineous families. Magnetic resonance imaging was performed. Exome sequencing data were examined for likely pathogenic variants. Candidate variants were checked for cosegregation with the phenotype using Sanger sequencing. Public databases including ExAC, GnomAD, dbSNP, and the 1,000 Genome Project as well as ethnically matched controls were checked to determine the frequencies of the alleles. Conservation of missense variants was ensured by aligning orthologous protein sequences from diverse vertebrate species. Results Reverse phenotyping identified spinocerebellar ataxia, autosomal recessive 1 [OMIM 606002, also referred to as ataxia oculomotor apraxia type 2 (AOA2)] and ataxia telangiectasia (OMIM 208900) in the two families. A novel homozygous missense mutation c.202 C>T (p.Arg68Cys) was identified within senataxin, SETX in the DNA of both patients in one of the families with AOA2. The patients in the second family were homozygous for a known variant in ataxia-telangiectasia mutated (ATM) gene: c.7327 C>T (p.Arg2443Ter). Both variants were absent from 100 ethnically matched control chromosomes and were either absent or present at very low frequencies in the public databases. Conclusions This report extends the allelic heterogeneity of SETX mutations causing AOA2 and also presents an asymptomatic patient with a pathogenic ATM variant.
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Affiliation(s)
- Huma Tariq
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Rashid Imran
- Punjab Institute of Neurosciences, Lahore General Hospital, Lahore, Pakistan
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.
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23
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Zhang Q, Ma C, Gearing M, Wang PG, Chin LS, Li L. Integrated proteomics and network analysis identifies protein hubs and network alterations in Alzheimer's disease. Acta Neuropathol Commun 2018; 6:19. [PMID: 29490708 PMCID: PMC5831854 DOI: 10.1186/s40478-018-0524-2] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 02/22/2018] [Indexed: 12/12/2022] Open
Abstract
Although the genetic causes for several rare, familial forms of Alzheimer’s disease (AD) have been identified, the etiology of the sporadic form of AD remains unclear. Here, we report a systems-level study of disease-associated proteome changes in human frontal cortex of sporadic AD patients using an integrated approach that combines mass spectrometry-based quantitative proteomics, differential expression analysis, and co-expression network analysis. Our analyses of 16 human brain tissues from AD patients and age-matched controls showed organization of the cortical proteome into a network of 24 biologically meaningful modules of co-expressed proteins. Of these, 5 modules are positively correlated to AD phenotypes with hub proteins that are up-regulated in AD, and 6 modules are negatively correlated to AD phenotypes with hub proteins that are down-regulated in AD. Our study generated a molecular blueprint of altered protein networks in AD brain and uncovered the dysregulation of multiple pathways and processes in AD brain, including altered proteostasis, RNA homeostasis, immune response, neuroinflammation, synaptic transmission, vesicular transport, cell signaling, cellular metabolism, lipid homeostasis, mitochondrial dynamics and function, cytoskeleton organization, and myelin-axon interactions. Our findings provide new insights into AD pathogenesis and suggest novel candidates for future diagnostic and therapeutic development.
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Abstract
The autosomal-recessive cerebellar ataxias comprise more than half of the known genetic forms of ataxia and represent an extensive group of clinically heterogeneous disorders that can occur at any age but whose onset is typically prior to adulthood. In addition to ataxia, patients often present with polyneuropathy and clinical symptoms outside the nervous system. The most common of these diseases is Friedreich ataxia, caused by mutation of the frataxin gene, but recent advances in genetic analysis have greatly broadened the ever-expanding number of causative genes to over 50. In this review, the clinical neurogenetics of the recessive cerebellar ataxias will be discussed, including updates on recently identified novel ataxia genes, advancements in unraveling disease-specific molecular pathogenesis leading to ataxia, potential treatments under development, technologic improvements in diagnostic testing such as clinical exome sequencing, and what the future holds for clinicians and geneticists.
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Affiliation(s)
- Brent L Fogel
- Program in Neurogenetics, Departments of Neurology and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, United States.
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25
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Choudry TN, Hilton-Jones D, Lennox G, Houlden H. Ataxia with oculomotor apraxia type 2: an evolving axonal neuropathy. Pract Neurol 2017; 18:52-56. [PMID: 29212862 DOI: 10.1136/practneurol-2017-001711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2017] [Indexed: 11/04/2022]
Abstract
A 23-year-old woman had presented initially to a podiatrist complaining of poorly fitting shoes during her adolescence. After extensive neurological review, she was diagnosed with ataxia with oculomotor apraxia type 2. This is a progressive autosomal recessive ataxia associated with cerebellar atrophy, peripheral neuropathy and an elevated serum α-fetoprotein. Within Europe, it is the most frequent autosomal recessive ataxia after Friedreich's ataxia and is due to mutations in the senataxin (SETX) gene. The age of onset is approximately 15 years.The diagnosis of oculomotor apraxia type 2 is often challenging. We provide a framework for assessing a young ataxic patient with or without oculomotor apraxia and review clues that will aid diagnosis. The prognosis, level of disability, cancer and immunosuppression risk all markedly differ between the conditions. Patients and their families need the correct diagnosis for genetic counselling, management and long-term surveillance with appropriate subspecialty services.
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Affiliation(s)
| | | | - Graham Lennox
- Department of Neurology, John Radcliffe Hospital, Oxford, UK
| | - Henry Houlden
- Reta Lila Weston Laboratories and Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
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26
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Pflieger LT, Dansithong W, Paul S, Scoles DR, Figueroa KP, Meera P, Otis TS, Facelli JC, Pulst SM. Gene co-expression network analysis for identifying modules and functionally enriched pathways in SCA2. Hum Mol Genet 2017; 26:3069-3080. [PMID: 28525545 PMCID: PMC5886232 DOI: 10.1093/hmg/ddx191] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/22/2017] [Accepted: 05/11/2017] [Indexed: 12/22/2022] Open
Abstract
Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disease caused by CAG repeat expansion in the ATXN2 gene. The repeat resides in an encoded region of the gene resulting in polyglutamine (polyQ) expansion which has been assumed to result in gain of function, predominantly, for the ATXN2 protein. We evaluated temporal cerebellar expression profiles by RNA sequencing of ATXN2Q127 mice versus wild-type (WT) littermates. ATXN2Q127 mice are characterized by a progressive motor phenotype onset, and have progressive cerebellar molecular and neurophysiological (Purkinje cell firing frequency) phenotypes. Our analysis revealed previously uncharacterized early and progressive abnormal patterning of cerebellar gene expression. Weighted Gene Coexpression Network Analysis revealed four gene modules that were significantly correlated with disease status, composed primarily of genes associated with GTPase signaling, calcium signaling and cell death. Of these genes, few overlapped with differentially expressed cerebellar genes that we identified in Atxn2-/- knockout mice versus WT littermates, suggesting that loss-of-function is not a significant component of disease pathology. We conclude that SCA2 is a disease characterized by gain of function for ATXN2.
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Affiliation(s)
| | - Warunee Dansithong
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Sharan Paul
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Daniel R. Scoles
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Karla P. Figueroa
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
| | - Pratap Meera
- Department of Neurobiology, University of California Los Angeles, Los Angeles, CA, USA
| | - Thomas S. Otis
- Department of Neurobiology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Stefan M. Pulst
- Department of Neurology, University of Utah, Salt Lake City, UT 84112, USA
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Choudhury SD, Vs A, Mushtaq Z, Kumar V. Altered translational repression of an RNA-binding protein, Elav by AOA2-causative Senataxin mutation. Synapse 2017; 71. [PMID: 28245518 DOI: 10.1002/syn.21969] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 02/20/2017] [Accepted: 02/22/2017] [Indexed: 11/09/2022]
Abstract
Mutations in Senataxin (SETX) gene causes two types of neurological disorders, Amyotrophic Lateral Sclerosis (ALS4) and Ataxia with Oculomotor Apraxia type 2 (AOA2). Recent studies in cultured cells suggest that SETX plays a crucial role at the interface of transcription and the DNA damage response. Whether SETX can alter translational of specific RNA is not known. In this study, we report that expressing AOA2-causative truncated form of human SETX in Drosophila neurons alters the development of neuromuscular junction (NMJ) synapses. Interestingly, we found that expressing this truncated form of SETX in Drosophila muscles resulted in an alteration of translational repression of an RNA-binding protein, Embryonic Lethal Abnormal Vision (Elav). Elav is transcribed in all tissues but remains translationally repressed except in neurons. Thus, our data suggest that an altered repression profile of RNA by SETX mutants could be one of the mechanisms underlying ALS4 or AOA2 pathogenesis.
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Affiliation(s)
- Saumitra Dey Choudhury
- Department of Biological Sciences, Laboratory of Neurogenetics, Indian Institute of Science Education and Research (IISER) Bhopal, Bhouri, Bhopal, Madhya Pradesh, India, 462 066
| | - Ancy Vs
- Department of Biological Sciences, Laboratory of Neurogenetics, Indian Institute of Science Education and Research (IISER) Bhopal, Bhouri, Bhopal, Madhya Pradesh, India, 462 066
| | - Zeeshan Mushtaq
- Department of Biological Sciences, Laboratory of Neurogenetics, Indian Institute of Science Education and Research (IISER) Bhopal, Bhouri, Bhopal, Madhya Pradesh, India, 462 066
| | - Vimlesh Kumar
- Department of Biological Sciences, Laboratory of Neurogenetics, Indian Institute of Science Education and Research (IISER) Bhopal, Bhouri, Bhopal, Madhya Pradesh, India, 462 066
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28
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Groh M, Albulescu LO, Cristini A, Gromak N. Senataxin: Genome Guardian at the Interface of Transcription and Neurodegeneration. J Mol Biol 2016; 429:3181-3195. [PMID: 27771483 DOI: 10.1016/j.jmb.2016.10.021] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/14/2016] [Accepted: 10/15/2016] [Indexed: 12/12/2022]
Abstract
R-loops comprise an RNA/DNA hybrid and a displaced single-stranded DNA. They play crucial biological functions and are implicated in neurological diseases, including ataxias, amyotrophic lateral sclerosis, nucleotide expansion disorders (Friedreich ataxia and fragile X syndrome), and cancer. Currently, it is unclear which mechanisms cause R-loop structures to become pathogenic. The RNA/DNA helicase senataxin (SETX) is one of the best characterised R-loop-binding factors in vivo. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). SETX is known to play a role in transcription, neurogenesis, and antiviral response. Here, we review the causes of R-loop dysregulation in neurodegenerative diseases and how these structures contribute to pathomechanisms. We will discuss the importance of SETX as a genome guardian in suppressing aberrant R-loop formation and analyse how SETX mutations can lead to neurodegeneration in AOA2/ALS4. Finally, we will discuss the implications for other R-loop-associated neurodegenerative diseases and point to future therapeutic approaches to treat these disorders.
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Affiliation(s)
- Matthias Groh
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK
| | - Laura Oana Albulescu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK
| | - Agnese Cristini
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK.
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29
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Ring KL, An MC, Zhang N, O'Brien RN, Ramos EM, Gao F, Atwood R, Bailus BJ, Melov S, Mooney SD, Coppola G, Ellerby LM. Genomic Analysis Reveals Disruption of Striatal Neuronal Development and Therapeutic Targets in Human Huntington's Disease Neural Stem Cells. Stem Cell Reports 2016; 5:1023-1038. [PMID: 26651603 PMCID: PMC4682390 DOI: 10.1016/j.stemcr.2015.11.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 11/02/2015] [Accepted: 11/12/2015] [Indexed: 12/29/2022] Open
Abstract
We utilized induced pluripotent stem cells (iPSCs) derived from Huntington's disease (HD) patients as a human model of HD and determined that the disease phenotypes only manifest in the differentiated neural stem cell (NSC) stage, not in iPSCs. To understand the molecular basis for the CAG repeat expansion-dependent disease phenotypes in NSCs, we performed transcriptomic analysis of HD iPSCs and HD NSCs compared to isogenic controls. Differential gene expression and pathway analysis pointed to transforming growth factor β (TGF-β) and netrin-1 as the top dysregulated pathways. Using data-driven gene coexpression network analysis, we identified seven distinct coexpression modules and focused on two that were correlated with changes in gene expression due to the CAG expansion. Our HD NSC model revealed the dysregulation of genes involved in neuronal development and the formation of the dorsal striatum. The striatal and neuronal networks disrupted could be modulated to correct HD phenotypes and provide therapeutic targets.
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Affiliation(s)
- Karen L Ring
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Mahru C An
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Ningzhe Zhang
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | | | - Eliana Marisa Ramos
- Departments of Neurology and Psychiatry, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Fuying Gao
- Departments of Neurology and Psychiatry, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Robert Atwood
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | | | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Sean D Mooney
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Giovanni Coppola
- Departments of Neurology and Psychiatry, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Lisa M Ellerby
- Buck Institute for Research on Aging, Novato, CA 94945, USA.
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30
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Kozela E, Juknat A, Gao F, Kaushansky N, Coppola G, Vogel Z. Pathways and gene networks mediating the regulatory effects of cannabidiol, a nonpsychoactive cannabinoid, in autoimmune T cells. J Neuroinflammation 2016; 13:136. [PMID: 27256343 PMCID: PMC4891926 DOI: 10.1186/s12974-016-0603-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/27/2016] [Indexed: 11/29/2022] Open
Abstract
Background Our previous studies showed that the non-psychoactive cannabinoid, cannabidiol (CBD), ameliorates the clinical symptoms in mouse myelin oligodendrocyte glycoprotein (MOG)35-55-induced experimental autoimmune encephalomyelitis model of multiple sclerosis (MS) as well as decreases the memory MOG35-55-specific T cell (TMOG) proliferation and cytokine secretion including IL-17, a key autoimmune factor. The mechanisms of these activities are currently poorly understood. Methods Herein, using microarray-based gene expression profiling, we describe gene networks and intracellular pathways involved in CBD-induced suppression of these activated memory TMOG cells. Encephalitogenic TMOG cells were stimulated with MOG35-55 in the presence of spleen-derived antigen presenting cells (APC) with or without CBD. mRNA of purified TMOG was then subjected to Illumina microarray analysis followed by ingenuity pathway analysis (IPA), weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) elucidation of gene interactions. Results were validated using qPCR and ELISA assays. Results Gene profiling showed that the CBD treatment suppresses the transcription of a large number of proinflammatory genes in activated TMOG. These include cytokines (Xcl1, Il3, Il12a, Il1b), cytokine receptors (Cxcr1, Ifngr1), transcription factors (Ier3, Atf3, Nr4a3, Crem), and TNF superfamily signaling molecules (Tnfsf11, Tnfsf14, Tnfrsf9, Tnfrsf18). “IL-17 differentiation” and “IL-6 and IL-10-signaling” were identified among the top processes affected by CBD. CBD increases a number of IFN-dependent transcripts (Rgs16, Mx2, Rsad2, Irf4, Ifit2, Ephx1, Ets2) known to execute anti-proliferative activities in T cells. Interestingly, certain MOG35-55 up-regulated transcripts were maintained at high levels in the presence of CBD, including transcription factors (Egr2, Egr1, Tbx21), cytokines (Csf2, Tnf, Ifng), and chemokines (Ccl3, Ccl4, Cxcl10) suggesting that CBD may promote exhaustion of memory TMOG cells. In addition, CBD enhanced the transcription of T cell co-inhibitory molecules (Btla, Lag3, Trat1, and CD69) known to interfere with T/APC interactions. Furthermore, CBD enhanced the transcription of oxidative stress modulators with potent anti-inflammatory activity that are controlled by Nfe2l2/Nrf2 (Mt1, Mt2a, Slc30a1, Hmox1). Conclusions Microarray-based gene expression profiling demonstrated that CBD exerts its immunoregulatory effects in activated memory TMOG cells via (a) suppressing proinflammatory Th17-related transcription, (b) by promoting T cell exhaustion/tolerance, (c) enhancing IFN-dependent anti-proliferative program, (d) hampering antigen presentation, and (d) inducing antioxidant milieu resolving inflammation. These findings put forward mechanism by which CBD exerts its anti-inflammatory effects as well as explain the beneficial role of CBD in pathological memory T cells and in autoimmune diseases. Electronic supplementary material The online version of this article (doi:10.1186/s12974-016-0603-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ewa Kozela
- The Dr Miriam and Sheldon G. Adelson Center for the Biology of Addictive Diseases, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel. .,Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Ana Juknat
- The Dr Miriam and Sheldon G. Adelson Center for the Biology of Addictive Diseases, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel.,Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Fuying Gao
- Departments of Psychiatry and Neurology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Nathali Kaushansky
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Giovanni Coppola
- Departments of Psychiatry and Neurology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Zvi Vogel
- The Dr Miriam and Sheldon G. Adelson Center for the Biology of Addictive Diseases, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel.,Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel
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31
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Cerebellar Transcriptome Profiles of ATXN1 Transgenic Mice Reveal SCA1 Disease Progression and Protection Pathways. Neuron 2016; 89:1194-1207. [PMID: 26948890 DOI: 10.1016/j.neuron.2016.02.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/22/2015] [Accepted: 02/03/2016] [Indexed: 12/13/2022]
Abstract
SCA1, a fatal neurodegenerative disorder, is caused by a CAG expansion encoding a polyglutamine stretch in the protein ATXN1. We used RNA sequencing to profile cerebellar gene expression in Pcp2-ATXN1[82Q] mice with ataxia and progressive pathology and Pcp2-ATXN1[30Q]D776 animals having ataxia in absence of Purkinje cell progressive pathology. Weighted Gene Coexpression Network Analysis of the cerebellar expression data revealed two gene networks that significantly correlated with disease and have an expression profile correlating with disease progression in ATXN1[82Q] Purkinje cells. The Magenta Module provides a signature of suppressed transcriptional programs reflecting disease progression in Purkinje cells, while the Lt Yellow Module reflects transcriptional programs activated in response to disease in Purkinje cells as well as other cerebellar cell types. Furthermore, we found that upregulation of cholecystokinin (Cck) and subsequent interaction with the Cck1 receptor likely underlies the lack of progressive Purkinje cell pathology in Pcp2-ATXN1[30Q]D776 mice.
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32
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Becherel OJ, Sun J, Yeo AJ, Nayler S, Fogel BL, Gao F, Coppola G, Criscuolo C, De Michele G, Wolvetang E, Lavin MF. A new model to study neurodegeneration in ataxia oculomotor apraxia type 2. Hum Mol Genet 2015; 24:5759-74. [PMID: 26231220 DOI: 10.1093/hmg/ddv296] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 07/20/2015] [Indexed: 12/18/2022] Open
Abstract
Ataxia oculomotor apraxia type 2 (AOA2) is a rare autosomal recessive cerebellar ataxia. Recent evidence suggests that the protein defective in this syndrome, senataxin (SETX), functions in RNA processing to protect the integrity of the genome. To date, only patient-derived lymphoblastoid cells, fibroblasts and SETX knockdown cells were available to investigate AOA2. Recent disruption of the Setx gene in mice did not lead to neurobehavioral defects or neurodegeneration, making it difficult to study the etiology of AOA2. To develop a more relevant neuronal model to study neurodegeneration in AOA2, we derived neural progenitors from a patient with AOA2 and a control by induced pluripotent stem cell (iPSC) reprogramming of fibroblasts. AOA2 iPSC and neural progenitors exhibit increased levels of oxidative damage, DNA double-strand breaks, increased DNA damage-induced cell death and R-loop accumulation. Genome-wide expression and weighted gene co-expression network analysis in these neural progenitors identified both previously reported and novel affected genes and cellular pathways associated with senataxin dysfunction and the pathophysiology of AOA2, providing further insight into the role of senataxin in regulating gene expression on a genome-wide scale. These data show that iPSCs can be generated from patients with the autosomal recessive ataxia, AOA2, differentiated into neurons, and that both cell types recapitulate the AOA2 cellular phenotype. This represents a novel and appropriate model system to investigate neurodegeneration in this syndrome.
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Affiliation(s)
- Olivier J Becherel
- UQ Centre for Clinical Research (UQCCR), School of Chemistry and Molecular Biosciences and
| | - Jane Sun
- Australian Institute for Bioengineering and Nanotechnology
| | - Abrey J Yeo
- UQ Centre for Clinical Research (UQCCR), School of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia
| | - Sam Nayler
- Australian Institute for Bioengineering and Nanotechnology
| | | | - Fuying Gao
- Department of Psychiatry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA and
| | - Giovanni Coppola
- Department of Neurology and Department of Psychiatry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA and
| | - Chiara Criscuolo
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, Federico II University, Napoli, Italy
| | - Giuseppe De Michele
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, Federico II University, Napoli, Italy
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Bartoletti-Stella A, Gasparini L, Giacomini C, Corrado P, Terlizzi R, Giorgio E, Magini P, Seri M, Baruzzi A, Parchi P, Brusco A, Cortelli P, Capellari S. Messenger RNA processing is altered in autosomal dominant leukodystrophy. Hum Mol Genet 2015; 24:2746-56. [PMID: 25637521 PMCID: PMC4406291 DOI: 10.1093/hmg/ddv034] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 01/27/2015] [Indexed: 02/06/2023] Open
Abstract
Adult-onset autosomal dominant leukodystrophy (ADLD) is a slowly progressive neurological disorder characterized by autonomic dysfunction, followed by cerebellar and pyramidal features. ADLD is caused by duplication of the lamin B1 gene (LMNB1), which leads to its increased expression. The molecular pathways involved in the disease are still poorly understood. Hence, we analyzed global gene expression in fibroblasts and whole blood of LMNB1 duplication carriers and used Gene Set Enrichment Analysis to explore their gene signatures. We found that LMNB1 duplication is associated with dysregulation of genes involved in the immune system, neuronal and skeletal development. Genes with an altered transcriptional profile clustered in specific genomic regions. Among the dysregulated genes, we further studied the role of RAVER2, which we found to be overexpressed at mRNA and protein level. RAVER2 encodes a putative trans regulator of the splicing repressor polypyrimidine tract binding protein (PTB) and is likely implicated in alternative splicing regulation. Functional studies demonstrated an abnormal splicing pattern of several PTB-target genes and of the myelin protein gene PLP1, previously demonstrated to be involved in ADLD. Mutant mice with different lamin B1 expression levels confirmed that Raver2 expression is dependent on lamin B1 in neural tissue and determines an altered splicing pattern of PTB-target genes and Plp1. Overall our results demonstrate that deregulation of lamin B1 expression induces modified splicing of several genes, likely driven by raver-2 overexpression, and suggest that an alteration of mRNA processing could be a pathogenic mechanism in ADLD.
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Affiliation(s)
- Anna Bartoletti-Stella
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40123, Italy
| | - Laura Gasparini
- Department of Neuroscience and Brain Techonologies, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - Caterina Giacomini
- Department of Neuroscience and Brain Techonologies, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - Patrizia Corrado
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40123, Italy
| | - Rossana Terlizzi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40123, Italy, IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Ospedale Bellaria, Bologna 40139, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, Torino 10126, Italy
| | - Pamela Magini
- Medical Genetics Unit, Department of Medical and Surgical Sciences, University of Bologna 40138, Italy and
| | - Marco Seri
- Medical Genetics Unit, Department of Medical and Surgical Sciences, University of Bologna 40138, Italy and
| | - Agostino Baruzzi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Ospedale Bellaria, Bologna 40139, Italy
| | - Piero Parchi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40123, Italy, IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Ospedale Bellaria, Bologna 40139, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino 10126, Italy, Città della Salute e della Scienza, University Hospital, Medical Genetics Unit, Torino 10126, Italy
| | - Pietro Cortelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40123, Italy, IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Ospedale Bellaria, Bologna 40139, Italy
| | - Sabina Capellari
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40123, Italy, IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Ospedale Bellaria, Bologna 40139, Italy,
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34
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Abstract
The RNA polymerase II transcription cycle is often divided into three major stages: initiation, elongation, and termination. Research over the last decade has blurred these divisions and emphasized the tightly regulated transitions that occur as RNA polymerase II synthesizes a transcript from start to finish. Transcription termination, the process that marks the end of transcription elongation, is regulated by proteins that interact with the polymerase, nascent transcript, and/or chromatin template. The failure to terminate transcription can cause accumulation of aberrant transcripts and interfere with transcription at downstream genes. Here, we review the mechanism, regulation, and physiological impact of a termination pathway that targets small noncoding transcripts produced by RNA polymerase II. We emphasize the Nrd1-Nab3-Sen1 pathway in yeast, in which the process has been extensively studied. The importance of understanding small RNA termination pathways is underscored by the need to control noncoding transcription in eukaryotic genomes.
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Affiliation(s)
- Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260;
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35
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Saccharomyces cerevisiae Sen1 as a model for the study of mutations in human Senataxin that elicit cerebellar ataxia. Genetics 2014; 198:577-90. [PMID: 25116135 DOI: 10.1534/genetics.114.167585] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The nuclear RNA and DNA helicase Sen1 is essential in the yeast Saccharomyces cerevisiae and is required for efficient termination of RNA polymerase II transcription of many short noncoding RNA genes. However, the mechanism of Sen1 function is not understood. We created a plasmid-based genetic system to study yeast Sen1 in vivo. Using this system, we show that (1) the minimal essential region of Sen1 corresponds to the helicase domain and one of two flanking nuclear localization sequences; (2) a previously isolated terminator readthrough mutation in the Sen1 helicase domain, E1597K, is rescued by a second mutation designed to restore a salt bridge within the first RecA domain; and (3) the human ortholog of yeast Sen1, Senataxin, cannot functionally replace Sen1 in yeast. Guided by sequence homology between the conserved helicase domains of Sen1 and Senataxin, we tested the effects of 13 missense mutations that cosegregate with the inherited disorder ataxia with oculomotor apraxia type 2 on Sen1 function. Ten of the disease mutations resulted in transcription readthrough of at least one of three Sen1-dependent termination elements tested. Our genetic system will facilitate the further investigation of structure-function relationships in yeast Sen1 and its orthologs.
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