1
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Kodavati M, Maloji Rao VH, Provasek VE, Hegde ML. Regulation of DNA damage response by RNA/DNA-binding proteins: Implications for neurological disorders and aging. Ageing Res Rev 2024; 100:102413. [PMID: 39032612 DOI: 10.1016/j.arr.2024.102413] [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: 06/03/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024]
Abstract
RNA-binding proteins (RBPs) are evolutionarily conserved across most forms of life, with an estimated 1500 RBPs in humans. Traditionally associated with post-transcriptional gene regulation, RBPs contribute to nearly every known aspect of RNA biology, including RNA splicing, transport, and decay. In recent years, an increasing subset of RBPs have been recognized for their DNA binding properties and involvement in DNA transactions. We refer to these RBPs with well-characterized DNA binding activity as RNA/DNA binding proteins (RDBPs), many of which are linked to neurological diseases. RDBPs are associated with both nuclear and mitochondrial DNA repair. Furthermore, the presence of intrinsically disordered domains in RDBPs appears to be critical for regulating their diverse interactions and plays a key role in controlling protein aggregation, which is implicated in neurodegeneration. In this review, we discuss the emerging roles of common RDBPs from the heterogeneous nuclear ribonucleoprotein (hnRNP) family, such as TAR DNA binding protein-43 (TDP43) and fused in sarcoma (FUS) in controlling DNA damage response (DDR). We also explore the implications of RDBP pathology in aging and neurodegenerative diseases and provide a prospective on the therapeutic potential of targeting RDBP pathology mediated DDR defects for motor neuron diseases and aging.
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Affiliation(s)
- Manohar Kodavati
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77047, USA.
| | - Vikas H Maloji Rao
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77047, USA
| | - Vincent E Provasek
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77047, USA; School of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Muralidhar L Hegde
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77047, USA; School of Medicine, Texas A&M University, College Station, TX 77843, USA; Department of Neurosurgery, Weill Medical College, New York, NY 10065, USA.
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2
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Lee S, Lee S, Choi N, Kim J, Kweon J, Miller K, Kim J. PCAF promotes R-loop resolution via histone acetylation. Nucleic Acids Res 2024; 52:8643-8660. [PMID: 38936834 PMCID: PMC11347145 DOI: 10.1093/nar/gkae558] [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: 03/05/2024] [Revised: 06/04/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024] Open
Abstract
R-loops cause genome instability, disrupting normal cellular functions. Histone acetylation, particularly by p300/CBP-associated factor (PCAF), is essential for maintaining genome stability and regulating cellular processes. Understanding how R-loop formation and resolution are regulated is important because dysregulation of these processes can lead to multiple diseases, including cancer. This study explores the role of PCAF in maintaining genome stability, specifically for R-loop resolution. We found that PCAF depletion promotes the generation of R-loop structures, especially during ongoing transcription, thereby compromising genome stability. Mechanistically, we found that PCAF facilitates histone H4K8 acetylation, leading to recruitment of the a double-strand break repair protein (MRE11) and exonuclease 1 (EXO1) to R-loop sites. These in turn recruit Fanconi anemia (FA) proteins, including FANCM and BLM, to resolve the R-loop structure. Our findings suggest that PCAF, histone acetylation, and FA proteins collaborate to resolve R-loops and ensure genome stability. This study therefore provides novel mechanistic insights into the dynamics of R-loops as well as the role of PCAF in preserving genome stability. These results may help develop therapeutic strategies to target diseases associated with genome instability.
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Affiliation(s)
- Seo Yun Lee
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Soo Hyeon Lee
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Nak Hun Choi
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Ja Young Kim
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Jun Hee Kweon
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jae Jin Kim
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
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3
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Jose L, Smith K, Crowner A, Androphy EJ, DeSmet M. Senataxin mediates R-loop resolution on HPV episomes. J Virol 2024; 98:e0100324. [PMID: 39046232 PMCID: PMC11334462 DOI: 10.1128/jvi.01003-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 06/29/2024] [Indexed: 07/25/2024] Open
Abstract
Three-stranded DNA-RNA structures known as R-loops that form during papillomavirus transcription can cause transcription-replication conflicts and lead to DNA damage. We found that R-loops accumulated at the viral early promoter in human papillomavirus (HPV) episomal cells but were greatly reduced in cells with integrated HPV genomes. RNA-DNA helicases unwind R-loops and allow for transcription and replication to proceed. Depletion of the RNA-DNA helicase senataxin (SETX) using siRNAs increased the presence of R-loops at the viral early promoter in HPV-31 (CIN612) and HPV-16 (W12) episomal HPV cell lines. Depletion of SETX reduced viral transcripts in episomal HPV cell lines. The viral E2 protein, which binds with high affinity to specific palindromes near the promoter and origin, complexes with SETX, and both SETX and E2 are present at the viral p97 promoter in CIN612 and W12 cells. SETX overexpression increased E2 transcription activity on the p97 promoter. SETX depletion also significantly increased integration of viral genomes in CIN612 cells. Our results demonstrate that SETX resolves viral R-loops to proceed with HPV transcription and prevent genome integration.IMPORTANCEPapillomaviruses contain small circular genomes of approximately 8 kilobase pairs and undergo unidirectional transcription from the sense strand of the viral genome. Co-transcriptional R-loops were recently reported to be present at high levels in cells that maintain episomal HPV and were also detected at the early viral promoter. R-loops can inhibit transcription and DNA replication. The process that removes R-loops from the PV genome and the requisite enzymes are unknown. We propose a model in which the host RNA-DNA helicase senataxin assembles on the HPV genome to resolve R-loops in order to maintain the episomal status of the viral genome.
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Affiliation(s)
- Leny Jose
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Keely Smith
- Indiana University Simon Comprehensive Cancer Center American Cancer Society Post-Baccalaureate Diversity in Cancer Research Education Program, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Anaiya Crowner
- Indiana University Simon Comprehensive Cancer Center American Cancer Society Post-Baccalaureate Diversity in Cancer Research Education Program, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Elliot J. Androphy
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Marsha DeSmet
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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4
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Rao S, Andrs M, Shukla K, Isik E, König C, Schneider S, Bauer M, Rosano V, Prokes J, Müller A, Janscak P. Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation. Nucleic Acids Res 2024:gkae673. [PMID: 39119900 DOI: 10.1093/nar/gkae673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 07/12/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
Replication forks stalled at co-transcriptional R-loops can be restarted by a mechanism involving fork cleavage-religation cycles mediated by MUS81 endonuclease and DNA ligase IV (LIG4), which presumably relieve the topological barrier generated by the transcription-replication conflict (TRC) and facilitate ELL-dependent reactivation of transcription. Here, we report that the restart of R-loop-stalled replication forks via the MUS81-LIG4-ELL pathway requires senataxin (SETX), a helicase that can unwind RNA:DNA hybrids. We found that SETX promotes replication fork progression by preventing R-loop accumulation during S-phase. Interestingly, loss of SETX helicase activity leads to nascent DNA degradation upon induction of R-loop-mediated fork stalling by hydroxyurea. This fork degradation phenotype is independent of replication fork reversal and results from DNA2-mediated resection of MUS81-cleaved replication forks that accumulate due to defective replication restart. Finally, we demonstrate that SETX acts in a common pathway with the DEAD-box helicase DDX17 to suppress R-loop-mediated replication stress in human cells. A possible cooperation between these RNA/DNA helicases in R-loop unwinding at TRC sites is discussed.
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Affiliation(s)
- Satyajeet Rao
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Andrs
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kaustubh Shukla
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Esin Isik
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Christiane König
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Stefan Schneider
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Michael Bauer
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Vinicio Rosano
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jiri Prokes
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anne Müller
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Pavel Janscak
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
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5
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Zannini L, Cardano M, Liberi G, Buscemi G. R-loops and impaired autophagy trigger cGAS-dependent inflammation via micronuclei formation in Senataxin-deficient cells. Cell Mol Life Sci 2024; 81:339. [PMID: 39120648 PMCID: PMC11335261 DOI: 10.1007/s00018-024-05380-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/17/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024]
Abstract
Senataxin is an evolutionarily conserved DNA/RNA helicase, whose dysfunctions are linked to neurodegeneration and cancer. A main activity of this protein is the removal of R-loops, which are nucleic acid structures capable to promote DNA damage and replication stress. Here we found that Senataxin deficiency causes the release of damaged DNA into extranuclear bodies, called micronuclei, triggering the massive recruitment of cGAS, the apical sensor of the innate immunity pathway, and the downstream stimulation of interferon genes. Such cGAS-positive micronuclei are characterized by defective membrane envelope and are particularly abundant in cycling cells lacking Senataxin, but not after exposure to a DNA breaking agent or in absence of the tumor suppressor BRCA1 protein, a partner of Senataxin in R-loop removal. Micronuclei with a discontinuous membrane are normally cleared by autophagy, a process that we show is impaired in Senataxin-deficient cells. The formation of Senataxin-dependent inflamed micronuclei is promoted by the persistence of nuclear R-loops stimulated by the DSIF transcription elongation complex and the engagement of EXO1 nuclease activity on nuclear DNA. Coherently, high levels of EXO1 result in poor prognosis in a subset of tumors lacking Senataxin expression. Hence, R-loop homeostasis impairment, together with autophagy failure and unscheduled EXO1 activity, elicits innate immune response through micronuclei formation in cells lacking Senataxin.
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Affiliation(s)
- Laura Zannini
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, 27100, Italy
| | - Miriana Cardano
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, 27100, Italy
| | - Giordano Liberi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, 27100, Italy.
| | - Giacomo Buscemi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, Pavia, 27100, Italy.
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6
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Ros‐Arlanzón P, Serrano‐Serrano B, Aledo‐Sala C, Guevara‐Dalrymple N, Martí‐Martínez S. Exploring the Pathogenicity of SETX I1942T Variant in Ataxia with Oculomotor Apraxia Type 2 Through Segregation Analysis. Mov Disord Clin Pract 2024; 11:1041-1043. [PMID: 38817201 PMCID: PMC11329564 DOI: 10.1002/mdc3.14128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 05/19/2024] [Indexed: 06/01/2024] Open
Affiliation(s)
- Pablo Ros‐Arlanzón
- Department of NeurologyDr. Balmis General University HospitalAlicanteSpain
- Alicante Institute for Health and Biomedical Research (ISABIAL)AlicanteSpain
| | | | - Carlos Aledo‐Sala
- Department of NeurologyDr. Balmis General University HospitalAlicanteSpain
- Alicante Institute for Health and Biomedical Research (ISABIAL)AlicanteSpain
| | - Natasha Guevara‐Dalrymple
- Department of NeurologyDr. Balmis General University HospitalAlicanteSpain
- Alicante Institute for Health and Biomedical Research (ISABIAL)AlicanteSpain
| | - Silvia Martí‐Martínez
- Department of NeurologyDr. Balmis General University HospitalAlicanteSpain
- Alicante Institute for Health and Biomedical Research (ISABIAL)AlicanteSpain
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7
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Chauhan AS, Jhujh SS, Stewart GS. E3 ligases: a ubiquitous link between DNA repair, DNA replication and human disease. Biochem J 2024; 481:923-944. [PMID: 38985307 PMCID: PMC11346458 DOI: 10.1042/bcj20240124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 07/11/2024]
Abstract
Maintenance of genome stability is of paramount importance for the survival of an organism. However, genomic integrity is constantly being challenged by various endogenous and exogenous processes that damage DNA. Therefore, cells are heavily reliant on DNA repair pathways that have evolved to deal with every type of genotoxic insult that threatens to compromise genome stability. Notably, inherited mutations in genes encoding proteins involved in these protective pathways trigger the onset of disease that is driven by chromosome instability e.g. neurodevelopmental abnormalities, neurodegeneration, premature ageing, immunodeficiency and cancer development. The ability of cells to regulate the recruitment of specific DNA repair proteins to sites of DNA damage is extremely complex but is primarily mediated by protein post-translational modifications (PTMs). Ubiquitylation is one such PTM, which controls genome stability by regulating protein localisation, protein turnover, protein-protein interactions and intra-cellular signalling. Over the past two decades, numerous ubiquitin (Ub) E3 ligases have been identified to play a crucial role not only in the initiation of DNA replication and DNA damage repair but also in the efficient termination of these processes. In this review, we discuss our current understanding of how different Ub E3 ligases (RNF168, TRAIP, HUWE1, TRIP12, FANCL, BRCA1, RFWD3) function to regulate DNA repair and replication and the pathological consequences arising from inheriting deleterious mutations that compromise the Ub-dependent DNA damage response.
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Affiliation(s)
- Anoop S. Chauhan
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Satpal S. Jhujh
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
| | - Grant S. Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
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8
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Kannan A, Gangadharan Leela S, Branzei D, Gangwani L. Role of senataxin in R-loop-mediated neurodegeneration. Brain Commun 2024; 6:fcae239. [PMID: 39070547 PMCID: PMC11277865 DOI: 10.1093/braincomms/fcae239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 06/14/2024] [Accepted: 07/13/2024] [Indexed: 07/30/2024] Open
Abstract
Senataxin is an RNA:DNA helicase that plays an important role in the resolution of RNA:DNA hybrids (R-loops) formed during transcription. R-loops are involved in the regulation of biological processes such as immunoglobulin class switching, gene expression and DNA repair. Excessive accumulation of R-loops results in DNA damage and loss of genomic integrity. Senataxin is critical for maintaining optimal levels of R-loops to prevent DNA damage and acts as a genome guardian. Within the nucleus, senataxin interacts with various RNA processing factors and DNA damage response and repair proteins. Senataxin interactors include survival motor neuron and zinc finger protein 1, with whom it co-localizes in sub-nuclear bodies. Despite its ubiquitous expression, mutations in senataxin specifically affect neurons and result in distinct neurodegenerative diseases such as amyotrophic lateral sclerosis type 4 and ataxia with oculomotor apraxia type 2, which are attributed to the gain-of-function and the loss-of-function mutations in senataxin, respectively. In addition, low levels of senataxin (loss-of-function) in spinal muscular atrophy result in the accumulation of R-loops causing DNA damage and motor neuron degeneration. Senataxin may play multiple functions in diverse cellular processes; however, its emerging role in R-loop resolution and maintenance of genomic integrity is gaining attention in the field of neurodegenerative diseases. In this review, we highlight the role of senataxin in R-loop resolution and its potential as a therapeutic target to treat neurodegenerative diseases.
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Affiliation(s)
| | - Shyni Gangadharan Leela
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Dana Branzei
- The AIRC Institute of Molecular Oncology Foundation, IFOM ETS, Milan 20139, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia 27100, Italy
| | - Laxman Gangwani
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
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9
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Riva N, Domi T, Pozzi L, Lunetta C, Schito P, Spinelli EG, Cabras S, Matteoni E, Consonni M, Bella ED, Agosta F, Filippi M, Calvo A, Quattrini A. Update on recent advances in amyotrophic lateral sclerosis. J Neurol 2024; 271:4693-4723. [PMID: 38802624 PMCID: PMC11233360 DOI: 10.1007/s00415-024-12435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/07/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
In the last few years, our understanding of disease molecular mechanisms underpinning ALS has advanced greatly, allowing the first steps in translating into clinical practice novel research findings, including gene therapy approaches. Similarly, the recent advent of assistive technologies has greatly improved the possibility of a more personalized approach to supportive and symptomatic care, in the context of an increasingly complex multidisciplinary line of actions, which remains the cornerstone of ALS management. Against this rapidly growing background, here we provide an comprehensive update on the most recent studies that have contributed towards our understanding of ALS pathogenesis, the latest results from clinical trials as well as the future directions for improving the clinical management of ALS patients.
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Affiliation(s)
- Nilo Riva
- 3Rd Neurology Unit and Motor Neuron Disease Centre, Fondazione IRCCS "Carlo Besta" Neurological Insitute, Milan, Italy.
| | - Teuta Domi
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Pozzi
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Christian Lunetta
- Istituti Clinici Scientifici Maugeri IRCCS, Neurorehabilitation Unit of Milan Institute, 20138, Milan, Italy
| | - Paride Schito
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Edoardo Gioele Spinelli
- Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Neuroimaging Research Unit, Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sara Cabras
- ALS Centre, 'Rita Levi Montalcini' Department of Neuroscience, University of Turin; SC Neurologia 1U, AOU città della Salute e della Scienza di Torino, Turin, Italy
| | - Enrico Matteoni
- ALS Centre, 'Rita Levi Montalcini' Department of Neuroscience, University of Turin; SC Neurologia 1U, AOU città della Salute e della Scienza di Torino, Turin, Italy
| | - Monica Consonni
- 3Rd Neurology Unit and Motor Neuron Disease Centre, Fondazione IRCCS "Carlo Besta" Neurological Insitute, Milan, Italy
| | - Eleonora Dalla Bella
- 3Rd Neurology Unit and Motor Neuron Disease Centre, Fondazione IRCCS "Carlo Besta" Neurological Insitute, Milan, Italy
| | - Federica Agosta
- Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Neuroimaging Research Unit, Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute Huniversity, Milan, Italy
| | - Massimo Filippi
- Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Neuroimaging Research Unit, Department of Neurology, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute Huniversity, Milan, Italy
| | - Andrea Calvo
- ALS Centre, 'Rita Levi Montalcini' Department of Neuroscience, University of Turin; SC Neurologia 1U, AOU città della Salute e della Scienza di Torino, Turin, Italy
| | - Angelo Quattrini
- Experimental Neuropathology Unit, Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, Milan, Italy
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10
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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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11
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Tazir M, Nouioua S. Distal hereditary motor neuropathies. Rev Neurol (Paris) 2024:S0035-3787(23)01111-6. [PMID: 38702287 DOI: 10.1016/j.neurol.2023.09.005] [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: 08/02/2022] [Revised: 07/30/2023] [Accepted: 09/29/2023] [Indexed: 05/06/2024]
Abstract
Distal hereditary motor neuropathies (dHMN) are a group of heterogeneous hereditary disorders characterized by a slowly progressive distal pure motor neuropathy. Electrophysiology, with normal motor and sensory conduction velocities, can suggest the diagnosis of dHMN and guide the genetic study. More than thirty genes are currently associated with HMNs, but around 60 to 70% of cases of dHMN remain uncharacterized genetically. Recent cohort studies showed that HSPB1, GARS, BICB2 and DNAJB2 are among the most frequent dHMN genes and that the prevalence of the disease was calculated as 2.14 and 2.3 per 100,000. The determination of the different genes involved in dHMNs made it possible to observe a genotypic overlap with some other neurogenetic disorders and other hereditary neuropathies such as CMT2, mainly with the HSPB1, HSPB8, BICD2 and TRPV4 genes of AD-inherited transmission and recently observed with SORD gene of AR transmission which seems relatively frequent and potentially curable. Distal hereditary motor neuropathy that predominates in the upper limbs is linked mainly to three genes: GARS, BSCL2 and REEP1, whereas dHMN with vocal cord palsy is associated with SLC5A7, DCTN1 and TRPV4 genes. Among the rare AR forms of dHMN like IGHMBP2 and DNAJB2, the SIGMAR1 gene mutations as well as VRK1 variants are associated with a motor neuropathy phenotype often associated with upper motoneuron involvement. The differential diagnosis of these latter arises with juvenile forms of amyotrophic lateral sclerosis, that could be caused also by variations of these genes, as well as hereditary spastic paraplegia. A differential diagnosis of dHMN related to Brown Vialetto Van Laere syndrome due to riboflavin transporter deficiency is important to consider because of the therapeutic possibility.
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Affiliation(s)
- Meriem Tazir
- Department of Neurology, University Hospital Mustapha Bacha, Algiers, Algeria; Neurosciences Laboratory, University Benyoucef Benkhedda, Algiers, Algeria.
| | - Sonia Nouioua
- Neurosciences Laboratory, University Benyoucef Benkhedda, Algiers, Algeria; Department of Neurology, EHS El Maham, Cherchell,Tipaza, Algeria
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12
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Xu Y, Jiao Y, Liu C, Miao R, Liu C, Wang Y, Ma C, Liu J. R-loop and diseases: the cell cycle matters. Mol Cancer 2024; 23:84. [PMID: 38678239 PMCID: PMC11055327 DOI: 10.1186/s12943-024-02000-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
The cell cycle is a crucial biological process that is involved in cell growth, development, and reproduction. It can be divided into G1, S, G2, and M phases, and each period is closely regulated to ensure the production of two similar daughter cells with the same genetic material. However, many obstacles influence the cell cycle, including the R-loop that is formed throughout this process. R-loop is a triple-stranded structure, composed of an RNA: DNA hybrid and a single DNA strand, which is ubiquitous in organisms from bacteria to mammals. The existence of the R-loop has important significance for the regulation of various physiological processes. However, aberrant accumulation of R-loop due to its limited resolving ability will be detrimental for cells. For example, DNA damage and genomic instability, caused by the R-loop, can activate checkpoints in the cell cycle, which in turn induce cell cycle arrest and cell death. At present, a growing number of factors have been proven to prevent or eliminate the accumulation of R-loop thereby avoiding DNA damage and mutations. Therefore, we need to gain detailed insight into the R-loop resolution factors at different stages of the cell cycle. In this review, we review the current knowledge of factors that play a role in resolving the R-loop at different stages of the cell cycle, as well as how mutations of these factors lead to the onset and progression of diseases.
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Affiliation(s)
- Yuqin Xu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Yue Jiao
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chengbin Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Rui Miao
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chunyan Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Yilong Wang
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chunming Ma
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Jiao Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China.
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13
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Scaravilli A, Tranfa M, Pontillo G, Brais B, De Michele G, La Piana R, Saccà F, Santorelli FM, Synofzik M, Brunetti A, Cocozza S. A Review of Brain and Pituitary Gland MRI Findings in Patients with Ataxia and Hypogonadism. CEREBELLUM (LONDON, ENGLAND) 2024; 23:757-774. [PMID: 37155088 DOI: 10.1007/s12311-023-01562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/26/2023] [Indexed: 05/10/2023]
Abstract
The association of cerebellar ataxia and hypogonadism occurs in a heterogeneous group of disorders, caused by different genetic mutations often associated with a recessive inheritance. In these patients, magnetic resonance imaging (MRI) plays a pivotal role in the diagnostic workflow, with a variable involvement of the cerebellar cortex, alone or in combination with other brain structures. Neuroimaging involvement of the pituitary gland is also variable. Here, we provide an overview of the main clinical and conventional brain and pituitary gland MRI imaging findings of the most common genetic mutations associated with the clinical phenotype of ataxia and hypogonadism, with the aim of helping neuroradiologists in the identification of these disorders.
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Affiliation(s)
- Alessandra Scaravilli
- Department of Advanced Biomedical Sciences, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy
| | - Mario Tranfa
- Department of Advanced Biomedical Sciences, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy
| | - Giuseppe Pontillo
- Department of Advanced Biomedical Sciences, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples "Federico II", Naples, Italy
| | - Bernard Brais
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, Montreal, Canada
| | - Giovanna De Michele
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, University of Naples "Federico II", Naples, Italy
| | - Roberta La Piana
- Department of Neurology and Neurosurgery, Montreal Neurological Hospital and Institute, Montreal, Canada
| | - Francesco Saccà
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, University of Naples "Federico II", Naples, Italy
| | | | - Matthis Synofzik
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
- Division Translational Genomics of Neurodegenerative Diseases, Center for Neurology and Hertie Institute for Clinical Brain Research, University of Tübingen, Otfried-Müller-Strasse 27, 72076, Tubingen, Germany
| | - Arturo Brunetti
- Department of Advanced Biomedical Sciences, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy
| | - Sirio Cocozza
- Department of Advanced Biomedical Sciences, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy.
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14
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Libri I, Cantoni V, Benussi A, Rivolta J, Ferrari C, Fancellu R, Synofzik M, Alberici A, Padovani A, Borroni B. Comparing Cerebellar tDCS and Cerebellar tACS in Neurodegenerative Ataxias Using Wearable Sensors: A Randomized, Double-Blind, Sham-Controlled, Triple-Crossover Trial. CEREBELLUM (LONDON, ENGLAND) 2024; 23:570-578. [PMID: 37349632 PMCID: PMC10951038 DOI: 10.1007/s12311-023-01578-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/09/2023] [Indexed: 06/24/2023]
Abstract
Cerebellar transcranial direct current stimulation (tDCS) represents a promising therapeutic approach for both motor and cognitive symptoms in neurodegenerative ataxias. Recently, transcranial alternating current stimulation (tACS) was also demonstrated to modulate cerebellar excitability by neuronal entrainment. To compare the effectiveness of cerebellar tDCS vs. cerebellar tACS in patients with neurodegenerative ataxia, we performed a double-blind, randomized, sham controlled, triple cross-over trial with cerebellar tDCS, cerebellar tACS or sham stimulation in twenty-six participants with neurodegenerative ataxia. Before entering the study, each participant underwent motor assessment with wearable sensors considering gait cadence (steps/minute), turn velocity (degrees/second) and turn duration (seconds), and a clinical evaluation with the scale for the Assessment and Rating of Ataxia (SARA) and the International Cooperative Ataxia Rating Scale (ICARS). After each intervention, participants underwent the same clinical assessment along with cerebellar inhibition (CBI) measurement, a marker of cerebellar activity. The gait cadence, turn velocity, SARA, and ICARS significantly improved after both tDCS and tACS, compared to sham stimulation (all p<0.010). Comparable effects were observed for CBI (p<0.001). Overall, tDCS significantly outperformed tACS on clinical scales and CBI (p<0.01). A significant correlation between changes of wearable sensors parameters from baseline and changes of clinical scales and CBI scores was detected. Cerebellar tDCS and cerebellar tACS are effective in ameliorating symptoms of neurodegenerative ataxias, with the former being more beneficial than the latter. Wearable sensors may serve as rater-unbiased outcome measures in future clinical trials. ClinicalTrial.gov Identifier: NCT05621200.
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Affiliation(s)
- Ilenia Libri
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Valentina Cantoni
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Alberto Benussi
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- Neurology Unit, Department of Neurological and Vision Sciences, ASST Spedali Civili, Brescia, Italy
| | - Jasmine Rivolta
- Neurology Unit, Department of Neurological and Vision Sciences, ASST Spedali Civili, Brescia, Italy
| | - Camilla Ferrari
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, Florence, Italy
| | - Roberto Fancellu
- UO Neurologia, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - Matthis Synofzik
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research and Centre of Neurology, Tübingen, Germany
- German Research Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Antonella Alberici
- Neurology Unit, Department of Neurological and Vision Sciences, ASST Spedali Civili, Brescia, Italy
| | - Alessandro Padovani
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
- Neurology Unit, Department of Neurological and Vision Sciences, ASST Spedali Civili, Brescia, Italy
| | - Barbara Borroni
- Neurology Unit, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy.
- Neurology Unit, Department of Neurological and Vision Sciences, ASST Spedali Civili, Brescia, Italy.
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15
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Vadla GP, Singh K, Lorson CL, Lorson MA. The contribution and therapeutic implications of IGHMBP2 mutations on IGHMBP2 biochemical activity and ABT1 association. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167091. [PMID: 38403020 PMCID: PMC10999323 DOI: 10.1016/j.bbadis.2024.167091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 02/27/2024]
Abstract
Mutations within immunoglobulin mu DNA binding protein (IGHMBP2), an RNA-DNA helicase, result in SMA with respiratory distress type I (SMARD1) and Charcot Marie Tooth type 2S (CMT2S). The underlying biochemical mechanism of IGHMBP2 is unknown as well as the functional significance of IGHMBP2 mutations in disease severity. Here we report the biochemical mechanisms of IGHMBP2 disease-causing mutations D565N and H924Y, and their potential impact on therapeutic strategies. The IGHMBP2-D565N mutation has been identified in SMARD1 patients, while the IGHMBP2-H924Y mutation has been identified in CMT2S patients. For the first time, we demonstrate a correlation between the altered IGHMBP2 biochemical activity associated with the D565N and H924Y mutations and disease severity and pathology in patients and our Ighmbp2 mouse models. We show that IGHMBP2 mutations that alter the association with activator of basal transcription (ABT1) impact the ATPase and helicase activities of IGHMBP2 and the association with the 47S pre-rRNA 5' external transcribed spacer. We demonstrate that the D565N mutation impairs IGHMBP2 ATPase and helicase activities consistent with disease pathology. The H924Y mutation alters IGHMBP2 activity to a lesser extent while maintaining association with ABT1. In the context of the compound heterozygous patient, we demonstrate that the total biochemical activity associated with IGHMBP2-D565N and IGHMBP2-H924Y proteins is improved over IGHMBP2-D565N alone. Importantly, we demonstrate that the efficacy of therapeutic applications may vary based on the underlying IGHMBP2 mutations and the relative biochemical activity of the mutant IGHMBP2 protein.
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Affiliation(s)
- Gangadhar P Vadla
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Kamal Singh
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Christian L Lorson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Monique A Lorson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA; Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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16
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Westover KR, Jin P, Yao B. Bridging the gap: R-loop mediated genomic instability and its implications in neurological diseases. Epigenomics 2024; 16:589-608. [PMID: 38530068 PMCID: PMC11160457 DOI: 10.2217/epi-2023-0379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024] Open
Abstract
R-loops, intricate three-stranded structures formed by RNA-DNA hybrids and an exposed non-template DNA strand, are fundamental to various biological phenomena. They carry out essential and contrasting functions within cellular mechanisms, underlining their critical role in maintaining cellular homeostasis. The specific cellular context that dictates R-loop formation determines their function, particularly emphasizing the necessity for their meticulous genomic regulation. Notably, the aberrant formation or misregulation of R-loops is implicated in numerous neurological disorders. This review focuses on the complex interactions between R-loops and double-strand DNA breaks, exploring how R-loop dysregulation potentially contributes to the pathogenesis of various brain disorders, which could provide novel insights into the molecular mechanisms underpinning neurological disease progression and identify potential therapeutic targets by highlighting these aspects.
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Affiliation(s)
- Katherine R Westover
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Bing Yao
- Department of Human Genetics, Emory University, School of Medicine, Atlanta, GA 30322, USA
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17
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Maliar NL, Talbot EJ, Edwards AR, Khoronenkova SV. Microglial inflammation in genome instability: A neurodegenerative perspective. DNA Repair (Amst) 2024; 135:103634. [PMID: 38290197 DOI: 10.1016/j.dnarep.2024.103634] [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: 08/31/2023] [Revised: 01/08/2024] [Accepted: 01/21/2024] [Indexed: 02/01/2024]
Abstract
The maintenance of genome stability is crucial for cell homeostasis and tissue integrity. Numerous human neuropathologies display chronic inflammation in the central nervous system, set against a backdrop of genome instability, implying a close interplay between the DNA damage and immune responses in the context of neurological disease. Dissecting the molecular mechanisms of this crosstalk is essential for holistic understanding of neuroinflammatory pathways in genome instability disorders. Non-neuronal cell types, specifically microglia, are major drivers of neuroinflammation in the central nervous system with neuro-protective and -toxic capabilities. Here, we discuss how persistent DNA damage affects microglial homeostasis, zooming in on the cytosolic DNA sensing cGAS-STING pathway and the downstream inflammatory response, which can drive neurotoxic outcomes in the context of genome instability.
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Affiliation(s)
- Nina L Maliar
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Emily J Talbot
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Abigail R Edwards
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
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18
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Zhang J, Chen F, Tang M, Xu W, Tian Y, Liu Z, Shu Y, Yang H, Zhu Q, Lu X, Peng B, Liu X, Xu X, Gullerova M, Zhu WG. The ARID1A-METTL3-m6A axis ensures effective RNase H1-mediated resolution of R-loops and genome stability. Cell Rep 2024; 43:113779. [PMID: 38358891 DOI: 10.1016/j.celrep.2024.113779] [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: 07/12/2023] [Revised: 12/02/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
R-loops are three-stranded structures that can pose threats to genome stability. RNase H1 precisely recognizes R-loops to drive their resolution within the genome, but the underlying mechanism is unclear. Here, we report that ARID1A recognizes R-loops with high affinity in an ATM-dependent manner. ARID1A recruits METTL3 and METTL14 to the R-loop, leading to the m6A methylation of R-loop RNA. This m6A modification facilitates the recruitment of RNase H1 to the R-loop, driving its resolution and promoting DNA end resection at DSBs, thereby ensuring genome stability. Depletion of ARID1A, METTL3, or METTL14 leads to R-loop accumulation and reduced cell survival upon exposure to cytotoxic agents. Therefore, ARID1A, METTL3, and METTL14 function in a coordinated, temporal order at DSB sites to recruit RNase H1 and to ensure efficient R-loop resolution. Given the association of high ARID1A levels with resistance to genotoxic therapies in patients, these findings open avenues for exploring potential therapeutic strategies for cancers with ARID1A abnormalities.
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Affiliation(s)
- Jun Zhang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Feng Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Ming Tang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai 200092, China
| | - Wenchao Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yuan Tian
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Zhichao Liu
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Yuxin Shu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Hui Yang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Qian Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiaopeng Lu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Bin Peng
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiangyu Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xingzhi Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Monika Gullerova
- Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Wei-Guo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China; Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518055, China; School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, China; Department of Biochemistry and Molecular Biology, Peking University Health Science Centre, Beijing 100191, China.
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19
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Lopergolo D, Rosini F, Pretegiani E, Bargagli A, Serchi V, Rufa A. Autosomal recessive cerebellar ataxias: a diagnostic classification approach according to ocular features. Front Integr Neurosci 2024; 17:1275794. [PMID: 38390227 PMCID: PMC10883068 DOI: 10.3389/fnint.2023.1275794] [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: 08/10/2023] [Accepted: 11/10/2023] [Indexed: 02/24/2024] Open
Abstract
Autosomal recessive cerebellar ataxias (ARCAs) are a heterogeneous group of neurodegenerative disorders affecting primarily the cerebellum and/or its afferent tracts, often accompanied by damage of other neurological or extra-neurological systems. Due to the overlap of clinical presentation among ARCAs and the variety of hereditary, acquired, and reversible etiologies that can determine cerebellar dysfunction, the differential diagnosis is challenging, but also urgent considering the ongoing development of promising target therapies. The examination of afferent and efferent visual system may provide neurophysiological and structural information related to cerebellar dysfunction and neurodegeneration thus allowing a possible diagnostic classification approach according to ocular features. While optic coherence tomography (OCT) is applied for the parametrization of the optic nerve and macular area, the eye movements analysis relies on a wide range of eye-tracker devices and the application of machine-learning techniques. We discuss the results of clinical and eye-tracking oculomotor examination, the OCT findings and some advancing of computer science in ARCAs thus providing evidence sustaining the identification of robust eye parameters as possible markers of ARCAs.
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Affiliation(s)
- Diego Lopergolo
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
- UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Francesca Rosini
- UOC Stroke Unit, Department of Emergenza-Urgenza, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
| | - Elena Pretegiani
- Unit of Neurology, Centre Hospitalier Universitaire Vaudoise Lausanne, Unit of Neurology and Cognitive Neurorehabilitation, Universitary Hospital of Fribourg, Fribourg, Switzerland
| | - Alessia Bargagli
- Evalab-Neurosense, Department of Medicine Surgery and Neuroscience, University of Siena, Siena, Italy
| | - Valeria Serchi
- Evalab-Neurosense, Department of Medicine Surgery and Neuroscience, University of Siena, Siena, Italy
| | - Alessandra Rufa
- Department of Medicine, Surgery and Neurosciences, University of Siena, Siena, Italy
- UOC Neurologia e Malattie Neurometaboliche, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Evalab-Neurosense, Department of Medicine Surgery and Neuroscience, University of Siena, Siena, Italy
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20
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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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21
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Yahia A, Li D, Lejerkrans S, Rajagopalan S, Kalnak N, Tammimies K. Whole exome sequencing and polygenic assessment of a Swedish cohort with severe developmental language disorder. Hum Genet 2024; 143:169-183. [PMID: 38300321 PMCID: PMC10881898 DOI: 10.1007/s00439-023-02636-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
Developmental language disorder (DLD) overlaps clinically, genetically, and pathologically with other neurodevelopmental disorders (NDD), corroborating the concept of the NDD continuum. There is a lack of studies to understand the whole genetic spectrum in individuals with DLD. Previously, we recruited 61 probands with severe DLD from 59 families and examined 59 of them and their families using microarray genotyping with a 6.8% diagnostic yield. Herein, we investigated 53 of those probands using whole exome sequencing (WES). Additionally, we used polygenic risk scores (PRS) to understand the within family enrichment of neurodevelopmental difficulties and examine the associations between the results of language-related tests in the probands and language-related PRS. We identified clinically significant variants in four probands, resulting in a 7.5% (4/53) molecular diagnostic yield. Those variants were in PAK2, MED13, PLCB4, and TNRC6B. We also prioritized additional variants for future studies for their role in DLD, including high-impact variants in PARD3 and DIP2C. PRS did not explain the aggregation of neurodevelopmental difficulties in these families. We did not detect significant associations between the language-related tests and language-related PRS. Our results support using WES as the first-tier genetic test for DLD as it can identify monogenic DLD forms. Large-scale sequencing studies for DLD are needed to identify new genes and investigate the polygenic contribution to the condition.
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Affiliation(s)
- Ashraf Yahia
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Danyang Li
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Sanna Lejerkrans
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
| | - Shyam Rajagopalan
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | - Nelli Kalnak
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden
- Department of Speech-Language Pathology, Helsingborg Hospital, Helsingborg, Sweden
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet, Region Stockholm, Stockholm, Sweden.
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden.
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22
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Jaiswal AS, Dutta A, Srinivasan G, Yuan Y, Zhou D, Shaheen M, Sadideen D, Kirby A, Williamson E, Gupta Y, Olsen SK, Xu M, Loranc E, Mukhopadhyay P, Pertsemlidis A, Bishop AR, Sung P, Nickoloff J, Hromas R. TATDN2 resolution of R-loops is required for survival of BRCA1-mutant cancer cells. Nucleic Acids Res 2023; 51:12224-12241. [PMID: 37953292 PMCID: PMC10711561 DOI: 10.1093/nar/gkad952] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/03/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
BRCA1-deficient cells have increased IRE1 RNase, which degrades multiple microRNAs. Reconstituting expression of one of these, miR-4638-5p, resulted in synthetic lethality in BRCA1-deficient cancer cells. We found that miR-4638-5p represses expression of TATDN2, a poorly characterized member of the TATD nuclease family. We discovered that human TATDN2 has RNA 3' exonuclease and endonuclease activity on double-stranded hairpin RNA structures. Given the cleavage of hairpin RNA by TATDN2, and that BRCA1-deficient cells have difficulty resolving R-loops, we tested whether TATDN2 could resolve R-loops. Using in vitro biochemical reconstitution assays, we found TATDN2 bound to R-loops and degraded the RNA strand but not DNA of multiple forms of R-loops in vitro in a Mg2+-dependent manner. Mutations in amino acids E593 and E705 predicted by Alphafold-2 to chelate an essential Mg2+ cation completely abrogated this R-loop resolution activity. Depleting TATDN2 increased cellular R-loops, DNA damage and chromosomal instability. Loss of TATDN2 resulted in poor replication fork progression in the presence of increased R-loops. Significantly, we found that TATDN2 is essential for survival of BRCA1-deficient cancer cells, but much less so for cognate BRCA1-repleted cancer cells. Thus, we propose that TATDN2 is a novel target for therapy of BRCA1-deficient cancers.
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Affiliation(s)
- Aruna S Jaiswal
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Arijit Dutta
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Gayathri Srinivasan
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Montaser Shaheen
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Doraid T Sadideen
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Austin Kirby
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Elizabeth A Williamson
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Yogesh K Gupta
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Shaun K Olsen
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Mingjiang Xu
- Department of Molecular Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Eva Loranc
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Pramiti Mukhopadhyay
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Alexander Pertsemlidis
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Alexander J R Bishop
- Department of Cell Systems and Anatomy and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology and the Greehey Children's Cancer Research Institute, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert Hromas
- Department of Medicine and the Mays Cancer Center, the University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA
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23
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Wu Y, Song T, Xu Q. R-LOOPs on Short Tandem Repeat Expansion Disorders in Neurodegenerative Diseases. Mol Neurobiol 2023; 60:7185-7195. [PMID: 37540313 DOI: 10.1007/s12035-023-03531-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/24/2023] [Indexed: 08/05/2023]
Abstract
Expansions of short tandem repeats (STRs) have been found to be present in more than 50 diseases and have a close connection with neurodegenerative diseases. Transcriptional silencing and R-LOOP formation, RNA-mediated sequestration of RNA-binding proteins (RBPs), gain-of-function (GOF) proteins containing expanded repeats, and repeat-associated non-AUG (RAN) translation of toxic repeat peptides are some potential molecular mechanisms underlying STR expansion disorders. R-LOOP, a byproduct of transcription, is a three-stranded nucleic acid structure with abnormal accumulation that participates in the pathogenesis of STR expansion disorders by inducing DNA damage and genome instability. R-LOOPs can engender a series of DNA damage, such as DNA double-strand breaks (DSBs), single-strand breaks (SSBs), DNA recombination, or mutations in the DNA replication, transcription, or repair processes. In this review, we provide an in-depth discussion of recent advancements in R-LOOP and systematically elaborate on its genetic destabilizing effects in several neurodegenerative diseases. These molecular mechanisms will provide novel targets for drug design and therapeutic upgrading of these devastating diseases.
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Affiliation(s)
- Yiting Wu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Tingwei Song
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qian Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.
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24
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Tsui A, Kouznetsova VL, Kesari S, Fiala M, Tsigelny IF. Role of Senataxin in Amyotrophic Lateral Sclerosis. J Mol Neurosci 2023; 73:996-1009. [PMID: 37982993 DOI: 10.1007/s12031-023-02169-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/23/2023] [Indexed: 11/21/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, uncurable neurodegenerative disorder characterized by the degradation of motor neurons leading to muscle impairment, failure, and death. Senataxin, encoded by the SETX gene, is a human helicase protein whose mutations have been linked with ALS onset, particularly in its juvenile ALS4 form. Using senataxin's yeast homolog Sen1 as a model for study, it is suggested that senataxin's N-terminus interacts with RNA polymerase II, whilst its C-terminus engages in helicase activity. Senataxin is heavily involved in transcription regulation, termination, and R-loop resolution, enabled by recruitment and interactions with enzymes such as ubiquitin protein ligase SAN1 and ribonuclease H (RNase H). Senataxin also engages in DNA damage response (DDR), primarily interacting with the exosome subunit Rrp45. The Sen1 mutation E1597K, alongside the L389S and R2136H gain-of-function mutations to senataxin, is shown to cause negative structural and thus functional effects to the protein, thus contributing to a disruption in WT functions, motor neuron (MN) degeneration, and the manifestation of ALS clinical symptoms. This review corroborates and summarizes published papers concerning the structure and function of senataxin as well as the effects of their mutations in ALS pathology in order to compile current knowledge and provide a reference for future research. The findings compiled in this review are indicative of the experimental and therapeutic potential of senataxin and its mutations as a target in future ALS treatment/cure discovery, with some potential therapeutic routes also being discussed in the review.
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Affiliation(s)
- Andrew Tsui
- REHS Program, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
- CureScience Institute, San Diego, CA, USA
- BiAna, San Diego, La Jolla, CA, USA
| | | | - Milan Fiala
- Department of Integrative Biology and Physiology, School of Medicine, UCLA, Los Angeles, CA, USA
| | - Igor F Tsigelny
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA.
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.
- CureScience Institute, San Diego, CA, USA.
- BiAna, San Diego, La Jolla, CA, USA.
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25
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Nickoloff JA, Jaiswal AS, Sharma N, Williamson EA, Tran MT, Arris D, Yang M, Hromas R. Cellular Responses to Widespread DNA Replication Stress. Int J Mol Sci 2023; 24:16903. [PMID: 38069223 PMCID: PMC10707325 DOI: 10.3390/ijms242316903] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Replicative DNA polymerases are blocked by nearly all types of DNA damage. The resulting DNA replication stress threatens genome stability. DNA replication stress is also caused by depletion of nucleotide pools, DNA polymerase inhibitors, and DNA sequences or structures that are difficult to replicate. Replication stress triggers complex cellular responses that include cell cycle arrest, replication fork collapse to one-ended DNA double-strand breaks, induction of DNA repair, and programmed cell death after excessive damage. Replication stress caused by specific structures (e.g., G-rich sequences that form G-quadruplexes) is localized but occurs during the S phase of every cell division. This review focuses on cellular responses to widespread stress such as that caused by random DNA damage, DNA polymerase inhibition/nucleotide pool depletion, and R-loops. Another form of global replication stress is seen in cancer cells and is termed oncogenic stress, reflecting dysregulated replication origin firing and/or replication fork progression. Replication stress responses are often dysregulated in cancer cells, and this too contributes to ongoing genome instability that can drive cancer progression. Nucleases play critical roles in replication stress responses, including MUS81, EEPD1, Metnase, CtIP, MRE11, EXO1, DNA2-BLM, SLX1-SLX4, XPF-ERCC1-SLX4, Artemis, XPG, FEN1, and TATDN2. Several of these nucleases cleave branched DNA structures at stressed replication forks to promote repair and restart of these forks. We recently defined roles for EEPD1 in restarting stressed replication forks after oxidative DNA damage, and for TATDN2 in mitigating replication stress caused by R-loop accumulation in BRCA1-defective cells. We also discuss how insights into biological responses to genome-wide replication stress can inform novel cancer treatment strategies that exploit synthetic lethal relationships among replication stress response factors.
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Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Aruna S. Jaiswal
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Elizabeth A. Williamson
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Manh T. Tran
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Dominic Arris
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Ming Yang
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
| | - Robert Hromas
- Department of Medicine and the Mays Cancer Center, The University of Texas Health Science Center San Antonio, San Antonio, TX 78229, USA; (A.S.J.); (M.T.T.); (R.H.)
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26
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Martínez-Rubio D, Hinarejos I, Argente-Escrig H, Marco-Marín C, Lozano MA, Gorría-Redondo N, Lupo V, Martí-Carrera I, Miranda C, Vázquez-López M, García-Pérez A, Marco-Hernández AV, Tomás-Vila M, Aguilera-Albesa S, Espinós C. Genetic Heterogeneity Underlying Phenotypes with Early-Onset Cerebellar Atrophy. Int J Mol Sci 2023; 24:16400. [PMID: 38003592 PMCID: PMC10671053 DOI: 10.3390/ijms242216400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Cerebellar atrophy (CA) is a frequent neuroimaging finding in paediatric neurology, usually associated with cerebellar ataxia. The list of genes involved in hereditary forms of CA is continuously growing and reveals its genetic complexity. We investigated ten cases with early-onset cerebellar involvement with and without ataxia by exome sequencing or by a targeted panel with 363 genes involved in ataxia or spastic paraplegia. Novel variants were investigated by in silico or experimental approaches. Seven probands carry causative variants in well-known genes associated with CA or cerebellar hypoplasia: SETX, CACNA1G, CACNA1A, CLN6, CPLANE1, and TBCD. The remaining three cases deserve special attention; they harbour variants in MAST1, PI4KA and CLK2 genes. MAST1 is responsible for an ultrarare condition characterised by global developmental delay and cognitive decline; our index case added ataxia to the list of concomitant associated symptoms. PIK4A is mainly related to hypomyelinating leukodystrophy; our proband presented with pure spastic paraplegia and normal intellectual capacity. Finally, in a patient who suffers from mild ataxia with oculomotor apraxia, the de novo novel CLK2 c.1120T>C variant was found. The protein expression of the mutated protein was reduced, which may indicate instability that would affect its kinase activity.
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Affiliation(s)
- Dolores Martínez-Rubio
- Rare Neurodegenerative Diseases Laboratory, Valencia Biomedical Research Foundation, Centro de Investigación Príncipe Felipe (CIPF), 46012 València, Spain
- Joint Unit CIPF-IIS La Fe Rare Diseases, 46012 València, Spain
| | - Isabel Hinarejos
- Rare Neurodegenerative Diseases Laboratory, Valencia Biomedical Research Foundation, Centro de Investigación Príncipe Felipe (CIPF), 46012 València, Spain
- Joint Unit CIPF-IIS La Fe Rare Diseases, 46012 València, Spain
| | | | - Clara Marco-Marín
- Structural Enzymopathology Unit, Instituto de Biomedicina de Valencia (IBV), Consejo Superior de Investigaciones Científicas (CSIC), 46022 València, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - María Ana Lozano
- Rare Neurodegenerative Diseases Laboratory, Valencia Biomedical Research Foundation, Centro de Investigación Príncipe Felipe (CIPF), 46012 València, Spain
| | - Nerea Gorría-Redondo
- Paediatric Neurology Unit, Department of Paediatrics, Hospital Universitario de Navarra, Navarrabiomed, 31008 Pamplona, Spain
| | - Vincenzo Lupo
- Rare Neurodegenerative Diseases Laboratory, Valencia Biomedical Research Foundation, Centro de Investigación Príncipe Felipe (CIPF), 46012 València, Spain
| | - Itxaso Martí-Carrera
- Paediatric Neurology Unit, Department of Paediatrics, Hospital Universitario Donostia, 20014 Donostia, Spain
| | - Concepción Miranda
- Paediatric Neurology Unit, Department of Paediatrics, Hospital General Universitario Gregorio Marañón, 28027 Madrid, Spain
| | - María Vázquez-López
- Paediatric Neurology Unit, Department of Paediatrics, Hospital General Universitario Gregorio Marañón, 28027 Madrid, Spain
| | - Asunción García-Pérez
- Paediatric Neurology Unit, Department of Paediatrics, Hospital Universitario Fundación Alcorcón, Alcorcón, 28922 Madrid, Spain
| | - Ana Victoria Marco-Hernández
- Paediatric Neurology Unit, Department of Paediatrics, Hospital Universitari Doctor, Peset, 46017 València, Spain
| | - Miguel Tomás-Vila
- Paediatric Neurology Unit, Department of Paediatrics, Hospital Universitari i Politècnic La Fe, 46026 València, Spain
| | - Sergio Aguilera-Albesa
- Paediatric Neurology Unit, Department of Paediatrics, Hospital Universitario de Navarra, Navarrabiomed, 31008 Pamplona, Spain
| | - Carmen Espinós
- Rare Neurodegenerative Diseases Laboratory, Valencia Biomedical Research Foundation, Centro de Investigación Príncipe Felipe (CIPF), 46012 València, Spain
- Joint Unit CIPF-IIS La Fe Rare Diseases, 46012 València, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
- Biotechnology Department, Universitat Politècnica de València, 46022 València, Spain
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27
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Bradley L, Savage KI. 'From R-lupus to cancer': Reviewing the role of R-loops in innate immune responses. DNA Repair (Amst) 2023; 131:103581. [PMID: 37832251 DOI: 10.1016/j.dnarep.2023.103581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
Cells possess an inherent and evolutionarily conserved ability to detect and respond to the presence of foreign and pathological 'self' nucleic acids. The result is the stimulation of innate immune responses, signalling to the host immune system that defence mechanisms are necessary to protect the organism. To date, there is a vast body of literature describing innate immune responses to various nucleic acid species, including dsDNA, ssDNA and ssRNA etc., however, there is limited information available on responses to R-loops. R-loops are 3-stranded nucleic acid structures that form during transcription, upon DNA damage and in various other settings. Emerging evidence suggests that innate immune responses may also exist for the detection of R-loop related nucleic acid structures, implicating R-loops as drivers of inflammatory states. In this review, we aim to summarise the evidence indicating that R-loops are immunogenic species that can trigger innate immune responses in physiological and pathological settings and discuss the implications of this in the study of various diseases and therapeutic development.
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Affiliation(s)
- Leanne Bradley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Rd, Belfast, United Kingdom
| | - Kienan I Savage
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Rd, Belfast, United Kingdom.
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28
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Yang S, Winstone L, Mondal S, Wu Y. Helicases in R-loop Formation and Resolution. J Biol Chem 2023; 299:105307. [PMID: 37778731 PMCID: PMC10641170 DOI: 10.1016/j.jbc.2023.105307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023] Open
Abstract
With the development and wide usage of CRISPR technology, the presence of R-loop structures, which consist of an RNA-DNA hybrid and a displaced single-strand (ss) DNA, has become well accepted. R-loop structures have been implicated in a variety of circumstances and play critical roles in the metabolism of nucleic acid and relevant biological processes, including transcription, DNA repair, and telomere maintenance. Helicases are enzymes that use an ATP-driven motor force to unwind double-strand (ds) DNA, dsRNA, or RNA-DNA hybrids. Additionally, certain helicases have strand-annealing activity. Thus, helicases possess unique positions for R-loop biogenesis: they utilize their strand-annealing activity to promote the hybridization of RNA to DNA, leading to the formation of R-loops; conversely, they utilize their unwinding activity to separate RNA-DNA hybrids and resolve R-loops. Indeed, numerous helicases such as senataxin (SETX), Aquarius (AQR), WRN, BLM, RTEL1, PIF1, FANCM, ATRX (alpha-thalassemia/mental retardation, X-linked), CasDinG, and several DEAD/H-box proteins are reported to resolve R-loops; while other helicases, such as Cas3 and UPF1, are reported to stimulate R-loop formation. Moreover, helicases like DDX1, DDX17, and DHX9 have been identified in both R-loop formation and resolution. In this review, we will summarize the latest understandings regarding the roles of helicases in R-loop metabolism. Additionally, we will highlight challenges associated with drug discovery in the context of targeting these R-loop helicases.
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Affiliation(s)
- Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lacey Winstone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sohaumn Mondal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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29
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Appel CD, Bermek O, Dandey VP, Wood M, Viverette E, Williams JG, Bouvette J, Riccio AA, Krahn JM, Borgnia MJ, Williams RS. Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2. Mol Cell 2023; 83:3692-3706.e5. [PMID: 37832548 PMCID: PMC10629462 DOI: 10.1016/j.molcel.2023.09.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/25/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
The senataxin (SETX, Sen1 in yeasts) RNA-DNA hybrid resolving helicase regulates multiple nuclear transactions, including DNA replication, transcription, and DNA repair, but the molecular basis for Sen1 activities is ill defined. Here, Sen1 cryoelectron microscopy (cryo-EM) reconstructions reveal an elongated inchworm-like architecture. Sen1 is composed of an amino terminal helical repeat Sen1 N-terminal (Sen1N) regulatory domain that is flexibly linked to its C-terminal SF1B helicase motor core (Sen1Hel) via an intrinsically disordered tether. In an autoinhibited state, the Sen1Sen1N domain regulates substrate engagement by promoting occlusion of the RNA substrate-binding cleft. The X-ray structure of an activated Sen1Hel engaging single-stranded RNA and ADP-SO4 shows that the enzyme encircles RNA and implicates a single-nucleotide power stroke in the Sen1 RNA translocation mechanism. Together, our data unveil dynamic protein-protein and protein-RNA interfaces underpinning helicase regulation and inactivation of human SETX activity by RNA-binding-deficient mutants in ataxia with oculomotor apraxia 2 neurodegenerative disease.
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Affiliation(s)
- C Denise Appel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Oya Bermek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Venkata P Dandey
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Makayla Wood
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Elizabeth Viverette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Jason G Williams
- Epigenetics and Stem Cell Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Jonathan Bouvette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Amanda A Riccio
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.
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Bennett CL, Dastidar S, Arnold FJ, McKinstry SU, Stockford C, Freibaum BD, Sopher BL, Wu M, Seidner G, Joiner W, Taylor JP, West RJH, La Spada AR. Senataxin helicase, the causal gene defect in ALS4, is a significant modifier of C9orf72 ALS G4C2 and arginine-containing dipeptide repeat toxicity. Acta Neuropathol Commun 2023; 11:164. [PMID: 37845749 PMCID: PMC10580588 DOI: 10.1186/s40478-023-01665-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023] Open
Abstract
Identifying genetic modifiers of familial amyotrophic lateral sclerosis (ALS) may reveal targets for therapeutic modulation with potential application to sporadic ALS. GGGGCC (G4C2) repeat expansions in the C9orf72 gene underlie the most common form of familial ALS, and generate toxic arginine-containing dipeptide repeats (DPRs), which interfere with membraneless organelles, such as the nucleolus. Here we considered senataxin (SETX), the genetic cause of ALS4, as a modifier of C9orf72 ALS, because SETX is a nuclear helicase that may regulate RNA-protein interactions involved in ALS dysfunction. After documenting that decreased SETX expression enhances arginine-containing DPR toxicity and C9orf72 repeat expansion toxicity in HEK293 cells and primary neurons, we generated SETX fly lines and evaluated the effect of SETX in flies expressing either (G4C2)58 repeats or glycine-arginine-50 [GR(50)] DPRs. We observed dramatic suppression of disease phenotypes in (G4C2)58 and GR(50) Drosophila models, and detected a striking relocalization of GR(50) out of the nucleolus in flies co-expressing SETX. Next-generation GR(1000) fly models, that show age-related motor deficits in climbing and movement assays, were similarly rescued with SETX co-expression. We noted that the physical interaction between SETX and arginine-containing DPRs is partially RNA-dependent. Finally, we directly assessed the nucleolus in cells expressing GR-DPRs, confirmed reduced mobility of proteins trafficking to the nucleolus upon GR-DPR expression, and found that SETX dosage modulated nucleolus liquidity in GR-DPR-expressing cells and motor neurons. These findings reveal a hitherto unknown connection between SETX function and cellular processes contributing to neuron demise in the most common form of familial ALS.
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Affiliation(s)
- Craig L Bennett
- Departments of Pathology, Laboratory Medicine, Neurology, and Biological Chemistry, UCI Center for Neurotherapeutics, University of California Irvine School of Medicine, Irvine, CA, 92697, USA
- Department of Neurology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Somasish Dastidar
- Department of Neurology, Duke University School of Medicine, Durham, NC, 27710, USA
- Center for Molecular Neurosciences, Kasturba Medical College, Manipal, 576104, India
| | - Frederick J Arnold
- Departments of Pathology, Laboratory Medicine, Neurology, and Biological Chemistry, UCI Center for Neurotherapeutics, University of California Irvine School of Medicine, Irvine, CA, 92697, USA
| | - Spencer U McKinstry
- Department of Neurology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Cameron Stockford
- Departments of Pathology, Laboratory Medicine, Neurology, and Biological Chemistry, UCI Center for Neurotherapeutics, University of California Irvine School of Medicine, Irvine, CA, 92697, USA
| | - Brian D Freibaum
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Bryce L Sopher
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, 98195, USA
| | - Meilin Wu
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Glen Seidner
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - William Joiner
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, 98195, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Ryan J H West
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, S10 2HQ, UK.
- Neuroscience Institute, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Albert R La Spada
- Departments of Pathology, Laboratory Medicine, Neurology, and Biological Chemistry, UCI Center for Neurotherapeutics, University of California Irvine School of Medicine, Irvine, CA, 92697, USA.
- Department of Neurology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Neurobiology and Behavior, University of California Irvine School of Biosciences, Irvine, CA, 92697, USA.
- UCI Center for Neurotherapeutics, University of California Irvine, Irvine, CA, 92697, USA.
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31
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Bohnsack KE, Yi S, Venus S, Jankowsky E, Bohnsack MT. Cellular functions of eukaryotic RNA helicases and their links to human diseases. Nat Rev Mol Cell Biol 2023; 24:749-769. [PMID: 37474727 DOI: 10.1038/s41580-023-00628-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
RNA helicases are highly conserved proteins that use nucleoside triphosphates to bind or remodel RNA, RNA-protein complexes or both. RNA helicases are classified into the DEAD-box, DEAH/RHA, Ski2-like, Upf1-like and RIG-I families, and are the largest class of enzymes active in eukaryotic RNA metabolism - virtually all aspects of gene expression and its regulation involve RNA helicases. Mutation and dysregulation of these enzymes have been linked to a multitude of diseases, including cancer and neurological disorders. In this Review, we discuss the regulation and functional mechanisms of RNA helicases and their roles in eukaryotic RNA metabolism, including in transcription regulation, pre-mRNA splicing, ribosome assembly, translation and RNA decay. We highlight intriguing models that link helicase structure, mechanisms of function (such as local strand unwinding, translocation, winching, RNA clamping and displacing RNA-binding proteins) and biological roles, including emerging connections between RNA helicases and cellular condensates formed through liquid-liquid phase separation. We also discuss associations of RNA helicases with human diseases and recent efforts towards the design of small-molecule inhibitors of these pivotal regulators of eukaryotic gene expression.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna, Cambridge, MA, USA.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Germany.
- Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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32
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Stump AL, Rioux DJ, Albright R, Melki GL, Prosser DC. Yeast Models of Amyotrophic Lateral Sclerosis Type 8 Mimic Phenotypes Seen in Mammalian Cells Expressing Mutant VAPB P56S. Biomolecules 2023; 13:1147. [PMID: 37509182 PMCID: PMC10377116 DOI: 10.3390/biom13071147] [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: 05/14/2023] [Revised: 07/09/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disease that results in the loss of motor neurons and can occur sporadically or due to genetic mutations. Among the 30 genes linked to familial ALS, a P56S mutation in VAPB, an ER-resident protein that functions at membrane contact sites, causes ALS type 8. Mammalian cells expressing VAPBP56S have distinctive phenotypes, including ER collapse, protein and/or membrane-containing inclusions, and sensitivity to ER stress. VAPB is conserved through evolution and has two homologs in budding yeast, SCS2 and SCS22. Previously, a humanized version of SCS2 bearing disease-linked mutations was described, and it caused Scs2-containing inclusions when overexpressed in yeast. Here, we describe a yeast model for ALS8 in which the two SCS genes are deleted and replaced with a single chromosomal copy of either wild-type or mutant yeast SCS2 or human VAPB expressed from the SCS2 promoter. These cells display ER collapse, the formation of inclusion-like structures, and sensitivity to tunicamycin, an ER stress-inducing drug. Based on the phenotypic similarity to mammalian cells expressing VAPBP56S, we propose that these models can be used to study the molecular basis of cell death or dysfunction in ALS8. Moreover, other conserved ALS-linked genes may create opportunities for the generation of yeast models of disease.
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Affiliation(s)
- AnnaMari L. Stump
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
- VCU Life Sciences, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Daniel J. Rioux
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
- VCU Life Sciences, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Richard Albright
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Guiliano L. Melki
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Derek C. Prosser
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA
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33
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Saadi SM, Cali E, Khalid LB, Yousaf H, Zafar G, Khan HN, Sher M, Vona B, Abdullah U, Malik NA, Klar J, Efthymiou S, Dahl N, Houlden H, Toft M, Baig SM, Fatima A, Iqbal Z. Genetic Investigation of Consanguineous Pakistani Families Segregating Rare Spinocerebellar Disorders. Genes (Basel) 2023; 14:1404. [PMID: 37510308 PMCID: PMC10379343 DOI: 10.3390/genes14071404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Spinocerebellar disorders are a vast group of rare neurogenetic conditions, generally characterized by overlapping clinical symptoms including progressive cerebellar ataxia, spastic paraparesis, cognitive deficiencies, skeletal/muscular and ocular abnormalities. The objective of the present study is to identify the underlying genetic causes of the rare spinocerebellar disorders in the Pakistani population. Herein, nine consanguineous families presenting different spinocerebellar phenotypes have been investigated using whole exome sequencing. Sanger sequencing was performed for segregation analysis in all the available individuals of each family. The molecular analysis of these families identified six novel pathogenic/likely pathogenic variants; ZFYVE26: c.1093del, SACS: c.1201C>T, BICD2: c.2156A>T, ALS2: c.2171-3T>G, ALS2: c.3145T>A, and B4GALNT1: c.334_335dup, and three already reported pathogenic variants; FA2H: c.159_176del, APTX: c.689T>G, and SETX: c.5308_5311del. The clinical features of all patients in each family are concurrent with the already reported cases. Hence, the current study expands the mutation spectrum of rare spinocerebellar disorders and implies the usefulness of next-generation sequencing in combination with clinical investigation for better diagnosis of these overlapping phenotypes.
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Affiliation(s)
- Saadia Maryam Saadi
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Elisa Cali
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Lubaba Bintee Khalid
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan
| | - Hammad Yousaf
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan
| | - Ghazala Zafar
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan
| | - Haq Nawaz Khan
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan
| | - Muhammad Sher
- Department of Allied Health Sciences, Iqra National University Swat Campus, Swat 19200, Pakistan
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Uzma Abdullah
- University Institute of Biochemistry and Biotechnology (UIBB), Pir Mehr Ali Shah Arid Agriculture University Rawalpindi (PMAS-AAUR), Rawalpindi 46300, Pakistan
| | - Naveed Altaf Malik
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, P.O. Box 815, 751 08 Uppsala, Sweden
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Uppsala University and Science for Life Laboratory, P.O. Box 815, 751 08 Uppsala, Sweden
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Mathias Toft
- Institute of Clinical Medicine, University of Oslo, P.O. Box 1171, N-0318 Oslo, Norway
- Department of Neurology, Oslo University Hospital, P.O. Box 4950 Nydalen, N-0424 Oslo, Norway
| | - Shahid Mahmood Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad 44000, Pakistan
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan
| | - Ambrin Fatima
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74000, Pakistan
| | - Zafar Iqbal
- Department of Neurology, Oslo University Hospital, P.O. Box 4950 Nydalen, N-0424 Oslo, Norway
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Gatti V, De Domenico S, Melino G, Peschiaroli A. Senataxin and R-loops homeostasis: multifaced implications in carcinogenesis. Cell Death Discov 2023; 9:145. [PMID: 37147318 PMCID: PMC10163015 DOI: 10.1038/s41420-023-01441-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/06/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
R-loops are inherent byproducts of transcription consisting of an RNA:DNA hybrid and a displaced single-stranded DNA. These structures are of key importance in controlling numerous physiological processes and their homeostasis is tightly controlled by the activities of several enzymes deputed to process R-loops and prevent their unproper accumulation. Senataxin (SETX) is an RNA/DNA helicase which catalyzes the unwinding of RNA:DNA hybrid portion of the R-loops, promoting thus their resolution. The key importance of SETX in R-loops homeostasis and its relevance with pathophysiological events is highlighted by the evidence that gain or loss of function SETX mutations underlie the pathogenesis of two distinct neurological disorders. Here, we aim to describe the potential impact of SETX on tumor onset and progression, trying to emphasize how dysregulation of this enzyme observed in human tumors might impact tumorigenesis. To this aim, we will describe the functional relevance of SETX in regulating gene expression, genome integrity, and inflammation response and discuss how cancer-associated SETX mutations might affect these pathways, contributing thus to tumor development.
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Affiliation(s)
- Veronica Gatti
- National Research Council of Italy, Institute of Translational Pharmacology, Rome, Italy
| | - Sara De Domenico
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, Rome, Italy
| | - Angelo Peschiaroli
- National Research Council of Italy, Institute of Translational Pharmacology, Rome, Italy.
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35
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Higuchi Y, Takashima H. Clinical genetics of Charcot-Marie-Tooth disease. J Hum Genet 2023; 68:199-214. [PMID: 35304567 DOI: 10.1038/s10038-022-01031-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/02/2022] [Accepted: 03/06/2022] [Indexed: 02/08/2023]
Abstract
Recent research in the field of inherited peripheral neuropathies (IPNs) such as Charcot-Marie-Tooth (CMT) disease has helped identify the causative genes provided better understanding of the pathogenesis, and unraveled potential novel therapeutic targets. Several reports have described the epidemiology, clinical characteristics, molecular pathogenesis, and novel causative genes for CMT/IPNs in Japan. Based on the functions of the causative genes identified so far, the following molecular and cellular mechanisms are believed to be involved in the causation of CMTs/IPNs: myelin assembly, cytoskeletal structure, myelin-specific transcription factor, nuclear related, endosomal sorting and cell signaling, proteasome and protein aggregation, mitochondria-related, motor proteins and axonal transport, tRNA synthetases and RNA metabolism, and ion channel-related mechanisms. In this article, we review the epidemiology, genetic diagnosis, and clinicogenetic characteristics of CMT in Japan. In addition, we discuss the newly identified novel causative genes for CMT/IPNs in Japan, namely MME and COA7. Identification of the new causes of CMT will facilitate in-depth characterization of the underlying molecular mechanisms of CMT, leading to the establishment of therapeutic approaches such as drug development and gene therapy.
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Affiliation(s)
- Yujiro Higuchi
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hiroshi Takashima
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.
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36
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Vadla GP, Ricardez Hernandez SM, Mao J, Garro-Kacher MO, Lorson ZC, Rice RP, Hansen SA, Lorson CL, Singh K, Lorson MA. ABT1 modifies SMARD1 pathology via interactions with IGHMBP2 and stimulation of ATPase and helicase activity. JCI Insight 2023; 8:e164608. [PMID: 36480289 PMCID: PMC9977310 DOI: 10.1172/jci.insight.164608] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
SMA with respiratory distress type 1 (SMARD1) and Charcot-Marie-Tooth type 2S (CMT2S) are results of mutations in immunoglobulin mu DNA binding protein 2 (IGHMBP2). IGHMBP2 is a UPF1-like helicase with proposed roles in several cellular processes, including translation. This study examines activator of basal transcription 1 (ABT1), a modifier of SMARD1-nmd disease pathology. Microscale thermophoresis and dynamic light scattering demonstrate that IGHMBP2 and ABT1 proteins directly interact with high affinity. The association of ABT1 with IGHMBP2 significantly increases the ATPase and helicase activity as well as the processivity of IGHMBP2. The IGHMBP2/ABT1 complex interacts with the 47S pre-rRNA 5' external transcribed spacer and U3 small nucleolar RNA (snoRNA), suggesting that the IGHMBP2/ABT1 complex is important for pre-rRNA processing. Intracerebroventricular injection of scAAV9-Abt1 decreases FVB-Ighmbp2nmd/nmd disease pathology, significantly increases lifespan, and substantially decreases neuromuscular junction denervation. To our knowledge, ABT1 is the first disease-modifying gene identified for SMARD1. We provide a mechanism proposing that ABT1 decreases disease pathology in FVB-Ighmbp2nmd/nmd mutants by optimizing IGHMBP2 biochemical activity (ATPase and helicase activity). Our studies provide insight into SMARD1 pathogenesis, suggesting that ABT1 modifies IGHMBP2 activity as a means to regulate pre-rRNA processing.
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Affiliation(s)
- Gangadhar P. Vadla
- Department of Veterinary Pathobiology, College of Veterinary Medicine, and
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Sara M. Ricardez Hernandez
- Department of Veterinary Pathobiology, College of Veterinary Medicine, and
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Jiude Mao
- Department of Veterinary Pathobiology, College of Veterinary Medicine, and
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Mona O. Garro-Kacher
- Department of Veterinary Pathobiology, College of Veterinary Medicine, and
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Zachary C. Lorson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, and
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Ronin P. Rice
- Department of Veterinary Pathobiology, College of Veterinary Medicine, and
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Sarah A. Hansen
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Christian L. Lorson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, and
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Kamal Singh
- Department of Veterinary Pathobiology, College of Veterinary Medicine, and
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Monique A. Lorson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, and
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
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37
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Faravelli I, Riboldi GM, Rinchetti P, Lotti F. The SMN Complex at the Crossroad between RNA Metabolism and Neurodegeneration. Int J Mol Sci 2023; 24:2247. [PMID: 36768569 PMCID: PMC9917330 DOI: 10.3390/ijms24032247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
In the cell, RNA exists and functions in a complex with RNA binding proteins (RBPs) that regulate each step of the RNA life cycle from transcription to degradation. Central to this regulation is the role of several molecular chaperones that ensure the correct interactions between RNA and proteins, while aiding the biogenesis of large RNA-protein complexes (ribonucleoproteins or RNPs). Accurate formation of RNPs is fundamentally important to cellular development and function, and its impairment often leads to disease. The survival motor neuron (SMN) protein exemplifies this biological paradigm. SMN is part of a multi-protein complex essential for the biogenesis of various RNPs that function in RNA metabolism. Mutations leading to SMN deficiency cause the neurodegenerative disease spinal muscular atrophy (SMA). A fundamental question in SMA biology is how selective motor system dysfunction results from reduced levels of the ubiquitously expressed SMN protein. Recent clarification of the central role of the SMN complex in RNA metabolism and a thorough characterization of animal models of SMA have significantly advanced our knowledge of the molecular basis of the disease. Here we review the expanding role of SMN in the regulation of gene expression through its multiple functions in RNP biogenesis. We discuss developments in our understanding of SMN activity as a molecular chaperone of RNPs and how disruption of SMN-dependent RNA pathways can contribute to the SMA phenotype.
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Affiliation(s)
- Irene Faravelli
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Center for Motor Neuron Biology and Diseases, Departments of Pathology & Cell Biology, and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Giulietta M. Riboldi
- Center for Motor Neuron Biology and Diseases, Departments of Pathology & Cell Biology, and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- The Marlene and Paolo Fresco Institute for Parkinson’s and Movement Disorders, NYU Langone Health, New York, NY 10017, USA
| | - Paola Rinchetti
- Center for Motor Neuron Biology and Diseases, Departments of Pathology & Cell Biology, and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Francesco Lotti
- Center for Motor Neuron Biology and Diseases, Departments of Pathology & Cell Biology, and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
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38
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Sarker AH, Cooper PK. Slot Blot Assay for Detection of R Loops. Methods Mol Biol 2023; 2701:149-156. [PMID: 37574480 DOI: 10.1007/978-1-0716-3373-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
R loops (DNA-RNA hybrid) are three-stranded nucleic acid structures that comprise of template DNA strand hybridized with the nascent RNA leaving the displaced non-template strand. Although a programmed R loop formation can serve as powerful regulators of gene expression, these structures can also turn into major sources of genomic instability and contribute to the development of diseases. Therefore, understanding how cells prevent the deleterious consequences of R loops yet allow R loop formation to participate in various physiological processes will help to understand how their homeostasis is maintained. Detection and quantitative measurements of R loops are critical that largely relied on S9.6 antibody. Immunofluorescence methods are frequently used to localize and quantify R loops in the cell but they require specialized tools for analysis and relatively expensive; therefore, they are not always useful for initial assessments of R loop accumulation. Here, we describe an improved slot blot protocol to detect and estimate R loops and show its sensitivity and specificity using the S9.6 antibody. Since specific factors protecting cells from harmful R loop accumulation are expanding, this protocol can be used to determine R loop accumulation in research and clinical settings.
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Affiliation(s)
- Altaf H Sarker
- Department of BioEngineering and BioMedical Sciences, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Priscilla K Cooper
- Department of BioEngineering and BioMedical Sciences, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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39
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Younger DS. Neurogenetic motor disorders. HANDBOOK OF CLINICAL NEUROLOGY 2023; 195:183-250. [PMID: 37562870 DOI: 10.1016/b978-0-323-98818-6.00003-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Advances in the field of neurogenetics have practical applications in rapid diagnosis on blood and body fluids to extract DNA, obviating the need for invasive investigations. The ability to obtain a presymptomatic diagnosis through genetic screening and biomarkers can be a guide to life-saving disease-modifying therapy or enzyme replacement therapy to compensate for the deficient disease-causing enzyme. The benefits of a comprehensive neurogenetic evaluation extend to family members in whom identification of the causal gene defect ensures carrier detection and at-risk counseling for future generations. This chapter explores the many facets of the neurogenetic evaluation in adult and pediatric motor disorders as a primer for later chapters in this volume and a roadmap for the future applications of genetics in neurology.
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Affiliation(s)
- David S Younger
- Department of Clinical Medicine and Neuroscience, CUNY School of Medicine, New York, NY, United States; Department of Medicine, Section of Internal Medicine and Neurology, White Plains Hospital, White Plains, NY, United States.
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Said M, Barra V, Balzano E, Talhaoui I, Pelliccia F, Giunta S, Naim V. FANCD2 promotes mitotic rescue from transcription-mediated replication stress in SETX-deficient cancer cells. Commun Biol 2022; 5:1395. [PMID: 36543851 PMCID: PMC9772326 DOI: 10.1038/s42003-022-04360-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Replication stress (RS) is a leading cause of genome instability and cancer development. A substantial source of endogenous RS originates from the encounter between the transcription and replication machineries operating on the same DNA template. This occurs predominantly under specific contexts, such as oncogene activation, metabolic stress, or a deficiency in proteins that specifically act to prevent or resolve those transcription-replication conflicts (TRCs). One such protein is Senataxin (SETX), an RNA:DNA helicase involved in resolution of TRCs and R-loops. Here we identify a synthetic lethal interaction between SETX and proteins of the Fanconi anemia (FA) pathway. Depletion of SETX induces spontaneous under-replication and chromosome fragility due to active transcription and R-loops that persist in mitosis. These fragile loci are targeted by the Fanconi anemia protein, FANCD2, to facilitate the resolution of under-replicated DNA, thus preventing chromosome mis-segregation and allowing cells to proliferate. Mechanistically, we show that FANCD2 promotes mitotic DNA synthesis that is dependent on XPF and MUS81 endonucleases. Importantly, co-depleting FANCD2 together with SETX impairs cancer cell proliferation, without significantly affecting non-cancerous cells. Therefore, we uncovered a synthetic lethality between SETX and FA proteins for tolerance of transcription-mediated RS that may be exploited for cancer therapy.
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Affiliation(s)
- Maha Said
- grid.14925.3b0000 0001 2284 9388CNRS UMR9019, Université Paris-Saclay, Gustave Roussy, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Viviana Barra
- grid.10776.370000 0004 1762 5517Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Elisa Balzano
- grid.7841.aDepartment of Biology & Biotechnology “Charles Darwin”, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Ibtissam Talhaoui
- grid.14925.3b0000 0001 2284 9388CNRS UMR9019, Université Paris-Saclay, Gustave Roussy, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Franca Pelliccia
- grid.7841.aDepartment of Biology & Biotechnology “Charles Darwin”, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Simona Giunta
- grid.7841.aDepartment of Biology & Biotechnology “Charles Darwin”, University of Rome Sapienza, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Valeria Naim
- grid.14925.3b0000 0001 2284 9388CNRS UMR9019, Université Paris-Saclay, Gustave Roussy, 114 rue Edouard Vaillant, 94805 Villejuif, France
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Rosenbohm A, Pott H, Thomsen M, Rafehi H, Kaya S, Szymczak S, Volk AE, Mueller K, Silveira I, Weishaupt JH, Tönnies H, Seibler P, Zschiedrich K, Schaake S, Westenberger A, Zühlke C, Depienne C, Trinh J, Ludolph AC, Klein C, Bahlo M, Lohmann K. Familial Cerebellar Ataxia and Amyotrophic Lateral Sclerosis/Frontotemporal Dementia with DAB1 and C9ORF72 Repeat Expansions: An 18-Year Study. Mov Disord 2022; 37:2427-2439. [PMID: 36148898 PMCID: PMC10900262 DOI: 10.1002/mds.29221] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/27/2022] [Accepted: 08/10/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Coding and noncoding repeat expansions are an important cause of neurodegenerative diseases. OBJECTIVE This study determined the clinical and genetic features of a large German family that has been followed for almost 2 decades with an autosomal dominantly inherited spinocerebellar ataxia (SCA) and independent co-occurrence of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). METHODS We carried out clinical examinations and telephone interviews, reviewed medical records, and performed magnetic resonance imaging and positron emission tomography scans of all available family members. Comprehensive genetic investigations included linkage analysis, short-read genome sequencing, long-read sequencing, repeat-primed polymerase chain reaction, and Southern blotting. RESULTS The family comprises 118 members across seven generations, 30 of whom were definitely and five possibly affected. In this family, two different pathogenic mutations were found, a heterozygous repeat expansion in C9ORF72 in four patients with ALS/FTD and a heterozygous repeat expansion in DAB1 in at least nine patients with SCA, leading to a diagnosis of DAB1-related ataxia (ATX-DAB1; SCA37). One patient was affected by ALS and SCA and carried both repeat expansions. The repeat in DAB1 had the same configuration but was larger than those previously described ([ATTTT]≈75 [ATTTC]≈40-100 [ATTTT]≈415 ). Clinical features in patients with SCA included spinocerebellar symptoms, sometimes accompanied by additional ophthalmoplegia, vertical nystagmus, tremor, sensory deficits, and dystonia. After several decades, some of these patients suffered from cognitive decline and one from additional nonprogressive lower motor neuron affection. CONCLUSION We demonstrate genetic and clinical findings during an 18-year period in a unique family carrying two different pathogenic repeat expansions, providing novel insights into their genotypic and phenotypic spectrums. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
| | - Hendrik Pott
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Mirja Thomsen
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Haloom Rafehi
- Division of Population Health and ImmunityThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
| | - Sabine Kaya
- Institute of Human GeneticsUniversity Hospital EssenEssenGermany
| | - Silke Szymczak
- Insitute of Medical Biometry and StatisticsUniversity of LübeckLübeckGermany
| | - Alexander E. Volk
- Institute of Human GeneticsUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | | | - Isabel Silveira
- i3S‐Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
| | - Jochen H. Weishaupt
- Division of Neurodegeneration, Neurology DepartmentUniversity Medicine Mannheim, Heidelberg UniversityMannheimGermany
| | - Holger Tönnies
- Institute of Human GeneticsChristian‐Albrechts‐UniversityKielGermany
| | - Philip Seibler
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | | | - Susen Schaake
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | | | | | | | - Joanne Trinh
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | - Albert C. Ludolph
- Department of NeurologyUniversity of UlmUlmGermany
- German Center for Neurodegenerative Diseases, Site UlmUlmGermany
| | | | - Melanie Bahlo
- Division of Population Health and ImmunityThe Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical BiologyThe University of MelbourneParkvilleAustralia
| | - Katja Lohmann
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
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Baviera-Muñoz R, Carretero-Vilarroig L, Vázquez-Costa JF, Morata-Martínez C, Campins-Romeu M, Muelas N, Sastre-Bataller I, Martínez-Torres I, Pérez-García J, Sivera R, Sevilla T, Vilchez JJ, Jaijo T, Espinós C, Millán JM, Bataller L, Aller E. Diagnostic Efficacy of Genetic Studies in a Series of Hereditary Cerebellar Ataxias in Eastern Spain. NEUROLOGY GENETICS 2022; 8:e200038. [DOI: 10.1212/nxg.0000000000200038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022]
Abstract
Background and ObjectivesTo determine the diagnostic efficacy of clinical exome-targeted sequencing (CES) and spinocerebellar ataxia 36 (SCA36) screening in a real-life cohort of patients with cerebellar ataxia (CA) from Eastern Spain.MethodsA total of 130 unrelated patients with CA, negative for common trinucleotide repeat expansions (SCA1, SCA2, SCA3, SCA6, SCA7, SCA8, SCA12, SCA17, dentatorubral pallidoluysian atrophy [DRPLA], and Friedreich ataxia), were studied with CES. Bioinformatic and genotype-phenotype analyses were performed to assess the pathogenicity of the variants encountered. Copy number variants were analyzed when appropriate. In undiagnosed dominant and sporadic cases, repeat primed PCR was used to screen for the presence of a repeat expansion in theNOP56gene.ResultsCES identified pathogenic or likely pathogenic variants in 50 families (39%), including 23 novel variants. Overall, there was a high genetic heterogeneity, and the most frequent genetic diagnosis wasSPG7(n = 15), followed bySETX(n = 6),CACNA1A(n = 5),POLR3A(n = 4), andSYNE1(n = 3). In addition, 17 families displayed likely pathogenic/pathogenic variants in 14 different genes:KCND3(n = 2),KIF1C(n = 2),CYP27A1A(n = 2),AFG3L2(n = 1),ANO10(n = 1),CAPN1(n = 1),CWF19L1(n = 1),ITPR1(n = 1),KCNA1(n = 1),OPA1(n = 1),PNPLA6(n = 1),SPG11(n = 1),SPTBN2(n = 1), andTPP1(n = 1). Twenty-two novel variants were characterized. SCA36 was diagnosed in 11 families, all with autosomal dominant (AD) presentation. SCA36 screening increased the total diagnostic rate to 47% (n = 61/130). Ultimately, undiagnosed patients showed delayed age at onset (p< 0.05) and were more frequently sporadic.DiscussionOur study provides insight into the genetic landscape of CA in Eastern Spain. Although CES was an effective approach to capture genetic heterogeneity, most patients remained undiagnosed. SCA36 was found to be a relatively frequent form and, therefore, should be tested prior to CES in familial AD presentations in particular geographical regions.
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Chen S, Du J, Jiang H, Zhao W, Wang N, Ying A, Li J, Chen S, Shen B, Zhou Y. Ataxia with oculomotor apraxia type 2 caused by a novel homozygous mutation in SETX gene, and literature review. Front Mol Neurosci 2022; 15:1019974. [DOI: 10.3389/fnmol.2022.1019974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/26/2022] [Indexed: 11/11/2022] Open
Abstract
ObjectivesAutosomal recessive inherited ataxia with oculomotor apraxia type 2 (AOA2), caused by SETX gene mutations, is characterized by early-onset, progressive cerebellar ataxia, peripheral neuropathy, oculomotor apraxia and elevated serum α-fetoprotein (AFP). This study aimed to expand and summarize the clinical and genetic characteristics of SETX variants related to AOA2.MethodsThe biochemical parameters, electromyogram and radiological findings of the patient were evaluated. Whole-exome sequencing (WES) was performed on the patient using next-generation sequencing (NGS), the variants were confirmed by Sanger sequencing and the pathogenicity of the variants was classified according to the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines. We reviewed 57 studies of AOA2 patients with SETX mutations and collected clinical and genetic information.ResultsThe patient was a 40-year-old Chinese woman who primarily presented with numbness and weakness of the lower limbs in her teenage years. She had elevated AFP, increased serum follicle-stimulating hormone (FSH) and luteinizing hormone (LH) and decreased anti-Müllerian hormone (AMH) levels. We identified a novel homozygous missense mutation of the SETX gene, c.7118 C>T (p. Thr2373Ile), in the patient via Whole-exome and Sanger sequencing. The variant was located in the DNA/RNA helicase domain and is highly conserved. The protein prediction analysis verified the SETX variant as a damaging alteration and ACMG/AMP guidelines classified it as likely pathogenic. Through a literature review, we identified 229 AOA2 cases with SETX variants, and among the variants, 156 SETX variants were exonic. We found that 107 (46.7%) patients were European, 50 (21.8%) were African and 48 (21.0%) were Asian. Among the Asian patients, five from two families were Mainland Chinese. The main clinical features were cerebellar ataxia (100%), peripheral neuropathy (94.6%), cerebellar atrophy (95.3%) and elevated AFP concentration (92.0%). Most reported SETX mutations in AOA2 patients were missense, frameshift and nonsense mutations.ConclusionWe discovered a novel homozygous variant of the SETX gene as a cause of AOA2 in the current patient and expanded the genotypic spectrum of AOA2. Moreover, the clinical features of AOA2 and genetic findings in SETX were assessed in reported cohorts and are summarized in the present study.
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R-Loop Formation in Meiosis: Roles in Meiotic Transcription-Associated DNA Damage. EPIGENOMES 2022; 6:epigenomes6030026. [PMID: 36135313 PMCID: PMC9498298 DOI: 10.3390/epigenomes6030026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/24/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
Meiosis is specialized cell division during gametogenesis that produces genetically unique gametes via homologous recombination. Meiotic homologous recombination entails repairing programmed 200–300 DNA double-strand breaks generated during the early prophase. To avoid interference between meiotic gene transcription and homologous recombination, mammalian meiosis is thought to employ a strategy of exclusively transcribing meiotic or post-meiotic genes before their use. Recent studies have shown that R-loops, three-stranded DNA/RNA hybrid nucleotide structures formed during transcription, play a crucial role in transcription and genome integrity. Although our knowledge about the function of R-loops during meiosis is limited, recent findings in mouse models have suggested that they play crucial roles in meiosis. Given that defective formation of an R-loop can cause abnormal transcription and transcription-coupled DNA damage, the precise regulatory network of R-loops may be essential in vivo for the faithful progression of mammalian meiosis and gametogenesis.
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Scarian E, Fiamingo G, Diamanti L, Palmieri I, Gagliardi S, Pansarasa O. The Role of VCP Mutations in the Spectrum of Amyotrophic Lateral Sclerosis-Frontotemporal Dementia. Front Neurol 2022; 13:841394. [PMID: 35273561 PMCID: PMC8902152 DOI: 10.3389/fneur.2022.841394] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/28/2022] [Indexed: 01/02/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) are two neurological diseases which, respectively, and primarily affect motor neurons and frontotemporal lobes. Although they can lead to different signs and symptoms, it is now evident that these two pathologies form a continuum and that hallmarks of both diseases can be present within the same person in the so-called ALS-FTD spectrum. Many studies have focused on the genetic overlap of these pathologies and it is now clear that different genes, such as C9orf72, TARDBP, SQSTM1, FUS, and p97/VCP can be mutated in both the diseases. VCP was one of the first genes associated with both FTD and ALS representing an early example of gene overlapping. VCP belongs to the type II AAA (ATPases Associated with diverse cellular activities) family and is involved in ubiquitinated proteins degradation, autophagy, lysosomal clearance and mitochondrial quality control. Since its numerous roles, mutations in this gene lead to different pathological features, first and foremost TDP-43 mislocalization. This review aims to outline recent findings on VCP roles and on how its mutations are linked to the neuropathology of ALS and FTD.
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Affiliation(s)
- Eveljn Scarian
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy.,Cellular Models and Neuroepigenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Giuseppe Fiamingo
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Luca Diamanti
- Neuroncology Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Ilaria Palmieri
- Department of Molecular Medicine, University of Pavia, Pavia, Italy.,Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Stella Gagliardi
- Molecular Biology and Transcriptomics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Orietta Pansarasa
- Cellular Models and Neuroepigenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
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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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Chavda V, Patel C, Modh D, Ertas YN, Sonak SS, Munshi NK, Anand K, Soni A, Pandey S. Therapeutic Approaches to Amyotrophic Lateral Sclerosis from the Lab to the Clinic. Curr Drug Metab 2022; 23:200-222. [PMID: 35272595 DOI: 10.2174/1389200223666220310113110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 01/07/2022] [Accepted: 02/02/2022] [Indexed: 11/22/2022]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a terminal neuro-degenerative disorder that is clinically recognized as a gradual degeneration of the upper and lower motor neurons, with an average duration of 3 to 5 years from initiation of symptoms to death. The mechanisms underlying the pathogenesis and progression of the disease are multifactorial. Therefore, to find effective treatments, it is necessary to understand this heterogeneity underlying the progression of ALS. Recent developments in gene therapy have opened a new avenue to treat this condition, especially for the characterized genetic types. Gene therapy methods have been studied in a variety of pre-clinical settings and clinical trials, and they may be a promising path for developing an effective and safe ALS cure. A growing body of evidence demonstrates abnormalities in energy metabolism at the cellular and whole-body level in animal models and in people living with ALS. The use and incorporation of high-throughput "omics" methods has radically transformed our thought about ALS, strengthening our understanding of the disease's dynamic molecular architecture, differentiating distinct patient subtypes, and creating a reasonable basis for the identification of biomarkers and novel individualised treatments. Future clinical and laboratory trials would also focus on the diverse relationships between metabolism and ALS to address the issue of whether targeting deficient metabolism in ALS is an effective way to change disease progression. In this review, we focus on the detailed pathogenesis of ALS and highlight principal genes, i.e., SOD1, TDP-43, C9orf72, and FUS, targeted therapeutic approaches of ALS. An attempt is made to provide up-to-date information on clinical outcomes, including various biomarkers which are thought to be important players in early ALS detection.
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Affiliation(s)
- Vivek Chavda
- Department of Pharmaceutic, L M College of Pharmacy, Ahmedabad - 380009 (India)
| | - Chirag Patel
- Department of Pharmacology, L M College of Pharmacy, Ahmedabad - 380009 (India)
| | - Dharti Modh
- Department of pharmaceutical chemistry, Poona college of pharmacy, Bharti vidhyapith, Pune - 411030 (India)
| | - Yavuz Nuri Ertas
- Department of Biomedical Engineering at Erciyes University, Kayseri, Turkey
- ERNAM - Nanotechnology Research and Application Center, Erciyes University, Kayseri 38039, Turkey
| | - Shreya S Sonak
- Department of pharmaceutical chemistry, Poona college of pharmacy, Bharti vidhyapith, Pune - 411030 (India)
| | - Nafisa K Munshi
- Department of pharmaceutical chemistry, Poona college of pharmacy, Bharti vidhyapith, Pune - 411030 (India)
| | - Krishna Anand
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences and National Health Laboratory Service, University of the Free State, Bloemfontein 9300, South Africa
| | - Arun Soni
- Department of Pharmacology, SSR College of Pharmacy, Silvassa, Dadra and Nagar Haveli - 396230(India)
| | - Sonal Pandey
- Research and Development, Meril Diagnostic Pvt. Ltd, Vapi - 396191 (India)
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Faecal Proteomics and Functional Analysis of Equine Melanocytic Neoplasm in Grey Horses. Vet Sci 2022; 9:vetsci9020094. [PMID: 35202347 PMCID: PMC8875177 DOI: 10.3390/vetsci9020094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 02/04/2023] Open
Abstract
Equine melanocytic neoplasm (EMN) is a common disease in older grey horses. The purpose of this study was to examine the potential proteins throughout EMN stages from faecal proteomic outlining using functional analysis. Faecal samples were collected from the rectum of 25 grey horses divided into three groups; normal group without EMN (n = 10), mild EMN (n = 6) and severe EMN (n = 9). Based on the results, 5910 annotated proteins out of 8509 total proteins were assessed from proteomic profiling. We observed differentially expressed proteins (DEPs) between the normal group and the EMN group, and 109 significant proteins were obtained, of which 28 and 81 were involved in metabolic and non-metabolic functions, respectively. We found 10 proteins that play a key role in lipid metabolism, affecting the tumour microenvironment and, consequently, melanoma progression. Interestingly, FOSL1 (FOS like 1, AP-1 transcription factor subunit) was considered as a potential highly expressed protein in a mild EMN group involved in melanocytes cell and related melanoma. Diacylglycerol kinase (DGKB), TGc domain-containing protein (Tgm2), structural maintenance of chromosomes 4 (SMC4) and mastermind-like transcriptional coactivator 2 (MAML2) were related to lipid metabolism, facilitating melanoma development in the severe-EMN group. In conclusion, these potential proteins can be used as candidate biomarkers for the monitoring of early EMN, the development of EMN, further prevention and treatment.
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A Novel SETX Mutation in a Taiwanese Patient with Autosomal Recessive Cerebellar Ataxia Detected by Targeted Next-Generation Sequencing, and a Literature Review. Brain Sci 2022; 12:brainsci12020173. [PMID: 35203940 PMCID: PMC8869917 DOI: 10.3390/brainsci12020173] [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: 01/05/2022] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/04/2022] Open
Abstract
Ataxia with oculomotor apraxia type 2 (AOA2), also known as autosomal recessive spinocerebellar ataxia with axonal neuropathy-2 (SCAN2) (OMIM #606002), is a neurodegenerative disorder characterized by early-onset progressive cerebellar ataxia, polyneuropathy, and elevated levels of alpha-fetoprotein. It is caused by mutations in the SETX (OMIM #608465) gene. The prevalence of this disease is widely varied, from non-existent up to 1/150,000, depending on the region. Until now, no cases of AOA2/SCAN2 have been reported in Taiwan. Methods: Next-generation sequencing was used to detect disease-causing mutations of SETX in a Taiwanese patient presenting with autosomal recessive cerebellar ataxia, polyneuropathy, and elevated alpha-fetoprotein. The candidate mutations were further confirmed by polymerase chain reaction (PCR) and Sanger sequencing. Results: A compound heterozygous mutation of SETX c.6859C > T (p.R2287X) and c.7034-7036del was identified. The c.6859C > T (p.R2287X) has been previously found in a Saudi Arabia family, whereas c.7034-7036del is a novel mutation. Both mutations were predicted by bioinformatics programs to be likely pathogenic (having a damaging effect). We also reviewed the literature to address the reported clinical features of AOA2 from different populations. Conclusions: To our knowledge, we are the first to report a Taiwanese patient with AOA2/SCAN2, a result obtained by utilizing next-generation sequencing. The literature review shows that ataxia, polyneuropathy, and elevated AFP are common features and ocular motor apraxia (OMA) is a variable sign of AOA2 from different populations. OMA is rare and saccadic ocular pursuit and nystagmus are common in East Asian AOA2.
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Kanagaraj R, Mitter R, Kantidakis T, Edwards MM, Benitez A, Chakravarty P, Fu B, Becherel O, Yang F, Lavin MF, Koren A, Stewart A, West SC. Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2. Proc Natl Acad Sci U S A 2022; 119:e2114314119. [PMID: 35042798 PMCID: PMC8795503 DOI: 10.1073/pnas.2114314119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/14/2021] [Indexed: 12/21/2022] Open
Abstract
Mutations in the SETX gene, which encodes Senataxin, are associated with the progressive neurodegenerative diseases ataxia with oculomotor apraxia 2 (AOA2) and amyotrophic lateral sclerosis 4 (ALS4). To identify the causal defect in AOA2, patient-derived cells and SETX knockouts (human and mouse) were analyzed using integrated genomic and transcriptomic approaches. A genome-wide increase in chromosome instability (gains and losses) within genes and at chromosome fragile sites was observed, resulting in changes to gene-expression profiles. Transcription stress near promoters correlated with high GCskew and the accumulation of R-loops at promoter-proximal regions, which localized with chromosomal regions where gains and losses were observed. In the absence of Senataxin, the Cockayne syndrome protein CSB was required for the recruitment of the transcription-coupled repair endonucleases (XPG and XPF) and RAD52 recombination protein to target and resolve transcription bubbles containing R-loops, leading to genomic instability. These results show that transcription stress is an important contributor to SETX mutation-associated chromosome fragility and AOA2.
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Affiliation(s)
- Radhakrishnan Kanagaraj
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom;
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | | | - Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Anaid Benitez
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Probir Chakravarty
- Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Beiyuan Fu
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Olivier Becherel
- Center for Clinical Research, University of Queensland, Herston, QLD 4029, Australia
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Martin F Lavin
- Center for Clinical Research, University of Queensland, Herston, QLD 4029, Australia
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Aengus Stewart
- Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Stephen C West
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom;
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