1
|
Kisby GE, Wilson DM, Spencer PS. Introducing the Role of Genotoxicity in Neurodegenerative Diseases and Neuropsychiatric Disorders. Int J Mol Sci 2024; 25:7221. [PMID: 39000326 PMCID: PMC11241460 DOI: 10.3390/ijms25137221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/21/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
Decades of research have identified genetic and environmental factors involved in age-related neurodegenerative diseases and, to a lesser extent, neuropsychiatric disorders. Genomic instability, i.e., the loss of genome integrity, is a common feature among both neurodegenerative (mayo-trophic lateral sclerosis, Parkinson's disease, Alzheimer's disease) and psychiatric (schizophrenia, autism, bipolar depression) disorders. Genomic instability is associated with the accumulation of persistent DNA damage and the activation of DNA damage response (DDR) pathways, as well as pathologic neuronal cell loss or senescence. Typically, DDR signaling ensures that genomic and proteomic homeostasis are maintained in both dividing cells, including neural progenitors, and post-mitotic neurons. However, dysregulation of these protective responses, in part due to aging or environmental insults, contributes to the progressive development of neurodegenerative and/or psychiatric disorders. In this Special Issue, we introduce and highlight the overlap between neurodegenerative diseases and neuropsychiatric disorders, as well as the emerging clinical, genomic, and molecular evidence for the contributions of DNA damage and aberrant DNA repair. Our goal is to illuminate the importance of this subject to uncover possible treatment and prevention strategies for relevant devastating brain diseases.
Collapse
Affiliation(s)
- Glen E. Kisby
- Department of Biomedical Sciences, College of Osteopathic Medicine of Pacific Northwest, Western University of Health Sciences, Lebanon, OR 97355, USA
| | - David M. Wilson
- Biomedical Research Institute, BIOMED, Hasselt University, 3500 Hasselt, Belgium;
| | - Peter S. Spencer
- Department of Neurology, School of Medicine, Oregon Institute of Occupational Health Sciences, Oregon Health & Sciences University (OHSU), Portland, OR 97239, USA
| |
Collapse
|
2
|
Chiu CL, Li CG, Verschueren E, Wen RM, Zhang D, Gordon CA, Zhao H, Giaccia AJ, Brooks JD. NUSAP1 Binds ILF2 to Modulate R-Loop Accumulation and DNA Damage in Prostate Cancer. Int J Mol Sci 2023; 24:6258. [PMID: 37047232 PMCID: PMC10093842 DOI: 10.3390/ijms24076258] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Increased expression of NUSAP1 has been identified as a robust prognostic biomarker in prostate cancer and other malignancies. We have previously shown that NUSAP1 is positively regulated by E2F1 and promotes cancer invasion and metastasis. To further understand the biological function of NUSAP1, we used affinity purification and mass spectrometry proteomic analysis to identify NUSAP1 interactors. We identified 85 unique proteins in the NUSAP1 interactome, including ILF2, DHX9, and other RNA-binding proteins. Using proteomic approaches, we uncovered a function for NUSAP1 in maintaining R-loops and in DNA damage response through its interaction with ILF2. Co-immunoprecipitation and colocalization using confocal microscopy verified the interactions of NUSAP1 with ILF2 and DHX9, and RNA/DNA hybrids. We showed that the microtubule and charged helical domains of NUSAP1 were necessary for the protein-protein interactions. Depletion of ILF2 alone further increased camptothecin-induced R-loop accumulation and DNA damage, and NUSAP1 depletion abolished this effect. In human prostate adenocarcinoma, NUSAP1 and ILF2 mRNA expression levels are positively correlated, elevated, and associated with poor clinical outcomes. Our study identifies a novel role for NUSAP1 in regulating R-loop formation and accumulation in response to DNA damage through its interactions with ILF2 and hence provides a potential therapeutic target.
Collapse
Affiliation(s)
- Chun-Lung Chiu
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caiyun G. Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Erik Verschueren
- ULUA Besloten Vennootschap, Arendstraat 29, 2018 Antwerpen, Belgium
| | - Ru M. Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dalin Zhang
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Catherine A. Gordon
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hongjuan Zhao
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Amato J. Giaccia
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Medical Research Council/Cancer Research United Kingdom Oxford Institute for Radiation Oncology and Gray Laboratory, University of Oxford, Oxford OX3 7DQ, UK
| | - James D. Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Cancer Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
3
|
Jauregui-Lozano J, Cottingham K, Hall H. Tissue-Specific, Genome-wide Mapping of R-loops in Drosophila Using MapR. Bio Protoc 2022; 12:e4516. [PMID: 36248608 PMCID: PMC9516225 DOI: 10.21769/bioprotoc.4516] [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: 03/23/2022] [Revised: 05/12/2022] [Accepted: 08/02/2022] [Indexed: 12/29/2022] Open
Abstract
R-loops, or RNA:DNA hybrids, are structures that arise co-transcriptionally when a nascent RNA hybridizes back with the template ssDNA, leading to a displaced ssDNA. Because accumulation of R-loops can lead to genomic instability and loss of cellular homeostasis, it is important to determine the genome-wide distribution of R-loops in different physiological conditions. Current R-loop mapping strategies are based on R-loop enrichment-mediated by the S9.6 antibody, such as DRIP-seq, or by the exonuclease RNase H1, such as MapR-or the latest R-loop CUT&Tag, based on an artificial R-loop sensor derived from an RNase H1 sub-domain. Because some of these techniques often require high input material or expensive reagents, we sought to apply MapR, which does not require expensive reagents and has been shown to be compatible with low input samples. Importantly, we demonstrate that incorporation of improved CUT&RUN steps into the MapR protocol yields R-loop-enriched DNA when using low input Drosophila nuclei. Graphical abstract: Workflow for mapping tissue-specific, genome-wide R-loops in Drosophila . Purify GST-tagged and catalytically inactive RNase H1 tethered MapR enzymes, GST-ΔRH-MNase, and GST-MNase, from transformed E. coli. Perform tissue-specific nuclei immuno-enrichment from UAS-EGFP.KASH-Msp300 Drosophila using magnetic bead-bound green fluorescent protein (GFP) antibody. Incubate isolated nuclei with MapR enzymes and activate MNase DNA cleavage with low salt/high calcium buffers. Purify released, R-loopenriched DNA fragments and generate sequencing-ready libraries. Align MapR data to reference genome and compare R-loop enrichment peaks in genome browser.
Collapse
Affiliation(s)
- Juan Jauregui-Lozano
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
,
*For correspondence:
;
| | | | - Hana Hall
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
,
Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
4
|
Pan X, Huang LF. Multi-omics to characterize the functional relationships of R-loops with epigenetic modifications, RNAPII transcription and gene expression. Brief Bioinform 2022; 23:6618633. [DOI: 10.1093/bib/bbac238] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 12/12/2022] Open
Abstract
Abstract
Abnormal accumulation of R-loops results in replication stress, genome instability, chromatin alterations and gene silencing. Little research has been done to characterize functional relationships among R-loops, histone marks, RNA polymerase II (RNAPII) transcription and gene regulation. We built extremely randomized trees (ETs) models to predict the genome-wide R-loops using RNAPII and multiple histone modifications chromatin immunoprecipitation (ChIP)-seq, DNase-seq, Global Run-On sequencing (GRO-seq) and R-loop profiling data. We compared the performance of ET models to multiple machine learning approaches, and the proposed ET models achieved the best and extremely robust performances. Epigenetic profiles are highly predictive of R-loops genome-widely and they are strongly associated with R-loop formation. In addition, the presence of R-loops is significantly correlated with RNAPII transcription activity, H3K4me3 and open chromatin around the transcription start site, and H3K9me1 and H3K9me3 around the transcription termination site. RNAPII pausing defects were correlated with 5′R-loops accumulation, and transcriptional termination defects and read-throughs were correlated with 3′R-loops accumulation. Furthermore, we found driver genes with 5′R-loops and RNAPII pausing defects express significantly higher and genes with 3′R-loops and read-through transcription express significantly lower than genes without R-loops. These driver genes are enriched with chromosomal instability, Hippo–Merlin signaling Dysregulation, DNA damage response and TGF-β pathways, indicating R-loops accumulating at the 5′ end of genes play oncogenic roles, whereas at the 3′ end of genes play tumor-suppressive roles in tumorigenesis.
Collapse
Affiliation(s)
- Xingxin Pan
- Division of Experimental Hematology and Cancer Biology , Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 , USA
| | - L Frank Huang
- Division of Experimental Hematology and Cancer Biology , Brain Tumor Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229 , USA
- Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH 45229 , USA
| |
Collapse
|
5
|
Cuartas J, Gangwani L. R-loop Mediated DNA Damage and Impaired DNA Repair in Spinal Muscular Atrophy. Front Cell Neurosci 2022; 16:826608. [PMID: 35783101 PMCID: PMC9243258 DOI: 10.3389/fncel.2022.826608] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/23/2022] [Indexed: 12/02/2022] Open
Abstract
Defects in DNA repair pathways are a major cause of DNA damage accumulation leading to genomic instability and neurodegeneration. Efficient DNA damage repair is critical to maintain genomicstability and support cell function and viability. DNA damage results in the activation of cell death pathways, causing neuronal death in an expanding spectrum of neurological disorders, such as amyotrophic lateral sclerosis (ALS), Parkinson’s disease (PD), Alzheimer’s disease (AD), and spinal muscular atrophy (SMA). SMA is a neurodegenerative disorder caused by mutations in the Survival Motor Neuron 1 (SMN1) gene. SMA is characterized by the degeneration of spinal cord motor neurons due to low levels of the SMN protein. The molecular mechanism of selective motor neuron degeneration in SMA was unclear for about 20 years. However, several studies have identified biochemical and molecular mechanisms that may contribute to the predominant degeneration of motor neurons in SMA, including the RhoA/ROCK, the c-Jun NH2-terminal kinase (JNK), and p53-mediated pathways, which are involved in mediating DNA damage-dependent cell death. Recent studies provided insight into selective degeneration of motor neurons, which might be caused by accumulation of R-loop-mediated DNA damage and impaired non-homologous end joining (NHEJ) DNA repair pathway leading to genomic instability. Here, we review the latest findings involving R-loop-mediated DNA damage and defects in neuron-specific DNA repair mechanisms in SMA and discuss these findings in the context of other neurodegenerative disorders linked to DNA damage.
Collapse
Affiliation(s)
- Juliana Cuartas
- Center of Emphasis in Neurosciences, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Laxman Gangwani
- Center of Emphasis in Neurosciences, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
- Francis Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
- *Correspondence: Laxman Gangwani
| |
Collapse
|
6
|
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.
Collapse
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)
| |
Collapse
|
7
|
Wu T, Nance J, Chu F, Fazzio TG. Characterization of R-Loop-Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression. Mol Cell Proteomics 2021; 20:100142. [PMID: 34478875 PMCID: PMC8461376 DOI: 10.1016/j.mcpro.2021.100142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 08/21/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Chromatin-associated RNAs have diverse roles in the nucleus. However, their mechanisms of action are poorly understood, in part because of the inability to identify proteins that specifically associate with chromatin-bound RNAs. Here, we address this problem for a subset of chromatin-associated RNAs that form R-loops-RNA-DNA hybrid structures that include a displaced strand of ssDNA. R-loops generally form cotranscriptionally and have important roles in regulation of gene expression, immunoglobulin class switching, and other processes. However, unresolved R-loops can lead to DNA damage and chromosome instability. To identify factors that may bind and regulate R-loop accumulation or mediate R-loop-dependent functions, we used a comparative immunoprecipitation/MS approach, with and without RNA-protein crosslinking, to identify a stringent set of R-loop-binding proteins in mouse embryonic stem cells. We identified 364 R-loop-interacting proteins, which were highly enriched for proteins with predicted RNA-binding functions. We characterized several R-loop-interacting proteins of the DEAD-box family of RNA helicases and found that these proteins localize to the nucleolus and, to a lesser degree, the nucleus. Consistent with their localization patterns, we found that these helicases are required for rRNA processing and regulation of gene expression. Surprisingly, depletion of these helicases resulted in misregulation of highly overlapping sets of protein-coding genes, including many genes that function in differentiation and development. We conclude that R-loop-interacting DEAD-box helicases have nonredundant roles that are critical for maintaining the normal embryonic stem cell transcriptome.
Collapse
Affiliation(s)
- Tong Wu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jennifer Nance
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Feixia Chu
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Thomas G Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
| |
Collapse
|
8
|
Dettori LG, Torrejon D, Chakraborty A, Dutta A, Mohamed M, Papp C, Kuznetsov VA, Sung P, Feng W, Bah A. A Tale of Loops and Tails: The Role of Intrinsically Disordered Protein Regions in R-Loop Recognition and Phase Separation. Front Mol Biosci 2021; 8:691694. [PMID: 34179096 PMCID: PMC8222781 DOI: 10.3389/fmolb.2021.691694] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
R-loops are non-canonical, three-stranded nucleic acid structures composed of a DNA:RNA hybrid, a displaced single-stranded (ss)DNA, and a trailing ssRNA overhang. R-loops perform critical biological functions under both normal and disease conditions. To elucidate their cellular functions, we need to understand the mechanisms underlying R-loop formation, recognition, signaling, and resolution. Previous high-throughput screens identified multiple proteins that bind R-loops, with many of these proteins containing folded nucleic acid processing and binding domains that prevent (e.g., topoisomerases), resolve (e.g., helicases, nucleases), or recognize (e.g., KH, RRMs) R-loops. However, a significant number of these R-loop interacting Enzyme and Reader proteins also contain long stretches of intrinsically disordered regions (IDRs). The precise molecular and structural mechanisms by which the folded domains and IDRs synergize to recognize and process R-loops or modulate R-loop-mediated signaling have not been fully explored. While studying one such modular R-loop Reader, the Fragile X Protein (FMRP), we unexpectedly discovered that the C-terminal IDR (C-IDR) of FMRP is the predominant R-loop binding site, with the three N-terminal KH domains recognizing the trailing ssRNA overhang. Interestingly, the C-IDR of FMRP has recently been shown to undergo spontaneous Liquid-Liquid Phase Separation (LLPS) assembly by itself or in complex with another non-canonical nucleic acid structure, RNA G-quadruplex. Furthermore, we have recently shown that FMRP can suppress persistent R-loops that form during transcription, a process that is also enhanced by LLPS via the assembly of membraneless transcription factories. These exciting findings prompted us to explore the role of IDRs in R-loop processing and signaling proteins through a comprehensive bioinformatics and computational biology study. Here, we evaluated IDR prevalence, sequence composition and LLPS propensity for the known R-loop interactome. We observed that, like FMRP, the majority of the R-loop interactome, especially Readers, contains long IDRs that are highly enriched in low complexity sequences with biased amino acid composition, suggesting that these IDRs could directly interact with R-loops, rather than being “mere flexible linkers” connecting the “functional folded enzyme or binding domains”. Furthermore, our analysis shows that several proteins in the R-loop interactome are either predicted to or have been experimentally demonstrated to undergo LLPS or are known to be associated with phase separated membraneless organelles. Thus, our overall results present a thought-provoking hypothesis that IDRs in the R-loop interactome can provide a functional link between R-loop recognition via direct binding and downstream signaling through the assembly of LLPS-mediated membrane-less R-loop foci. The absence or dysregulation of the function of IDR-enriched R-loop interactors can potentially lead to severe genomic defects, such as the widespread R-loop-mediated DNA double strand breaks that we recently observed in Fragile X patient-derived cells.
Collapse
Affiliation(s)
- Leonardo G Dettori
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Diego Torrejon
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Arijita Chakraborty
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Arijit Dutta
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Mohamed Mohamed
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Csaba Papp
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States.,Department of Urology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Vladimir A Kuznetsov
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, United States.,Bioinformatics Institute, ASTAR Biomedical Institutes, Singapore, Singapore
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, United States
| | - Wenyi Feng
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Alaji Bah
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States
| |
Collapse
|
9
|
Patel PS, Abraham KJ, Guturi KKN, Halaby MJ, Khan Z, Palomero L, Ho B, Duan S, St-Germain J, Algouneh A, Mateo F, El Ghamrasni S, Barbour H, Barnes DR, Beesley J, Sanchez O, Berman HK, Brown GW, El Bachir Affar, Chenevix-Trench G, Antoniou AC, Arrowsmith CH, Raught B, Pujana MA, Mekhail K, Hakem A, Hakem R. RNF168 regulates R-loop resolution and genomic stability in BRCA1/2-deficient tumors. J Clin Invest 2021; 131:140105. [PMID: 33529165 PMCID: PMC7843228 DOI: 10.1172/jci140105] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 12/09/2020] [Indexed: 12/23/2022] Open
Abstract
Germline mutations in BRCA1 and BRCA2 (BRCA1/2) genes considerably increase breast and ovarian cancer risk. Given that tumors with these mutations have elevated genomic instability, they exhibit relative vulnerability to certain chemotherapies and targeted treatments based on poly (ADP-ribose) polymerase (PARP) inhibition. However, the molecular mechanisms that influence cancer risk and therapeutic benefit or resistance remain only partially understood. BRCA1 and BRCA2 have also been implicated in the suppression of R-loops, triple-stranded nucleic acid structures composed of a DNA:RNA hybrid and a displaced ssDNA strand. Here, we report that loss of RNF168, an E3 ubiquitin ligase and DNA double-strand break (DSB) responder, remarkably protected Brca1-mutant mice against mammary tumorigenesis. We demonstrate that RNF168 deficiency resulted in accumulation of R-loops in BRCA1/2-mutant breast and ovarian cancer cells, leading to DSBs, senescence, and subsequent cell death. Using interactome assays, we identified RNF168 interaction with DHX9, a helicase involved in the resolution and removal of R-loops. Mechanistically, RNF168 directly ubiquitylated DHX9 to facilitate its recruitment to R-loop-prone genomic loci. Consequently, loss of RNF168 impaired DHX9 recruitment to R-loops, thereby abrogating its ability to resolve R-loops. The data presented in this study highlight a dependence of BRCA1/2-defective tumors on factors that suppress R-loops and reveal a fundamental RNF168-mediated molecular mechanism that governs cancer development and vulnerability.
Collapse
Affiliation(s)
- Parasvi S. Patel
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Karan Joshua Abraham
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Kiran Kumar Naidu Guturi
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Marie-Jo Halaby
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Zahra Khan
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Luis Palomero
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Brandon Ho
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Shili Duan
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Jonathan St-Germain
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Arash Algouneh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Francesca Mateo
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Haithem Barbour
- Centre de Recherche, Hôpital Maisonneuve-Rosemont, Montreal, Quebec, Canada
| | - Daniel R. Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan Beesley
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Otto Sanchez
- University of Ontario Institute of Technology, Oshawa, Ontario, Canada
| | - Hal K. Berman
- Toronto General Research Institute, Toronto, Ontario, Canada
| | - Grant W. Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - El Bachir Affar
- Centre de Recherche, Hôpital Maisonneuve-Rosemont, Montreal, Quebec, Canada
| | | | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Cheryl H. Arrowsmith
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Miquel Angel Pujana
- Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Anne Hakem
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
| | - Razqallah Hakem
- Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, and
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
10
|
Giannini M, Bayona-Feliu A, Sproviero D, Barroso SI, Cereda C, Aguilera A. TDP-43 mutations link Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage. PLoS Genet 2020; 16:e1009260. [PMID: 33301444 PMCID: PMC7755276 DOI: 10.1371/journal.pgen.1009260] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 12/22/2020] [Accepted: 11/08/2020] [Indexed: 12/16/2022] Open
Abstract
TDP-43 is a DNA and RNA binding protein involved in RNA processing and with structural resemblance to heterogeneous ribonucleoproteins (hnRNPs), whose depletion sensitizes neurons to double strand DNA breaks (DSBs). Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disorder, in which 97% of patients are familial and sporadic cases associated with TDP-43 proteinopathies and conditions clearing TDP-43 from the nucleus, but we know little about the molecular basis of the disease. After showing with the non-neuronal model of HeLa cells that TDP-43 depletion increases R loops and associated genome instability, we prove that mislocalization of mutated TDP-43 (A382T) in transfected neuronal SH-SY5Y and lymphoblastoid cell lines (LCLs) from an ALS patient cause R-loop accumulation, R loop-dependent increased DSBs and Fanconi Anemia repair centers. These results uncover a new role of TDP-43 in the control of co-transcriptional R loops and the maintenance of genome integrity by preventing harmful R-loop accumulation. Our findings thus link TDP-43 pathology to increased R loops and R loop-mediated DNA damage opening the possibility that R-loop modulation in TDP-43-defective cells might help develop ALS therapies. Amyotrophic Lateral Sclerosis (ALS) is an adult onset, progressive neurodegenerative disease, caused by the selective loss of upper and lower motor neurons in the cerebral cortex, brainstem and spinal cord. The nuclear TDP-43 RNA binding protein, is encoded by a major gene for ALS susceptibility whose mutations are found in 3% of familial and 2% of sporadic ALS cases. Thanks to its ability to recognize DNA and RNA, TDP-43 is involved in different steps of mRNA metabolism and in several mechanisms of genome integrity. This, together with the fact that R loops or DNA-RNA hybrids are a common source of genome instability, prompted us to investigate whether TDP-43 deficiency has any role in R loop homeostasis that could explain previously described DNA damage response defects of ALS cells. We show that TDP-43 plays a role in preventing R loop-accumulation and associated genome instability in neuronal and non-neuronal cells, as well as in patient cell lines. Thus, our study opens the possibility that R loop-modulation in TDP-43-defective cells might help develop ALS therapies.
Collapse
Affiliation(s)
- Marta Giannini
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Aleix Bayona-Feliu
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Daisy Sproviero
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Sonia I. Barroso
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Cristina Cereda
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
- * E-mail: (CC); (AA)
| | - Andrés Aguilera
- Andalusian Center of Molecular Biology and Regenerative Medicine-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
- * E-mail: (CC); (AA)
| |
Collapse
|
11
|
Perego MGL, Galli N, Nizzardo M, Govoni A, Taiana M, Bresolin N, Comi GP, Corti S. Current understanding of and emerging treatment options for spinal muscular atrophy with respiratory distress type 1 (SMARD1). Cell Mol Life Sci 2020; 77:3351-3367. [PMID: 32123965 PMCID: PMC11104977 DOI: 10.1007/s00018-020-03492-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 02/08/2020] [Accepted: 02/20/2020] [Indexed: 12/11/2022]
Abstract
Spinal muscular atrophy (SMA) with respiratory distress type 1 (SMARD1) is an autosomal recessive motor neuron disease that is characterized by distal and proximal muscle weakness and diaphragmatic palsy that leads to respiratory distress. Without intervention, infants with the severe form of the disease die before 2 years of age. SMARD1 is caused by mutations in the IGHMBP2 gene that determine a deficiency in the encoded IGHMBP2 protein, which plays a critical role in motor neuron survival because of its functions in mRNA processing and maturation. Although it is rare, SMARD1 is the second most common motor neuron disease of infancy, and currently, treatment is primarily supportive. No effective therapy is available for this devastating disease, although multidisciplinary care has been an essential element of the improved quality of life and life span extension in these patients in recent years. The objectives of this review are to discuss the current understanding of SMARD1 through a summary of the presently known information regarding its clinical presentation and pathogenesis and to discuss emerging therapeutic approaches. Advances in clinical care management have significantly extended the lives of individuals affected by SMARD1 and research into the molecular mechanisms that lead to the disease has identified potential strategies for intervention that target the underlying causes of SMARD1. Gene therapy via gene replacement or gene correction provides the potential for transformative therapies to halt or possibly prevent neurodegenerative disease in SMARD1 patients. The recent approval of the first gene therapy approach for SMA associated with mutations in the SMN1 gene may be a turning point for the application of this strategy for SMARD1 and other genetic neurological diseases.
Collapse
Affiliation(s)
- Martina G L Perego
- Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Noemi Galli
- Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Monica Nizzardo
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Alessandra Govoni
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Michela Taiana
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Nereo Bresolin
- Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Giacomo P Comi
- Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
- Neuromuscular and Rare Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Stefania Corti
- Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy.
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122, Milan, Italy.
| |
Collapse
|
12
|
Ishiguro A, Kimura N, Noma T, Shimo-Kon R, Ishihama A, Kon T. Molecular dissection of ALS-linked TDP-43 - involvement of the Gly-rich domain in interaction with G-quadruplex mRNA. FEBS Lett 2020; 594:2254-2265. [PMID: 32337711 DOI: 10.1002/1873-3468.13800] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/15/2020] [Accepted: 04/20/2020] [Indexed: 12/12/2022]
Abstract
TDP-43 is the major pathogenic protein of amyotrophic lateral sclerosis (ALS). Previously, we identified that TDP-43 interacts with G-quadruplex (G4)-containing RNA and is involved in their long-distance transport in neurons. For the molecular dissection of the TDP-43 and G4-RNA interaction, we analyzed it here in vitro and in cultured cells using a set of 10 mutant TDP-43 proteins from familial and sporadic ALS patients as well as using the TDP-43 C-terminal Gly-rich domain alone. Our results altogether indicate the involvement of the Gly-rich region of TDP-43 in the initial recognition and binding of G4-RNA, which then induces tight binding of TDP-43 with target RNAs, supposedly in conjunction with its RNA recognition motifs.
Collapse
Affiliation(s)
- Akira Ishiguro
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
| | - Nobuyuki Kimura
- Section of Cell Biology and Pathology, Department of Alzheimer's Disease Research, Center for Development of Advanced Medicine for Dementia, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Takashi Noma
- Department of Biological Science, Graduate School of Science, and Faculty of Science Osaka University, Toyonaka, Japan
| | - Rieko Shimo-Kon
- Department of Biological Science, Graduate School of Science, and Faculty of Science Osaka University, Toyonaka, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Japan
| | - Takahide Kon
- Department of Biological Science, Graduate School of Science, and Faculty of Science Osaka University, Toyonaka, Japan
| |
Collapse
|
13
|
Ain Q, Schmeer C, Wengerodt D, Witte OW, Kretz A. Extrachromosomal Circular DNA: Current Knowledge and Implications for CNS Aging and Neurodegeneration. Int J Mol Sci 2020; 21:E2477. [PMID: 32252492 PMCID: PMC7177960 DOI: 10.3390/ijms21072477] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
Still unresolved is the question of how a lifetime accumulation of somatic gene copy number alterations impact organ functionality and aging and age-related pathologies. Such an issue appears particularly relevant in the broadly post-mitotic central nervous system (CNS), where non-replicative neurons are restricted in DNA-repair choices and are prone to accumulate DNA damage, as they remain unreplaced over a lifetime. Both DNA injuries and consecutive DNA-repair strategies are processes that can evoke extrachromosomal circular DNA species, apparently from either part of the genome. Due to their capacity to amplify gene copies and related transcripts, the individual cellular load of extrachromosomal circular DNAs will contribute to a dynamic pool of additional coding and regulatory chromatin elements. Analogous to tumor tissues, where the mosaicism of circular DNAs plays a well-characterized role in oncogene plasticity and drug resistance, we suggest involvement of the "circulome" also in the CNS. Accordingly, we summarize current knowledge on the molecular biogenesis, homeostasis and gene regulatory impacts of circular extrachromosomal DNA and propose, in light of recent discoveries, a critical role in CNS aging and neurodegeneration. Future studies will elucidate the influence of individual extrachromosomal DNA species according to their sequence complexity and regional distribution or cell-type-specific abundance.
Collapse
Affiliation(s)
- Quratul Ain
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
| | - Christian Schmeer
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Diane Wengerodt
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
| | - Otto W. Witte
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Alexandra Kretz
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| |
Collapse
|
14
|
Zhang LH, Zhang XY, Hu T, Chen XY, Li JJ, Raida M, Sun N, Luo Y, Gao X. The SUMOylated METTL8 Induces R-loop and Tumorigenesis via m3C. iScience 2020; 23:100968. [PMID: 32199293 PMCID: PMC7082549 DOI: 10.1016/j.isci.2020.100968] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/08/2020] [Accepted: 03/03/2020] [Indexed: 01/26/2023] Open
Abstract
R-loops, three-stranded DNA-DNA:RNA hybrid structures, are best known for their deleterious effects on genome stability. The regulatory factors of this fundamental genetic structure remain unclear. Here, we reveal an epigenetic factor that controls R-loop stability. METTL8, a member of the methyltransferase-like protein family that methylates 3-methylcytidine (m3C), is a key factor in the R-loop regulating methyltransferase complex. Biochemical studies show that METTL8 forms a large SUMOylated nuclear RNA-binding protein complex (∼0.8 mega daltons) that contains well-reported R-loop related factors. Genetic ablation of METTL8 results in an overall reduction of R-loops in cells. Interaction assays indicated METTL8 binds to RNAs and is responsible for R-loop stability on selected gene regions. Our results demonstrate that the SUMOylated METTL8 promotes tumorigenesis by affecting genetic organization primarily in, or in close proximity to, the nucleolus and impacts the formation of regulatory R-loops through its methyltransferase activity on m3C. DNA:RNA hybrid structures are regulated by RNA methyltransferase via 3-methylcytidine SUMOylation stabilizes the RNA methyltransferase complex in the nucleus Dysregulation of DNA:RNA hybrids may induce tumorigenesis in mammalian cells
Collapse
Affiliation(s)
- Li-Hong Zhang
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Hangzhou 310009, China
| | - Xue-Yun Zhang
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Hangzhou 310009, China
| | - Tao Hu
- Department of Spine Surgery, Shanghai East Hospital, Tongji University, Shanghai 200092, China
| | - Xin-Yun Chen
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jing-Jia Li
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Hangzhou 310009, China
| | - Manfred Raida
- Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Ning Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yan Luo
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Hangzhou 310009, China.
| | - Xiang Gao
- Department of Biochemistry and Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Key Laboratory of Cancer Prevention and Intervention of China National Ministry of Education, Hangzhou 310009, China.
| |
Collapse
|
15
|
Kaushal S, Freudenreich CH. The role of fork stalling and DNA structures in causing chromosome fragility. Genes Chromosomes Cancer 2019; 58:270-283. [PMID: 30536896 DOI: 10.1002/gcc.22721] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/13/2018] [Accepted: 12/03/2018] [Indexed: 12/19/2022] Open
Abstract
Alternative non-B form DNA structures, also called secondary structures, can form in certain DNA sequences under conditions that produce single-stranded DNA, such as during replication, transcription, and repair. Direct links between secondary structure formation, replication fork stalling, and genomic instability have been found for many repeated DNA sequences that cause disease when they expand. Common fragile sites (CFSs) are known to be AT-rich and break under replication stress, yet the molecular basis for their fragility is still being investigated. Over the past several years, new evidence has linked both the formation of secondary structures and transcription to fork stalling and fragility of CFSs. How these two events may synergize to cause fragility and the role of nuclease cleavage at secondary structures in rare and CFSs are discussed here. We also highlight evidence for a new hypothesis that secondary structures at CFSs not only initiate fragility but also inhibit healing, resulting in their characteristic appearance.
Collapse
Affiliation(s)
- Simran Kaushal
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, Massachusetts.,Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts
| |
Collapse
|
16
|
|
17
|
Freudenreich CH. R-loops: targets for nuclease cleavage and repeat instability. Curr Genet 2018; 64:789-794. [PMID: 29327083 PMCID: PMC6039234 DOI: 10.1007/s00294-018-0806-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/03/2018] [Accepted: 01/08/2018] [Indexed: 01/09/2023]
Abstract
R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias. Recently, it was found that R-loops at an expanded CAG/CTG repeat tract cause DNA breaks as well as repeat instability (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Two factors were identified as causing R-loop-dependent breaks at CAG/CTG tracts: deamination of cytosines and the MutLγ (Mlh1-Mlh3) endonuclease, defining two new mechanisms for how R-loops can generate DNA breaks (Su and Freudenreich, Proc Natl Acad Sci USA 114, E8392-E8401, 2017). Following R-loop-dependent nicking, base excision repair resulted in repeat instability. These results have implications for human repeat expansion diseases and provide a paradigm for how RNA:DNA hybrids can cause genome instability at structure-forming DNA sequences. This perspective summarizes mechanisms of R-loop-induced fragility at G-rich repeats and new links between DNA breaks and repeat instability.
Collapse
Affiliation(s)
- Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, MA, 02155, USA.
- Program in Genetics, Tufts University, Boston, MA, 02111, USA.
| |
Collapse
|
18
|
Garcia-Vaquero ML, Gama-Carvalho M, Rivas JDL, Pinto FR. Searching the overlap between network modules with specific betweeness (S2B) and its application to cross-disease analysis. Sci Rep 2018; 8:11555. [PMID: 30068933 PMCID: PMC6070533 DOI: 10.1038/s41598-018-29990-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/23/2018] [Indexed: 12/14/2022] Open
Abstract
Discovering disease-associated genes (DG) is strategic for understanding pathological mechanisms. DGs form modules in protein interaction networks and diseases with common phenotypes share more DGs or have more closely interacting DGs. This prompted the development of Specific Betweenness (S2B) to find genes associated with two related diseases. S2B prioritizes genes frequently and specifically present in shortest paths linking two disease modules. Top S2B scores identified genes in the overlap of artificial network modules more than 80% of the times, even with incomplete or noisy knowledge. Applied to Amyotrophic Lateral Sclerosis and Spinal Muscular Atrophy, S2B candidates were enriched in biological processes previously associated with motor neuron degeneration. Some S2B candidates closely interacted in network cliques, suggesting common molecular mechanisms for the two diseases. S2B is a valuable tool for DG prediction, bringing new insights into pathological mechanisms. More generally, S2B can be applied to infer the overlap between other types of network modules, such as functional modules or context-specific subnetworks. An R package implementing S2B is publicly available at https://github.com/frpinto/S2B .
Collapse
Affiliation(s)
- Marina L Garcia-Vaquero
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016, Lisboa, Portugal
| | - Margarida Gama-Carvalho
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016, Lisboa, Portugal
| | - Javier De Las Rivas
- Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), Salamanca, Spain
| | - Francisco R Pinto
- University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, C8 bdg, 1749-016, Lisboa, Portugal.
| |
Collapse
|
19
|
Abstract
R loops are transient three-stranded nucleic acid structures that form physiologically during transcription when a nascent RNA transcript hybridizes with the DNA template strand, leaving a single strand of displaced nontemplate DNA. However, aberrant persistence of R-loops can cause DNA damage by inducing genomic instability. Indeed, evidence has emerged that R-loops might represent a key element in the pathogenesis of human diseases, including cancer, neurodegeneration, and motor neuron disorders. Mutations in genes directly involved in R-loop biology, such as SETX (senataxin), or unstable DNA expansion eliciting R-loop generation, such as C9ORF72 HRE, can cause DNA damage and ultimately result in motor neuron cell death. In this review, we discuss current advancements in this field with a specific focus on motor neuron diseases associated with deregulation of R-loop structures. These mechanisms can represent novel therapeutic targets for these devastating, incurable diseases.
Collapse
|
20
|
Abstract
Spinal muscular atrophy (SMA) is a motor neuron disease caused by mutations/deletions within the survival of motor neuron 1 (SMN1) gene that lead to a pathological reduction of SMN protein levels. SMN is part of a multiprotein complex, functioning as a molecular chaperone that facilitates the assembly of spliceosomal small nuclear ribonucleoproteins (snRNP). In addition to its role in spliceosome formation, SMN has also been found to interact with mRNA-binding proteins (mRBPs), and facilitate their assembly into mRNP transport granules. The association of protein and RNA in RNP complexes plays an important role in an extensive and diverse set of cellular processes that regulate neuronal growth, differentiation, and the maturation and plasticity of synapses. This review discusses the role of SMN in RNP assembly and localization, focusing on molecular defects that affect mRNA processing and may contribute to SMA pathology.
Collapse
|
21
|
Shen W, Sun H, De Hoyos CL, Bailey JK, Liang XH, Crooke ST. Dynamic nucleoplasmic and nucleolar localization of mammalian RNase H1 in response to RNAP I transcriptional R-loops. Nucleic Acids Res 2017; 45:10672-10692. [PMID: 28977560 PMCID: PMC5737507 DOI: 10.1093/nar/gkx710] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/04/2017] [Indexed: 12/29/2022] Open
Abstract
An R-loop is a DNA:RNA hybrid formed during transcription when a DNA duplex is invaded by a nascent RNA transcript. R-loops accumulate in nucleoli during RNA polymerase I (RNAP I) transcription. Here, we report that mammalian RNase H1 enriches in nucleoli and co-localizes with R-loops in cultured human cells. Co-migration of RNase H1 and R-loops from nucleoli to perinucleolar ring structures was observed upon inhibition of RNAP I transcription. Treatment with camptothecin which transiently stabilized nucleolar R-loops recruited RNase H1 to the nucleoli. It has been reported that the absence of Topoisomerase and RNase H activity in Escherichia coli or Saccharomyces cerevisiae caused R-loop accumulation along rDNA. We found that the distribution of RNase H1 and Top1 along rDNA coincided at sites where R-loops accumulated in mammalian cells. Loss of either RNase H1 or Top1 caused R-loop accumulation, and the accumulation of R-loops was exacerbated when both proteins were depleted. Importantly, we observed that protein levels of Top1 were negatively correlated with the abundance of RNase H1. We conclude that Top1 and RNase H1 are partially functionally redundant in mammalian cells to suppress RNAP I transcription-associate R-loops.
Collapse
Affiliation(s)
- Wen Shen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Cheryl L De Hoyos
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Jeffrey K Bailey
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA
| |
Collapse
|
22
|
Abraham KJ, Ostrowski LA, Mekhail K. Non-Coding RNA Molecules Connect Calorie Restriction and Lifespan. J Mol Biol 2017; 429:3196-3214. [DOI: 10.1016/j.jmb.2016.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/10/2016] [Accepted: 08/15/2016] [Indexed: 01/05/2023]
|
23
|
Functions of long non-coding RNAs in human disease and their conservation in Drosophila development. Biochem Soc Trans 2017; 45:895-904. [PMID: 28673935 DOI: 10.1042/bst20160428] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/18/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023]
Abstract
Genomic analysis has found that the transcriptome in both humans and Drosophila melanogaster features large numbers of long non-coding RNA transcripts (lncRNAs). This recently discovered class of RNAs regulates gene expression in diverse ways and has been involved in a large variety of important biological functions. Importantly, an increasing number of lncRNAs have also been associated with a range of human diseases, including cancer. Comparative analyses of their functions among these organisms suggest that some of their modes of action appear to be conserved. This highlights the importance of model organisms such as Drosophila, which shares many gene regulatory networks with humans, in understanding lncRNA function and its possible impact in human health. This review discusses some known functions and mechanisms of action of lncRNAs and their implication in human diseases, together with their functional conservation and relevance in Drosophila development.
Collapse
|
24
|
Ataxin-2: From RNA Control to Human Health and Disease. Genes (Basel) 2017; 8:genes8060157. [PMID: 28587229 PMCID: PMC5485521 DOI: 10.3390/genes8060157] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/23/2017] [Accepted: 05/31/2017] [Indexed: 12/13/2022] Open
Abstract
RNA-binding proteins play fundamental roles in the regulation of molecular processes critical to cellular and organismal homeostasis. Recent studies have identified the RNA-binding protein Ataxin-2 as a genetic determinant or risk factor for various diseases including spinocerebellar ataxia type II (SCA2) and amyotrophic lateral sclerosis (ALS), amongst others. Here, we first discuss the increasingly wide-ranging molecular functions of Ataxin-2, from the regulation of RNA stability and translation to the repression of deleterious accumulation of the RNA-DNA hybrid-harbouring R-loop structures. We also highlight the broader physiological roles of Ataxin-2 such as in the regulation of cellular metabolism and circadian rhythms. Finally, we discuss insight from clinically focused studies to shed light on the impact of molecular and physiological roles of Ataxin-2 in various human diseases. We anticipate that deciphering the fundamental functions of Ataxin-2 will uncover unique approaches to help cure or control debilitating and lethal human diseases.
Collapse
|
25
|
Hall AC, Ostrowski LA, Pietrobon V, Mekhail K. Repetitive DNA loci and their modulation by the non-canonical nucleic acid structures R-loops and G-quadruplexes. Nucleus 2017; 8:162-181. [PMID: 28406751 DOI: 10.1080/19491034.2017.1292193] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cells have evolved intricate mechanisms to maintain genome stability despite allowing mutational changes to drive evolutionary adaptation. Repetitive DNA sequences, which represent the bulk of most genomes, are a major threat to genome stability often driving chromosome rearrangements and disease. The major source of repetitive DNA sequences and thus the most vulnerable constituents of the genome are the rDNA (rDNA) repeats, telomeres, and transposable elements. Maintaining the stability of these loci is critical to overall cellular fitness and lifespan. Therefore, cells have evolved mechanisms to regulate rDNA copy number, telomere length and transposon activity, as well as DNA repair at these loci. In addition, non-canonical structure-forming DNA motifs can also modulate the function of these repetitive DNA loci by impacting their transcription, replication, and stability. Here, we discuss key mechanisms that maintain rDNA repeats, telomeres, and transposons in yeast and human before highlighting emerging roles for non-canonical DNA structures at these repetitive loci.
Collapse
Affiliation(s)
- Amanda C Hall
- a Department of Laboratory Medicine and Pathobiology , Faculty of Medicine, University of Toronto , Toronto, Ontario , Canada
| | - Lauren A Ostrowski
- a Department of Laboratory Medicine and Pathobiology , Faculty of Medicine, University of Toronto , Toronto, Ontario , Canada
| | - Violena Pietrobon
- a Department of Laboratory Medicine and Pathobiology , Faculty of Medicine, University of Toronto , Toronto, Ontario , Canada
| | - Karim Mekhail
- a Department of Laboratory Medicine and Pathobiology , Faculty of Medicine, University of Toronto , Toronto, Ontario , Canada.,b Canada Research Chairs Program ; Faculty of Medicine, University of Toronto , Toronto, Ontario , Canada
| |
Collapse
|
26
|
Jangi M, Fleet C, Cullen P, Gupta SV, Mekhoubad S, Chiao E, Allaire N, Bennett CF, Rigo F, Krainer AR, Hurt JA, Carulli JP, Staropoli JF. SMN deficiency in severe models of spinal muscular atrophy causes widespread intron retention and DNA damage. Proc Natl Acad Sci U S A 2017; 114:E2347-E2356. [PMID: 28270613 PMCID: PMC5373344 DOI: 10.1073/pnas.1613181114] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spinal muscular atrophy (SMA), an autosomal recessive neuromuscular disease, is the leading monogenic cause of infant mortality. Homozygous loss of the gene survival of motor neuron 1 (SMN1) causes the selective degeneration of lower motor neurons and subsequent atrophy of proximal skeletal muscles. The SMN1 protein product, survival of motor neuron (SMN), is ubiquitously expressed and is a key factor in the assembly of the core splicing machinery. The molecular mechanisms by which disruption of the broad functions of SMN leads to neurodegeneration remain unclear. We used an antisense oligonucleotide (ASO)-based inducible mouse model of SMA to investigate the SMN-specific transcriptome changes associated with neurodegeneration. We found evidence of widespread intron retention, particularly of minor U12 introns, in the spinal cord of mice 30 d after SMA induction, which was then rescued by a therapeutic ASO. Intron retention was concomitant with a strong induction of the p53 pathway and DNA damage response, manifesting as γ-H2A.X positivity in neurons of the spinal cord and brain. Widespread intron retention and markers of the DNA damage response were also observed with SMN depletion in human SH-SY5Y neuroblastoma cells and human induced pluripotent stem cell-derived motor neurons. We also found that retained introns, high in GC content, served as substrates for the formation of transcriptional R-loops. We propose that defects in intron removal in SMA promote DNA damage in part through the formation of RNA:DNA hybrid structures, leading to motor neuron death.
Collapse
Affiliation(s)
- Mohini Jangi
- Computational Biology & Genomics, Biogen, Cambridge, MA 02142
| | - Christina Fleet
- Computational Biology & Genomics, Biogen, Cambridge, MA 02142
| | - Patrick Cullen
- Computational Biology & Genomics, Biogen, Cambridge, MA 02142
| | - Shipra V Gupta
- Computational Biology & Genomics, Biogen, Cambridge, MA 02142
| | | | - Eric Chiao
- Stem Cell Research, Biogen, Cambridge, MA 02142
| | - Norm Allaire
- Computational Biology & Genomics, Biogen, Cambridge, MA 02142
| | - C Frank Bennett
- Neuroscience Drug Discovery, Ionis Pharmaceuticals, Carlsbad, CA 92008
| | - Frank Rigo
- Neuroscience Drug Discovery, Ionis Pharmaceuticals, Carlsbad, CA 92008
| | | | - Jessica A Hurt
- Computational Biology & Genomics, Biogen, Cambridge, MA 02142
| | - John P Carulli
- Computational Biology & Genomics, Biogen, Cambridge, MA 02142;
| | | |
Collapse
|
27
|
Gama-Carvalho M, L Garcia-Vaquero M, R Pinto F, Besse F, Weis J, Voigt A, Schulz JB, De Las Rivas J. Linking amyotrophic lateral sclerosis and spinal muscular atrophy through RNA-transcriptome homeostasis: a genomics perspective. J Neurochem 2017; 141:12-30. [PMID: 28054357 DOI: 10.1111/jnc.13945] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/02/2016] [Accepted: 12/24/2016] [Indexed: 12/11/2022]
Abstract
In this review, we present our most recent understanding of key biomolecular processes that underlie two motor neuron degenerative disorders, amyotrophic lateral sclerosis, and spinal muscular atrophy. We focus on the role of four multifunctional proteins involved in RNA metabolism (TDP-43, FUS, SMN, and Senataxin) that play a causal role in these diseases. Recent results have led to a novel scenario of intricate connections between these four proteins, bringing transcriptome homeostasis into the spotlight as a common theme in motor neuron degeneration. We review reported functional and physical interactions between these four proteins, highlighting their common association with nuclear bodies and small nuclear ribonucleoprotein particle biogenesis and function. We discuss how these interactions are turning out to be particularly relevant for the control of transcription and chromatin homeostasis, including the recent identification of an association between SMN and Senataxin required to ensure the resolution of DNA-RNA hybrid formation and proper termination by RNA polymerase II. These connections strongly support the existence of common pathways underlying the spinal muscular atrophy and amyotrophic lateral sclerosis phenotype. We also discuss the potential of genome-wide expression profiling, in particular RNA sequencing derived data, to contribute to unravelling the underlying mechanisms. We provide a review of publicly available datasets that have addressed both diseases using these approaches, and highlight the value of investing in cross-disease studies to promote our understanding of the pathways leading to neurodegeneration.
Collapse
Affiliation(s)
- Margarida Gama-Carvalho
- Universidade de Lisboa, Faculdade de Ciências, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisboa, Portugal
| | - Marina L Garcia-Vaquero
- Universidade de Lisboa, Faculdade de Ciências, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisboa, Portugal
| | - Francisco R Pinto
- Universidade de Lisboa, Faculdade de Ciências, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Joachim Weis
- Institute of Neuropathology, RWTH Aachen University, Aachen, Germany
| | - Aaron Voigt
- Department of Neurology, University Hospital, RWTH Aachen University, Aachen, Germany.,JARA-Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich GmbH and RWTH Aachen University, Aachen, Germany
| | - Jörg B Schulz
- Department of Neurology, University Hospital, RWTH Aachen University, Aachen, Germany.,JARA-Institute Molecular Neuroscience and Neuroimaging, Forschungszentrum Jülich GmbH and RWTH Aachen University, Aachen, Germany
| | - Javier De Las Rivas
- Cancer Research Center (CiC-IBMCC, CSIC/USAL/IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) and Universidad de Salamanca (USAL), Salamanca, Spain
| |
Collapse
|
28
|
Nascent Connections: R-Loops and Chromatin Patterning. Trends Genet 2016; 32:828-838. [PMID: 27793359 DOI: 10.1016/j.tig.2016.10.002] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/03/2016] [Accepted: 10/06/2016] [Indexed: 11/22/2022]
Abstract
RNA molecules, such as long noncoding RNAs (lncRNAs), have critical roles in regulating gene expression, chromosome architecture, and the modification states of chromatin. Recent developments suggest that RNA also influences gene expression and chromatin patterns through the interaction of nascent transcripts with their DNA template via the formation of co-transcriptional R-loop structures. R-loop formation over specific, conserved, hotspots occurs at thousands of genes in mammalian genomes and represents an important and dynamic feature of mammalian chromatin. Here, focusing primarily on mammalian systems, I describe the accumulating connections and possible mechanisms linking R-loop formation and chromatin patterning. The possible contribution of aberrant R-loops to pathological conditions is also discussed.
Collapse
|
29
|
Guerrero EN, Wang H, Mitra J, Hegde PM, Stowell SE, Liachko NF, Kraemer BC, Garruto RM, Rao KS, Hegde ML. TDP-43/FUS in motor neuron disease: Complexity and challenges. Prog Neurobiol 2016; 145-146:78-97. [PMID: 27693252 PMCID: PMC5101148 DOI: 10.1016/j.pneurobio.2016.09.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/19/2016] [Accepted: 09/20/2016] [Indexed: 01/05/2023]
Abstract
Amyotrophic lateral sclerosis (ALS), a common motor neuron disease affecting two per 100,000 people worldwide, encompasses at least five distinct pathological subtypes, including, ALS-SOD1, ALS-C9orf72, ALS-TDP-43, ALS-FUS and Guam-ALS. The etiology of a major subset of ALS involves toxicity of the TAR DNA-binding protein-43 (TDP-43). A second RNA/DNA binding protein, fused in sarcoma/translocated in liposarcoma (FUS/TLS) has been subsequently associated with about 1% of ALS patients. While mutations in TDP-43 and FUS have been linked to ALS, the key contributing molecular mechanism(s) leading to cell death are still unclear. One unique feature of TDP-43 and FUS pathogenesis in ALS is their nuclear clearance and simultaneous cytoplasmic aggregation in affected motor neurons. Since the discoveries in the last decade implicating TDP-43 and FUS toxicity in ALS, a majority of studies have focused on their cytoplasmic aggregation and disruption of their RNA-binding functions. However, TDP-43 and FUS also bind to DNA, although the significance of their DNA binding in disease-affected neurons has been less investigated. A recent observation of accumulated genomic damage in TDP-43 and FUS-linked ALS and association of FUS with neuronal DNA damage repair pathways indicate a possible role of deregulated DNA binding function of TDP-43 and FUS in ALS. In this review, we discuss the different ALS disease subtypes, crosstalk of etiopathologies in disease progression, available animal models and their limitations, and recent advances in understanding the specific involvement of RNA/DNA binding proteins, TDP-43 and FUS, in motor neuron diseases.
Collapse
Affiliation(s)
- Erika N. Guerrero
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030, USA
- Centre for Neuroscience, Institute for Scientific Research and Technology Services (INDICASAT-AIP), City of Knowledge, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Haibo Wang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030, USA
| | - Joy Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030, USA
| | - Pavana M. Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030, USA
| | - Sara E. Stowell
- Department of Anthropology, Binghamton University, State University of New York, Binghamton, New York
| | - Nicole F Liachko
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, 98108, USA
| | - Brian C. Kraemer
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, 98108, USA
| | - Ralph M. Garruto
- Department of Anthropology, Binghamton University, State University of New York, Binghamton, New York
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, New York
| | - K. S. Rao
- Centre for Neuroscience, Institute for Scientific Research and Technology Services (INDICASAT-AIP), City of Knowledge, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Muralidhar L. Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, Texas 77030, USA
- Houston Methodist Neurological Institute, Houston, Texas 77030 USA
- Weill Medical College of Cornell University, New York
| |
Collapse
|
30
|
Wang H, Dharmalingam P, Vasquez V, Mitra J, Boldogh I, Rao KS, Kent TA, Mitra S, Hegde ML. Chronic oxidative damage together with genome repair deficiency in the neurons is a double whammy for neurodegeneration: Is damage response signaling a potential therapeutic target? Mech Ageing Dev 2016; 161:163-176. [PMID: 27663141 DOI: 10.1016/j.mad.2016.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/13/2016] [Accepted: 09/19/2016] [Indexed: 12/14/2022]
Abstract
A foremost challenge for the neurons, which are among the most oxygenated cells, is the genome damage caused by chronic exposure to endogenous reactive oxygen species (ROS), formed as cellular respiratory byproducts. Strong metabolic activity associated with high transcriptional levels in these long lived post-mitotic cells render them vulnerable to oxidative genome damage, including DNA strand breaks and mutagenic base lesions. There is growing evidence for the accumulation of unrepaired DNA lesions in the central nervous system (CNS) during accelerated aging and progressive neurodegeneration. Several germ line mutations in DNA repair or DNA damage response (DDR) signaling genes are uniquely manifested in the phenotype of neuronal dysfunction and are etiologically linked to many neurodegenerative disorders. Studies in our lab and elsewhere revealed that pro-oxidant metals, ROS and misfolded amyloidogenic proteins not only contribute to genome damage in CNS, but also impede their repair/DDR signaling leading to persistent damage accumulation, a common feature in sporadic neurodegeneration. Here, we have reviewed recent advances in our understanding of the etiological implications of DNA damage vs. repair imbalance, abnormal DDR signaling in triggering neurodegeneration and potential of DDR as a target for the amelioration of neurodegenerative diseases.
Collapse
Affiliation(s)
- Haibo Wang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Prakash Dharmalingam
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Velmarini Vasquez
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Centre for Neuroscience, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), City of Knowledge, Panama City, Panama; Department of Biotechnology, Acharya Nagarjuna University, Guntur, AP, India; Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Joy Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - K S Rao
- Centre for Neuroscience, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), City of Knowledge, Panama City, Panama
| | - Thomas A Kent
- Department of Neurology, Baylor College of Medicine and Center for Translational Research on Inflammatory Diseases Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX 77030, USA
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Weill Medical College of Cornell University, New York, USA
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA; Houston Methodist Neurological Institute, Houston, TX 77030, USA; Weill Medical College of Cornell University, New York, USA.
| |
Collapse
|
31
|
Richard P, Manley JL. R Loops and Links to Human Disease. J Mol Biol 2016; 429:3168-3180. [PMID: 27600412 DOI: 10.1016/j.jmb.2016.08.031] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/26/2016] [Accepted: 08/31/2016] [Indexed: 12/13/2022]
Abstract
Aberrant R-loop structures are increasingly being realized as an important contributor to human disease. R loops, which are mainly co-transcriptional, abundant RNA/DNA hybrids, form naturally and can indeed be beneficial for transcription regulation at certain loci. However, their unwanted persistence elsewhere or in particular situations can lead to DNA double-strand breaks, chromosome rearrangements, and hypermutation, which are all sources of genomic instability. Mutations in genes involved in R-loop resolution or mutations leading to R-loop formation at specific genes affect the normal physiology of the cell. We discuss here the examples of diseases for which a link with R loops has been described, as well as how disease-causing mutations might participate in the development and/or progression of diseases that include repeat-associated conditions, other neurological disorders, and cancers.
Collapse
Affiliation(s)
- Patricia Richard
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| |
Collapse
|
32
|
Abraham KJ, Chan JNY, Salvi JS, Ho B, Hall A, Vidya E, Guo R, Killackey SA, Liu N, Lee JE, Brown GW, Mekhail K. Intersection of calorie restriction and magnesium in the suppression of genome-destabilizing RNA-DNA hybrids. Nucleic Acids Res 2016; 44:8870-8884. [PMID: 27574117 PMCID: PMC5063000 DOI: 10.1093/nar/gkw752] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/20/2016] [Indexed: 12/14/2022] Open
Abstract
Dietary calorie restriction is a broadly acting intervention that extends the lifespan of various organisms from yeast to mammals. On another front, magnesium (Mg2+) is an essential biological metal critical to fundamental cellular processes and is commonly used as both a dietary supplement and treatment for some clinical conditions. If connections exist between calorie restriction and Mg2+ is unknown. Here, we show that Mg2+, acting alone or in response to dietary calorie restriction, allows eukaryotic cells to combat genome-destabilizing and lifespan-shortening accumulations of RNA–DNA hybrids, or R-loops. In an R-loop accumulation model of Pbp1-deficient Saccharomyces cerevisiae, magnesium ions guided by cell membrane Mg2+ transporters Alr1/2 act via Mg2+-sensitive R-loop suppressors Rnh1/201 and Pif1 to restore R-loop suppression, ribosomal DNA stability and cellular lifespan. Similarly, human cells deficient in ATXN2, the human ortholog of Pbp1, exhibit nuclear R-loop accumulations repressible by Mg2+ in a process that is dependent on the TRPM7 Mg2+ transporter and the RNaseH1 R-loop suppressor. Thus, we identify Mg2+ as a biochemical signal of beneficial calorie restriction, reveal an R-loop suppressing function for human ATXN2 and propose that practical magnesium supplementation regimens can be used to combat R-loop accumulation linked to the dysfunction of disease-linked human genes.
Collapse
Affiliation(s)
- Karan J Abraham
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Janet N Y Chan
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Jayesh S Salvi
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Brandon Ho
- Department of Biochemistry and Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Amanda Hall
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Elva Vidya
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Ru Guo
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Samuel A Killackey
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Nancy Liu
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada Canada Research Chairs Program, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada Canada Research Chairs Program, Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
33
|
Mellor J, Woloszczuk R, Howe FS. The Interleaved Genome. Trends Genet 2016; 32:57-71. [DOI: 10.1016/j.tig.2015.10.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 09/29/2015] [Accepted: 10/23/2015] [Indexed: 12/25/2022]
|
34
|
Highley JR, Lorente Pons A, Cooper-Knock J, Wharton SB, Ince PG, Shaw PJ, Wood J, Kirby J. Motor neurone disease/amyotrophic lateral sclerosis associated with intermediate-length CAG repeat expansions inAtaxin-2does not have 1C2-positive polyglutamine inclusions. Neuropathol Appl Neurobiol 2015; 42:377-89. [DOI: 10.1111/nan.12254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/14/2015] [Indexed: 12/13/2022]
Affiliation(s)
- John Robin Highley
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Alejandro Lorente Pons
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Stephen B. Wharton
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Paul G. Ince
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Pamela J. Shaw
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Jon Wood
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience (SITraN); University of Sheffield; Sheffield UK
| |
Collapse
|
35
|
Szafranski K, Abraham KJ, Mekhail K. Non-coding RNA in neural function, disease, and aging. Front Genet 2015; 6:87. [PMID: 25806046 PMCID: PMC4353379 DOI: 10.3389/fgene.2015.00087] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/18/2015] [Indexed: 12/03/2022] Open
Abstract
Declining brain and neurobiological function is arguably one of the most common features of human aging. The study of conserved aging processes as well as the characterization of various neurodegenerative diseases using different genetic models such as yeast, fly, mouse, and human systems is uncovering links to non-coding RNAs. These links implicate a variety of RNA-regulatory processes, including microRNA function, paraspeckle formation, RNA–DNA hybrid regulation, nucleolar RNAs and toxic RNA clearance, amongst others. Here we highlight these connections and reveal over-arching themes or questions related to recently appreciated roles of non-coding RNA in neural function and dysfunction across lifespan.
Collapse
Affiliation(s)
- Kirk Szafranski
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto Toronto, ON, Canada
| | - Karan J Abraham
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto Toronto, ON, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto Toronto, ON, Canada ; Canada Research Chairs Program, Faculty of Medicine, University of Toronto Toronto, ON, Canada
| |
Collapse
|