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Huang WP, Ellis BCS, Hodgson RE, Sanchez Avila A, Kumar V, Rayment J, Moll T, Shelkovnikova TA. Stress-induced TDP-43 nuclear condensation causes splicing loss of function and STMN2 depletion. Cell Rep 2024; 43:114421. [PMID: 38941189 DOI: 10.1016/j.celrep.2024.114421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 04/04/2024] [Accepted: 06/14/2024] [Indexed: 06/30/2024] Open
Abstract
TDP-43 protein is dysregulated in several neurodegenerative diseases, which often have a multifactorial nature and may have extrinsic stressors as a "second hit." TDP-43 undergoes reversible nuclear condensation in stressed cells including neurons. Here, we demonstrate that stress-inducible nuclear TDP-43 condensates are RNA-depleted, non-liquid assemblies distinct from the known nuclear bodies. Their formation requires TDP-43 oligomerization and ATP and is inhibited by RNA. Using a confocal nanoscanning assay, we find that amyotrophic lateral sclerosis (ALS)-linked mutations alter stress-induced TDP-43 condensation by changing its affinity to liquid-like ribonucleoprotein assemblies. Stress-induced nuclear condensation transiently inactivates TDP-43, leading to loss of interaction with its protein binding partners and loss of function in splicing. Splicing changes are especially prominent and persisting for STMN2 RNA, and STMN2 protein becomes rapidly depleted early during stress. Our results point to early pathological changes to TDP-43 in the nucleus and support therapeutic modulation of stress response in ALS.
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Affiliation(s)
- Wan-Ping Huang
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Brittany C S Ellis
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Rachel E Hodgson
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Anna Sanchez Avila
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Vedanth Kumar
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Jessica Rayment
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Tobias Moll
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience and Neuroscience Institute, University of Sheffield, Sheffield, UK.
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2
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Lambert-Smith IA, Shephard VK, McAlary L, Yerbury JJ, Saunders DN. High-content analysis of proteostasis capacity in cellular models of amyotrophic lateral sclerosis (ALS). Sci Rep 2024; 14:13844. [PMID: 38879591 PMCID: PMC11180180 DOI: 10.1038/s41598-024-64366-0] [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: 11/22/2021] [Accepted: 06/07/2024] [Indexed: 06/19/2024] Open
Abstract
Disrupted proteome homeostasis (proteostasis) in amyotrophic lateral sclerosis (ALS) has been a major focus of research in the past two decades. However, the proteostasis processes that become disturbed in ALS are not fully understood. Obtaining more detailed knowledge of proteostasis disruption in association with different ALS-causing mutations will improve our understanding of ALS pathophysiology and may identify novel therapeutic targets and strategies for ALS patients. Here we describe the development and use of a novel high-content analysis (HCA) assay to investigate proteostasis disturbances caused by the expression of several ALS-causing gene variants. This assay involves the use of conformationally-destabilised mutants of firefly luciferase (Fluc) to examine protein folding/re-folding capacity in NSC-34 cells expressing ALS-associated mutations in the genes encoding superoxide dismutase-1 (SOD1A4V) and cyclin F (CCNFS621G). We demonstrate that these Fluc isoforms can be used in high-throughput format to report on reductions in the activity of the chaperone network that result from the expression of SOD1A4V, providing multiplexed information at single-cell resolution. In addition to SOD1A4V and CCNFS621G, NSC-34 models of ALS-associated TDP-43, FUS, UBQLN2, OPTN, VCP and VAPB mutants were generated that could be screened using this assay in future work. For ALS-associated mutant proteins that do cause reductions in protein quality control capacity, such as SOD1A4V, this assay has potential to be applied in drug screening studies to identify candidate compounds that can ameliorate this deficiency.
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Affiliation(s)
- Isabella A Lambert-Smith
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia.
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia.
| | - Victoria K Shephard
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Luke McAlary
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Darren N Saunders
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, 2522, Australia.
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3
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Wang H, Zeng R. Aberrant protein aggregation in amyotrophic lateral sclerosis. J Neurol 2024:10.1007/s00415-024-12485-z. [PMID: 38869826 DOI: 10.1007/s00415-024-12485-z] [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: 03/12/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/14/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal disease. As its pathological mechanisms are not well understood, there are no efficient therapeutics for it at present. While it is highly heterogenous both etiologically and clinically, it has a common salient hallmark, i.e., aberrant protein aggregation (APA). The upstream pathogenesis and the downstream effects of APA in ALS are sophisticated and the investigation of this pathology would be of consequence for understanding ALS. In this paper, the pathomechanism of APA in ALS and the candidate treatment strategies for it are discussed.
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Affiliation(s)
- Huaixiu Wang
- Department Neurology, Shanxi Provincial Peoples Hospital: Fifth Hospital of Shanxi Medical University, Taiyuan, 030012, China.
- Beijing Ai-Si-Kang Medical Technology Co. Ltd., No. 18 11th St Economical & Technological Development Zone, Beijing, 100176, China.
| | - Rong Zeng
- Department Neurology, Shanxi Provincial Peoples Hospital: Fifth Hospital of Shanxi Medical University, Taiyuan, 030012, China
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4
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Wang Y, Chembazhi UV, Yee D, Chen S, Ji J, Wang Y, Nguyen KL, Lin P, Ratti A, Hess R, Qiao H, Ko C, Yang J, Kalsotra A, Mei W. PTBP1 mediates Sertoli cell actin cytoskeleton organization by regulating alternative splicing of actin regulators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598725. [PMID: 38915624 PMCID: PMC11195235 DOI: 10.1101/2024.06.12.598725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Spermatogenesis is a biological process within the testis that produces haploid spermatozoa for the continuity of species. Sertoli cells are somatic cells in the seminiferous epithelium that orchestrate spermatogenesis. Cyclic reorganization of Sertoli cell actin cytoskeleton is vital for spermatogenesis, but the underlying mechanism remains largely unclear. Here, we report that RNA-binding protein PTBP1 controls Sertoli cell actin cytoskeleton reorganization by programming alternative splicing of actin cytoskeleton regulators. This splicing control enables ectoplasmic specializations, the actin-based adhesion junctions, to maintain the blood-testis barrier and support spermatid transport and transformation. Particularly, we show that PTBP1 promotes actin bundle formation by repressing the inclusion of exon 14 of Tnik , a kinase present at the ectoplasmic specialization. Our results thus reveal a novel mechanism wherein Sertoli cell actin cytoskeleton dynamics is controlled post-transcriptionally by utilizing functionally distinct isoforms of actin regulatory proteins, and PTBP1 is a critical regulatory factor in generating such isoforms.
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5
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Kim JM, Kim WR, Park EG, Lee DH, Lee YJ, Shin HJ, Jeong HS, Roh HY, Kim HS. Exploring the Regulatory Landscape of Dementia: Insights from Non-Coding RNAs. Int J Mol Sci 2024; 25:6190. [PMID: 38892378 PMCID: PMC11172830 DOI: 10.3390/ijms25116190] [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: 04/26/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Dementia, a multifaceted neurological syndrome characterized by cognitive decline, poses significant challenges to daily functioning. The main causes of dementia, including Alzheimer's disease (AD), frontotemporal dementia (FTD), Lewy body dementia (LBD), and vascular dementia (VD), have different symptoms and etiologies. Genetic regulators, specifically non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are known to play important roles in dementia pathogenesis. MiRNAs, small non-coding RNAs, regulate gene expression by binding to the 3' untranslated regions of target messenger RNAs (mRNAs), while lncRNAs and circRNAs act as molecular sponges for miRNAs, thereby regulating gene expression. The emerging concept of competing endogenous RNA (ceRNA) interactions, involving lncRNAs and circRNAs as competitors for miRNA binding, has gained attention as potential biomarkers and therapeutic targets in dementia-related disorders. This review explores the regulatory roles of ncRNAs, particularly miRNAs, and the intricate dynamics of ceRNA interactions, providing insights into dementia pathogenesis and potential therapeutic avenues.
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Affiliation(s)
- Jung-min Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hae Jin Shin
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hyeon-su Jeong
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (J.-m.K.); (W.R.K.); (E.G.P.); (D.H.L.); (Y.J.L.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hyun-Young Roh
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
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6
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Joglekar A, Hu W, Zhang B, Narykov O, Diekhans M, Marrocco J, Balacco J, Ndhlovu LC, Milner TA, Fedrigo O, Jarvis ED, Sheynkman G, Korkin D, Ross ME, Tilgner HU. Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain. Nat Neurosci 2024; 27:1051-1063. [PMID: 38594596 PMCID: PMC11156538 DOI: 10.1038/s41593-024-01616-4] [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: 04/22/2023] [Accepted: 03/07/2024] [Indexed: 04/11/2024]
Abstract
RNA isoforms influence cell identity and function. However, a comprehensive brain isoform map was lacking. We analyze single-cell RNA isoforms across brain regions, cell subtypes, developmental time points and species. For 72% of genes, full-length isoform expression varies along one or more axes. Splicing, transcription start and polyadenylation sites vary strongly between cell types, influence protein architecture and associate with disease-linked variation. Additionally, neurotransmitter transport and synapse turnover genes harbor cell-type variability across anatomical regions. Regulation of cell-type-specific splicing is pronounced in the postnatal day 21-to-postnatal day 28 adolescent transition. Developmental isoform regulation is stronger than regional regulation for the same cell type. Cell-type-specific isoform regulation in mice is mostly maintained in the human hippocampus, allowing extrapolation to the human brain. Conversely, the human brain harbors additional cell-type specificity, suggesting gain-of-function isoforms. Together, this detailed single-cell atlas of full-length isoform regulation across development, anatomical regions and species reveals an unappreciated degree of isoform variability across multiple axes.
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Affiliation(s)
- Anoushka Joglekar
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Wen Hu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Bei Zhang
- Spatial Genomics, Inc., Pasadena, CA, USA
| | - Oleksandr Narykov
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Mark Diekhans
- UC Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jordan Marrocco
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Biology, Touro University, New York, NY, USA
- Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, USA
| | - Jennifer Balacco
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Lishomwa C Ndhlovu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Fedrigo
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
| | - Erich D Jarvis
- Vertebrate Genome Lab, The Rockefeller University, New York, NY, USA
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Gloria Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA, USA
| | - Dmitry Korkin
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA, USA
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - M Elizabeth Ross
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Hagen U Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA.
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7
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Tsekrekou M, Giannakou M, Papanikolopoulou K, Skretas G. Protein aggregation and therapeutic strategies in SOD1- and TDP-43- linked ALS. Front Mol Biosci 2024; 11:1383453. [PMID: 38855322 PMCID: PMC11157337 DOI: 10.3389/fmolb.2024.1383453] [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: 02/07/2024] [Accepted: 05/02/2024] [Indexed: 06/11/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with severe socio-economic impact. A hallmark of ALS pathology is the presence of aberrant cytoplasmic inclusions composed of misfolded and aggregated proteins, including both wild-type and mutant forms. This review highlights the critical role of misfolded protein species in ALS pathogenesis, particularly focusing on Cu/Zn superoxide dismutase (SOD1) and TAR DNA-binding protein 43 (TDP-43), and emphasizes the urgent need for innovative therapeutic strategies targeting these misfolded proteins directly. Despite significant advancements in understanding ALS mechanisms, the disease remains incurable, with current treatments offering limited clinical benefits. Through a comprehensive analysis, the review focuses on the direct modulation of the misfolded proteins and presents recent discoveries in small molecules and peptides that inhibit SOD1 and TDP-43 aggregation, underscoring their potential as effective treatments to modify disease progression and improve clinical outcomes.
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Affiliation(s)
- Maria Tsekrekou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Maria Giannakou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- Department of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Katerina Papanikolopoulou
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
- ResQ Biotech, Patras Science Park, Rio, Greece
- Institute for Bio-innovation, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
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8
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Scherer NM, Maurel C, Graus M, McAlary L, Richter G, Radford RW, Hogan A, Don E, Lee A, Yerbury J, Francois M, Chung R, Morsch M. RNA-binding properties orchestrate TDP-43 homeostasis through condensate formation in vivo. Nucleic Acids Res 2024; 52:5301-5319. [PMID: 38381071 PMCID: PMC11109982 DOI: 10.1093/nar/gkae112] [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: 06/23/2023] [Revised: 01/12/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Insoluble cytoplasmic aggregate formation of the RNA-binding protein TDP-43 is a major hallmark of neurodegenerative diseases including Amyotrophic Lateral Sclerosis. TDP-43 localizes predominantly in the nucleus, arranging itself into dynamic condensates through liquid-liquid phase separation (LLPS). Mutations and post-translational modifications can alter the condensation properties of TDP-43, contributing to the transition of liquid-like biomolecular condensates into solid-like aggregates. However, to date it has been a challenge to study the dynamics of this process in vivo. We demonstrate through live imaging that human TDP-43 undergoes nuclear condensation in spinal motor neurons in a living animal. RNA-binding deficiencies as well as post-translational modifications can lead to aberrant condensation and altered TDP-43 compartmentalization. Single-molecule tracking revealed an altered mobility profile for RNA-binding deficient TDP-43. Overall, these results provide a critically needed in vivo characterization of TDP-43 condensation, demonstrate phase separation as an important regulatory mechanism of TDP-43 accessibility, and identify a molecular mechanism of how functional TDP-43 can be regulated.
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Affiliation(s)
- Natalie M Scherer
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Cindy Maurel
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Matthew S Graus
- The David Richmond Laboratory for Cardio-Vascular Development: gene regulation and editing, Centenary Institute, The University of Sydney, School of Medical Sciences, Sydney, NSW 2006, Australia
- Genome Imaging Centre, Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Luke McAlary
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Grant Richter
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Rowan A W Radford
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Alison Hogan
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily K Don
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Albert Lee
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Justin Yerbury
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Mathias Francois
- The David Richmond Laboratory for Cardio-Vascular Development: gene regulation and editing, Centenary Institute, The University of Sydney, School of Medical Sciences, Sydney, NSW 2006, Australia
- Genome Imaging Centre, Centenary Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Roger S Chung
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Marco Morsch
- Faculty of Medicine, Health & Human Sciences, Macquarie Medical School, MND Research Centre, Macquarie University, Sydney, NSW 2109, Australia
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9
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Arnold FJ, Putka AF, Raychaudhuri U, Hsu S, Bedlack RS, Bennett CL, La Spada AR. Revisiting Glutamate Excitotoxicity in Amyotrophic Lateral Sclerosis and Age-Related Neurodegeneration. Int J Mol Sci 2024; 25:5587. [PMID: 38891774 PMCID: PMC11171854 DOI: 10.3390/ijms25115587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is the most common motor neuron disorder. While there are five FDA-approved drugs for treating this disease, each has only modest benefits. To design new and more effective therapies for ALS, particularly for sporadic ALS of unknown and diverse etiologies, we must identify key, convergent mechanisms of disease pathogenesis. This review focuses on the origin and effects of glutamate-mediated excitotoxicity in ALS (the cortical hyperexcitability hypothesis), in which increased glutamatergic signaling causes motor neurons to become hyperexcitable and eventually die. We characterize both primary and secondary contributions to excitotoxicity, referring to processes taking place at the synapse and within the cell, respectively. 'Primary pathways' include upregulation of calcium-permeable AMPA receptors, dysfunction of the EAAT2 astrocytic glutamate transporter, increased release of glutamate from the presynaptic terminal, and reduced inhibition by cortical interneurons-all of which have been observed in ALS patients and model systems. 'Secondary pathways' include changes to mitochondrial morphology and function, increased production of reactive oxygen species, and endoplasmic reticulum (ER) stress. By identifying key targets in the excitotoxicity cascade, we emphasize the importance of this pathway in the pathogenesis of ALS and suggest that intervening in this pathway could be effective for developing therapies for this disease.
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Affiliation(s)
- Frederick J. Arnold
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA 92617, USA
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; (A.F.P.)
| | - Alexandra F. Putka
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; (A.F.P.)
| | - Urmimala Raychaudhuri
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA 92617, USA
| | - Solomon Hsu
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA 92617, USA
| | - Richard S. Bedlack
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; (A.F.P.)
| | - Craig L. Bennett
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA 92617, USA
- Department of Neurology, University of California Irvine, Irvine, CA 92617, USA
| | - Albert R. La Spada
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA 92617, USA
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; (A.F.P.)
- Department of Neurology, University of California Irvine, Irvine, CA 92617, USA
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92617, USA
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA 92697, USA
- UCI Center for Neurotherapeutics, University of California Irvine, Irvine, CA 92697, USA
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10
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Provasek VE, Bacolla A, Rangaswamy S, Mitra J, Kodavati M, Yusuf IO, Malojirao VH, Vasquez V, Britz GW, Li GM, Xu Z, Mitra S, Garruto RM, Tainer JA, Hegde ML. RNA/DNA Binding Protein TDP43 Regulates DNA Mismatch Repair Genes with Implications for Genome Stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594552. [PMID: 38798341 PMCID: PMC11118483 DOI: 10.1101/2024.05.16.594552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
TDP43 is an RNA/DNA binding protein increasingly recognized for its role in neurodegenerative conditions including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). As characterized by its aberrant nuclear export and cytoplasmic aggregation, TDP43 proteinopathy is a hallmark feature in over 95% of ALS/FTD cases, leading to the formation of detrimental cytosolic aggregates and a reduction in nuclear functionality within neurons. Building on our prior work linking TDP43 proteinopathy to the accumulation of DNA double-strand breaks (DSBs) in neurons, the present investigation uncovers a novel regulatory relationship between TDP43 and DNA mismatch repair (MMR) gene expressions. Here, we show that TDP43 depletion or overexpression directly affects the expression of key MMR genes. Alterations include MLH1, MSH2, MSH3, MSH6, and PMS2 levels across various primary cell lines, independent of their proliferative status. Our results specifically establish that TDP43 selectively influences the expression of MLH1 and MSH6 by influencing their alternative transcript splicing patterns and stability. We furthermore find aberrant MMR gene expression is linked to TDP43 proteinopathy in two distinct ALS mouse models and post-mortem brain and spinal cord tissues of ALS patients. Notably, MMR depletion resulted in the partial rescue of TDP43 proteinopathy-induced DNA damage and signaling. Moreover, bioinformatics analysis of the TCGA cancer database reveals significant associations between TDP43 expression, MMR gene expression, and mutational burden across multiple cancers. Collectively, our findings implicate TDP43 as a critical regulator of the MMR pathway and unveil its broad impact on the etiology of both neurodegenerative and neoplastic pathologies.
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Affiliation(s)
- Vincent E Provasek
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- School of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Suganya Rangaswamy
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Joy Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Manohar Kodavati
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Issa O Yusuf
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Vikas H Malojirao
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Velmarini Vasquez
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Gavin W Britz
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Neurosurgery and Department of Neuroscience, Weill Cornell Medical College, New York, NY 10065, USA
| | - Guo-Min Li
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zuoshang Xu
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
| | - Sankar Mitra
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Ralph M Garruto
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY 13902
| | - John A Tainer
- Department of Molecular and Cellular Oncology, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Muralidhar L Hegde
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Neuroscience, Weill Cornell Medical College, New York, NY 10065, USA
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11
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Leventoux N, Morimoto S, Ishikawa M, Nakamura S, Ozawa F, Kobayashi R, Watanabe H, Supakul S, Okamoto S, Zhou Z, Kobayashi H, Kato C, Hirokawa Y, Aiba I, Takahashi S, Shibata S, Takao M, Yoshida M, Endo F, Yamanaka K, Kokubo Y, Okano H. Aberrant CHCHD2-associated mitochondriopathy in Kii ALS/PDC astrocytes. Acta Neuropathol 2024; 147:84. [PMID: 38750212 DOI: 10.1007/s00401-024-02734-w] [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: 10/13/2023] [Revised: 02/28/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Amyotrophic Lateral Sclerosis/Parkinsonism-Dementia Complex (ALS/PDC), a rare and complex neurological disorder, is predominantly observed in the Western Pacific islands, including regions of Japan, Guam, and Papua. This enigmatic condition continues to capture medical attention due to affected patients displaying symptoms that parallel those seen in either classical amyotrophic lateral sclerosis (ALS) or Parkinson's disease (PD). Distinctly, postmortem examinations of the brains of affected individuals have shown the presence of α-synuclein aggregates and TDP-43, which are hallmarks of PD and classical ALS, respectively. These observations are further complicated by the detection of phosphorylated tau, accentuating the multifaceted proteinopathic nature of ALS/PDC. The etiological foundations of this disease remain undetermined, and genetic investigations have yet to provide conclusive answers. However, emerging evidence has implicated the contribution of astrocytes, pivotal cells for maintaining brain health, to neurodegenerative onset, and likely to play a significant role in the pathogenesis of ALS/PDC. Leveraging advanced induced pluripotent stem cell technology, our team cultivated multiple astrocyte lines to further investigate the Japanese variant of ALS/PDC (Kii ALS/PDC). CHCHD2 emerged as a significantly dysregulated gene when disease astrocytes were compared to healthy controls. Our analyses also revealed imbalances in the activation of specific pathways: those associated with astrocytic cilium dysfunction, known to be involved in neurodegeneration, and those related to major neurological disorders, including classical ALS and PD. Further in-depth examinations revealed abnormalities in the mitochondrial morphology and metabolic processes of the affected astrocytes. A particularly striking observation was the reduced expression of CHCHD2 in the spinal cord, motor cortex, and oculomotor nuclei of patients with Kii ALS/PDC. In summary, our findings suggest a potential reduction in the support Kii ALS/PDC astrocytes provide to neurons, emphasizing the need to explore the role of CHCHD2 in maintaining mitochondrial health and its implications for the disease.
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Affiliation(s)
- Nicolas Leventoux
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Satoru Morimoto
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- Keio Regenerative Medicine Research Centre, Keio University, Kanagawa, Japan
- Division of Neurodegenerative Disease Research, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
- Department of Oncologic Pathology, Mie University Graduate School of Medicine, Mie, Japan
| | - Mitsuru Ishikawa
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Shiho Nakamura
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- Keio Regenerative Medicine Research Centre, Keio University, Kanagawa, Japan
- Division of Neurodegenerative Disease Research, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Fumiko Ozawa
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- Keio Regenerative Medicine Research Centre, Keio University, Kanagawa, Japan
- Division of Neurodegenerative Disease Research, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Reona Kobayashi
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Hirotaka Watanabe
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- Keio Regenerative Medicine Research Centre, Keio University, Kanagawa, Japan
| | - Sopak Supakul
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Satoshi Okamoto
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Zhi Zhou
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Hiroya Kobayashi
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- Keio Regenerative Medicine Research Centre, Keio University, Kanagawa, Japan
- Division of Neurodegenerative Disease Research, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Chris Kato
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- Keio Regenerative Medicine Research Centre, Keio University, Kanagawa, Japan
- Division of Neurodegenerative Disease Research, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Yoshifumi Hirokawa
- Department of Oncologic Pathology, Mie University Graduate School of Medicine, Mie, Japan
| | - Ikuko Aiba
- Department of Neurology, NHO, Higashinagoya National Hospital, Aichi, Japan
| | - Shinichi Takahashi
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- Keio Regenerative Medicine Research Centre, Keio University, Kanagawa, Japan
- Department of Neurology and Stroke, International Medical Centre, Saitama Medical University, Saitama, Japan
| | - Shinsuke Shibata
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
- Division of Microscopic Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masaki Takao
- Department of Clinical Laboratory, National Centre of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Mari Yoshida
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Aichi, Japan
| | - Fumito Endo
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Aichi, Japan
| | - Koji Yamanaka
- Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Aichi, Japan
| | - Yasumasa Kokubo
- Kii ALS/PDC Research Centre, Mie University Graduate School of Regional Innovation Studies, Mie, Japan.
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan.
- Keio Regenerative Medicine Research Centre, Keio University, Kanagawa, Japan.
- Division of Neurodegenerative Disease Research, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan.
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12
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Bak M, van Nimwegen E, Kouzel IU, Gur T, Schmidt R, Zavolan M, Gruber AJ. MAPP unravels frequent co-regulation of splicing and polyadenylation by RNA-binding proteins and their dysregulation in cancer. Nat Commun 2024; 15:4110. [PMID: 38750024 PMCID: PMC11096328 DOI: 10.1038/s41467-024-48046-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
Maturation of eukaryotic pre-mRNAs via splicing and polyadenylation is modulated across cell types and conditions by a variety of RNA-binding proteins (RBPs). Although there exist over 1,500 RBPs in human cells, their binding motifs and functions still remain to be elucidated, especially in the complex environment of tissues and in the context of diseases. To overcome the lack of methods for the systematic and automated detection of sequence motif-guided pre-mRNA processing regulation from RNA sequencing (RNA-Seq) data we have developed MAPP (Motif Activity on Pre-mRNA Processing). Applying MAPP to RBP knock-down experiments reveals that many RBPs regulate both splicing and polyadenylation of nascent transcripts by acting on similar sequence motifs. MAPP not only infers these sequence motifs, but also unravels the position-dependent impact of the RBPs on pre-mRNA processing. Interestingly, all investigated RBPs that act on both splicing and 3' end processing exhibit a consistently repressive or activating effect on both processes, providing a first glimpse on the underlying mechanism. Applying MAPP to normal and malignant brain tissue samples unveils that the motifs bound by the PTBP1 and RBFOX RBPs coordinately drive the oncogenic splicing program active in glioblastomas demonstrating that MAPP paves the way for characterizing pre-mRNA processing regulators under physiological and pathological conditions.
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Affiliation(s)
- Maciej Bak
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Erik van Nimwegen
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Ian U Kouzel
- Department of Biology, University of Konstanz, D-78464, Konstanz, Germany
| | - Tamer Gur
- Department of Biology, University of Konstanz, D-78464, Konstanz, Germany
| | - Ralf Schmidt
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Mihaela Zavolan
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Andreas J Gruber
- Department of Biology, University of Konstanz, D-78464, Konstanz, Germany.
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13
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Koike Y. Molecular mechanisms linking loss of TDP-43 function to amyotrophic lateral sclerosis/frontotemporal dementia-related genes. Neurosci Res 2024:S0168-0102(24)00063-4. [PMID: 38723906 DOI: 10.1016/j.neures.2024.05.001] [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: 03/08/2024] [Revised: 04/18/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are characterized by nuclear depletion and cytoplasmic aggregation of TAR DNA-binding protein-43 (TDP-43). TDP-43 plays a key role in regulating the splicing of numerous genes, including TARDBP. This review aims to delineate two aspects of ALS/FTD pathogenesis associated with TDP-43 function. First, we provide novel mechanistic insights into the splicing of UNC13A, a TDP-43 target gene. Single nucleotide polymorphisms (SNPs) in UNC13A are the most common risk factors for ALS/FTD. We found that TDP-43 represses "cryptic exon" inclusion during UNC13A RNA splicing. A risk-associated SNP in this exon results in increased RNA levels of UNC13A retaining the cryptic exon. Second, we described the perturbation of the TDP-43 autoregulatory mechanism caused by age-related DNA demethylation. Aging is a major risk factor for sporadic ALS/FTD. Typically, TDP-43 levels are regulated via alternative splicing of TARDBP mRNA. We hypothesized that TARDBP methylation is altered by aging, thereby disrupting TDP-43 autoregulation. We found that demethylation reduces the efficiency of alternative splicing and increases TARDBP mRNA levels. Moreover, we demonstrated that, with aging, this region is demethylated in the human motor cortex and is associated with the early onset of ALS.
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Affiliation(s)
- Yuka Koike
- Department of Molecular Neuroscience, Brain Research Institute, Niigata University, Japan.
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14
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Li S, Zhao S, Sinson JC, Bajic A, Rosenfeld JA, Neeley MB, Pena M, Worley KC, Burrage LC, Weisz-Hubshman M, Ketkar S, Craigen WJ, Clark GD, Lalani S, Bacino CA, Machol K, Chao HT, Potocki L, Emrick L, Sheppard J, Nguyen MTT, Khoramnia A, Hernandez PP, Nagamani SC, Liu Z, Eng CM, Lee B, Liu P. The clinical utility and diagnostic implementation of human subject cell transdifferentiation followed by RNA sequencing. Am J Hum Genet 2024; 111:841-862. [PMID: 38593811 PMCID: PMC11080285 DOI: 10.1016/j.ajhg.2024.03.007] [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: 10/04/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
RNA sequencing (RNA-seq) has recently been used in translational research settings to facilitate diagnoses of Mendelian disorders. A significant obstacle for clinical laboratories in adopting RNA-seq is the low or absent expression of a significant number of disease-associated genes/transcripts in clinically accessible samples. As this is especially problematic in neurological diseases, we developed a clinical diagnostic approach that enhanced the detection and evaluation of tissue-specific genes/transcripts through fibroblast-to-neuron cell transdifferentiation. The approach is designed specifically to suit clinical implementation, emphasizing simplicity, cost effectiveness, turnaround time, and reproducibility. For clinical validation, we generated induced neurons (iNeurons) from 71 individuals with primary neurological phenotypes recruited to the Undiagnosed Diseases Network. The overall diagnostic yield was 25.4%. Over a quarter of the diagnostic findings benefited from transdifferentiation and could not be achieved by fibroblast RNA-seq alone. This iNeuron transcriptomic approach can be effectively integrated into diagnostic whole-transcriptome evaluation of individuals with genetic disorders.
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Affiliation(s)
- Shenglan Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sen Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jefferson C Sinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Aleksandar Bajic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Advanced Technology Cores, Baylor College of Medicine, Houston, TX, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Matthew B Neeley
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
| | - Mezthly Pena
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Monika Weisz-Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Gary D Clark
- Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Seema Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Keren Machol
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA; Cain Pediatric Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, USA
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Lisa Emrick
- Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Jennifer Sheppard
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - My T T Nguyen
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
| | - Anahita Khoramnia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Sandesh Cs Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Section of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics, Houston, TX, USA
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Baylor Genetics, Houston, TX, USA.
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15
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Ayala I, Bahrami A, Pan Y, Spencer C, Flanagan ME, Mesulam MM, Gefen T, Geula C. Loss and microglia phagocytosis of synaptic proteins in frontotemporal lobar degeneration with TDP-43 proteinopathy. Neurochem Int 2024; 175:105719. [PMID: 38452814 PMCID: PMC11003416 DOI: 10.1016/j.neuint.2024.105719] [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: 04/05/2023] [Revised: 11/07/2023] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Cortical synaptic loss has emerged as an early abnormality in Alzheimer's disease (AD) with a strong relationship to cognitive performance. However, the status of synapses in frontotemporal lobar degeneration (FTLD) has received meager experimental attention. The purpose of this study was to investigate changes in cortical synaptic proteins in FTLD with tar DNA binding protein-43 (TDP-43) proteinopathy. A second aim was to study phagocytosis of synaptic proteins by microglia as a surrogate for synaptic pruning. Western blot analysis in frozen tissue from the middle frontal gyrus revealed decreased levels of the presynaptic protein synaptophysin, but slightly increased levels of the postsynaptic density protein 95 (PSD95) in FTLD-TDP. Levels of the dendritic spine protein spinophilin displayed the largest decrease. Double immunofluorescent staining visualized aggregate or punctate synaptic protein immunoreactivity in microglia. Overall, the proportion of microglia containing synaptic proteins was larger in FTLD-TDP when compared with normal controls. The increase in PSD95 levels may represent reactive upregulation of this protein, as suggested in AD. While greater numbers of microglia containing synaptic proteins is consistent with loss of synapses in FTLD-TDP, it may also be an indication of abnormal synaptic pruning by microglia.
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Affiliation(s)
- Ivan Ayala
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Atousa Bahrami
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Yuting Pan
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Callen Spencer
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Margaret E Flanagan
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - M-Marsel Mesulam
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Tamar Gefen
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Changiz Geula
- Mesulam Center for Cognitive Neurology and Alzheimer's Disease, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
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16
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Dupont M, Krischuns T, Gianetto QG, Paisant S, Bonazza S, Brault JB, Douché T, Arragain B, Florez-Prada A, Perez-Perri JI, Hentze MW, Cusack S, Matondo M, Isel C, Courtney DG, Naffakh N. The RBPome of influenza A virus NP-mRNA reveals a role for TDP-43 in viral replication. Nucleic Acids Res 2024:gkae291. [PMID: 38686810 DOI: 10.1093/nar/gkae291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 03/22/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Genome-wide approaches have significantly advanced our knowledge of the repertoire of RNA-binding proteins (RBPs) that associate with cellular polyadenylated mRNAs within eukaryotic cells. Recent studies focusing on the RBP interactomes of viral mRNAs, notably SARS-Cov-2, have revealed both similarities and differences between the RBP profiles of viral and cellular mRNAs. However, the RBPome of influenza virus mRNAs remains unexplored. Herein, we identify RBPs that associate with the viral mRNA encoding the nucleoprotein (NP) of an influenza A virus. Focusing on TDP-43, we show that it binds several influenza mRNAs beyond the NP-mRNA, and that its depletion results in lower levels of viral mRNAs and proteins within infected cells, and a decreased yield of infectious viral particles. We provide evidence that the viral polymerase recruits TDP-43 onto viral mRNAs through a direct interaction with the disordered C-terminal domain of TDP-43. Notably, other RBPs found to be associated with influenza virus mRNAs also interact with the viral polymerase, which points to a role of the polymerase in orchestrating the assembly of viral messenger ribonucleoproteins.
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Affiliation(s)
- Maud Dupont
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Tim Krischuns
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Quentin Giai Gianetto
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France
| | - Sylvain Paisant
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Stefano Bonazza
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, BelfastBT9 7BL, Northern Ireland
| | - Jean-Baptiste Brault
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - Thibaut Douché
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
| | - Benoît Arragain
- European Molecular Biology Laboratory, 38042Grenoble, France
| | | | | | | | - Stephen Cusack
- European Molecular Biology Laboratory, 38042Grenoble, France
| | - Mariette Matondo
- Institut Pasteur, Université Paris Cité, CNRS UAR2024, Proteomics Platform, Mass Spectrometry for Biology, Paris, France
| | - Catherine Isel
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
| | - David G Courtney
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, BelfastBT9 7BL, Northern Ireland
| | - Nadia Naffakh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, RNA Biology and Influenza Viruses, Paris, France
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17
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Fakim H, Vande Velde C. The implications of physiological biomolecular condensates in amyotrophic lateral sclerosis. Semin Cell Dev Biol 2024; 156:176-189. [PMID: 37268555 DOI: 10.1016/j.semcdb.2023.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023]
Abstract
In recent years, there has been an emphasis on the role of phase-separated biomolecular condensates, especially stress granules, in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). This is largely due to several ALS-associated mutations occurring in genes involved in stress granule assembly and observations that pathological inclusions detected in ALS patient neurons contain stress granule proteins, including the ALS-linked proteins TDP-43 and FUS. However, protein components of stress granules are also found in numerous other phase-separated biomolecular condensates under physiological conditions which are inadequately discussed in the context of ALS. In this review, we look beyond stress granules and describe the roles of TDP-43 and FUS in physiological condensates occurring in the nucleus and neurites, such as the nucleolus, Cajal bodies, paraspeckles and neuronal RNA transport granules. We also discuss the consequences of ALS-linked mutations in TDP-43 and FUS on their ability to phase separate into these stress-independent biomolecular condensates and perform their respective functions. Importantly, biomolecular condensates sequester multiple overlapping protein and RNA components, and their dysregulation could contribute to the observed pleiotropic effects of both sporadic and familial ALS on RNA metabolism.
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Affiliation(s)
- Hana Fakim
- Department of Neurosciences, Université de Montréal, and CHUM Research Center, Montréal, QC, Canada
| | - Christine Vande Velde
- Department of Neurosciences, Université de Montréal, and CHUM Research Center, Montréal, QC, Canada.
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18
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Klickstein JA, Johnson MA, Antonoudiou P, Maguire J, Paulo JA, Gygi SP, Weihl C, Raman M. ALS-related p97 R155H mutation disrupts lysophagy in iPSC-derived motor neurons. Stem Cell Reports 2024; 19:366-382. [PMID: 38335961 PMCID: PMC10937112 DOI: 10.1016/j.stemcr.2024.01.002] [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: 07/11/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/12/2024] Open
Abstract
Mutations in the AAA+ ATPase p97 cause multisystem proteinopathy 1, which includes amyotrophic lateral sclerosis; however, the pathogenic mechanisms that contribute to motor neuron loss remain obscure. Here, we use two induced pluripotent stem cell models differentiated into spinal motor neurons to investigate how p97 mutations perturb the motor neuron proteome. Using quantitative proteomics, we find that motor neurons harboring the p97 R155H mutation have deficits in the selective autophagy of lysosomes (lysophagy). p97 R155H motor neurons are unable to clear damaged lysosomes and have reduced viability. Lysosomes in mutant motor neurons have increased pH compared with wild-type cells. The clearance of damaged lysosomes involves UBXD1-p97 interaction, which is disrupted in mutant motor neurons. Finally, inhibition of the ATPase activity of p97 using the inhibitor CB-5083 rescues lysophagy defects in mutant motor neurons. These results add to the evidence that endo-lysosomal dysfunction is a key aspect of disease pathogenesis in p97-related disorders.
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Affiliation(s)
- Jacob A Klickstein
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA
| | - Michelle A Johnson
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA
| | | | - Jamie Maguire
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Steve P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Chris Weihl
- Department of Neurology, Washington University at St. Louis, St. Louis, MO
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA.
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19
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Zhong J, Wang C, Zhang D, Yao X, Zhao Q, Huang X, Lin F, Xue C, Wang Y, He R, Li XY, Li Q, Wang M, Zhao S, Afridi SK, Zhou W, Wang Z, Xu Y, Xu Z. PCDHA9 as a candidate gene for amyotrophic lateral sclerosis. Nat Commun 2024; 15:2189. [PMID: 38467605 PMCID: PMC10928119 DOI: 10.1038/s41467-024-46333-5] [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: 05/18/2023] [Accepted: 02/23/2024] [Indexed: 03/13/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease. To identify additional genetic factors, we analyzed exome sequences in a large cohort of Chinese ALS patients and found a homozygous variant (p.L700P) in PCDHA9 in three unrelated patients. We generated Pcdhα9 mutant mice harboring either orthologous point mutation or deletion mutation. These mice develop progressive spinal motor loss, muscle atrophy, and structural/functional abnormalities of the neuromuscular junction, leading to paralysis and early lethality. TDP-43 pathology is detected in the spinal motor neurons of aged mutant mice. Mechanistically, we demonstrate that Pcdha9 mutation causes aberrant activation of FAK and PYK2 in aging spinal cord, and dramatically reduced NKA-α1 expression in motor neurons. Our single nucleus multi-omics analysis reveals disturbed signaling involved in cell adhesion, ion transport, synapse organization, and neuronal survival in aged mutant mice. Together, our results present PCDHA9 as a potential ALS gene and provide insights into its pathogenesis.
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Affiliation(s)
- Jie Zhong
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaodong Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Disease, Beijing, 100053, China.
| | - Dan Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoli Yao
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Quanzhen Zhao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xusheng Huang
- Department of Neurology, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Feng Lin
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Chun Xue
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Yaqing Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Ruojie He
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xu-Ying Li
- Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Disease, Beijing, 100053, China
| | - Qibin Li
- Shenzhen Clabee Biotechnology Incorporation, Shenzhen, 518057, China
| | - Mingbang Wang
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, 201102, China
| | - Shaoli Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Shabbir Khan Afridi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenhao Zhou
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, 201102, China
| | - Zhanjun Wang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, National Clinical Research Center for Geriatric Disease, Beijing, 100053, China
| | - Yanming Xu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
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20
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Carrick BH, Crittenden SL, Chen F, Linsley M, Woodworth J, Kroll-Conner P, Ferdous AS, Keleş S, Wickens M, Kimble J. PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans. Dev Cell 2024; 59:661-675.e7. [PMID: 38290520 DOI: 10.1016/j.devcel.2024.01.005] [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: 07/31/2023] [Revised: 11/10/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Protein-RNA regulatory networks underpin much of biology. C. elegans FBF-2, a PUF-RNA-binding protein, binds over 1,000 RNAs to govern stem cells and differentiation. FBF-2 interacts with multiple protein partners via a key tyrosine, Y479. Here, we investigate the in vivo significance of partnerships using a Y479A mutant. Occupancy of the Y479A mutant protein increases or decreases at specific sites across the transcriptome, varying with RNAs. Germline development also changes in a specific fashion: Y479A abolishes one FBF-2 function-the sperm-to-oocyte cell fate switch. Y479A's effects on the regulation of one mRNA, gld-1, are critical to this fate change, though other network changes are also important. FBF-2 switches from repression to activation of gld-1 RNA, likely by distinct FBF-2 partnerships. The role of RNA-binding protein partnerships in governing RNA regulatory networks will likely extend broadly, as such partnerships pervade RNA controls in virtually all metazoan tissues and species.
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Affiliation(s)
- Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fan Chen
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - MaryGrace Linsley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer Woodworth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peggy Kroll-Conner
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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21
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Rajabi D, Khanmohammadi S, Rezaei N. The role of long noncoding RNAs in amyotrophic lateral sclerosis. Rev Neurosci 2024; 0:revneuro-2023-0155. [PMID: 38452377 DOI: 10.1515/revneuro-2023-0155] [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: 12/14/2023] [Accepted: 02/18/2024] [Indexed: 03/09/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease with a poor prognosis leading to death. The diagnosis and treatment of ALS are inherently challenging due to its complex pathomechanism. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides involved in different cellular processes, incisively gene expression. In recent years, more studies have been conducted on lncRNA classes and interference in different disease pathologies, showing their promising contribution to diagnosing and treating neurodegenerative diseases. In this review, we discussed the role of lncRNAs like NEAT1 and C9orf72-as in ALS pathogenesis mechanisms caused by mutations in different genes, including TAR DNA-binding protein-43 (TDP-43), fused in sarcoma (FUS), superoxide dismutase type 1 (SOD1). NEAT1 is a well-established lncRNA in ALS pathogenesis; hence, we elaborate on its involvement in forming paraspeckles, stress response, inflammatory response, and apoptosis. Furthermore, antisense lncRNAs (as-lncRNAs), a key group of transcripts from the opposite strand of genes, including ZEB1-AS1 and ATXN2-AS, are discussed as newly identified components in the pathology of ALS. Ultimately, we review the current standing of using lncRNAs as biomarkers and therapeutic agents and the future vision of further studies on lncRNA applications.
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Affiliation(s)
- Darya Rajabi
- School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
| | - Shaghayegh Khanmohammadi
- School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
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22
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Huang Y, Chen J, Hsiung CH, Bai Y, Tan Z, Ye S, Zhang X. Detecting protein-protein interaction during liquid-liquid phase separation using fluorogenic protein sensors. Mol Biol Cell 2024; 35:ar41. [PMID: 38231854 PMCID: PMC10916855 DOI: 10.1091/mbc.e23-11-0442] [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: 11/20/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/19/2024] Open
Abstract
The formation of cellular condensates, akin to membraneless organelles, is typically mediated by liquid-liquid phase separation (LLPS), during which proteins and RNA molecules interact with each other via multivalent interactions. Gaining a comprehensive understanding of these interactions holds significance in unraveling the mechanisms underlying condensate formation and the pathology of related diseases. In an attempt toward this end, fluorescence microscopy is often used to examine the colocalization of target proteins/RNAs. However, fluorescence colocalization is inadequate to reliably identify protein interaction due to the diffraction limit of traditional fluorescence microscopy. In this study, we achieve this goal through adopting a novel chemical biology approach via the dimerization-dependent fluorescent proteins (ddFPs). We succeeded in utilizing ddFPs to detect protein interaction during LLPS both in vitro and in living cells. The ddFPs allow us to investigate the interaction between two important LLPS-associated proteins, FUS and TDP-43, as cellular condensates formed. Importantly, we revealed that their interaction was associated with RNA binding upon LLPS, indicating that RNA plays a critical role in mediating interactions between RBPs. More broadly, we envision that utilization of ddFPs would reveal previously unknown protein-protein interaction and uncover their functional roles in the formation and disassembly of biomolecular condensates.
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Affiliation(s)
- Yanan Huang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Junlin Chen
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Chia-Heng Hsiung
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Zizhu Tan
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Songtao Ye
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, Hangzhou 310030, Zhejiang, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang Province, China
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23
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Alexovič M, Uličná C, Sabo J, Davalieva K. Human peripheral blood mononuclear cells as a valuable source of disease-related biomarkers: Evidence from comparative proteomics studies. Proteomics Clin Appl 2024; 18:e2300072. [PMID: 37933719 DOI: 10.1002/prca.202300072] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/08/2023] [Accepted: 10/26/2023] [Indexed: 11/08/2023]
Abstract
PURPOSE The discovery of specific and sensitive disease-associated biomarkers for early diagnostic purposes of many diseases is still highly challenging due to various complex molecular mechanisms triggered, high variability of disease-related interactions, and an overlap of manifestations among diseases. Human peripheral blood mononuclear cells (PBMCs) contain protein signatures corresponding to essential immunological interplay. Certain diseases stimulate PBMCs and contribute towards modulation of their proteome which can be effectively identified and evaluated via the comparative proteomics approach. EXPERIMENTAL DESIGN In this review, we made a detailed survey of the PBMCS-derived protein biomarker candidates for a variety of diseases, published in the last 15 years. Articles were preselected to include only comparative proteomics studies. RESULTS PBMC-derived biomarkers were investigated for cancer, glomerular, neurodegenerative/neurodevelopmental, psychiatric, chronic inflammatory, autoimmune, endocrinal, infectious, and other diseases. A detailed review of these studies encompassed the proteomics platforms, proposed candidate biomarkers, their immune cell type specificity, and potential clinical application. CONCLUSIONS Overall, PBMCs have shown a solid potential in giving early diagnostic and prognostic biomarkers for many diseases. The future of PBMC biomarker research should reveal its full potential through well-designed comparative studies and extensive testing of the most promising protein biomarkers identified so far.
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Affiliation(s)
- Michal Alexovič
- Department of Medical and Clinical Biophysics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Csilla Uličná
- Department of Medical and Clinical Biophysics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Ján Sabo
- Department of Medical and Clinical Biophysics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Katarina Davalieva
- Research Centre for Genetic Engineering and Biotechnology "Georgi D Efremov", Macedonian Academy of Sciences and Arts, Skopje, North Macedonia
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24
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Demongin C, Tranier S, Joshi V, Ceschi L, Desforges B, Pastré D, Hamon L. RNA and the RNA-binding protein FUS act in concert to prevent TDP-43 spatial segregation. J Biol Chem 2024; 300:105716. [PMID: 38311174 PMCID: PMC10912363 DOI: 10.1016/j.jbc.2024.105716] [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: 09/12/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
FUS and TDP-43 are two self-adhesive aggregation-prone mRNA-binding proteins whose pathological mutations have been linked to neurodegeneration. While TDP-43 and FUS form reversible mRNA-rich compartments in the nucleus, pathological mutations promote their respective cytoplasmic aggregation in neurons with no apparent link between the two proteins except their intertwined function in mRNA processing. By combining analyses in cellular context and at high resolution in vitro, we unraveled that TDP-43 is specifically recruited in FUS assemblies to form TDP-43-rich subcompartments but without reciprocity. The presence of mRNA provides an additional scaffold to promote the mixing between TDP-43 and FUS. Accordingly, we also found that the pathological truncated form of TDP-43, TDP-25, which has an impaired RNA-binding ability, no longer mixes with FUS. Together, these results suggest that the binding of FUS along nascent mRNAs enables TDP-43, which is highly aggregation-prone, to mix with FUS phase to form mRNA-rich subcompartments. A functional link between FUS and TDP-43 may explain their common implication in amyotrophic lateral sclerosis.
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Affiliation(s)
- Clément Demongin
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | - Samuel Tranier
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Vandana Joshi
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | - Léa Ceschi
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | | | - David Pastré
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France
| | - Loic Hamon
- SABNP, Univ Evry, INSERM, U1204, Université Paris-Saclay, Evry, France.
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25
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Shi Y, Huang L, Dong H, Yang M, Ding W, Zhou X, Lu T, Liu Z, Zhou X, Wang M, Zeng B, Sun Y, Zhong S, Wang B, Wang W, Yin C, Wang X, Wu Q. Decoding the spatiotemporal regulation of transcription factors during human spinal cord development. Cell Res 2024; 34:193-213. [PMID: 38177242 PMCID: PMC10907391 DOI: 10.1038/s41422-023-00897-x] [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: 05/26/2023] [Accepted: 11/02/2023] [Indexed: 01/06/2024] Open
Abstract
The spinal cord is a crucial component of the central nervous system that facilitates sensory processing and motor performance. Despite its importance, the spatiotemporal codes underlying human spinal cord development have remained elusive. In this study, we have introduced an image-based single-cell transcription factor (TF) expression decoding spatial transcriptome method (TF-seqFISH) to investigate the spatial expression and regulation of TFs during human spinal cord development. By combining spatial transcriptomic data from TF-seqFISH and single-cell RNA-sequencing data, we uncovered the spatial distribution of neural progenitor cells characterized by combinatorial TFs along the dorsoventral axis, as well as the molecular and spatial features governing neuronal generation, migration, and differentiation along the mediolateral axis. Notably, we observed a sandwich-like organization of excitatory and inhibitory interneurons transiently appearing in the dorsal horns of the developing human spinal cord. In addition, we integrated data from 10× Visium to identify early and late waves of neurogenesis in the dorsal horn, revealing the formation of laminas in the dorsal horns. Our study also illuminated the spatial differences and molecular cues underlying motor neuron (MN) diversification, and the enrichment of Amyotrophic Lateral Sclerosis (ALS) risk genes in MNs and microglia. Interestingly, we detected disease-associated microglia (DAM)-like microglia groups in the developing human spinal cord, which are predicted to be vulnerable to ALS and engaged in the TYROBP causal network and response to unfolded proteins. These findings provide spatiotemporal transcriptomic resources on the developing human spinal cord and potential strategies for spinal cord injury repair and ALS treatment.
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Affiliation(s)
- Yingchao Shi
- Guangdong Institute of Intelligence Science and Technology, Guangdong, China.
| | - Luwei Huang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Dong
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Meng Yang
- Changping Laboratory, Beijing, China
| | - Wenyu Ding
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Xiang Zhou
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tian Lu
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Xin Zhou
- Changping Laboratory, Beijing, China
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Mengdi Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Zeng
- Changping Laboratory, Beijing, China
| | - Yinuo Sun
- Changping Laboratory, Beijing, China
| | - Suijuan Zhong
- Changping Laboratory, Beijing, China
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Bosong Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China
| | - Wei Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Xiaoqun Wang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Changping Laboratory, Beijing, China.
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China.
| | - Qian Wu
- Changping Laboratory, Beijing, China.
- State Key Laboratory of Cognitive Neuroscience and Learning, IDG/McGovern Institute for Brain Research, New Cornerstone Science Laboratory, Beijing Normal University, Beijing, China.
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26
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Hu W, Foord C, Hsu J, Fan L, Corley MJ, Bhatia TN, Xu S, Belchikov N, He Y, Pang AP, Lanjewar SN, Jarroux J, Joglekar A, Milner TA, Ndhlovu LC, Zhang J, Butelman E, Sloan SA, Lee VM, Gan L, Tilgner HU. ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.24.581897. [PMID: 38464236 PMCID: PMC10925193 DOI: 10.1101/2024.02.24.581897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Multimodal measurements have become widespread in genomics, however measuring open chromatin accessibility and splicing simultaneously in frozen brain tissues remains unconquered. Hence, we devised Single-Cell-ISOform-RNA sequencing coupled with the Assay-for-Transposase-Accessible-Chromatin (ScISOr-ATAC). We utilized ScISOr-ATAC to assess whether chromatin and splicing alterations in the brain convergently affect the same cell types or divergently different ones. We applied ScISOr-ATAC to three major conditions: comparing (i) the Rhesus macaque (Macaca mulatta) prefrontal cortex (PFC) and visual cortex (VIS), (ii) cross species divergence of Rhesus macaque versus human PFC, as well as (iii) dysregulation in Alzheimer's disease in human PFC. We found that among cortical-layer biased excitatory neuron subtypes, splicing is highly brain-region specific for L3-5/L6 IT_RORB neurons, moderately specific in L2-3 IT_CUX2.RORB neurons and unspecific in L2-3 IT_CUX2 neurons. In contrast, at the chromatin level, L2-3 IT_CUX2.RORB neurons show the highest brain-region specificity compared to other subtypes. Likewise, when comparing human and macaque PFC, strong evolutionary divergence on one molecular modality does not necessarily imply strong such divergence on another molecular level in the same cell type. Finally, in Alzheimer's disease, oligodendrocytes show convergently high dysregulation in both chromatin and splicing. However, chromatin and splicing dysregulation most strongly affect distinct oligodendrocyte subtypes. Overall, these results indicate that chromatin and splicing can show convergent or divergent results depending on the performed comparison, justifying the need for their concurrent measurement to investigate complex systems. Taken together, ScISOr-ATAC allows for the characterization of single-cell splicing and chromatin patterns and the comparison of sample groups in frozen brain samples.
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Affiliation(s)
- Wen Hu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Careen Foord
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Justine Hsu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Li Fan
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Helen and Robert Appel Alzheimer's Disease Research Institute
| | - Michael J Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Tarun N Bhatia
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Siwei Xu
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Natan Belchikov
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics & Systems Biology Program, Weill Cornell Medicine, New York, NY, USA
| | - Yi He
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Alina Ps Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Samantha N Lanjewar
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Julien Jarroux
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Anoushka Joglekar
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Lishomwa C Ndhlovu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Eduardo Butelman
- Neuropsychoimaging of Addiction and Related Conditions Research Program, Dept. of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven A Sloan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Virginia My Lee
- Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Li Gan
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Helen and Robert Appel Alzheimer's Disease Research Institute
| | - Hagen U Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
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Gomez N, Hsieh C, Li X, Dykstra M, Waksmacki J, Altheim C, Bechar Y, Klim J, Zaepfel B, Rothstein J, Tank EE, Barmada SJ. Counter-regulation of RNA stability by UPF1 and TDP43. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578310. [PMID: 38352350 PMCID: PMC10862862 DOI: 10.1101/2024.01.31.578310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
RNA quality control is crucial for proper regulation of gene expression. Disruption of nonsense mediated mRNA decay (NMD), the primary RNA decay pathway responsible for the degradation of transcripts containing premature termination codons (PTCs), can disrupt development and lead to multiple diseases in humans and other animals. Similarly, therapies targeting NMD may have applications in hematological, neoplastic and neurological disorders. As such, tools capable of accurately quantifying NMD status could be invaluable for investigations of disease pathogenesis and biomarker identification. Toward this end, we assemble, validate, and apply a next-generation sequencing approach (NMDq) for identifying and measuring the abundance of PTC-containing transcripts. After validating NMDq performance and confirming its utility for tracking RNA surveillance, we apply it to determine pathway activity in two neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) characterized by RNA misprocessing and abnormal RNA stability. Despite the genetic and pathologic evidence implicating dysfunctional RNA metabolism, and NMD in particular, in these conditions, we detected no significant differences in PTC-encoding transcripts in ALS models or disease. Contrary to expectations, overexpression of the master NMD regulator UPF1 had little effect on the clearance of transcripts with PTCs, but rather restored RNA homeostasis through differential use and decay of alternatively poly-adenylated isoforms. Together, these data suggest that canonical NMD is not a significant contributor to ALS/FTD pathogenesis, and that UPF1 promotes neuronal survival by regulating transcripts with abnormally long 3'UTRs.
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Qneibi M, Bdir S, Bdair M, Aldwaik SA, Sandouka D, Heeh M, Idais TI. AMPA receptor neurotransmission and therapeutic applications: A comprehensive review of their multifaceted modulation. Eur J Med Chem 2024; 266:116151. [PMID: 38237342 DOI: 10.1016/j.ejmech.2024.116151] [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: 12/14/2023] [Revised: 01/02/2024] [Accepted: 01/11/2024] [Indexed: 02/05/2024]
Abstract
The neuropharmacological community has shown a strong interest in AMPA receptors as critical components of excitatory synaptic transmission during the last fifteen years. AMPA receptors, members of the ionotropic glutamate receptor family, allow rapid excitatory neurotransmission in the brain. AMPA receptors, which are permeable to sodium and potassium ions, manage the bulk of the brain's rapid synaptic communications. This study thoroughly examines the recent developments in AMPA receptor regulation, focusing on a shift from single chemical illustrations to a more extensive investigation of underlying processes. The complex interplay of these modulators in modifying the function and structure of AMPA receptors is the main focus, providing insight into their influence on the speed of excitatory neurotransmission. This research emphasizes the potential of AMPA receptor modulation as a therapy for various neurological disorders such as epilepsy and Alzheimer's disease. Analyzing these regulators' sophisticated molecular details enhances our comprehension of neuropharmacology, representing a significant advancement in using AMPA receptors for treating intricate neurological conditions.
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Affiliation(s)
- Mohammad Qneibi
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine.
| | - Sosana Bdir
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Mohammad Bdair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Samia Ammar Aldwaik
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Dana Sandouka
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | | | - Tala Iyad Idais
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
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29
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Hruska-Plochan M, Wiersma VI, Betz KM, Mallona I, Ronchi S, Maniecka Z, Hock EM, Tantardini E, Laferriere F, Sahadevan S, Hoop V, Delvendahl I, Pérez-Berlanga M, Gatta B, Panatta M, van der Bourg A, Bohaciakova D, Sharma P, De Vos L, Frontzek K, Aguzzi A, Lashley T, Robinson MD, Karayannis T, Mueller M, Hierlemann A, Polymenidou M. A model of human neural networks reveals NPTX2 pathology in ALS and FTLD. Nature 2024; 626:1073-1083. [PMID: 38355792 PMCID: PMC10901740 DOI: 10.1038/s41586-024-07042-7] [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: 09/28/2021] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
Human cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1, which involve human-specific mechanisms2-5 that cannot be directly studied in animal models. Here, to explore the emergence and consequences of TDP-43 pathologies, we generated induced pluripotent stem cell-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors6. Single-cell transcriptomics and comparison to independent neural stem cells7 showed that iCoMoNSCs are uniquely homogenous and self-renewing. Differentiated iCoMoNSCs formed a self-organized multicellular system consisting of synaptically connected and electrophysiologically active neurons, which matured into long-lived functional networks (which we designate iNets). Neuronal and glial maturation in iNets was similar to that of cortical organoids8. Overexpression of wild-type TDP-43 in a minority of neurons within iNets led to progressive fragmentation and aggregation of the protein, resulting in a partial loss of function and neurotoxicity. Single-cell transcriptomics revealed a novel set of misregulated RNA targets in TDP-43-overexpressing neurons and in patients with TDP-43 proteinopathies exhibiting a loss of nuclear TDP-43. The strongest misregulated target encoded the synaptic protein NPTX2, the levels of which are controlled by TDP-43 binding on its 3' untranslated region. When NPTX2 was overexpressed in iNets, it exhibited neurotoxicity, whereas correcting NPTX2 misregulation partially rescued neurons from TDP-43-induced neurodegeneration. Notably, NPTX2 was consistently misaccumulated in neurons from patients with amyotrophic lateral sclerosis and frontotemporal lobar degeneration with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby revealing a TDP-43-dependent pathway of neurotoxicity.
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Affiliation(s)
| | - Vera I Wiersma
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Katharina M Betz
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Izaskun Mallona
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Silvia Ronchi
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- MaxWell Biosystems AG, Zurich, Switzerland
| | - Zuzanna Maniecka
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Eva-Maria Hock
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Elena Tantardini
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Florent Laferriere
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Sonu Sahadevan
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Vanessa Hoop
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Igor Delvendahl
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Beatrice Gatta
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Martina Panatta
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | | | - Dasa Bohaciakova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University Brno, Brno, Czech Republic
| | - Puneet Sharma
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
- NCCR RNA and Disease Technology Platform, Bern, Switzerland
| | - Laura De Vos
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Karl Frontzek
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological diseases, Department of Movement Disorders, UCL Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | - Mark D Robinson
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | | | - Martin Mueller
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Andreas Hierlemann
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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30
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Dos Passos PM, Hemamali EH, Mamede LD, Hayes LR, Ayala YM. RNA-mediated ribonucleoprotein assembly controls TDP-43 nuclear retention. PLoS Biol 2024; 22:e3002527. [PMID: 38422113 DOI: 10.1371/journal.pbio.3002527] [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: 08/22/2023] [Revised: 03/12/2024] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
TDP-43 is an essential RNA-binding protein strongly implicated in the pathogenesis of neurodegenerative disorders characterized by cytoplasmic aggregates and loss of nuclear TDP-43. The protein shuttles between nucleus and cytoplasm, yet maintaining predominantly nuclear TDP-43 localization is important for TDP-43 function and for inhibiting cytoplasmic aggregation. We previously demonstrated that specific RNA binding mediates TDP-43 self-assembly and biomolecular condensation, requiring multivalent interactions via N- and C-terminal domains. Here, we show that these complexes play a key role in TDP-43 nuclear retention. TDP-43 forms macromolecular complexes with a wide range of size distribution in cells and we find that defects in RNA binding or inter-domain interactions, including phase separation, impair the assembly of the largest species. Our findings suggest that recruitment into these macromolecular complexes prevents cytoplasmic egress of TDP-43 in a size-dependent manner. Our observations uncover fundamental mechanisms controlling TDP-43 cellular homeostasis, whereby regulation of RNA-mediated self-assembly modulates TDP-43 nucleocytoplasmic distribution. Moreover, these findings highlight pathways that may be implicated in TDP-43 proteinopathies and identify potential therapeutic targets.
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Affiliation(s)
- Patricia M Dos Passos
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Erandika H Hemamali
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Lohany D Mamede
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Lindsey R Hayes
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yuna M Ayala
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
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31
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Arribas V, Onetti Y, Ramiro-Pareta M, Villacampa P, Beck H, Alberola M, Esteve-Codina A, Merkel A, Sperandio M, Martínez-Estrada OM, Schmid B, Montanez E. Endothelial TDP-43 controls sprouting angiogenesis and vascular barrier integrity, and its deletion triggers neuroinflammation. JCI Insight 2024; 9:e177819. [PMID: 38300714 PMCID: PMC11143933 DOI: 10.1172/jci.insight.177819] [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: 11/20/2023] [Accepted: 01/30/2024] [Indexed: 02/03/2024] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is a DNA/RNA-binding protein that regulates gene expression, and its malfunction in neurons has been causally associated with multiple neurodegenerative disorders. Although progress has been made in understanding the functions of TDP-43 in neurons, little is known about its roles in endothelial cells (ECs), angiogenesis, and vascular function. Using inducible EC-specific TDP-43-KO mice, we showed that TDP-43 is required for sprouting angiogenesis, vascular barrier integrity, and blood vessel stability. Postnatal EC-specific deletion of TDP-43 led to retinal hypovascularization due to defects in vessel sprouting associated with reduced EC proliferation and migration. In mature blood vessels, loss of TDP-43 disrupted the blood-brain barrier and triggered vascular degeneration. These vascular defects were associated with an inflammatory response in the CNS with activation of microglia and astrocytes. Mechanistically, deletion of TDP-43 disrupted the fibronectin matrix around sprouting vessels and reduced β-catenin signaling in ECs. Together, our results indicate that TDP-43 is essential for the formation of a stable and mature vasculature.
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Affiliation(s)
- Víctor Arribas
- Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona and Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet del Llobregat, Spain
| | - Yara Onetti
- Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona and Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet del Llobregat, Spain
| | - Marina Ramiro-Pareta
- Celltec-UB, Department of Cell Biology, Physiology, and Immunology, Faculty of Biology, and
- Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - Pilar Villacampa
- Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona and Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet del Llobregat, Spain
| | - Heike Beck
- Walter Brendel Centre of Experimental Medicine, Biomedical Center, Institute of Cardiovascular Physiology and Pathophysiology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Mariona Alberola
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Angelika Merkel
- Josep Carreras Leukemia Research Institute (IJC), Barcelona, Spain
| | - Markus Sperandio
- Walter Brendel Centre of Experimental Medicine, Biomedical Center, Institute of Cardiovascular Physiology and Pathophysiology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Ofelia M. Martínez-Estrada
- Celltec-UB, Department of Cell Biology, Physiology, and Immunology, Faculty of Biology, and
- Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - Bettina Schmid
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Eloi Montanez
- Department of Physiological Sciences, Faculty of Medicine and Health Sciences, University of Barcelona and Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet del Llobregat, Spain
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32
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Zeng Y, Lovchykova A, Akiyama T, Liu C, Guo C, Jawahar VM, Sianto O, Calliari A, Prudencio M, Dickson DW, Petrucelli L, Gitler AD. TDP-43 nuclear loss in FTD/ALS causes widespread alternative polyadenylation changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.575730. [PMID: 38328059 PMCID: PMC10849503 DOI: 10.1101/2024.01.22.575730] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
In frontotemporal dementia and amyotrophic lateral sclerosis, the RNA-binding protein TDP-43 is depleted from the nucleus. TDP-43 loss leads to cryptic exon inclusion but a role in other RNA processing events remains unresolved. Here, we show that loss of TDP-43 causes widespread changes in alternative polyadenylation, impacting expression of disease-relevant genes (e.g., ELP1, NEFL, and TMEM106B) and providing evidence that alternative polyadenylation is a new facet of TDP-43 pathology.
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Affiliation(s)
- Yi Zeng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tetsuya Akiyama
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Chang Liu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Caiwei Guo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Vidhya Maheswari Jawahar
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Odilia Sianto
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna Calliari
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Mercedes Prudencio
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Dennis W. Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
- Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub – San Francisco, San Francisco, CA, USA
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33
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Zhu L, Deng F, Bai D, Hou J, Jia Q, Zhang C, Ou K, Li S, Li XJ, Yin P. Loss of TDP-43 mediates severe neurotoxicity by suppressing PJA1 gene transcription in the monkey brain. Cell Mol Life Sci 2024; 81:16. [PMID: 38194085 PMCID: PMC11072099 DOI: 10.1007/s00018-023-05066-2] [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: 09/12/2023] [Revised: 11/19/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024]
Abstract
The nuclear loss and cytoplasmic accumulation of TDP-43 (TAR DNA/RNA binding protein 43) are pathological hallmarks of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Previously, we reported that the primate-specific cleavage of TDP-43 accounts for its cytoplasmic mislocalization in patients' brains. This prompted us to investigate further whether and how the loss of nuclear TDP-43 mediates neuropathology in primate brain. In this study, we report that TDP-43 knockdown at the similar effectiveness, induces more damage to neuronal cells in the monkey brain than rodent mouse. Importantly, the loss of TDP-43 suppresses the E3 ubiquitin ligase PJA1 expression in the monkey brain at transcriptional level, but yields an opposite upregulation of PJA1 in the mouse brain. This distinct effect is due to the species-dependent binding of nuclear TDP-43 to the unique promoter sequences of the PJA1 genes. Further analyses reveal that the reduction of PJA1 accelerates neurotoxicity, whereas overexpressing PJA1 diminishes neuronal cell death by the TDP-43 knockdown in vivo. Our findings not only uncover a novel primate-specific neurotoxic contribution to the loss of function theory of TDP-43 proteinopathy, but also underscore a potential therapeutic approach of PJA1 to the loss of nuclear TDP-43.
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Affiliation(s)
- Longhong Zhu
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Fuyu Deng
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Dazhang Bai
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
- Department of Neurology, Affiliated Hospital of North Sichuan Medical College, North Sichuan Medical College, Nanchong, 637000, China
- Institute of Neurological Diseases, North Sichuan Medical College, Nanchong, 637000, China
| | - Junqi Hou
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Qingqing Jia
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Chen Zhang
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Kaili Ou
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Shihua Li
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
- Ministry of Education Key Laboratory of CNS Regeneration, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
- Ministry of Education Key Laboratory of CNS Regeneration, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
| | - Peng Yin
- Guangdong Key Laboratory of Non-Human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
- Ministry of Education Key Laboratory of CNS Regeneration, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, 510632, China.
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34
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Agra Almeida Quadros AR, Li Z, Wang X, Ndayambaje IS, Aryal S, Ramesh N, Nolan M, Jayakumar R, Han Y, Stillman H, Aguilar C, Wheeler HJ, Connors T, Lopez-Erauskin J, Baughn MW, Melamed Z, Beccari MS, Olmedo Martínez L, Canori M, Lee CZ, Moran L, Draper I, Kopin AS, Oakley DH, Dickson DW, Cleveland DW, Hyman BT, Das S, Ertekin-Taner N, Lagier-Tourenne C. Cryptic splicing of stathmin-2 and UNC13A mRNAs is a pathological hallmark of TDP-43-associated Alzheimer's disease. Acta Neuropathol 2024; 147:9. [PMID: 38175301 PMCID: PMC10766724 DOI: 10.1007/s00401-023-02655-0] [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: 05/29/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Nuclear clearance and cytoplasmic accumulations of the RNA-binding protein TDP-43 are pathological hallmarks in almost all patients with amyotrophic lateral sclerosis (ALS) and up to 50% of patients with frontotemporal dementia (FTD) and Alzheimer's disease. In Alzheimer's disease, TDP-43 pathology is predominantly observed in the limbic system and correlates with cognitive decline and reduced hippocampal volume. Disruption of nuclear TDP-43 function leads to abnormal RNA splicing and incorporation of erroneous cryptic exons in numerous transcripts including Stathmin-2 (STMN2, also known as SCG10) and UNC13A, recently reported in tissues from patients with ALS and FTD. Here, we identify both STMN2 and UNC13A cryptic exons in Alzheimer's disease patients, that correlate with TDP-43 pathology burden, but not with amyloid-β or tau deposits. We also demonstrate that processing of the STMN2 pre-mRNA is more sensitive to TDP-43 loss of function than UNC13A. In addition, full-length RNAs encoding STMN2 and UNC13A are suppressed in large RNA-seq datasets generated from Alzheimer's disease post-mortem brain tissue. Collectively, these results open exciting new avenues to use STMN2 and UNC13A as potential therapeutic targets in a broad range of neurodegenerative conditions with TDP-43 proteinopathy including Alzheimer's disease.
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Affiliation(s)
- Ana Rita Agra Almeida Quadros
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Zhaozhi Li
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Xue Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, FL, USA
| | - I Sandra Ndayambaje
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sandeep Aryal
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Nandini Ramesh
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Matthew Nolan
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Rojashree Jayakumar
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Han
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hannah Stillman
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Corey Aguilar
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hayden J Wheeler
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Theresa Connors
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jone Lopez-Erauskin
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Michael W Baughn
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ze'ev Melamed
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Melinda S Beccari
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Laura Olmedo Martínez
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Canori
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Chao-Zong Lee
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura Moran
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Derek H Oakley
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Bradley T Hyman
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sudeshna Das
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA.
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Neurology, MassGeneral Institute for Neurodegenerative Diseases (MIND), Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA.
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López-Erauskin J, Bravo-Hernandez M, Presa M, Baughn MW, Melamed Z, Beccari MS, Agra de Almeida Quadros AR, Arnold-Garcia O, Zuberi A, Ling K, Platoshyn O, Niño-Jara E, Ndayambaje IS, McAlonis-Downes M, Cabrera L, Artates JW, Ryan J, Hermann A, Ravits J, Bennett CF, Jafar-Nejad P, Rigo F, Marsala M, Lutz CM, Cleveland DW, Lagier-Tourenne C. Stathmin-2 loss leads to neurofilament-dependent axonal collapse driving motor and sensory denervation. Nat Neurosci 2024; 27:34-47. [PMID: 37996528 PMCID: PMC10842032 DOI: 10.1038/s41593-023-01496-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/16/2023] [Indexed: 11/25/2023]
Abstract
The mRNA transcript of the human STMN2 gene, encoding for stathmin-2 protein (also called SCG10), is profoundly impacted by TAR DNA-binding protein 43 (TDP-43) loss of function. The latter is a hallmark of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Using a combination of approaches, including transient antisense oligonucleotide-mediated suppression, sustained shRNA-induced depletion in aging mice, and germline deletion, we show that stathmin-2 has an important role in the establishment and maintenance of neurofilament-dependent axoplasmic organization that is critical for preserving the caliber and conduction velocity of myelinated large-diameter axons. Persistent stathmin-2 loss in adult mice results in pathologies found in ALS, including reduced interneurofilament spacing, axonal caliber collapse that drives tearing within outer myelin layers, diminished conduction velocity, progressive motor and sensory deficits, and muscle denervation. These findings reinforce restoration of stathmin-2 as an attractive therapeutic approach for ALS and other TDP-43-dependent neurodegenerative diseases.
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Affiliation(s)
- Jone López-Erauskin
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Mariana Bravo-Hernandez
- Department of Anesthesiology and Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | | | - Michael W Baughn
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ze'ev Melamed
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Medical Neurobiology, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Melinda S Beccari
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ana Rita Agra de Almeida Quadros
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Olatz Arnold-Garcia
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain
- CIBERNED, ISCIII (CIBER, Carlos III Institute, Spanish Ministry of Sciences and Innovation), Madrid, Spain
| | | | - Karen Ling
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | - Oleksandr Platoshyn
- Department of Anesthesiology and Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Elkin Niño-Jara
- Department of Anesthesiology and Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - I Sandra Ndayambaje
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Melissa McAlonis-Downes
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Larissa Cabrera
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Jonathan W Artates
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | | | - Anita Hermann
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, University of California at San Diego, La Jolla, CA, USA
| | | | | | - Frank Rigo
- Ionis Pharmaceuticals Inc., Carlsbad, CA, USA
| | - Martin Marsala
- Department of Anesthesiology and Stem Cell Program and Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | | | - Don W Cleveland
- Ludwig Institute and Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.
| | - Clotilde Lagier-Tourenne
- Department of Neurology, The Sean M. Healey and AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
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36
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Nolan M, Scott C, Hof PR, Ansorge O. Betz cells of the primary motor cortex. J Comp Neurol 2024; 532:e25567. [PMID: 38289193 PMCID: PMC10952528 DOI: 10.1002/cne.25567] [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: 08/09/2023] [Revised: 11/11/2023] [Accepted: 11/17/2023] [Indexed: 02/01/2024]
Abstract
Betz cells, named in honor of Volodymyr Betz (1834-1894), who described them as "giant pyramids" in the primary motor cortex of primates and other mammalian species, are layer V extratelencephalic projection (ETP) neurons that directly innervate α-motoneurons of the brainstem and spinal cord. Despite their large volume and circumferential dendritic architecture, to date, no single molecular criterion has been established that unequivocally distinguishes adult Betz cells from other layer V ETP neurons. In primates, transcriptional signatures suggest the presence of at least two ETP neuron clusters that contain mature Betz cells; these are characterized by an abundance of axon guidance and oxidative phosphorylation transcripts. How neurodevelopmental programs drive the distinct positional and morphological features of Betz cells in humans remains unknown. Betz cells display a distinct biphasic firing pattern involving early cessation of firing followed by delayed sustained acceleration in spike frequency and magnitude. Few cell type-specific transcripts and electrophysiological characteristics are conserved between rodent layer V ETP neurons of the motor cortex and primate Betz cells. This has implications for the modeling of disorders that affect the motor cortex in humans, such as amyotrophic lateral sclerosis (ALS). Perhaps vulnerability to ALS is linked to the evolution of neural networks for fine motor control reflected in the distinct morphomolecular architecture of the human motor cortex, including Betz cells. Here, we discuss histological, molecular, and functional data concerning the position of Betz cells in the emerging taxonomy of neurons across diverse species and their role in neurological disorders.
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Affiliation(s)
- Matthew Nolan
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Department of NeurologyMassachusetts General HospitalBostonMassachusettsUSA
| | - Connor Scott
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
| | - Patrick. R. Hof
- Nash Family Department of Neuroscience and Friedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Olaf Ansorge
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
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37
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McKeever PM, Sababi AM, Sharma R, Khuu N, Xu Z, Shen SY, Xiao S, McGoldrick P, Orouji E, Ketela T, Sato C, Moreno D, Visanji N, Kovacs GG, Keith J, Zinman L, Rogaeva E, Goodarzi H, Bader GD, Robertson J. Single-nucleus multiomic atlas of frontal cortex in amyotrophic lateral sclerosis with a deep learning-based decoding of alternative polyadenylation mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.22.573083. [PMID: 38187588 PMCID: PMC10769403 DOI: 10.1101/2023.12.22.573083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The understanding of how different cell types contribute to amyotrophic lateral sclerosis (ALS) pathogenesis is limited. Here we generated a single-nucleus transcriptomic and epigenomic atlas of the frontal cortex of ALS cases with C9orf72 (C9) hexanucleotide repeat expansions and sporadic ALS (sALS). Our findings reveal shared pathways in C9-ALS and sALS, characterized by synaptic dysfunction in excitatory neurons and a disease-associated state in microglia. The disease subtypes diverge with loss of astrocyte homeostasis in C9-ALS, and a more substantial disturbance of inhibitory neurons in sALS. Leveraging high depth 3'-end sequencing, we found a widespread switch towards distal polyadenylation (PA) site usage across ALS subtypes relative to controls. To explore this differential alternative PA (APA), we developed APA-Net, a deep neural network model that uses transcript sequence and expression levels of RNA-binding proteins (RBPs) to predict cell-type specific APA usage and RBP interactions likely to regulate APA across disease subtypes.
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Dogan EO, Bouley J, Zhong J, Harkins AL, Keeler AM, Bosco DA, Brown RH, Henninger N. Genetic ablation of Sarm1 attenuates expression and mislocalization of phosphorylated TDP-43 after mouse repetitive traumatic brain injury. Acta Neuropathol Commun 2023; 11:206. [PMID: 38124145 PMCID: PMC10731794 DOI: 10.1186/s40478-023-01709-4] [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: 08/15/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Traumatic brain injury (TBI), particularly when moderate-to-severe and repetitive, is a strong environmental risk factor for several progressive neurodegenerative disorders. Mislocalization and deposition of transactive response DNA binding protein 43 (TDP-43) has been reported in both TBI and TBI-associated neurodegenerative diseases. It has been hypothesized that axonal pathology, an early event after TBI, may promote TDP-43 dysregulation and serve as a trigger for neurodegenerative processes. We sought to determine whether blocking the prodegenerative Sarm1 (sterile alpha and TIR motif containing 1) axon death pathway attenuates TDP-43 pathology after TBI. We subjected 111 male Sarm1 wild type, hemizygous, and knockout mice to moderate-to-severe repetitive TBI (rTBI) using a previously established injury paradigm. We conducted serial neurological assessments followed by histological analyses (NeuN, MBP, Iba-1, GFAP, pTDP-43, and AT8) at 1 month after rTBI. Genetic ablation of the Sarm1 gene attenuated the expression and mislocalization of phosphorylated TDP-43 (pTDP-43) and accumulation of pTau. In addition, Sarm1 knockout mice had significantly improved cortical neuronal and axonal integrity, functional deficits, and improved overall survival after rTBI. In contrast, removal of one Sarm1 allele delayed, but did not prevent, neurological deficits and neuroaxonal loss. Nevertheless, Sarm1 haploinsufficient mice showed significantly less microgliosis, pTDP-43 pathology, and pTau accumulation when compared to wild type mice. These data indicate that the Sarm1-mediated prodegenerative pathway contributes to pathogenesis in rTBI including the pathological accumulation of pTDP-43. This suggests that anti-Sarm1 therapeutics are a viable approach for preserving neurological function after moderate-to-severe rTBI.
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Affiliation(s)
- Elif O Dogan
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA
| | - James Bouley
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA
| | - Jianjun Zhong
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ashley L Harkins
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA
- Graduate Program in Neuroscience, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, 01655, USA
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Allison M Keeler
- Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
- NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, MA, 01605, USA
| | - Daryl A Bosco
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA
| | - Nils Henninger
- Department of Neurology, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA.
- Department of Psychiatry, University of Massachusetts Chan Medical School, 55 Lake Ave, North, Worcester, MA, 01655, USA.
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Zhao B, Cowan CM, Coutts JA, Christy DD, Saraph A, Hsueh SCC, Plotkin SS, Mackenzie IR, Kaplan JM, Cashman NR. Targeting RACK1 to alleviate TDP-43 and FUS proteinopathy-mediated suppression of protein translation and neurodegeneration. Acta Neuropathol Commun 2023; 11:200. [PMID: 38111057 PMCID: PMC10726565 DOI: 10.1186/s40478-023-01705-8] [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: 10/09/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) and Fused in Sarcoma/Translocated in Sarcoma (FUS) are ribonucleoproteins associated with pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Under physiological conditions, TDP-43 and FUS are predominantly localized in the nucleus, where they participate in transcriptional regulation, RNA splicing and metabolism. In disease, however, they are typically mislocalized to the cytoplasm where they form aggregated inclusions. A number of shared cellular pathways have been identified that contribute to TDP-43 and FUS toxicity in neurodegeneration. In the present study, we report a novel pathogenic mechanism shared by these two proteins. We found that pathological FUS co-aggregates with a ribosomal protein, the Receptor for Activated C-Kinase 1 (RACK1), in the cytoplasm of spinal cord motor neurons of ALS, as previously reported for pathological TDP-43. In HEK293T cells transiently transfected with TDP-43 or FUS mutant lacking a functional nuclear localization signal (NLS; TDP-43ΔNLS and FUSΔNLS), cytoplasmic TDP-43 and FUS induced co-aggregation with endogenous RACK1. These co-aggregates sequestered the translational machinery through interaction with the polyribosome, accompanied by a significant reduction of global protein translation. RACK1 knockdown decreased cytoplasmic aggregation of TDP-43ΔNLS or FUSΔNLS and alleviated associated global translational suppression. Surprisingly, RACK1 knockdown also led to partial nuclear localization of TDP-43ΔNLS and FUSΔNLS in some transfected cells, despite the absence of NLS. In vivo, RACK1 knockdown alleviated retinal neuronal degeneration in transgenic Drosophila melanogaster expressing hTDP-43WT or hTDP-43Q331K and improved motor function of hTDP-43WT flies, with no observed adverse effects on neuronal health in control knockdown flies. In conclusion, our results revealed a novel shared mechanism of pathogenesis for misfolded aggregates of TDP-43 and FUS mediated by interference with protein translation in a RACK1-dependent manner. We provide proof-of-concept evidence for targeting RACK1 as a potential therapeutic approach for TDP-43 or FUS proteinopathy associated with ALS and FTLD.
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Affiliation(s)
- Beibei Zhao
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada
- ProMIS Neurosciences, Cambridge, MA, 02142, USA
| | - Catherine M Cowan
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada
| | - Juliane A Coutts
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada
| | - Darren D Christy
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada
| | - Ananya Saraph
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada
| | - Shawn C C Hsueh
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Stephen S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Ian R Mackenzie
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada
| | | | - Neil R Cashman
- University of British Columbia, Djavad Mowafaghian Centre for Brain Health, Vancouver, BC, V6T 1Z3, Canada.
- ProMIS Neurosciences, Cambridge, MA, 02142, USA.
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40
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Kahriman A, Bouley J, Tuncali I, Dogan EO, Pereira M, Luu T, Bosco DA, Jaber S, Peters OM, Brown RH, Henninger N. Repeated mild traumatic brain injury triggers pathology in asymptomatic C9ORF72 transgenic mice. Brain 2023; 146:5139-5152. [PMID: 37527465 PMCID: PMC11046056 DOI: 10.1093/brain/awad264] [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: 10/14/2022] [Revised: 07/06/2023] [Accepted: 07/24/2023] [Indexed: 08/03/2023] Open
Abstract
Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are fatal neurodegenerative diseases that represent ends of the spectrum of a single disease. The most common genetic cause of FTD and ALS is a hexanucleotide repeat expansion in the C9orf72 gene. Although epidemiological data suggest that traumatic brain injury (TBI) represents a risk factor for FTD and ALS, its role in exacerbating disease onset and course remains unclear. To explore the interplay between traumatic brain injury and genetic risk in the induction of FTD/ALS pathology we combined a mild repetitive traumatic brain injury paradigm with an established bacterial artificial chromosome transgenic C9orf72 (C9BAC) mouse model without an overt motor phenotype or neurodegeneration. We assessed 8-10 week-old littermate C9BACtg/tg (n = 21), C9BACtg/- (n = 20) and non-transgenic (n = 21) mice of both sexes for the presence of behavioural deficits and cerebral histopathology at 12 months after repetitive TBI. Repetitive TBI did not affect body weight gain, general neurological deficit severity, nor survival over the 12-month observation period and there was no difference in rotarod performance, object recognition, social interaction and acoustic characteristics of ultrasonic vocalizations of C9BAC mice subjected to repetitive TBI versus sham injury. However, we found that repetitive TBI increased the time to the return of the righting reflex, reduced grip force, altered sociability behaviours and attenuated ultrasonic call emissions during social interactions in C9BAC mice. Strikingly, we found that repetitive TBI caused widespread microglial activation and reduced neuronal density that was associated with loss of histological markers of axonal and synaptic integrity as well as profound neuronal transactive response DNA binding protein 43 kDa mislocalization in the cerebral cortex of C9BAC mice at 12 months; this was not observed in non-transgenic repetitive TBI and C9BAC sham mice. Our data indicate that repetitive TBI can be an environmental risk factor that is sufficient to trigger FTD/ALS-associated neuropathology and behavioural deficits, but not paralysis, in mice carrying a C9orf72 hexanucleotide repeat expansion.
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Affiliation(s)
- Aydan Kahriman
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - James Bouley
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Idil Tuncali
- Department of Psychological and Brain Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Elif O Dogan
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Mariana Pereira
- Department of Psychological and Brain Sciences, University of Massachusetts, Amherst, MA 01003, USA
| | - Thuyvan Luu
- Department of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Daryl A Bosco
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Samer Jaber
- Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Owen M Peters
- School of Biosciences, UK Dementia Research Institute, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Nils Henninger
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
- Department of Psychiatry, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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41
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García Morato J, Gloeckner CJ, Kahle PJ. Proteomics elucidating physiological and pathological functions of TDP-43. Proteomics 2023; 23:e2200410. [PMID: 37671599 DOI: 10.1002/pmic.202200410] [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: 05/19/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
Trans-activation response DNA binding protein of 43 kDa (TDP-43) regulates a great variety of cellular processes in the nucleus and cytosol. In addition, a defined subset of neurodegenerative diseases is characterized by nuclear depletion of TDP-43 as well as cytosolic mislocalization and aggregation. To perform its diverse functions TDP-43 can associate with different ribonucleoprotein complexes. Combined with transcriptomics, MS interactome studies have unveiled associations between TDP-43 and the spliceosome machinery, polysomes and RNA granules. Moreover, the highly dynamic, low-valency interactions regulated by its low-complexity domain calls for innovative proximity labeling methodologies. In addition to protein partners, the analysis of post-translational modifications showed that they may play a role in the nucleocytoplasmic shuttling, RNA binding, liquid-liquid phase separation and protein aggregation of TDP-43. Here we review the various TDP-43 ribonucleoprotein complexes characterized so far, how they contribute to the diverse functions of TDP-43, and roles of post-translational modifications. Further understanding of the fluid dynamic properties of TDP-43 in ribonucleoprotein complexes, RNA granules, and self-assemblies will advance the understanding of RNA processing in cells and perhaps help to develop novel therapeutic approaches for TDPopathies.
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Affiliation(s)
- Jorge García Morato
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Christian Johannes Gloeckner
- Research Group Functional Neuroproteomics, German Center of Neurodegenerative Diseases, Tübingen, Germany
- Core Facility for Medical Bioanalytics, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Philipp J Kahle
- Laboratory of Functional Neurogenetics, Department of Neurodegeneration, German Center of Neurodegenerative Diseases and Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Department of Biochemistry, University of Tübingen, Tübingen, Germany
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42
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Ke H, Liu K, Jiao B, Zhao L. Implications of TDP-43 in non-neuronal systems. Cell Commun Signal 2023; 21:338. [PMID: 37996849 PMCID: PMC10666381 DOI: 10.1186/s12964-023-01336-5] [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: 07/27/2023] [Accepted: 09/26/2023] [Indexed: 11/25/2023] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) is a versatile RNA/DNA-binding protein with multifaceted processes. While TDP-43 has been extensively studied in the context of degenerative diseases, recent evidence has also highlighted its crucial involvement in diverse life processes beyond neurodegeneration. Here, we mainly reviewed the function of TDP-43 in non-neurodegenerative physiological and pathological processes, including spermatogenesis, embryonic development, mammary gland development, tumor formation, and viral infection, highlighting its importance as a key regulatory factor for the maintenance of normal functions throughout life. TDP-43 exhibits diverse and sometimes opposite functionality across different cell types through various mechanisms, and its roles can shift at distinct stages within the same biological system. Consequently, TDP-43 operates in both a context-dependent and a stage-specific manner in response to a variety of internal and external stimuli. Video Abstract.
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Affiliation(s)
- Hao Ke
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 330031, China
| | - Kang Liu
- Ganzhou People's Hospital, Ganzhou, 341000, China
| | - Baowei Jiao
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Limin Zhao
- Human Aging Research Institute (HARI) and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang, 330031, China.
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Poller W, Sahoo S, Hajjar R, Landmesser U, Krichevsky AM. Exploration of the Noncoding Genome for Human-Specific Therapeutic Targets-Recent Insights at Molecular and Cellular Level. Cells 2023; 12:2660. [PMID: 37998395 PMCID: PMC10670380 DOI: 10.3390/cells12222660] [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: 10/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
While it is well known that 98-99% of the human genome does not encode proteins, but are nevertheless transcriptionally active and give rise to a broad spectrum of noncoding RNAs [ncRNAs] with complex regulatory and structural functions, specific functions have so far been assigned to only a tiny fraction of all known transcripts. On the other hand, the striking observation of an overwhelmingly growing fraction of ncRNAs, in contrast to an only modest increase in the number of protein-coding genes, during evolution from simple organisms to humans, strongly suggests critical but so far essentially unexplored roles of the noncoding genome for human health and disease pathogenesis. Research into the vast realm of the noncoding genome during the past decades thus lead to a profoundly enhanced appreciation of the multi-level complexity of the human genome. Here, we address a few of the many huge remaining knowledge gaps and consider some newly emerging questions and concepts of research. We attempt to provide an up-to-date assessment of recent insights obtained by molecular and cell biological methods, and by the application of systems biology approaches. Specifically, we discuss current data regarding two topics of high current interest: (1) By which mechanisms could evolutionary recent ncRNAs with critical regulatory functions in a broad spectrum of cell types (neural, immune, cardiovascular) constitute novel therapeutic targets in human diseases? (2) Since noncoding genome evolution is causally linked to brain evolution, and given the profound interactions between brain and immune system, could human-specific brain-expressed ncRNAs play a direct or indirect (immune-mediated) role in human diseases? Synergistic with remarkable recent progress regarding delivery, efficacy, and safety of nucleic acid-based therapies, the ongoing large-scale exploration of the noncoding genome for human-specific therapeutic targets is encouraging to proceed with the development and clinical evaluation of novel therapeutic pathways suggested by these research fields.
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Affiliation(s)
- Wolfgang Poller
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
| | - Susmita Sahoo
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1030, New York, NY 10029, USA;
| | - Roger Hajjar
- Gene & Cell Therapy Institute, Mass General Brigham, 65 Landsdowne St, Suite 143, Cambridge, MA 02139, USA;
| | - Ulf Landmesser
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Anna M. Krichevsky
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
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Pisciottani A, Croci L, Lauria F, Marullo C, Savino E, Ambrosi A, Podini P, Marchioretto M, Casoni F, Cremona O, Taverna S, Quattrini A, Cioni JM, Viero G, Codazzi F, Consalez GG. Neuronal models of TDP-43 proteinopathy display reduced axonal translation, increased oxidative stress, and defective exocytosis. Front Cell Neurosci 2023; 17:1253543. [PMID: 38026702 PMCID: PMC10679756 DOI: 10.3389/fncel.2023.1253543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, lethal neurodegenerative disease mostly affecting people around 50-60 years of age. TDP-43, an RNA-binding protein involved in pre-mRNA splicing and controlling mRNA stability and translation, forms neuronal cytoplasmic inclusions in an overwhelming majority of ALS patients, a phenomenon referred to as TDP-43 proteinopathy. These cytoplasmic aggregates disrupt mRNA transport and localization. The axon, like dendrites, is a site of mRNA translation, permitting the local synthesis of selected proteins. This is especially relevant in upper and lower motor neurons, whose axon spans long distances, likely accentuating their susceptibility to ALS-related noxae. In this work we have generated and characterized two cellular models, consisting of virtually pure populations of primary mouse cortical neurons expressing a human TDP-43 fusion protein, wt or carrying an ALS mutation. Both forms facilitate cytoplasmic aggregate formation, unlike the corresponding native proteins, giving rise to bona fide primary culture models of TDP-43 proteinopathy. Neurons expressing TDP-43 fusion proteins exhibit a global impairment in axonal protein synthesis, an increase in oxidative stress, and defects in presynaptic function and electrical activity. These changes correlate with deregulation of axonal levels of polysome-engaged mRNAs playing relevant roles in the same processes. Our data support the emerging notion that deregulation of mRNA metabolism and of axonal mRNA transport may trigger the dying-back neuropathy that initiates motor neuron degeneration in ALS.
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Affiliation(s)
- Alessandra Pisciottani
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Croci
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Povo, Italy
| | - Chiara Marullo
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisa Savino
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Ambrosi
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paola Podini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Filippo Casoni
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ottavio Cremona
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
| | - Stefano Taverna
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angelo Quattrini
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Jean-Michel Cioni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Franca Codazzi
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - G. Giacomo Consalez
- Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milan, Italy
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
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45
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Dubowsky M, Theunissen F, Carr JM, Rogers ML. The Molecular Link Between TDP-43, Endogenous Retroviruses and Inflammatory Neurodegeneration in Amyotrophic Lateral Sclerosis: a Potential Target for Triumeq, an Antiretroviral Therapy. Mol Neurobiol 2023; 60:6330-6345. [PMID: 37450244 PMCID: PMC10533598 DOI: 10.1007/s12035-023-03472-y] [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: 04/12/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease (MND), is a progressive neurological disorder, characterised by the death of upper and lower motor neurons. The aetiology of ALS remains unknown, and treatment options are limited. Endogenous retroviruses (ERVs), specifically human endogenous retrovirus type K (HERV-K), have been proposed to be involved in the propagation of neurodegeneration in ALS. ERVs are genomic remnants of ancient viral infection events, with most being inactive and not retaining the capacity to encode a fully infectious virus. However, some ERVs retain the ability to be activated and transcribed, and ERV transcripts have been found to be elevated within the brain tissue of MND patients. A hallmark of ALS pathology is altered localisation of the transactive response (TAR) DNA binding protein 43 kDa (TDP-43), which is normally found within the nucleus of neuronal and glial cells and is involved in RNA regulation. In ALS, TDP-43 aggregates within the cytoplasm and facilitates neurodegeneration. The involvement of ERVs in ALS pathology is thought to occur through TDP-43 and neuroinflammatory mediators. In this review, the proposed involvement of TDP-43, HERV-K and immune regulators on the onset and progression of ALS will be discussed. Furthermore, the evidence supporting a therapy based on targeting ERVs in ALS will be reviewed.
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Affiliation(s)
- Megan Dubowsky
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia.
| | - Frances Theunissen
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | - Jillian M Carr
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - Mary-Louise Rogers
- College of Medicine and Public Health and Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
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46
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Theme 05 - Human Cell Biology and Pathology. Amyotroph Lateral Scler Frontotemporal Degener 2023; 24:140-160. [PMID: 37966320 DOI: 10.1080/21678421.2023.2260195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
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47
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Corcia P, Vourc'h P, Bernard E, Cassereau J, Codron P, Fleury MC, Guy N, Mouzat K, Pradat PF, Soriani MH, Couratier P. French National Protocol for genetic of amyotrophic lateral sclerosis. Rev Neurol (Paris) 2023; 179:1020-1029. [PMID: 37735015 DOI: 10.1016/j.neurol.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 09/23/2023]
Abstract
Relationships between genes and amyotrophic lateral sclerosis (ALS) have been widely accepted since the first studies highlighting pathogenic mutations in the SOD1 gene 30years ago. Over the last three decades, scientific literature has clearly highlighted the central role played by genetic factors in the disease, in both clinics and pathophysiology, as well as in therapeutics. This implies that health professionals who care for patients with ALS are increasingly faced with patients and relatives eager to have answers to questions related to the role of genetic factors in the occurrence of the disease and the risk for their relatives to develop ALS. In order to address these public health issues, the French ALS network FILSLAN proposed to the Haute Autorité de santé (HAS) the drafting of a French National Protocol (PNDS) on ALS genetics. This PNDS was developed according to the "method for developing a national diagnosis and care protocol for rare diseases" published by the HAS in 2012 (methodological guide for PNDS available on the HAS website: http://www.has-sante.fr/). This document aims to provide the most recent data on the role of genes in ALS and to detail the implications for diagnosis and care.
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Affiliation(s)
- P Corcia
- CRMR SLA, CHRU Bretonneau, Tours, France; UMR 1253 iBrain, Tours, France.
| | - P Vourc'h
- UMR 1253 iBrain, Tours, France; Laboratoire de biochimie et biologie moléculaire, CHRU Bretonneau, Tours, France
| | | | | | - P Codron
- CRMR SLA, CHU d'Angers, Angers, France
| | - M-C Fleury
- CRC SLA, CHU de Strasbourg, Strasbourg, France
| | - N Guy
- CRC SLA, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - K Mouzat
- Laboratoire de biochimie et biologie moléculaire, CHU de Nîmes, Nîmes, France
| | - P-F Pradat
- CRMR SLA, CHU Pitié-Salpêtrière, Paris, France
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Zhu H, Yang Y, Wang Y, Wang F, Huang Y, Chang Y, Wong KC, Li X. Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet. Nat Commun 2023; 14:6824. [PMID: 37884495 PMCID: PMC10603054 DOI: 10.1038/s41467-023-42547-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
RNA-binding proteins play crucial roles in the regulation of gene expression, and understanding the interactions between RNAs and RBPs in distinct cellular conditions forms the basis for comprehending the underlying RNA function. However, current computational methods pose challenges to the cross-prediction of RNA-protein binding events across diverse cell lines and tissue contexts. Here, we develop HDRNet, an end-to-end deep learning-based framework to precisely predict dynamic RBP binding events under diverse cellular conditions. Our results demonstrate that HDRNet can accurately and efficiently identify binding sites, particularly for dynamic prediction, outperforming other state-of-the-art models on 261 linear RNA datasets from both eCLIP and CLIP-seq, supplemented with additional tissue data. Moreover, we conduct motif and interpretation analyses to provide fresh insights into the pathological mechanisms underlying RNA-RBP interactions from various perspectives. Our functional genomic analysis further explores the gene-human disease associations, uncovering previously uncharacterized observations for a broad range of genetic disorders.
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Affiliation(s)
- Haoran Zhu
- School of Artificial Intelligence, Jilin University, 130012, Changchun, China
| | - Yuning Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Yunhe Wang
- School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
| | - Fuzhou Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Yujian Huang
- College of Computer Science and Cyber Security, Chengdu University of Technology, 610059, Chengdu, China
| | - Yi Chang
- School of Artificial Intelligence, Jilin University, 130012, Changchun, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, Hong Kong SAR.
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, 130012, Changchun, China.
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Li C, Wei Q, Hou Y, Lin J, Ou R, Zhang L, Jiang Q, Xiao Y, Liu K, Chen X, Yang T, Song W, Zhao B, Wu Y, Shang H. Genome-wide analyses identify NEAT1 as genetic modifier of age at onset of amyotrophic lateral sclerosis. Mol Neurodegener 2023; 18:77. [PMID: 37872557 PMCID: PMC10594666 DOI: 10.1186/s13024-023-00669-6] [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: 02/07/2023] [Accepted: 10/16/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Patients with amyotrophic lateral sclerosis (ALS) demonstrate great heterogeneity in the age at onset (AAO), which is closely related to the course of disease. However, most genetic studies focused on the risk of ALS, while the genetic background underlying AAO of ALS is still unknown. METHODS To identify genetic determinants influencing AAO of ALS, we performed genome-wide association analysis using a Cox proportional hazards model in 2,841 patients with ALS (Ndiscovery = 2,272, Nreplication = 569) in the Chinese population. We further conducted colocalization analysis using public cis-eQTL dataset, and Mendelian randomization analysis to identify risk factors for AAO of ALS. Finally, functional experiments including dual-luciferase reporter assay and RT-qPCR were performed to explore the regulatory effect of the target variant. RESULTS The total heritability of AAO of ALS was ~ 0.24. One novel locus rs10128627 (FRMD8) was significantly associated with earlier AAO by ~ 3.15 years (P = 1.54E-08, beta = 0.31, SE = 0.05). This locus was cis-eQTL of NEAT1 in multiple brain tissues and blood. Colocalization analysis detected association signals at this locus between AAO of ALS and expression of NEAT1. Furthermore, functional exploration supported the variant rs10128627 was associated with upregulated expression of NEAT1 in cell models and patients with ALS. Causal inference suggested higher total cholesterol, low-density lipoprotein, and eosinophil were nominally associated with earlier AAO of ALS, while monocyte might delay the AAO. CONCLUSIONS Collective evidence from genetic, bioinformatic, and functional results suggested NEAT1 as a key player in the disease progression of ALS. These findings improve the current understanding of the genetic role in AAO of ALS, and provide a novel target for further research on the pathogenesis and therapeutic options to delay the disease onset.
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Affiliation(s)
- Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Qianqian Wei
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Yanbing Hou
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Junyu Lin
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Ruwei Ou
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Lingyu Zhang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Qirui Jiang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Yi Xiao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Kuncheng Liu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Xueping Chen
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - TianMi Yang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Wei Song
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Bi Zhao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Ying Wu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, West China Hospital, National Clinical Research Center for Geriatric, Sichuan University, Chengdu, China.
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50
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Godfrey RK, Alsop E, Bjork RT, Chauhan BS, Ruvalcaba HC, Antone J, Gittings LM, Michael AF, Williams C, Hala'ufia G, Blythe AD, Hall M, Sattler R, Van Keuren-Jensen K, Zarnescu DC. Modelling TDP-43 proteinopathy in Drosophila uncovers shared and neuron-specific targets across ALS and FTD relevant circuits. Acta Neuropathol Commun 2023; 11:168. [PMID: 37864255 PMCID: PMC10588218 DOI: 10.1186/s40478-023-01656-0] [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: 08/03/2023] [Accepted: 09/19/2023] [Indexed: 10/22/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) comprise a spectrum of neurodegenerative diseases linked to TDP-43 proteinopathy, which at the cellular level, is characterized by loss of nuclear TDP-43 and accumulation of cytoplasmic TDP-43 inclusions that ultimately cause RNA processing defects including dysregulation of splicing, mRNA transport and translation. Complementing our previous work in motor neurons, here we report a novel model of TDP-43 proteinopathy based on overexpression of TDP-43 in a subset of Drosophila Kenyon cells of the mushroom body (MB), a circuit with structural characteristics reminiscent of vertebrate cortical networks. This model recapitulates several aspects of dementia-relevant pathological features including age-dependent neuronal loss, nuclear depletion and cytoplasmic accumulation of TDP-43, and behavioral deficits in working memory and sleep that occur prior to axonal degeneration. RNA immunoprecipitations identify several candidate mRNA targets of TDP-43 in MBs, some of which are unique to the MB circuit and others that are shared with motor neurons. Among the latter is the glypican Dally-like-protein (Dlp), which exhibits significant TDP-43 associated reduction in expression during aging. Using genetic interactions we show that overexpression of Dlp in MBs mitigates TDP-43 dependent working memory deficits, conistent with Dlp acting as a mediator of TDP-43 toxicity. Substantiating our findings in the fly model, we find that the expression of GPC6 mRNA, a human ortholog of dlp, is specifically altered in neurons exhibiting the molecular signature of TDP-43 pathology in FTD patient brains. These findings suggest that circuit-specific Drosophila models provide a platform for uncovering shared or disease-specific molecular mechanisms and vulnerabilities across the spectrum of TDP-43 proteinopathies.
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Affiliation(s)
- R Keating Godfrey
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA.
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, 3215 Hull Road, Gainesville, FL, 32611, USA.
| | - Eric Alsop
- Translational Genomics Research Institute, 445 N 5th St., Phoenix, AZ, 85004, USA
| | - Reed T Bjork
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Brijesh S Chauhan
- Cellular and Molecular Physiology, Penn State College of Medicine, 500 University Drive Crescent Building C4605, Hershey, PA, 17033, USA
| | - Hillary C Ruvalcaba
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Jerry Antone
- Translational Genomics Research Institute, 445 N 5th St., Phoenix, AZ, 85004, USA
| | - Lauren M Gittings
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | - Allison F Michael
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Christi Williams
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Grace Hala'ufia
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Alexander D Blythe
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA
| | - Megan Hall
- Translational Genomics Research Institute, 445 N 5th St., Phoenix, AZ, 85004, USA
| | - Rita Sattler
- Department of Translational Neuroscience, Barrow Neurological Institute, 350 W Thomas Road, Phoenix, AZ, 85013, USA
| | | | - Daniela C Zarnescu
- Department of Molecular and Cellular Biology, Life Sciences South, University of Arizona, 1007 E. Lowell St., Tucson, AZ, 85721, USA.
- Cellular and Molecular Physiology, Penn State College of Medicine, 500 University Drive Crescent Building C4605, Hershey, PA, 17033, USA.
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